Month: February 2025

We excluded hospitalizations that included liver transplantation , and used the cohort of those who did not receive liver transplantation as the primary cohort. The primary outcome was ODS at any point during hospitalization . Patient age, sex, race, etiology of liver disease, general medical comorbidities, complications of cirrhosis, and hospital outcomes including discharge disposition, length of stay, and inflation-adjusted total cost were also extracted as described in depth elsewhere. In brief, we identified specific complications of cirrhosis using discharge diagnosis codes ; we identified specific patient comorbidities such as congestive heart failure using the Clinical Classification Software; and identified paracenteses and thoracenteses with procedure codes. Charlson Comorbidity Index was used as a marker of general illness severity/degree of comorbidities, stratified into three groups: mild , moderate ,severe . Baveno IV consensus criteria was used as a marker of cirrhosis illness severity, where those with Stages 3 , and 4 represented decompensated cirrhosis. For descriptive statistics we presented categorical variables as percentages and continuous variables as medians with respective interquartile ranges . To compare characteristics between patients with vs. without ODS, we used Pearson chi-square test for dichotomous variables; non-parametric Kruskal-Wallis to compare categorical variables; and Wilcoxon rank-sum for continuous variables. We used univariable logistic regression to assess unadjusted odds ratios associated with ODS, square plant pot and used stepwise backward selection to determine the final multi-variable logistic model. Statistical analysis were performed using Stata .

In this investigation of the National Inpatient Sample, 2009-2013, we found that the prevalence of ODS in hospitalized patients with cirrhosis was extremely rare, and much lower than the prevalence reported in patients undergoing liver transplantation.2-6,8 Alcohol related cirrhosis, younger age, and female gender were associated with an inpatient diagnosis of ODS. Notably, markers for cirrhotic decompensation and severity of comorbid illness were not found to be associated with ODS. This included no evidence for an association with ascites, which ran counter to our hypothesis that those with portal hypertension might be at higher risk for ODS due to labile serum sodium levels during hospitalization. Our findings that those with vs. without ODS experienced longer hospital stays, higher hospitalizations costs, and increased chance of receiving a discharge disposition to somewhere other than home help to quantify the burden of ODS on the health care system. Furthermore, the increased health care burden and poorer outcomes we found in those with vs. without ODS provide additional evidence that we appropriately identified pronounced cases of ODS with our selection methods. We acknowledge our study’s limitations. As with all large database investigations, our results are susceptible to case ascertainment and measurement biases. While ICD-9 codes have been well-validated for the selected measures of cirrhosis and overall disease,7 ICD-9 codes for ODS have not been systematically validated. In particular, we cannot know whether subtler cases of ODS might have gone unrecognized in the hospital setting only to be diagnosed at outpatient follow-up upon review of MRI imaging. Our low prevalence estimate likely reflects this, underestimating the total prevalence of ODS by failing to detect these subtler cases. That being said, we aimed to capture clinically-apparent cases of ODS, for which ICD-9 coding would be most specific. Finally, our study was limited by a paucity of sodium level data.

Unfortunately, the NIS does not contain laboratory values, so we couldn’t associate serum sodium changes with ODS. Additionally, hyponatremia as detected by ICD9 coding has been demonstrated to be variable and often lacking, representing perhaps only one third of inpatients experiencing hyponatremia.9 Because of this, and because hyponatremia is already known as a major precipitant of ODS, we elected to focus our research questions on other risk factors beyond it.1 In conclusion, our investigation of a large nationwide database demonstrates that ODS is extremely rare, occurring in 0.02% of hospitalized patients with cirrhosis. ODS is associated with alcohol-related cirrhosis, younger age, and female gender. ODS is not associated with specific cirrhosis complications including ascites, nor with overall liver disease severity or general comorbid disease severity. These data may help inform management of hyponatremia in patients with cirrhosis by reassuring providers of the rarity of ODS, while reinforcing the consideration of a broad range of differential diagnoses in cirrhosis patients exhibiting altered mental status after hyponatremia correction.Cobalt monosilicide crystalizes in a chiral structure in the P213 space group inset. It has been intensely studied as a potential thermoelectric material due to its large power factor at room temperature. Recent theoretical works have found that CoSi and its isostructural siblings possess a chiral double sixfold-degenerate spin-1 Weyl fermion at R point and a fourfold-degenerate chiral fermion at Γ point in their Brillouin zone. These “new fermions” with large topological charges are connected by long, robust Fermi arcs on the surface which have been later confirmed by angle-resolved photoemission spectroscopy experiments. However, no transport properties of CoSi directly related to its topological nature have been reported until now. As far as we are aware, previous reported CoSi single crystals manifest relatively low carrier mobilities and no quantum oscillations have been observed in their electrical properties under magnetic field. It is difficult to bridge the transport properties with its topological band structure due to low sample quality.

Here we report our crystal growth and a survey of the electrical transport properties of single-crystalline CoSi. Tellurium was found to be an appropriate metal flux for the growth of CoSi which yields high-quality single crystals with large magneto-resistance and carrier mobilities. Although there is plenty of research work on the thermopower of CoSi, few of them have paid attention to its magneto-Seebeck and Nernst effect. Combining the high quality of our Te-flux grown samples and the sensitivity of thermoelectricity measurement, we are able to observe, for the first time, QOs in the thermoelectric signals of CoSi. By analyzing the QOs in magneto-Seebeck and Nernst signals at different temperatures and magnetic field directions, we reveal two spherical Fermi surfaces around the BZ corner R point, which is consistent with our density functional theory calculations. The extracted Berry phases of electron orbit equal zero, agreeing well with the scenario of −2 chiral charge at R point. We also found that the spin-orbit coupling induced band-splitting is lessthan 2 meV near the Fermi level and this result is one order smaller than our DFT calculations. We also report a large Nernst effect in CoSi due to the combination of high mobility and phonon-drag contribution at intermediate temperatures. As a consequence, a relatively large Nernst-Ettinshausen figure of merit of around 0.03 is achieved at 42 K in 14 T.Grape berries undergo a series of complex physiological and biochemical changes during their development that determine their characteristics at harvest . Genome-wide expression studies using microarray and, more recently, RNA sequencing revealed that berry development involves the expression and modulation of approximately 23,000 genes and that the ripening transition is associated with a major transcriptome shift . Transcriptomic studies characterized the ripening program across grapevine cultivars , identifying key ripening-related genes and determining the impact of stress and viticultural practices on ripening . This knowledge increases the possibility of exerting control over the ripening process, improving fruit composition under suboptimal or adverse conditions, and enhancing desirable traits in a crop with outstanding cultural and commercial significance . These genome-wide expression analyses were possible because a highly contiguous assembly for the species was produced ;this first effort used a grape line created by several rounds of back crossing to reduce heterozygosity, facilitating genome assembly . Though poor by current standards, this pioneering, square pot chromosome-resolved assembly served as the basis for numerous publications. However, the structural diversity of grape genomes makes using a single one-size-fits-all reference genome inappropriate . There is substantial unshared gene content between cultivars, with 8–10% of the genes missing when two cultivars are compared . Although many of these genes are not essential for plant survival, they can account for 80% of the expression within their respective families and expand key gene families possibly associated with cultivar-specific traits . Assembling genome references for all interesting cultivars is impractical, in part because its cost remains prohibitive and because of genomic features that impede the development of high-quality genome assemblies for any grape cultivar. Although the V. vinifera genome is relatively small and as repetitive as other plant genomes of similar size , it is highly heterozygous . Most domesticated grape cultivars are crosses between distantly related parents; this and clonal propagation cause the high heterozygosity observed in the species . Earlier attempts using short reads struggled to resolve complex, highly heterozygous genomes . A limited ability to call consensus polymorphic regions yields highly fragmented assemblies where structural ambiguity occurs and alternative alleles at heterozygous sites are excluded altogether . Single Molecule Real Time DNA sequencing has emerged as the leading technology for reconstructing highly contiguous, diploid assemblies of long, repetitive genomes that include phased information about heterozygous sites . Recently, we used Vitis vinifera cv. Cabernet Sauvignon to test the ability of SMRT reads and the FALCON-Unzip assembly pipeline to resolve both alleles at heterozygous sites in the genome .

The assembly produced was significantly more contiguous than the original PN40024 assembly and provided the first phased sequences of the diploid V. vinifera genome . Despite recent advances in genome reconstruction methodologies, assembling a complex plant genome is still costly. Transcriptome reconstruction is the only alternative strategy to depict known and unknown gene content information . De novo assembly of RNA-seq reads is widely used for this purpose . SMRT technology was recently deployed to investigate expressed gene isoforms in a variety of organisms, including a handful of plant species . Long reads delivered by this methodology report full-length transcripts sequenced from their 59-ends to polyadenylated tails , making Iso-Seq an ideal technology for reconstructing a transcriptome without a reference genome sequence and without assembling fragments to resolve the complete isoform sequence . Moreover, alternative transcripts that contribute to the gene space complexity and vary with cell type , developmental stage , and stress cannot be definitively characterized without full-length transcript information. The objective of this study was to test whether full-length cDNA sequencing with Iso-Seq technology is a suitable alternative to traditional genome sequencing, assembly, and annotation for reconstructing a grape transcriptome reference for transcriptional profiling. We compared how Cabernet Sauvignon’s Iso-Seq transcriptome fares as a reference for RNA-seq analysis vs. its annotated genome. We sequenced the full-length transcripts of ripening berries with Iso-Seq and Illumina RNA-seq reads. The high-coverage short-read data were used to profile gene expression and to error-correct low-expression isoforms that would have been otherwise lost by the standard Iso-Seq pipeline. The transcriptome reference built with Iso-Seq data represented most of the expressed genes in the grape berries and included cultivarspecific or “private” genes. When used as the reference for RNAseq, Iso-Seq generated transcriptome profiles quantitatively similar to those obtained by mapping on a complete genome reference. These results support using Iso-Seq to capture the gene space of a plant and build a comprehensive reference for transcriptional pro- filing without a pre-defined reference genome.Grape berries from Cabernet Sauvignon FPS clone 08 were collected in Summer 2016 from vines grown in the Foundation Plant Services Classic Foundation Vineyard . Between 10 and 15 berries were sampled at pre-véraison, véraison, post-véraison, and at commercial maturity. Table S1 provides weather information for the sampling days. The ripening stages were visually assessed based on color development and confirmed by measurements of soluble solids . On the day of sampling, berries were deseeded, frozen in liquid nitrogen, and ground to powder . Total RNA was isolated using a Cetyltrimethyl Ammonium Bromide -based extraction protocol as described in Blanco-Ulate et al. . RNA purity was evaluated with a Nanodrop 2000 spectrophotometer . RNA was quantified with a Qubit 2.0 Fluorometer using the RNA broad range kit . RNA integrity was assessed using electrophoresis and an Agilent 2100 Bioanalyzer . Only RNA with integrity number greater than 8.0 was used for SMRTbell library preparation. One mg of the pooled RNA was used for cDNA synthesis and for SMRTbell library construction using the SMARTer PCR cDNA synthesis kit . First-strand cDNA synthesis was performed using the SMRTScribe Reverse Transcriptase . Each developmental stage was individually barcoded . To minimize artifacts during largescale amplification, a cycle optimization step was performed by collecting five 5 ml aliquots at 10, 12, 14, 16, and 18 PCR cycles.

Given the later fruit development of grapevine and the grape chemistry requirements for red wine making , the length of the growing season is often a limitation for achieving the desired ripening and vintage quality in cool climates . Thus, yield is often sacrificed to balance source-to-sink ratio in favor of accelerated fruit ripening or to mitigate the effects of early fall frosts . Although the initial control of crop level comes during pruning , the number of dormant buds retained at pruning time is maintained constant through the years in warm climate regions. Cluster thinning is a management practice fine-tuned each year to achieve vine balance . This effect could be exacerbated with high nitrogen amounts inhibiting anthocyanin biosynthesis , the absence of water stress, or changes of cluster microclimate due to mutual shading , and thus, not by the under cropping itself. Therefore, grapevine canopy development is managed through the control of inputs, vine spacing, irrigation, rootstocks, pruning, leaf removal, hedging, or cover crops, among others. A great part of the carbon assimilated through the growing season is incorporated into cellulose or lignin in roots, trunks, and shoots . However, blueberry grow bag resumption of a new season’s growth depends on the carbon stored as nonstructural carbohydrates, majorly in the form of starch, but also soluble carbohydrates such as sucrose, glucose, and fructose .

Roots are the greatest sink of non-structural carbohydrates and root-derived carbohydrates constitute the principal reserve source for annual resumption of growth in the spring. The grapevine’s capacity for replenishment of these carbohydrate reserves increases at mid-ripening, when canopies are at their maximum and fruit demand slows down sugar accumulation in perennial parts . Therefore, the loss of photosynthetically active leaf area or excessive number of clusters may impair the reconstitution of reserves . In addition, high crop levels may delay fruit maturation and shorten the post-harvest period and subsequently reduce the time needed to accumulate reserve carbohydrates. Grape growing systems based on high yields are typically in warm to hot regions, relying on early harvest to replenish these reserves. However, it is common that excessive yields lead to a reduction in yields the following season . Loss of photosynthetically active leaf area or excessive number of clusters may deplete these reserves. High crop levels may reduce the reserve carbohydrate accumulation and delayed fruit maturation and may shorten the postharvest period. Therefore, the grapevine may not have sufficient time to accumulate carbohydrates for the following season in cool climates. Conversely, there is not consensus in literature regarding the effect of high cropping levels on storage reserves . This was explained by sink limitation as the grapevine was able to maintain equilibrium by adjusting physiological processes . In addition to the modulation of berry ripening and storage reserves, other compensatory mechanisms have been described in response to over and under cropping. Components of yield, which include clusters per vine, berries per cluster, and berry mass, are susceptible to change together with berry ripening in compensation of each other . Although grapevine pruning, canopy, and crop load management are the most frequently reported case of study for source-to-sink ratios, most studies may not offer direct observations , enough combinations, duration of the study, or range of source-to-sink ratios to respond to some fundamental questions.

The aim of this study was to determine the in-season and carryover effects of carbon source and sink imbalances in grapevine. Specifically, we investigated the combined effects of defoliation and fruit removal on components of yield, canopy area, and seasonal integrals of leaf gas exchange, shifts in phenology, carbohydrate, and soluble sugar concentration in the roots.The experimental design was a factorial arrangement of treatments. There were three levels of manual defoliation by three levels of manual fruit removal applied . The treatments were applied as follows. Leaves were removed on every shoot in an alternating pattern. For instance, 66% of leaf treatments retained leaves in positions 1st, 2nd, 4th, 5th, 7th, 8th etc. while 33% of leaf treatments kept leaves in positions 1st, 4th, 7th, etc. in every shoot . The fruit removal treatments retained a percentage of clusters after standardizing the cluster numbers in each year. Each treatment combination was replicated four times and each treatment-replicate consisted of three experimental units. In 2017, all vines were standardized at fruit set to 20 shoots and 30 clusters per vine, and laterals were removed prior to defoliation and fruit removal treatments. In 2018, all vines were standardized to 24 shoots and 45 clusters and laterals were removed prior to treatment application. Treatments were applied at pepper-corn size . In 2019, after two seasons of growth under the nine combinations of treatments, the carryover effects were studied by leaving all vines untreated . For each experimental unit one vine was shoot thinned to 24 shoots, and others were left unmanaged . All clusters at pepper-corn size in all treatment-replicates were dipped in a 5.5% kaolin solution to provide protection from the afternoon sun due to the row orientation of the vineyard in every year of the experiment.Percentage of bud break , flowering , veraison , and leaf senescence per plant were recorded at time intervals of either 1, 2, or 3 times a week depending on weather and phenology events . A leaf was considered senescent when 50% of its area was yellow.

Measurements started soon after the application of treatments in 2017 until leaf senescence 2019. In 2019, only grapevines thinned to 24 shoots per vine were followed.Leaf gas exchange was measured bi-weekly in all years of the experiment with an infra-red gas analyzer . Three sun-exposed leaves were selected from the main shoot axis in each experimental unit, and three readings were taken from each leaf. Gas exchange measurements were taken when the sunlight conditions were close to saturating levels in all instances. The relative humidity was set at 40%, the reference CO2 concentration was set at 400 µmol CO2 mol−1 as the standard environmental condition setting in CIRAS-3. Net carbon assimilation rate and stomatal conductance were obtained. To express the season-long response of AN, and gs , their integrals were calculated by using natural cubic splines for plant water status and gas exchange measurements to assess the cumulative values for these parameters over the whole experiment period during the growing season. Then, these cumulative values were normalized as divided by the number of days elapsed between the first measurement date and the last measurement date to make the data comparable to each individual measurement.After harvest, leaves from one vine per replicate were collected, weighted, and dried in a forced-air oven at 80◦C for 3 days. Dry leaf weights were converted into area by measuring the area of a subsample of 50 random leaves with a leaf area meter as reported previously . On 12 December 2018, after the second season of treatments, one vine per experimental unit of the most extreme treatments were pruned, coppiced, blueberry grow bag size and the root systems were removed with a back-hoe. The sectioned grapevine portions were weighed on a top loading scale, and dried in a forced-air oven at 60◦C until no weight change of tissue was detected. At harvest , clusters were removed, counted, and weighed for each plant in the experiment. Total soluble solids were measured from 55 berries collected randomly at harvest point. The berries were crushed by hand and filtered to obtain must. A digital refractometer was then used to measure total soluble solids of must.Soon after the harvest of 2017 was completed, root tissues were sampled every 2 months. The top layer of soil was removed until the roots were visible. Each grapevine root zone was divided into four quadrants and on each date and one single quadrant was sampled, leaving the other 11 quadrants undisturbed. Roots were gently cleaned with water, freeze-dried, and ground to a fine powder with a tissue lyser . Thirty milligrams of the resultant powder were extracted in 80:20 ethanol solution. A 1.5 mL aliquot of the extract was then placed in a 90◦C water bath for 10 min, then centrifuged at 10,000 rpm for 1 min. The supernatant was collected for total soluble sugars determination. The same procedure was repeated for starch determination, in which the pellet was collected for its determination.

Total soluble sugars in the roots were determined as reported elsewhere by Torres et al. . Briefly, the 1.5 mL sample was filtered by PTFE membrane filters and transferred into high performance liquid chromatography vials. Equipment consisted of a reversed-phase HPLC system Agilent 1100 coupled to a diode array detector and an Agilent Infinity Refractive Index Detector . The reversed-phase column was Luna Omega Sugar with a guard column of 5 mm. The temperature of the column compartment was maintained at 40◦C and the RID flow cell was kept at 35◦C. The mobile phase system consisted in an isocratic elution with acetonitrile:water at a flow rate of 1.0 mL•min−1 with a run time of 22 min. Standard solutions of 10 mg/L of D-glucose, D-fructose, D-sucrose, and D-raffinose were injected to obtain the retention time for each compound, and detection was conducted by RID. Sugar standards were purchased from VWR . Sugar concentration of each sample was determined by comparison of the peak area and retention time with standard sample curves. Starch content of roots was measured using the Starch Assay Kit SA-20 following the manufacturer’s instructions. Briefly, pellets of root tissues were dissolved in 1 mL DMSO, and incubated for 5 min in a water bath at 100◦C. Starch digestion was started by adding 10 µL α- amylase and incubated in boiling water for another 5 min. then, the ddH2O was added to a total volume of 5 mL. Then, 500 µL of the above sample and 500 µL of starch assay reagent were mixed and incubated for 15 min at 60◦C. Negative controls with the starch assay reagent blank, sample blank, and glucose assay reagent blank and positive controls with starch from wheat and corn were performed. Reaction started with the incubation of 500 µL of each sample and 1 ml of glucose assay reagent at 37◦C and was stopped with the addition of 1 mL of 6 M Sulfuric acid after 30 min. Reaction was followed with analytical measurements with a Cary 100 Series UV-Vis Spectrophotometer and starch content expressed as mg of starch per tissue dried weight.In our experiment the results indicated that there was an interaction of year and defoliation on cluster weight, berries per cluster and yield per vine . When we analyzed the data by year, the effect of defoliation was clearer. In both experimental years , there was a strong linear trend of defoliationon all components of yield except for cluster number; which was only affected by the fruit removal treatments. In 2017 defoliating 66% of the leaves resulted in an 8% decrease in berry weight. The differences were exacerbated in cluster weight , berries/cluster , and yield when 66% of the leaf area was removed. In 2018, the effect of defoliation was evident with a 12% decrease in berry weight. As in the previous year, we saw a diminution in cluster weight, berries/cluster, and yield. However, the decline in yield in 2018 was 56% when 66% of the leaves were defoliated. Fruit removal was effective in modulating the cluster number and thus the yield in both experimental years as expected . Furthermore, we measured a strong linear decrease in cluster weight in 2017. However, the same response was not evident in 2018. Removing 66% of the cluster resulted in a 55 and 60% decrease in yield of Cabernet Sauvignon in 2017 and 2018, respectively. Surprisingly, we did not measure an interaction of defoliation and fruit removal on components of year in either of the experimental years . The carry-over effects of source-sink adjustments on components of yield in 2019 were strongly evident ; even though no defoliation or fruit removal treatments were applied. Berry weight, cluster number per vine, cluster weight, and yield per vine were all affected by the carry over effects of defoliation from the previous 2 years. They all declined linearly with the 33% defoliation treatment. Conversely, we did not measure a carryover effect of fruit removal in 2019 in the majority of components of yield monitored. There was an interaction of defoliation and fruit removal in 2019 on the number of berries per cluster.

Although such effects with regard to child care type have been rather mixed, there is some reason to suspect that heightened exposure to peers—such as often found in center-based child care—may be a salient stressor for young children . For instance, at abehavioral level, the replicated link between greater exposure to center-based child care and subsequently heightened levels of aggression in childhood has been shown to be at least partially explained by the typically higher levels of peer exposure faced by these children . That said, the potential effects of peer exposure on HPA axis functioning in infancy and toddlerhood are largely unknown. Indeed, some work has suggested that heightened peer exposure may be associated with lower levels of HPA activity. For instance, in their generative study of infants and toddlers, Watamura and colleagues found that toddlers who spent more time playing with their peers tended to show lower cortisol levels than their less social classmates. Of course, the direction of this relation remains unclear; for example, perhaps less physiologically stressed children choose to play more with peers . However, it nonetheless raises the possibility that peer exposure may provide valuable opportunities for young children to learn to negotiate such complex social contexts.With rare exception, the extant literature concerning child care and children’s early adrenocortical functioning has been based on rather small, homogeneous samples of children from middle- to upper income families. Informed by findings from studies of children’s behavioral outcomes, plastic grow bag there is increasing evidence to suggest that child care effects for children growing up in poverty may be quite different those for children from more affluent home families .

Accumulating findings indicate that the beneficial effects of high-quality child care may be comparatively more pronounced for children from high-risk contexts. For instance, some work has shown that greater exposure to high-quality child care , or even simply attending regular non-maternal care , may mitigate the detrimental effects of economic adversity or low levels of maternal education on children’s subsequent academic achievement. Similar buffering effects have been noted with respect to children’s language development, such that exposure to high-quality language environments in child care may mitigate the negative effects of low-quality language environments experienced at home . Related findings also extend to children’s social development. For example, contrary to the replicated finding that more extensive hours in child care are predictive of heightened levels of aggression , increasing evidence suggests that the opposite may be true for children from high-risk home environments. Greater hours in high-quality child care have been linked with lower levels of internalizing and externalizing behavior in samples of low-income children . Similarly, using data from a large Canadian sample, Côté and colleagues found that the prototypically positive relation between non-maternal care and aggression in childhood was evident only for children from middle- to upper class families. Indeed, although it failed to reach statistical significance, there was a descriptive indication that non-maternal care was associated with better socialoutcomes for low-income children. We and our colleagues have recently shown similar findings with respect to child care exposure and several outcomes in pre-kindergarten .

Specifically, we found that for children experiencing high levels of household chaos across early childhood, greater weekly hours in child care were predictive of comparatively fewer behavior problems. In particular, consistent with the idea of a buffering effect, greater child care exposure ameliorated the detrimental relation between household chaos and children’s social problems. We have also recently shown similar interactive relations with respect to children’s HPA axis functioning at 48 months of age ; specifically, using the same sample as in the present study, we found that the direction of the relation between child care exposure and children’s cortisol levels at 48 months varied as a function children’s broader environmental risk. For children from low-risk households, greater weekly hours of child care were predictive of higher cortisol levels. In contrast, for children facing substantial cumulative risks at home, greater hours of child care exposure were predictive of lower cortisol levels. Of note, and contrary to our hypotheses, is that other aspects of children’s experiences, such as caregiver responsivity and child care type, were unrelated to children’s cortisol level, irrespective of children’s home contexts. As such, the potential mechanisms underlying these relations remain unclear. Furthermore, this work was concerned with HPA axis functioning just prior to children’s transition to school in relation to their average child care experiences across early childhood. Although this represents an important development span, we know little about the extent to which similar conditional relations are evident much earlier in development. Also, unlike the elegant within-person designs adopted by prior work that has considered links between child care and children’s diurnal rhythms on child care versus non–child care days, our findings comprised only between-child analyses. Within person designs afford important methodological advantages.

Most notably, they strengthen the internal validity of one’s inferences by essentially treating each individual as his or her own control group. In so doing, this holds all possible time-invariant confounds constant.Informed by our prior work, we hypothesized that increases in child care exposure would be associated with contemporaneous increases in children’s cortisol levels for those facing low levels of environmental risk. In contrast, we hypothesized that this within-child relation of child care exposure and cortisol levels would be comparatively more negative for those experiencing higher levels of risk—possibly to the extent to which the conditional relation reverses direction, such that increases in child care are predictive of contemporaneous decreases in children’s cortisol levels. Given that our prior work showed evidence of a similar interaction effect at approximately 48 months of age , we expected this conditional relation to extend downwardly to children in toddlerhood. However, consistent with cross-sectional findings by others , we allowed for the possibility that the relation might be comparatively weaker in early infancy. In our prior work we have found little evidence of effects of child care type or caregiver responsivity with respect to 48-month cortisol. Yet, informed by prior studies by others , we nonetheless conjectured that the high-quality and center-based care might play a particularly important role in children’s cortisol levels for those from high-risk home environments. Finally, informed by that idea that peer relations may support optimal behavioral and physiological regulation for children in child care , we hypothesized that within-child increases in positive peer exposure would be associated with cotemporaneous decreases in children’s cortisol levels—perhaps, particularly so for children experiencing heightened levels environmental risk. Our hypotheses with respect to between-child differences in children’s child care experiences were substantively identical to the within-person representations above.The Family Life Project was designed to study young children and their families in two of the four major geographical areas of the United States with high poverty rates —eastern North Carolina and central Pennsylvania; specifically, 1,292 children whose families resided in one of the six counties at the time of the child’s birth were sampled. Lowincome families in both states and African American families in NC were oversampled. A comprehensive description of the sampling plan was provided by Vernon-Feagans and colleagues . The present analytic sample comprises the 1,155 children with child care data for at least one of the three points at which child care information was collected between the time children were 7 and 24 months of age. Those excluded from the analytic sample did not differ from the present sample with respect to race or family income or primary caregiver education level at 7 months.In the present study we focused on data collected across infancy and toddlerhood. Children’s mothers were interviewed regarding demographic and personal information when their children were approximately 2 months of age. The demographic data used to calculate economic adversity, pe grow bag as well as information about child care usage, were collected from mothers during interviews when their children were 7, 15, and 24 months of age. At the ages of 7, 15, and 24 months, saliva samples were collected from children during home visits to assess resting or “non- stimulated” cortisol levels. Saliva samples were collected after the data collectors had been in the home for at least 1 hour interviewing the primary caregiver and prior to conducting a number of assessments with children.

The modal time of collection was approximately 10:00 a.m. at each wave of collection; however, there was some variability. Within-child differences in saliva sampling times across the three home observation points, as well as between-child differences in the saliva sampling times were adjusted statistically in all models. We use the term resting given that no active, purposeful stimulation was present, and children were given ample time to return to baseline after the arrival of the research assistants . We cannot rule out, however, that our “resting” cortisol levels partly capture HPA axis stimulation due to the visit. Unstimulated whole saliva was collected using either cotton or hydrocellulose absorbent material and expressing the sample into 2-ml cryogenic storage vials using a needleless syringe or by centrifugation . Prior studies have indicated no differences in cortisol concentrations associated with the two collection techniques . Children’s saliva samples were immediately frozen at −20° C and subsequently stored at −80° C. Intra- and interassay coefficients of variability for cortisol were, on average, less than 10% and 15%, respectively. When children were in non-parental care for at least 10 hours per week, interactions between the child care caregiver and the child were rated for caregiver responsivity by independent raters.Salivary cortisol—All samples from the 7-, 15-, and 24-month assessments were assayed for salivary cortisol using a highly sensitive enzyme immunoassay US FDA 510k cleared for use as an in vitro diagnostic measure of adrenal function . The samples were assayed in duplicate, with the average of the duplicates was used in all analyses. We examined child temperature and use of medications as influences on child cortisol); no relations were evident, after adjusting for the time of day when the saliva sample was collected. Saliva collection times were included as both time varying and time-invariant control covariates. Child care quantity—Children’s primary caregivers provided the average hours per week that the child attended non-parental child care when the child was 7, 15, and 24 months old. non-parental caregiver responsivity—Traditional measures of child care quality, such as the Early Childhood Environment Rating Scale or the Observational Record of the Caregiving Environment were unavailable in these data. We thus used independent ratings of the non-maternal caregivers’ behavior toward the child, as scored with Home Observation Measure of the Environment scale , as a proxy for process quality in child care. Indeed, although the HOME Responsivity scale is not a measure of child care quality, per se—like the process quality measure used in the NICHD Study of Early Child Care and Youth Development —it taps the sensitivity and responsivity of the non-parental caregiver to the child’s needs in ways that are comparable across different types of child care. HOME scale observations were made when the child was 7, 15, and 24 months old. Informed by prior psychometric work , we fitted a series of confirmatory factor analytic models, based on 10 items tapping caregiver responsiveness and affection toward the child. We hypothesized that a single latent factor explained observed caregiver responsivity across the items within a given time point. Because items were scored dichotomously these models were fitted using a robust weighted least-squares estimator . Descriptions of the CFA models are provided in the online supporting materials on the Family Relations website. In short, the results discussed below are based on factor scores estimated from a longitudinal CFA, constrained for partial measurement invariance. Higher values reflect higher levels of caregiver responsivity. Child care type—Child care type was reported by independent observers during child care visits conducted when the target child was 7, 15, and 24 months of age . Child care peer exposure—The numbers of peers in the classroom were based on counts conducted by independent observers during child care visits at 7, 15, and 24 months of age. Cumulative risk—Informed by extensive prior work with these data , we created a cumulative-risk composite comprising seven variables— family income, maternal education, constant spouse/partner living in the home, hours of employment, occupational prestige, household density, and neighborhood noise and safety—that were measured across infancy and toddlerhood. As described in detail in the online supporting materials, we created a continuous cumulative-risk index by reverse scoring the positively framed variables, standardizing each risk measure, and averaging across the risks.

Overall, insectivorous birds are the most abundant on coffee farms and hold great potential as bio-control of many insect pests . Details on bird densities on Costa Rica coffee farms used in the model are expanded on below .To our knowledge, there is little information about population densities of CBB in coffee plantations at the start of the growing season. We first initialized the coffee berry borer population model with 100 dispersing females . The start of CBB reproduction commenced 120 days after coffee flowering and continued until 305 days after flowering, yielding a 185-day CBB breeding season. We confirmed CBB reproduction was possible within this period for Central Valley Costa Rica using degree day calculations from Jaramillo et al. based on CBB thermal tolerance. We then calculated how much the dispersing adult survival rate would have to be reduced to cause a 50% reduction in adult female borer population size on day 185. To determine how many CBB would need to be consumed by birds to achieve this goal, we found the difference between daily borer population sizes of unsuppressed and suppressed populations and summed the differences across the CBB reproductive season. We used sensitivity analysis to estimate the degree to which changes in each vital rate affects population growth rate . All models were implemented using the popbio package in R . R code for all analyses is provided in the Supporting Information . We also wanted our model to project CBB population growth that represented “low” and “high” infestations observed in the field. To start, we estimated probable CBB densities using data on the number of dispersing females collected in alcohol-lure traps. At peak dispersal, CBB numbers have been recorded as high as 1000–6120 CBB/trap/week to as low as 50–105 CBB/trap/week .

Using these trap counts, plastic square flower bucket we calculated potential CBB densities per hectare via reported trap densities and converted weekly capture estimates to the number of daily dispersers to complement our daily population model. We used a density independent model, a standard first step in many population models. However, note that we would need to divide CBB numbers by plant density to evaluate the impacts of CBB population growth on yield. We also would need empirical data on how the demography of CBB populations change with coffee-plant density to implement a revised model, and we are unaware of published data on this. Consequently, this analysis is beyond the scope of this paper . Using data from Aristizabal et al. , we selected a high peak dispersal count from farms with large infestations and a low peak dispersal count from farms with small infestations to represent peak dispersal on Day 185 in our model. We used our calculated values of 269 and 5 as our “high” and “low” initial population sizes of gravid females at the start of the coffee season and used 100 CBB to represent “medium” initial population size.Parameters for our Leslie matrix for coffee berry borers are broadly consistent with expectations and general knowledge . For example, our conversion of fecundity to a daily value, F1 = 1.341, is consistent with published literature stating that 1–2 eggs are laid per day by CBB . Model projections showed that across a 185-day CBB breeding period starting at the point of first ovipositing, an initial population size of 100 female dispersers would produce 1.3 million offspring, resulting in a new adult population of 70,245 females . Assuming
99% of colonizing females successfully bore and oviposit in a coffee cherry on Day 0, the first generation of new dispersing females does not appear until day 37.

At Day 38, the adult population begins to increase, and continues to do so exponentially.The daily growth rate of this population converged on 1.042. Sensitivity analysis revealed that survival of adult females had the largest impact on overall population growth , followed by daily survival of pupa , juveniles , eggs and larvae and dispersing females . In addition to modeling growth with 100 initial colonists , we projected the population growth of low and high starting populations calculated from observed weekly alcohol-lure trap catches during peak dispersal . Comparing the three population projections, peak number of dispersers at Day 185 varied considerably, with 162, 3259, and 8768 daily dispersers for low, medium, and high colonizing populations, respectively. In the high population projection, the adult population toward the end of the growing season reached over 18,800 individuals. Note that because these are density-independent models, the number of CBB does not depend on plant density. However, the impacts of the CBB population on yield would depend on coffee plant density. To reduce the final adult population by 50%, the daily survival rate of dispersing females would have to be reduced from 0.99602 to 0.83202. This change represents a 16.4% reduction in daily survival when dispersing. The number of CBB that birds need to eat to reduce the adult population at this rate was driven by the initial population size as a straight line, y = 79.23 N0 . At medium starting population , birds need to consume 7628 CBB during the borer breeding season, while at high starting population , about 20,500 dispersing CBB must be consumed by birds. Daily consumption rates by birds would have to increase over time as the CBB population grows and could vary from 15 to 750 CBB being consumed a day, depending on starting population size . Overall, we calculated that for every female CBB in the initial colonization, birds need to consume 79 CBB to reduce the end of season population by half.We estimated that the caloric content of a 195 μg adult CBB to be 1.09 calories per gram dry weight, or 0.00109 kcal. At 5%–10% of a bird’s daily diet based on number of prey items, birds would consume <7 CBB per day. This represents 0.03%–0.05% of daily caloric requirements of our average insectivorous bird. At these feeding rates, our models suggest that by the time of peak dispersal, 4, 88, and 236 birds are required at low, medium, and high starting population sizes, respectively, to reduce CBB populations by 50% on day 185 .Our model suggests that avian predation is likely to be effective at reducing CBB populations by 50% only during small infestations , or during the early stages of larger infestations . Birds appear unable to successfully suppress medium and large infestations because the number of CBB that need to be eaten in a season requires higher bird densities than are reported in the literature. Karp et al. estimated 4–12 birds/ha of species that are confirmed or suspected CBB predators. Flocks of migratory birds on coffee farms are estimated at 19/ha and 24/ha , but these values are also short of our estimates of necessary densities for suppressing larger CBB outbreaks. One caveat to our conclusions is that our calculations were based on CBB accounting for 5%–10% of a bird’s daily diet . This assumption meant birds would only eat a set maximum of 7 CBB per day. Sherry et al. reported up to 116 CBB in the stomach contents of a single warbler, suggesting under certain circumstances in the field, birds eat more CBB. Generalist insectivores, particularly Neotropical migrants, have flexible foraging preferences and would likely feed opportunistically on CBB in response to dramatic dispersal peaks. Therefore, birds might be expected to increase feeding rates as CBB disperser abundances increase, though it may depend on the relative abundances of other prey. Better data on CBB consumption rates by birds under different circumstances would improve our estimates of the circumstances under which birds can control CBB populations.

A second caveat is that bird densities used in the model may not represent the potential for CBB control because bird densities depend on the structure of the agricultural landscape, which the current model does not consider. On coffee farms, plastic plant pot birds are more abundant when native tree cover is highest and natural forests are close by . Across tropical and temperate regions, the propensity for birds to forage on farms, and thus exert pressure on agricultural pests, is correlated with the physical complexity and diversity of the agroecosystem . For example, birds make more frequent foraging trips to apple orchards with high native tree coverage . In alfalfa fields, edge habitat complexity supports greater avian richness leading to lower pest abundances . Under some circumstances, the density of birds foraging in certain areas may be higher than average densities would imply, leading to greater control potential than our models suggest. More generally, our CBB population model is density independent and assumes environmental conditions and sufficient resources to allow CBB populations to increase without restriction. As a result, our model is limited, as it does not consider localized effects of weather and temperature fluctuations on CBB developmental time , nor characteristics of coffee farms that influence both CBB infestation and bird density. We assumed maximal capacity for CBB population growth and used estimates of bird densities from the literature that only included birds known to consume CBB, perhaps underestimating the potential for avian control. Models are an important tool for estimating population dynamics, but as with any species, the growth potential for CBB and availability of its predators, is context dependent. Our study echoes Kendall et al.’s conclusion that, even though errors in model construction are common, these seldom change qualitative conclusions. From our population matrix, CBB daily growth rate converged on λdaily = 1.042 around day 124, with an observed rate of population change across the entire coffee-growing season of 705 . Our λdaily is higher than Mariño et al.’s reported lambda of 1.32 over 50– 56 days, which corresponds to λdaily ≈ 1.006 . Part of this discrepancy may come from the fact that Marino et al. combined vital rates across life stages with different time steps. Nonetheless, both models are consistent in predicting rapidly growing populations. Observed CBB population growth rates are similar to ours: Baker, Barrera, & Rivas, calculated a 1.067 growth rate in wild populations and RuizC ardenas and Baker reported 1.047 in CBB reared in laboratory settings. In their sensitivity analysis, Mariño et al. reported that adult female survival, and transitions from larva to pupa and pupa to juvenile had high sensitivity in contributing to population growth rate, with adult survival the highest . We found a similar peak sensitivity value for female adult survival in our matrix , supporting the idea that CBB population growth is most sensitive to adult survival rate. Interestingly, dispersal survival from our matrix was estimated to have low impact on population growth , even though this life stage is when CBB are vulnerable to bird predation. Thus, our analysis superficially suggests that population control once CBB are established should focus on reducing adult survival rather than on trapping dispersing females , if the same impact on numbers could be achieved. However, dispersing females are much more accessible to control methods like spraying fungal bio-insecticide than are adult females, which are inside the coffee cherries, so despite the tremendous difference in sensitivity values, management of an established population is likely to be more cost effective by continuing to focus on dispersing females . Population models specific to CBB have been criticized for not being representative of wild populations, since more generations are estimated through modeling than are observed in field studies . We analyzed CBB population growth using a deterministic model, with an even distribution of dispersal and a fixed predation pressure. While CBB dispersal is continuous, there can be dramatic intraseasonal peaks in numbers that were not captured by our model . In addition, reported longevity of female CBB varies widely from 55 to 380 days, though some studies looked at CBB reared on artificial diet . Refinements of survival in natural settings would, therefore, improve models of CBB population growth, and the potential for control by birds. If field data on CBB vital rate stochasticity become available, and bird densities opportunistically increase during CBB peak numbers, it could affect our conclusions about the capacity of birds to control larger CBB outbreaks. Based on our analyses, there is a population density of CBB above which their capacity to produce more adults exceeds the ability of birds to control their numbers, at least to limit the population size by 50%.

As pointed out in Ref., the Berry phase has a profound geometrical origin because an adiabatic and cyclic process of a quantum state is mathematically equivalent to parallel transporting it along a loop, which connects to the concept of holonomy in geometry. Hence, the Berry phase bridges physics and geometry, making it extremely important in the understanding of topological phenomena, such as integer quantum Hall effect, topological insulators and superconductors, and others. The description of the Berry phase relies on the properties of a pure state of a quantum systems at zero temperature. Meanwhile, mixed quantum states, including thermal state at finite temperatures, are more common. Therefore, mixed-state generalizations of the Berry phase have been an important task. Uhlmann made a breakthrough by constructing the Uhlmann connection for exploring the topology of finite-temperature systems. As the Berry holonomy arises from parallel transport of a state-vector along a closed path, the Uhlmann holonomy is generated by parallel-transporting the amplitude of a density matrix. defined by W = √ρU. Here the amplitude W is the mixed-state counterpart of the wavefunction, and U is a phase factor. A geometrical phase is deduced from the initial and final amplitudes. However, Uhlmann’s definition of parallel transport is rather abstract and may involve non-unitary processes, complicating a direct and clear physical interpretation. Moreover, the fiber bundle built upon Uhlmann’s formalism is trivial, which severely restricts its applications in physical systems.Purification of a mixed state leads to purified state, round flower buckets a state-vector equivalent to the amplitude of a density matrix. The lack of a one-to-one correspondence between the density matrix and its purified states gives rise to a phase factor, similar to the phase of a wave function.

In a branch of quantum field theory called thermal field theory, there is a similar structure for describing the thermal-equilibrium state of a system by constructing the corresponding thermal vacuum by duplicating the system state as an ancilla and forming a composite state. It plays a crucial role in the formalism of traversable wormholes induced by the holographic correspondence between a quantum field theory and a gravitational theory of one higher dimensions. Importantly, purified states of a two level system has been demonstrated on the IBM quantum computer while the thermal vacuum of a transverse field Ising model in its approximate form has been realized on a trapped-ion quantum computer. Despite the superficial similarity, a major difference between a thermal vacuum and a purified state is a partial transposition of the ancilla to ensure the Hilbert-Schmidt product is well defined. In quantum information theory, a partial transposition is closely related to entanglement of mixed states. Importantly, partial transpositions of composite systems have been approximately realized in experiments by utilizing structural physical approximations in suitable quantum computing platforms. Although ordinary observables cannot discern the partial transposition between the purified state and thermal vacuum, here we will show that at least two types of generalizations of the Berry phase to mixed states are capable of differentiating the two representations of finite temperature systems. Among many attempts to generalize the Berry phase or related geometric concepts to mixed states , a frequently mentioned approach was proposed in Ref.. Instead of decomposing the density matrix to obtain a matrix-valued phase factor, a geometrical phase is di-rectly assigned to a mixed state after parallel transport by an analogue of the optical process of the MachZehnder interferometer. Hence, the geometrical phase generated in this way is often referred to as the interferometric phase. The interferometric phase has been generalized to nonunitary processes, but the transformations are still on the system only. Moreover, it is essentially different from Uhlmann’s theory since the conceptual structure of holonomy is not incorporated.

We will first derive a mixed-state generalization of the parallel-transport condition for generalizing the Berry phase without invoking holonomy. This approach unifies the necessary condition for both the interferometric phase and Uhlmann phase . Two ways to implement the parallel-transport condition based on how the system of interest undergoes adiabatic evolution will be introduced, and they lead to different generalizations of the Berry phase. We will name one thermal Berry phase and the other generalized Berry phase. Importantly, the partial transposition of the ancilla between a purified state and thermal vacuum will be shown to produces observable geometrical effects in both thermal Berry phase and generalized Berry phase. Through explicit examples, the two generalized phases are shown to differentiate the two finite-temperature representations, a task beyond the capability of the conventional interferometric phase or Uhlmann phase. The rest of the paper is organized as follows. Sec. II summarizes the Berry phase in a geometrical framework with an introduction of the parallel-transport condition for pure quantum states. In Sec. III, we review the representations of mixed states via purified states and thermal vacua and then explain the difference of the partial transposition of the ancilla. In Sec. IV, we introduce the thermal Berry phase via generalized adiabatic processes. While the thermal Berry phase can differentiate a purified state from a thermal vacuum, it may contain non-geometrical contributions. In Sec. V, we generalize the parallel-transport condition to involve the system and ancilla and derive the general Berry phase according to the generalized condition. While the generalized Berry phase only carries geometrical information, its ability of differentiating a purified state from a thermal vacuum depends on the setup and protocol. We present examples of the thermal and generalized Berry phases. Sec. VI concludes our study. Some details and derivations are given in the Appendix.While purified states of a two-level system incorporating environmental effects have been simulated on the IBM quantum platform, thermal vacua of the transverse Ising model has been experimentally realized on an ion-trap quantum computer by the quantum approximate optimization algorithm. Moreover, partial transposition of a composite system has been approximately realized on quantum computers with various numbers of qubits. Therefore, a comparison of the geometric effects reflected by the generalizations of the Berry phase of purified states or thermal vacua is expected to be achievable in future experiments on quantum computers or quantum simulators. For example, one may consider two identical composite quantum systems of Example V.1 of the generalized Berry phase and then apply a partial transposition to one of the composite systems. As a consequence, the composite system with a partial transposition corresponds to a purified state while the one without partial transposition may be viewed as a thermal vacuum. By applying parallel transport that involves the ancilla to both composite systems and extract their generalized Berry phase after a cycle, a π-phase difference is expected between the two composite systems. Given the large phase difference between them after a cycle, the result is robust against small perturbations or noise from the hardware and offers another demonstration of geometrical protection of information. We have presented two generalizations of the Berry phase, the thermal Berry phase and generalized Berry phase, for distinguishing the two state-vector representations of mixed states via the purified state and thermal vacuum. From the geometrical and physical points of view, the generalized Berry phase has more desirable properties since the thermal Berry phase is generated by a temperature-dependent thermal Hamiltonian and may carry non-geometrical information. We caution that while the transformations can be on the system, ancilla, or both in the construction of the generalized Berry phase, an operation on the ancilla is necessary if we want to differentiate the purified state and thermal vacuum.The earliest classification of the forms of matter we see around us, typically presented to us in our early school days, consists of solids, liquids and gases.

High school physics textbooks and experience later teach us that solids can be further classified based on their electronic properties as conductors and insulators. Solid state physics courses in college add semiconductors, semimetals and superconductors to that list, plastic flower buckets wholesale and explain the basic physics that governs the electronic properties of these phases. More precisely, as long as the electrons in a solid are non-interacting, solids with partially filled bands are shown to be metals or conductors while those with no partially filled bands and a gap between the valence and the conduction bands are insulators or semiconductors. If the gap is extremely small or vanishing or if there is a very small overlap between the valence and the conduction bands, the material is semimetallic. Superconductors are argued to be the fate of a metal cooled to extremely low temperatures. However, vast quantitative as well as qualitative differences between the properties of materials within a single category are often observed. For instance, some insulators have conducting surfaces while others do not. Moreover, the surface conduction is stable against perturbations as well as deformations in the band structure as long as the underlying symmetries of the system are preserved and the system remains insulating after the deformations. Similarly, interactions and certain perturbations can gap out some semimetals and turn them insulating but not others . These observations call for further refinement in the classification of solids, especially one that explains why the properties of some phases are robust to certain deformations, interactions and perturbations. In other words, an understanding for why some phases are topological while other are not, is required. The study of the topology of the bands provides a powerful unifying framework for accomplishing this task. Topology shows up in two distinct ways in the band structures of non-interacting Hamiltonians depending on whether the spectrum is gapped or gapless. In systems with gapped band structures, which include insulators and most superconductors, the wavefunctions wind non-trivially across the Brillouin zone in the topological phases, as described in Sec. 1.1. What constitutes a non-trivial winding depends strongly on the symmetries and the dimensionality of the system under consideration, thus, revealing a rich substrucutre within the insulating and superconducting phases. On the other hand, gapless band structures contain topological objects in momentum space which can be characterized by the winding of theGreen’s function around the object, as exemplified in Sec. 1.2. A key feature of topological media is that they typically have unconventional surface states which, in many cases, cannot exist independently of the bulk phase in one lower dimension. For instance, the two dimensional surface of a three dimensional topological insulator hosts pseudorelativistic electrons and cannot exist as an independent two dimensional system. Because of this intimate surface-bulk connection and because the surface is usually more accessible than the bulk, experiments usually probe the surface states in order to identify the bulk topological phase. The surface states are also extremely valuable from a practical point of view, since the unconventional properties bestowed upon them by the non-trivial bulk topology may be exploited to design novel electronic devices.The role topology plays in the band structures of gapped non-interacting Hamiltonians is analogous to its manifestation in an early example of topology in physics – Gauss’s law in electrostatics. Gauss’s law states that the total electric flux piercing a closed surface is determined only by the charge enclosed by it and is independent of its shape or the precise charge distribution. Thus, the total flux through each surface in Figure 1.1.1 is four units. For gapped noninteracting lattice Hamiltonians, the analog of the Gaussian surface is the Brillouin zone, and different Gaussian surfaces correspond to different Brillouin zones in the extended zone scheme or to different bands in the reduced zone scheme. The electric charge, then, maps to an appropriate topological invariant whose exact form depends on the symmetries of the system under consideration. This topological invariant can be written as an integral over the Brillouin zone of an appropriate field derived from the Bloch functions of the occupied bands, analogous to how the electric charge enclosed by a Gaussian surface is equal to an integral of the electric field over it. The analogy is generalizable to continuum Hamiltonians, defined over all of momentum space, as well, provided the points at infinity are identified. This identification compactifies momentum space to the topological equivalent of a sphere, which, being a closed surface, permits the application of Gauss’s law. Next, assuming every charge that exists in the universe is inside a Gaussian surface, the only way to change the amount of charge enclosed by a single surface is by fusing it with another Gaussian surface, moving charges across the junction and pinching the junction ofto get the original surfaces back, as illustrated in Figure 1.1.2. Similarly, for band structures, topological invariants can only be defined for Brillouin zones wave functions in the extended zone scheme or equivalently, for bands in the more common reduced zone scheme.

Higher synthesis coupled with reduced transporter activity may act to elevate synaptic dopamine concentrations in older adults, potentially reflecting compensatory mechanisms for counteracting losses in receptor density. However, research to date has not supported a clear role of elevated synthesis in benefiting cognition . Indeed, inverted-U-shaped relationships are observed for dopamine synthesis , suggesting higher synthesis levels may, in some cases, be detrimental. Therefore, it may not be sufficient to consider aging as simply a hypodopaminergic state, but instead may be a dysregulated state characterized by a loss of balance between presynaptic and postsynaptic components of the system. Similar conceptualizations of dopamine dysregulation may be applied to psychological and psychiatric disorders including schizophrenia, ADHD, and addiction . This dysregulation may critically affect the precision of dopamine signaling, increasing the variability of its temporal dynamics and noise . There is emerging evidence that regulation of dopamine receptors and age-related decline in receptor density is not spatially homogeneous . Rieckmann and colleagues report age-related reductions in interregional correlations in D1 BPND using [11C]SCH23390. Their findings suggested that aging is associated with a dissociation in D1 receptor regulation between nigrostriatal and mesocortical/mesolimbic pathways. Seaman and colleagues evaluated regional differences in estimated rates of percentage of change in D2/3 BPND using [18F]fally pride . Their findings revealed tremendous heterogeneity across regions in the estimated rate of decline, which was variably linear or curvilinear. Even after correcting for differences in gray matter volume, procona system they estimated the most extreme reductions in subgenual frontal cortex and superior temporal gyrus and less pronounced reductions in ventral striatum, pallidum and hippocampus .

Altogether, findings in aging indicate that changes in the dopamine system vary across individuals, vary across different presynaptic and postsynaptic components, and vary spatially across the brain. In the following three sections, we highlight instances in which accounting for these three sources of variability may shed light on reported effects in valuebased decision-making.Loss of dopamine has been linked with propensity to avoid punishment rather than approach reward. The probabilistic selection task is a well-known decision-making task that has been used to study these questions and has been applied to healthy adults and a variety of patient populations including those with Parkinson’s disease and schizophrenia . It ostensibly taps into processes of modelfree reinforcement learning, with some evidence suggesting it is preferentially associated with striatal rather than PFC dopamine function . Despite links to dopamine, there have been largely null findings in previous studies examining consistent group-wise effects of age on performance. Here we provide background on the PST, and models of dopamine’s role via the D1-mediated “direct” and D2-mediated“indirect” pathways. We propose that any measure that captures individual differences in dopamine function may useful in clarifying these null effects. Further, we discuss specific ways in which D1 and D2/3 receptor imaging can be leveraged to contribute to our basic understanding of the role of these pathways in human decision-making as well as individual differences in performance in aging. The PST is composed of both a probabilistic learning phase and a choice phase. Its design aims to assess potential biases in choice action to approach reward versus choice action to avoid punishment.

Briefly, three sets of Japanese hiragana characters are presented in randomized order and are associated with differing probabilities of reward or punishment . During the learning phase, participants learn to select the stimuli associated with reward. However, this learning could be driven by positive reinforcement from reward or negative reinforcement from punishment . The choice phase of the PST is designed to dissociate these possibilities. The stimuli are presented in novel pairs to reveal underlying choice biases in incentive motivation to either approach reward or avoid punishment . The bias to avoid punishment was demonstrated in Parkinson’s patients tested off medication, but was reversed when patients were tested on medication in presumably dopamine-replete states . Since the original description of the PST task, there has been significant interest in understanding how age-related changes in dopamine function may affect biases in decision-making. A simple hypodopaminergic account of aging would predict that age effects mimic those observed in Parkinson’s disease, but to a lesser degree given the relative sparing of dopaminergic function . Such biases, if they produce inoptimal choice behavior, would be a prime target for intervention in aging. Behavioral evidence of age-related biases in choice selection is mixed, with greater individual differences reported for older adults. A bias to avoid punishment has been shown in an older subset of older adults, but not in a younger subset . Some studies report greater individual differences in the balance between positively and negatively motivated choices in aging , or have shown selective reduction in positive learning but not negative learning . Other aging studies have found no effects of valence . We posit that accounting for individual differences in the decline of dopamine function using specific dopamine targets in striatum or neuromelanin-sensitive MR will clarify these null and mixed results. Previous research using MR approaches for assessing midbrain dopaminergic nuclei suggest a benefit of greater structural integrity for reward learning .

We predict that the subgroup of older adults with a positive choice bias to approach reward will have greater midbrain neuromelanin MR signal than older adults with a negative choice bias .The proposed mechanisms of dopamine’s involvement in approaching reward versus avoiding punishment involve the weighting of two circuits, the direct pathway versus the indirect pathway, involving substantia nigra, striatum, globus pallidus, and thalamus. Activation of the direct “go” pathway leads to the disinhibition of thalamus, facilitating outputs to cortex. Conversely, activation of the indirect “no-go” pathway suppresses thalamic output to cortex. The direct pathway is associated with reward-based learning and approach, which may be mediated by stimulation of striatal D1 expressing medium spiny neurons . The indirect pathway is associated with aversion-based learning and avoidance, which may be mediated by stimulation of striatal D2 expressing medium spiny neurons . Frank and colleagues suggest that low tonic dopamine amplifies learning through D2 negative reinforcement mechanisms and accounts for biases to avoid punishment in Parkinson’s patients tested off medication . A recent PETstudy in healthy young adults directly probed relationships between individual differences in D1 and D2/3 BPND and propensity to approach reward versus avoid punishment in the PST . However, higher D2/3 BPND was not clearly related to a bias to avoid punishment in this young adult sample. It is currently not known whether D2/3 effects would emerge if these healthy subjects were tested in a dopamine depleted state . It is possible that individual differences in relative ratios of D1 and D2/3 receptor densities may underlie between-subject variability in PST performance in older adults, or variability in performance on other tasks, such as tasks involving risky gambles, which tap into approach versus avoidance mechanisms. There is some evidence, though limited, suggesting D1 and D2/3 receptor densities decline at different rates across the lifespan . Estimated rates of decline are numerically greater for D1 receptors than D2/3 receptors for between-subject comparisons of PET data and within-subject analyses of postmortem tissue . However, additional research is needed to establish whether there are asymmetric effects of aging on D1 versus D2/3 receptors. It is unclear what the underlying physiological mechanism might be for the relative vulnerability of D1 receptors or relative resilience of D2/3 receptors in aging. D1 and D2-expressing medium spiny neurons have distinct morphological and electrophysiological properties which may confer unique susceptibilities. In culture, D2, rather than D1 receptors, procona valencia buckets may be more vulnerable to excitotoxic insults . However, observations in early Parkinson’s disease reveal upregulation of D2/3 receptors, but not D1 receptors . This leaves open the possibility that differences in the capacity for receptor upregulation may underlie reductions of the ratio between D1 and D2/3 in healthy aging. Regardless of mechanism, the direction of these effects observed in aging is generally consistent with the view that aging shifts choice behavior toward a bias to avoid punishment rather than approach reward.There is, however, significant inter individual variability in the trajectory of age-related changes in the dopamine system, which would warrant examination of within-subject ratios of D1 to D2/3 receptor densities and their relationship with performance. For the PST, evaluation of individual subject performance has revealed subgroups of older adults with a “positive” choice bias to approach reward and subgroups with a “negative” bias to avoid punishment . Subjects with losses in D1 receptors but relative preservation of D2/3 receptors may show reduced choice behavior to approach reward , and greater choice behavior to avoid punishment . Subjects with losses in D2/3 receptors but relative preservation of D1 receptors could be expected to show the opposite pattern of results .

In vivo PET imaging could resolve the underlying neural basis of these individual differences in positively and negatively motivated choices in aging. Further, complementary studies in animal models could test whether selective knock-down of D1 versus D2 receptors generates a similar pattern of results.While the density of dopamine receptors declines with age, there is evidence for counteracting increases in dopamine synthesis and decreases in dopamine reuptake via reduced transporter BPND . If imbalance in the tuning of pre and postsynaptic components occurs in aging, this dysregulation may lead to reduced precision of RPEs implicated in value-based reinforcement learning . Such dysregulation would be expected to result in slower model-free reinforcement learning. Behavioral evidence suggests that while older adults perform comparably to young adults when cue reward contingencies are deterministic older adults show impaired performance in situations in which outcomes are probabilistic or require learning from feedback . Though behavioral evidence indicates impaired reward-based learning in older adults, it is not clear that neural activity associated with reward anticipation or reward outcome is systematically altered in aging. Ventral striatum/nucleus accumbens activation in response to reward-predicting cues is the same in young and older adults . Further, responses to rewarding outcomes in ventral striatum and medial PFC have been shown to be similar in young and older adults . These measures of BOLD activation suggest there are no systematic differences in reward responsivity in aging. However, these measures typically rely on averages across many trials, and may not capture age-differences in trial-to-trial variability. Fruitful lines of research in aging have linked reward-based learning with neurocomputational approaches to examine age differences in RPE-like BOLD signal that rely on trial-based estimates. Together, these studies suggest that aging reduces correlations between RPEs derived from reward learning tasks and BOLD activation in ventral striatum/ nucleus accumbens and ventromedial PFC . Few studies have linked age-related reductions in these correlations with alteration in dopamine function in aging. In one notable exception, Chowdhury, Guitart-Masip, Lambert, Dayan, et al. pharmacologically manipulated dopamine to examine its effects on learning and RPEs. This study demonstrated that treatment of older adults with levodopa increased both RPE-like signals in ventral striatum and rates of learning. A recent study using the same task probed relationships between striatal D1 BPND and nucleus accumbens RPE’s in young and older adults . Surprisingly, they did not find striatal RPE-like responses in either young or older adults. D1 BPND was not correlated with performance for either group but was positively related to ventromedial PFC signal associated with reward anticipation. Moving forward, it will be valuable to consider how dopamine changes in aging may fundamentally alter the reliability in dopamine signaling to affect reward-based learning. This can be achieved in studies in animal models that examine the effects of age on the amplitude and timing of phasic responses. In humans, foundational studies could investigate whether neuromelanin-sensitive MR measures of midbrain dopamine function are related to the strength of correlations between RPEs derived from reward learning tasks and striatal BOLD signal in older adults. Higher correlations may be predicted in older adults with higher midbrain neuromelanin MR contrast-to-noise ratios. Applying PET methods, future studies could consider relationships between presynaptic and postsynaptic components within subject. For example, individual differences in the ratio of dopamine transporter availability and D2/3 receptor availability within subject may correlate with rates of learning . One may predict an inverted-U-shaped relationship between a presynaptic/ postsynaptic composite measure and learning suggesting that an optimal balance in dopamine receptor binding and reuptake is associated with more precise RPEs and more efficient learning rates in aging.

Fixed nitrogen is often a limiting nutrient for primary productivity in the surface ocean, and consequently influences the dynamics of oceanic carbon sequestration . Nitrogen fixation by marine cyanobacteria is an important source of oceanic fixed nitrogen, adding an estimated 100–200 Tg-N annually to open ocean ecosystems . This nitrogen fixation is often associated with cyanobacterial trichomes or aggregates colonized by heterotrophic bacteria, picoeukaryotes and metazoans . Respiratory activity within these so-called ‘pseudobenthic’ environments can create ephemeral suboxic to anoxic zones, establishing a niche for facultative anaerobes within otherwise oxygenated surface waters . Emerging evidence suggests that denitrification occurs within these anoxic habitats, coupling processes of nitrogen-fixation and loss at the microscale . While initial studies of marine biological nitrogen fixation focused on colonial filamentous Trichodesmium species and symbiotic, heterocystous Richelia species , more recent work has demonstrated the importance of unicellular diazotrophic cyanobacteria from the order Chroococcales . Diazotrophic UCYN have been studied extensively in the global oceans by surveys of the nitrogenase gene nifH diversity, blueberry in pot which revealed three phylogenetically distinct clades . UCYN-A are small , metabolically streamlined, uncultured cyanobacteria that lack the oxygen-producing photosystem II and live as endosymbionts within haptophytes, a lineage of eukaryotic algae .

UCYN clades B and C are larger , free-living cyanobacteria and include cultured representatives, such as Crocosphaera watsonii and Cyanothece sp. ATCC51142. Studies of aggregate-associated nitrogen fixation have focused predominantly on Trichodesmium sp. colonies and rafts , or filamentous heterocystous cyanobacterial colonies . However, some Crocosphaera watsonii strains have been observed to produce copious quantities of exopolysaccharides and have been linked to the formation of transparent exopolymer particles . These gel-like particles provide microhabitats for other microorganisms, and thus have the potential to play an important role in marine biogeochemical cycling . Here, we report a new species of uncultured, unicellular cyanobacteria from the order Chroococcales which forms millimeter-sized aggregates together with diatoms and other putatively heterotrophic bacteria. These macroscopic aggregates, which we call “green berries,” are found in the muddy, intertidal pools of Little and Great Sippewissett salt marshes . They are found interspersed with previously described, sulfur-cycling “pink berry” consortia . Using a combination of metagenomic sequencing and ecophysiological measurements, we demonstrate that the green berries are characterized by diazotrophy and rapid rates of photosynthesis and respiration that produce steep oxygen gradients. Heterotrophic bacteria within the green berries are closely related to other marine epiphytic marine strains and encode key genes in the denitrification pathway.

The green berries are found in the same organic-rich, intertidal pools of Little Sippewissett salt marsh on Cape Cod where both multicellular magnetotactic bacteria and pink berries have been previously studied . Though less abundant than the pink berries found in these pools , the green berries form similar irregular ellipsoid aggregates measuring 1–8 mm in diameter, with an average equivalent spherical diameter of 1.7 mm ± 0.1 mm . Green berries were dense and compact aggregates that were typically observed at the sediment-water interface, but were occasionally found to float at the water surface when suspended by bubbles. Microscopic observation of the green berries revealed abundant coccoid unicellular cyanobacteria 5–7 µm in diameter , interspersed with pennate diatoms . Filamentous cyanobacteria were observed occasionally, but were rare compared to the unicellular GB-CYN1 morphotype. A clear, extracellular matrix coated these aggregates of phototrophic cells, and was colonized by a variety of smaller bacteria . GB-CYN1 exhibited absorption maxima at 620, 660, and 680 nm corresponding to thepresence of phycocyanin, allophycocyanin and chlorophyll a, respectively.Sequencing of 18S rRNA genes from the green berries indicated that the eukaryotic community was predominantly made up of two different pennate diatom species related to Navicula cari strain AT-82.04c and Amphora pediculus strain AT-117.11 . These same diatom species were also the dominant eukaryotic 18S rRNA gene sequences recovered from pink berry aggregates, though diatoms were more abundant in green berries than in pink berries, as observed by microscopy and the relative abundance of 16S rRNA chloroplast sequences .

Bacterial 16S rRNA gene sequences amplified from the green berries were dominated by sequences related to either diatom chloroplasts or Chroococcales unicellular cyanobacteria . Unassembled metagenomic sequence reads assigned to rRNA sequences and protein-coding regions support the observed abundance of Chroococcales , but did not recover comparable proportions of diatom chloroplasts . FIGURE 2 | Comparison of green berry bacterial diversity estimates from16S rDNA PCR amplified clones library with unassembled Roche 454 metagenomic sequence reads. Taxonomic assignment of metagenomic reads matching ribosomal RNA reads was conducted using the M5RNA database in MG-RAST . A similar taxonomic assignment was conducted with metagenomic reads matching protein coding sequences in the M5NR database . Note that the 16S rRNA clone library abundance data for the Bacillariophyta was obtained from diatom chloroplasts sequences, which are likely present in multiple copies in the cell and thus not directly comparable to metagenomic 18S rRNA sequences for this group . The overall bacterial community structure of the green berries was significantly different from coexisting pink berry consortia . Some abundant taxa from the pink berries co-occurred in the green berries as rare OTUs, such as the purple sulfur bacterial species Thiohalocapsa sp. PB-PSB1 , and a Winogradskyella species . The persistence of these distinct, co-occurring pink and green berry consortia suggests that the process of macroscopic aggregation enables niche partitioning between oxygenic and anoxygenic phototrophs in these marsh pools. Most of the non-cyanobacterial sequences in the green berry consortia are related to aerobic and facultatively anaerobic marine heterotrophs from the Bacteroidetes, Alphaproteobacteria, and Gammaproteobacteria . Many of these sequences were most closely related to environmental 16S rRNA sequences associated with aggregates of oxygenic phototrophs. Examples of such habitats included phytodetrital aggregates collected from euphotic and hadal environments , and epiphytes of marine macroalgae . The occurrence of related phylotypes in such environments suggests that taxa may be well adapted to an attached lifestyle, degradation of photosynthate, and the fluctuating oxygen conditions in an aggregate environment.Metagenomic data indicate that the orders Rhizobiales and Rhodobacterales of the Alphaproteobacteria are abundant in the green berry consortia. While these groups were rarely detected in the PCR-based 16S rRNA survey, we have previously observed this same PCR bias from the 8F primer during studies of the pink berry consortia . We find the abundance of these clades in the green berries particularly interesting as they include lineages of marine denitrifying bacteria. For example, pelagic Rhizobiales have been linked to denitrification when found in association with macroscopic Trichodesmium sp. aggregates in oxic waters bordering oxygen minimum zones .The cyanobacterial 16S rRNA gene sequences from the green berries grouped into two closely related OTUs , GB-CYN1a and GB-CYN1b, that can be confidently placed in the order Chroococcales . The GB-CYN1 monophyletic cluster formed a clade basal to the UCYNA clade . Using 29 concatenated single-copy phylogenetic marker genes assembled from the metagenome , plastic planters wholesale we reconstructed a phylogenetic tree that placed the GB-CYN1 within a clade including Crocosphaera watsonii and Cyanothece sp. ATCC 51142 as a sister taxa to “Candidatus Atelocyanobacterium thalassa” isolate ALOHA . A phylogenetic tree inferred from nifH gene sequences reveals that the near full-length nifH gene recovered from the GB-CYN1 metagenomic data affiliated with the UCYN-B clade, and was most closely related to Cyanothece sp. 8801/8802 and Crocosphaera watsonii . We conclude that the observed discordance between 16S rRNA, concatenated, and nifH gene phylogenies involving species such as Cyanothece sp. 8801, Gloeothece sp. KO68DGA, and the cyanobacterial endosymbiont of Rhopalodia gibba is most likely due to lateral gene transfer of the nifH gene. Lateral transfer of nifH has been observed in many other species, including mat-forming filamentous cyanobacteria .A full suite of nitrogenase genes were found in the green berry metagenome and were consistently assigned to GB-CYN1, indicating the metabolic potential for nitrogen fixation characteristic of other members of the UCYN A-C clades . In two separate experiments , we measured rates of 11 and 20 nanomoles acetylene reduced per hour per milligram of aggregate dry weight . These rates are comparable, though faster than the rates of 3–6 nmol mg−1 hr−1 reported in macroscopic aggregates of filamentous cyanobacteria from Bogue Sound, North Carolina . Rates measured from actively growing Cyanothece cultures were two orders of magnitude larger than the rates in the green berries.

The total aggregate elemental composition was analyzed using elemental analyzer isotope ratio mass spectrometry . The mean observed C:N ratio in the green berries, 7.1 ± 0.6 , falls within range of the Redfield molar ratio . This observed C:N ratio is higher than that the ratio of 5.4 ± 0.4 observed in similarly large, anoxic, diazotrophic Nodularia spumigena aggregates from the Baltic Sea . Cultures of Crocosphaera watsonii exhibit wide diel fluctuations in C:N ratios as a result of temporal partitioning of carbon and nitrogen fixation activities . Our samples, collected in the late afternoon on a 14 h light/10 h dark photoperiod, are comparable to reports of C:N = 7 from C. wastsonii at similar late afternoon times in a 16 h light/8 h dark photoperiod . Future studies investigating the temporal partitioning for such activities in the green berry aggregate would be informative to elucidate the dynamics of carbon and nitrogen flow in the consortia.Oxygen microsensors were used to characterize the balance between respiration and photosynthesis in the green berry aggregates. Aggregates examined were relatively symmetric ellipsoids of similar size with an equivalent spherical diameter of 1.7 ± 0.1 mm . Photosynthesis produced supersaturated oxygen concentrations within the aggregates: 380 µM O2 with illumination at 170 µE m−2 s −1 and 520 µM O2 at 320 µE m−2 s −1 . During these experiments, bubbles were not observed on aggregate surfaces and the aggregates never floated. Oxygen production rates per aggregate were calculated from these profiles as 13 and 31 nmol O2 per hour at 170 µE m−2 s −1 and 320 µE m−2 s −1 , respectively . We did not rigorously determine the saturating light intensity; however, we observed that illumination with a third lamp failed to stimulate increased oxygen production beyond that with two lamps , suggesting that the saturating light intensity lies in the range of 170 – 320 µE m−2 s −1 . This rate, equivalent to a volumetric rate of 6.8 µmol cm−3 hr−1 , is well above the theoretical threshold for respiration rates capable of causing oxygen diffusional limitation from surrounding seawater . In light-dark shifts, we observed a rapid response where the aggregate core transitioned from steady state supersaturation to full anoxia in 5–8 min . Volumetric gross photosynthetic rates were calculated by two methods: from depth microprofiles via the sum of net photosynthesis and dark respiration and via the light-dark shift technique performed at a single point in the aggregate center . At both light intensities examined, rates calculated via the light-dark shift method were found to be 4.5 µmol cm−3 hr−1 , lower than those from depth microprofiles. While this difference could arise from biological variability between aggregates, we suspect that the light-dark shift rates measured at the aggregate core were lower than those we might have measured closer to the aggregate surface. Future depth integrated studies of photosynthetic rates will help to clarify this difference and allow better characterization of respiratory activity in the light. Comparing the green berries’ dark respiration and gross photosynthesis to other photosynthetic mats and aggregates, we find them similar to the high rates measured for large , filamentous aggregates of the heterocystous cyanobacterium, Nodularia spumigena from the Baltic Sea . Indeed, our estimates of carbon fixation are close to prediction of 349 ng C per aggregate per hour calculated using Ploug et al.’s regression of volume to gross photosynthesis from a 2009 Nodularia bloom. The green berry dark respiration rate was similar, though slightly higher than that observed for Nodularia aggregates of similar diameter; however, the ratio of dark respiration to gross photosynthesis of 0.38 was identical to that observed for 7 mm3 aggregates found late in the bloom . In large Nodularia aggregates, dark anoxia is associated with active dissimilatory nitrogen cycling, including denitrification, dissimilatory reduction of nitrate to ammonia , and significant rates of cryptic nitrification .

Sections were then transferred to 1.5 ml of 0.15% Proteinase K solution and mixed at 55°C and 300 RPM rotation for 14 days with an Eppendorf Thermomixer . Samples were then washed in DI water and placed into an 0.1% amylase solution for 24 hours at 50°C. Samples were then washed in DI water again, lyophilized overnight, mounted on aluminum stubs, and viewed under a Field Emission Scanning Electron Microscope . Sieve plates were viewed under low vacuum , 20- KV of accelerating voltage and a spot size of 2.5.Phloem anatomy was a stronger predictor of maximum sugar accumulation rates than vine carbon gain or water stress. Maximum sugar accumulation rates were not significantly correlated with photosynthesis or midday leaf water potentials . Including photosynthesis and midday leaf water potential as additional predictors also did not substantively improve the relationships between maximum sugar accumulation rates and petiole or pedicel cross-sectional phloem areas. Akaike Information Criterion corrected for small sample size values were higher for the larger models than the univariate models predicting maximum accumulation rates from petiole or pedicel phloem area alone, indicating that accounting for vine carbon gain and water stress did not improve predictive capacity for sugar accumulation . In addition, only one correlation was found between phloem petiole area and minimum mid-day water potential , while other average photosynthesis and water potential variables did not correlate with the phloem anatomical parameters. Finally, a previous dataset measuring leaf area for each cultivar did not find any significant correlations with °Brix accumulation, or other parameters measured .Overall, collection pot we found that total cross-sectional phloem area in the pedicels and the petioles significantly predicted maximum °Brix accumulation rates in the berries , as well as sieve element area in pedicels .

Other sieve tube traits, such as sieve plate porosity, were not correlated with sugar accumulation rates, indicating that grapevines mainly increase their maximum capacity for sugar transport by adding more and wider sieve tubes to the transport pathway. Total cross-sectional areas were significantly lower in cultivars typically grown in hot than warm growing regions, suggesting these cultivars have been inadvertently selected for smaller phloem areas to slow sugar accumulation, delay ripening, and achieve an optimal flavor profile provided by longer grape maturation times prior to harvest . Further, although there wasn’t a significant difference in sieve element area between cultivar climate category in the pedicel phloem, sieve element area did significantly predict brix accumulation rate. Phloem area was also a stronger predictor for sugar accumulation rates than the typical vegetative physiology parameters of gas exchange and water potential . This study points to a new anatomical phenotype that can be used by grape breeders to select for cultivars with smaller petiole or pedicel phloem areas to decrease sugar accumulation rates to berries as an adaptation to increasing temperature.Our phloem area and °Brix accumulation results align with findings from trait comparisons in other crop species and experiments manipulating phloem area in grape and other crops. In grapevine , abscisic acid and gibberellin hormone treatments increased the phloem cross-sectional area in the midveins, pedicels, and stems along with berry sugar concentrations, despite reduced photosynthetic assimilation . The increased phloem area enhances the hydraulic conductivity of the transport pathway , facilitating the transport of sugars from source to sink .

Phloem area has also been linked to fruit growth and sugar accumulation in other crop species. For example, modifying the expression of a phloem cell proliferation regulatory gene in tomato increased phloem area, yield, and fruit sugar concentration . Similarly, in giant pumpkin varieties, the phloem area in pedicels and petioles was positively correlated with fruit yield . These findings highlight the potential for optimizing phloem area to enhance plant productivity by matching source production and sink utilization. Additionally, our study suggests that targeting phloem/xylem in petioles could be an efficient approach for plant breeders to improve yield by enhancing hydraulic conductance and carbon export to fruits .One of the goals of this study was to investigate how cultivars adapted to different climate regimes varied in sugar accumulation and vascular anatomy traits under common garden conditions. Approximately half of the variance in berry sugar concentration is attributable to climate , making common garden experiments crucial to isolate the effects of plant traits on sugar accumulation. We found that, for red varieties, total phloem cross sectional area in the petioles and pedicels was significantly larger in the varieties typically grown in warm regions than hot regions . This could be an adaptation unknowingly selected by generations of winemakers to slow sugar accumulation and synchronize sugar and flavor development in hot climates. For white varieties, phloem area did not increase significantly from hot to warm regions . There could have been less selective pressure to increase sugar accumulation in the warm-climate white than red varieties, since white wines are typically made with lower alcohol content, and the absence of anthocyanin production could reduce metabolic demands for sugar .

Phloem anatomy is influenced by both the climate that plants have adapted to and the climate plants experience during the growing season . This suggests that more work is needed to evaluate how plastic responses to inter annual or geographic variability to climate influence cultivar differences in phloem anatomy and sugar transport capacity. In Arabidopsis, the effects of growing conditions on phloem anatomy depended strongly on the climate the genotypes evolved in. Comparisons between cool and hot growing conditions showed that high temperatures reduced the proportion of phloem area in the minor veins, and that these reductions were larger in Arabidopsis genotypes that evolved in cool than hot climates . These results suggested that phloem plasticity in response to growing conditions outside evolved temperature ranges was greater ingenotypes adapted to cool climates, increasing genotypic differences in phloem anatomy under hot growing conditions. Interestingly, we found the opposite pattern in grape, that phloem area in the pedicel and petiole was significantly larger in the cultivars typically grown in warm than hot climates, even though our common garden experiment was in a hot growing region . Comparisons in different regions or in years with different climatic conditions are needed to determine how strongly the cultivar differences in anatomy observed here depend on the conditions during phloem development.Xylem and phloem area scaled in the midvein, petiole, and pedicel, which produced similar relationships in xylem and phloem areas with maximum °Brix accumulation rates and climate groupings . The relationships with xylem area could simply reflect selection for phloem traits and developmental constraints that make xylem and phloem differentiation proportional, or both xylem and phloem area could impact °Brix accumulation rates. °Brix is a concentration and determined by water and sugar contents. The phloem supplies most of the water to the berries after veraison . The total volume of phloem water influx is generally much larger than the volume of the berries, forcing the berries to export water to the canopy through the xylem to avoid cracking or splitting . A larger phloem area would increase the water influx into the berries, which could require a larger xylem area to compensate for water export. Further, the xylem accounted for most of the vascular area in each organ, and the ratio of xylem to phloem area increased with stem cross sectional area, which also made this ratio significantly larger in warm- than hot-climate cultivars . This larger xylem:phloem ratio could accelerate °Brix accumulation by increasing the capacity for water export relative to influx. Thus, selecting for a lower xylem:phloem ratio could slowberry sugar accumulation. Xylem and phloem areas also scale in other species, including ash , Pelargonium , fir , poplar, and ginkgo , and, notably, xylem: phloem ratios were smaller in species with larger fruit . However, some grape cultivars produce blockages in the pedicel xylem during ripening that reduce conductivity and water efflux, 10 plastic plant pots which could make the ratio of xylem to phloem area less important to °Brix accumulation rates. Overall, more work is needed to clarify the effects of individual tissue areas and xylem: phloem area ratios on ripening.Another interesting findings from the current study was that sieve element area was a significant predictor of brix accumulation rate , while porosity of the elements , most of the smaller sieve element area/ lower brix accumulation rate cultivars were from the warm climate category. These findings suggest that grapevines have primarily adapted to control sugar accumulation rate by changing the number and width of sieve elements, although these two traits were not correlated . Conversely, phloem cross sectional area and mean sieve element area were correlated in the pedicels for other species, including pumpkin and tomato . However, similar to our findings, variation in sieve element area was small for pumpkin, and the differences between cultivars were not significant .

Cooler growing regions are typically more humid and prone to disease pressure , and less porous sieve plates can facilitate the faster formation of callose blockages to more quickly restrict pathogen spread through the phloem . Future work may consider the transcriptional abundance of sugar unloading proteins , and how this relates with phloem anatomical characteristics related to pathway resistance.Phloem anatomy was a stronger predictor of berry sugar accumulation rates than vegetative physiology parameters capturing vine carbon gain and water status. This was unexpected, since photosynthesis determines the carbon available for ripening, and water stress has been shown to strongly impact sugar accumulation rates in many of the cultivars tested here . However, our experimental vines were irrigated during the ripening period to maintain leaf water potentials in a relatively narrow range . This irrigation regime follows standard commercial practices for California, which could have limited cultivar differences in vine water stress and photosynthesis and thus, their impacts on sugar accumulation. These findings suggest that measuring phloem anatomy could provide more insight into plant capacity for berry sugar accumulation under standard, irrigated conditions than conventional vegetative physiology traits. Alternatively, leaf-level photosynthesis could have been decoupled from °Brix accumulation by variation in vine balance , which would impact the ratio of whole-plant carbon supply to demand. A larger ratio of canopy area to fruit mass would increase maximum °Brix accumulation rates. Future work should estimate leaf area per cultivar to ensure that relationships between phloem anatomy and maximum °Brix accumulation rates scale with variation in vine balance.Overall, we found that phloem cross-sectional area in the petioles and pedicels was the most predictive trait for the maximum rate of sugar accumulation in the berries across winegrape cultivars tested. Carbon dioxide in the atmosphere is expected to double by centuries’ end, and the dual effects on plant carbon availability and growing season temperature are projected to strongly accelerate sugar accumulation and exacerbate the detrimental impacts on wine quality . We suggest that reduced phloem areas could be a useful and novel phenotype to screen for in existing cultivars to slow carbon transport rates in hotter growing regions, allowing more time for flavor development. If petiole phloem area is well-conserved across life stages and under different growing conditions, this would be an especially useful trait to accelerate phenotyping since grapevines must mature for several years to begin producing fruit. However, future work is still needed to clarify how xylem area and vine balance influence sugar concentrations, and how interannual and site-specific environmental variability influence anatomical traits and sugar accumulation.Age-related macular degeneration is the leading cause of blindness among seniors in developed countries, and third worldwide after uncorrected refractive errors and cataracts. In early stages, the disease is characterized by small to intermediate drusen with pigmentary changes that may progress rapidly to more advanced forms such as choroidal neovascularization or central geographic atrophy with loss of central vision. Lutein , zeaxanthin , and the isomer meso-zeaxanthin are macular pigments that filter damaging blue light and provide oxidative defense in the macula. These pigments are found in plants as xanthophylls, with increased dietary intake proposed to reduce the development and progression of AMD. The relative concentration of xanthophyll carotenoids in the retina can be measured non-invasively by psychophysical and objective methods, expressed as macular pigment optical density. Numerous epidemiological studies report that individuals with a low MPOD level are at an increased risk of AMD. Dietary L and Z are found in certain fruits and vegetables with red, yellow, or orange color, egg yolk, and in some green leafy vegetables.

Orienting vineyards N-S on a flat terrain allowed for uniform canopy and cluster exposure to solar radiation, since radiation is approximately symmetric about the N-S axis . However, the berry temperature on the west side of the vine significantly increased in the afternoon compared to the east side because hysteresis in air temperature causes asymmetry about solar noon. On average, berry temperature on the west side of the vines was greater than 35◦C for about 1-2.5 hours longer than the east side . Interestingly, although there was temporal asymmetry due to air temperature and temperature extremes, the net daily accumulation of berry growing degree hours was virtually identical between each side of the vine . On flat terrain, rows oriented NW-SE increased light interception and fruit overexposure in the afternoon and E-W reduced light interception and fruit overexposure in the afternoon . The high exposure to direct sunlight in NW-SE oriented rows resulted in simulated berry temperatures up to 7.8◦C higher on the SE side compared to the NW side . Compared to rows oriented NE-SW, best indoor plant pots rows oriented NW-SE had an additional 3 hours of canopy light interception above 200 W m−2 between 14:00 and 17:00 and berry temperatures greater than 35◦C for 2 additional hours . Narrow spacing affected berry temperature by potentially reducing the duration of berry exposure due to shading from neighboring vines.

Compared to the wider row spacing, the berries in narrow row spacing in N-S rows on a flat terrain intercepted up to 36% less sunlight and reduced elevated berry temperatures on the west-facing side . In the E-W row orientation, the number of hours with berry temperatures greater than 35◦C was also reduced with the narrow row spacing due to the shading from neighboring vines . The most balanced sunlight exposure and growing degree hours between each side of the vine was achieved in the N-S row orientation, although notable hourly berry temperature differences were present for both narrow and wider row spacing. For example, west-facing berries exceeded35◦C for about 1 hour for the narrower row spacing and about 3.6 hours for the wider row spacing .Adding a 30◦ slope to each of the simulations had a considerable effect on berry temperature, and could significantly change its behavior relative to flat terrain. Furthermore, the conditional inference tree results showed that the slope aspect had the strongest effect on the imbalance in temperature between different sides of the vines . In general, sloping to the south or west tended to increase light interception, berry temperatures, and berry temperature imbalance relative to north- or east-facing slopes. For example, compared to the vines oriented NW-SE on flat terrain, the vines oriented NW-SE on a southwest-facing slope increased the number of hours of Tberry > 35◦C up to 1.25 h on the southwest side . In contrast, situating these vines on a northeast-facing slope decreased the number of hours of Tberry > 35◦C up to 2 h on the northeast side . 、

For N-S oriented vines, slope had a minimal effect on daily integrated quantities such as daily light interception and berry growing degree hours, but did significantly affect short-term increases in berry temperature. N-S rows on west-facing slope increased the number of hours of Tberry > 35◦C for west-facing berries by over 2 h relative to flat terrain. However, these effects tended to be averaged out in N-S rows to maintain good symmetry over a daily period. The NE-SW oriented vines maintained good protection from berry temperature spikes and relatively good symmetry between sides of the vine as slope was added. For NE-SW oriented rows, the northwest-facing slope had more hours with Tberry > 35◦C than for the southeast-facing slope, but the opposite was true for daily-integrated quantities. This illustrates that exposure due to partially western-facing slope was more effective at generating temperature extremes than a partially southern-facing slope, but the opposite is true for daily-integrated quantities.The efficacy of shade cloth in reducing or equalizing berry temperature strongly depended on the row orientation and slope aspect . In general, adding shade cloth to the side of the row with partial or full south or west exposure tended to produce a significant reduction in berry temperatures and heat accumulation, as is to be intuitively expected. Adding shade cloth to sides of the vine with partial or full north or east exposure typically had weaker effect, and could actually increase temperatures on north-facing berries due to trapping of energy transmitted from the south. While avoiding fruit overexposure reduces fruit temperature, in some cases, controlling the amount of direct radiation received by berries with shade cloths consistently maintained the berry temperature below 35 ◦C.

For instance, in vines oriented N-S and NW-SE with wider rows, 50%and 70% shade cloth significantly reduced the time berry temperature was above 35◦C late in the afternoon in west facing berries . It was possible in several cases to achieve near-equal heat accumulation between sides of the vine while also minimizing berry temperature extremes by applying shade cloth to one side of the vine. For example, applying 70% shade cloth to the SE side of the vine in NE-SW oriented rows on flat terrain effectively balanced heat accumulation while also eliminating berry temperatures above 35◦C. E-W oriented rows always had high imbalance in heat accumulation regardless of shade cloth density or slope aspect.Comparisons between measured and modeled berry temperature indicated that the model is able to reproduce general spatial and temporal patterns of temperature, and can capture the additional effects of shade cloth. This is in addition to prior validation efforts demonstrating excellent model performance in the absence of shade cloth. Experimental validation of 3D, spatially explicit models is complicated by high sensitivity of localized model predictions to specifics of the canopy geometry. However, overall close agreement between measurements and model predictions in an average sense suggested that the model is robust to variation in vineyard architecture, topography, and the addition of shade cloth. For model validation purposes, local measurements of ambient berry microclimate were used to drive simulations. Effects of large-scale microclimatic variation was not included within this model, which could affect the predictive ability of the model as large-scale features are varied such as topography. Variation in topography could induce changes in wind speed or sensible heating of the air independent of vineyard structure, which was not represented in the model. However, radiation exposure is the primary driver of berry temperature deviations from ambient, and other microclimatic effects due to large-scale topography are likely to be secondary and establish the baseline temperature state similar to changing weather.The results of this study for flat terrain largely confirmed conclusions of previous work regarding design of vertically-trained vineyards for berry temperature management, but revealed some additional trade-offs for consideration. Similar to previous findings, the NE-SW row orientation on flat terrain is likely to be the best compromise between canopy and berry light interception, reduction of elevated berry temperatures, and balancing of heating between opposing sides of the vine, which was also argued by Tarara et al.. A trade-off of this vineyard design is that it modestly reduces overall vine light interception relative to the more common N-S row orientation. Additionally, there are still significant differences in berry heat accumulation and exposure between sides of the vine in a NE-SW row orientation. However, for VSP vineyards on flat terrain with no shade cloth, the NE-SW row orientation appeared to be the best overall at equalizing exposure between sides of the vine and reducing berry temperature extremes. For N-S oriented rows on flat terrain, previously well-documented imbalances in berry temperature between sides of the vine were also observed. It is intuitive to understand that the higher air temperatures and lower humidity that occur in the afternoon, blueberry container size when combined with berry exposure to the west sun, creates higher berry temperature than in the morning when ambient conditions are cooler. There is strong evidence that the accumulation of berry anthocyanin is a function of temperature and light Buttrose et al., Downey et al., Hunteret al., Spayd et al. and that the temperature difference between sides of the vine can create imbalance in the mass of the berries, as well as on tritable acidity, pH and phenolic compounds.

If row access by mechanical equipment is not a concern, decreasing row spacing could offer some protection against berry temperature extremes, although this is not effective at balancing opposing sides of the vine. Interestingly, results indicated that although there was high berry temperature imbalance localized to the afternoon, daily integrated metrics such as daily growing degree hours and daily berry light interception were almost perfectly balanced between sides of the vine in N-S rows. However, it is possible this was coincidental, or that abnormal diurnal temperature fluctuations such as that caused by clouds could break this symmetry. The NW-SE row orientation on flat terrain resulted in the most elevated berry temperatures. Berries on the southwest side of the vine spent nearly 4 hours above 35◦C, and shade cloth did little to mitigate these temperatures because the sun was nearly perpendicular to the shade cloth at the hottest time of day. Most previous work examining the effects of shade cloth does so for a single site and vineyard design, but results indicated that details of topography and vineyard architecture can have a significant effect on shade cloth performance. In N-S oriented rows on flat terrain, smaller row spacing relative to canopy height significantly reduced the hours of berry exposure to direct sunlight in the east and west side of the vine due to shading from neighboring vines. While berry temperatures were reduced in vineyards with narrower row spacing, grape and wine quality could decline at some point when row spacing is reduced due to excessive berry shading. Mechanical equipment access may be impeded below some threshold row spacing. Full-size equipment generally requires a minimum row spacing of around 3 m for single canopy systems. Thus, depending on the availability of equipment for mechanization and the vineyard design, shade cloth appeared to be a viable option for mitigation of berry overexposure in widely spaced rows. This study considered only VSP trellis systems at a single fruiting height, which resulted in the potential for high fruit exposure. Other trellis systems that reduce berry exposure are becoming more popular in warm climate regions. However, since it is usually undesirable to completely shade clusters because of its negative effect on berry quality, it is still necessary to understand the interaction effects between canopy architecture and berry exposure. While the results of this work can provide some initial guidance in this regard, future work analyzing different trellis types is still needed. Because of the spatially explicit nature of the model presented in this work, it is likely that only minimal adjustments to the model are needed to accommodate different trellis types.For most cases, it was observed that planting on a slope fully or partially facing south or west increased berry exposure and elevated temperatures relative to north- or east-facing slopes or flat terrain . Furthermore, a west-facing slope tended to increase temperatures more relative to a south-facing slope. This is intuitive given that the sun spends most of the day to the south, and the sun is to the west during the warmest time of a typical day. In several cases, slope had the negative effect of increasing the imbalance in heat accumulation between sides of the vine. This was especially true for the E-W row orientation, which caused very large imbalance that could not be effectively mitigated by shade cloth. For N-S and NE-SW oriented rows, the impact of slope on the berry temperature metrics was generally small. Shade cloth was able to mitigate the negative effects of slope in many cases. Applying 70% shade cloth in the sloped cases achieved excellent balance in heat accumulation between sides of the vine with N-S, NW-SE, and NE-SW orientations. The 70% shade cloth was also able to reduce the time above 35◦C to 1 hour or lower in all but the case with N-S rows on a west-facing slope, and NW-SE rows on flat terrain. The 3D model developed in this work was able to represent the effects of shade cloth on berry temperature and, thus, provided a viable tool for quantification of interactions between hypothetical vineyard designs and shade cloth on metrics related to berry temperature.

The presence of topologically non-trivial electronic band structures in condensed matter systems leads to a number of unusual consequences. A rich variety of phenomena have been discovered in gapless topological materials, such as those exhibiting Dirac-fermion excitations near the points of linear crossings of bands close to the Fermi energy EF. The breaking of either spatial inversion symmetry or time reversal symmetry splits the degeneracy of the Dirac points, leading to a pair of topologically protected Weyl points. Weyl fermions have been found to cause distinct experimental signatures, such as the chiral anomaly in transport measurements, a topological Hall effect, and Fermi arcs. Weyl fermions have mainly been studied in weakly correlated electron systems, while strong electronic correlations are frequently found to lead to novel electronic properties beyond those of simple metals or insulators, and heavy fermion systems are the prototype examples showing phenomena characteristic for strongly correlated electron systems. Here, due to strong Kondo coupling between the f-electron and conduction-band states, below the Kondo temperature , the electronic bands in the vicinity of EF may become strongly renormalized, showing a strong f-character and a huge enhancement of the quasiparticle mass. When the chemical potential lies within the hybridization gap, insulating behavior is found at low temperatures and in the topological Kondo insulators, such as has been proposed for SmB6, square plant pots the resulting electronic structure is topologically non-trivial, again leading to conducting states on the surface.

It is therefore of particular interest to look for topological heavy fermion semimetals with gapless excitations, i.e. Weyl fermions in the presence of strongly renormalized bands. Such a Weyl–Kondo semimetal phase has been predicted from calculations based on the periodic Anderson model with broken inversion symmetry. While it was proposed that Ce3Bi4Pd3 displays the low-temperature thermodynamic signatures of a Weyl–Kondo semimetal, other signatures of Weyl fermions such as the chiral anomaly have not been reported. A Weyl heavy fermion state was also proposed for CeRu4Sn6 from ab initio calculations, but no experimental evidence for Weyl fermions has been demonstrated. Consequently, whether Weyl fermions exist in the presence of a strong Kondo effect needs to be determined experimentally. Furthermore, the influence of electronic correlations on Weyl fermions is to be explored, specifically how such a system evolves from high temperatures, where the f-electrons are well localized, to low temperatures where there is a strong Kondo interaction and a reconstruction of the electronic bands. It was recently found that the half-Heusler GdPtBi, which has a strongly localized 4f-electron shell, shows evidence for Weyl fermions in an applied magnetic field due to the presence of the chiral anomaly and topological Hall effect. Here, we examine the isostructural compound YbPtBi. Although at high temperatures the Yb 4f-electrons are localized similar to GdPtBi, upon cooling YbPtBi becomes a prototypical heavy-fermion semimetal, where the enormous Sommerfeld coefficient of γ ≈ 8 J mol−1 K−2 demonstrates the enhanced effective mass of the charge carriers. This compound is therefore highly suited to look for Weyl fermions, which are strongly affected by electronic correlations. In this work, we report evidence for Weyl fermions in YbPtBi, where the bands hosting the Weyl points are strongly modified as the Kondo coupling strengthens at low temperatures.

Electronic structure calculations and angle-resolved photoemission spectroscopy measurements indicate the presence of triply degenerate fermion points in the high-temperature regime, which will each split into a Weyl node and a trivial crossing in applied fields. At these temperatures, evidence for the chiral anomaly is revealed by field-angle-dependent magnetotransport measurements. As the temperature is lowered, the chiral anomaly is not detected in the magnetotransport, but experimental signatures of Weyl fermions are found in measurements of the specific heat. This is consistent with a greatly reduced Fermi velocity due to the influence of the Kondo effect on the electronic bands near the Weyl points. Furthermore, the observation of a topological Hall effect contribution, which can arise from the Berry curvature generated by the Weyl nodes, provides additional evidence for the existence of Weyl fermions at both low and elevated temperatures.At higher temperatures, the band structure of YbPtBi can be calculated treating f-electrons as core states, as displayed in Fig. 1. The Λ6 bands cross the two hole bands near EF, forming two triply degenerate fermion points. Under amagnetic field, each triply degenerate point will further split into a Weyl point and a trivial crossing, with energies close to the bottom of the electron bands. The calculated bulk band structure with triply degenerate points is in good agreement with the ARPES results in Fig. 1b, which shows the energy–momentum dispersion relations along the surface ΓMdirection. Note that the sample can only be cleaved well with the orientation.

Along this orientation, the symmetry-equivalent bulk ΓL direction projects on the surface ΓM direction at a slanted angle, allowing for the dispersion in the vicinity of the triply degenerate points to be revealed via a careful comparison with the projected bulk band structure calculations . Two hole bands crossing EF can be clearly identified in the ARPES experiments, as well as an additional electron band with a band bottom right below EF. These experimentally observed bands are confirmed to be three dimensional bulk bands based on their photon energy dependence, and they correspond well to the theoretical calculations. The direct observation of both electron and hole pockets and their close proximity with different group velocities confirms the existence of the triply degenerate fermion points near EF, which is not affected by the slight discrepancy between the experimental results and calculations. This discrepancy is mainly related to the details of the separation and slope of the two hole bands, which could be caused by the limitations of frozen f-shell calculations and correlation effects not taken into account by the local density approximation. The good correspondence between ARPES measurements and density functional theory calculations therefore provides evidence for Weyl fermions at elevated temperatures.Based on the above experimental findings, we propose the diagram shown in Fig. 5 to describe the Weyl fermions in YbPtBi. At high temperatures there are Weyl nodes formed from the conduction bands, while the f electrons are well localized. This is consistently shown from electronic structure calculations, ARPES, and magnetotransport measurements. At lower temperatures, the strong band renormalization due to Kondo coupling enhances the effective quasiparticle mass, which modifies the dispersion ofthe bands in the vicinity of the topologically protected Weyl points, as shown schematically in the diagram. The renormalization also leads to a greatly reduced effective Fermi velocity v* compared to the bare band value, which eventually causes the disappearance of the chiral anomaly in transport measurements, but allows for the observation of a sizeable specific heat contribution C ~ 3. Importantly, there is evidence for the Berry curvature associated with the Weyl nodes from the anomalous Hall effect, which can be detected in both the intermediate and low-temperature regimes. Our results highlight the existence of Weyl fermions in YbPtBi, where we find evidence for their modification as the Kondo coupling is strengthened upon lowering the temperature. How precisely the Weyl points are modified as the electronic correlations become stronger needs to be determined by future studies. While the topological Hall effect and specific heat provide evidence for the survival of Weyl fermions at low temperatures, looking for spectroscopic evidence from ARPES or scanning tunneling spectroscopy is very important. One possible approach to reveal Weyl fermions in the heavy fermion state from f-bands is resonant photo emission. However, plastic potting pots our measurements across the Yb N edge do not show obvious resonance contrast . Although ARPES measurements with hν > 100 eV indeed reveal the bulk f bands near EF , resolving the hybridized bands deep inside the heavy fermion state is still challenging, and therefore further ARPES measurements with greater energy and momentum resolution are highly desirable. The presence of Weyl fermions in YbPtBi is different from the cases of both CeSb and GdPtBi, where the bands hosting Weyl fermions do not have a significant f-electron contribution.

Meanwhile, evidence for Weyl fermions has also been found in some magnetic d-electron systems such as Mn3Sn and YbMnBi2, where in the case of Mn3Sn a significant topological Hall effect is also observed. On the other hand, it is of great interest to look for the kind of dichotomy observed here for YbPtBi in other potential Weyl heavy-fermion semimetals, such as Ce3Bi4Pd3 where a similarly small v* was inferred from the specific heat, yet evidence for the chiral anomaly at elevated temperatures has not yet been reported. Furthermore, the strength of the Kondo interaction in heavy fermion systems can be readily tuned by non-thermal control parameters, such as pressure and magnetic field, and in particular, a quantum critical point can be reached in YbPtBi at a critical field of 0.4 T. Therefore, our findings may open up the opportunity to explore the exciting relationship between Weyl fermions, electron–electron correlations and quantum criticality.Increasing temperatures and temperature variability associated with a changing climate have become a major concern for many wine grape growing regions due to their effect on grape and wine composition. As is true for other crops, adequate sun exposure is vital because grapevines need sunlight for photosynthesis, growth, and development, and absorbed radiation by the berries is crucial for the biochemical and physiological processes that determine grape berry quality. Regrettably, excess sunlight and elevated temperatures are negatively affecting grape productivity in many growing regions. In California, minimum and maximum annual temperatures have increased from 1985 to 2011 by 2.34◦C and 1.77◦C, respectively, and in the summers by 3.88◦C and 3.31◦C, respectively . In Oakville, CA, Mart´ınez-Luscher et al. ¨ reported that elevated temperatures for grape clusters resulted in unbalanced wines with higher pH and lower levels of anthocyanins. Other research in Murrumbidgee, Australia reported that temperatures exceeding 40◦C result in delaying ripening and causing berry sunburn. Thus, strategies to minimize harmful berry temperatures are needed to sustain production in warm climates. It is challenging to manage the grapevine canopy to reduce the effect of excess temperature because of the complex interactions between plant architecture and the environment. Traditionally, it has been recommended to time canopy management to maintain sun-exposure for young fruits, but also to allow some shading of mature grape clusters to prevent excess sun exposure. Although increasing the shade in vineyards palliates the effect of elevated temperature, trade-offs need to be evaluated as well. For instance, shaded clusters can cause delay in fruit ripening, reduce wine quality, and increase disease prevalence due to pathogens such as bunch rot and powdery mildew. The negative effects of elevated temperature on grape berries could likely be mitigated in many cases if the complex interactions between canopy architecture and microclimate were better understood and predicted at the berry level. Developing and evaluating proposed mitigation strategies experimentally based on field trials is costly and time-consuming, which can limit their breadth and generalizability. Crop models can have the potential to extrapolate the results of a limited set of experiments through systematic variation of relevant variables, however, there are currently no models available that can represent varying grapevine architectures and their effect on spatial and temporal fluctuations in grape berry temperature. Through three different studies, this dissertation aims to 1) investigate the impact of the heterogeneous and anisotropic vegetation structure characteristic of grapevines on light interception, 2) develop a 3D model to simulate grape berry temperature in response to varying vineyard architecture and topography, and 3) identify strategies that have the potential to mitigate unfavorable temperatures in grape berries. Chapter 2 evaluates widely used assumptions when modeling solar radiation interception in plant canopies. The solar radiation intercepted by plant canopies is a fundamental driver of biophysical processes on Earth, and thus, quantifying such interception is a critical part of understanding and predicting a wide range of processes occurring at the land-atmosphere interface. The study showed that using a 1D model to simulate light interception for discontinuous canopies resulted in overestimation of light interception by up to 115% for the cases considered.