Ecological characteristics explain neutral genetic variation of three coastal sparrow species.

Eco-phylogeographic approaches to comparative population genetic analyses allow for the inclusion of intrinsic influences as drivers of intraspecific genetic structure. This insight into microevolutionary processes, including changes within a species or lineage, provides better mechanistic understanding of species-specific interactions and enables predictions of evolutionary responses to environmental change. In this study, we used single nucleotide polymorphisms (SNPs) identified from reduced representation sequencing to compare neutral population structure, isolation by distance (IBD), genetic diversity and effective population size (Ne) across three closely related and co-distributed saltmarsh sparrow species differing along a specialization gradient-Nelson's (Ammospiza nelsoni subvirgata), saltmarsh (A. caudacuta) and seaside sparrows (A. maritima maritima). Using an eco-phylogeographic lens within a conservation management context, we tested predictions about species' degree of evolutionary history and ecological specialization to tidal marshes, habitat, current distribution and population status on population genetic metrics. Population structure differed among the species consistent with their current distribution and habitat factors, rather than degree of ecological specialization: seaside sparrows were panmictic, saltmarsh sparrows showed hierarchical structure and Nelson's sparrows were differentiated into multiple, genetically distinct populations. Neutral population genetic theory and demographic/evolutionary history predicted patterns of genetic diversity and Ne rather than degree of ecological specialization. Patterns of population variation and evolutionary distinctiveness (Shapely metric) suggest different conservation measures for long-term persistence and evolutionary potential in each species. Our findings contribute to a broader understanding of the complex factors influencing genetic variation, beyond specialist-generalist status and support the role of an eco-phylogeographic approach in population and conservation genetics.

Plumage microorganism communities of tidal marsh sparrows.

Microorganism communities can shape host phenotype evolution but are often comprised of thousands of taxa with varied impact on hosts. Identification of taxa influencing host evolution relies on first describing microorganism communities and acquisition routes. Keratinolytic (keratin-degrading) microorganisms are hypothesized to be abundant in saltmarsh sediments and to contribute to plumage evolution in saltmarsh-adapted sparrows. Metabarcoding was used to describe plumage bacterial (16S rRNA) and fungal (ITS) communities in three sparrow species endemic to North America's Atlantic coast saltmarshes. Results describe limited within-species variability and moderate host species-level patterns in microorganism diversity and community composition. A small percentage of overall microorganism diversity was comprised of potentially keratinolytic microorganisms, warranting further functional studies. Distinctions between plumage and saltmarsh sediment bacteria, but not fungal, communities were detected, suggesting multiple bacterial acquisition routes and/or vertebrate host specialization. This research lays groundwork for future testing of causal links between microorganisms and avian host evolution.

An examination of obsessive-compulsive symptom domains, depression, and quality of life within an online survey sample.

Obsessive-compulsive disorder (OCD) is a heterogeneous and highly impairing disorder that is frequently comorbid with other conditions. Participants in this study were 212 individuals recruited through Mechanical Turk who filled out validated measures of obsessive-compulsive symptoms, quality of life (QoL), generalized anxiety, and depressive symptoms. Analyses examined the influences of each symptom variable on QoL and the mediating role of depression as an indirect link between unacceptable thoughts (UT) and QoL. Depressive symptoms had a significant negative relationship with multiple domains of functioning. Generalized anxiety was not significant. Higher endorsement of UT symptoms was related to lower physical, emotional, and social QoL. Depression partially mediated the relationship between UT symptoms and physical, emotional, and social health. Depressive symptoms are important to consider in clinical work surrounding OCD. The significant associations between UT symptoms and QoL in a nonclinical population illustrate a relevant area for future intervention, public awareness, and education.

Point of Care Molecular Testing: Community-Based Rapid Next-Generation Sequencing to Support Cancer Care.

Purpose: Biomarker data are critical to the delivery of precision cancer care. The average turnaround of next-generation sequencing (NGS) reports is over 2 weeks, and in-house availability is typically limited to academic centers. Lengthy turnaround times for biomarkers can adversely affect outcomes. Traditional workflows involve moving specimens through multiple facilities. This study evaluates the feasibility of rapid comprehensive NGS using the Genexus integrated sequencer and a novel streamlined workflow in a community setting. Methods: A retrospective chart review was performed to assess the early experience and performance characteristics of a novel approach to biomarker testing at a large community center. This approach to NGS included an automated workflow utilizing the Genexus integrated sequencer, validated for clinical use. NGS testing was further integrated within a routine immunohistochemistry (IHC) service, utilizing histotechnologists to perform technical aspects of NGS, with results reported directly by anatomic pathologists. Results: Between October 2020 and October 2021, 578 solid tumor samples underwent genomic profiling. Median turnaround time for biomarker results was 3 business days (IQR: 2-5). Four hundred eighty-one (83%) of the cases were resulted in fewer than 5 business days, and 66 (11%) of the cases were resulted simultaneously with diagnosis. Tumor types included lung cancer (310), melanoma (97), and colorectal carcinoma (68), among others. NGS testing detected key driver alterations at expected prevalence rates: lung EGFR (16%), ALK (3%), RET (1%), melanoma BRAF (43%), colorectal RAS/RAF (67%), among others. Conclusion: This is the first study demonstrating clinical implementation of rapid NGS. This supports the feasibility of automated comprehensive NGS performed and interpreted in parallel with diagnostic histopathology and immunohistochemistry. This novel approach to biomarker testing offers considerable advantages to clinical cancer care.

Mercury exposure of tidal marsh songbirds in the northeastern United States and its association with nest survival.

The biogeochemistry of tidal marsh sediments facilitates the transformation of mercury (Hg) into the biologically available form methylmercury (MeHg), resulting in elevated Hg exposures to tidal marsh wildlife. Saltmarsh and Acadian Nelson's sparrows (Ammospiza caudacutua and A. nelsoni subvirgatus, respectively) exclusively inhabit tidal marshes, potentially experiencing elevated risk to Hg exposure, and have experienced range-wide population declines. To characterize spatial and temporal variation of Hg exposure in these species, we sampled total mercury (THg) in blood collected from 9 populations spanning 560 km of coastline, including individuals resampled within and among years. Using concurrent nesting studies, we tested whether THg was correlated with nest survival probabilities, an index of fecundity. Blood THg ranged from 0.074-3.373 µg/g ww across 170 samples from 127 individuals. We detected high spatial variability in Hg exposure, observing differences of more than 45-fold across all individuals and 8-fold in mean blood THg among all study plots, including 4-fold between study plots within 4 km. Intraindividual changes in blood Hg exposure did not vary systematically in time but were considerable, varying by up to 2-fold within and among years. Controlling for both species differences and maximum water level, the dominant driver of fecundity in this system, nest survival probability decreased by 10% across the full range of female blood THg concentrations observed. We conclude that Hg has the potential to impair songbird reproduction, potentially exacerbating known climate-change driven population declines from sea-level rise in saltmarsh and Acadian Nelson's sparrows.

Meta-analysis: Congruence of genomic and phenotypic differentiation across diverse natural study systems.

Linking genotype to phenotype is a primary goal for understanding the genomic underpinnings of evolution. However, little work has explored whether patterns of linked genomic and phenotypic differentiation are congruent across natural study systems and traits. Here, we investigate such patterns with a meta-analysis of studies examining population-level differentiation at subsets of loci and traits putatively responding to divergent selection. We show that across the 31 studies (88 natural population-level comparisons) we examined, there was a moderate (R 2 = 0.39) relationship between genomic differentiation (F ST ) and phenotypic differentiation (P ST ) for loci and traits putatively under selection. This quantitative relationship between P ST and F ST for loci under selection in diverse taxa provides broad context and cross-system predictions for genomic and phenotypic adaptation by natural selection in natural populations. This context may eventually allow for more precise ideas of what constitutes "strong" differentiation, predictions about the effect size of loci, comparisons of taxa evolving in nonparallel ways, and more. On the other hand, links between P ST and F ST within studies were very weak, suggesting that much work remains in linking genomic differentiation to phenotypic differentiation at specific phenotypes. We suggest that linking genotypes to specific phenotypes can be improved by correlating genomic and phenotypic differentiation across a spectrum of diverging populations within a taxon and including wide coverage of both genomes and phenomes.

Geographic variation of mercury in breeding tidal marsh sparrows of the northeastern United States.

Saltmarsh sparrows (Ammospiza caudacuta) and seaside sparrows (A. maritima) are species of conservation concern primarily due to global sea-level rise and habitat degradation. Environmental mercury (Hg) contamination may present additional threats to their reproductive success and survival. To assess site-specific total mercury (THg) exposure and identify environmental correlates of THg detection, we sampled blood from adult male saltmarsh and seaside sparrows at 27 sites between Maine and Virginia, USA. The mean THg concentration (±1 SD) throughout the entire sampling range was 0.531 ± 0.287 µg/g wet weight (ww) for saltmarsh sparrows and 0.442 ± 0.316 µg/g ww for seaside sparrows. Individual THg concentrations ranged from 0.135-1.420 µg/g ww for saltmarsh sparrows and 0.153-1.530 µg/g ww for seaside sparrows. Model averaging from a suite of linear mixed models showed that saltmarsh sparrows averaged 20.1% higher blood THg concentrations than seaside sparrows, potentially due to differences in diet or foraging behavior. We found no evidence for a relationship between sparrow THg concentrations and land cover surrounding sampled marshes or average precipitation-based Hg deposition. Overall, our results suggest considerable, unexplained variation in tidal marsh sparrow blood THg concentrations over their co-occurring breeding ranges.

Beyond Thin Films: Clarifying the Impact of c-Li15Si4 Formation in Thin Film, Nanoparticle, and Porous Si Electrodes.

The formation of the c-Li15Si4 phase has well-established detrimental effects on the capacity retention of thin film silicon electrodes. However, the role of this crystalline phase with respect to the loss of capacity is somewhat ambiguous in nanoscale morphologies. In this work, three silicon-based morphologies are examined, including planar films, porous planar films, and silicon nanoparticle composite powder electrodes. The cycling conditions are used as the lever to induce, or not induce, the formation of c-Li15Si4 through application of constant-current (CC) or constant-current constant-voltage (CCCV) steps. In this manner, the role of this phase on capacity retention and Coulombic efficiency can be determined with few other convoluting factors such as alteration of the composition or morphology of the silicon electrodes themselves. The results here confirm that the c-Li15Si4 phase increases the rate of capacity decay in planar films but has no major effect on capacity retention in half-cells based on porous silicon films or silicon nanoparticle composite powder electrodes, although this conclusion is nuanced. Besides using a constant-voltage step, formation of the c-Li15Si4 phase is influenced by the dimensions of the Si material and the lithiation cutoff voltage. Porous Si films, which, in this work, comprise primary Si particle sizes that are smaller than those in the preformed Si nanoparticle slurries, do not undergo the formation of c-Li15Si4 at 50 mV, whereas Si nanoparticle slurries are accompanied by the formation of c-Li15Si4 up to 80 mV. The solid-electrolyte interphase (SEI) formed from reaction of the c-Li15Si4 with the carbonate-based electrolyte causes polarization in both nanoparticle and porous film silicon electrodes and lowers the average Coulombic efficiency. A comparison of the cumulative irreversibilities due to SEI formation between different lithiation cutoff voltages in silicon nanoparticle slurry electrodes confirmed the connection between higher SEI buildup and formation of the c-Li15Si4 phase. This work indicates that concerns about the c-Li15Si4 phase in silicon nanoparticles and porous silicon electrodes should mainly focus on the stability of the SEI and a reduction of irreversible electrolyte reactions.

Solvent Vapor Annealing, Defect Analysis, and Optimization of Self-Assembly of Block Copolymers Using Machine Learning Approaches.

Self-assembly of block copolymers (BCPs) is an alternative patterning technique that promises high resolution and density multiplication with lower costs. The defectivity of the resulting nanopatterns remains too high for many applications in microelectronics and is exacerbated by small variations of processing parameters, such as film thickness, and fluctuations of solvent vapor pressure and temperature, among others. In this work, a solvent vapor annealing (SVA) flow-controlled system is combined with design of experiments (DOE) and machine learning (ML) approaches. The SVA flow-controlled system enables precise optimization of the conditions of self-assembly of the high Flory-Huggins interaction parameter (χ) hexagonal dot-array forming BCP, poly(styrene-b-dimethylsiloxane) (PS-b-PDMS). The defects within the resulting patterns at various length scales are then characterized and quantified. The results show that the defectivity of the resulting nanopatterned surfaces is highly dependent upon very small variations of the initial film thicknesses of the BCP, as well as the degree of swelling under the SVA conditions. These parameters also significantly contribute to the quality of the resulting pattern with respect to grain coarsening, as well as the formation of different macroscale phases (single and double layers and wetting layers). The results of qualitative and quantitative defect analyses are then compiled into a single figure of merit (FOM) and are mapped across the experimental parameter space using ML approaches, which enable the identification of the narrow region of optimum conditions for SVA for a given BCP. The result of these analyses is a faster and less resource intensive route toward the production of low-defectivity BCP dot arrays via rational determination of the ideal combination of processing factors. The DOE and machine learning-enabled approach is generalizable to the scale-up of self-assembly-based nanopatterning for applications in electronic microfabrication.

Bipolar Resistive Switching in Junctions of Gallium Oxide and p-type Silicon.

In this work, native GaOx is positioned between bulk gallium and degenerately doped p-type silicon (p+-Si) to form Ga/GaOx/SiOx/p+-Si junctions. These junctions show memristive behavior, exhibiting large current-voltage hysteresis. When cycled between -2.5 and 2.5 V, an abrupt insulator-metal transition is observed that is reversible when the polarity is reversed. The ON/OFF ratio between the high and low resistive states in these junctions can reach values on the order of 108 and retain the ON and OFF resistive states for up to 105 s with an endurance exceeding 100 cycles. The presence of a nanoscale layer of gallium oxide is critical to achieving reversible resistive switching by formation and dissolution of the gallium filament across the switching layer.

Patterns of introgression vary within an avian hybrid zone.

BACKGROUND: Exploring hybrid zone dynamics at different spatial scales allows for better understanding of local factors that influence hybrid zone structure. In this study, we tested hypotheses about drivers of introgression at two spatial scales within the Saltmarsh Sparrow (Ammospiza caudacuta) and Nelson's Sparrow (A. nelsoni) hybrid zone. Specifically, we evaluated the influence of neutral demographic processes (relative species abundance), natural selection (exogenous environmental factors and genetic incompatibilities), and sexual selection (assortative mating) in this mosaic hybrid zone. By intensively sampling adults (n = 218) and chicks (n = 326) at two geographically proximate locations in the center of the hybrid zone, we determined patterns of introgression on a fine scale across sites of differing habitat. We made broadscale comparisons of patterns from the center with those of prior studies in the southern edge of the hybrid zone. RESULTS: A panel of fixed SNPs (135) identified from ddRAD sequencing was used to calculate a hybrid index and determine genotypic composition/admixture level of the populations. Another panel of polymorphic SNPs (589) was used to assign paternity and reconstruct mating pairs to test for sexual selection. On a broad-scale, patterns of introgression were not explained by random mating within marshes. We found high rates of back-crossing and similarly low rates of recent-generation (F1/F2) hybrids in the center and south of the zone. Offspring genotypic proportions did not meet those expected from random mating within the parental genotypic distribution. Additionally, we observed half as many F1/F2 hybrid female adults than nestlings, while respective male groups showed no difference, in support of Haldane's Rule. The observed proportion of interspecific mating was lower than expected when accounting for mate availability, indicating assortative mating was limiting widespread hybridization. On a fine spatial scale, we found variation in the relative influence of neutral and selective forces between inland and coastal habitats, with the smaller, inland marsh influenced primarily by neutral demographic processes, and the expansive, coastal marsh experiencing higher selective pressures in the form of natural (exogenous and endogenous) and sexual selection. CONCLUSIONS: Multiple drivers of introgression, including neutral and selective pressures (exogenous, endogenous, and sexual selection), are structuring this hybrid zone, and their relative influence is site and context-dependent.

Laboratory practices for manual blood film review: Results of an IQMH patterns of practice survey.

INTRODUCTION: Examination of a blood film is the second most common hematology test, after the complete blood count. Interpretation of a peripheral blood film by trained laboratory professionals provides valuable diagnostic information. The Institute for Quality Management in Healthcare (IQMH) Hematology Scientific Committee developed a questionnaire to gather information regarding current practices for manual blood film review and reporting from laboratories participating in IQMH Morphology proficiency testing (PT) surveys. METHODS: An online survey was distributed to 174 laboratories, 97% submitted results. RESULTS: Of the respondents, the majority (82%) indicated affiliation with small- or medium-sized hospitals (<500 beds). 80% of respondents had core laboratory technologists performing manual blood film reviews, while only 2% utilized dedicated hematology technologists with morphology expertise. All respondents had a policy for manual blood film review by a technologist, 70% did not have blood films reviewed by a senior/charge technologist prior to review by a physician. The majority (88%) of participants included morphological findings in their critical result list; of these, 98% include malaria and 88% include the first-time finding of blasts as critical results. 59% of participants indicated that they have a procedure in place to ensure that interpretation and confirmation of first-time potentially significant morphological findings are available from a physician at all times. CONCLUSION: This survey identified significant variation in blood film review and reporting practices across participating laboratories. The IQMH Hematology Scientific Committee will develop best practice recommendations to guide and standardize practice.

Optimization of the Bulk Heterojunction of All-Small-Molecule Organic Photovoltaics Using Design of Experiment and Machine Learning Approaches.

All-small-molecule organic photovoltaic (OPV) cells based upon the small-molecule donor, DRCN5T, and nonfullerene acceptors, ITIC, IT-M, and IT-4F, were optimized using Design of Experiments (DOE) and machine learning (ML) approaches. This combination enables rational sampling of large parameter spaces in a sparse but mathematically deliberate fashion and promises economies of precious resources and time. This work focused upon the optimization of the core layer of the OPV device, the bulk heterojunction (BHJ). Many experimental processing parameters play critical roles in the overall efficiency of a given device and are often correlated and thus are difficult to parse individually. DOE was applied to the (i) solution concentration of the donor and acceptor ink used for spin-coating, (ii) the donor fraction, (iii) the temperature, and (iv) duration of the annealing of these films. The ML-based approach was then used to derive maps of the power conversion efficiencies (PCE) landscape for the first and second rounds of optimization to be used as guides to determine the optimal values of experimental processing parameters with respect to PCE. This work shows that with little knowledge of a potential combination of components for a given BHJ, a large parameter space can be effectively screened and investigated to rapidly determine its potential for high-efficiency OPVs.

van der Waals Epitaxy of Soft Twisted Bilayers: Lattice Relaxation and Mass Density Waves.

Interfaces comprising incommensurate or twisted hexagonal lattices are ubiquitous and of great interest, from adsorbed organic/inorganic interfaces in electronic devices, to superlubricants, and more recently to van der Waals bilayer heterostructures (vdWHs) of graphene and other 2D materials that demonstrate a range of properties such as superconductivity and ferromagnetism. Here we show how growth of 2D crystalline domains of soft block copolymers (BCPs) on patterned hard hexagonal lattices provide fundamental insights into van der Waals heteroepitaxy. At moderate registration forces, it is experimentally found that these BCP-hard lattice vdWHs do not adopt a simple moiré superstructure, but instead adopt local structural relaxations known as mass density waves (MDWs). Simulations reveal that MDWs are a primary mechanism of energy minimization and are the origin of the observed preferential twist angle between the lattices.

Redox Flow Batteries: How to Determine Electrochemical Kinetic Parameters.

Redox flow batteries (RFBs) are promising energy storage candidates for grid deployment of intermittent renewable energy sources such as wind power and solar energy. Various new redox-active materials have been introduced to develop cost-effective and high-power-density next-generation RFBs. Electrochemical kinetics play critical roles in influencing RFB performance, notably the overpotential and cell power density. Thus, determining the kinetic parameters for the employed redox-active species is essential. In this Perspective, we provide the background, guidelines, and limitations for a proposed electrochemical protocol to define the kinetics of redox-active species in RFBs.

Mercury exposure in migrating songbirds: correlations with physical condition.

Many migratory songbirds are at high risk of methylmercury (MeHg) exposure due to their trophic position and foraging in and around wetland habitats. Methylmercury has the potential to alter migratory behaviors and physiology via neurological impairment or reduced flight performance and can be remobilized from songbird muscle tissue during migration, increasing the risk of acute MeHg exposure. To document MeHg exposure and its relationship with physical condition in migratory songbirds, we sampled passerine blood and feathers at a migration stopover site on Key Biscayne, FL during fall and spring from 2009 to 2012. We found evidence that spring blood total mercury (THg) concentrations decreased throughout the day and that fall feather THg concentrations changed over the migratory season. Total mercury exposure was marginally correlated with migratory fat stores and related to changes in pectoral muscle thickness by time of day. These patterns suggest that environmentally relevant levels of THg are related to, and may be influencing, the physical condition of free-living migrating songbirds. Further research and monitoring during the migratory period will be important to elucidate exposure risk across multiple species and assess the potential for effects during this complex period of the annual cycle.

Water-soluble pH-switchable cobalt complexes for aqueous symmetric redox flow batteries.

A water soluble octahedral Co(ii) complex, BCPIP-Co(ii), with 4 appended carboxylic groups on the ligand periphery is utilized as both posolyte and negolyte in an aqueous, symmetric redox flow battery (RFB). The full RFB demonstrates coulombic efficiencies >99% for up to 100 cycles.

Contrasting drivers of diversification rates on islands and continents across three passerine families.

Diversification rates vary greatly among taxa. Understanding how species-specific traits influence speciation rates will help elucidate mechanisms driving biodiversity over broad spatio-temporal scales. Ecological specialization and range size are two hypothesized drivers of speciation rates, yet each mechanism predicts both increases and decreases in speciation. We constructed a continuous index of specialization using avian bill morphology to determine the relative effect of specialization and range size and shape on speciation rates across 559 species within the Emberizoidea superfamily, a morphologically diverse New World clade. We found a significant positive correlation between specialization and speciation rate and a negative correlation with range size. Only the effect of specialization persisted after removing island endemics, however, suggesting that ecological specialization is an important driver of diversity across large macroevolutionary scales, and the relative importance of specific drivers may differ between islands and continents.

Framework for quantifying population responses to disturbance reveals that coastal birds are highly resilient to hurricanes.

Changes in the frequency and severity of extreme weather may introduce new threats to species that are already under stress from gradual habitat loss and climate change. We provide a probabilistic framework that quantifies potential threats by applying concepts from ecological resilience to single populations. Our approach uses computation to compare disturbance-impacted projections to a population's normal range of variation, quantifying the full range of potential impacts. We illustrate this framework with projection models for coastal birds, which are commonly depicted as vulnerable to disturbances, especially hurricanes and oil spills. We found that populations of coastal specialists are resilient to extreme disturbances, with high resistance to the effects of short-term reductions in vital rates and recovery within 20 years. Applying the general framework presented here across disturbance-prone species and ecosystems would improve understanding of population resilience and generate specific projections of resilience that are needed for effective conservation planning.

Genomics of rapid ecological divergence and parallel adaptation in four tidal marsh sparrows.

Theory suggests that different taxa having colonized a similar, challenging environment will show parallel or lineage-specific adaptations to shared selection pressures, but empirical examples of parallel evolution in independent taxa are exceedingly rare. We employed comparative genomics to identify parallel and lineage-specific responses to selection within and among four species of North American sparrows that represent four independent, post-Pleistocene colonization events by an ancestral, upland subspecies and a derived salt marsh specialist. We identified multiple cases of parallel adaptation in these independent comparisons following salt marsh colonization, including selection of 12 candidate genes linked to osmoregulation. In addition to detecting shared genetic targets of selection across multiple comparisons, we found many novel, species-specific signatures of selection, including evidence of selection of loci associated with both physiological and behavioral mechanisms of osmoregulation. Demographic reconstructions of all four species highlighted their recent divergence and small effective population sizes, as expected given their rapid radiation into saline environments. Our results highlight the interplay of both shared and lineage-specific selection pressures in the colonization of a biotically and abiotically challenging habitat and confirm theoretical expectations that steep environmental clines can drive repeated and rapid evolutionary diversification in birds.