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Using data from a multi-institutional grounded theory study, this paper details the thoughts, feelings, and behaviors that 59 U.S. college students with disabilities used to cope with ableist stressors in postsecondary learning environments. Specifically, this manuscript highlights the varied coping strategies students adopted as they responded to the following stressors: (a) bullying; (b) labels, assumptions, and stereotypes; and (c) low expectations and discouragement. The paper concludes with recommendations for practice.

Abstract We evaluate deconvolution methods, which infer levels of immune infiltration from bulk expression of tumor samples, through a community-wide DREAM Challenge. We assess six published and 22 community-contributed methods using in vitro and in silico transcriptional profiles of admixed cancer and healthy immune cells. Several published methods predict most cell types well, though they either were not trained to evaluate all functional CD8+ T cell states or do so with low accuracy. Several community-contributed methods address this gap, including a deep learning-based approach, whose strong performance establishes the applicability of this paradigm to deconvolution. Despite being developed largely using immune cells from healthy tissues, deconvolution methods predict levels of tumor-derived immune cells well. Our admixed and purified transcriptional profiles will be a valuable resource for developing deconvolution methods, including in response to common challenges we observe across methods, such as sensitive identification of functional CD4+ T cell states.

Using data from a grounded theory study with 59 college students with disabilities, this article documents the complex process of developing self-advocacy during the transition from K--12 to post-secondary school settings. This article draws on rich student narratives to illuminate the nuanced self-advocacy processes that college students with disabilities adopted as they transitioned from extensive K-12 school-based and familial supports to more independent higher education contexts. Our findings point to evolving relationships students had with their parents/caregivers as they transitioned into college. The process of learning to self-advocate was also shaped by bureaucratic collegiate contexts that required students to develop new levels of self-awareness, assertiveness, and understanding of their legal rights regarding access to collegiate accommodations and resources.

We show that the notion of critical droplets is central to an understanding of the nature of ground states in the Edwards–Anderson–Ising model of a spin glass in arbitrary dimensions. Given a specific ground state, we suppose that the coupling value for a given edge is varied with all other couplings held fixed. Beyond some specific value of the coupling, a droplet will flip, leading to a new ground state; we refer to this as the critical droplet for that edge and ground state. We show that the distribution of sizes and energies over all edges for a specific ground state can be used to determine which of the leading scenarios for the spin glass phase is correct. In particular, the existence of low-energy interfaces between incongruent ground states, as predicted by replica symmetry breaking, is equivalent to the presence of critical droplets, whose boundaries comprise a positive fraction of edges in the infinite lattice.

Quantitative precipitation forecasts (QPF) from numerical weather prediction models need systematic verification to enable rigorous assessment and informed use, as well as model improvements. The United States (US) National Oceanic and Atmospheric Administration (NOAA) recently made a major update to its regional tropical cyclone modeling capabilities, introducing two new operational configurations of the Hurricane Analysis and Forecast System (HAFS). NOAA performed multi-season retrospective forecasts using the HAFS configurations during the period that the Hurricane Weather and Forecasting (HWRF) model was operational, which was used to assess HAFS performance for key tropical cyclone forecast metrics. However, systematic QPF verification was not an integral part of the initial evaluation. The first systematic QPF evaluation of the operational HAFS version 1 configurations is presented here for the 2021 and 2022 season re-forecasts as well as the first HAFS operational season, 2023. A suite of techniques, tools, and metrics within the enhanced Model Evaluation Tools (METplus) software suite are used. This includes shifting forecasts to mitigate track errors, regridding model and observed fields to a storm relative coordinate system, as well as object oriented verification. The HAFS configurations have better performance than HWRF for equitable threat score (ETS), but larger over forecast biases than HWRF. Storm relative and object oriented verification show the HAFS configurations have larger precipitation areas and less intense precipitation near the TC center as compared to observations and HWRF. HAFS QPF performance decreased for the 2023 season, but the general spatial patterns of the model QPF were very similar to 2021-2022.

Abstract Cerebrospinal fluid tumor-derived DNA (CSF-tDNA) analysis is a promising approach for monitoring the neoplastic processes of the central nervous system. We applied a lung cancer-specific sequencing panel (CAPP-Seq) to 81 CSF, blood, and tissue samples from 24 lung cancer patients who underwent lumbar puncture (LP) for suspected leptomeningeal disease (LMD). A subset of the cohort (N = 12) participated in a prospective trial of osimertinib for refractory LMD in which serial LPs were performed before and during treatment. CSF-tDNA variant allele fractions (VAFs) were significantly higher than plasma circulating tumor DNA (ctDNA) VAFs (median CSF-tDNA, 32.7%; median plasma ctDNA, 1.8%; P

Background The objective was to summarize the methodology used to reach consensus for recommended minimum data elements that should be collected and reported when conducting injury surveillance research in military settings. This paper summarizes the methodology used to develop the international Minimum Data Elements for surveillance and Reporting of Musculoskeletal Injuries in the MILitary (ROMMIL) statement. Methods A Delphi methodology was employed to reach consensus for minimum reporting elements. Preliminary steps included conducting a literature review and surveying a convenience sample of military stakeholders to 1) identify barriers and facilitators of military musculoskeletal injury (MSKI) prevention programs, 2) identify relevant knowledge/information gaps and 3) establish future research priorities. The team then led a sequential three-round Delphi consensus survey, including relevant stakeholders from militaries around the world, and then conducted asynchronous mixed knowledge user meeting to explore level of agreement among subject matter experts. Knowledge users, including former and current military service members, civil servant practitioners, and global-wide subject matter experts having experience with policy, execution, or clinical investigation of MSKI mitigation programs, MSKI diagnoses, and MSKI risk factors in military settings. For each round, participants scored each question on a Likert scale of 1-5. Scores ranged from No Importance (1) to Strong Importance (5). Results Literature review and surveys helped informed the scope of potential variables to vote on. Three rounds were necessary to reach minimum consensus. Ninety-five, 65 and 42 respondents participated in the first, second and third rounds of the Delphi consensus, respectively. Ultimately, consensus recommendations emerged consisting of one data principle and 33 minimum data elements. Conclusions Achieving consensus across relevant stakeholders representing military organizations globally can be challenging. This paper details the methodology employed to reach consensus for a core minimum data elements checklist for conducting MSKI research in military settings and improve data harmonization and scalability efforts. These methods can be used as a resource to assist in future consensus endeavors of similar nature.

Abstract The El Niño‐Southern Oscillation (ENSO) phenomenon—the dominant source of climate variability on seasonal to multi‐year timescales—is predictable a few seasons in advance. Forecast skill at longer multi‐year timescales has been found in a few models and forecast systems, but the robustness of this predictability across models has not been firmly established owing to the cost of running dynamical model predictions at longer lead times. In this study, we use a massive collection of multi‐model hindcasts performed using model analogs to show that multi‐year ENSO predictability is robust across models and arises predominantly due to skillful prediction of multi‐year La Nina events following strong El Niño events.

Nε-lysine acetylation is recognized as a prevalent post-translational modification (PTM) that regulates proteins across all three domains of life. In Bacillus subtilis, the histone-like protein HBsu is acetylated at seven sites, which regulates DNA compaction and the process of sporulation. In Mycobacteria, DNA compaction is a survival strategy in response antibiotic exposure. Acetylation of the HBsu ortholog HupB decondenses the chromosome to escape this drug-induced, non-growing state, and in addition, regulates the formation of drug-tolerant subpopulations by altering gene expression. We hypothesized that the acetylation of HBsu plays similar regulatory roles. First, we measured nucleoid area by fluorescence microscopy and in agreement, we found that wild-type cells compacted their nucleoids upon kanamycin exposure, but not exposure to tetracycline. We analyzed a collection of HBsu mutants that contain lysine substitutions that mimic the acetylated (glutamine) or unacetylated (arginine) forms of the protein. Our findings indicate that some level of acetylation is required at K3 for a proper response and K75 must be deacetylated. Next, we performed time-kill assays of wild-type and mutant strains in the presence of different antibiotics and found that interfering with HBsu acetylation led to faster killing rates. Finally, we examined the persistent subpopulation and found that altering the acetylation status of HBsu led to an increase in persister cell formation. In addition, we found that most of the deacetylation-mimic mutants, which have compacted nucleoids, were delayed in resuming growth following removal of the antibiotic, suggesting that acetylation is required to escape the persistent state. Together, this data adds an additional regulatory role for HBsu acetylation and further supports the existence of a histone-like code in bacteria.

Abstract There is significant clinical interest in targeting adenosine-mediated immunosuppression, with several small molecule inhibitors having been developed for targeting the A2AR receptor. Understanding of the mechanism by which A2AR is regulated has been hindered by difficulty in identifying the cell types that express A2AR due to a lack of robust antibodies for these receptors. To overcome this limitation, here an A2AR eGFP reporter mouse is developed, enabling the expression of A2AR during ongoing anti-tumor immune responses to be assessed. This reveals that A2AR is highly expressed on all tumor-infiltrating lymphocyte subsets including Natural Killer (NK) cells, NKT cells, γδ T cells, conventional CD4+ and CD8+ T lymphocytes and on a MHCIIhiCD86hi subset of type 2 conventional dendritic cells. In response to PD-L1 blockade, the emergence of PD-1+A2AR- cells correlates with successful therapeutic responses, whilst IL-18 is identified as a cytokine that potently upregulates A2AR and synergizes with A2AR deficiency to improve anti-tumor immunity. These studies provide insight into the biology of A2AR in the context of anti-tumor immunity and reveals potential combination immunotherapy approaches.

Abstract T cells are important in the pathogenesis of acute kidney injury (AKI), and TCR+CD4-CD8- (double negative-DN) are T cells that have regulatory properties. However, there is limited information on DN T cells compared to traditional CD4+ and CD8+ cells. To elucidate the molecular signature and spatial dynamics of DN T cells during AKI, we performed single-cell RNA sequencing (scRNA-seq) on sorted murine DN, CD4+, and CD8+ cells combined with spatial transcriptomic profiling of normal and post AKI mouse kidneys. scRNA-seq revealed distinct transcriptional profiles for DN, CD4+, and CD8+ T cells of mouse kidneys with enrichment of Kcnq5, Klrb1c, Fcer1g, and Klre1 expression in DN T cells compared to CD4+ and CD8+ T cells in normal kidney tissue. We validated the expression of these four genes in mouse kidney DN, CD4+ and CD8+ T cells using RT-PCR and Kcnq5, Klrb1, and Fcer1g genes with the NIH human kidney precision medicine project (KPMP). Spatial transcriptomics in normal and ischemic mouse kidney tissue showed a localized cluster of T cells in the outer medulla expressing DN T cell genes including Fcer1g. These results provide a template for future studies in DN T as well as CD4+ and CD8+ cells in normal and diseased kidneys.

The purpose of the present study was to conduct a process evaluation of intervention delivery for a randomized controlled trial (RCT) conducted during the COVID-19 pandemic (NCT 03915548). The RCT tested the effects of a telephone-delivered behavioral intervention on changes in breast cancer survivors’ satisfaction with social roles and activities, as compared to an attention control condition. This process evaluation examined (a) fidelity monitoring scores; (b) participants’ perceived benefit ratings for gaining confidence, reducing distress, adjusting habits and routines, setting goals, and increasing exercise; and (c) field notes, email communications, and transcripts of coach supervision and debriefing sessions. The behavioral and attention control conditions were delivered with a high degree of fidelity (global quality rating score for the BA/PS condition was M = 4.6 (SD = 0.6) and M = 4.9 (SD = 0.3) for the attention control condition, where “5” is the highest rating). The behavioral intervention participants perceived greater benefits than the control participants pertaining to goal setting, t(248) = 5.73, p = t(248) = 2.94, p = 0.0036, and increasing exercise, t(248) = 4.66, p =

ABSTRACT Immunodominant and highly conserved flavivirus envelope proteins can trigger cross-reactive IgG antibodies against related flaviviruses, which shapes subsequent protection or disease severity. This study examined how prior dengue serotype 3 (DENV-3) infection affects subsequent Zika virus (ZIKV) plasmablast responses in rhesus macaques (n = 4). We found that prior DENV-3 infection was not associated with diminished ZIKV-neutralizing antibodies or magnitude of plasmablast activation. Rather, characterization of 363 plasmablasts and their derivative 177 monoclonal antibody supernatants from acute ZIKV infection revealed that prior DENV-3 infection was associated with a differential isotype distribution toward IgG, lower somatic hypermutation, and lesser B cell receptor variable gene diversity as compared with repeat ZIKV challenge. We did not find long-lasting DENV-3 cross-reactive IgG after a ZIKV infection but did find persistent ZIKV-binding cross-reactive IgG after a DENV-3 infection, suggesting non-reciprocal cross-reactive immunity. Infection with ZIKV after DENV-3 boosted pre-existing DENV-3-neutralizing antibodies by two- to threefold, demonstrating immune imprinting. These findings suggest that the order of DENV and ZIKV infections has impact on the quality of early B cell immunity which has implications for optimal immunization strategies.IMPORTANCEThe Zika virus epidemic of 2015–2016 in the Americas revealed that this mosquito-transmitted virus could be congenitally transmitted during pregnancy and cause birth defects in newborns. Currently, there are no interventions to mitigate this disease and Zika virus is likely to re-emerge. Understanding how protective antibody responses are generated against Zika virus can help in the development of a safe and effective vaccine. One main challenge is that Zika virus co-circulates with related viruses like dengue, such that prior exposure to one can generate cross-reactive antibodies against the other which may enhance infection and disease from the second virus. In this study, we sought to understand how prior dengue virus infection impacts subsequent immunity to Zika virus by single-cell sequencing of antibody producing cells in a second Zika virus infection. Identifying specific qualities of Zika virus immunity that are modulated by prior dengue virus immunity will enable optimal immunization strategies.

Abstract Host‐associated bacterial microbiomes can facilitate host acclimation to seasonal environmental change and are hypothesized to help hosts cope with recent anthropogenic environmental perturbations (e.g., landscape modification). However, it is unclear how recurrent and recent forms of environmental change interact to shape variation in the microbiome. The majority of wildlife microbiome research occurs within a single seasonal context. Meanwhile, the few studies of seasonal variation in the microbiome often restrict focus to a single environmental context. By sampling urban and exurban eastern grey squirrel populations in the spring, summer, autumn, and winter, we explored whether seasonal rhythms in the grey squirrel gut microbiome differed across environments using a 16S amplicon sequencing approach. Differences in the microbiome between urban and exurban squirrels persisted across most of the year, which we hypothesize is linked to anthropogenic food consumption, but we also observed similarities in the urban and exurban grey squirrel microbiome during the autumn, which we attribute to engrained seed caching instincts in preparation for the winter. Host behaviour and diet selection may therefore be capable of maintaining similarities in microbiome structure between disparate environments. However, the depletion of an obligate host mucin glycan specialist (Akkermansia) during the winter in both urban and exurban squirrels was among the strongest differential abundance patterns we observed. In summary, urban grey squirrels showed different seasonal patterns in their microbiome than squirrels from exurban forests; however, in some instances, host behaviour and physiological responses might be capable of maintaining similar microbiome responses across seasons.

Measurement(s) SARS-CoV-2 seroprevalence Technology Type(s) serology assay Factor Type(s) geography • age • sex • race/ethnicity • Collection date Sample Characteristic - Organism Homo sapiens Sample Characteristic - Environment spatiotemporal region Sample Characteristic - Location United States of America

Air surveillance offers a potential means of monitoring airborne pathogens without the need for individual sampling. Here, the authors perform continuous air sampling in 15 community settings in the US for 29 weeks and demonstrate its feasibility for routine detection of SARS-CoV-2 and other respiratory pathogens.

Abstract Climate models exhibit known systematic errors in their representation of the El Niño‐Southern Oscillation (ENSO). In this study, we show that such simulation errors are largely present in tropical seasonal prediction, even for short lead times. Regressing monthly forecast errors from 11 different operational models upon the observed ENSO state, we find that predicted ENSO‐related sea surface temperature anomalies (of either sign) for winter/spring are significantly extended or shifted to the west and are also too persistent during the ENSO decay phase, both common climate model errors. There are also corresponding precipitation forecast errors, most notably a robust westward shift of the ENSO‐related precipitation dipole that may impact predictions of extratropical teleconnections. These ENSO‐related errors develop within days after initialization regardless of month, including significant errors appearing in anomalous surface trade winds, and saturate so rapidly that they primarily depend upon the seasonal cycle rather than lead time.

Cumulative cultural evolution is ubiquitous in humans, but is rarely observed in non-human animals. Here, Williams et al. report elaboration of songs over several decades in Savannah sparrows, consistent with cumulative cultural evolution.

Obesity and Western-like diet consumption leads to gut microbiome dysbiosis, which is associated with the development of cardio-metabolic diseases and poor health outcomes. The objective of this study was to reduce Western diet-mediated gut microbial dysbiosis, metabolic dysfunction, and systemic inflammation through the administration of a novel combined intervention strategy (oral probiotic bacteria supplements and muscadine grape extract (MGE)). To do so, adult female C57BL/6 mice were fed a low-fat control or Western-style diet and sub-grouped into diet alone, probiotic intervention, antibiotic treatments, MGE supplementation, a combination of MGE and probiotics, or MGE and antibiotics for 13 weeks. Mouse body weight, visceral adipose tissue (VAT), liver, and mammary glands (MG) were weighed at the end of the study. Fecal 16S rRNA sequencing was performed to determine gut bacterial microbiome populations. Collagen, macrophage, and monocyte chemoattractant protein-1 (MCP-1) in the VAT and MG tissue were examined by immunohistochemistry. Adipocyte diameter was measured in VAT. Immunohistochemistry of intestinal segments was used to examine villi length, muscularis thickness, and goblet cell numbers. We show that dietary interventions in Western diet-fed mice modulated % body weight gain, visceral adiposity, MG weight, gut microbial populations, and inflammation. Intervention strategies in both diets effectively reduced VAT and MG fibrosis, VAT and MG macrophages, adipocyte diameter, and VAT and MG MCP-1. Interventions also improved intestinal health parameters. In conclusion, dietary intervention with MGE and probiotics modulates several microbial, inflammatory, and metabolic factors reducing poor health outcomes associated with Western diet intake.

Despite acral melanoma being the most common melanoma subtype in non-White individuals, its molecular drivers remain unknown. Here, the authors integrate genomic and clinical data from 104 patients and identify late-arising focal amplifications of chr22q11.21 and LZTR1 as a key tumour promoter in this region.

Abstract The development and expansion of wind energy is considered a key threat to bat populations in North America and globally. Several approaches to mitigating the impacts of wind energy development on bat populations have been developed, including curtailing wind turbine operation at night during lower wind speeds when bats are thought to be more active. Blanket curtailment approaches have shown substantial promise in reducing bat fatalities at wind energy facilities, but they also reduce the amount of energy extracted from the wind by turbines. A related approach, referred to as smart curtailment, uses bat activity and other variables to predict when bats will be at the greatest risk at a given wind facility. In some contexts, a smart curtailment approach might reduce bat fatalities while also reducing energy loss relative to blanket curtailment. However, it has not been clear how to compare blanket curtailment and smart curtailment approaches in terms of annual energy production at wind facilities. Here, we describe a new approach to simulating the influence of blanket and smart curtailment approaches on energy production at wind energy facilities, and demonstrate the approach using 6 wind energy development areas in the Canadian province of Alberta. We show how stakeholders involved can explore the potential influences of various kinds of bat activity on energy production. We present the results of our Alberta analysis and conclude with some caveats and recommendations for future work on simulating the influences of bat curtailment on energy production at wind energy facilities.

In the 2016 Zika virus (ZIKV) pandemic, a previously unrecognized risk of birth defects surfaced in babies whose mothers were infected with Asian-lineage ZIKV during pregnancy. Less is known about the impacts of gestational African-lineage ZIKV infections. Given high human immunodeficiency virus (HIV) burdens in regions where African-lineage ZIKV circulates, we evaluated whether pregnant rhesus macaques infected with simian immunodeficiency virus (SIV) have a higher risk of African-lineage ZIKV-associated birth defects. Remarkably, in both SIV+ and SIV- animals, ZIKV infection early in the first trimester caused a high incidence (78%) of spontaneous pregnancy loss within 20 days. These findings suggest a significant risk for early pregnancy loss associated with African-lineage ZIKV infection and provide the first consistent ZIKV-associated phenotype in macaques for testing medical countermeasures.

Abstract Offshore wind energy is a growing industry in the United States, and renewable energy from offshore wind is estimated to double the country's total electricity generation. There is growing concern that land‐based wind development in North America is negatively impacting bat populations, primarily long‐distance migrating bats, but the impacts to bats from offshore wind energy are unknown. Bats are associated with the terrestrial environment, but have been observed over the ocean. In this review, we synthesize historic and contemporary accounts of bats observed and acoustically recorded in the North American marine environment to ascertain the spatial and temporal distribution of bats flying offshore. We incorporate studies of offshore bats in Europe and of bat behavior at land‐based wind energy studies to examine how offshore wind development could impact North American bat populations. We find that most offshore bat records are of long‐distance migrating bats and records occur during autumn migration, the period of highest fatality rates for long‐distance migrating bats at land‐based wind facilities in North America. We summarize evidence that bats may be attracted to offshore turbines, potentially increasing their exposure to risk of collision. However, higher wind speeds offshore can potentially reduce the amount of time that bats are exposed to risk. We identify knowledge gaps and hypothesize that a combination of operational minimization strategies may be the most effective approach for reducing impacts to bats and maximizing offshore energy production.

Abstract Emerging infectious diseases in wildlife can threaten vulnerable host populations. Actions targeting habitat improvements to aid population resilience and recovery may be beneficial long‐term strategies, yet testing the efficacy of such strategies before major conservation investments are made can be challenging. The disease white‐nose syndrome (WNS) has caused severe declines in several species of North American hibernating bats. We tested a novel conservation approach targeted at improving foraging conditions near bat hibernacula by experimentally manipulating insect density in the pre‐hibernation fattening period and spring emergence recovery period. We measured foraging (feeding buzzes) and echolocation activity of little brown bats Myotis lucifugus at ultraviolet (UV) light lures to determine behavioural response to augmented foraging conditions and characterized insect availability at UV light lures. In the fall, bat foraging activity was three times greater (95% CI: 1.5–5.8; p = 0.002) when UV lights were on, but there was no statistical support for differences in echolocation activity response when our experimental design alternated between nights with lights on and off. In the spring, we allowed UV light lures to run consistently each night and compared with a control location in similar habitat. Bat foraging activity was 8.5 times greater (95% CI: 4.5–16.0; p

To assess the performance and scalability of the Unified Forecast System (UFS) Short-Range Weather (SRW) application, case studies are chosen to cover a wide variety of forecast applications. Here, model forecasts of Hurricane Barry (July 2019) are examined and analyzed. Several versions of the Global Forecast System (GFS) and Rapid Refresh Forecast System (RRFS) physics suites are run in the UFS-SRW at grid spacings of 25 km, 13 km, and 3 km. All model configurations produce significant track errors of up to 350 km at landfall. The track errors are investigated, and several commonalities are seen between model configurations. A westerly bias in the environmental steering flow surrounding the tropical cyclone (TC) is seen across forecasts, and this bias is coincident with a warm sea surface temperature (SST) bias and overactive convection on the eastern side of the forecasted TC. Positive feedback between the surface winds, latent heating, moisture, convection, and TC intensification is initiated by this SST bias. The asymmetric divergent flow induced by the excess convection results in all model TC tracks being diverted to the east as compared to the track derived from reanalysis. The large differences between runs using the same physics packages at different grid spacing suggest a deficiency in the scalability of these packages with respect to hurricane forecasting in vertical wind shear.

Countermeasures against Zika virus (ZIKV), including vaccines, are frequently tested in nonhuman primates (NHP). Macaque models are important for understanding how ZIKV infections impact human pregnancy due to similarities in placental development. The lack of consistent adverse pregnancy outcomes in ZIKV-affected pregnancies poses a challenge in macaque studies where group sizes are often small (4-8 animals). Studies in small animal models suggest that African-lineage Zika viruses can cause more frequent and severe fetal outcomes. No adverse outcomes were observed in macaques exposed to 1x104 PFU (low dose) of African-lineage ZIKV at gestational day (GD) 45. Here, we exposed eight pregnant rhesus macaques to 1x108 PFU (high dose) of African-lineage ZIKV at GD 45 to test the hypothesis that adverse pregnancy outcomes are dose-dependent. Three of eight pregnancies ended prematurely with fetal death. ZIKV was detected in both fetal and placental tissues from all cases of early fetal loss. Further refinements of this exposure system (e.g., varying the dose and timing of infection) could lead to an even more consistent, unambiguous fetal loss phenotype for assessing ZIKV countermeasures in pregnancy. These data demonstrate that high-dose exposure to African-lineage ZIKV causes pregnancy loss in macaques and also suggest that ZIKV-induced first trimester pregnancy loss could be strain-specific.

Abstract Background Host-associated microbiota are integral to the ecology of their host and may help wildlife species cope with rapid environmental change. Urbanization is a globally replicated form of severe environmental change which we can leverage to better understand wildlife microbiomes. Does the colonization of separate cities result in parallel changes in the intestinal microbiome of wildlife, and if so, does within-city habitat heterogeneity matter? Using 16S rRNA gene amplicon sequencing, we quantified the effect of urbanization (across three cities) on the microbiome of eastern grey squirrels (Sciurus carolinensis). Grey squirrels are ubiquitous in rural and urban environments throughout their native range, across which they display an apparent coat colour polymorphism (agouti, black, intermediate). Results Grey squirrel microbiomes differed between rural and city environments; however, comparable variation was explained by habitat heterogeneity within cities. Our analyses suggest that operational taxonomic unit (OTU) community structure was more strongly influenced by local environmental conditions (rural and city forests versus human built habitats) than urbanization of the broader landscape (city versus rural). The bacterial genera characterizing the microbiomes of built-environment squirrels are thought to specialize on host-derived products and have been linked in previous research to low fibre diets. However, despite an effect of urbanization at fine spatial scales, phylogenetic patterns in the microbiome were coat colour phenotype dependent. City and built-environment agouti squirrels displayed greater phylogenetic beta-dispersion than those in rural or forest environments, and null modelling results indicated that the phylogenetic structure of urban agouti squirrels did not differ greatly from stochastic expectations. Conclusions Squirrel microbiomes differed between city and rural environments, but differences of comparable magnitude were observed between land classes at a within-city scale. We did not observe strong evidence that inter-environmental differences were the result of disparate selective pressures. Rather, our results suggest that microbiota dispersal and ecological drift are integral to shaping the inter-environmental differences we observed. However, these processes were partly mediated by squirrel coat colour phenotype. Given a well-known urban cline in squirrel coat colour melanism, grey squirrels provide a useful free-living system with which to study how host genetics mediate environment x microbiome interactions.

Bottlenecks in qPCR-based COVID-19 diagnostics include the lengthy multistep process and reagent shortages. Here the authors report OIL-TAS which integrates RNA extraction and detection into a single device.

Abstract Background The objective of this study was to increase understanding of the complex interactions between diet, obesity, and the gut microbiome of adult female non-human primates (NHPs). Subjects consumed either a Western (n=15) or Mediterranean (n=14) diet designed to represent human dietary patterns for 31 months. Body composition was determined using CT, fecal samples were collected, and shotgun metagenomic sequencing was performed. Gut microbiome results were grouped by diet and adiposity. Results Diet was the main contributor to gut microbiome bacterial diversity. Adiposity within each diet was associated with subtle shifts in the proportional abundance of several taxa. Mediterranean diet-fed NHPs with lower body fat had a greater proportion of Lactobacillus animalis than their higher body fat counterparts. Higher body fat Western diet-fed NHPs had more Ruminococcus champaneliensis and less Bacteroides uniformis than their low body fat counterparts. Western diet-fed NHPs had significantly higher levels of Prevotella copri than Mediterranean diet NHPs. Western diet-fed subjects were stratified by P. copri abundance (P. copri HIGH versus P. copri LOW), which was not associated with adiposity. Overall, Western diet-fed animals in the P. copri HIGH group showed greater proportional abundance of B. ovatus, B. faecis, P. stercorea, P. brevis, and Faecalibacterium prausnitzii than those in the Western P. copri LOW group. Western diet P. copri LOW subjects had a greater proportion of Eubacterium siraeum. E. siraeum negatively correlated with P. copri proportional abundance regardless of dietary consumption. In the Western diet group, Shannon diversity was significantly higher in P. copri LOW when compared to P. copri HIGH subjects. Furthermore, gut E. siraeum abundance positively correlated with HDL plasma cholesterol indicating that those in the P. copri LOW population may represent a more metabolically healthy population. Untargeted metabolomics on urine and plasma from Western diet-fed P. copri HIGH and P. copri LOW subjects suggest early kidney dysfunction in Western diet-fed P. copri HIGH subjects. Conclusions In summary, the data indicate diet to be the major influencer of gut bacterial diversity. However, diet and adiposity must be considered together when analyzing changes in abundance of specific bacterial taxa. Interestingly, P. copri appears to mediate metabolic dysfunction in Western diet-fed NHPs. Video abstract

Background Cardiac arrest survivorship refers to the lived experience of long‐term survivors of cardiac arrest and the many postdischarge challenges they experience. We aimed to gather a nuanced understanding of these challenges and of survivors' perceptions of ways to improve the recovery process. Methods and Results We conducted 15 semistructured, one‐on‐one interviews with cardiac arrest survivor members of the Sudden Cardiac Arrest Foundation; the interviews were conducted by telephone and recorded and transcribed verbatim. We used thematic analysis, informed by the Framework Method, to identify underlying themes regarding cardiac arrest survivorship challenges and recommendations to improve cardiac arrest survivorship. Regarding challenges, the overarching theme was a feeling of unpreparedness to confront postarrest challenges because of lack of resources, education, and appropriate expectations for recovery. Regarding recommendations, we uncovered 3 overarching themes including systemic recommendations (eg, providing appropriate resources and expectations, educating providers about survivorship, following up with survivors, including caregivers in treatment planning), social recommendations (eg, attending peer support groups, spending time with loved ones, providing support resources for family members), and individual coping recommendations (eg, acceptance, resilience, regaining control, seeking treatment, focusing on meaning and purpose). Conclusions We described common challenges that survivors of cardiac arrest face, such as lacking resources, education, and appropriate expectations for recovery. Additionally, we identified promising pathways that may improve cardiac arrest survivorship at systemic, social, and individual coping levels. Future studies could use our findings as targets for interventions to support and improve survivorship.

Synechococcus sp. PCC 7002 is a unicellular cyanobacterium capable of fast growth and tolerance to high light intensity and high salinity. These attributes along with genetic tractability make Synechococcus sp. PCC 7002 an attractive candidate for industrial scale production of specialty and commodity chemicals. Synechococcus sp. PCC 7002 LS (Davies et al., Front Bioeng Biotechnol, 2014, 2, 21–11) produces limonene, an energy dense diesel jet fuel drop-in additive, at a titer of 4 mg/L over a 4-day incubation period. In this study, we use the state-of-the-art whole-cell characterization tool, isotopically non-stationary 13C metabolic flux analysis (INST-13CMFA) to determine intracellular fluxes through the pathways of central metabolism for the limonene producing strain and wild type strain of Synechococcus sp. PCC 7002. We find similar flux distribution in the Calvin-Benson-Bassham cycle, photorespiration, oxidative pentose phosphate pathway, and oxidative tricarboxylic acid cycle. The key difference between strains is observed in the production of pyruvate. The limonene producing strain displays significantly higher flux through the amphibolic pathways of phosphoenolpyruvate carboxylase and the malic enzyme to synthesize pyruvate, while the wild type strain uses pyruvate kinase in a single step. Our findings suggest that this flux distribution is a mechanism to recover a physiologically optimal ratio of ATP to NADPH. The upregulation of this amphibolic pathway may act to restore the physiological ATP:NADPH ratio that has been disturbed by limonene biosynthesis. This study demonstrates the value of INST-13CMFA as a tool for cyanobacterial strain engineering and provides new avenues of research for improving limonene production in Synechococcus.

Traumatic cyclodialysis clefts, a rare diagnosis after blunt injury to the eye, are typically amenable to closure with either medical therapy or direct surgical cyclopexy. However, when cyclodialysis clefts cannot be closed through these methods, unorthodox techniques may be required. We describe a method to close a traumatic cyclodialysis cleft involving simultaneous vitrectomy, capsular tension ring placement, and insertion of an intraocular lens.

There are currently no approved drugs to treat Zika virus (ZIKV) infection during pregnancy. Hyperimmune globulin products such as VARIZIG and WinRho are FDA-approved to treat conditions during pregnancy such as Varicella Zoster virus infection and Rh-incompatibility. We administered ZIKV-specific human immune globulin as a treatment in pregnant rhesus macaques one day after subcutaneous ZIKV infection. All animals controlled ZIKV viremia following the treatment and generated robust levels of anti-Zika virus antibodies in their blood. No adverse fetal or infant outcomes were identified in the treated animals, yet the placebo control treated animals also did not have signs related to congenital Zika syndrome (CZS). Human immune globulin may be a viable prophylaxis and treatment option for ZIKV infection during pregnancy, however, more studies are required to fully assess the impact of this treatment to prevent CZS.

Avian pathogenic E. coli is the causative agent of extra-intestinal infections in birds known as colibacillosis, which can manifest as localized or systemic infections. The disease affects all stages of poultry production, resulting in economic losses that occur due to morbidity, carcass condemnation and increased mortality of the birds. APEC strains have a diverse virulence trait repertoire, which includes virulence factors involved in adherence to and invasion of the host cells, serum resistance factors, and toxins. However, the pathogenesis of APEC infections remains to be fully elucidated. The Type 6 secretion (T6SS) system has recently gained attention due to its role in the infection process and protection of bacteria from host defenses in human and animal pathogens. Previous work has shown that T6SS components are involved in the adherence to and invasion of host cells, as well as in the formation of biofilm, and intramacrophage bacterial replication. Here, we analyzed the frequency of T6SS genes hcp, impK, evpB, vasK and icmF in a collection of APEC strains and their potential role in virulence-associated phenotypes of APECO18. The T6SS genes were found to be significantly more prevalent in APEC than in fecal E. coli isolates from healthy birds. Expression of T6SS genes was analyzed in culture media and upon contact with host cells. Mutants were generated for hcp, impK, evpB, and icmF and characterized for their impact on virulence-associated phenotypes, including adherence to and invasion of host model cells, and resistance to predation by Dictyostelium discoideum. Deletion of the aforementioned genes did not significantly affect adherence and invasion capabilities of APECO18. Deletion of hcp reduced resistance of APECO18 to predation by D. discoideum, suggesting that T6SS is involved in the virulence of APECO18.

The authors report a co-occurrence of the U2AF1 S34F splicing factor mutation and ROS1 translocations in lung adenocarcinomas and profile effects of S34F on transcriptome-wide RNA binding. They further show that U2AF1 S34F enhances invasive potential and alters splicing of ROS1 fusion transcripts

Pulmonary arterial hypertension (PAH) is characterised by progressive pulmonary vascular remodelling. Here, Arnold et al. develop a therapeutic antibody targeting osteoprotegerin and find it attenuates pulmonary vascular remodelling in multiple rodent models of PAH, alone or in combination with standard of care vasodilator therapy.

Abstract: FOXO1 has an oncogenic role in adult germinal center–derived lymphomas, in which mutations, predominately within the AKT recognition motif, cause nuclear retention of FOXO1, resulting in increased cell proliferation. To determine the prevalence and distribution of FOXO1 mutations in pediatric Burkitt lymphoma (BL), we sequenced a large number of sporadic and endemic BL patient samples. We report a high frequency of FOXO1 mutations in both sporadic and endemic BL at diagnosis, occurring in 23/78 (29%) and 48/89 (54%) samples, respectively, as well as 8/16 (50%) cases at relapse. Mutations of T24 were the most common in sporadic BL but were rare in endemic cases, in which mutations of residue S22, also within the AKT recognition motif, were the most frequent. FOXO1 mutations were almost always present in the major tumor cell clone but were not associated with outcome. Analysis of other recurrent mutations reported in BL revealed that FOXO1 mutations were associated with mutations of DDX3X and ARID1A, but not MYC, TCF3/ID3, or members of the phosphatidylinositol 3-kinase signaling pathway. We further show common nuclear retention of the FOXO1 protein, irrespective of mutation status, suggesting alternative unknown mechanisms for maintaining FOXO1 transcriptional activity in BL. CRISPR/Cas9 knockout of FOXO1 in an endemic cell line produced a significant decrease in cell proliferation, supporting an oncogenic role for FOXO1 in endemic BL. Thus, FOXO1 is frequently mutated in both sporadic and endemic BL and may offer a potential therapeutic target for pediatric BL patients worldwide.

Abstract Background The vocalizations of birds are dynamic traits that often vary in output with time of day and time of year. By quantifying patterns of diel and seasonal variation in vocal output, we can gain insight into the ecology and evolution of birds and the function of their vocalizations. In this investigation, we quantified diel and seasonal variation in song output by studying a breeding population of Savannah Sparrows (Passerculus sandwichensis). Methods We used autonomous recorders to collect extensive recordings across the breeding season in a long-term, colour-marked study population of Savannah Sparrows in eastern Canada. We described diel and seasonal variation across five different breeding stages based on recordings of more than 50,000 songs from 34 males. Results During the pre-breeding stage, prior to female arrival, males sang a pronounced dawn chorus with a peak in song output during the early morning. During the breeding stage, in contrast, the dawn chorus was diminished and males instead exhibited a pronounced dusk chorus with a peak in song output during the evening. Across the breeding season, the highest levels of song output occurred in late April and early May, soon after males arrived on the breeding grounds, and the lowest levels occurred in August, prior to the departure of birds for the wintering grounds. Conclusions These patterns suggest that Savannah Sparrows’ early-season dawn choruses are directed at males and serve a territorial defense function. Later-season dusk choruses, in contrast, appear to play a role in attracting mates and possibly acoustic mate guarding.

Abstract Urban ecosystems are rapidly expanding throughout the world, but how urban growth affects the evolutionary ecology of species living in urban areas remains largely unknown. Urban ecology has advanced our understanding of how the development of cities and towns change environmental conditions and alter ecological processes and patterns. However, despite decades of research in urban ecology, the extent to which urbanization influences evolutionary and eco‐evolutionary change has received little attention. The nascent field of urban evolutionary ecology seeks to understand how urbanization affects the evolution of populations, and how those evolutionary changes in turn influence the ecological dynamics of populations, communities, and ecosystems. Following a brief history of this emerging field, this Perspective article provides a research agenda and roadmap for future research aimed at advancing our understanding of the interplay between ecology and evolution of urban‐dwelling organisms. We identify six key questions that, if addressed, would significantly increase our understanding of how urbanization influences evolutionary processes. These questions consider how urbanization affects nonadaptive evolution, natural selection, and convergent evolution, in addition to the role of urban environmental heterogeneity on species evolution, and the roles of phenotypic plasticity versus adaptation on species’ abundance in cities. Our final question examines the impact of urbanization on evolutionary diversification. For each of these six questions, we suggest avenues for future research that will help advance the field of urban evolutionary ecology. Lastly, we highlight the importance of integrating urban evolutionary ecology into urban planning, conservation practice, pest management, and public engagement.

SIRPa is most commonly known as a phagocytosis inhibitory receptor expressed by myeloid cells. Here the authors show SIRPa is expressed on a subset of CD8+ T cells with higher proliferative and effector activity during the chronic phase of the immune response to viral infection.

Concerns have arisen that pre-existing immunity to dengue virus (DENV) could enhance Zika virus (ZIKV) disease, due to the homology between ZIKV and DENV and the observation of antibody-dependent enhancement (ADE) among DENV serotypes. To date, no study has examined the impact of pre-existing DENV immunity on ZIKV pathogenesis during pregnancy in a translational non-human primate model. Here we show that macaques with a prior DENV-2 exposure had a higher burden of ZIKV vRNA in maternal-fetal interface tissues as compared to DENV-naive macaques. However, pre-existing DENV immunity had no detectable impact on ZIKV replication kinetics in maternal plasma, and all pregnancies progressed to term without adverse outcomes or gross fetal abnormalities detectable at delivery. Understanding the risks of ADE to pregnant women worldwide is critical as vaccines against DENV and ZIKV are developed and licensed and as DENV and ZIKV continue to circulate.

Zika virus (ZIKV) is an arthropod-borne virus (arbovirus) and is primarily transmitted by Aedes species mosquitoes; however, ZIKV can also be sexually transmitted. During the initial epidemic and in places where ZIKV is now considered endemic, it is difficult to disentangle the risks and contributions of sexual versus vector-borne transmission to adverse pregnancy outcomes. To examine the potential impact of sexual transmission of ZIKV on pregnancy outcome, we challenged three rhesus macaques (Macaca mulatta) three times intravaginally with 1 x 107 PFU of a low passage, African lineage ZIKV isolate (ZIKV-DAK) in the first trimester (~30 days gestational age). Samples were collected from all animals initially on days 3 through 10 post challenge, followed by twice, and then once weekly sample collection; ultrasound examinations were performed every 3-4 days then weekly as pregnancies progressed. All three dams had ZIKV RNA detectable in plasma on day 3 post-ZIKV challenge. At approximately 45 days gestation (17-18 days post-challenge), two of the three dams were found with nonviable embryos by ultrasound. Viral RNA was detected in recovered tissues and at the maternal-fetal interface (MFI) in both cases. The remaining viable pregnancy proceeded to near term (~155 days gestational age) and ZIKV RNA was detected at the MFI but not in fetal tissues. These results suggest that sexual transmission of ZIKV may represent an underappreciated risk of pregnancy loss during early gestation.

Colibacillosis caused by avian pathogenic Escherichia coli (APEC) is a devastating disease of poultry that results in multi-million-dollar losses annually to the poultry industry. Disease syndromes associated with APEC includes colisepticemia, cellulitis, air sac disease, peritonitis, salpingitis, omphalitis, and osteomyelitis among others. A total of 61 APEC isolates collected during the Fall of 2018 (Aug–Dec) from submitted diagnostic cases of poultry diagnosed with colibacillosis were assessed for the presence of 44 virulence-associated genes, 24 antimicrobial resistance genes and 17 plasmid replicon types. Each isolate was also screened for its ability to form biofilm using the crystal violet assay and antimicrobial susceptibility to 14 antimicrobials using the NARMS panel. Overall, the prevalence of virulence genes ranged from 1.6% to >90% with almost all strains harboring genes that are associated with the ColV plasmid—the defining trait of the APEC pathotype. Overall, 58 strains were able to form biofilms and only three strains formed negligible biofilms. Forty isolates displayed resistance to antimicrobials of the NARMS panel ranging from one to nine agents. This study highlights that current APEC causing disease in poultry possess virulence and resistance traits and form biofilms which could potentially lead to challenges in colibacillosis control.

Aim: To estimate the proportion of significant posttraumatic stress (PTS) in both cardiac survivors with good neurologic recovery and informal caregivers, and to pilot test the hypothesis that greater PTS are associated with worse quality of life (QoL) in both cardiac arrest survivors and informal caregivers of cardiac arrest survivors. Methods: We distributed an online survey to survivor and caregiver members of the Sudden Cardiac Arrest Foundation. Participants provided demographic and cardiac arrest characteristics and completed the PTSD Checklist-5 (PCL-5), the Lawton Instrumental Activities of Daily Living scale, and the WHOQOL-BREF. We identified covariates through bivariate correlations or linear regressions as appropriate. Six multiple regression models (three each for survivors and caregivers) examined associations between PCL-5 scores with each QoL subscale, adjusted for covariates identified from the bivariate models. Results: We included 169 survivors (mean months since arrest: 62.8, positive PTS screen: 24.9%) and 52 caregivers (mean months since arrest: 43.2, positive PTS screen: 34.6%). For survivors, the following showed significant bivariate associations with QoL: Lawton scores, daily memory problems, sex, months since arrest, age, and income; for caregivers, months since arrest, age, and income. In adjusted models, greater PCL-5 scores were associated with worse QoL (β: −0.35 to −0.53, p < .05). Conclusions: Our pilot results suggest that PTS are prevalent years after the initial cardiac arrest and are associated with worse QoL in survivors and informal caregivers. Further study is needed to validate these findings in a larger, representative sample.