Climate change drives migratory range shift via individual plasticity in shearwaters.

How individual animals respond to climate change is key to whether populations will persist or go extinct. Yet, few studies investigate how changes in individual behavior underpin these population-level phenomena. Shifts in the distributions of migratory animals can occur through adaptation in migratory behaviors, but there is little understanding of how selection and plasticity contribute to population range shift. Here, we use long-term geolocator tracking of Balearic shearwaters (Puffinus mauretanicus) to investigate how year-to-year changes in individual birds' migrations underpin a range shift in the post-breeding migration. We demonstrate a northward shift in the post-breeding range and show that this is brought about by individual plasticity in migratory destination, with individuals migrating further north in response to changes in sea-surface temperature. Furthermore, we find that when individuals migrate further, they return faster, perhaps minimizing delays in return to the breeding area. Birds apparently judge the increased distance that they will need to migrate via memory of the migration route, suggesting that spatial cognitive mechanisms may contribute to this plasticity and the resulting range shift. Our study exemplifies the role that individual behavior plays in populations' responses to environmental change and highlights some of the behavioral mechanisms that might be key to understanding and predicting species persistence in response to climate change.

Genomic perspectives on human dispersals during the Holocene.

Nearly 20 y ago, Jared Diamond and Peter Bellwood reviewed the evidence for the associated spread of farming and large language families by the demographic expansions of farmers. Since then, advances in obtaining and analyzing genomic data from modern and ancient populations have transformed our knowledge of human dispersals during the Holocene. Here, we provide an overview of Holocene dispersals in the light of genomic evidence and conclude that they have a complex history. Even when there is a demonstrated connection between a demographic expansion of people, the spread of agriculture, and the spread of a particular language family, the outcome in the results of contact between expanding and resident groups is highly variable. Further research is needed to identify the factors and social circumstances that have influenced this variation and complex history.

Sex-linked gene traffic underlies the acquisition of sexually dimorphic UV color vision in Heliconius butterflies.

The acquisition of novel sexually dimorphic traits poses an evolutionary puzzle: How do new traits arise and become sex-limited? Recently acquired color vision, sexually dimorphic in animals like primates and butterflies, presents a compelling model for understanding how traits become sex-biased. For example, some Heliconius butterflies uniquely possess UV (ultraviolet) color vision, which correlates with the expression of two differentially tuned UV-sensitive rhodopsins, UVRh1 and UVRh2. To discover how such traits become sexually dimorphic, we studied Heliconius charithonia, which exhibits female-specific UVRh1 expression. We demonstrate that females, but not males, discriminate different UV wavelengths. Through whole-genome shotgun sequencing and assembly of the H. charithonia genome, we discovered that UVRh1 is present on the W chromosome, making it obligately female-specific. By knocking out UVRh1, we show that UVRh1 protein expression is absent in mutant female eye tissue, as in wild-type male eyes. A PCR survey of UVRh1 sex-linkage across the genus shows that species with female-specific UVRh1 expression lack UVRh1 gDNA in males. Thus, acquisition of sex linkage is sufficient to achieve female-specific expression of UVRh1, though this does not preclude other mechanisms, like cis-regulatory evolution from also contributing. Moreover, both this event, and mutations leading to differential UV opsin sensitivity, occurred early in the history of Heliconius. These results suggest a path for acquiring sexual dimorphism distinct from existing mechanistic models. We propose a model where gene traffic to heterosomes (the W or the Y) genetically partitions a trait by sex before a phenotype shifts (spectral tuning of UV sensitivity).

Horizontal transmission enables flexible associations with locally adapted symbiont strains in deep-sea hydrothermal vent symbioses.

SignificanceIn marine ecosystems, transmission of microbial symbionts between host generations occurs predominantly through the environment. Yet, it remains largely unknown how host genetics, symbiont competition, environmental conditions, and geography shape the composition of symbionts acquired by individual hosts. To address this question, we applied population genomic approaches to four species of deep-sea hydrothermal vent snails that live in association with chemosynthetic bacteria. Our analyses show that environment is more important to strain-level symbiont composition than host genetics and that symbiont strains show genetic variation indicative of adaptation to the distinct geochemical conditions at each vent site. This corroborates a long-standing hypothesis that hydrothermal vent invertebrates affiliate with locally adapted symbiont strains to cope with the variable conditions characterizing their habitats.

Neo-sex chromosome evolution shapes sex-dependent asymmetrical introgression barrier.

Sex chromosomes play a special role in the evolution of reproductive barriers between species. Here we describe conflicting roles of nascent sex chromosomes on patterns of introgression in an experimental hybrid swarm. Drosophila nasuta and Drosophila albomicans are recently diverged, fully fertile sister species that have different sex chromosome systems. The fusion between an autosome (Muller CD) with the ancestral X and Y gave rise to neo-sex chromosomes in D. albomicans, while Muller CD remains unfused in D. nasuta. We found that a large block containing overlapping inversions on the neo-sex chromosome stood out as the strongest barrier to introgression. Intriguingly, the neo-sex chromosome introgression barrier is asymmetrical and sex-dependent. Female hybrids showed significant D. albomicans­biased introgression on Muller CD (neo-X excess), while males showed heterosis with excessive (neo-X, D. nasuta Muller CD) genotypes. We used a population genetic model to dissect the interplay of sex chromosome drive, heterospecific pairing incompatibility between the neo-sex chromosomes and unfused Muller CD, neo-Y disadvantage, and neo-X advantage in generating the observed sex chromosome genotypes in females and males. We show that moderate neo-Y disadvantage and D. albomicans specific meiotic drive are required to observe female-specific D. albomicans­biased introgression in this system, together with pairing incompatibility and neo-X advantage. In conclusion, this hybrid swarm between a young species pair sheds light onto the multifaceted roles of neo-sex chromosomes in a sex-dependent asymmetrical introgression barrier at a species boundary.

Predicted structural proteome of Sphagnum divinum and proteome-scale annotation.

MOTIVATION: Sphagnum-dominated peatlands store a substantial amount of terrestrial carbon. The genus is undersampled and under-studied. No experimental crystal structure from any Sphagnum species exists in the Protein Data Bank and fewer than 200 Sphagnum-related genes have structural models available in the AlphaFold Protein Structure Database. Tools and resources are needed to help bridge these gaps, and to enable the analysis of other structural proteomes now made possible by accurate structure prediction. RESULTS: We present the predicted structural proteome (25 134 primary transcripts) of Sphagnum divinum computed using AlphaFold, structural alignment results of all high-confidence models against an annotated nonredundant crystallographic database of over 90,000 structures, a structure-based classification of putative Enzyme Commission (EC) numbers across this proteome, and the computational method to perform this proteome-scale structure-based annotation. AVAILABILITY AND IMPLEMENTATION: All data and code are available in public repositories, detailed at https://github.com/BSDExabio/SAFA. The structural models of the S. divinum proteome have been deposited in the ModelArchive repository at https://modelarchive.org/doi/10.5452/ma-ornl-sphdiv.

A WNT mimetic with broad spectrum FZD-specificity decreases fibrosis and improves function in a pulmonary damage model.

BACKGROUND: Wnt/ß-catenin signaling is critical for lung development and AT2 stem cell maintenance in adults, but excessive pathway activation has been associated with pulmonary fibrosis, both in animal models and human diseases such as idiopathic pulmonary fibrosis (IPF). IPF is a detrimental interstitial lung disease, and although two approved drugs limit functional decline, transplantation is the only treatment that extends survival, highlighting the need for regenerative therapies. METHODS: Using our antibody-based platform of Wnt/ß-catenin modulators, we investigated the ability of a pathway antagonist and pathway activators to reduce pulmonary fibrosis in the acute bleomycin model, and we tested the ability of a WNT mimetic to affect alveolar organoid cultures. RESULTS: A WNT mimetic agonist with broad FZD-binding specificity (FZD1,2,5,7,8) potently expanded alveolar organoids. Upon therapeutic dosing, a broad FZD-binding specific Wnt mimetic decreased pulmonary inflammation and fibrosis and increased lung function in the bleomycin model, and it impacted multiple lung cell types in vivo. CONCLUSIONS: Our results highlight the unexpected capacity of a WNT mimetic to effect tissue repair after lung damage and support the continued development of Wnt/ß-catenin pathway modulation for the treatment of pulmonary fibrosis.

Are Instagram Gym Advertisements Working Out? An Experimental Study of Model Body-Size and Slogan-Type.

Previous health communication research has demonstrated the negative psychological and health effects of depicting thin-sized models in mass media advertisements including on social media sites such as Instagram. However, gym advertisements are one common source for the presentation of lean and thin-sized models on Instagram. Therefore, the current study guided by social comparison theory and signaling theory aimed to experimentally examine the effect of thin-sized models relative to plus-sized models as well as slogan-type (health and wellness versus physique-based) on women's appearance comparison, body satisfaction, perceived gym fit, and intentions to join the gym. A sample of 217 undergraduate students who identified as women were randomly assigned to one of four Instagram gym advertisement conditions varying in model body-size and slogan-type. Appearance comparisons, perceived gym fit, and intentions to join the gym were measured post advertisement exposure and body satisfaction was measured pre-and-post advertisement exposure. As expected, exposure to Instagram gym advertisements featuring thin-sized models resulted in greater appearance comparisons and lower body satisfaction than exposure to Instagram gym advertisements featuring plus-sized models. Moreover, the combination of plus-sized models with health and wellness slogans in Instagram gym advertisements resulted in greater gym fit perceptions although there was no effect of model body-size and slogan-type on intentions to join the gym. This study supports social comparison theory, signaling theory, and practically the findings indicate that Instagram gym advertisements that depict plus-sized models (versus thin) with health-and-wellness slogans (versus physique) generate fewer body image concerns and lead to greater gym fit perceptions.

Impact of a pharmacist-driven COPD clinic on outcomes related to COPD in a federally qualified health center.

BACKGROUND: Chronic obstructive pulmonary disease (COPD) affects many patients across the United States. Morbidity related to COPD can lead to increased financial strain to health care system. The United States is also shifting toward value-based payments, which rely on satisfying quality measures. Pharmacists are equipped with knowledge in adjusting medications based on symptom burden and guideline recommendations in COPD and are equipped with the proper knowledge to address quality measures. OBJECTIVE: This project aimed to determine the impact of a clinical pharmacy service centered around inhaler education and optimization on COPD morbidity and Uniform Data System (UDS) quality measure satisfaction in a federally qualified health center. METHODS: This quality improvement project consisted of patient referrals by and reports from a population health software for the pharmacy service from November 2022 to March 2023. The outcomes in this study included symptom change measured by follow-up modified Medical Research Council (mMRC) Dyspnea Scale in addition to changes in compliance with UDS quality measures. At follow-up, patients were administered another mMRC to evaluate treatment effect and determine quality measure satisfaction. RESULTS: Thirteen patient visits were conducted. Most patients were female (84.6%) with an exacerbation in the previous year (46.1%). All patients received an adjustment in their pharmacotherapy along with inhaler education. The average baseline mMRC score decreased from 2.1 to 0.6, indicating a decrease in overall COPD symptoms. Five quality measures of 13 were satisfied during the follow-up period. CONCLUSION: The COPD clinical pharmacy service led to an increase in guideline-driven pharmacotherapy regimens for patients with COPD while having an overall decrease in morbidity. Quality measures were also addressed and satisfied after the appointment. Continuation of this quality improvement service will ensure proper assessment of COPD along with addressing UDS quality measures.

Reprint of: Impact of a pharmacist-driven COPD clinic on outcomes related to COPD in a federally qualified health center.

BACKGROUND: Chronic obstructive pulmonary disease (COPD) affects many patients across the United States. Morbidity related to COPD can lead to increased financial strain to health care system. The United States is also shifting toward value-based payments, which rely on satisfying quality measures. Pharmacists are equipped with knowledge in adjusting medications based on symptom burden and guideline recommendations in COPD and are equipped with the proper knowledge to address quality measures. OBJECTIVE: This project aimed to determine the impact of a clinical pharmacy service centered around inhaler education and optimization on COPD morbidity and Uniform Data System (UDS) quality measure satisfaction in a federally qualified health center. METHODS: This quality improvement project consisted of patient referrals by and reports from a population health software for the pharmacy service from November 2022 to March 2023. The outcomes in this study included symptom change measured by follow-up modified Medical Research Council (mMRC) Dyspnea Scale in addition to changes in compliance with UDS quality measures. At follow-up, patients were administered another mMRC to evaluate treatment effect and determine quality measure satisfaction. RESULTS: Thirteen patient visits were conducted. Most patients were female (84.6%) with an exacerbation in the previous year (46.1%). All patients received an adjustment in their pharmacotherapy along with inhaler education. The average baseline mMRC score decreased from 2.1 to 0.6, indicating a decrease in overall COPD symptoms. Five quality measures of 13 were satisfied during the follow-up period. CONCLUSION: The COPD clinical pharmacy service led to an increase in guideline-driven pharmacotherapy regimens for patients with COPD while having an overall decrease in morbidity. Quality measures were also addressed and satisfied after the appointment. Continuation of this quality improvement service will ensure proper assessment of COPD along with addressing UDS quality measures.

Sexual Minority Identity and Risky Alcohol Use: the Moderating Role of Aggressive Behavior.

Adolescent alcohol use has significant consequences for concurrent and longitudinal health and wellbeing, with sexual minority youth consistently reporting higher levels of alcohol use than their heterosexual peers. Understanding how individual-difference variables like aggressive behavior are associated with variability in sexual minority adolescents' higher levels of alcohol use offers novel theoretical insight into this vulnerability. The 81,509 participants were drawn from the Profiles of Student life: Attitudes and Behavior Study. They were ages 14-17 years (M = 15.38, SD = 1.09) and 50.1% were cisgender girls. For sexual identity, 88% were heterosexual, 5% were mostly heterosexual, were 4% bisexual, were 1% mostly gay or lesbian, and were 1% being gay or lesbian. Participants reported on alcohol use, aggressive behavior, and sexual identity. Gay/lesbian and mostly gay/lesbian adolescents who reported higher aggressive behavior had higher levels of alcohol use than their heterosexual peers who also reported higher aggressive behavior. The way in which aggressive behavior amplified the link between mostly gay/lesbian and gay/lesbian identities and alcohol use suggests the need for more research examining how this trait may heighten both exposure and reaction to minority stressors among some subgroups of sexual minority youth.

Examining Audiences' Psychological Reactance to Christian-Sourced Excessive Alcohol Consumption Messages in the United States.

This study experimentally investigated the effect of dogmatic and suggestive language in Christian-sourced excessive alcohol consumption messages among college-aged participants who identify as Christians or non-Christians, as well as the role of perceived similarity with the message source, on their self-reported freedom-threat, psychological reactance, and behavioral intentions to consume alcohol. The results from this study support psychological reactance theory and demonstrate the various message strategies to effectively communicate the negative health effects of excessive alcohol consumption to individuals who identify either as Christians or non-Christians.

Predicting transfer RNA gene activity from sequence and genome context.

Transfer RNA (tRNA) genes are among the most highly transcribed genes in the genome owing to their central role in protein synthesis. However, there is evidence for a broad range of gene expression across tRNA loci. This complexity, combined with difficulty in measuring transcript abundance and high sequence identity across transcripts, has severely limited our collective understanding of tRNA gene expression regulation and evolution. We establish sequence-based correlates to tRNA gene expression and develop a tRNA gene classification method that does not require, but benefits from, comparative genomic information and achieves accuracy comparable to molecular assays. We observe that guanine + cytosine (G + C) content and CpG density surrounding tRNA loci is exceptionally well correlated with tRNA gene activity, supporting a prominent regulatory role of the local genomic context in combination with internal sequence features. We use our tRNA gene activity predictions in conjunction with a comprehensive tRNA gene ortholog set spanning 29 placental mammals to estimate the evolutionary rate of functional changes among orthologs. Our method adds a new dimension to large-scale tRNA functional prediction and will help prioritize characterization of functional tRNA variants. Its simplicity and robustness should enable development of similar approaches for other clades, as well as exploration of functional diversification of members of large gene families.

OpenMDlr: parallel, open-source tools for general protein structure modeling and refinement from pairwise distances.

SUMMARY: Easy-to-use, open-source, general-purpose programs for modeling a protein structure from inter-atomic distances are needed for modeling from experimental data and refinement of predicted protein structures. OpenMDlr is an open-source Python package for modeling protein structures from pairwise distances between any atoms, and optionally, dihedral angles. We provide a user-friendly input format for harnessing modern biomolecular force fields in an easy-to-install package that can efficiently make use of multiple compute cores. AVAILABILITY AND IMPLEMENTATION: OpenMDlr is available at https://github.com/BSDExabio/OpenMDlr-amber. The package is written in Python (versions 3.x). All dependencies are open-source and can be installed with the Conda package management system. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

NF2 mutations are associated with resistance to radiation therapy for grade 2 and grade 3 recurrent meningiomas.

PURPOSE: High grade meningiomas have a prognosis characterized by elevated recurrence rates and radiation resistance. Recent work has highlighted the importance of genomics in meningioma prognostication. This study aimed to assess the relationship between the most common meningioma genomic alteration (NF2) and response to postoperative radiation therapy (RT). METHODS: From an institutional tissue bank, grade 2 and 3 recurrent meningiomas with both > 30 days of post-surgical follow-up and linked targeted next-generation sequencing were identified. Time to radiographic recurrence was determined with retrospective review. The adjusted hazard of recurrence was estimated using Cox-regression for patients treated with postoperative RT stratified by NF2 mutational status. RESULTS: Of 53 atypical and anaplastic meningiomas (29 NF2 wild-type, 24 NF2 mutant), 19 patients underwent postoperative RT. When stratified by NF2 wild-type, postoperative RT in NF2 wild-type patients was associated with a 78% reduction in the risk of recurrence (HR 0.216; 95%CI 0.068-0.682; p = 0.009). When stratified by NF2 mutation, there was a non-significant increase in the risk of recurrence for NF2 mutant patients who received postoperative RT compared to those who did not (HR 2.43; 95%CI 0.88-6.73, p = 0.087). CONCLUSION: This study demonstrated a protective effect of postoperative RT in NF2 wild-type patients with recurrent high grade meningiomas. Further, postoperative RT may be associated with no improvement and perhaps an accelerated time to recurrence in NF2 mutant tumors. These differences in recurrence rates provide evidence that NF2 may be a valuable prognostic marker in treatment decisions regarding postoperative RT. Further prospective studies are needed to validate this relationship.

tinyIFD: A High-Throughput Binding Pose Refinement Workflow Through Induced-Fit Ligand Docking.

A critical step in structure-based drug discovery is predicting whether and how a candidate molecule binds to a model of a therapeutic target. However, substantial protein side chain movements prevent current screening methods, such as docking, from accurately predicting the ligand conformations and require expensive refinements to produce viable candidates. We present the development of a high-throughput and flexible ligand pose refinement workflow, called "tinyIFD". The main features of the workflow include the use of specialized high-throughput, small-system MD simulation code mdgx.cuda and an actively learning model zoo approach. We show the application of this workflow on a large test set of diverse protein targets, achieving 66% and 76% success rates for finding a crystal-like pose within the top-2 and top-5 poses, respectively. We also applied this workflow to the SARS-CoV-2 main protease (Mpro) inhibitors, where we demonstrate the benefit of the active learning aspect in this workflow.

On the origins of spontaneous spherical symmetry-breaking in open-shell atoms through polymer self-consistent field theory.

An alternative approach to density functional theory based on self-consistent field theory for ring polymers is applied to neutral atoms hydrogen to neon in their ground-states. The spontaneous emergence of an atomic shell structure and spherical symmetry-breaking of the total electron density are predicted by the model using the ideas of polymer excluded-volume between pairs of electrons to enforce the Pauli-exclusion principle and an exact electron self-interaction correction. The Pauli potential is approximated by neglecting inter-atomic correlations along with other types of correlations, and comparisons to Hartree-Fock theory are made, which also ignores correlations. The model shows excellent agreement with Hartree-Fock theory to within the standards of orbital-free density functional theory for the atomic binding energies and density profiles of the first six elements, providing exact matches for the elements hydrogen and helium. The predicted shell structure starts to deviate significantly past the element neon, and spherical symmetry-breaking is first predicted to occur at carbon instead of boron. The self-consistent field theory energy functional that describes the model is decomposed into thermodynamic components to trace the origin of spherical symmetry-breaking. It is found to arise from the electron density approaching closer to the nucleus in non-spherical distributions, which lowers the energy despite resulting in frustration between the quantum kinetic energy, electron-electron interaction, and the Pauli exclusion interaction. The symmetry-breaking effect is found to have a minimal impact on the binding energies, which suggests that the spherical-averaging approximation used in previous work is physically reasonable when investigating atomic systems. The pair density contour plots display behavior similar to polymer macro-phase separation, where individual electron pairs occupy single lobe structures that together form a dumbbell shape analogous to the 2p orbital shape. It is further shown that the predicted densities satisfy known constraints and produce the same total electronic density profile that is predicted by other formulations of quantum mechanics.

Diminishing Psychological Reactance Through Self-Transcendent Media Experiences: A Self-Report and Psychophysiological Investigation.

Health communication scholars have provided ample evidence demonstrating the ways in which freedom-threatening language used in persuasive health messages evokes freedom-threat perceptions, state psychological reactance, and intentions to engage in behaviors opposite of those recommended by the health message. This study examined a novel mitigation strategy for diminishing these outcomes. We examined whether prior exposure to entertainment portrayals of moral virtue (versus a neutral video) can dampen audiences' psychological reactance, intentions to consume alcohol, and defensive message processing via their psychophysiological responses to a subsequent, freedom-threatening excessive alcohol consumption public service announcement (PSA). The results revealed that participants who viewed entertainment portrayals of moral virtue (N = 50 college-aged participants) self-reported higher levels of elevation, moved, and inspiration relative to participants in the control condition (N = 50 college-aged participants). Participants who were exposed to entertainment portrayals of moral virtue prior to the excessive alcohol consumption PSA also self-reported less psychological reactance and fewer behavioral intentions to consume alcohol following the excessive alcohol consumption PSA than participants in the control condition. Consistent with these self-report data, participants in the entertainment portrayals of moral virtue condition exhibited less defensive message processing of the excessive alcohol consumption PSA via their psychophysiological responses relative to the control group. The results indicate that initial exposure to entertainment portrayals of moral virtue can dampen audiences' cognitive, emotional, and behavioral responses to a subsequent, freedom-threatening health message, thereby increasing the chances of improved health outcomes.

Racial-ethnic socialization, racial discrimination, and internalization of the model minority myth in East Asian families.

Guided by the integrative model, this study investigated the moderating effect of East Asian American youth-reported (N = 143) racial-ethnic socialization (RES) in the relationship between the youth's experiences of discrimination and internalization of the model minority myth. The results suggest that there was a significant interaction between youth's racial discrimination and youth-reported awareness of discrimination on youth's internalization of the model minority myth (b = 3.52, p < .05). No significant interaction effect emerged between racial discrimination and maintenance of heritage culture on internalization of model minority myth. The findings offer several contributions to inform research, family, and communities in understanding the ways caregivers respond to youth's racialized settings, which also contribute to youth's positive outcomes.

Comparing sexual orientation identity development in plurisexual versus monosexual latinx sexual minority youth.

INTRODUCTION: Plurisexual individuals represent 50% of sexual minority adolescent communities. However, most studies of sexual minority adolescents analyze this population as a homogeneous group rather than attending to plausible differences between plurisexual and monosexual sexual minority youth. This study examined whether plurisexual Latinx youth differed from monosexual youth on three facets of sexual orientation identity (SOI) development (exploration, resolution, and affirmation). Further, we examined whether plurisexual (vs. monosexual) identity moderated the relationship between SOI development and depressive symptoms and self-esteem. METHODS: The sample included 365 Latinx sexual minority youth (14-24 years) living in the United States or US Territory. The majority of participants identified as monosexual (84.1%); 15.9% were plurisexual. The sample was 75.6% male, 19.5% female, and 2.0% transgender. Participants were asked to complete an online, cross-sectional survey that asked questions pertaining to ethnicity and sexual orientation. This data was collected in the fall of 2014. RESULTS: Latinx plurisexual youth had higher levels of SOI affirmation, exploration, and resolution than monosexual youth. SOI affirmation and exploration and were positively associated with self-esteem for all youth. SOI affirmation was significantly negatively associated with depressive symptoms for monosexual youth but not for plurisexual youth. SOI exploration and resolution were not significantly associated with depressive symptoms. CONCLUSIONS: This study demonstrates that there are significant differences between plurisexual and monosexual Latinx adolescent populations in reference to identity affirmation, exploration, and resolution, and that these sexual orientations should be treated distinctly in future research. In addition, all three aspects of identity development were significantly related to higher self-esteem for all youth regardless of identity, providing evidence for the importance of developing these three factors.