Viviparity imparts a macroevolutionary signature of ecological opportunity in the body size of female Liolaemus lizards.

Viviparity evolved ~115 times across squamate reptiles, facilitating the colonization of cold habitats, where oviparous species are scarce or absent. Whether the ecological opportunity furnished by such colonization reconfigures phenotypic diversity and accelerates evolution is unclear. We investigated the association between viviparity and patterns and rates of body size evolution in female Liolaemus lizards, the most species-rich tetrapod genus from temperate regions. Here, we discover that viviparous species evolve ~20% larger optimal body sizes than their oviparous relatives, but exhibit similar rates of body size evolution. Through a causal modeling approach, we find that viviparity indirectly influences body size evolution through shifts in thermal environment. Accordingly, the colonization of cold habitats favors larger body sizes in viviparous species, reconfiguring body size diversity in Liolaemus. The catalyzing influence of viviparity on phenotypic evolution arises because it unlocks access to otherwise inaccessible sources of ecological opportunity, an outcome potentially repeated across the tree of life.

Protein embeddings predict binding residues in disordered regions.

The identification of protein binding residues helps to understand their biological processes as protein function is often defined through ligand binding, such as to other proteins, small molecules, ions, or nucleotides. Methods predicting binding residues often err for intrinsically disordered proteins or regions (IDPs/IDPRs), often also referred to as molecular recognition features (MoRFs). Here, we presented a novel machine learning (ML) model trained to specifically predict binding regions in IDPRs. The proposed model, IDBindT5, leveraged embeddings from the protein language model (pLM) ProtT5 to reach a balanced accuracy of 57.2 ± 3.6% (95% confidence interval). Assessed on the same data set, this did not differ at the 95% CI from the state-of-the-art (SOTA) methods ANCHOR2 and DeepDISOBind that rely on expert-crafted features and evolutionary information from multiple sequence alignments (MSAs). Assessed on other data, methods such as SPOT-MoRF reached higher MCCs. IDBindT5's SOTA predictions are much faster than other methods, easily enabling full-proteome analyses. Our findings emphasize the potential of pLMs as a promising approach for exploring and predicting features of disordered proteins. The model and a comprehensive manual are publicly available at https://github.com/jahnl/binding_in_disorder .

Correction: Social vulnerability during the COVID-19 pandemic in Peru.

[This corrects the article DOI: 10.1371/journal.pgph.0001330.].

Higher prevalence of sacbrood virus in Apis mellifera (Hymenoptera: Apidae) colonies after pollinating highbush blueberries.

Highbush blueberry pollination depends on managed honey bees (Apis mellifera) L. for adequate fruit sets; however, beekeepers have raised concerns about the poor health of colonies after pollinating this crop. Postulated causes include agrochemical exposure, nutritional deficits, and interactions with parasites and pathogens, particularly Melisococcus plutonius [(ex. White) Bailey and Collins, Lactobacillales: Enterococcaceae], the causal agent of European foulbrood disease, but other pathogens could be involved. To broadly investigate common honey bee pathogens in relation to blueberry pollination, we sampled adult honey bees from colonies at time points corresponding to before (t1), during (t2), at the end (t3), and after (t4) highbush blueberry pollination in British Columbia, Canada, across 2 years (2020 and 2021). Nine viruses, as well as M. plutonius, Vairimorpha ceranae, and V. apis [Tokarev et al., Microsporidia: Nosematidae; formerly Nosema ceranae (Fries et al.) and N. apis (Zander)], were detected by PCR and compared among colonies located near and far from blueberry fields. We found a significant interactive effect of time and blueberry proximity on the multivariate pathogen community, mainly due to differences at t4 (corresponding to ~6 wk after the beginning of the pollination period). Post hoc comparisons of pathogens in near and far groups at t4 showed that detections of sacbrood virus (SBV), which was significantly higher in the near group, not M. plutonius, was the primary driver. Further research is needed to determine if the association of SBV with highbush blueberry pollination is contributing to the health decline that beekeepers observe after pollinating this crop.

Synthesis and Characterization of a Semiconductor Diodic Bilayer PbS/CdS Made by the Chemical Bath Deposition Technique.

In this work, we report a heterojunction formed by a PbS/CdS bilayer using the chemical bath deposition (CBD) technique because it is a relatively simple, fast, and low-cost technique; is permitted to obtain high-quality thin films (TFs); and also covers large areas. Some characterizations have been carried out to confirm the identity of the involved bilayer. For the cadmium sulfide (CdS) film, optical properties such as absorption, transmission, reflection, extinction coefficient, and refractive index were measured. Moreover, the bandgap was calculated, and morphology was obtained by scanning electron microscopy (SEM). Also, X-ray diffraction (XRD) and high-resolution transmission electron microscopy (TEM) were performed for the synthesis of CdS films. On the other hand, for the synthesis of lead sulfide (PbS) films, we performed TEM, energy-dispersive spectroscopy, and XRD. A surface morphological SEM image of the PbS film synthesized was also taken. The multiheterojunction PbS/CdS bilayer was characterized by the current-voltage (I-V) curve, and the behavior of the bilayer was evaluated under the conditions of darkness and controlled fixed lighting, detecting a very slight photosensitivity of the complete diodic device through those measurements. The calculated bandgap for the CdS TF was E g = 2.55 eV, while after a chosen thermal annealing, the bandgap decreased to 2.38 eV. On the other hand, the PbS film presented a cubic structure.

Endoscopic Normalization and Transition of J-Pouch Phenotypes Over Time in Patients With Inflammatory Bowel Disease.

BACKGROUND: Patients with inflammatory bowel disease (IBD) who undergo proctocolectomy with ileal pouch-anal anastomosis may develop pouchitis. We previously proposed a novel endoscopic classification of pouchitis describing 7 phenotypes with differing outcomes. This study assessed phenotype transitions over time. METHODS: We classified pouch findings into 7 main phenotypes: (1) normal, (2) afferent limb (AL) involvement, (3) inlet (IL) involvement, (4) diffuse, (5) focal inflammation of the pouch body, (6) cuffitis, and (7) pouch-related fistulas noted more than 6 months after ileostomy takedown. Among 2 endoscopic phenotypes, the phenotype that was first identified was defined as the primary phenotype, and the phenotype observed later was defined as the subsequent phenotype. RESULTS: We retrospectively reviewed 1359 pouchoscopies from 426 patients (90% preoperative diagnosis of ulcerative colitis). The frequency of primary phenotype was 31% for AL involvement, 42% for IL involvement, 28% for diffuse inflammation, 72% for focal inflammation, 45% for cuffitis, 18% for pouch-related fistulas, and 28% for normal pouch. The most common subsequent phenotype was focal inflammation (64.8%), followed by IL involvement (38.6%), cuffitis (37.8%), AL involvement (25.6%), diffuse inflammation (23.8%), normal pouch (22.8%), and pouch-related fistulas (11.9%). Subsequent diffuse inflammation, pouch-related fistulas, and AL or IL stenoses significantly increased the pouch excision risk. Patients who achieved subsequent normal pouch were less likely to have pouch excision than those who did not (8.1% vs 15.7%; P = .15). CONCLUSIONS: Pouch phenotype and the risk of pouch loss can change over time. In patients with pouch inflammation, subsequent pouch normalization is feasible and associated with favorable outcome.

Endoscopic pouch phenotypes can change over time and subsequent development of diffuse inflammation, pouch-related fistulas, and afferent limb/inlet stenoses significantly worsen pouch outcomes. In patients with pouch inflammation, subsequent pouch normalization is feasible and associated with favorable outcomes.

Secure Messaging and Telephone Use for Clinician-to-Clinician Communication.

This cohort study investigates the association of use of text-based secured messaging with telephone use among resident physicians.

A His bundle pacing protocol for suppressing ventricular arrhythmia maintenance and improving defibrillation efficacy.

BACKGROUND: The excitable gap (EG), defined as the excitable tissue between two subsequent wavefronts of depolarization, is critical for maintaining reentry that underlies deadly ventricular arrhythmias. EG in the His-Purkinje Network (HPN) plays an important role in the maintenance of electrical wave reentry that underlies these arrhythmias. OBJECTIVE: To determine if rapid His bundle pacing (HBP) during reentry reduces the amount of EG in the HPN and ventricular myocardium to suppress reentry maintenance and/or improve defibrillation efficacy. METHODS: In a virtual human biventricular model, reentry was initiated with rapid line pacing followed by HBP delivered for 3, 6, or 9 s at pacing cycle lengths (PCLs) ranging from 10 to 300 ms (n=30). EG was calculated independently for the HPN and myocardium over each PCL. Defibrillation efficacy was assessed for each PCL by stimulating myocardial surface EG with delays ranging from 0.25 to 9 s (increments of 0.25 s, n=36) after the start of HBP. Defibrillation was successful if reentry terminated within 1 s after EG stimulation. This defibrillation protocol was repeated without HBP. To test the approach under different pathological conditions, all protocols were repeated in the model with right (RBBB) or left (LBBB) bundle branch block. RESULTS: Compared to without pacing, HBP for >3 seconds reduced average EG in the HPN and myocardium across a broad range of PCLs for the default, RBBB, and LBBB models. HBP >6 seconds terminated reentrant arrhythmia by converting HPN activation to a sinus rhythm behavior in the default (6/30 PCLs) and RBBB (7/30 PCLs) models. Myocardial EG stimulation during HBP increased the number of successful defibrillation attempts by 3%-19% for 30/30 PCLs in the default model, 3%-6% for 14/30 PCLs in the RBBB model, and 3%-11% for 27/30 PCLs in the LBBB model. CONCLUSION: HBP can reduce the amount of excitable gap and suppress reentry maintenance in the HPN and myocardium. HBP can also improve the efficacy of low-energy defibrillation approaches targeting excitable myocardium. HBP during reentrant arrhythmias is a promising anti-arrhythmic and defibrillation strategy.

White-tailed deer population dynamics in a multipredator landscape shaped by humans.

Large terrestrial mammals increasingly rely on human-modified landscapes as anthropogenic footprints expand. Land management activities such as timber harvest, agriculture, and roads can influence prey population dynamics by altering forage resources and predation risk via changes in habitat, but these effects are not well understood in regions with diverse and changing predator guilds. In northeastern Washington state, USA, white-tailed deer (Odocoileus virginianus) are vulnerable to multiple carnivores, including recently returned gray wolves (Canis lupus), within a highly human-modified landscape. To understand the factors governing predator-prey dynamics in a human context, we radio-collared 280 white-tailed deer, 33 bobcats (Lynx rufus), 50 cougars (Puma concolor), 28 coyotes (C. latrans), and 14 wolves between 2016 and 2021. We first estimated deer vital rates and used a stage-structured matrix model to estimate their population growth rate. During the study, we observed a stable to declining deer population (lambda = 0.97, 95% confidence interval: 0.88, 1.05), with 74% of Monte Carlo simulations indicating population decrease and 26% of simulations indicating population increase. We then fit Cox proportional hazard models to evaluate how predator exposure, use of human-modified landscapes, and winter severity influenced deer survival and used these relationships to evaluate impacts on overall population growth. We found that the population growth rate was dually influenced by a negative direct effect of apex predators and a positive effect of timber harvest and agricultural areas. Cougars had a stronger effect on deer population dynamics than wolves, and mesopredators had little influence on the deer population growth rate. Areas of recent timber harvest had 55% more forage biomass than older forests, but horizontal visibility did not differ, suggesting that timber harvest did not influence predation risk. Although proximity to roads did not affect the overall population growth rate, vehicle collisions caused a substantial proportion of deer mortalities, and reducing these collisions could be a win-win for deer and humans. The influence of apex predators and forage indicates a dual limitation by top-down and bottom-up factors in this highly human-modified system, suggesting that a reduction in apex predators would intensify density-dependent regulation of the deer population owing to limited forage availability.

Adenosine modifications impede SARS-CoV-2 RNA-dependent RNA transcription.

SARS-CoV-2, the causative virus of the COVID-19 pandemic, follows SARS and MERS as recent zoonotic coronaviruses causing severe respiratory illness and death in humans. The recurrent impact of zoonotic coronaviruses demands a better understanding of their fundamental molecular biochemistry. Nucleoside modifications, which modulate many steps of the RNA lifecycle, have been found in SARS-CoV-2 RNA, although whether they confer a pro- or anti-viral effect is unknown. Regardless, the viral RNA-dependent RNA polymerase will encounter these modifications as it transcribes through the viral genomic RNA. We investigated the functional consequences of nucleoside modification on the pre-steady state kinetics of SARS-CoV-2 RNA-dependent RNA transcription using an in vitro reconstituted transcription system with modified RNA templates. Our findings show that N6-methyladenosine and 2'O-methyladenosine modifications slow the rate of viral transcription at magnitudes specific to each modification, which has the potential to impact SARS-CoV-2 genome maintenance.

Image Analysis Using the Fluorescence Imaging of Nuclear Staining (FINS) Algorithm.

Finding appropriate image analysis techniques for a particular purpose can be difficult. In the context of the analysis of immunocytochemistry images, where the key information lies in the number of nuclei containing co-localised fluorescent signals from a marker of interest, researchers often opt to use manual counting techniques because of the paucity of available tools. Here, we present the development and validation of the Fluorescence Imaging of Nuclear Staining (FINS) algorithm for the quantification of fluorescent signals from immunocytochemically stained cells. The FINS algorithm is based on a variational segmentation of the nuclear stain channel and an iterative thresholding procedure to count co-localised fluorescent signals from nuclear proteins in other channels. We present experimental results comparing the FINS algorithm to the manual counts of seven researchers across a dataset of three human primary cell types which are immunocytochemically stained for a nuclear marker (DAPI), a biomarker of cellular proliferation (Ki67), and a biomarker of DNA damage (γH2AX). The quantitative performance of the algorithm is analysed in terms of consistency with the manual count data and acquisition time. The FINS algorithm produces data consistent with that achieved by manual counting but improves the process by reducing subjectivity and time. The algorithm is simple to use, based on software that is omnipresent in academia, and allows data review with its simple, intuitive user interface. We hope that, as the FINS tool is open-source and is custom-built for this specific application, it will streamline the analysis of immunocytochemical images.

PARticular MARks: Histone ADP-ribosylation and the DNA damage response.

Cellular and molecular responses to DNA damage are highly orchestrated and dynamic, acting to preserve the maintenance and integrity of the genome. Histone proteins bind DNA and organize the genome into chromatin. Post-translational modifications of histones have been shown to play an essential role in orchestrating the chromatin response to DNA damage by regulating the DNA damage response pathway. Among the histone modifications that contribute to this intricate network, histone ADP-ribosylation (ADPr) is emerging as a pivotal component of chromatin-based DNA damage response (DDR) pathways. In this review, we survey how histone ADPr is regulated to promote the DDR and how it impacts chromatin and other histone marks. Recent advancements have revealed histone ADPr effects on chromatin structure and the regulation of DNA repair factor recruitment to DNA lesions. Additionally, we highlight advancements in technology that have enabled the identification and functional validation of histone ADPr in cells and in response to DNA damage. Given the involvement of DNA damage and epigenetic regulation in human diseases including cancer, these findings have clinical implications for histone ADPr, which are also discussed. Overall, this review covers the involvement of histone ADPr in the DDR and highlights potential future investigations aimed at identifying mechanisms governed by histone ADPr that participate in the DDR, human diseases, and their treatments.

Potential association between suicide risk, aggression, impulsivity, and the somatosensory system.

Aggression and impulsivity are linked to suicidal behaviors, but their relationship to the suicidal crisis remains unclear. This magnetoencephalography (MEG) study investigated the link between aggression, impulsivity, and resting-state MEG power and connectivity. Four risk groups were enrolled: high-risk (HR; n = 14), who had a recent suicidal crisis; lower-risk (LR; n = 41), who had a history of suicide attempts but no suicide attempt or ideation in the past year; clinical control (CC; n = 38), who had anxiety/mood disorders but no suicidal history; and minimal risk (MR; n = 28), who had no psychiatric/suicidal history. No difference in resting-state MEG power was observed between the groups. Individuals in the HR group with high self-reported aggression and impulsivity scores had reduced MEG power in regions responsible for sensory/emotion regulation vs. those in the HR group with low scores. The HR group also showed downregulated bidirectional glutamatergic feedback between the precuneus (PRE) and insula (INS) compared to the LR, CC, and MR groups. High self-reported impulsivity was linked to reduced PRE to INS feedback, whereas high risk-taking impulsivity was linked to upregulated INS to postcentral gyrus (PCG) and PCG to INS feedback. These preliminary findings suggest that glutamatergic-mediated sensory and emotion-regulation processes may function as potential suicide risk markers.

City divided: Unveiling family ties and genetic structuring of coyotes in Seattle.

Linear barriers pose significant challenges for wildlife gene flow, impacting species persistence, adaptation, and evolution. While numerous studies have examined the effects of linear barriers (e.g., fences and roadways) on partitioning urban and non-urban areas, understanding their influence on gene flow within cities remains limited. Here, we investigated the impact of linear barriers on coyote (Canis latrans) population structure in Seattle, Washington, where major barriers (i.e., interstate highways and bodies of water) divide the city into distinct quadrants. Just under 1000 scats were collected to obtain genetic data between January 2021 and December 2022, allowing us to identify 73 individual coyotes. Notably, private allele analysis underscored limited interbreeding among quadrants. When comparing one quadrant to each other, there were up to 16 private alleles within a single quadrant, representing nearly 22% of the population allelic diversity. Our analysis revealed weak isolation by distance, and despite being a highly mobile species, genetic structuring was apparent between quadrants even with extremely short geographic distance between individual coyotes, implying that Interstate 5 and the Ship Canal act as major barriers. This study uses coyotes as a model species for understanding urban gene flow and its consequences in cities, a crucial component for bolstering conservation of rarer species and developing wildlife friendly cities.

Investigating turbulence distribution in the lower atmosphere using time-lapse imagery from a camera bank.

The atmosphere's surface layer (first 50-100 m above the ground) is extremely dynamic and is influenced by surface radiative properties, roughness, and atmospheric stability. Understanding the distribution of turbulence in the surface layer is critical to many applications, such as directed energy and free space optical communications. Several measurement campaigns in the past have relied on weather balloons or sonic detection and ranging (SODAR) to measure turbulence up to the atmospheric boundary layer. However, these campaigns had limited measurements near the surface. We have developed a time-lapse imaging technique to profile atmospheric turbulence from turbulence-induced differential motion or tilts between features on a distant target, sensed between pairs of cameras in a camera bank. This is a low-cost and portable approach to remotely sense turbulence from a single site without the deployment of sensors at the target location. It is thus an excellent approach to study the distribution of turbulence in low altitudes with sufficiently high resolution. In the present work, the potential of this technique was demonstrated. We tested the method over a path with constant turbulence. We explored the turbulence distribution with height in the first 20 m above the ground by imaging a 30 m water tower over a flat terrain on three clear days in summer. In addition, we analyzed time-lapse data from a second water tower over a sloped terrain. In most of the turbulence profiles extracted from these images, the drop in turbulence with altitude in the first 15 m or so above the ground showed a h m dependence, where the exponent m varied from -0.3 to -1.0, quite contrary to the widely used value of -4/3.

Integrating social media, body shame and psychological distress within the Elaborated Sociocultural Model.

The Elaborated Sociocultural Model proposes exposure to sociocultural appearance pressures increases women's internalisation of the thin ideal, their engagement in social comparison and body surveillance, and subsequent body dissatisfaction and disturbances in eating (Fitzsimmons-Craft et al., 2011). Although this model has received some empirical support, it is limited in that it does not currently account for social media as a contemporary source of appearance pressure, nor include additional known outcomes of thin ideal internalisation (i.e., body shame, psychological distress). The current study tested the integration of these variables within the Elaborated Sociocultural Model. Using structural equation modelling with latent variables, the extended model provided acceptable to good fit to the data in a sample of 271 female participants. A latent variable representing sociocultural appearance pressures originating from social media, traditional media, family and peers was found to significantly predict thin ideal internalisation and body image concerns. Furthermore, both social comparison and body surveillance emerged as indirect mediators of the relationship between thin ideal internalisation and body image concerns, which in turn, increased report of restrained eating and psychological distress. Aligning with previous research, this extended model offers a useful and comprehensive framework for investigating women's body image.

Polysaccharide functionalization reduces lipid vesicle stiffness.

The biophysical properties of lipid vesicles are important for their stability and integrity, key parameters that control the performance when these vesicles are used for drug delivery. The vesicle properties are determined by the composition of lipids used to form the vesicle. However, for a given lipid composition, they can also be tailored by tethering polymers to the membrane. Typically, synthetic polymers like polyethyleneglycol are used to increase vesicle stability, but the use of polysaccharides in this context is much less explored. Here, we report a general method for functionalizing lipid vesicles with polysaccharides by binding them to cholesterol. We incorporate the polysaccharides on the outer membrane leaflet of giant unilamellar vesicles (GUVs) and investigate their effect on membrane mechanics using micropipette aspiration. We find that the presence of the glycolipid functionalization produces an unexpected softening of GUVs with fluid-like membranes. By contrast, the functionalization of GUVs with polyethylene glycol does not reduce their stretching modulus. This work provides the potential means to study membrane-bound meshworks of polysaccharides similar to the cellular glycocalyx; moreover, it can be used for tuning the mechanical properties of drug delivery vehicles.

Owner survey suggests cats may be undertreated for pain compared to dogs after an elective ovariohysterectomy or orchiectomy.

OBJECTIVE: To investigate differences in pain management between dogs and cats after surgical sterilization. We hypothesized that dogs would be more likely to be discharged with analgesics after sterilization compared to cats and that owner compliance would be better in dogs. ANIMALS: 175 respondents owning 92 dogs and 83 cats from a high-volume, low-cost veterinary clinic in Michigan during August 2022. METHODS: Owners received an online survey designed to assess their pet's postoperative analgesic care. They were asked demographic information about themselves and their pets. Additionally, they were asked if their pet was discharged with analgesics, if they were administered as prescribed, and if their pet was painful at home. Dogs and cats were included if they were sterilized within 6 months of survey completion and in the owner's care at the time of the procedure. RESULTS: The survey was distributed to 5,241 owners and received 227 responses, a response rate of 4.4%. Analgesics were prescribed for 19 of 162 (12%) pets: 14 of 88 (16%) dogs and 5 of 74 (6.7%) cats. There was no difference in the prescription of analgesics between dogs and cats after ovariohysterectomy (P = .09) or orchiectomy (P = .73). 15 of 19 owners reported their compliance in administering analgesics at 78.9%. Owners' subjective assessments showed that 24 of 86 (28%) dogs and 12 of 68 (17%) cats appeared painful at home. CLINICAL RELEVANCE: Postoperative pain in cats may not be appropriately managed.

National HIV and HCV Screening Rates for Hospitalized People who Use Drugs Are Suboptimal and Heterogeneous Across 11 US Hospitals.

Background: To end the HIV and hepatitis C virus (HCV) epidemics, people who use drugs (PWUD) need more opportunities for testing. While inpatient hospitalizations are an essential opportunity to test people who use drugs (PWUD) for HIV and HCV, there is limited research on rates of inpatient testing for HIV and HCV among PWUD. Methods: Eleven hospital sites were included in the study. Each site created a cohort of inpatient encounters associated with injection drug use. From these cohorts, we collected data on HCV and HIV testing rates and HIV testing consent policies from 65 276 PWUD hospitalizations. Results: Hospitals had average screening rates of 40% for HIV and 32% for HCV, with widespread heterogeneity in screening rates across facilities. State consent laws and opt-out testing policies were not associated with statistically significant differences in HIV screening rates. On average, hospitals that reflexed HCV viral load testing on HCV antibody testing did not have statistically significant differences in HCV viral load testing rates. We found suboptimal testing rates during inpatient encounters for PWUD. As treatment (HIV) and cure (HCV) are necessary to end these epidemics, we need to prioritize understanding and overcoming barriers to testing.