Miracle-dz/UniFAR-FTUs huggingface dataset:
Novel inductively-coupled ear-bars (ICEs) for fMRI signal enhancement in rat entorhinal cortex

Entorhinal cortex (EC) is a potential target of deep brain stimulation in Alzheimer’s disease (AD) and fMRI can enable whole-brain dynamic mapping noninvasively. However, it remains challenging to study EC-based fMRI connectivity in rodents due to image signal loss and the lower sensitivity of the surface coil ring or array coil for deep brain areas. To reduce the magnetic susceptibility artifacts driven signal loss issue, we introduced baby cream into the middle ear. To improve detection sensitivity, we implemented novel inductively-coupled ear-bars (ICEs) in the 7 T Bruker scanner, which resulted in an approximately 2-fold signal-to-noise ratio (SNR) increase in EC over the conventional surface array. The ICE can be conveniently utilized as an add-on device, with no modulation to the scanner interface. To demonstrate the applicability of ICEs for both task and resting-state (rs) fMRI, whole-brain echo-planar imaging (EPI) was performed in anesthetized rats modeling AD mixed dementia. Seed-based rs-fMRI connectivity maps emanating from the left entorhinal cortex demonstrated its connectivity to the hippocampus, piriform cortex, septal nuclei, and prefrontal cortex. Hence, this work demonstrates an optimized procedure for ICE by acquiring large scale networks emanating from a seed region that was not easily accessible by conventional MRI detectors, enabling better observation of EC-based brain fMRI connectivity studies with a higher signal-to-noise ratio in rodent models of dementia.
What causes bird‐building collision risk? Seasonal dynamics and weather drivers

Bird-building collisions are a major source of wild bird mortality, with hundreds of millions of fatalities each year in the United States and Canada alone. Here, we use two decades of daily citizen-science monitoring to characterize day-to-day variation in building collisions and determine the factors that predict the highest risk times in two North American cities. We use these analyses to evaluate three potential causes of increased collision risk: heightened migration traffic during benign weather, increased navigational and flight errors during inclement weather, and increased errors in response to highly directional sunlight that enhances reflected images. The seasonal phenology of collisions was consistent across sites and years, with daily collision rates approximately two-fold higher in autumn as compared to spring. During both migration seasons, collision risk was best predicted by the weather conditions at dawn. In spring, peak collision risk occurs on days with warm temperatures, south winds, and a lack of precipitation at dawn. In autumn, peak collision occurs on days with cool temperatures, north winds, high atmospheric pressure, a lack of precipitation, and clear conditions with high visibility. Based on these results, we hypothesize that collisions are influenced by two main weather-driven mechanisms. First, benign weather at dawn with winds that are favorable for migration flight causes an increase in migration traffic in both spring and autumn, creating greater opportunity for collisions to occur. Second, for autumnal migrants, cold clear conditions may cause an additional increase in collision risk. We propose that these conditions may be particularly hazardous in autumn because of the high abundance of naïve and diurnal migrants at that time of year. Our analysis also establishes that a relatively small proportion of days (15%) are responsible for 50% of the total collision mortality within a season, highlighting the importance of targeting mitigation strategies to the most hazardous times.
We the Hunted

Classic depictions of human evolutionary ecology cast Homo as predator and other hominins, including Paranthropus robustus, as prey. Such hypotheses rest on a small number of fossils that exhibit evidence of carnivore predation, including the iconic SK 54 cranium from Swartkrans in South Africa. Here we demonstrate that the SK 54 cranium shares its closest affinities with H. erectus rather than P. robustus. Demonstrating that Homo was prey for leopards at Swartkrans weakens the historically significant hypothesis that Homo was better able to avoid predation because of being behaviourally and technologically advanced compared to Paranthropus. Subsequent ideas about hominin paleobiology derived from this hypothesis warrant reconsideration.
Environmental DNA concentrations of Japanese eels in relation to habitat characteristics

The Japanese eel (Anguilla japonica), is listed as “Endangered” by the IUCN. Understanding eel riverine habitat is useful in considering conservation strategies. This study sought to determine the relationship between environmental DNA (eDNA) concentrations derived from Japanese eels, water quality, and river structure in three small rivers in Nagasaki, Japan. eDNA was detected at 14 of 15 sites (93%). The concentration of eDNA in brackish water was significantly higher than that in freshwater and was correlated with water depth. Eel occurrence throughout the river suggests a need to conserve a diversity of habitats.
Gains and losses of the epiphytic lifestyle in epidendroid orchids: review and new analyses with succulence traits

Background and Aims Epiphytism has evolved repeatedly in plants and has resulted in a considerable number of species with original characteristics. Succulent forms in particular are thought to have evolved as an adaptation to the epiphytic environment, because the water supply is generally erratic compared to soils’. However, succulent organs also exist in terrestrial plants, and the question of the concomitant evolution of epiphytism and succulence has received little attention, not even in the epidendroid orchids, which account for 68% of vascular epiphytes. Methods We reconstructed a new time-calibrated phylogenetic tree of Epidendroideae with 203 genera treated in Genera Orchidacearum, from which we reconstructed the evolution of epiphytism and other traits including stem and leaf succulence, while testing the correlated evolution between lifestyle and morphological traits. Furthermore, we reconstructed the ancestral geographic ranges to interpret major character changes during the Cenozoic. Key Results Epiphytism evolved at least 7.1 My ago in the neotropical Sobralieae, 11.5 My ago in the Arethuseae in Southeast Asia and Australia, and 39.0 My ago in the common ancestor of the Dendrobieae and Cymbidieae in the three previous areas, and was notably lost in the Malaxideae, Collabieae, Calypsoeae, Bletiinae, and Eulophiinae. Stem succulence is inferred to have evolved once, in a terrestrial ancestor 43.1 My ago, thus preceding the evolution of epiphytism by at least 4.1 My. If lost, stem succulence was almost systematically replaced by leaf succulence in epiphytic lineages. Conclusions Epiphytism probably evolved from terrestrial orchids already possessing succulent stems, which appeared during Eocene climatic cooling. Both epiphytic and secondary terrestrial Epidendroideae may have appeared in seasonally-dry forests. Thus, we believe that the emergence of stem succulence in early epidendroids was a key innovation in the evolution of orchids, facilitating the colonisation of epiphytic environments that led to the greatest diversification of orchids.
Protein Language Model Predicts Mutation Pathogenicity and Clinical Prognosis

Accurately predicting the effects of mutations in cancer has the potential to improve existing treatments and identify novel therapeutic targets. In this paper, we evidence for the first time that the large-scale pre-trained protein language models (PPLMs) are zero-shot predictors for two clinically relevant tasks: identifying diseasecausing mutations and predicting patient survival rate. Then we benchmark a series of state-of-the-art (SOTA) PPLMs on 2279 protein variants across 20 cancer-related genes. Our empirical results show that the PPLMs outperform the SOTA baseline, EVE [1], trained on multiple sequence alignment (MSA) data. We also demonstrate that the evolutionary index score, generated from the PPLM’s softmax layer, is good indicator for both mutation pathogenicity and patient survival rate. Our paper has taken a key step toward the clinical utility of large-scale PPLMs.
The origins of haplotype 58 (H58) Salmonella enterica serovar Typhi

Antimicrobial resistance (AMR) poses a serious threat to the clinical management of typhoid fever. AMR in Salmonella Typhi (S. Typhi) is associated with the H58 lineage, which arose comparatively recently before becoming globally disseminated. To better understand when and how this lineage emerged and became dominant, we performed detailed phylogenetic and phylodynamic analyses on contemporary genome sequences from S. Typhi isolated in the period spanning the emergence. Our dataset, which contains the earliest described H58 S. Typhi, indicates that the prototype H58 organisms were multi-drug resistant (MDR). These organisms emerged spontaneously in India in 1987 and became radially distributed throughout South Asia and then globally in the ensuing years. These early organisms were associated with a single long branch, possessing mutations associated with increased bile tolerance, suggesting that the first H58 organism was generated during chronic carriage. The subsequent use of fluoroquinolones led to several independent mutations in gyrA. The ability of H58 to acquire and maintain AMR genes continues to pose a threat, as extensively drug-resistant (XDR; MDR plus resistance to ciprofloxacin and third generation cephalosporins) variants, have emerged recently in this lineage. Understanding where and how H58 S. Typhi originated and became successful is key to understand how AMR drives successful lineages of bacterial pathogens. Additionally, these data can inform optimal targeting of typhoid conjugate vaccines (TCVs) for reducing the potential for emergence and the impact of new drug-resistant variants. Emphasis should also be placed upon the prospective identification and treatment of chronic carriers to prevent the emergence of new drug resistant variants with the ability to spread efficiently.
Volatile metabolites in lavage fluid are correlated to Valley fever disease severity in murine model lung infections

Coccidioides immitis and Coccidioides posadasii are soil-dwelling fungi of arid regions in North and South America that are responsible for Valley fever (coccidioidomycosis). Forty percent of patients with Valley fever exhibit symptoms ranging from mild, self-limiting respiratory infections, to severe, life-threatening pneumonia that requires treatment. Misdiagnosis as bacterial pneumonia commonly occurs in symptomatic Valley fever cases, resulting in inappropriate treatment with antibiotics, increased medical costs, and delay in diagnosis. In this study, we explored the feasibility of developing breath-based diagnostics for Valley fever using a murine lung infection model. To investigate potential volatile biomarkers of Valley fever that arise from host-pathogen interactions, we infected C57BL/6J mice with C. immitis RS and C. posadasii Silveira via intranasal inoculation. We measured fungal dissemination and collected bronchoalveolar lavage fluid (BALF) for cytokine profiling and for untargeted volatile metabolomics via solid phase microextraction (SPME) and two-dimensional gas chromatography coupled to time-of-flight mass spectrometry (GC×GC-TOFMS). We identified 36 volatile organic compounds (VOCs) that were significantly correlated to cytokine abundances and clustered mice by disease severity. These 36 VOCs were also able to separate mice with a moderate to high disease severity by infection strain. The data presented here show that Coccidioides and/or the host produce volatile metabolites that may yield biomarkers for a Valley fever breath test that can detect Coccidioidal infection and provide clinically relevant information on disease severity. IMPORTANCE Coccidioidomycosis, or Valley fever, is a fungal disease endemic to the North and South American arid regions. Forty percent of individuals infected with Valley fever will exhibit symptoms consistent with community-acquired pneumonia. However, misdiagnosis frequently occurs in these cases, resulting in inappropriate treatment with antibiotics, increased medical costs, and delay in receiving an accurate diagnosis. Herein, we used a murine lung infection model as a step towards developing a breath-based diagnostic for Valley fever. We infected C57BL/6J mice with C. immitis RS and C. posadasii Silveira and collected bronchoalveolar lavage fluid for untargeted volatile metabolomics. We observed that volatile metabolites in the bronchoalveolar lavage fluid of Cocci-inoculated mice were significantly correlated to disease severity, as measured by immune response. The data presented here show that Coccidioides and/or the host produce volatile metabolites that may yield biomarkers for a Valley fever breath test.
Fitness benefits from co-display favour subdominant male–male partnerships between phenotypes

Male-male competition over matings is a key driving force in the evolution of courtship. Typically, competition is an individual affair selecting for dominance and aggression. Yet, some males forgo direct confrontation and improve their reproductive success through cooperation. Occasionally, this leads to specialized alternative reproductive tactics that operate at the intersection of cooperation and conflict. We used a community game model, informed with empirical data derived from previous studies, to examine cooperation dynamics between lekking male ruffs (Calidris pugnax) using two different tactics: resident and satellite. Residents defend display courts against other residents on leks. In contrast, satellites forgo court defence and engage in cooperative co-display with selected residents. Co-displaying appears to alter female mate choice, yet the exact mechanism and consequences remain unclear. We modelled individual male mating success as a function of lek size, resident rank, and satellite competitiveness. Our most realistic model assumed that co-display draws copulations from residents proportional to the existing mating skew among them. Under this assumption, all residents benefit from co-display over single display when a satellite is on the lek, except for α-residents co-displaying with the most competitive satellites on large leks. Thus, satellites could nearly always choose their preferred co-display partner, but achieved the highest copulation rates with lower ranking (subdominant) residents on intermediate sized leks. Co-display between the satellite and lower ranking residents reduced the mating skew among residents. However, since copulations for satellites were similar over a range of potential co-display partners, a variety of co-displaying dyads is to be expected, which is consistent with observations in nature. We conclude that, given our model assumptions, co-displaying reduces the impact of male dominance on reproductive success and ultimately alters the course of sexual selection.
Condition-dependence resolves the paradox of missing plasticity costs

Phenotypic plasticity plays a key role in adaptation to changing environments. However, plasticity is neither perfect nor ubiquitous, implying that fitness costs must limit the evolution of phenotypic plasticity in nature. The measurement of such costs of plasticity has proved elusive; decades of experiments show that fitness costs of plasticity are often weak or nonexistent. Here, we show that this paradox can be at least partially explained by condition-dependence. We develop two models differing in their assumptions about how condition-dependence arises; both models show that variation in condition can readily mask costs of plasticity even when such costs are substantial. This can be shown simply in a model where costly plasticity itself evolves condition-dependence. Yet similar effects emerge from an alternative model where trait expression is condition-dependent. In this more complex model, average condition in each environment and genetic covariance in condition across environments both determine when costs of plasticity can be revealed. Analogous to the paradox of missing trade-offs between life history traits, our models show that variation in condition masks costs of plasticity even when costs exist, and suggests this conclusion may be robust to the details of how condition affects trait expression. Our models demonstrate that condition dependence can also account for the often-observed pattern of elevated plasticity costs inferred in stressful environments, the maintenance of genetic variance in plasticity, and provides insight into experimental and biological scenarios ideal for revealing a cost of phenotypic plasticity.
Regulation of Polyhomeotic Condensates by Intrinsically Disordered Sequences That Affect Chromatin Binding

The Polycomb group (PcG) complex PRC1 localizes in the nucleus in the form of condensed structures called Polycomb bodies. The PRC1 subunit Polyhomeotic (Ph) contains an oligomerizing sterile alpha motif (SAM) that is implicated in both PcG body formation and chromatin organization in Drosophila and mammalian cells. A truncated version of Ph containing the SAM (mini-Ph), forms phase separated condensates with DNA or chromatin in vitro, suggesting PcG bodies may form by SAM-driven phase separation. In cells, Ph forms multiple small condensates, while mini-Ph typically forms a single large nuclear condensate. We therefore hypothesize that sequences outside of mini-Ph, which are predicted to be intrinsically disordered, are required for proper condensate formation. We identified three distinct low complexity regions in Ph based on sequence composition. We systematically tested the role of each of these sequences in Ph condensates using live imaging of transfected Drosophila S2 cells. Each sequence uniquely affects Ph SAM-dependent condensate size, number, and morphology, but the most dramatic effects occur when the central, glutamine rich IDR is removed, which results in large Ph condensates. Like mini-Ph condensates, these condensates exclude chromatin. Chromatin fractionation experiments indicate that removal of the glutamine rich IDR reduces chromatin binding, while removal of either of the other IDRs increases chromatin binding. Our data suggest all three IDRs, and functional interactions among them, regulate Ph condensate size and number. Our results can be explained by a model in which tight chromatin binding by Ph IDRs antagonizes Ph SAM driven phase separation and highlight the complexity of regulation of biological condensates housed in single proteins.
Digital and Non-Digital Solidarity between Older Parents and Their Middle-Aged Children: Associations with Mental Health during the COVID-19 Pandemic

We incorporated intergenerational digital communication (frequency of texting, video call, and social media interaction) into the intergenerational solidarity paradigm and identified new types of intergenerational and digital solidarity with adult children among older parents during the COVID-19 pandemic. In addition, we examined whether those types are associated with older parents’ mental health (depressive symptoms, psychological well-being, and self-esteem). We used the 2021/2022 wave of the Longitudinal Study of Generations (LSOG), and a sample of 519 older parents (mean age = 69 years). Latent class analysis identified four classes describing intergenerational and digital solidarity with adult children (distant-but-digitally connected, tight-knit-traditional, detached, and ambivalent). We found that older parents who had distant-but-digitally connected and tight-knit-traditional relationships with their adult children reported better mental health, compared to those who had detached and ambivalent relationships with their adult children during the COVID-19 pandemic. Our findings suggest that intergenerational digital communication should be considered as a digital solidarity in intergenerational solidarity paradigm, which is useful for measuring multidimension of intergenerational relationships within family members during and after the pandemic.
Whole-Genome Resequencing Highlights the Unique Characteristics of Kecai Yaks

Simple Summary Kecai yaks are an important genetic resource in Gansu Province, China. These yaks, produced through the crossbreeding of Gannan yaks and wild yaks, exhibit excellent production performance and high fecundity. Despite these beneficial characteristics, the genetic characteristics, population structure, and other properties of Kecai yaks have not been effectively characterized to date. Accordingly, this study was developed to explore the genetic diversity and population structure of Kecai yaks through whole-genome resequencing. These analyses ultimately revealed the status of Kecai yaks as an independent group within the overall Chinese yak population. Abstract Kecai yaks are regarded as an important genetic resource in China owing to their high fecundity and flavorful meat. However, the genetic characteristics of Kecai yaks have not been effectively characterized to date, and the relationship between Kecai yaks and other yak breeds remains to be fully characterized. In this paper, the resequencing of the Kecai yak genome is performed leading to the identification of 11,491,383 high-quality single nucleotide polymorphisms (SNPs). Through principal component, phylogenetic, and population genetic structure analyses based on these SNPs, Kecai yaks were confirmed to represent an independent population of yaks within China. In this study, marker and functional enrichment analysis of genes related to positive selection in Kecai yak was carried out, and the results show that such selection in Kecai yaks is associated with the adaptation to alpine environments and the deposition of muscle fat. Overall, these results offer a theoretical foundation for the future utilization of Kecai yak genetic resources.
Well-Being during the Pandemic–Insights from a Rapid Review on the Mental Health of Disadvantaged Youth and Young Adults

The spread of the COVID-19 pandemic had a wide range of impacts on living conditions, opportunities and mental health. As discussed by society and supported by some studies, young people were particularly affected. The aim of this review was to provide an overview of research that explicitly addressed the mental health outcomes of adolescents’ and young adults’ transition. A systematic literature search in PubMed, PsycInfo, PSYNDEX, Embase and LIVIVO was conducted in February 2022. 42 of 2562 screened publications from industrialized/high-income countries were included and analyzed. All included publications show that the mental health of young people worsened during the pandemic. Several studies suggest(ed) that youths with less education and low socioeconomic status were affected most. Regarding different stages of adolescence, study results are heterogeneous. Evidence indicates that schools as institutions are important settings for everyday lives, personal development and education of young people. The review shows that there is a need for research and scientifically validated recommendations for practice. Further consideration should focus on the implementation of sustainable structures on the local level to strengthen resilience, minimize risk factors for young people’s mental health and create opportunities for valuable transitions.