bluuebunny/crossref_metadata_2025_split huggingface dataset:
DROUGHT-INDUCED BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE enhances drought tolerance in rice
Authors: Shim Jae Sung , Jeong Hye In , Bang Seung Woon , Jung Se Eun , Kim Goeun , Kim Youn Shic , Redillas Mark Christian Felipe R , Oh Se-Jun , Seo Jun Sung , Kim Ju-Kon 
Published: December 2022

Abstract
Plants accumulate several metabolites in response to drought stress, including branched-chain amino acids (BCAAs). However, the roles of BCAAs in plant drought responses and the underlying molecular mechanisms for BCAA accumulation remain elusive. Here, we demonstrate that rice (Oryza sativa) DROUGHT-INDUCED BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE (OsDIAT) mediates the accumulation of BCAAs in rice in response to drought stress. An in vitro enzyme activity assay indicated that OsDIAT is a branched-chain amino acid aminotransferase, and subcellular localization analysis revealed that OsDIAT localizes to the cytoplasm. The expression of OsDIAT was induced in plants upon exposure to abiotic stress. OsDIAT-overexpressing (OsDIATOX) plants were more tolerant to drought stress, whereas osdiat plants were more susceptible to drought stress compared with nontransgenic (NT) plants. Amino acid analysis revealed that BCAA levels were higher in OsDIATOX but lower in osdiat compared with in NT plants. Finally, the exogenous application of BCAAs improved plant tolerance to osmotic stress compared with that in control plants. Collectively, these findings suggest that OsDIAT mediates drought tolerance by promoting the accumulation of BCAAs.
Neurological complications of COVID-19
Authors: Dai X , Cao X , Jiang Q , Wu B , Lou T , Shao Y , Hu Y , Lan Q 
Published: December 2022

AbstractCorona Virus Disease 2019 (COVID-19) has caused several pandemic peaks worldwide due to its high variability and infectiousness, and COVID-19 has become a long-standing global public health problem. There is growing evidence that severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) frequently causes multi-organ injuries and more severe neurological manifestations. Therefore, increased awareness of possible neurological complications is beneficial in preventing and mitigating the impact of long-term sequelae and improving the prognostic outcome of critically ill patients with COVID-19. Here, we review the main pathways of SARS-CoV-2 neuroinvasion and the potential mechanisms causing neurological damage. We also discuss in detail neurological complications, aiming to provide cutting-edge basis for subsequent related basic research and clinical studies of diagnosis and treatment.
Brain-Derived Neurotrophic Factor Val66Met Genotype Modulates Latent Inhibition: Relevance for Schizophrenia
Authors: Buhusi Mona , Griffin Daniel , Buhusi Catalin V 
Published: December 2022

AbstractBackground and HypothesisLatent inhibition (LI) is a measure of selective attention and learning relevant to Schizophrenia (SZ), with 2 abnormality poles: Disrupted LI in acute SZ, thought to underlie positive symptoms, and persistent LI (PLI) in schizotypy and chronic SZ under conditions where normal participants fail to show LI. We hypothesized that Brain-Derived Neurotrophic Factor (BDNF)-Met genotype shifts LI toward the PLI pole.Study DesignWe investigated the role of BDNF-Val66Met polymorphism and neural activation in regions involved in LI in mice, and the interaction between the BDNF and CHL1, a gene associated with SZ.Study ResultsNo LI differences occurred between BDNF-wild-type (WT) (Val/Val) and knock-in (KI) (Met/Met) mice after weak conditioning. Chronic stress or stronger conditioning disrupted LI in WT but not KI mice. Behavior correlated with activation in infralimbic and orbitofrontal cortices, and nucleus accumbens. Examination of LI in CHL1-KO mice revealed no LI with no Met alleles (BDNF-WTs), PLI in CHL1-WT mice with 1 Met allele (BDNF-HETs), and PLI in both CHL1-WTs and CHL1-KOs with 2 Met alleles (BDNF-KIs), suggesting a shift to LI persistence with the number of BDNF-Met alleles in the CHL1 model of acute SZ.ConclusionsResults support a role for BDNF polymorphisms in gene-gene and gene-environment interactions relevant to SZ. BDNF-Met allele may reduce expression of some acute SZ symptoms, and may increase expression of negative symptoms in individuals with chronic SZ. Evaluation of (screening for) SZ phenotypes associated with mutations at a particular locus (eg, CHL1), may be masked by strong effects at different loci (eg, BDNF).
The use of residual serum samples to perform serological surveillance of severe acute respiratory syndrome coronavirus 2 in Dili and regional areas of Timor-Leste
Authors: Sarmento Nevio , Ico Lourenço C , Sheridan Sarah L , Tanesi Maria Y , Santos Celia G , Barreto Ismael , Gomes Nelia , Oakley Tessa , Draper Anthony D K , Fancourt Nicholas S S , Yan Jennifer , Macartney Kristine , Francis Joshua R , Arkell Paul 
Published: December 2022

ABSTRACTBackgroundLack of access to diagnostic testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection can limit disease surveillance in remote areas. Serological surveillance can indicate the true extent and distribution of infections in such settings.MethodsThis study monitored SARS-CoV-2 seroprevalence in residual serum samples salvaged from laboratories at five healthcare facilities across Timor-Leste from March to October 2021.ResultsSeroprevalence increased from 8.3% to 87.0% during the study period. Potential immunity gaps were identified among children aged 0–15 y (who had not been eligible for vaccination) and individuals aged &gt;60 y.ConclusionsEfforts to vaccinate vulnerable individuals including older people should be maintained. Residual serum samples can be analysed to give local, contemporary information about the extent and distribution of antibodies to infections, especially SARS-CoV-2, in areas where epidemiological information is limited.
Bullying in Academic Medicine: Experiences of Women Physician Leaders
Authors: Iyer Maya S. , Way David P. , MacDowell Doug J. , Overholser Barbara M. , Spector Nancy D. , Jagsi Reshma 
Published: December 2022

Purpose
Bullying is defined as offenders abusing positions of authority and intentionally targeting individuals through persistent negative behaviors to impede education or career growth. This study sought to estimate the prevalence and nature of bullying experienced by women physician leaders in academic medicine.

Method
In this survey-based study, 547 physician graduates of an executive women’s leadership training program were invited to complete a survey that measured workplace bullying in 2021. Participants were asked whether and when they had been bullied, how it impacted their careers, and remedies for bullying. Descriptive statistics were used to profile mistreatment and bullying experienced by the respondents during their professional careers and the nature of bullying. Content analysis of open-ended comments was used to describe how bullying impacted women physicians and outline recommendations for bullying prevention and mitigation.

Results
The survey response rate was 64.7% (354/547). Most women (302/354 [85.3%]) had experienced mistreatment during their careers, with more than half experiencing bullying while an attending physician (198/302 [65.6%]). Many women (187/302 [61.9%]) who screened positive for mistreatment also reported that they had been bullied at work. Of these 187 respondents, 173 (92.5%) experienced bullying from men and 121 (64.7%) reporting bullying from women (effect size = 0.34, P ≤ .001), and 115 (61.5%) reported that bullies were their immediate supervisors. Qualitative findings suggested that bullying harmed individuals’ career advancement, mental health, reputation, and relationships with others. Many had to change roles or leave jobs. Participants proposed that initiatives by top-level leaders, clear definitions of bullying behavior, reporting mechanisms, and upstander training for faculty and staff could mitigate bullying.

Conclusions
Most women physician leaders have experienced bullying. These results highlight the need to address bullying in academic medicine so that women can reach their full career potential.
The influence of low-level viremia on CD4+ cell count in human immunodeficiency virus–infected patients
Authors: Lee Cheng-Te , Chen Hsin-Pai , Lin Hsi-Hsun , Ke Meng-Yu , Wu Ping-Feng 
Published: December 2022

Background:
Following initiation of combined antiretroviral therapy, the majority of human immunodeficiency virus–infected patients experience immune reconstitution indicated by virologic suppression and an increase in peripheral CD4+ T-cell counts. Some patients may suffer from low-level viremia, which was reported to be significantly associated with acquired immunodeficiency syndrome cases, virologic failure, and death. We aimed to further investigate the influence of low-level viremia on CD4+ T-cell count.

Methods:
In our study, we included human immunodeficiency virus-seropositive patients on combined antiretroviral therapy, for at least 6 months, who received at least one assessment of human immunodeficiency virus plasma viral load and CD4+ cell count every 6 months, from January 2009 to January 2019. The copy-year viremia was determined by calculating the area under the curve of the plasma human immunodeficiency virus viral load.

Results:
When comparing patients with a mean CD4+ cell count <200 cells/μL, there was no significant difference between patients with a mean viral load <1000 copies/mL and patients with a mean viral load ≥1000 copies/mL (p = 0.219). Among those with a mean viral load <1000 copies/mL, a higher proportion of patients had a mean CD4+ cell count ≥500 cells/µL (p < 0.001). The mean CD4+ cell count of patients with copy-years viremia (log10) <4 (577.7, interquartile range 429.2-736.7) was significantly higher than that of patients with copy-years viremia (log10) ≥4 (443.3, interquartile range 319.0-558.4) (p < 0.001). In multivariate logistic regression analysis, we observed that malignancy without history, lower copy-years viremia, and high nadir CD4+ cell count were independent predictors of mean CD4+ cell count ≥500 cells/µL.

Conclusion:
Human immunodeficiency virus–infected patients with a history of malignancy, high copy-year viremia, and lower nadir CD4+ cell counts should be monitored carefully in clinical settings.
Vitamin A-treated natural killer cells reduce interferon-gamma production and support regulatory T cell differentiation
Authors: Jeong Mingeum , See Jia-Xiang , De La Torre Carolina , Cerwenka Adelheid , Stojanovic Ana 
Published: December 2022

AbstractNatural killer (NK) cells are innate cytotoxic lymphocytes that contribute to immune responses against stressed, transformed or infected cells. NK cell effector functions are regulated by microenvironmental factors, including cytokines, metabolites and nutrients. Vitamin A is an essential micronutrient that plays an indispensable role in embryogenesis and development, but was also reported to regulate immune responses. However, the role of vitamin A in regulating NK cell functions remains poorly understood. Here, we show that the most prevalent vitamin A metabolite, all-transretinoic acid (atRA), induces transcriptional and functional changes in NK cells leading to altered metabolism and reduced IFN-γ production in response to a wide range of stimuli. atRA-exposed NK cells display a reduced ability to support dendritic cell (DC) maturation and to eliminate immature DCs. Moreover, they support the polarization and proliferation of regulatory T cells. These results imply that in vitamin A-enriched environments, NK cells can acquire regulatory-like functions and might promote tolerogenic immunity and/or immunosuppression.
PADAPT 1.0 – the Pannonian Database of Plant Traits
Authors: Sonkoly Judit , Tóth Edina , Balogh Nóra , Balogh Lajos , Bartha Dénes , Bata Kinga , Bátori Zoltán , Békefi Nóra , Botta-Dukát Zoltán , Bölöni János , Csecserits Anikó , Csiky János , Csontos Péter , Dancza István , Deák Balázs , Dobolyi Zoltán Konstantin , E-Vojtkó Anna , Gyulai Ferenc , Hábenczyus Alida Anna , Henn Tamás , Horváth Ferenc , Höhn Mária , Jakab Gusztáv , Kelemen András , Király Gergely , Kis Szabolcs , Kovacsics-Vári Gergely , Kun András , Lehoczky Éva , Lengyel Attila , Lhotsky Barbara , Löki Viktor , Lukács Balázs András , Matus Gábor , McIntosh-Buday Andrea , Mesterházy Attila , Miglécz Tamás , Molnár V. Attila , Molnár Zsolt , Morschhauser Tamás , Papp László , Pósa Patrícia , Rédei Tamás , Schmidt Dávid , Szmorad Ferenc , Takács Attila , Tamás Júlia , Tiborcz Viktor , Tölgyesi Csaba , Tóth Katalin , Tóthmérész Béla , Valkó Orsolya , Virók Viktor , Wirth Tamás , Török Péter 
Published: December 2022

AbstractWe present PADAPT 1.0, the Pannonian Database of Plant Traits which relies on regional data sources and integrates existing data and new measurements on a wide range of traits and attributes of the plant species of the Pannonian Biogeographical Region and makes it freely accessible atwww.padapt.eu. The current version covers the species of the region occurring in Hungary (cc. 90% of the region’s flora) and consists of 126,337 records on 2745 taxa. There are 53 plant attributes in PADAPT 1.0 organised in six major groups: (i) Habitus and strategy, (ii) Reproduction, (iii) Kariology, (iv) Distribution and conservation, (v) Ecological indicator values, and (vi) Leaf traits. By including species of the eastern part of Europe not covered by other databases, PADAPT can facilitate studying the flora and vegetation of the eastern part of the continent. Data collection will continue in the future and the PADAPT team welcomes researchers interested in contributing with data. The main task before an updated version of the database is to include species of the Pannonian region not covered by the current version. In conclusion, although data coverage is far from complete, PADAPT meets the longstanding need for a regional database of the Pannonian flora.
IL-6 prevents Th2 cell polarization by promoting SOCS3-dependent suppression of IL-2 signaling
Authors: Bachus Holly , McLaughlin Erin , Lewis Crystal , Papillion Amber M. , Benveniste Etty N. , Hill Dave Durrell , Rosenberg Alexander F. , Ballesteros-Tato André , León Beatriz 
Published: December 2022

AbstractDefective interleukin-6 (IL-6) signaling has been associated with Th2 bias and elevated IgE. However, the underlying mechanism by which IL-6 prevents the development of Th2-driven diseases remains unknown. Using a model of house-dust-mite (HDM)-induced Th2 differentiation and allergic airway inflammation, we show that IL-6 signaling in allergen-specific T cells was required to prevent Th2 development and subsequent IgE response and allergic inflammation. Th2 cell lineage commitment required strong sustained IL-2 signaling. Importantly, we found that IL-6 turned off IL-2 signaling during early T cell activation and thus inhibited Th2 priming. Mechanistically, we found that IL-6-driven inhibition of IL-2 signaling in responding T cells was mediated by upregulation of Suppressor Of Cytokine Signaling 3 (SOCS3). This mechanism could be mimicked by pharmacological Janus Kinase-1 (JAK1) inhibition. Collectively, our results identify an unrecognized mechanism that prevents the development of unwanted Th2 cell responses and associated diseases and outline potential preventive interventions.
“Sharing my story has been part of my healing process”: how Native women survivors heal from IPV
Authors: Park Susanna Y 
Published: December 2022

AbstractFour out of five Native women experience intimate partner violence (IPV) in their lifetime. Culture, Native identity, and other socioeconomic factors influence how survivors experience seeking support and healing. High rates of IPV among Native women indicate an urgent public health need to address the long-term implications of being a survivor. This study explores how Native women in California seek healing as survivors of violence through stories shared in Community Circles and Oral Histories supported by collaborations with local Indigenous community organizations in Southern California. Seeking support and healing for Native women survivors of IPV are layered with their identities as Indigenous women, historical oppression, and its resulting intergenerational traumas. Healing from the violence has cultural implications, amplifying the need for community-based systems of support that are Indigenous-centered. For AIAN women survivors of IPV, healing transcends beyond their selves, extending to their families, tribal communities, and future generations. Culturally-rooted systems of support that cultivate Indigenous values of connection and healing are needed.
Identifying B-cell epitopes using AlphaFold2 predicted structures and pretrained language model
Authors: Zeng Yuansong , Wei Zhuoyi , Yuan Qianmu , Chen Sheng , Yu Weijiang , Lu Yutong , Gao Jianzhao , Yang Yuedong 
Published: December 2022

AbstractMotivationIdentifying the B-cell epitopes is an essential step for guiding rational vaccine development and immunotherapies. Due to experimental approaches being expensive and time-consuming, many computational methods have been designed to assist B-cell epitope prediction. However, existing sequence-based methods have limited performance since they only use contextual features of the sequential neighbors while neglecting structural information.ResultsBased on the recent breakthrough of AlphaFold2 in protein structure prediction, we propose GraphBepi, a novel graph-based model for accurate B-cell epitope prediction. GraphBepi first generates the effective information sequence representations and protein structures from antigen sequences through the pretrained language model and AlphaFold2, respectively. GraphBepi then applies the edge-enhanced deep graph neural network (EGNN) to capture the spatial information from predicted protein structures and leverages the bidirectional long short-term memory neural networks (BiLSTM) to capture long-range dependencies from sequences. The low-dimensional representation learned by EGNN and BiLSTM is then combined to predict B-cell epitopes through a multilayer perceptron. Through comprehensive tests on the curated epitope dataset, GraphBepi was shown to outperform the state-of-the-art methods by more than 5.5% and 44.0% in terms of AUC and AUPR, respectively. We also provide the GraphBepi web server that is freely available athttps://biomed.nscc-gz.cn/apps/GraphBepi.AvailabilityThe datasets, pre-computed features, source codes, and the pretrained model of GraphBepi are available athttps://github.com/biomed-AI/GraphBepi.Contactyangyd25@mail.sysu.edu.cnorgaojz@nankai.edu.cn
Using light for energy: examining the evolution of phototrophic metabolism through synthetic construction
Authors: Peterson Autumn , Baskett Carina , Ratcliff William C. , Burnetti Anthony 
Published: December 2022

AbstractThe origin of phototrophy was pivotal in increasing the size and scale of the biosphere, as it allowed organisms to utilize light-driven energy transport to drive biological processes. Retinalophototrophy, one of two independently evolved phototrophic pathways, consists of a simple system of microbial rhodopsins which have spread broadly through the tree of life via horizontal gene transfer. Here, we sought to determine whetherSaccharomyces cerevisiae, a heterotrophic fungus with no known evolutionary history of phototrophy, can function as a facultative artificial phototroph after acquiring a single rhodopsin gene. We transformedS. cerevisiaeinto a facultative phototroph by inserting a rhodopsin protein fromUstilago maydisinto the yeast vacuole, allowing light to pump protons into the vacuolar compartment, a function typically driven by consuming ATP. We show that yeast with rhodopsins gain a selective advantage when grown under green light, growing more rapidly than their non-phototrophic ancestor or rhodopsin-bearing yeast cultured in the dark. These results underscore the remarkable ease with which rhodopsins may be horizontally transferred even in eukaryotes, providing novel biological function without first requiring evolutionary optimization.
Low-pass Whole Genome Imputation Enables the Characterization of Polygenic Breast Cancer Risk in the Indigenous Arab Population
Authors: Al-Jumaan Mohammed , Chu Hoyin , Al-Sulaiman Abdullah , Camp Sabrina Y. , Han Seunghun , Gillani Riaz , Al Marzooq Yousef , Almulhim Fatmah , Vatte Chittibabu , Al Nemer Areej , Almuhanna Afnan , Van Allen Eliezer M , Al-Ali Amein , AlDubayan Saud H 
Published: December 2022

AbstractThe indigenous Arab population has traditionally been underrepresented in cancer genomics studies, and as a result the polygenic risk landscape of breast cancer in the population remains elusive. Here we show by utilizing low-pass whole genome sequencing (lpWGS), we can accurately impute population-specific variants with high exome concordance (median dosage correlation: 0.9459, Interquartile range: 0.9410-0.9490) and construct breast cancer burden-sensitive polygenic risk scores (PRS) using publicly available resources. After adjusting the PRS to the Arab population, we found significant associations between PRS performance in risk prediction and first-degree relative breast cancer history prediction (Spearman rho=0.43, p = 0.03), where breast cancer patients in the top PRS decile are 5.53 (95% CI: 1.76-17.97, p = 0.003) times more likely to also have a first degree relative diagnosed with breast cancer compared to those in the middle deciles. In addition, we found evidence for the genetic liability threshold model of breast cancer where among patients with a family history of breast cancer, pathogenic rare variant carriers had significantly lower PRS than non-carriers (p = 0.0205, M.W.U.) while for non-carriers every standard deviation increase in PRS corresponded to 4.52 years (95% CI: 8.88-0.17, p = 0.042) earlier age of presentation. Overall, our study provides a viable strategy utilizing lpWGS to assess polygenic risk in an understudied population and took steps in addressing existing global health disparities.
Identification of fibroinflammatory and fibrotic transcriptomic subsets of human sclerotic cutaneous chronic graft-versus-host disease
Authors: Rosenstein Rachel K. , Rose Jeremy J. , Brooks Stephen R. , Tsai Wanxia L. , Gadina Massimo , Pavletic Steven Z. , Nagao Keisuke , Cowen Edward W. 
Published: December 2022

ABSTRACTCutaneous sclerotic chronic graft-versus-host disease (cGVHD) is a common and highly morbid complication of allogeneic hematopoietic stem cell transplantation (HSCT). We identified genes that are significantly upregulated in the skin of sclerotic cGVHD patients (n = 17) compared to HSCT patients without sclerotic cGVHD (n = 9) by bulk RNA sequencing. This revealed two transcriptomic groups of affected patients: those with fibrotic and inflammatory/Th1 gene expression, the fibroinflammatory group, and those with predominantly fibrotic/TGFβ-associated expression, the fibrotic group. This transcriptomic heterogeneity was also associated with histopathologic heterogeneity, with the fibroinflammatory sub-cluster showing more histopathologic features of epidermal cGVHD and inflammation. Further study will help elucidate if these gene expression and histopathologic findings can be used to tailor treatment decisions. Multiple highly induced genes in the skin (SFRP4, SERPINE2, COMP) were also found to be significantly induced in sclerotic cGVHD patient plasma (n = 16) compared to control HSCT patients without sclerotic cGVHD (n = 17), suggesting these TGFβ and Wnt pathway mediators as candidate blood biomarkers of disease.