bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unraveling the small proteome of the plant symbiontSinorhizobium melilotiby ribosome profiling and proteogenomics
Authors: Hadjeras Lydia , Heiniger Benjamin , Maaß Sandra , Scheuer Robina , Gelhausen Rick , Azarderakhsh Saina , Barth-Weber Susanne , Backofen Rolf , Becher Dörte , Ahrens Christian H , Sharma Cynthia M , Evguenieva-Hackenberg Elena 
Published: March 2023

AbstractThe soil-dwelling plant symbiont Sinorhizobium meliloti is a major model organism of Alphaproteobacteria. Despite numerous detailed OMICS studies, information about small open reading frame (sORF)-encoded proteins (SEPs) is largely missing, because sORFs are poorly annotated and SEPs are hard to detect experimentally. However, given that SEPs can fulfill important functions, identification of translated sORFs is critical for analyzing their roles in bacterial physiology. Ribosome profiling (Ribo-seq) can detect translated sORFs with high sensitivity, but is not yet routinely applied to bacteria because it must be adapted for each species. Here, we established a Ribo-seq procedure for S. meliloti 2011 based on RNase I digestion and detected translation for 60% of the annotated coding sequences during growth in minimal medium. Using ORF prediction tools based on Ribo-seq data, subsequent filtering, and manual curation, the translation of 37 non-annotated sORFs with ≤ 70 amino acids was predicted with confidence. The Ribo-seq data were supplemented by mass spectrometry (MS) analyses from three sample preparation approaches and two integrated proteogenomic search database (iPtgxDB) types. Searches against standard and 20-fold smaller Ribo-seq data-informed custom iPtgxDBs confirmed 47 annotated SEPs and identified 11 additional novel SEPs. Epitope tagging and Western blot analysis confirmed the translation of 15 out of 20 SEPs selected from the translatome map. Overall, by combining MS and Ribo-seq approaches, the small proteome of S. meliloti was substantially expanded by 48 novel SEPs. Several of them are part of predicted operons and/or are conserved from Rhizobiaceae to Bacteria, suggesting important physiological functions.
Microbiology education: a significant path to sustainably improve the human and biosphere condition
Authors: Timmis Kenneth 
Published: March 2023

AbstractIn this short piece, I connect the dots between the pervasive influence of microbial activities on our health and that of the planet, including their positive and negative roles in current polycrises, our ability to influence microbes to promote their positive influences and mitigate their negative impacts, the roles of everyone as stewards and stakeholders in personal, family, community, national, and global wellbeing, the need for stewards and stakeholders to possess relevant information in order to fulfil their roles and obligations, and the compelling case for microbiology literacy and introduction of a societally relevant microbiology curriculum in school.
Residential Segregation and Depressive Symptoms in Older Chinese Immigrants: The Mediating Role of Social Processes
Authors: Tang Fengyan , Jiang Yanping , Li Ke , Rosso Andrea L 
Published: March 2023

AbstractBackground and ObjectivesOlder Chinese immigrants are at risk for depression due to acculturative stress and language barriers. Residential segregation with respect to language use plays an important role in the mental health of historically marginalized populations. Previous research provided mixed evidence about the segregation effect among older Latino and Asian immigrants. Guided by a model of social processes, we examined the direct and indirect effects of residential segregation on depressive symptoms via multiple mechanisms of acculturation, discrimination, social network, social support, social strain, and social engagement.Research Design and MethodsFour waves of depressive symptoms were assessed in the Population Study of Chinese Elderly (2011–19, N = 1,970), and linked to the 2010–14 American Community Survey estimates of neighborhood context. Residential segregation was measured by the Index of Concentrations at the Extremes which simultaneously assesses Chinese and English language use within a given census tract. Latent growth curve models with adjusted cluster robust standard errors were estimated after controlling for individual-level factors.ResultsResidents of segregated Chinese-speaking neighborhoods had fewer baseline depressive symptoms but a slower rate of symptom reduction than those living in neighborhoods segregated with English-only speakers. Racial discrimination, social strain, and social engagement partially mediated the association between segregation and baseline depressive symptoms; social strain and social engagement partially mediated the association with long-term reduction in depressive symptoms.Discussion and ImplicationsThis study demonstrates the importance of residential segregation and social processes in shaping mental well-being among older Chinese immigrants and suggests potential mechanisms to alleviate mental health risks.
How to estimate life history ratios to simplify data-poor fisheries assessment
Authors: Prince Jeremy D , Wilcox Chris , Hall Norman 
Published: March 2023

Abstract
Less variable than life history parameters (LHPs), it is life history ratios (LHRs) that define how taxa allocate energy between growth, maintenance and reproduction, and respond to fishing pressure. Limited by small samples, variable data quality, and a focus on LHP estimation, previous meta-analyses have failed to settle debate about the extent to which LHRs are relatively invariant across all taxa or characteristic of specific taxa. We collected de novo 1335 published studies and applying rigorous standardization and quality control procedures developed, and make available, a database of high-quality M/K and Lm/L∞ estimates. We describe two parallel but independent meta-analyses: a cross-validation study of the predictability of M/K by taxonomic category and an evaluation of alternative relationships between the LHRs using Akaike information criteria. These analyses demonstrate that the LHRs are correlated and vary predictably by taxa, with aggregation to the level of family and genera having the most predictive power in our database. We postulate that the LHRs of taxa may relate to their stoichiometric niches, which could open up interesting lines for ecological research and provide new tools for predicting the LHRs of poorly studied taxa.
Behavioural responses of wild, spawning Atlantic cod (Gadus morhua L.) to seismic airgun exposure
Authors: McQueen K , Skjæraasen J E , Nyqvist D , Olsen E M , Karlsen Ø , Meager J J , Kvadsheim P H , Handegard N O , Forland T N , de Jong K , Sivle L D 
Published: March 2023

Abstract
Seismic airgun surveys to map petroleum deposits in the seabed may impact behaviour of marine animals over large distances. Understanding whether fish spawning behaviour is affected by this anthropogenic noise source is important because reproductive success may be impacted. The fine-scale behavioural responses of Atlantic cod to airgun exposure over an extended period were investigated using an acoustic telemetry positioning system on a spawning ground in Norway. During 2019 to 2021, 135 spawning cod were equipped with telemetry sensor tags and were exposed to airgun shooting during the spawning periods of 2020 and 2021, with varying received sound levels comparable to a full-scale survey at distances of 5 to &gt;40 km. Cod demonstrated only weak responses to the disturbance from repeated 3-h treatment periods over 5-d, swimming on average slightly deeper during seismic exposure compared to silent control periods. This response varied between individuals. Longer-term effects of seismic exposure on swimming depth were not detected. No changes in swimming acceleration, displacement, or area use occurred. These results suggest that relatively distant seismic surveys do not substantially alter cod behaviour during the spawning period at received sound exposure levels varying between 115 and 145 dB re 1 µPa2s over a 5-d period.
Practical considerations for specifying a super learner
Authors: Phillips Rachael V , van der Laan Mark J , Lee Hana , Gruber Susan 
Published: March 2023

AbstractCommon tasks encountered in epidemiology, including disease incidence estimation and causal inference, rely on predictive modelling. Constructing a predictive model can be thought of as learning a prediction function (a function that takes as input covariate data and outputs a predicted value). Many strategies for learning prediction functions from data (learners) are available, from parametric regressions to machine learning algorithms. It can be challenging to choose a learner, as it is impossible to know in advance which one is the most suitable for a particular dataset and prediction task. The super learner (SL) is an algorithm that alleviates concerns over selecting the one ‘right’ learner by providing the freedom to consider many, such as those recommended by collaborators, used in related research or specified by subject-matter experts. Also known as stacking, SL is an entirely prespecified and flexible approach for predictive modelling. To ensure the SL is well specified for learning the desired prediction function, the analyst does need to make a few important choices. In this educational article, we provide step-by-step guidelines for making these decisions, walking the reader through each of them and providing intuition along the way. In doing so, we aim to empower the analyst to tailor the SL specification to their prediction task, thereby ensuring their SL performs as well as possible. A flowchart provides a concise, easy-to-follow summary of key suggestions and heuristics, based on our accumulated experience and guided by SL optimality theory.
National Identity and Public Attitudes Toward the World Health Organization
Authors: Ariely Gal 
Published: March 2023

AbstractThis article examines whether assumptions about the contradiction between national identity and support for international organizations are reflected in public support of the World Health Organization (WHO). Study 1 uses a comparative multilevel analysis to examine the link between national identification and confidence in the WHO as well as the influence of globalization on these attitudes. Study 2, which is based on a panel survey in Israel, explores whether attitudes toward the WHO have changed over time and under the influence of the COVID-19 pandemic and whether relations between national identification, national chauvinism, and perceptions of the WHO have also changed. Overall, the findings indicate that there is no clear-cut contradiction between national identity and public support for the WHO.
Narrowing the Gap in the Access to Justice for Child Victims in Postconflict Societies: An Analysis Stemming from the Construction of Child Soldiers in International Law and Policy
Authors: Molima Bameka Christelle 
Published: March 2023

ABSTRACT∞
A controversial approach characterizes international law and policy on children affected by armed conflict: it is much more concerned with child soldiers’ victimization than with their victims’ situation. This approach leads to (1) the prioritization of the former over the child victims of their crimes before judicial and non-judicial mechanisms and (2) a significant disparity in how international law and policy respond to the victimization of war-affected children in the presence of those categorized as ‘child soldiers.’ To narrow this gap, this article explores the potential of defining child soldiers as victims who victimize during trials. It does so by discussing the practice observed in local juvenile courts in the North and South Kivu provinces in the Democratic Republic of Congo.
Nonexercise machine learning models for maximal oxygen uptake prediction in national population surveys
Authors: Liu Yuntian , Herrin Jeph , Huang Chenxi , Khera Rohan , Dhingra Lovedeep Singh , Dong Weilai , Mortazavi Bobak J , Krumholz Harlan M , Lu Yuan 
Published: March 2023

AbstractObjectiveNonexercise algorithms are cost-effective methods to estimate cardiorespiratory fitness (CRF), but the existing models have limitations in generalizability and predictive power. This study aims to improve the nonexercise algorithms using machine learning (ML) methods and data from US national population surveys.Materials and MethodsWe used the 1999–2004 data from the National Health and Nutrition Examination Survey (NHANES). Maximal oxygen uptake (VO2 max), measured through a submaximal exercise test, served as the gold standard measure for CRF in this study. We applied multiple ML algorithms to build 2 models: a parsimonious model using commonly available interview and examination data, and an extended model additionally incorporating variables from Dual-Energy X-ray Absorptiometry (DEXA) and standard laboratory tests in clinical practice. Key predictors were identified using Shapley additive explanation (SHAP).ResultsAmong the 5668 NHANES participants in the study population, 49.9% were women and the mean (SD) age was 32.5 years (10.0). The light gradient boosting machine (LightGBM) had the best performance across multiple types of supervised ML algorithms. Compared with the best existing nonexercise algorithms that could be applied to the NHANES, the parsimonious LightGBM model (RMSE: 8.51 ml/kg/min [95% CI: 7.73–9.33]) and the extended LightGBM model (RMSE: 8.26 ml/kg/min [95% CI: 7.44–9.09]) significantly reduced the error by 15% and 12% (P &lt; .001 for both), respectively.DiscussionThe integration of ML and national data source presents a novel approach for estimating cardiovascular fitness. This method provides valuable insights for cardiovascular disease risk classification and clinical decision-making, ultimately leading to improved health outcomes.ConclusionOur nonexercise models provide improved accuracy in estimating VO2 max within NHANES data as compared to existing nonexercise algorithms.
Cultural Competence in the Care of LGBTQ+ Patients: A Primer for Breast/Chest Centers
Authors: Mehta Tejas S , Thompson Julie , Applegate Julia M , Wahab Rifat A 
Published: March 2023

Abstract
The number of individuals identifying as lesbian, gay, bisexual, transgender, queer/questioning (LGBTQ+) has doubled over the past 10 years, and this figure continues to rise. The LGBTQ+ community is diverse, encompassing a vast array of differences in gender identity and sexual orientation. Additionally, it is inclusive of people from all races, ethnicities, religions, and socioeconomic backgrounds. This intersectionality of identities and experiences impacts both access to health care and its delivery. Barriers to care for this population are multifactorial and include stigma, discrimination, bias, limited role models, issues with insurance coverage, lack of education and training for health care providers, and lack of research on LGBTQ+ health–related issues. Specific to breast cancer, the screening recommendations for this group are influenced not only by risk but also by gender-affirming hormonal and surgical therapies. This article will provide an overview of the LGBTQ+ population, review breast cancer screening compliance and recommendations, summarize the multitude of health disparities, and offer potential interventions to improve care delivery at the individual, facility, organizational, and health policy levels.
Gene cloning, expression pattern, and response to dietary total lipids and phospholipids of hormone-sensitive lipase (HSL) in the Oriental river prawnMacrobrachium nipponenseDe Haan, 1849 (Decapoda: Caridea: Palaemonidae)
Authors: Wang Qianqian , Cai Chunfang , Zhang Junbiao , Shui Dianzhang , Cui Guangtong , Wang Zhi , Ren Shengjie , Wu Ping , Ye Yuantu 
Published: March 2023

AbstractHormone-sensitive lipase (HSL) is an important regulator of cellular lipid homeostasis and catalyzes the hydrolysis of stored triacylglycerol. We identified and cloned for the first time the full-length cDNA sequence of HSL of the prawn Macrobrachium nipponense De Haan, 1849 [De Haan, 1833–1850] from a hepatopancreas cDNA library. The complete HSL sequence is 3,575 bp and encoded a 785 amino acid peptide with the catalytic core (GXSXG) containing a serine residue. The phylogenetic tree revealed that the gene of HSL of M. nipponense is closely related with that of Penaeus vanmameiBoone, 1931. The tissue distribution showed that the mRNA expression level of HSL in the hepatopancreas was significantly higher than that in other tissues (P &lt; 0.05). Furthermore, the HSL expression in hepatopancreas was upregulated with the increase of dietary lipids but partially inhibited when the ratio of phospholipids was increased in the lipid mixture. These results demonstrate that HSL is involved in the lipid metabolism of M. nipponense and highlights the importance of phospholipids in lipid metabolism.
Pipecolic acid synthesis is required for systemic acquired resistance and plant-to-plant-induced immunity in barley
Authors: Brambilla Alessandro , Lenk Miriam , Ghirardo Andrea , Eccleston Laura , Knappe Claudia , Weber Baris , Lange Birgit , Imani Jafargholi , Schäffner Anton R , Schnitzler Jörg-Peter , Vlot A Corina 
Published: March 2023

Abstract
Defense responses in plants are based on complex biochemical processes. Systemic acquired resistance (SAR) helps to fight infections by (hemi-)biotrophic pathogens. One important signaling molecule in SAR is pipecolic acid (Pip), accumulation of which is dependent on the aminotransferase ALD1 in Arabidopsis. While exogenous Pip primes defense responses in the monocotyledonous cereal crop barley (Hordeum vulgare), it is currently unclear if endogenous Pip plays a role in disease resistance in monocots. Here, we generated barley ald1 mutants using CRISPR/Cas9, and assessed their capacity to mount SAR. Endogenous Pip levels were reduced after infection of the ald1 mutant, and this altered systemic defense against the fungus Blumeria graminis f. sp. hordei. Furthermore, Hvald1 plants did not emit nonanal, one of the key volatile compounds that are normally emitted by barley plants after the activation of SAR. This resulted in the inability of neighboring plants to perceive and/or respond to airborne cues and prepare for an upcoming infection, although HvALD1 was not required in the receiver plants to mediate the response. Our results highlight the crucial role of endogenous HvALD1 and Pip for SAR, and associate Pip, in particular together with nonanal, with plant-to-plant defense propagation in the monocot crop barley.
Membrane Protein Detection and Morphological Analysis of Red Blood Cells in Hereditary Spherocytosis by Confocal Laser Scanning Microscopy
Authors: Rey-Barroso Laura , Roldán Mónica , Burgos-Fernández Francisco J , Isola Ignacio , Ruiz Llobet Anna , Gassiot Susanna , Sarrate Edurne , Vilaseca Meritxell 
Published: March 2023

AbstractIn hereditary spherocytosis (HS), genetic mutations in the cell membrane and cytoskeleton proteins cause structural defects in red blood cells (RBCs). As a result, cells are rigid and misshapen, usually with a characteristic spherical form (spherocytes), too stiff to circulate through microcirculation regions, so they are prone to undergo hemolysis and phagocytosis by splenic macrophages. Mild to severe anemia arises in HS, and other derived symptoms like splenomegaly, jaundice, and cholelithiasis. Although abnormally shaped RBCs can be identified under conventional light microscopy, HS diagnosis relies on several clinical factors and sometimes on the results of complex molecular testing. It is specially challenging when other causes of anemia coexist or after recent blood transfusions. We propose two different approaches to characterize RBCs in HS: (i) an immunofluorescence assay targeting protein band 3, which is affected in most HS cases and (ii) a three-dimensional morphology assay, with living cells, staining the membrane with fluorescent dyes. Confocal laser scanning microscopy (CLSM) was used to carry out both assays, and in order to complement the latter, a software was developed for the automated detection of spherocytes in blood samples. CLSM allowed the precise and unambiguous assessment of cell shape and protein expression.
NGTS clusters survey – IV. Search for Dipper stars in the Orion Nebular Cluster
Authors: Moulton Tyler , Hodgkin Simon T , Smith Gareth D , Briegal Joshua T , Gillen Edward , Acton Jack S , Battley Matthew P , Burleigh Matthew R , Casewell Sarah L , Gill Samuel , Goad Michael R , Henderson Beth A , Kendall Alicia , Ramsay Gavin , Tilbrook Rosanna H , Wheatley Peter J 
Published: March 2023

ABSTRACTThe dipper is a novel class of young stellar object associated with large drops in flux on the order of 10–50 per cent lasting for hours to days. Too significant to arise from intrinsic stellar variability, these flux drops are currently attributed to disc warps, accretion streams, and/or transiting circumstellar dust. Dippers have been previously studied in young star-forming regions, including the Orion Complex. Using Next Generation Transit Survey (NGTS) data, we identified variable stars from their light curves. We then applied a machine learning random forest classifier for the identification of new dipper stars in Orion using previous variable classifications as a training set. We discover 120 new dippers, of which 83 are known members of the Complex. We also investigated the occurrence rate of discs in our targets, again using a machine learning approach. We find that all dippers have discs, and most of these are full discs. We use dipper periodicity and model-derived stellar masses to identify the orbital distance to the inner disc edge for dipper objects, confirming that dipper stars exhibit strongly extended sublimation radii, adding weight to arguments that the inner disc edge is further out than predicted by simple models. Finally, we determine a dipper fraction (the fraction of stars with discs which are dippers) for known members of 27.8 ± 2.9 per cent. Our findings represent the largest population of dippers identified in a single cluster to date.
Intergenic Regions of Saccharomycotina Yeasts are Enriched in Potential to Encode Transmembrane Domains
Authors: Tassios Emilios , Nikolaou Christoforos , Vakirlis Nikolaos 
Published: March 2023

AbstractIntergenic genomic regions have essential regulatory and structural roles that impose constraints on their sequences. But regions that do not currently encode proteins also carry the potential to do so in the future. De novo gene emergence, the evolution of novel genes out of previously noncoding sequences has now been established as a potent force for genomic novelty. Recently, it was shown that intergenic regions in the genome of Saccharomyces cerevisiae harbor pervasive cryptic potential to, if theoretically translated, form transmembrane domains (TM domains) more frequently than expected by chance given their nucleotide composition, a property that we refer to as TM-forming enrichment. The source and biological relevance of this property is unknown. Here, we expand the investigation into the TM-forming potential of intergenic regions to the entire Saccharomycotina budding yeast subphylum, in an effort to explain this property and understand its importance. We find pervasive but variable enrichment in TM-forming potential across the subphylum regardless of the composition and average size of intergenic regions. This cryptic property is evenly spread across the genome, cannot be explained by the hydrophobic content of the sequence, and does not appear to localize to regions containing regulatory motifs. This TM-forming enrichment specifically, and not the actual TM-forming potential, is associated, across genomes, with more TM domains in evolutionarily young genes. Our findings shed light on this newly discovered feature of yeast genomes and constitute a first step toward understanding its evolutionary importance.