bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chronic alcohol consumption dysregulates innate immune response to SARS-CoV-2 in the lung
Authors: Lewis Sloan A. , Cinco Isaac R. , Doratt Brianna M. , Blanton Madison B. , Hoagland Cherise , Davies Michael , Grant Kathleen A. , Messaoudi Ilhem 
Published: May 2023

AbstractAlcohol consumption is widespread with over half of the individuals over 18 years of age in the U.S. reporting alcohol use in the last 30 days. Moreover, 9 million Americans engaged in binge or chronic heavy drinking (CHD) in 2019. CHD negatively impacts pathogen clearance and tissue repair, including in the respiratory tract, thereby increasing susceptibility to infection. Although, it has been hypothesized that chronic alcohol consumption negatively impacts COVID-19 outcomes; the interplay between chronic alcohol use and SARS-CoV-2 infection outcomes has yet to be elucidated. Therefore, in this study we investigated the impact of chronic alcohol consumption on SARS-CoV-2 anti-viral responses in bronchoalveolar lavage cell samples from humans with alcohol use disorder and rhesus macaques that engaged in chronic drinking. Our data show that in both humans and macaques, the induction of key antiviral cytokines and growth factors was decreased with chronic ethanol consumption. Moreover, in macaques fewer differentially expressed genes mapped to Gene Ontology terms associated with antiviral immunity following 6 month of ethanol consumption while TLR signaling pathways were upregulated. These data are indicative of aberrant inflammation and reduced antiviral responses in the lung with chronic alcohol drinking.
Syntheses of Pyrimidine-Modified Seleno-DNAs as Stable Antisense Molecules
Authors: Fang Ziyuan , Dantsu Yuliya , Chen Cen , Zhang Wen , Huang Zhen 
Published: May 2023

ABSTRACTChemically modified antisense oligonucleotides (ASO) currently in pre-clinical and clinical experiments mainly focus on the 2′-position derivatizations to enhance stability and targeting affinity. Considering the possible incompatibility of 2′-modifications with RNase H stimulation and activity, we have hypothesized that the atom specific modifications on nucleobases can retain the complex structure and RNase H activity, while enhancing ASO’s binding affinity, specificity, and stability against nucleases. Herein we report a novel strategy to explore our hypothesis by synthesizing the deoxynucleoside phosphoramidite building block with the seleno-modification at 5-position of thymidine, as well as its Se-oligonucleotides. Via X-ray crystal structural study, we found that the Se-modification was located in the major groove of nucleic acid duplex and didn’t cause the thermal and structural perturbations. Surprisingly, our nucleobase-modified Se-DNAs were exceptionally resistant to nuclease digestion, while compatible with RNase H activity. This affords a novel avenue for potential antisense modification in the form of Se-antisense oli-gonucleotides (Se-ASO).
How environmental drivers of spatial synchrony interact
Authors: Reuman Daniel C. , Castorani Max C.N. , Cavanaugh Kyle C. , Sheppard Lawrence W. , Walter Jonathan A. , Bell Tom W. 
Published: May 2023

AbstractSpatial synchrony, the tendency for populations across space to show correlated fluctuations, is a fundamental feature of population dynamics, linked to central topics of ecology such as population cycling, extinction risk, and ecosystem stability. A common mechanism of spatial synchrony is the Moran effect, whereby spatially synchronized environmental signals drive population dynamics and hence induce population synchrony. After reviewing recent progress in understanding Moran effects, we here elaborate a general theory of how Moran effects of different environmental drivers acting on the same populations can interact, either synergistically or destructively, to produce either substantially more or markedly less population synchrony than would otherwise occur. We provide intuition for how this newly recognized mechanism works through theoretical case studies and application of our theory to California populations of giant kelp. We argue that Moran interactions should be common. Our theory and analysis explain an important new aspect of a fundamental feature of spatiotemporal population dynamics.
Parallel Evolution of Linezolid ResistantStaphylococcus aureusin Patients with Cystic Fibrosis
Authors: Pitcher Nicholas J. , Feder Andries , Bolden Nicholas , Zirbes Christian F. , Pamatmat Anthony J. , Boyken Linda , Hill Jared J. , Thurman Andrew L. , Reeb Valérie C. , Porterfield Harry S. , Moustafa Ahmed M. , Planet Paul J. , Fischer Anthony J. 
Published: May 2023

AbstractBackgroundLinezolid is an antibiotic used to treat seriousStaphylococcus aureusinfections. Resistance to linezolid is considered rare but could emerge with repeated dosing. We recently reported widespread prescription of linezolid for a cohort of patients with cystic fibrosis (CF).ObjectivesThe goals of this study were to determine the incidence of linezolid resistance in CF and identify molecular mechanisms for linezolid resistance.MethodsWe identified patients withS. aureusresistant to linezolid (MIC > 4) at the University of Iowa CF Center between 2008 and 2018. We obtained isolates from these patients and retested susceptibility to linezolid using broth microdilution. We used whole genome sequencing to perform phylogenetic analysis of linezolid resistant isolates and examine sequences for mutations or accessory genes that confer linezolid resistance.Main ResultsBetween 2008 and 2018, 111 patients received linezolid and 4 of these patients cultured linezolid resistantS. aureus. We sequenced 11 resistant and 21 susceptible isolates from these 4 subjects. Phylogenetic analysis indicated that linezolid resistance developed in ST5 or ST105 backgrounds. Three individuals had linezolid resistantS. aureuswith a G2576T mutation in 23S rRNA. One of these subjects additionally had amutS-mutL-hypermutatingS. aureusthat produced 5 resistant isolates with multiple ribosomal subunit mutations. In one subject, the genetic basis for linezolid resistance was unclear.ConclusionsLinezolid resistance evolved in 4 of 111 patients in this study. Linezolid resistance occurred by multiple genetic mechanisms. All resistant strains developed in ST5 or ST105 MRSA backgrounds.Key PointLinezolid resistance arises through multiple genetic mechanisms and could be facilitated by mutator phenotypes. Linezolid resistance was transient, possibly due to growth disadvantage.
Genetic manipulation of candidate phyla radiation bacteria provides functional insights into microbial dark matter
Authors: Wang Yaxi , Gallagher Larry A. , Andrade Pia A. , Liu Andi , Humphreys Ian R. , Turkarslan Serdar , Cutler Kevin J. , Arrieta-Ortiz Mario L. , Li Yaqiao , Radey Matthew C. , McLean Jeffrey S. , Cong Qian , Baker David , Baliga Nitin S. , Peterson S. Brook , Mougous Joseph D. 
Published: May 2023

SummaryThe study of bacteria has yielded fundamental insights into cellular biology and physiology, biotechnological advances and many therapeutics. Yet due to a lack of suitable tools, the significant portion of bacterial diversity held within the candidate phyla radiation (CPR) remains inaccessible to such pursuits. Here we show that CPR bacteria belonging to the phylum Saccharibacteria exhibit natural competence. We exploit this property to develop methods for their genetic manipulation, including the insertion of heterologous sequences and the construction of targeted gene deletions. Imaging of fluorescent protein-labeled Saccharibacteria provides high spatiotemporal resolution of phenomena accompanying epibiotic growth and a transposon insertion sequencing genome-wide screen reveals the contribution of enigmatic Saccharibacterial genes to growth on their Actinobacteria hosts. Finally, we leverage metagenomic data to provide cutting-edge protein structure-based bioinformatic resources that support the strainSouthlakia epibionticumand its corresponding host,Actinomyces israelii, as a model system for unlocking the molecular underpinnings of the epibiotic lifestyle.
Synergistic Binding of the Halide and Cationic Prime Substrate of the l-Lysine 4-Chlorinase, BesD, in Both Ferrous and Ferryl States
Authors: Slater Jeffrey W. , Neugebauer Monica E. , McBride Molly J. , Sil Debangsu , Lin Chi-Yun , Katch Bryce J. , Boal Amie K. , Chang Michelle C.Y. , Silakov Alexey , Krebs Carsten , Bollinger J. Martin 
Published: May 2023

ABSTRACTAn aliphatic halogenase requires four substrates: 2-oxoglutarate (2OG), halide (Cl−or Br−), the halogenation target (“prime substrate”), and dioxygen. In well-studied cases, the three non-gaseous substrates must bind to activate the enzyme’s Fe(II) cofactor for efficient capture of O2. Halide, 2OG, and (lastly) O2all coordinate directly to the cofactor to initiate its conversion to acis-halo-oxo-iron(IV) (haloferryl) complex, which abstracts hydrogen (H•) from the non-coordinating prime substrate to enable radicaloid carbon-halogen coupling. We dissected the kinetic pathway and thermodynamic linkage in binding of the first three substrates of thel-lysine 4-chlorinase, BesD. After 2OG adds, subsequent coordination of the halide to the cofactor and binding of cationicl-Lys near the cofactor are associated with strong heterotropic cooperativity. Progression to the haloferryl intermediate upon addition of O2does not trap the substrates in the active site and, in fact, markedly diminishes cooperativity between halide andl-Lys. The surprising lability of the BesD•[Fe(IV)=O]•Cl•succinate•l-Lys complex engenders pathways for decay of the haloferryl intermediate that do not result inl-Lys chlorination, especially at low chloride concentrations; one identified pathway involves oxidation of glycerol. The mechanistic data imply that (i) BesD may have evolved from a hydroxylase ancestor either relatively recently or under weak selective pressure for efficient chlorination and (ii) that acquisition of its activity may have involved the emergence of linkage betweenl-Lys binding and chloride coordination following loss of the anionic protein-carboxylate iron ligand present in extant hydroxylases.
Characterizing spatiotemporal population receptive fields in human visual cortex with fMRI
Authors: Kim Insub , Kupers Eline R. , Lerma-Usabiaga Garikoitz , Grill-Spector Kalanit 
Published: May 2023

AbstractThe use of fMRI and computational modeling has advanced understanding of spatial characteristics of population receptive fields (pRFs) in human visual cortex. However, we know relatively little about the spatiotemporal characteristics of pRFs because neurons’ temporal properties are one to two orders of magnitude faster than fMRI BOLD responses. Here, we developed an image-computable framework to estimate spatiotemporal pRFs from fMRI data. First, we developed a simulation software that predicts fMRI responses to a time varying visual input given a spatiotemporal pRF model and solves the model parameters. The simulator revealed that ground-truth spatiotemporal parameters can be accurately recovered at the millisecond resolution from synthesized fMRI responses. Then, using fMRI and a novel stimulus paradigm, we mapped spatiotemporal pRFs in individual voxels across human visual cortex in 10 participants. We find that a compressive spatiotemporal (CST) pRF model better explains fMRI responses than a conventional spatial pRF model across visual areas spanning the dorsal, lateral, and ventral streams. Further, we find three organizational principles of spatiotemporal pRFs: (i) from early to later areas within a visual stream, spatial and temporal integration windows of pRFs progressively increase in size and show greater compressive nonlinearities, (ii) later visual areas show diverging spatial and temporal integration windows across streams, and (iii) within early visual areas (V1-V3), both spatial and temporal integration windows systematically increase with eccentricity. Together, this computational framework and empirical results open exciting new possibilities for modeling and measuring fine-grained spatiotemporal dynamics of neural responses in the human brain using fMRI.Significance StatementWe developed a computational framework for estimating spatiotemporal receptive fields of neural populations using fMRI. This framework pushes the boundary of fMRI measurements, enabling quantitative evaluation of neural spatial and temporal processing windows at the resolution of visual degrees and milliseconds, which was thought to be unattainable with fMRI. We not only replicate well-established visual field and pRF size maps, but also estimates of temporal summation windows from electrophysiology. Notably, we find that spatial and temporal windows as well as compressive nonlinearities progressively increase from early to later visual areas in multiple visual processing streams. Together, this framework opens exciting new possibilities for modeling and measuring fine-grained spatiotemporal dynamics of neural responses in the human brain using fMRI.
Colon resident CD8+ T cells from people with HIV on antiretroviral therapy exhibit mitochondrial dysfunction and impaired responses
Authors: Adhikari Upasana Das , Shah Palak V. , Froehle Leah M. , Linder Alice H. , Flagg Meaghan , Rawlings Crystal , Junca Muntsa R. , Folarin Lilian , Karim Farina , Li Jonathan , Kloverpris Henrik , Kwon Douglas S. 
Published: May 2023

ABSTRACTCD8+ tissue-resident memory T cells (CD8+ TRM) play an important role in mediating immune responses against HIV in the gastrointestinal (GI) mucosa. Antiretroviral therapy (ART) successfully supresses HIV replication in the blood, but fails to restore GI homeostasis, particularly within gut associated lymphoid tissue (GALT). The importance of cellular metabolism in shaping CD8+ TRM antiviral function has emerged as a crucial aspect of general immunoregulation. To gain better insight into the immunoregulation of CD8+ TRM during HIV, we characterized the function of blood and colon CD8+ T cells in people with HIV (PWH) on ART and HIV-uninfected individuals. We show that a higher proportion of activated CD8+ TRM persisted in the colon of PWH on ART, and these cells exhibited weaker immune response and compromised mitochondrial function compared to their peripheral counterparts. We also observed decreased mitochondrial function in CD8+ T cell in the colon compared to peripheral blood in PWH on ART. The study indicates that mitochondrial bioenergetic properties may be an indicator of colonic CD8+ TRM dysfunction in PWH on ART and highlights the importance of understanding cellular metabolism in shaping CD8+ TRM function to develop targeted immunotherapies for PWH.
A Systematic Review of Peruvian Contributions to Scientific Publications on Experimental Research Against COVID-19
Authors: Coronel-Monje Katiusca , Candia-Puma Mayron Antonio , Vilca-Alosilla Juan Jeferson , Goyzueta-Mamani Luis Daniel , Aguilar Bravo Herbert Mishaelf , Sánchez Zegarra Jorge Augusto , Barazorda-Ccahuana Haruna Luz , Ferraz Coelho Eduardo Antonio , Chávez-Fumagalli Miguel Angel 
Published: May 2023

AbstractOne of the countries most adversely affected by the COVID-19 outbreak was Peru. Worldwide scientific knowledge creation has significantly grown because of this pandemic. This systematic study aims to examine several facets of Peru’s experimental scientific production concerning COVID-19. Between December 2019 and June 2022, searches were made in the PubMed database for experimental scientific articles created in Peruvian institutions. The systematic review resulted in nine studies that meet the requirements. Data were extracted and analyzed on the type of biomedical research, the study’s applicability, the thematic area and specific thematic, journal impact factor and quartile, funding, grants, and institution of affiliation for the first and correspondence authors. The results revealed that Peru needs to promote policies to boost research funding and the number of researchers to produce information that will be useful for managing diseases in the future. Yet, despite the funding provided by national organizations like National Council for Science, Technology, and Technological Innovation (CONCYTEC), there were few publications and little international collaboration. The studies that have been published focus mostly on applied research in the areas of diagnostics, sanitary products, and treatment and transmission, and they have great visibility because they are indexed in Q1 journals. This thorough study revealed Peru’s inadequate reaction to COVID-19 regarding experimental scientific research. Peruvian authorities should think about supporting the required policies to boost the number of researchers and financial aid to produce information that may be utilized to manage potential new diseases in the future.
A brainstem to hypothalamic arcuate nucleus GABAergic circuit drives feeding
Authors: Martinez de Morentin Pablo B , Gonzalez J Antonio , Dowsett Georgina K.C. , Martynova Yuliia , Yeo Giles S.H. , Sylantyev Sergiy , Heisler Lora K 
Published: May 2023

AbstractThe obesity epidemic is principally driven by the consumption of more calories than the body requires. It is therefore essential that the mechanisms underpinning feeding behavior are defined. The brainstem nucleus of the solitary tract (NTS) receives direct information from the digestive system and projects to second order regions in the brain. Though γ-Aminobutyric acid is widely expressed in the NTS (GABANTS), its function has not been defined. Characterization of GABA cells using single nucleus RNA sequencing (Nuc-Seq) identified at least 19 clusters. Here we provide insight into the function of GABANTScells, revealing that selective activation of GABANTSneurons significantly controls food intake and body weight. Optogenetic interrogation of GABANTScircuitry identified GABANTS→arcuate nucleus of the hypothalamus (ARC) projections as appetite suppressive without creating aversion. Electrophysiological analysis revealed GABANTS→ARC stimulation inhibits hunger promoting agouti-related protein/neuropeptide Y (AgRP/NPY) neurons via GABA release. Adopting an intersectional genetics strategy, we clarify that the GABANTS→ARC circuit induces satiety. These data identify GABANTSas a new modulator of feeding behavior, body weight and controller of orexigenic AgRP/NPY activity, thereby providing insight into the neural underpinnings of obesity.HighlightsNucleus of the solitary tract (NTS) GABA neurons are responsive to nutritional status.Chemogenetic GABANTSneuron activation reduces food intake and body weight.GABANTSprojections to the hypothalamic arcuate nucleus (ARC) promote satiety.Optogenetic GABANTS→ARC stimulation inhibits orexigenic AgRP/NPY neurons.In BriefMartinez de Morentin et al. identify GABAergic neurons in the nucleus of the solitary tract as a new player in the circuit governing feeding behavior and body weight.
Discovering knowledge map and evolutionary path of HRM and ER: using the STM combined with Word2vec
Authors: Yu Dejian , Xiang Bo 
Published: May 2023

PurposeThe purpose of this study is to comprehensively review the human resource management (HRM) and employment relations (ERs) field and explore the knowledge map, knowledge evolution trends and paths and paradigm shifts within this field.Design/methodology/approachThe Structural Topic Model in combination with Word2vec is proposed and applied in this work. First, this paper detects and interprets the research topics by reviewing 23,786 papers from 29 important journals in this field from 1990 to 2021. Then, this research explores popularity trends by aggregating topic proportions from a temporal perspective. Finally, this work explores the research topic evolution from the semantic perspective.FindingsThis paper obtains the following findings: (1) Sixteen research topics are identified, which provide the basic research overview of the whole field. (2) The changes in topic popularity over time map the tendency for employee benefits to be valued. (3) The evolutionary trajectories of temporal local topics are provided, which reflect the mechanisms of the paradigm and ideological migration and fusion.Originality/valueThis work adopts state-of-the-art textual as well as semantic mining techniques to establish a comprehensive knowledge map for HRM and ER research. Furthermore, these results uniquely demonstrate the pluralistic ideological orientation at the social level is gradually integrated into more micro levels, such as enterprises and individuals. These are the contents that were mentioned from previous studies by scholars, but not meticulously verified and interpreted.
Measuring implicit motivations: a qualitative approach
Authors: Nazarpour Mohammad Mahdi , Askari Azadeh 
Published: May 2023

Purpose
The present study aims to investigate the psychometric properties of the picture story exercise (PSE), a tool for measuring implicit motivations in Iran.

Design/methodology/approach
The research method is descriptive correlation and was conducted in two studies. In the first study 24 psychology master’s students were selected by convenience sampling method and tested them to check retest and inter-coder reliability. The second study investigated the correlation between self-reports and the PSE test on a sample of managers. Its statistical population comprised all the managers of a refinery company, 50 people were selected by convenience sampling method. To check the concurrent validity of the PSE test, the participants of the second study, completing the PSE, also completed the needs questionnaire of Steers and Porter (1979).

Findings
The findings showed that the PSE test in the Iranian sample had high retest reliability (0.62 on mean) and inter-coder reliability (0.87 on mean), and, following previous research, it does not show a significant relationship with self-reported motives.

Practical implications
PSE can be used in future research as a tool that has demonstrated its reliability and validity in the Iranian sample.

Originality/value
Measurement of implicit motives is a practical factor for predicting people’s behavior, the necessity of using tools that can accurately evaluate implicit motives is strongly felt. Taking into account the fact that so far, in Iranian samples, implicit motivations have not been measured, therefore, the current research is trying to answer this question, whether one of the most important and prominent tools that were made for this purpose and used in various studies can also be used in Iranian samples.