bluuebunny/crossref_metadata_2025_split huggingface dataset:
Streptococcus parasanguinis: An emerging pathogen causing neonatal endocarditis: A case report
Authors: Shrimali Twishi , Malhotra Shikhir , Relhan Nidhi , Tak Vibhor , Choudhary Sushil Kumar , Gupta Neeraj , Singh Arun Kumarendu 
Published: May 2023

Background
The microbial infection of the endocardium, popularly known as Infective Endocarditis (IE), is typically classified on the basis of anatomy, valve nativity and its associated microbiology. As per the associated microbiology, Staphylococcus aureus is the most common microorganism responsible for the cause of IE. Even though, Streptococcus group accounts for a smaller percentage of IE, however this doesn’t give us the liberty of ignoring the high mortality and morbidity associated with this pathogen.
Case presentation
We report an unusual case of neonatal sepsis, complicated with endocarditis, caused by penicillin resistant Streptococcus parasanguinis. The neonate however died of the same despite all efforts. The said baby was given birth by a mother with gestational diabetes mellitus.
Conclusion
High index of clinical suspicion and prompt diagnosis are the most important factors of patient management, especially in cases of life threatening neonatal infections. In such conditions a coordinated interdepartmental approach is very much needed.
Concurrent measurement of O2and isoprene production during photosynthesis: pros, cons, and metabolic implications
Authors: Som Suman , Gallo Luiza , Sunder Aatish , Demus Jilian , Dominges Tomas F. , Wistrom Christina M. , Gu Lianhong , Tcherkez Guillaume , Jardine Kolby J. 
Published: May 2023

AbstractDuring oxygenic photosynthesis, oxygen (O2) is generated from water photolysis, which provides reducing power to sustain CO2assimilation. To date, traditional leaf gas-exchange experiments have been focused on net CO2exchange (Anet), with limited observations of net oxygen production (NOP). Here, we present the first gas-exchange/fluorescence system, coupling CO2/H2O analysis (photosynthesis and transpiration) with NOP and isoprene emission measurements. This configuration allowed us to calculate the assimilatory quotient (AQ = Anet/NOP) and thus obtain a more complete picture of the photosynthetic redox budget via photosynthetic production of O2, electron transport rate (ETR), and isoprene biosynthesis. We used cottonwood leaves (Populus trichocarpa) and carried out response curves to light, CO2and temperature along with18O-labelling with18O-enriched water. We found that Anetand NOP were linearly correlated across environmental variables with AQ of 1.27 +/- 0.12 regardless of light, CO2, and temperature. Anetand NOP had optimal temperatures (Topt) of 31°C, while ETR (35°C) and isoprene emissions (39°C) had distinctly higher Topt. Leaves labelled with H218O produced labeled (18O16O) oxygen with the same Toptas ETR (35°C). The results confirm a tight connection between water oxidation and ETR and are consistent with a suppression of Anetand NOP at high temperature driven by an acceleration of (photo)respiration. The findings support the view of isoprene biosynthesis primarily driven by excess photosynthetic ATP/NADPH not consumed by the Calvin cycle during photorespiratory conditions as an important thermotolerance mechanism linked with high rates of CO2and O2recycling.KeywordsPhotosynthesis, net oxygen production, gross oxygen production, H218O labelingOne sentence summaryA leaf gas-exchange system is presented enabling a more complete picture of the photosynthetic redox budget and calculation of the assimilatory quotient.
Gap junction and amino acid import in somatic cells promote germ cell growth
Authors: Vachias Caroline , Tourlonias Camille , Grelée Louis , Gueguen Nathalie , Renaud Yoan , Venugopal Parvathy , Richard Graziella , Pouchin Pierre , Brasset Émilie , Mirouse Vincent 
Published: May 2023

AbstractGap junctions allow the exchange of small molecules between cells. How this function could be used to promote cell growth is not yet fully understood. DuringDrosophilaovarian follicle development, germ cells, which are surrounded by epithelial somatic cells, undergo massive growth. We found that this growth depends on gap junctions between these cell populations, with a requirement for Innexin4 and Innexin2, in the germ cells and the somatic cells, respectively. Translatomic analyses revealed that somatic cells express enzymes and transporters involved in amino acid metabolism that are absent in germ cells. Among them, we identified an amino acid transporter required for germline growth. Its ectopic expression in the germline can compensate for its absence in somatic cells. Moreover, affecting either gap junctions or amino-acid import in somatic cells induces P-bodies in the germ cells, a feature associated with an arrest of translation. Finally, in somatic cells, innexin2 expression and gap junction assembly are regulated by the insulin receptor/PI3K kinase pathway. Overall, these results support the view that metabolic transfer through gap junction promotes cell growth and illustrate how such a mechanism can be integrated into a developmental programme, coupling growth control by extrinsic systemic signals with the intrinsic coordination between cell populations.
Deciphering interplay between biology and physics: finite element method-implemented vertex organoid model raises the challenge
Authors: Laussu J. , Michel D. , Magne L. , Segonds S. , Marguet S. , Hamel D. , Quaranta-Nicaise M. , Barreau F. , Mas E. , Velay V. , Bugarin F. , Ferrand A. 
Published: May 2023

Understanding the intertwining of biology and mechanics in tissue architecture is a challenging issue, especially when it comes to the 3D tissue organization. Addressing this challenge requires both a biological model allowing multiscale observations from the cell to the tissue, and theoretical and computational approaches allowing the generation of a synthetic model, relevant to the biological model, and allowing access to the mechanical constraints experienced by the tissue.Here, using human colon epithelium monolayer organoid as biological model, and combining vertex and FEM approaches, we generated a comprehensive elastic finite element model of the human colon organoid and demonstrated its flexibility. This FEM model provides a basis for relating cell shape, tissue deformation, and strain at the cellular level due to imposed stresses.In conclusion, we demonstrated that the combination of vertex and FEM approaches allows for better modeling of the alteration of organoid morphology over time and better assessment of the mechanical cues involved in establishing the architecture of the human colon epithelium.
Synthetic Cooling Agent and Candy Flavors in California-marketed “non-Menthol” Cigarettes
Authors: Jabba Sairam V. , Erythropel Hanno C. , Anastas Paul T. , Zimmerman Julie B. , Jordt Sven E. 
Published: May 2023

ABSTRACTRATIONALEThe ban of menthol cigarettes is one of the key strategies to promote smoking cessation in the United States. Menthol cigarettes are preferred by young beginning smokers for smoking initiation. Almost 90% of African American smokers use menthol cigarettes, a result of decades-long targeted industry marketing. Several states and municipalities already banned menthol cigarettes, most recently California, effective on December 21, 2022. In the weeks before California’s ban took effect, the tobacco industry introduced several “non-menthol” cigarette products in California, replacing previously mentholated brands. Here, we hypothesize that tobacco companies replaced menthol with synthetic cooling agents to create a cooling effect without using menthol. Similar to menthol, these agents activate the TRPM8 cold-menthol receptor in sensory neurons innervating the upper and lower airways.METHODSCalcium microfluorimetry in HEK293t cells expressing the TRPM8 cold/menthol receptors was used to determine sensory cooling activity of extracts prepared from these “non-menthol” cigarette brands, and compared to standard menthol cigarette extracts of the same brands. Specificity of receptor activity was validated using TRPM8-selective inhibitor, AMTB. Gas chromatography mass spectrometry (GCMS) was used to determine presence and amounts of any flavoring chemicals, including synthetic cooling agents, in the tobacco rods, wrapping paper, filters and crushable capsule (if present) of these “non-menthol” cigarettes.RESULTSCompared to equivalent menthol cigarette extracts, several California-marketed “non-menthol” cigarette extracts activated cold/menthol receptor TRPM8 at higher dilutions and with stronger efficacies, indicating substantial pharmacological activity to elicit robust cooling sensations. Synthetic cooling agent, WS-3, was detected in tobacco rods of several of these “non-menthol” cigarette brands. Crushable capsules added to certain “non-menthol” crush varieties contained neither WS-3 nor menthol but included several “sweet” flavorant chemicals, including vanillin, ethyl vanillin and anethole.CONCLUSIONTobacco companies have replaced menthol with the synthetic cooling agent, WS-3, in California-marketed “non-menthol” cigarettes. WS-3 creates a cooling sensation similar to menthol, but lacks menthol’s characteristic “minty” odor. The measured WS-3 content is sufficient to elicit cooling sensations in smokers, similar to menthol, that facilitate smoking initiation and act as a reinforcing cue. Regulators need to act quickly to prevent the tobacco industry from bypassing menthol bans by substituting menthol with synthetic cooling agents, and thereby thwarting smoking cessation efforts.
Minimal effective dose of oral bedaquiline and activity of a long acting formulation of bedaquiline in the murine model of leprosy Bedaquiline for the treatment of leprosy
Authors: Chauffour Aurélie , Lounis Nacer , Andries Koen , Jarlier Vincent , Veziris Nicolas , Aubry Alexandra 
Published: May 2023

AbstractBackgroundBedaquiline (BDQ), by targeting the electron transport chain and having a long half-life, is a good candidate to simplify leprosy treatment. Our objectives were to (i) determine the minimal effective dose (MED) of oral BDQ, (ii) evaluate the benefit of adding another inhibitor of the respiratory chain to oral BDQ (i.e.clofazimine (CFZ)) and (iii) evaluate the benefit of an intramuscular injectable long-acting formulation of BDQ (intramuscular BDQ; BDQ-LA IM), in a murine model of leprosy.Methodology/ Principal FindingsTo determine the MED of oral BDQ and the benefit of adding CFZ, 100 four-week-old female nude mice were inoculated in the footpads with 5.103bacilli ofM. lepraestrain THAI53. Mice were randomly allocated into: 1 untreated group, 5 groups treated with oral BDQ (0.10 to 25 mg/kg), 3 groups treated with CFZ 20 mg/kg alone or combined with oral BDQ 0.10 or 0.33 mg/kg, and 1 group treated with rifampicin (RIF) 10 mg/kg. Mice were treated 5 days a week during 24 weeks.To evaluate the benefit of the BDQ-LA IM, 340 four-week-old female Swiss mice were inoculated in the footpads with 5.103to 5.101bacilli (or 5.100for the untreated control group) ofM. lepraestrain THAI53. Mice were randomly allocated into the following 11 groups treated with a single dose (SD) or 3 doses (3D) 24h after the inoculation: 1 untreated group, 2 treated with RIF 10 mg/kg SD or 3D, 8 treated with oral BDQ or BDQ-LA IM 2 or 20 mg/kg, SD or 3D.Twelve months later, mice were sacrificed andM. lepraebacilli enumerated in the footpad. All the footpads became negative with BDQ at 3.3 mg/kg. The MED of oral BDQ againstM. lepraein this model is therefore 3.3 mg/kg. The addition of CFZ to a dose of BDQ 10-fold lower than this MED increased the bactericidal activity of BDQ suggesting synergies between both drugs. The BDQ-LA IM displayed similar or lower bactericidal activity than the oral BDQ.ConclusionWe demonstrated that the MED of oral BDQ againstM. lepraewas 3.3 mg/kg in mice and the addition of CFZ to oral BDQ may improve the efficacy of BDQ. BDQ-LA IM was similar or less active than oral BDQ at equivalent dosing and frequency but should be tested at higher dosing in order to reach equivalent exposure in further experiments.
Investigating mitochondrial gene expression patterns inDrosophila melanogasterusing network analysis to understand aging mechanisms
Authors: Mangoni Manuel , Petrizzelli Francesco , Liorni Niccolò , Bianco Salvatore Daniele , Biagini Tommaso , Napoli Alessandro , Adinolfi Marta , Guzzi Pietro Hiram , Novelli Antonio , Caputo Viviana , Mazza Tommaso 
Published: May 2023

AbstractThe process of aging is a complex phenomenon that involves a progressive decline in physiological functions required for survival and fertility. To better understand the mechanisms underlying this process, the scientific community has utilized several tools. Among them, mitochondrial DNA has emerged as a crucial factor in biological aging, given that mitochondrial dysfunction is thought to significantly contribute to this phenomenon. Additionally,Drosophila melanogasterhas proven to be a valuable model organism for studying aging due to its low cost, capacity to generate large populations, and ease of genetic manipulation and tissue dissection. Moreover, graph theory has been employed to understand the dynamic changes in gene expression patterns associated with aging and to investigate the interactions between aging and aging-related diseases. In this study, we have integrated these approaches to examine the patterns of gene co-expression inDrosophila melanogasterat various stages of development. By applying graph-theory techniques, we have identified modules of co-expressing genes, highlighting those that contain a significantly high number of mitochondrial genes. We found important mitochondrial genes involved in aging and age-related diseases inDrosophila melanogaster, including UQCR-C1, ND-B17.2, ND-20, and Pdhb. Our findings shed light on the role of mitochondrial genes in the aging process and demonstrate the utility ofDrosophila melanogasteras a model organism and graph theory in aging research.
Benchmarking of Hi-C tools for scaffolding de novo genome assemblies
Authors: Obinu Lia , Trivedi Urmi , Porceddu Andrea 
Published: May 2023

AbstractThe implementation of Hi-C reads in thede novogenome assembly allows to order large regions of the genome in scaffolds, obtaining chromosome-level assemblies. Several bioinformatics tools have been developed for genome scaffolding with Hi-C, and all have pros and cons which need to be carefully evaluated before adoption.We developed assemblyQC, a bash pipeline that combines QUAST, BUSCO, Merqury and, optionally, Liftoff, plus a gene positioning validation script to evaluate and benchmark the performance of three scaffolders, 3d-dna, SALSA2, and YaHS, on two de novo assembly of Arabidopsis thaliana obtained from the same raw PacBio HiFi and ONT data.In our analysis, YaHS proved to be the best-performing bioinformatic tool for scaffolding ofde novogenome assembly.
ExMove: An open-source toolkit for processing and exploring animal tracking data in R
Authors: Langley Liam Patrick , Lang Stephen , Ozsanlav-Harris Luke , Trevail Alice 
Published: May 2023

AbstractOngoing technological advances have led to a rapid increase in the number, type, and scope of animal tracking studies. In response, many software tools have been developed to analyse animal movement data. These tools generally focus on movement modelling, but the steps required to clean raw data files from different tracking devices have been largely ignored. Such pre-processing steps are often time-consuming and involve a steep learning curve but are crucial for the creation of high quality, standardised, and shareable data. Moreover, decisions made at this early stage can substantially influence subsequent analyses, and in the current age of reproducibility crisis, the transparency of this process is vital.Here we present an open-access, reproducible toolkit written in the programming language R for processing raw data files into a single cleaned data set for analyses and upload to online tracking databases (found here:https://github.com/ExMove/ExMove). The toolkit comprises well documented and flexible code to facilitate data processing and user understanding, both of which can increase user confidence and improve the uptake of sharing open and reproducible code. Additionally, we provide an overview website (found here:https://exmove.github.io/) and a Shiny app to help users visualise tracking data and assist with parameter determination during data cleaning.The toolkit is generalisable to different data formats and device types, uses modern ‘tidy coding’ practices, and relies on few well-maintained packages. Amongst these, we perform spatial manipulations using the packagesf, providing a timely resource for movement ecologists following the recent deprecation of the widely-usedsppackage.Overall, by collating all required steps from data collection to archiving on open access databases into a single, robust pipeline, our toolkit provides a valuable resource for anyone conducting animal movement analyses and represents an important step towards increased standardisation and reproducibility in animal movement ecology.
Distinct Local and Global Functions of Aβ Low-Threshold Mechanoreceptors in Mechanical Pain Transmission
Authors: Gautam Mayank , Yamada Akihiro , Yamada Ayaka I , Wu Qinxue , Kridsada Kim , Ling Jennifer , Yu Huasheng , Dong Peter , Ma Minghong , Gu Jianguo , Luo Wenqin 
Published: May 2023

SummaryThe roles of Aβ low-threshold mechanoreceptors (LTMRs) in transmitting mechanical hyperalgesia and in alleviating chronic pain have been of great interest but remain contentious. Here we utilized intersectional genetic tools, optogenetics, and high-speed imaging to specifically examine functions ofSplitCrelabeled Aβ-LTMRs in this regard. Genetic ablation of SplitCre-Aβ-LTMRs increased mechanical pain but not thermosensation in both acute and chronic inflammatory pain conditions, indicating their modality-specific role in gating mechanical pain transmission. Local optogenetic activation of SplitCre-Aβ-LTMRs triggered nociception after tissue inflammation, whereas their broad activation at the dorsal column still alleviated mechanical hypersensitivity of chronic inflammation. Taking all data into consideration, we propose a new model, in which Aβ-LTMRs play distinctive local and global roles in transmitting and alleviating mechanical hyperalgesia of chronic pain, respectively. Our model suggests a new strategy of global activation plus local inhibition of Aβ-LTMRs for treating mechanical hyperalgesia.
VirB, a key transcriptional regulator ofShigellavirulence, requires a CTP ligand for its regulatory activities
Authors: Gerson Taylor M. , Ott Audrey M. , Karney Monika MA. , Socea Jillian N. , Ginete Daren R. , Iyer Lakshminarayan M. , Aravind L. , Gary Ronald K. , Wing Helen J. 
Published: May 2023

AbstractThe VirB protein, encoded by the large virulence plasmid ofShigellaspp., is a key transcriptional regulator of virulence genes. Without a functionalvirBgene,Shigellacells are avirulent. On the virulence plasmid, VirB functions to offset transcriptional silencing mediated by the nucleoid structuring protein, H-NS, which binds and sequesters AT-rich DNA, making it inaccessible for gene expression. Thus, gaining a mechanistic understanding of how VirB counters H-NS-mediated silencing is of considerable interest. VirB is unusual in that it does not resemble classic transcription factors. Instead, its closest relatives are found in the ParB superfamily, where the best-characterized members function in faithful DNA segregation before cell division. Here, we show that VirB is a fast-evolving member of this superfamily and report for the first time that the VirB protein binds a highly unusual ligand, CTP. VirB binds this nucleoside triphosphate preferentially and with specificity. Based on alignments with the best-characterized members of the ParB family, we identify amino acids of VirB likely to bind CTP. Substitutions in these residues disrupt several well-documented activities of VirB, including its anti-silencing activity at a VirB-dependent promoter, its role in generating a Congo red positive phenotype inShigella, and the ability of the VirB protein to form foci in the bacterial cytoplasm when fused to GFP. Thus, this work is the first to show that VirB is a bona fide CTP-binding protein and linksShigellavirulence phenotypes to the nucleoside triphosphate, CTP.ImportanceShigellaspecies cause bacillary dysentery (shigellosis), the second leading cause of diarrheal deaths worldwide. With growing antibiotic resistance, there is a pressing need to identify novel molecular drug targets.Shigellavirulence phenotypes are controlled by the transcriptional regulator, VirB. We show that VirB belongs to a fast-evolving, primarily plasmid-borne clade of the ParB superfamily, which has diverged from versions that have a distinct cellular role – DNA partitioning. We are the first to report that, like classic members of the ParB family, VirB binds a highly unusual ligand, CTP. Mutants predicted to be defective in CTP binding are compromised in a variety of virulence attributes controlled by VirB. This study i) reveals that VirB binds CTP, ii) provides a link between VirB-CTP interactions andShigellavirulence phenotypes, and iii) broadens our understanding of the ParB superfamily, a group of bacterial proteins that play critical roles in many different bacteria.
Interpretable modeling of time-resolved single-cell gene-protein expression using CrossmodalNet
Authors: Yang Yongjian , Lin Yu-Te , Li Guanxun , Zhong Yan , Xu Qian , Cai James J. 
Published: May 2023

AbstractCell-surface proteins play a critical role in cell function and are primary targets for therapeutics. CITE-seq is a single-cell technique that enables simultaneous measurement of gene and surface protein expression. It is powerful but costly and technically challenging. Computational methods have been developed to predict surface protein expression using gene expression information such as from single-cell RNA sequencing (scRNA-seq) data. Existing methods however are computationally demanding and lack the interpretability to reveal underlying biological processes. We propose CrossmodalNet, an interpretable machine learning model, to predict surface protein expression from scRNA-seq data. Our model with a customized adaptive loss accurately predicts surface protein abundances. When samples from multiple time points are given, our model encodes temporal information into an easy-to-interpret time embedding to make prediction in a time point-specific manner able to uncover noise-free causal gene-protein relationships. Using two publicly available time-resolved CITE-seq data sets, we validate the performance of our model by comparing it to benchmarking methods and evaluate its interpretability. Together, we show our method accurately and interpretably profiles surface protein expression using scRNA-seq data, thereby expanding the capacity of CITE-seq experiments for investigating molecular mechanisms involving surface proteins.