bluuebunny/crossref_metadata_2025_split huggingface dataset:
Establishment of Tuberculosis Meningitis Mouse Model Using Aerosol Route ofW. BeijingHN878 strain
Authors: Khatri Bhagwati , Goulding Sara , Rannow Vicky , Dagg Belinda , Ho Mei Mei 
Published: July 2023

AbstractIn this study, we report the development of a tuberculosis meningitis (TBM) mouse model using the HN878 strain via the aerosol route. Three genetically different strains of mice, CB6F1, C57BL/6 and BALB/c mice, were used to determine the dissemination of HN878 in the brain. The 8 x 108CFU/ml of HN878 dose was used to infect CB6F1 mice and deposited approximately 3.8 (0.07, SD) log10CFU in the lungs. The burden of HN878 in the brain of the control group (administered saline) after approximately 16/17 days post-infection for CB6F1, C57BL/6 and BALB/c were 4.00 (0.47 SD), 3.79 (0.27, SD) and 2.12 (0.41, SD) log10CFU/brain, respectively. The log10CFU/brain in the BCG vaccinated CB6F1, C57BL/6 and BALB/c mice were 1.05 (0.61, SD), 2.13 (0.33, SD) and 1.42 (0.38, SD) respectively, which, if compared to the control groups, BCG vaccinated mice inhibited dissemination of HN878 in the brain by an impressive 2.94 (CB6F1), 1.66 (C57BL/6) and 0.69 (BALB/c) log10CFU/brain reduction. In conclusion, we have established a relatively inexpensive TBM mouse model using an aerosol, a natural route of infection, which will advance research in understanding TBM dissemination to the brain, and preclinical tuberculosis vaccine/drug discovery/drug regimens against TBM.
Quantification of Covid-19 Vaccine Coercion in India: A Survey Study
Authors: Raman Bhaskaran , Banerjee Amitav , Vajjala Sai Mahesh 
Published: July 2023

AbstractIntroductionInformed consent is the cornerstone of medical ethics, enshrined in the constitution of most countries, as well as in international documents. However, mandates for Covid-19 vaccination as well as coercion was prevalent in many places in the world, including in India. Against this background, we did a cross sectional study to assess and quantify the extent of Covid-19 vaccine coercion in India.MethodsA cross sectional study was conducted after obtaining ethical clearance from IIT Bombay. This survey was conducted using a pretested questionnaire anonymously amongst the college students and adults in Mumbai from October 2022 to December 2022. The questionnaire contained details of why the vaccine was taken, and if the participant was a student. Descriptive analysis was conducted and frequencies, percentages along with 95% confidence intervals were used to summarize the findings.ResultsA total of 483 participants responded, which included both students and non-students, of which 470 participants reported having taken the vaccine. A total of 106 (21.95%, 95% C.I. 18.48%-25.85%) reported to have pressured into taking the vaccine. The level of coercion was similar among college students 78 (21.61%, 95% C.I. 17.67%-26.14%) and non-student adults 28 (22.95%, 95% C.I. 15.82% – 31.43%).ConclusionA significant proportion was coerced into taking the vaccines, violating the requirement for informed consent. These results are of paramount importance for future policies as well as for posterity.
Cuprizone drives divergent neuropathological changes in different mouse models of Alzheimer’s disease
Authors: Cheng Gerald Wai-Yeung , Ma Iris Wai-Ting , Huang Jianpan , Yeung Sunny Hoi-Sang , Ho Paolo , Chen Zilin , Mak Henry Ka Fung , Herrup Karl , Chan Kannie Wai Yan , Tse Kai-Hei 
Published: July 2023

ABSTRACTMyelin degradation is a normal feature of brain aging that accelerates in Alzheimer’s disease (AD). To date, however, the underlying biological basis of this correlation remains elusive. The amyloid cascade hypothesis predicts that demyelination is caused by increased levels of the β-amyloid (Aβ) peptide. Here we report on work supporting the alternative hypothesis that early demyelination is upstream of amyloid. We challenged two different mouse models of AD (R1.40 and APP/PS1) using cuprizone-induced demyelination and tracked the responses with both neuroimaging and neuropathology. In oppose to amyloid cascade hypothesis, R1.40 mice, carrying only a single human mutant APP (Swedish; APPSWE) transgene, showed a more abnormal changes of magnetization transfer ratio and diffusivity than in APP/PS1 mice, which carry both APPSWEand a second PSEN1 transgene (delta exon 9; PSEN1dE9). Although cuprizone targets oligodendrocytes (OL), magnetic resonance spectroscopy and targeted RNA-seq data in R1.40 mice suggested a possible metabolic alternation in axons. In support of alternative hypotheses, cuprizone induced significant intraneuronal amyloid deposition in young APP/PS1, but not in R1.40 mice, and it suggested the presence of PSEN deficiencies, may accelerate Aβ deposition upon demyelination. In APP/PS1, mature OL is highly vulnerable to cuprizone with significant DNA double strand breaks (53BP1+) formation. Despite these major changes in myelin, OLs, and Aβ immunoreactivity, no cognitive impairment or hippocampal pathology was detected in APP/PS1 mice after cuprizone treatment. Together, our data supports the hypothesis that myelin loss can be the cause, but not the consequence, of AD pathology.SIGNIFICANCE STATEMENTThe causal relationship between early myelin loss and the progression of Alzheimer’s disease remains unclear. Using two different AD mouse models, R1.40 and APP/PS1, our study supports the hypothesis that myelin abnormalities are upstream of amyloid production and deposition. We find that acute demyelination initiates intraneuronal amyloid deposition in the frontal cortex. Further, the loss of oligodendrocytes, coupled with the accelerated intraneuronal amyloid deposition, interferes with myelin tract diffusivity at a stage before any hippocampus pathology or cognitive impairments occur. We propose that myelin loss could be the cause, not the consequence, of amyloid pathology during the early stages of Alzheimer’s disease.
ScopeViewer: A Browser-Based Solution for Visualizing Spatial Transcriptomics Data
Authors: Luo Danni , Robertson Sophie , Zhan Yuanchun , Rong Ruichen , Wang Shidan , Jiang Xi , Yang Sen , Palmer Suzette , Jia Liwei , Li Qiwei , Xiao Guanghua , Zhan Xiaowei 
Published: July 2023

AbstractMotivationSpatial transcriptomics (ST) enables a high-resolution interrogation of molecular characteristics within specific spatial contexts and tissue morphology. Despite its potential, visualization of ST data is a challenging task due to the complexities in handling, sharing and visualizing large image datasets together with molecular information.ResultsWe introduce ScopeViewer, a browser-based software designed to overcome these challenges. ScopeViewer offers the following functionalities: (1) It visualizes large image data and associated annotations at various zoom levels, allowing for intricate exploration of the data; (2) It enables dual interactive viewing of the original images along with their annotations, providing a comprehensive understanding of the context; (3) It displays spatial molecular features with optimized bandwidth, ensuring a smooth user experience; and (4) It bolsters data security by circumventing data transfers.AvailabilityScopeViewer is available at:https://datacommons.swmed.edu/scopeviewerContactXiaowei.Zhan@UTSouthwestern.edu,Guanghua.Xiao@UTSouthwestern.eduSupplementary informationSupplementary data are available at Bioinformatics online.
A Strategy for Differential Abundance Analysis of Sparse Microbiome Data with Group-wise Structured Zeros
Authors: Abegaz Fentaw , Abedini Davar , White Fred , Guerrieri Alessandra , Zancarini Anouk , Dong Lemeng , Westerhuis Johan A. , van Eeuwijk Fred , Bouwmeester Harro , Smilde Age K. 
Published: July 2023

AbstractComparing the abundance of microbial communities between different groups or obtained under different experimental conditions using count sequence data is a challenging task due to various issues such as inflated zero counts, overdispersion, and non-normality. Several methods and procedures based on counts, their transformation and compositionality have been proposed in the literature to detect differentially abundant species in datasets containing hundreds to thousands of microbial species. Despite efforts to address the the large numbers of zeros present in microbiome datasets, even after careful data preprocessing, the performance of existing methods is impaired by the presence of inflated zero counts and group-wise structured zeros (i.e., all zero counts in a group). We propose and validate using extensive simulations an approach combining two differential abundance testing methods, namely DESeq2-ZINBWaVE and DESeq2, to address the issues of zero-inflation and group-wise structured zeros, respectively. This combined approach was subsequently successfully applied to two plant microbiome datasets that revealed a number of taxa as interesting candidates for further experimental validation.
Mechanisms of extracellular electron transfer in anaerobic methanotrophic archaea
Authors: Ouboter Heleen T , Mesman Rob , Sleutels Tom , Postma Jelle , Wissink Martijn , Jetten Mike S M , Heijne Annemiek ter , Berben Tom , Welte Cornelia U 
Published: July 2023

AbstractAnaerobic methanotrophic (ANME) archaea are environmentally important uncultivated microorganisms mitigating the release of the potent greenhouse gas methane. During methane oxidation ANME archaea engage in extracellular electron transfer (EET) with other microorganisms, metal oxides, and electrodes, through a currently unknown mechanism. To shed light on this mechanism, we cultivated ANME-2d archaea (’Ca. Methanoperedens’) in bioelectrochemical systems and observed strong methane-dependent current (91-93% of total current) associated with high enrichment of ‘Ca. Methanoperedens’ on the anode (up to 82% of the community) determined by metagenomics and transmission electron microscopy. Electrochemistry and metatranscriptomics indicated that the EET mechanism was similar at various electrode potentials pointing to the involvement of an so far uncharacterized short-range electron transport protein complex and OmcZ nanowires, suggesting a unique EET pathway in all ANME-2 archaea. Our findings furthermore indicate that bioelectrochemical cells might be powerful tools for the cultivation, and possibly isolation, of uncultured electroactive microorganisms.
Revealing and evaluation of antivirals targeting multiple druggable sites of RdRp complex in SARS-CoV-2
Authors: Rani Ruchi , Nehul Sanketkumar , Choudhary Shweta , Upadhyay Anushka , Sharma Gaurav Kumar , Kumar Pravindra , Tomar Shailly 
Published: July 2023

AbstractSARS-CoV-2 RNA-dependent RNA polymerase (RdRp) complex consisting of nsp12, nsp7, and nsp8 as the key enzyme for viral genome replication and is a proven antiviral drug target. In this study, molecular interactions of nsp7 and nsp8 with nsp12 and the active site of nsp12 were coterminously targeted usingin-silicoscreening of small molecule libraries to identify potential antivirals. Surface plasmon resonance (SPR) based assay using purified nsp7 and nsp8 proteins was developed, and the binding of identified molecules to targets was validated. The antiviral efficacy of identified small molecules was evaluated using cell-based assays, and potent antiviral effect with EC50values of 0.56 μM, 0.73 μM, and 2.8 μM was demonstrated by fangchinoline, cepharanthine, and sennoside B, respectively. Furtherin vivo,investigation usinghACE2mice is being conducted. This is the first study that targets multiple sites in the RdRp complex of SARS-CoV-2 using a structure-based molecular repurposing approach and suggests potential therapeutic options for emerging variants of SARS-CoV-2.
tUbe net: a generalisable deep learning tool for 3D vessel segmentation
Authors: Holroyd Natalie , Li Zhongwang , Walsh Claire , Brown Emmeline , Shipley Rebecca , Walker-Samuel Simon 
Published: July 2023

AbstractDeep learning has become an invaluable tool for bioimage analysis but, while open-source cell annotation software such as cellpose are widely used, an equivalent tool for three-dimensional (3D) vascular annotation does not exist. With the vascular system being directly impacted by a broad range of diseases, there is significant medical interest in quantitative analysis for vascular imaging. However, existing deep learning approaches for this task are specialised to particular tissue types or imaging modalities. We present a new deep learning model for segmentation of vasculature that is generalisable across tissues, modalities, scales and pathologies. To create a generalisable model, a 3D convolutional neural network was trained using data from multiple modalities including optical imaging, computational tomography and photoacoustic imaging. Through this varied training set, the model was forced to learn common features of vessels cross-modality and scale. Following this, the general model was fine-tuned to different applications with a minimal amount of manually labelled ground truth data. It was found that the general model could be specialised to segment new datasets, with a high degree of accuracy, using as little as 0.3% of the volume of that dataset for fine-tuning. As such, this model enables users to produce accurate segmentations of 3D vascular networks without the need to label large amounts of training data.
Vaginal Community State Types (CSTs) Alter Environmental Cues and Production of theStaphylococcus aureusToxic Shock Syndrome Toxin-1 (TSST-1)
Authors: Maduta Carla S. , McCormick John K. , Dufresne Karine 
Published: July 2023

ABSTRACTMenstrual toxic shock syndrome (mTSS) is a rare but life-threatening disease associated with use of high-absorbency tampons. The production of theStaphylococcus aureustoxic shock syndrome toxin-1 (TSST-1) is involved in nearly all cases of mTSS and is tightly controlled by regulators responding to the environment. In the prototypic mTSS strainS. aureusMN8, the major repressor of TSST-1 is the carbon catabolite protein A (CcpA), which responds to glucose concentrations in the vaginal tract. Healthy vaginalLactobacillusspecies also depend on glucose for both growth and acidification of the vaginal environment through lactic acid production. We hypothesized that interactions between the vaginal microbiota (herein referred to as Community State Types, or CSTs) and MN8 depend on environmental cues, and that these interactions subsequently affect TSST-1 production. Using MN8 Δ1ccpAat various glucose levels, we demonstrate that the supernatants from different CSTs grown in vaginally defined media (VDM) significantly decreasetstexpression. When co-culturing CST species with MN8 ΔccpA, we show thatL. jenseniicompletely inhibits TSST-1 production in conditions mimicking healthy menstruation or mTSS. Finally, we show that growingS. aureusin “unhealthy” or “transitional” CST supernatants results in higher IL-2 production from T cells. These findings suggest that dysbiotic CSTs may encourage TSST-1 production in the vaginal tract, and further indicates that the CSTs are likely important for the development of mTSS.IMPORTANCEIn this study, we investigate the impact of the vaginal microbiota againstS. aureusin conditions mimicking the vaginal environment at various stages of the menstrual cycle. We demonstrate thatL. jenseniican inhibit TSST-1 production, suggesting the potential for probiotic activity in treating mTSS. On the other side of the spectrum, “unhealthy” or “transient” bacteria such asG. vaginalisandL. inerssupport more TSST-1 production byS. aureus, suggesting that CSTs are important in the development of mTSS. This study sets forward a model for examining contact-independent interactions between pathogenic bacteria and the vaginal microbiota. It also demonstrates the necessity of replicating the environment when studying one as dynamic as the vagina.
TIAM-1 regulates polarized protrusions during dorsal intercalation in theC. elegansembryo through both its GEF and N-terminal domains
Authors: Zhu Yuyun , Hardin Jeff 
Published: July 2023

AbstractMediolateral cell intercalation is a morphogenetic strategy used throughout animal development to reshape tissues. Dorsal intercalation in theC. elegansembryo involves the mediolateral intercalation of two rows of dorsal epidermal cells to create a single row that straddles the dorsal midline, and so is a simple model to study cell intercalation. Polarized protrusive activity during dorsal intercalation requires theC. elegansRac and RhoG orthologs CED-10 and MIG-2, but how these GTPases are regulated during intercalation has not been thoroughly investigated. In this study, we characterize the role of the Rac-specific guanine nucleotide exchange factor (GEF), TIAM-1, in regulating actin-based protrusive dynamics during dorsal intercalation. We find that TIAM-1 can promote protrusion formation through its canonical GEF function, while its N-terminal domains function to negatively regulate this activity, preventing the generation of ectopic protrusions in intercalating cells. We also show that the guidance receptor UNC-5 inhibits ectopic protrusive activity in dorsal epidermal cells, and that this effect is in part mediated via TIAM-1. These results expand the network of proteins that regulate basolateral protrusive activity during directed cell rearrangement.Summary statementTIAM-1 activates the Rac pathway to promote protrusion formation via its GEF domain, while its N-terminal domains suppress ectopic protrusions during dorsal intercalation in theC. elegansembryo.
The Role of the Tyrosine-Based Sorting Signals of the ORF3a Protein of SARS-CoV-2 on Intracellular Trafficking, Autophagy, and Apoptosis
Authors: Henke Wyatt , Kalamvoki Maria , Stephens Edward B 
Published: July 2023

ABSTRACTThe open reading frame 3a (ORF3a) is an accessory transmembrane protein that is important to the pathogenicity of SARS-CoV-2. The cytoplasmic domain of ORF3a has three canonical tyrosine-based sorting signals (YxxΦ; where x is any amino acid and Φ is a hydrophobic amino acid with a bulky -R group). They have been implicated in the trafficking of membrane proteins to the cell plasma membrane and to intracellular organelles. Previous studies have indicated that mutation of the160YSNV163motif abrogated plasma membrane expression and inhibited ORF3a-induced apoptosis. However, two additional canonical tyrosine-based sorting motifs (211YYQL213,233YNKI236) exist in the cytoplasmic domain of ORF3a that have not been assessed. We removed all three potential tyrosine-based motifs and systematically restored them to assess the importance of each motif or combination of motifs that restored efficient trafficking to the cell surface and lysosomes. Our results indicate that the YxxΦ motif at position 160 was insufficient for the trafficking of ORF3a to the cell surface. Our studies also showed that ORF3a proteins with an intact YxxΦ at position 211 or at 160 and 211 were most important. We found that ORF3a cell surface expression correlated with the co-localization of ORF3a with LAMP-1 near the cell surface. These results suggest that YxxΦ motifs within the cytoplasmic domain may act cooperatively in ORF3a transport to the plasma membrane and endocytosis to lysosomes. Further, our results indicate that certain tyrosine mutants failed to activate caspase 3 and did not correlate with autophagy functions associated with this protein.IMPORTANCEOpen reading frame 3a (ORF3a) encodes for the largest of the SARS-CoV-2 accessory proteins. While deletion of the ORF3a gene from SARS-CoV-2 results in a virus that replicates slightly less efficiently in cell culture, deletion also results in a virus that is less pathogenic in mouse models of SARS-CoV-2 infections. The ORF3a has been reported to be a viroporin, induces apoptosis and incomplete autophagy in cells. Thus, determining the domains involved in these functions will further our understanding of how this protein influences virus assembly and pathogenesis. Here, we investigated the role of the three potential tyrosine-based sorting signals in the cytoplasmic domain of the ORF3a on intracellular protein trafficking, apoptosis, and in the initiation of autophagy. Our results indicate that more than one YxxΦ motif is required for efficient transport of ORF3a, ORF3a expression resulted in minimal apoptosis, and cell surface expression was not required for autophagy.
Pre-existing heterogeneity facilitates development of heteroresistance upon gene acquisition
Authors: Jaggavarapu Siddharth , Hufnagel David A. , Weiss David S. 
Published: July 2023

AbstractAntibiotic resistance causes 1.27 million global deaths annually and is predicted to worsen. Heteroresistance is a form of resistance in which only a minor and unstable subpopulation of cells of a bacterial isolate are resistant to a given antibiotic, and are therefore often undetected by clinical diagnostics. These infrequent and undetected resistant cells can be selected during antibiotic therapy, expand in number, and cause unexplained treatment failures. A major question is how heteroresistance evolves. Here, studying the antibiotic fosfomycin, we report that heteroresistance can develop from a pre-existing state of phenotypic heterogeneity in which an isolate harbors a subpopulation with increased minimum inhibitory concentration (MIC), but below the clinical resistance breakpoint. We call this phenomenon heterosusceptibility and demonstrate that acquisition of a resistance gene,fosA, increases the MIC of the subpopulation beyond the breakpoint, making the isolate heteroresistant. Conversely, deletion offosAfrom a heteroresistant isolate led to reduction of the MIC of the resistant subpopulation without a loss of heterogeneity, thus generating heterosusceptibility. A survey of 103 carbapenem-resistant Enterobacterales (CRE) revealed that theEscherichia sp. isolates lacked thefosAgene and uniformly exhibited fosfomycin heterosusceptibility, whereas theKlebsiellaandEnterobacterencoded thefosAgene and were almost exclusively heteroresistant. Furthermore, some isolates exhibited heterosusceptibility to other antibiotics, demonstrating that this is a widespread phenomenon. These results highlight a mechanism for the evolution of heteroresistance and suggest that surveillance for heterosusceptibility may facilitate the prediction of impending heteroresistance before it evolves.