bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enabling global-scale nucleic acid repositories through versatile, scalable biochemical selection from room-temperature archives
Authors: Berleant Joseph D. , Banal James L. , Rao Dhriti K. , Bathe Mark 
Published: April 2024

ABSTRACTConventional collection, preservation, and retrieval of nucleic acid specimens, particularly unstable RNA, require costly cold-chain infrastructure and rely on inefficient robotic sample handling, hindering downstream analyses. These generate critical bottlenecks for global pathogen surveillance and genomic biobanking efforts, prohibiting large-scale nucleic acid sample collection and analyses that are needed to empower pathogen tracing, as well as rare disease diagnostics1. Here, we introduce a scalable nucleic acid storage system that enables rapid and precise retrieval on pooled nucleic acid samples—stored at room-temperature with minimal physical footprint2,3—using versatile database-like queries on barcoded, encapsulated samples. Queries can incorporate numerical ranges, categorical filters, and combinations thereof, which is a significant advancement beyond previous demonstrations limited to single-sample retrieval or Boolean classifiers. We apply our system to a pool of ninety-six mock SARS-CoV-2 genomic samples identified with theoretical patient data including patient age, geographic location, and diagnostic state, allowing rapid, multiplexed nucleic acid sample retrieval in a scalable manner to empower genomic analyses. By avoiding expensive and cumbersome freezer storage and retrieval systems, our approach in principle scales to millions of samples without loss of fidelity or throughput, thereby supporting the development of large-scale pathogen and genomic repositories in under-resourced or isolated regions of the US and worldwide.
Molecular characterization of antimicrobial resistance organisms from drinking water and wastewater in a metropolitan city
Authors: Akhtar Khursheda , Farhana Nasreen , Hossain Alamgir , Khanam Fahmida 
Published: April 2024

AbstractBackgroundAntimicrobial resistant (AMR) organisms in environment may harm people. This study assessed the phenotypic and genotypic characteristics of AMR organisms from drinking and wastewater.Materials and methodsThis cross-sectional study conducted randomly on 30 samples (15 drinking water samples from household places; 15 sewage lifts stations) and collected aseptically, filtered, inoculated and isolated from culture plates, identified biochemically of pathogenic bacteria, and disc diffusion tested for antibiotic susceptibility. The primers of the targeted antimicrobial resistance genes were used for molecular amplification.ResultsTwenty-five bacteria were isolated from 30 drinking and wastewater samples.Pseudomonasspp. (36%),Enterobacterspp. (28%),Escherichia coli(20%),Citrobacterspp.(4%), Acinetobacterspp (4%) andKlebsiella oxytoca(4%) were isolated. Most of the isolates exhibited resistance to multiple groups of antibiotics, with meropenem, imipenem, gentamicin, ciprofloxacin, and amikacin showing the highest sensitivity against the isolates. Multiplex PCR confirmed the presence of two ESBL genes (blaSHV andblaCTX-M-15) and five carbapenemase genes (blaIMP,blaVIM,blaKPC,blaOXA1,blaNDM1) in resistant bacteria andblaCTX-M-15 (53.3%) followed byblaKPC (46.7%) genes were the most prevalent from drinking and wastewater samples respectively. According to WHO’s sanitary inspection risk score classification, 60% of drinking water samples scored 4 out of 11, categorizing them as intermediate risk based on hazard score.ConclusionsThis study addresses antimicrobial resistance in the environment, emphasizing public health implications; advocating for improved environmental regulations to mitigate AMR organism discharge through wastewater and drinking water.The significance of the studyThe study attempted to determine the pattern of antimicrobial resistance of microorganisms using phenotypic and genotypic methods by polymerase chain reaction (PCR), targeting particular genes with specific sequence of primers. As in Bangladesh very few studies for antimicrobial resistance organisms from drinking water and wastewater around household and hospital environments in Dhaka city, yet finished to change public health perspectives, and inform respective authorities for making decision. Thus the research contributes to generating some evidence-based information about the reservoir of antimicrobial resistance in environment.
In situinvestigation of extracellular vesicles in viscous formulations: interplay of nanoparticle transport and nano rheology through interferometric light microscopy analysis
Authors: Alexandre Lucile , Dubrova Anastasiia , Kunduru Aruna , Berger Marie , Boucenna Imane , Gazeau Florence , Silva Amanda K. A. , Mangenot Stéphanie , Aubertin Kelly 
Published: April 2024

SummaryWhile extracellular vesicles (EVs) demonstrate growing potential as innovative therapeutics in diverse medical context (cancer, regenerative medicine, etc.) or as naturally circulant diagnostic / prognostic probes, their physical properties (size, transport, etc.) remains a critical concern. Here, we introduce a pipeline that relies on interferometric light microscopy (ILM) for measuring not only nanoparticle concentration and size distribution but also for analyzing the interactions of these nanoparticles with their environment. The analysis of interference patterns allows for the physical characterization of (bio)nanoparticles not only in aqueous solutions but also in challenging media with relatively high viscosity, particularly pertinent for characterizing gel-based EV-delivery systems. Through exploration of the instrument’s functionality and the use of calibrated NPs of various known sizes, we successfully obtained information about the local viscosity characteristics of a complex fluid embedding EVs. We present a proof-of-concept for characterizing EVs suspended in unconventional media and their interactions with their surroundings. Leveraging the outcomes of this investigation, we not only highlight the advantages of using ILM for characterizing EVs in complex fluid, particularly pertinent for the development of optimized biological carriers for targeted drug delivery and therapeutic applications, but we also validate a new method for measuring viscosity at the nanoscale.
p53 mediated regulation of LINE1 retrotransposition derived R-loops
Authors: Paul Pratyashaa , Kumar Arun , De Astik Kumar , Parida Ankita Subhadarsani , Bhadke Gauri , Khatua Satyajeet , Pattanayak Fizalin , Tiwari Bhavana 
Published: April 2024

AbstractLong Interspersed Nuclear Element 1 (LINE1/L1) retrotransposons, comprising around 17% of the human genome, typically remain quiescent in healthy somatic cells but become activated in various cancer types. Our recent investigation reveals that p53 silences L1 transposons in human somatic cells, potentially constituting a tumor suppressive pathway. In this study, we demonstrate that p53 silences both L1mRNA-gDNA (cis L1 R-loops) and L1mRNA-cDNA hybrids (trans L1 R-loops) formed during retrotransposition. The activation of L1 transposons by HDAC inhibitors (HDACi) led to accumulation of these cis and trans L1 R-loops in p53-/-cells, which were mitigated by treatment with a reverse transcriptase inhibitor. Furthermore, p53 established re-silencing of hyperactivated L1 transposons induced by HDACi. The p53-mediated restoration of silencing was accompanied by recruiting histone repressive marks specifically H3K9me3 and H3K27me3 and inhibiting the deposition of H3K4me3 and H3K9ac marks at the L1 promoter. This study elucidates a novel role of p53 in regulating the formation of RNA-DNA hybrids, a pivotal intermediate component of retrotransposition, and initiating the suppression of hyperactivated L1 elements. These findings underscore the significance of p53 in preserving genome stability through the regulation of L1-derived R-loops.In BriefThe role of L1 transposon derived L1mRNA-cDNA hybrids; an intermediate product formed during retrotransposition, in DNA damage and inflammation is not clear. Paul et al. reveals that p53 prevents L1cDNA derived RNA-DNA hybrids to control DNA damage and activation of inflammatory genes. The findings also elucidate the role of p53 in initiating the repression of hyperactivated transposons by facilitating the recruitment of epigenetic repressive marks and preventing the deposition of activating marks at L1-5’UTR.Highlightsp53 loss facilitates accumulation of both cis (L1mRNA-gDNA) and trans (L1mRNA-cDNA) forms of L1 R-loops.The youngest, actively retrotransposing full-length L1s contribute to the formation of trans (L1mRNA-cDNA) R-loops.p53 aids immediate L1 re-silencing by restoring deposition of epigenetic repressive and inhibition of activating marks.Reverse transcriptase inhibitor prevents L1 mediated DNA damage.Subject Categories: L1/LINE1, p53, Retrotransposons, RNA-DNA hybrids, Cis R loops, Trans R-loop, L1/LINE1Graphical
The ER Thioredoxin-Related Transmembrane Protein TMX2 Controls Redox-Mediated Tethering of ER-Mitochondria Contacts (ERMCS)
Authors: Chen Junsheng , Yap Megan C. , Bassot Arthur , Pascual Danielle M. , Makio Tadashi , Zimmermann Jannik , Mast Heather , Bhat Rakesh , Fleury Samuel G. , Fan Yuxiang , Buzatto Adriana Zardini , Moore Jack , Ballanyi Klaus , Li Liang , Overduin Michael , Lemieux M. Joanne , Lemieux Hélène , Tan Wen-Hann , Mancini Grazia M.S. , Morgan Bruce , Marcogliese Paul C. , Simmen Thomas 
Published: April 2024

SummaryThioredoxin-related transmembrane proteins (TMX) of the endoplasmic reticulum (ER) have emerged as key regulators of ER membrane properties. Within the ER lumen, TMX proteins and other ER redox enzymes determine oxidative conditions, which control the formation of ER-mitochondria membrane contacts (ERMCS) and determine their function. ERMCS exhibit cytoplasmic redox nanodomains, derived from ER and mitochondrial reactive oxygen species (ROS), whose mechanistic regulation is uncharacterized. Our research has identified the ER protein TMX2, which uses its unique cytosolic thioredoxin domain to prevent cytosolic sulfenylation of mitochondrial outer membrane proteins such as TOM70 through a functional interaction with peroxiredoxin-1 (PRDX1). By doing so, TMX2 interferes with the TOM70 ERMCS tethering function and reduces mitochondrial Ca2+flux and metabolism. Recently, TMX2 mutations have been identified to cause a neurodevelopmental disorder with microcephaly, cortical malformations, and spasticity (NEDMCMS). Using TMX2-mutated NEDMCMS patient cells, we demonstrate that compromising TMX2 through mutation reproduces mitochondrial defects. In a flyin vivomodel, TMX2 knockdown manifests predominantly in glial cells. Our results therefore provide important mechanistic insight into NEDMCMS and mechanistically link TMX2-mediated control of ERMCS to brain development and function.Graphical AbstractThe transmembrane thioredoxin-related TMX2 prevents TOM70 sulfenylation at ERMCS, thus maintaining normal mitochondria metabolism in wild-type cells. TMX2 knockout leads to TOM70 sulfenylation and tight ERMCS formation. This then increases ROS production, unbalances mitochondrial lipids, and relatively shifts OXPHOS electron supply to complex II.
Hyperacetylation mimetics within the tau filament core inhibits prion-like propagation of misfolded tau
Authors: Smith Ethan D , McKenna Robert , Mietzsch Mario , Borchelt David R , Prokop Stefan , Chakrabarty Paramita 
Published: April 2024

AbstractAcetylation of key Lysine residues characterizes aggregates of the microtubule-associated protein tau constituting the neuropathological hallmark of many neurodegenerative diseases, such as Alzheimer’s disease (AD) and Progressive Supranuclear Palsy (PSP). This has led to the idea that acetylation influences tau aggregation. Using a HEK293 cell-based aggregation assay, we tested whether acetylation-mimicking substitutions (K→Q) on five AD-associated acetyl-modified sites (AcK-311, 353, 369, 370, 375) influenced its propensity to aggregate when exposed to tau seeds derived from two clinically distinctive diseases – AD and PSP. In combination, the presence of 5K→Q sites ablated tau aggregation induced by seeds from both AD and PSP patients, indicating that acetylation within the filament core domain of tau could have an inhibitory effect on seed-mediated aggregation. We had previously identified that a phosphorylation-mimetic on Ser305 (S→E) abrogated tau aggregation by seeds from AD patients, without affecting seeding by PSP patients. Combining the S305→E to the 5K→Q acetyl-modified sites, we found that this tau could now be seeded only by PSP patients, but not by AD patients, confirming Ser305 as a critical determinant of strain-specific tau seeding. On the other hand, acetylation-nullifying substitutions (K→R or K→A) on these same Lys sites did not alter tau seeding abilities compared to the parental tau construct. Notably, the combined acetylation-nullifying Alanine substitutions on these 5 Lys sites resulted in spontaneous self-aggregation, with the filaments resembling amorphous deposits. All together, we demonstrate that cooperative acetyl-occupancy in the tau filament core influences seeded propagation of misfolded tau as well as drives self-aggregation.
A novel method to guide biomarker combinations to optimize the sensitivity
Authors: Ghasem Seyyed Mahmood , Fahrmann Johannes F. , Hanash Samir , Do Kim-Anh , Long James P. , Irajizad Ehsan 
Published: April 2024

AbstractLogistic regression has demonstrated its utility in classifying binary labeled datasets through the maximum likelihood approach. However, in numerous biological and clinical contexts, the aim is often to determine coefficients that yield the highest sensitivity at the pre-specified specificity or vice versa. Therefore, the application of logistic regression is limited in such settings. To this end, we have developed an improved regression framework, SMAGS, for binary classification that, for a given specificity, finds the linear decision rule that yields the maximum sensitivity. Furthermore, we employed the method for feature selection to find the features that are satisfying the sensitivity maximization goal. We compared our method with normal logistic regression by applying it to real clinical data as well as synthetic data. In the real application data (colorectal cancer dataset), we found 14% improvement of sensitivity at 98.5% specificity.Availability and implementationSoftware is made available in Python (https://github.com/smahmoodghasemi/SMAGS)
CD4-mediated immunity shapes neutrophil-driven tuberculous pathology
Authors: Gern Benjamin H , Klas Josepha M , Foster Kimberly A , Cohen Sara B , Plumlee Courtney R , Duffy Fergal J , Neal Maxwell L , Halima Mehnaz , Gustin Andrew T , Diercks Alan H , Aderem Alan , Gale Michael , Aitchison John D , Gerner Michael Y , Urdahl Kevin B 
Published: April 2024

SummaryPulmonaryMycobacterium tuberculosis(Mtb) infection results in highly heterogeneous lesions ranging from granulomas with central necrosis to those primarily comprised of alveolitis. While alveolitis has been associated with prior immunity in human post-mortem studies, the drivers of these distinct pathologic outcomes are poorly understood. Here, we show that these divergent lesion structures can be modeled in C3HeB/FeJ mice and are regulated by prior immunity. Using quantitative imaging, scRNAseq, and flow cytometry, we demonstrate that Mtb infection in the absence of prior immunity elicits dysregulated neutrophil recruitment and necrotic granulomas. In contrast, prior immunity induces rapid recruitment and activation of T cells, local macrophage activation, and diminished late neutrophil responses. Depletion studies at distinct infection stages demonstrated that neutrophils are required for early necrosis initiation and necrosis propagation at chronic stages, whereas early CD4 T cell responses prevent neutrophil feedforward circuits and necrosis. Together, these studies reveal fundamental determinants of tuberculosis lesion structure and pathogenesis, which have important implications for new strategies to prevent or treat tuberculosis.
Unlocking TAS2R14 activation through intricate multi-ligand binding networks
Authors: Hu Xiaolong , Ao Weizhen , Gao Mingxin , Wu Lijie , Pei Yuan , Liu Shenhui , Sun Qianqian , Liu Junlin , Jiang Longquan , Wu Yiran , Wang Xin , Li Yan , Tan Qiwen , Cheng Jie , Yang Fan , Yang Chi , Sun Jinpeng , Hua Tian , Liu Zhi-Jie 
Published: April 2024

AbstractBitter taste receptors, particularly TAS2R14, play central roles in discerning a wide array of bitter substances, ranging from dietary components to pharmaceutical agents1–3. In addition, TAS2R14 has broad expression in non-gustatory tissues, suggesting its important roles in selective physiological processes and therapeutic potential4. Here, we present cryo-electron microcopy structures of TAS2R14 in complex with flufenamic acid and aristolochic acid, coupling with G protein subtypes gustducin and Gi. Distinct from most known GPCRs, agonists of TAS2R14 bind to multiple intracellular pockets. We highlight the cholesterol molecules occupying an upper transmembrane site, typically the orthosteric pocket in other GPCRs, also binding in the entrance to an intracellular agonist binding pocket, suggesting an endogenous modulatory function5. The structural and mutagenesis analysis illuminate the receptor’s broad-spectrum ligand recognition and activation via intricate multiple ligand-binding sites. Furthermore, we unveil the structural configuration of gustducin and its interaction with TAS2R14, as well as the coupling mode of Gi1. This investigation should be instrumental in advancing our knowledge of the mechanisms underlying bitter taste recognition and response, with broader relevance to sensory biology and pharmacology.
Rbpjdeletion in hepatic progenitor cells attenuates endothelial responses in a mouse model of cholestatic liver disease
Authors: Lee Sanghoon , Ren Lu , Paranjpe Aditi , Zhou Ping , Potter Andrew , Huppert Stacey S. , Shin Soona 
Published: April 2024

ABSTRACTBackground and AimsSince the role of hepatic progenitor cells (HPCs) constituting ductular reactions in pathogenesis remains ambiguous, we aimed to establish the in vivo cause-and-effect relationship between HPCs and angiogenesis, a process associated with chronic liver disease progression. We previously demonstrated that peritumoral ductules are associated with angiogenesis in liver tumors and forkhead box L1 (Foxl1)- expressing murine HPCs secrete angiogenic factors in vitro. Therefore, we hypothesized that HPCs are capable of remodeling the vascular microenvironment and this function of HPCs is dependent on recombination signal binding protein for immunoglobulin kappa J region (RBPJ), a key effector of the Notch signaling pathway.Approach and ResultsWe generated HPC-specificRbpjconditional knockout mice usingFoxl1-Creand treated them with the 3,5-diethoxycarbonyl-1,4-dihydrocollidine-supplemented diet to induce cholestatic liver disease. Knockout mice displayed significant reduction of HPC proliferation and ductular reactions as well as attenuated vascular and fibrotic areas compared to control mice. Assessment of vascular endothelial growth factor A-positive areas in vivo and the effects ofRbpjshRNAs in vitro indicated thatRbpjknockout in HPCs reduces the total number of angiogenic factor-expressing cells rather than affecting angiogenic factor expression within HPCs. Single-nucleus RNA sequencing analysis indicated that conditionalRbpjknockout in HPCs induces transcriptional changes in endothelial cells and alters expression of genes involved in various functions of the endothelium.ConclusionOur findings indicate that HPCs regulate endothelial responses to cholestatic liver disease andRbpjdeletion in HPCs attenuates these responses, identifying novel targets for modulating angiogenesis during disease progression.
Parameter quantification for oxygen transport in the human brain
Authors: Bing Yun , Józsa Tamás I. , Payne Stephen J. 
Published: April 2024

AbstractOxygen is carried to the brain by blood flow through generations of vessels across a wide range of length scales. This multi-scale nature of blood flow and oxygen transport poses challenges on investigating the mechanisms underlying both healthy and pathological states through imaging techniques alone. Recently, multi-scale models describing whole brain perfusion and oxygen transport have been developed. Such models rely on effective parameters that represent the microscopic properties. While parameters of the perfusion models have been characterised, those for oxygen transport are still lacking. In this study, we set to quantify the parameters associated with oxygen transport and their uncertainties. We first present a multi-scale, multi-compartment oxygen transport model based on a porous continuum approach. We then determine the effective values of the model parameters. By using statistically accurate capillary networks, geometric parameters (vessel volume fraction and surface area to volume ratio) that capture the microvascular topologies are found to be 1.42% and 627 [mm2/mm3], respectively. These values compare well with those obtained from human and monkey vascular samples. In addition, maximum consumption rates of oxygen are optimised to uniquely define the oxygen distribution over depth. Simulation results from a one-dimensional tissue column show qualitative agreement with experimental measurements of tissue oxygen partial pressure in rats. We highlight the importance of anatomical accuracy through simulation performed within a patient-specific brain mesh. Finally, one-at-a-time sensitivity analysis reveals that the oxygen model is not sensitive to most of its parameters; however, perturbations in oxygen solubilities and plasma to whole blood oxygen concentration ratio have a considerable impact on the tissue oxygenation. These findings demonstrate the validity of using a porous continuum approach to model organ-scale oxygen transport and draw attention to the significance of anatomy and certain parameter values.
Mol-AE: Auto-Encoder Based Molecular Representation Learning With 3D Cloze Test Objective
Authors: Yang Junwei , Zheng Kangjie , Long Siyu , Nie Zaiqing , Zhang Ming , Dai Xinyu , Ma Wei-Ying , Zhou Hao 
Published: April 2024

Abstract3D molecular representation learning has gained tremendous interest and achieved promising performance in various downstream tasks. A series of recent approaches follow a prevalent framework: an encoder-only model coupled with a coordinate denoising objective. However, through a series of analytical experiments, we prove that the encoderonly model with coordinate denoising objective exhibits inconsistency between pre-training and downstream objectives, as well as issues with disrupted atomic identifiers. To address these two issues, we propose Mol-AE for molecular representation learning, an auto-encoder model using positional encoding as atomic identifiers. We also propose a new training objective named 3D Cloze Test to make the model learn better atom spatial relationships from real molecular substructures. Empirical results demonstrate that Mol-AE achieves a large margin performance gain compared to the current state-of-the-art 3D molecular modeling approach. The source codes of Mol-AE are publicly available athttps://github.com/yjwtheonly/MolAE.