bluuebunny/crossref_metadata_2025_split huggingface dataset:
Drivers of inappropriate use of antimicrobials in South Asia: A systematic review of qualitative literature
Authors: Murray Jennifer L. , Leung Daniel T. , Hanson Olivia R. , Ahmed Sharia M. , Pavia Andrew T. , Khan Ashraful I. , Szymczak Julia E. , Vaughn Valerie M. , Patel Payal K. , Biswas Debashish , Watt Melissa H. 
Published: September 2023

AbstractAntimicrobial resistance is a global public health crisis. Effective antimicrobial stewardship requires an understanding of the factors and context that contribute to inappropriate use of antimicrobials. The goal of this qualitative systematic review was to synthesize themes across levels of the social ecological framework that drive inappropriate use of antimicrobials in South Asia. In September 2023, we conducted a systematic search using the electronic databases PubMed and Embase. Search terms, identifieda priori, were related to research methods, topic, and geographic location. We identified 165 articles from the initial search and 8 upon reference review (n=173); after removing duplicates and preprints (n=12) and excluding those that did not meet eligibility criteria (n=115), 46 articles were included in the review. We assessed methodological quality using the qualitative Critical Appraisal Skills Program checklist. The studies represented 6 countries in South Asia, and included data from patients, health care providers, community members, and policy makers. For each manuscript, we wrote a summary memo to extract the factors that impede antimicrobial stewardship. We coded memos using NVivo software; codes were organized by levels of the social ecological framework. Barriers were identified at multiple levels including the patient (self-treatment with antimicrobials; perceived value of antimicrobials), the provider (antimicrobials as a universal therapy; gaps in knowledge and skills; financial or reputational incentives), the clinical setting (lack of resources; poor regulation of the facility), the community (access to formal health care; informal drug vendors; social norms), and policy (absence of a regulatory framework; poor implementation of existing policies). The findings highlight the importance of working across multiple sectors to design and implement approaches to antimicrobial stewardship in South Asia.
Regulation of Toxic RNA Foci and MutantDMPKTranscripts: Role of MBNL Proteins and RNA Decay Pathways
Authors: Xing Xiaomeng , Markus Robert , Ghosh Tushar , Buxton Sarah , Nieves Daniel J. , Wojciechowska Marzena , Brook J. David 
Published: September 2023

AbstractMyotonic dystrophy type 1 (DM1) is a progressive, multisystemic disorder caused by an expansion of CTG repeats in the 3’ untranslated region of theDMPKgene. When transcribed the mutant RNAs accumulate in affected tissues appearing as distinct foci when visualised byin situhybridisation. The RNA foci are aggregates of CUG repeat-containing RNAs that sequester RNA-binding proteins, particularly muscleblind-like (MBNL) proteins, leading to their dysfunction and causing downstream molecular and cellular defects. Here we show the double knock-out ofMBNL1and2prevents RNA foci formation and nuclear retention of mutantDMPKmRNA in DM1 cells as well as promoting their degradation and nuclear export. Using stochastic optical reconstruction microscopy (STORM), we find the presence of both large foci and micro foci in DM1 cells. Large foci consist of multiple DMPK transcripts, while many micro foci are (CUG)n fragments. The absence of MBNL proteins not only prevents the aggregation of multipleDMPKtranscripts into large foci, but also promotes their degradation and nuclear processing. However, although a substantial amount of MBNL1 proteins are bound to the mutant transcripts, the pools of free MBNL1 proteins are similar in DM1 nuclei to those in controls. Furthermore, we have identified several factors that are involved in the control of mutantDMPKmRNA turnover, including XRN2, EXOSC10, UPF1 and STAU1. Our study indicates that these factors are implicated in the RNA foci accumulation and the degradation of mutantDMPKmRNA. UPF1 and STAU1 may have additional roles beyond degradation, impacting the nuclear processing of mutantDMPKmRNA. Our study also highlights the critical role of MBNL proteins in regulating mutantDMPKmRNA metabolism: the absence of MBNLs in DM1 appears to expedite the processing of mutantDMPKmRNA mediated by these RNA decay factors.Significance statementOur investigations uncovered valuable data on the RNA foci dynamics in DM1, revealing the intricate mechanisms that underlie their formation, stability, and turnover. Our findings also contributed to delineate the complex pathways involved in the transportation and degradation of the mutant mRNA and provided insights into the critical role played by MBNL proteins in these processes. Studying the degradation mechanism of mutantDMPKmRNA in myotonic dystrophy may provide a foundation for comprehending the mechanisms of RNA degradation in other diseases caused by short tandem repeat (STR) mutations, such as Huntington’s disease, Fragile X syndrome, and several types of ataxia. Additionally, the use of cutting-edge STORM technology can provide a valuable tool for investigating RNA foci in other STR expansion disorders.
A taxonomy for human social perception: Data-driven modelling with cinematic stimuli
Authors: Santavirta Severi , Malén Tuulia , Erdemli Asli , Nummenmaa Lauri 
Published: September 2023

AbstractEvery day, humans encounter complex social situations that need to be encoded effectively to allow interaction with others. Yet, principles for organizing the perception of social features from the external world remain poorly characterised. In this large-scale study we investigated the principles of social perception in dynamic scenes. In the primary dataset, we presented 234 movie clips (41 minutes) containing various social situations to 1140 participants and asked them to evaluate the presence of 138 social features in each clip. Analyses of the social feature ratings revealed that some features are perceived categorically (present or absent) and others continuously (intensity) and simple social features requiring immediate response are perceived most consistently across participants. To establish the low-dimensional perceptual organization for social features based on movies, we used principal coordinate analysis and consensus clustering for the feature ratings. These dimension reduction analyses revealed that the social perceptual structure can be modelled with eight main dimensions and that behaviourally relevant perceptual categories emerge from these main dimensions. This social perceptual structure generalized from the perception of unrelated Hollywood movie clips to the perception of a full Finnish movie (70 min), and to the perception of static images (n = 468) and across three independent sets of participants (n = 2254). Based on the results, we proposeeight basic dimensions of social perceptionas a model for rapid social perception where social situations are perceived along eight orthogonal perceptual dimensions (most importantly emotional valence, empathy versus dominance, and cognitive versus physical behaviour).
Open top multi sample dual view light sheet microscope for live imaging of large multicellular systems
Authors: Moos F. , Suppinger S. , de Medeiros G. , Oost K. , Boni A. , Rémy C. , Weevers S. , Tsiairis C. , Strnad P. , Liberali P. 
Published: September 2023

AbstractMulticellular systems grow over the course of weeks from single cells to tissues or even full organisms composed of several thousands of cells, making live imaging of such samples challenging. To bridge these wide spatiotemporal scales, we present an open top dual view and dual illumination light sheet microscope dedicated for live imaging of large specimens at single cell resolution. The novel configuration of objectives together with a flexible and customizable multi-well mounting system combines dual view with high throughput multi-position imaging. We use the newly developed microscope to image a wide variety of samples and highlight its capabilities to gain quantitative single-cell information in large specimens such as mature intestinal organoids and gastruloids.
Differential utilisation of subcellular skeletal muscle glycogen pools: A comparative analysis between 1 and 15 minutes of maximal exercise
Authors: Schytz Camilla Tvede , Ørtenblad Niels , Gejl Kasper Degn , Nielsen Joachim 
Published: September 2023

AbstractDistinct subcellular pools of glycogen particles exist within skeletal muscle fibres, distributed both within and between myofibrils and can be found in proximity to, or at a distance from mitochondria. Their precise localisation may influence their degradation rate and role in muscle function. Here, we investigated how exercise at different intensities (1- and 15-min maximal exercise) with known variations in glycogenolytic rate and relative contribution from anaerobic metabolism affects the utilisation of the distinct pools. Further, we investigated how lowered carbohydrate and energy intake affected glycogen volume densities and the storage of glycogen particles (i.e., localisation, size, and number) and their subsequent utilisation during the exercises. Using a randomized, counterbalanced, cross-over design, participants performed two maximal cycle tests of either 1 (n=10) or 15 min (n=10), conducted following consumption of two distinct diets with either high or lowered carbohydrate and energy contents. Muscle biopsies fromm. vastus lateraliswere obtained before and after the exercises. Intermyofibrillar glycogen was preferentially utilised during the 1-min exercise, whereas intramyofibrillar glycogen was preferentially utilised during the 15-min exercise. The lowered carbohydrate and energy intake decreased the particle size across all subcellular pools and reduced the numerical density in the intramyofibrillar and subsarcolemmal pools, with no effects on the glycogen utilisation during the subsequent exercise. In conclusion, the distinct subcellular glycogen pools were differentially utilised during 1-min and 15-min maximal exercise. Additionally, lowered carbohydrate and energy consumption reduces particle size and numerical density, depending on subcellular localisation.
Contributions of hyperactive mutations in Mprofrom SARS-CoV-2 to drug resistance
Authors: Flynn Julia M. , Zvornicanin Sarah N. , Shaqra Ala M. , Yilmaz Nese Kurt , Moquin Stephanie , Dovala Dustin , Schiffer Celia S. , Bolon Daniel N.A. 
Published: September 2023

AbstractThe appearance and spread of mutations that cause drug resistance in rapidly evolving diseases, including infections by SARS-CoV-2 virus, are major concerns for human health. Many drugs target enzymes, and resistance-conferring mutations impact inhibitor binding and/or enzyme activity. Nirmatrelvir, the most widely used inhibitor currently used to treat SARS-CoV-2 infections, targets the main protease (Mpro) preventing it from processing the viral polyprotein into active subunits. Our previous work systematically analyzed resistance mutations in Mprothat reduce binding to inhibitors; here we investigate mutations that affect enzyme function. Hyperactive mutations that increase Mproactivity can contribute to drug resistance but had not been thoroughly studied. To explore how hyperactive mutations contribute to resistance, we comprehensively assessed how all possible individual mutations in Mproaffect enzyme function using a mutational scanning approach with a FRET-based yeast readout. We identified hundreds of mutations that significantly increased Mproactivity. Hyperactive mutations occurred both proximal and distal to the active site, consistent with protein stability and/or dynamics impacting activity. Hyperactive mutations were observed three times more than mutations which reduced apparent binding to nirmatrelvir in recent studies of laboratory grown viruses selected for drug resistance. Hyperactive mutations were also about three times more prevalent than nirmatrelvir-binding mutations in sequenced isolates from circulating SARS-CoV-2. Our findings indicate that hyperactive mutations are likely to contribute to the natural evolution of drug resistance in Mproand provide a comprehensive list for future surveillance efforts.
A Small Multidrug Resistance Transporter inPseudomonas aeruginosaConfers Substrate-Specific Resistance or Susceptibility
Authors: Wegrzynowicz Andrea K. , Heelan William J. , Demas Sydnye P. , McLean Maxwell S. , Peters Jason M. , Henzler-Wildman Katherine A. 
Published: September 2023

ABSTRACTSmall Multidrug Resistance (SMR) transporters are key players in the defense of multidrug-resistant pathogens to toxins and other homeostasis-perturbing compounds. However, recent evidence demonstrates that EmrE, an SMR fromEscherichia coliand a model for understanding transport, can also induce susceptibility to some compounds by drug-gated proton leak. This runs down the ΔpH component of the Proton Motive Force (PMF), reducing viability of the affected bacteria. Proton leak may provide an unexplored drug target distinct from the targets of most known antibiotics. Activating proton leak requires an SMR to be merely present, rather than be the primary resistance mechanism, and dissipates the energy source for many other efflux pumps. PAsmr, an EmrE homolog fromP. aeruginosa, transports many EmrE substrates in cells and purified systems. We hypothesized that PAsmr, like EmrE, may confer susceptibility to some compounds via drug-gated proton leak. Growth assays ofE. coliexpressing PAsmr displayed substrate-dependent resistance and susceptibility phenotypes, andin vitrosolid-supported membrane electrophysiology experiments revealed that PAsmr performs both antiport and substrate-gated proton uniport, demonstrating the same functional promiscuity observed in EmrE. Growth assays ofP. aeruginosastrain PA14 demonstrated that PAsmr contributes resistance to some antimicrobial compounds, but no growth defect is observed with susceptibility substrates, suggestingP. aeruginosacan compensate for the proton leak occurring through PAsmr. These phenotypic differences betweenP. aeruginosaandE. coliadvance our understanding of underlying resistance mechanisms inP. aeruginosaand prompt further investigation into the role that SMRs play in antibiotic resistance in pathogens.IMPORTANCESmall multidrug resistance transporters are a class of efflux pumps found in many pathogens, but whose contributions to antibiotic resistance are not fully understood. We hypothesize that these transporters may confer not only resistance, but also susceptibility, by dissipating the proton-motive force. This means to use an SMR transporter as a target, it merely needs to be present (as opposed to being the primary resistance mechanism). Here, we test this hypothesis with an SMR transporter found inPseudomonas aeruginosaand find that it can perform both antiport (conferring resistance) and substrate-gated proton leak. Proton leak is detrimental to growth inE. colibut notP. aeruginosa, suggesting thatP. aeruginosaresponds differently to or can altogether prevent ΔpH dissipation.
High density aromatic peptides protect retinal ganglion cells in mouse retina following optic nerve crush injury
Authors: MacNeil Margaret A. , Garcia-Marin Virginia , Birk Alexander 
Published: September 2023

AbstractPurposeMitochondrial dysfunction plays a significant role in the death of retinal ganglion cells (RGCs) and their axons in retinal neurodegenerative diseases. We studied the effect of the mitochondrial-targeted HDAP2 (High Density Aromatic Peptide 2) to protect MDBK cells following serum starvation in cultured cells, and in mouse retinal ganglion cells following optic nerve crush.MethodsUptake, toxicity, and efficacy of HDAP2 was studied in cultured cells under conditions of serum starvation. Once preliminary safety and efficacy of the peptide was establishedin vitro, HDAP2 was administered to mice following unilateral optic nerve crush and the distribution and survival of RBPMS-labeled RGCs was assessed.ResultsWe found that water-soluble HDAP2 localizes to mitochondria and improves the mitochondrial membrane potential, prevents oxidative stress, and reduces death of cells grown in serum-free culture media. In mice treated systemically with biotinylated peptide, we found that HDAP2 labeled all layers of the retina in a pattern similar to the mitochondrial marker Cox IV, and that the peptide was colocalized with retinal ganglion cells and Müller glia. Animals treated with HDAP2 following optic nerve crush showed significantly greater survival of retinal ganglion cells compared to untreated animals at all retinal eccentricities.ConclusionOur results demonstrate that HDAP2 protects cells against serum starvation-induced decreases in mitochondrial membrane potential and leads to significant protection of retinal ganglion cells in the mouse retina following optic nerve crushin vivo.These results suggest that therapeutic agents preserving the mitochondrial membrane potential may help protect neurons following trauma or from neurodegenerative disease.
mRNA N1-2’O-methylation by CMTR1 affects NVL2 mRNA splicing
Authors: Wolter Steven , Hennig Thomas , Wallerath Christina , Schlee-Guimaraes Thais M. , Kirchhoff Alexander , Urban Christian , Piras Antonio , Stukalov Alexey , Juranek Stefan , Engelke Michael , Boehm Volker , Gehring Niels H. , Hartmann Gunther , Pichlmair Andreas , Friedel Caroline C. , Dölken Lars , Schlee Martin 
Published: September 2023

ABSTRACTCap0-mRNA is characterized by a 5’-5’triphosphate-linked N7-methylated guanosine(m7G). In higher eukaryotes, the methyltransferase CMTR1 additionally methylates the 2’O-position of the penultimate mRNA nucleotide(N1) ribose (cap1-mRNA). While the m7G cap is essential for mRNA export and translation initiation by the eIF4F complex, the N1-2’O-methylation prevents recognition of cap1-mRNA by the antiviral RNA receptors RIG-I and IFIT1, but a function beyond immunotolerance remained elusive. Here, we generatedCMTR1-knockout(CMTR1-/-) cells and found that type-I-interferon(IFN-I) treatment resulted in IFIT1-mediated reduction of cell viability and broad mRNA translation. Consequently, stimulation of the antiviral receptor RIG-I inCMTR1-/-cells revealed an IFIT1 dependent dramatic reduction of IFN-I and chemokine protein induction, demonstrating the importance of N1-2’O-methylation for antiviral responses.Additionally, IFN-I- and IFIT1-independent effects were observed:CMTR1-/-cells were smaller, divided slower, and exhibited a reduced transcription of mRNAs coding ribosomal proteins (RP), 5’TOP-RNA and snoRNA host genes(SNHG). Additionally, proteome and transcriptome analysis revealed that expression of NVL2, an essential factor in ribosome biogenesis, is strongly suppressed by an alternative-splicing event ofNVL2 mRNAin CMTR1-/-cells. This reduction could only be rescued by catalytically active CMTR1. Altogether, besides antiviral immunity N1-2’O-methylation by CMTR1 has broad effects on cellular physiology and controls splicing of NVL2.
Statistics to prioritize rare variants in family-based sequencing studies with disease subtypes
Authors: Nieuwoudt Christina , Farooq Fabiha Binte , Brooks-Wilson Angela , Bureau Alexandre , Graham Jinko 
Published: September 2023

AbstractFamily-based sequencing studies are increasingly used to find rare genetic variants of high risk for disease traits with familial clustering. In some studies, families with multiple disease subtypes are collected and the exomes of affected relatives are sequenced for shared rare variants. Since different families can harbor different causal variants and each family harbors many rare variants, tests to detect causal variants can have low power in this study design. Our goal is rather to prioritize shared variants for further investigation by, e.g., pathway analyses or functional studies. The transmission-disequilibrium test prioritizes variants based on departures from Mendelian transmission in parent-child trios. Extending this idea to families, we propose methods to prioritize rare variants shared in affected relatives with two disease subtypes, with one subtype more heritable than the other. Global approaches condition on a variant being observed in the study and assume a known probability of carrying a causal variant. In contrast, local approaches condition on a variant being observed in specific families to eliminate the carrier probability. Our simulation results indicate that global approaches are robust to mis-specification of the carrier probability and prioritize more effectively than local approaches even when the carrier probability is misspecified.
Standard methods for marking caudate amphibians do not impair animal welfare over the short term: an experimental approach
Authors: Daversa DR , Baxter E , Rosa GM , Sergeant C , Garner TWJ 
Published: September 2023

AbstractMajor advancements in ecology and biodiversity conservation have been made thanks to methods for marking and individually tracking animals. Marking animals is both widely used and controversial due to the potential consequences to animal welfare, which are often incompletely evaluated before implementation. Two outstanding knowledge gaps concerning the welfare consequences of individual marking concerns their short-term behavioural impacts and the relative impacts from marking versus the handling of animals while carrying out procedures. We addressed these knowledge gaps through an experimental study of alpine newts (Ichthyosaura alpestris) in which we varied handling and marking procedures. Examining individual responses to handling, toe-clipping and visible implant elastomer (VIE) injection over 21 days showed that handling and marking elicited increased newt activity and hesitancy to feed compared to animals that did not get handled or marked. These effects were apparent even when animals were handled only (not marked), and marking did not further increase the magnitude of responses. Increases in newt activity and feeding hesitancy were transient; they were not observed in the weeks following handling and marking. Whereas previous studies emphasize the welfare impacts of marking procedures themselves, these findings highlight that handling alone can elicit behavioural changes with possible costs to welfare. Yet, the transient nature of behavioural responses observed here suggests that immediate costs of handling may be subsequently compensated for.