bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel mouse allele of the DNA/RNA helicase senataxin (Setxspcar3) causing meiotic arrest of spermatocytes and male infertility
Authors: Fujiwara Yasuhiro , Saito Kouhei , Sun Fengyun , Petri Sabrina , Inoue Erina , Schimenti John , Okada Yuki , Handel Mary Ann 
Published: April 2023

ABSTRACTAn unbiased screen for discovering novel genes for fertility identified thespcar3, spermatocyte arrest 3,mutant phenotype. Thespcar3mutation identified a new allele of theSetxgene, encoding senataxin, a DNA/RNA helicase that regulates transcription termination by resolving DNA/RNA hybrid R-loop structures. Although mutations in the humanSETXgene cause neural disorders,Setxspcar3mutant mice do not show any apparent neural phenotype, but instead exhibit male infertility and female subfertility. Histology of theSetxspcar3mutant testes revealed absence of spermatids and mature spermatozoa in the seminiferous tubules. Cytological analysis of chromosome spread preparations of theSetxspcar3mutant spermatocytes revealed normal synapsis, but aberrant DNA damage in the autosomes, and defective formation of the sex body. Furthermore,Setxspcar3testicular cells exhibited abnormal accumulation of R-loops compared to wild type testicular cells. Transient expression assays identified regions of the senataxin protein required for sub-nuclear localization. Together, these results not only confirm that senataxin is required for normal meiosis and spermatogenesis but also provide a new resource for determination of its role in maintaining R-loop formation and genome integrity.
Population ageing, incarceration and the growing digital divide: understanding the effects of digital literacy inequity experienced by older people leaving prison
Authors: Hwang Ye In (Jane) , Hagos Amanuel , Withall Adrienne , Hampton Stephen , Snoyman Phillip , Butler Tony 
Published: April 2023

AbstractBackgroundDigital inequity refers to the inequality and exclusion experienced by those who lack the same opportunities or circumstances to support the development of digital skills as the rest of modern society. One rapidly growing and highly vulnerable group to digital inequity is older people attempting to reintegrate into society after release from prison, where technology access is limited. Inadequate support for digital skills in this population entails widespread consequences for public health, human rights, social welfare and recidivism. This qualitative study is the first to: examine digital inequity experienced by older people who have been incarcerated, understand the effects of this on reintegration to society, and begin informing appropriate solutions.MethodSemi-structured interviews were conducted with N=15 older people (mean age= 57) who had been released from an Australian prison in the last two years, regarding their experiences of digital literacy since leaving prison. Reflexive thematic analysis was conducted under a critical realist lens.ResultsThe analysis resulted in six themes that illustrated the extent of digital inequity experienced by this population, and key challenges for improving digital literacy: ‘surviving in a digital world’, ‘stranger in a foreign world’, ‘questioning the digital divide’, ‘overcoming your “old” self’, ‘don’t like what you don’t know’, and ‘seeking versus finding help’.ConclusionsThe digital inequity that older people experience during and after incarceration creates additional challenges for a growing group who are already medically and socially marginalised. Prioritisation of this group for digital literacy initiatives both during incarceration and in the community will have benefits for their health, social and financial reintegration. Their unique life experiences should be considered in designing and delivering these programs.
Co-immobilization of ciprofloxacin and chlorhexidine as a long-term, broad-spectrum antimicrobial dual-drug coating for polyvinyl chloride (PVC)-based endotracheal tubes
Authors: Alves Diana , Pereira Maria Olívia , Lopes Susana Patrícia 
Published: April 2023

AbstractThe endotracheal tube (ETT) affords support for intubated patients, but the rising incidence of ventilator-associated pneumonia (VAP) is jeopardizing its application. ETT surfaces promote (poly)microbial colonization and biofilm formation, with a heavy burden for VAP. Devising safe, broad-spectrum antimicrobial materials to tackle ETT bioburden is needful. Herein, we immobilized ciprofloxacin (CIP) and/or chlorhexidine (CHX), through polydopamine (pDA)-based functionalization, onto polyvinyl chloride (PVC) surfaces. These surfaces were characterized and challenged with single and polymicrobial cultures of VAP-relevant bacteria (Pseudomonas aeruginosa;Acinetobacter baumannii;Klebsiella pneumoniae;Staphylococcus aureus;Staphylococcus epidermidis) and fungi (Candida albicans). The coatings imparted PVC surfaces with homogeneous morphology, varied wettability, and low roughness. Coated surfaces exhibited sustained CIP/CHX release, retaining long-term (10 days) stability. Surfaces evidencing no A549 lung cell toxicity exhibited broad-spectrum anti-biofilm activity. CIP/CHX co-immobilization resulted in better outcomes than CIP or CHX coatings, reducing bacteria up to >7 Log10, and modestly distressing (ca. 1 Log10)C. albicans. The anti-biofilm effectiveness of coated surfaces endured for dual biofilms, substantially preventing bacterial populations and fungi (ca. 2.7 Log10) inP. aeruginosa/C. albicansconsortia. A less pronounced antifungal effect (ca. 1 Log10reduction) was found in triple-species communities, but fully preventingP. aeruginosaandS. aureuspopulations. CIP/CHX co-immobilization holds a safe and robust broad-spectrum antimicrobial coating for PVC-ETTs, with the promise laying in reducing VAP incidence.
Genome editing in the mouse brain with minimally immunogenic Cas9 RNPs
Authors: Stahl Elizabeth C. , Sabo Jennifer K. , Kang Min Hyung , Allen Ryan , Applegate Elizabeth , Kim Shin Eui , Kwon Yoonjin , Seth Anmol , Lemus Nicholas , Salinas-Rios Viviana , Soczek Katarzyna , Trinidad Marena , Vo Linda T. , Jeans Chris , Wozniak Anna , Morris Timothy , Kimberlin Athen , Foti Thomas , Savage David F. , Doudna Jennifer A. 
Published: April 2023

AbstractTransient delivery of CRISPR-Cas9 ribonucleoproteins (RNPs) into the central nervous system (CNS) for therapeutic genome editing could avoid limitations of viral vector-based delivery including cargo capacity, immunogenicity, and cost. Here we tested the ability of cell penetrant Cas9 RNPs to edit the mouse striatum when introduced using a convection enhanced delivery system. These transient Cas9 RNPs showed comparable editing of neurons and reduced adaptive immune responses relative to one formulation of Cas9 delivered using AAV serotype 9. The production of ultra-low-endotoxin Cas9 protein manufactured at scale further improved innate immunity. We conclude that injection-based delivery of minimally immunogenic CRISPR genome editing RNPs into the CNS provides a valuable alternative to virus-mediated genome editing.
Ensembles for improved detection of invasive breast cancer in histological images
Authors: Solorzano Leslie , Robertson Stephanie , Hartman Johan , Rantalainen Mattias 
Published: April 2023

AbstractAccurate detection of invasive breast cancer (IC) can provide decision support to pathologists as well as improve downstream computational analyses, where detection of IC is a first step. Tissue containing IC is characterized by the presence of specific morphological features, which can be learned by convolutional neural networks (CNN). Here, we compare the use of a single CNN model versus an ensemble of several base models with the same CNN architecture, and we evaluate prediction performance as well as variability across ensemble based model predictions.Two in-house datasets comprising 587 WSI are used to train an ensemble of ten InceptionV3 models whose consensus is used to determine the presence of IC. A novel visualization strategy was developed to communicate ensemble agreement spatially. Performance was evaluated in an internal test set with 118 WSIs, and in an additional external dataset (TCGA breast cancer) with 157 WSI.We observed that the ensemble-based strategy outperformed the single CNN-model alternative with respect to accuracy on tile level in 89% of all WSIs in the test set. The overall accuracy was 0.92 (DICE coefficient, 0.90) for the ensemble model, and 0.85 (DICE coefficient, 0.83) for the single CNN alternative in the internal test set. For TCGA the ensemble outperformed the single CNN in 96.8% of the WSI, with an accuracy of 0.87 (DICE coefficient 0.89), the single model provides an accuracy of 0.75 (DICE coefficient 0.78)The results suggest that an ensemble-based modeling strategy for breast cancer invasive cancer detection consistently outperforms the conventional single model alternative. Furthermore, visualization of the ensemble agreement and confusion areas provide direct visual interpretation of the results. High performing cancer detection can provide decision support in the routine pathology setting as well as facilitate downstream computational analyses.
Separate attentional processes in the two visual systems of jumping spiders
Authors: Ferrante Federico , Loconsole Maria , Giacomazzi Davide , De Agrò Massimo 
Published: April 2023

1AbstractBy selectively focusing on a specific portion of the environment, animals can solve the problem of information overload, toning down irrelevant inputs and concentrate only on the relevant ones. This may be of particular relevance for animals such as the jumping spider, which possess a wide visual field of almost 360° and thus could benefit from a low-cost system for sharpening attention. Jumping spiders have a modular visual system composed of four pairs of eyes, of which only the two frontal eyes (i.e., AMEs) are motile, whereas the other secondary pairs remain immobile. We hypothesized that jumping spiders can exploit both primary and secondary eyes for stimulus detection and attentional shift, with the two systems working synergistically. In Experiment 1 we investigated AMEs’ attentional responses following a spatial cue presented to the secondary eyes. In Experiment 2, we tested for enhanced attention in the secondary eyes’ visual field congruent with the direction of the AMEs’ focus. In both experiments, we observed that animals were faster and more accurate in detecting a target when it appeared in a direction opposite to that of the initial cue. In contrast with our initial hypothesis, these results would suggest that attention is segregated across eyes, while each system works to compensate the other by attending to different spatial locations, rather than sharing a common attentional focus.
Development, Characterization, and Structural Analysis of a Genetically Encoded Red Fluorescent Peroxynitrite Biosensor
Authors: Pang Yu , Huang Mian , Fan Yichong , Yeh Hsien-Wei , Xiong Ying , Ng Ho Leung , Ai Hui-wang 
Published: April 2023

ABSTRACTBoronic acid-containing fluorescent molecules have been widely used to sense hydrogen peroxide and peroxynitrite, which are important reactive oxygen and nitrogen species in biological systems. However, it has been challenging to gain specificity. Our previous studies developed genetically encoded, green fluorescent peroxynitrite biosensors by genetically incorporating a boronic acid-containing noncanonical amino acid (ncAA),p-boronophenylalanine (pBoF), into the chromophore of circularly permuted green fluorescent proteins (cpGFPs). In this work, we introducedpBoF to amino acid residues spatially close to the chromophore of an enhanced circularly permuted red fluorescent protein (ecpApple). Our effort has resulted in two responsive ecpApple mutants: one bestows reactivity toward both peroxynitrite and hydrogen peroxide, while the other, namely pnRFP, is a selective red fluorescent peroxynitrite biosensor. We characterized pnRFPin vitroand in live mammalian cells. We further studied the structure and sensing mechanism of pnRFP using X-ray crystallography,11B-NMR, and computational methods. The boron atom in pnRFP adopts an sp2-hybridization geometry in a hydrophobic pocket, and the reaction of pnRFP with peroxynitrite generates a product with a twisted chromophore, corroborating the observed “turn-off” fluorescence response. Thus, this study extends the color palette of genetically encoded peroxynitrite biosensors, provides insight into the response mechanism of the new biosensor, and demonstrates the versatility of using protein scaffolds to modulate chemoreactivity.
Effects of B lymphocytes Invitro Treatment with Rose Extract on Transmembrane Ligands
Authors: Arokiaraj Mark Christopher , Menesson Eric 
Published: April 2023

AbstractAimsThe study was performed to evaluate the role of red rose extract (Pierre de Ronsard) on B lymphocytes. Specifically the gene expression of CD20, CD30, CD40, and CCR5 in human B cells were studied after treatment with rose extract.MethodsRed rose extract was prepared at the dilution of 0.0075% (v/v) and stored until use at -20°C. Cell treatment was performed at 37°C on B cells. The cells were plated in 6 well plates at 1.5×106cells per well and stored at -80°C. Total RNA extraction and quality control were performed. RTq-PCR was performed according to Genecopoeia’s instructions. The cycle threshold method (ΔΔCt) was used for data analysis.ResultsThe comparative Ct method quantification (2^-ΔCt) and fold change for CD20, CD 30, CD 40 and CCR5 were - 5.65E+01, 4.80E-01, N/A, 2.47E-01; and 0.954,0.377, N/A and 0.577, respectively. The amount of total RNA extracted from about 4.5×106cells was low and did not allow us to measure the RNA profile. The A260/A230 ratios were very low due to the low amount of RNA. The analysis of gene expression by qRT-PCR showed that CD40 was not expressed in untreated cells and cells treated with rose extract with the Ct values over 32. All other genes were expressed and well-measured in both B cell samples.ConclusionThe treatment with rose extract at 0.0075% (v/v) did not modify the expression of CD20. However, the expression of CD30 and CCR5 decreased with the rose extract treatment. The range of the fold change showed that the result of CD30 expression was more accurate than for CCR5.
Loss of the extracellular matrix protein Perlecan disrupts axonal and synaptic stability duringDrosophiladevelopment
Authors: Guss Ellen J. , Akbergenova Yulia , Cunningham Karen L. , Littleton J. Troy 
Published: April 2023

AbstractHeparan sulfate proteoglycans (HSPGs) form essential components of the extracellular matrix (ECM) and basement membrane (BM) and have both structural and signaling roles. Perlecan is a secreted ECM-localized HSPG that contributes to tissue integrity and cell-cell communication. Although a core component of the ECM, the role of Perlecan in neuronal structure and function is less understood. Here we identify a role forDrosophilaPerlecan in the maintenance of larval motoneuron axonal and synaptic stability. Loss of Perlecan causes alterations in the axonal cytoskeleton, followed by axonal breakage and synaptic retraction of neuromuscular junctions. These phenotypes are not prevented by blocking Wallerian degeneration and are independent of Perlecan’s role in Wingless signaling. Expression of Perlecan solely in motoneurons cannot rescue synaptic retraction phenotypes. Similarly, removing Perlecan specifically from neurons, glia or muscle does not cause synaptic retraction, indicating the protein is secreted from multiple cell types and functions non-cell autonomously. Within the peripheral nervous system, Perlecan predominantly localizes to the neural lamella, a specialized ECM surrounding nerve bundles. Indeed, the neural lamella is disrupted in the absence of Perlecan, with axons occasionally exiting their usual boundary in the nerve bundle. In addition, entire nerve bundles degenerate in a temporally coordinated manner across individual hemi-segments throughout larval development. These observations indicate disruption of neural lamella ECM function triggers axonal destabilization and synaptic retraction of motoneurons, revealing a role for Perlecan in axonal and synaptic integrity during nervous system development.
Dual functioning by the PhoR sensor is a key determinant toMycobacterium tuberculosisvirulence
Authors: Singh Prabhat Ranjan , Goar Harsh , Paul Partha , Mehta Khushboo , Bamniya Bhanwar , Vijjamarri Anil Kumar , Bansal Roohi , Khan Hina , Karthikeyan Subramanian , Sarkar Dibyendu 
Published: April 2023

AbstractPhoP-PhoR empowersM. tuberculosisto adapt to diverse environmental conditions, and remains essential for virulence. Although PhoP and PhoR have been structurally characterized, the signal(s) that this TCS responds to remains unknown. In this study, we show that PhoR is a sensor of acidic pH/high salt conditions, which activate PhoP via phosphorylation. Transcriptomic studies uncover that acidic pH-inducible expression of PhoP regulon is significantly inhibited in a PhoR-deletedM. tuberculosis. Using genome-wide screening we further identify a non-canonical mechanism of PhoP phosphorylation by the sensor kinase PrrB. To investigate how phosphorylation of PhoP is regulated, we discovered that PhoR functions as a phosphatase. Our results identify the motif/residues responsible for contrasting kinase/phosphatase dual functioning of PhoP, and collectively determine the homeostatic regulation of intra-mycobacterial P~PhoP which controls the final output of PhoP regulon. Together, these data uncover that PhoR plays a central role in mycobacterial adaptation to low pH conditions within the host macrophage phagosome. Consistent with these results a PhoR-deletedM. tuberculosisremains significantly attenuated in macrophages and animal models.
How reliable are DAO supplements? — A comparison of over-the-counter Diamine oxidase products
Authors: Alemany-Fornes Marc , Bori Jaume , Tintoré Maria , Cuñé Jordi , de Lecea Carlos 
Published: April 2023

AbstractDiamine oxidase (DAO) supplements have gained increasing attention in recent years due to their potential to support DAO deficiency, histamine intolerance and related symptoms. However, choosing a reliable and trustworthy DAO supplement can be a challenging task for patients and Healthcare practitioners. One of the main concerns is the lack of regulatory oversight on dietary supplements, which may result in misleading or incomplete labelling, incorrect dosages, and inadequate quality control. Such situations may lead to patients consuming supplements with insufficient amounts of active enzyme or with questionable purity, potentially resulting in undesired health outcomes. Thus, we tested the DAO activity of a variety of already in-the-market supplements and compared them with one another and against the specified activity, if any, by the manufacturer. Our results show a great discrepancy in most of the products and significant differences in DAO activity between different manufacturers.
Do NSm virulence factors in the Bunyavirales viral order originate from Gn gene duplication?
Authors: Lefebvre Victor , Foun Lin Ravy Leon , Cole Laura , Cosset François-Loïc , Fogeron Marie-Laure , Böckmann Anja 
Published: April 2023

AbstractOne-third of the nine WHO shortlisted pathogens prioritized for research and development in public health emergencies belong to theBunyaviralesorder. SeveralBunyaviralesspecies carry an NSm protein that acts as a virulence factor. We predicted the structures of these NSm protein and unexpectedly found that in two families, its cytosolic domain is inferred to have a similar fold to the cytosolic domain of the viral envelope-forming glycoprotein N (Gncyto) encoded on the same genome fragment. We show that although the sequence identity between the NSmcytoand Gncytodomains is low, the conservation of the two zinc finger-forming CCHC motifs explains the predicted structural conservation. Importantly, our predictions provide a first glimpse into the long unknown structure of NSm and its link to virulence. Also, these predictions suggest that NSm is the result of a gene duplication event in theBunyavirales NairoviridaeandPeribunyaviridaefamilies, and that such events may be common in the recent evolutionary history of RNA viruses.
A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats
Authors: de Jong Tristan V , Pan Yanchao , Rastas Pasi , Munro Daniel , Tutaj Monika , Akil Huda , Benner Chris , Chen Denghui , Chitre Apurva S , Chow William , Colonna Vincenza , Dalgard Clifton L , Demos Wendy M , Doris Peter A , Garrison Erik , Geurts Aron M , Gunturkun Hakan M , Guryev Victor , Hourlier Thibaut , Howe Kerstin , Huang Jun , Kalbfleisch Ted , Kim Panjun , Li Ling , Mahaffey Spencer , Martin Fergal J , Mohammadi Pejman , Ozel Ayse Bilge , Polesskaya Oksana , Pravenec Michal , Prins Pjotr , Sebat Jonathan , Smith Jennifer R , Woods Leah C Solberg , Tabakoff Boris , Tracey Alan , Uliano-Silva Marcela , Villani Flavia , Wang Hongyang , Sharp Burt M , Telese Francesca , Jiang Zhihua , Saba Laura , Wang Xusheng , Murphy Terence D , Palmer Abraham A , Kwitek Anne E , Dwinell Melinda R , Williams Robert W , Li Jun Z , Chen Hao 
Published: April 2023

SummaryThe seventh iteration of the reference genome assembly forRattus norvegicus— mRatBN7.2—corrects numerous misplaced segments and reduces base-level errors by approximately 9-fold and increases contiguity by 290-fold compared to its predecessor. Gene annotations are now more complete, significantly improving the mapping precision of genomic, transcriptomic, and proteomics data sets. We jointly analyzed 163 short-read whole genome sequencing datasets representing 120 laboratory rat strains and substrains using mRatBN7.2. We defined ∼20.0 million sequence variations, of which 18.7 thousand are predicted to potentially impact the function of 6,677 genes. We also generated a new rat genetic map from 1,893 heterogeneous stock rats and annotated transcription start sites and alternative polyadenylation sites. The mRatBN7.2 assembly, along with the extensive analysis of genomic variations among rat strains, enhances our understanding of the rat genome, providing researchers with an expanded resource for studies involving rats.