bluuebunny/crossref_metadata_2025_split huggingface dataset:
Small bowel obstruction caused by a mango phytobezoar within a Meckel’s diverticulum
Authors: Hulf Toby , Ben-David Matan 
Published: November 2023

Abstract
A fit and well gentleman in his 40s presented with vomiting and obstipation. His only relevant history being recent ingestion of a large quantity of mangoes. A computer tomography demonstrated a small bowel obstruction with a transition point in the right iliac fossa, but no other pathological findings. After a short period of non-operative management he proceeded to surgery, where a phytobezoar was identified at a Meckel’s diverticulum causing a pantaloon shaped intra-luminal obstruction. A small bowel resection and primary anastomosis was performed and the patient had an uncomplicated post-operative course. Meckel’s diverticuli are a relatively common phenomenon and may pre-dispose to bowel obstructions through a number of different mechanisms. This unusual case highlights the importance of considering this as a differential, and one that will likely require timely operative intervention.
Coeliac artery avulsion secondary to high velocity blunt abdominal trauma: a case report
Authors: Kay Tegan J , Rahman Zafreen , Musicki Korana , Atkinson Noel , Martin Katherine 
Published: November 2023

Abstract
Coeliac artery (CA) injuries are an extremely rare subset of blunt abdominal trauma with a reported incidence of only 0.01%. Patterns of CA injury include intimal tear, dissection, thrombosis and pseudoaneurysm, with the most rare being complete CA avulsion. These complex injuries pose a treatment challenge due to rapid blood loss and anatomical difficultly in achieving proximal and multiple points of distal vascular control. To our knowledge, this case of CA avulsion from blunt polytrauma is only the 7th case reported in the literature. To assist in management, we report a case of blunt traumatic CA avulsion managed successfully with open ligation following endovascular balloon occlusion of the juxta-coeliac aorta for haemorrhage control.
Cultural specificities of online dictionaries for English learners: Evidence from a user survey and a multimodal discourse analysis
Authors: Zhong Shuneng , Liu Xiqin 
Published: November 2023

Abstract
This study examines three popular e-dictionary platforms using a quantitative user survey coupled with a qualitative multimodal discourse analysis (MDA): Chinese Youdao, Cambridge English-Mandarin Chinese Dictionary (Cambridge), and the Free Dictionary (FD). The survey (N = 478) revealed that, despite its language flaws, Youdao was preferred by most Chinese EFL (English as a Foreign Language) learners mainly due to its search functionality and personalization. In contrast, English majors and postgraduates preferred Cambridge for its reliability and multimodal resources. FD ranked the lowest in popularity mainly for perceived inconvenience of searching and less accessibility of personalized functions. Multinomial logistic regressions and structural equation modelling showed that dictionary selection by users was contingent upon their perception of its features and their use strategies. Furthermore, MDA revealed how each dictionary contributed to the construction of a cultural identity. Youdao seemed to be a toolbox for personal use, with raw texts of varying quality, but with a clear and practical vision, in addition to customization options. Cambridge portrayed itself as a welcoming language community through appealing imagery, interactive options, and diverse navigational styles. FD was comparable to a dynamic and cluttered library, archiving large blocks of hyperlinked texts and word lists accompanied by musical animations. In brief, multimodal and cultural factors partially explained Chinese EFL learners’ preferences for a specific dictionary, highlighting the importance of adaptation to the linguistic and cultural background of the user, including customization. A general cultural and semiotic framework is proposed to examine the representation of cultural identity in e-dictionaries.
Statistical Comparison of Substructures in Pure Aluminum Before and After Creep Deformation, Based on EBSD Image Data
Authors: Rieder Philipp , Petrich Lukas , Serrano-Munoz Itziar , Fernández Ricardo , Bruno Giovanni , Schmidt Volker 
Published: November 2023

Abstract
Electron backscatter diffraction (EBSD) images of extruded pure aluminum were statistically analyzed to investigate creep-induced subgrain structures after applying two different levels of creep stress, corresponding to the power law (PL) and power-law breakdown (PLB) regimes. Kernel average misorientation analysis of EBSD measurements revealed 2D morphologies, which were subdivided by a multi-step segmentation procedure into subgranular arrangements. Various descriptors were employed to characterize the “subgrains” quantitatively, including their size, shape, spatial arrangement, and crystallographic orientation. In particular, the analysis of the orientations of subgrains was conducted by neglecting rotations around the loading axis. This approach facilitated the individual investigation of the {001} and {111} subgrain families with respect to the loading axis for two investigated stress levels plus a reference specimen. For the PL regime, the statistical analysis of subgrain descriptors computed from segmented image data revealed a similar degree of strain accumulation for {111} and {001} subgrains. In contrast, for the PLB regime, the analyzed descriptors indicate that {111} subgrains tend to accumulate significantly more strain than {001} ones. These observations suggest that the mechanisms leading to PLB may be associated with strain localization dependent on intergranular stress, hindering the recovery process within {111} grains.
A Short Historical Review of Water-Soluble Aminoplastic Resin Use for Lipid Ultrastructure Research
Authors: Gao Johnson K 
Published: November 2023

Abstract
In 1982, a water-soluble aminoplastic resin embedding method for electron microscopy (EM) was developed to study lipids. It involves a silylation technique for processing cured resins by converting them from hydrophilic to hydrophobic status, facilitating ultra-thin sectioning. The technique offers better preservation of lipovitellin material in frog (Rana amurensis) yolk platelets, and it shows membrane ultrastructure better than traditional epoxy embedding methods. An early (1982) pseudo-colored TEM image processing technique applied to the micrographs obtained by EM of silylated aminoplastic thin sections revealed the lipovitellin molecules, in relation to the biosynthesis of new membranes in the first cleavage of the egg, with remarkable clarity and explains the lipovitellin molecules in relation to the biosynthesis of new membranes. Because the original article was written in Chinese and published in China before its open policy, many scientists may not be aware of the publication. Thus, in this short review, the essential components of the procedure are presented in English to help guide investigators who might be interested in the use of water-soluble embedding methods for lipid research.
Tissue Clearing: An Overview of Methods, Considerations, and Applications
Authors: Padgett Caleb A 
Published: November 2023

Abstract
Since the advent of confocal microscopy, advances in tissue clearing have allowed researchers to push the limits of imaging depth and dive deeper into the precise 3D structures of biological specimens. As clearing methods are discovered, refined, and retired, it behooves the prudent microscopist to consider the pros and cons of various tissue clearing methods and systematically evaluate whether tissue clearing is beneficial to answer their research questions. Herein, I will briefly discuss the evolution of tissue clearing, pros and cons of more popular methods and techniques related to fluorescence microscopy, and key considerations for selecting a method most likely to yield experimental success.
Igniting New Confocal Imaging Potential – Nikon AX R Series with NSPARC
Authors: Delattre Sabrina 
Published: November 2023

Abstract
The Nikon AX/AX R microscope with the recently developed Nikon Spatial Array Detector (NSPARC) provides rapid, super-resolution image acquisition of fixed and living cells. Here, we discuss the structure and function of the NSPARC, which provides excellent resolution and signal-to-noise (S/N) capabilities, and show applications related to in vitro neutrophil movement within pancreatic blood vessels and dynamic changes in mitochondrial morphology occurring over a matter of seconds. The large field-of-view and associated AI software facilitates acquisition and analysis of large 3D samples.
Addressing Burnout in the Primary Care Setting: The Impact of an Evidence-Based Mindfulness Toolkit
Authors: Christensen Andrew J , Virnig Jonathan P , Case Nicole L , Hayes Stephanie S , Heyne Rebecca , Taylor Laura A , Allen Micheal P 
Published: November 2023

ABSTRACT

Background
Burnout is insidious and manifests over prolonged, repeated exposure to occupational stressors. There is a growing crisis among health care workers (HCWs) due to high levels of burnout and associated adverse outcomes. Identifying and addressing burnout can be problematic due to extensive variances of perceived occupational stressors across HCWs.

Purpose
Mindfulness-based training can enhance individual HCWs’ abilities to perceive and constructively respond to stresses endemic in the health care environment. It can reduce the prevalence of burnout in the primary care setting. An evidence-based multimodal Mindfulness-Based Stress Reduction toolkit (MBSR TK) was designed, implemented, and evaluated for its impact on HCWs’ self-reported stress levels (SRSL).

Implementation Strategies
A pre-post-program evaluation explored the impact of a multimodal toolkit program on HCW SRSL with the Mini-Z burnout survey (MZBS). The MBSR TK program, consisting of a 45 minute introduction and 4 biweekly 15 minute mindfulness sessions offering acupressure, meditation, journaling for gratitude, and self-compassion was designed, delivered, and evaluated with HCWs across 2 military primary care clinics in South Texas.

Results
All HCWs across 2 Air Force family practice clinics were invited to participate in all toolkit components. Seventy percent of all HCWs (N = 90) attended the introduction session. Thirty-seven (41%) HCWs completed pre and post MZBSs, and these responses are included in the data analysis section. The most represented HCWs were registered nurses, physician assistants, and technicians, respectively, at 24%, 21%, and 18%. The Wilcoxon Signed-Rank test examined changes in HCWs’ SRSL after participation in the MBSR TK program. HCWs who attended the introduction plus one biweekly session showed statistically significant decreases in self-reported stress (P = 0.018) and burnout (P = 0.045) and a significant increase in electronic health record proficiency (P = 0.033).

Conclusions
Multimodal mindfulness toolkits to address SRSL burnout are practical, accessible, easily implemented, adaptive to any environment, and can decrease burnout with participation with just one 15 minute session. This MBSR TK implementation effectively lowered self-reported stress in HCWs who are repeatedly challenged to adapt to various settings around the world during peacetime, wars, natural disasters, humanitarian crises, and now, pandemics.
Discovery of a one-sided radio filament of PSR J0538+2817 in S147: escape of relativistic PWN leptons into surrounding supernova remnant?
Authors: Khabibullin I I , Churazov E M , Bykov A M , Chugai N N , Zinchenko I I 
Published: November 2023

ABSTRACT
We report the discovery of a faint radio filament near PSR J0538+2817 in the NVSS, CGPS, and the Rapid ASKAP Continuum Survey data. This pulsar is plausibly associated with the supernova that gave rise to the Spaghetti nebula (Simeis 147). The structure is one-sided and appears to be almost aligned (within 17 degrees) with the direction of the pulsar’s proper motion, but in contrast to the known cases of pulsar radio tails, it is located ahead of the pulsar. At the same time, this direction is also approximately (within 5 degrees) perpendicular to the axis of the extended non-thermal X-ray emission around the pulsar. No X-ray or optical emission is detected from the filament region, although the end point of the radio filament appears to be adjacent to a filament of Hα emission. We speculate that this structure might represent a filament connecting pulsar wind nebula (PWN) with the ambient interstellar medium filled with relativistic electrons escaping the pulsar nebula, i.e. a radio analogue of X-ray filaments of Guitar and Lighthouse PWNs and filaments of non-thermal radio emission in the Galactic Centre.
Uridine–cytidine kinase 2 potentiates the mutagenic influence of the antiviral β-d-N4-hydroxycytidine
Authors: Xu Zhen , Flensburg Christoffer , Bilardi Rebecca A , Majewski Ian J 
Published: November 2023

Abstract
Molnupiravir (EIDD-2801) is an antiviral that received approval for the treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) infection. Treatment of bacteria or cell lines with the active form of molnupiravir, β-d-N4-hydroxycytidine (NHC, or EIDD-1931), induces mutations in DNA. Yet these results contrast in vivo genotoxicity studies conducted during registration of the drug. Using a CRISPR screen, we found that inactivating the pyrimidine salvage pathway component uridine–cytidine kinase 2 (Uck2) renders cells more tolerant of NHC. Short-term exposure to NHC increased the mutation rate in a mouse myeloid cell line, with most mutations being T:A to C:G transitions. Inactivating Uck2 impaired the mutagenic activity of NHC, whereas over-expression of Uck2 enhanced mutagenesis. UCK2 is upregulated in many cancers and cell lines. Our results suggest differences in ribonucleoside metabolism contribute to the variable mutagenicity of NHC observed in cancer cell lines and primary tissues.
VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center in 2023
Authors: Alvarez-Jarreta Jorge , Amos Beatrice , Aurrecoechea Cristina , Bah Saikou , Barba Matthieu , Barreto Ana , Basenko Evelina Y , Belnap Robert , Blevins Ann , Böhme Ulrike , Brestelli John , Brown Stuart , Callan Danielle , Campbell Lahcen I , Christophides George K , Crouch Kathryn , Davison Helen R , DeBarry Jeremy D , Demko Richard , Doherty Ryan , Duan Yikun , Dundore Walter , Dyer Sarah , Falke Dave , Fischer Steve , Gajria Bindu , Galdi Daniel , Giraldo-Calderón Gloria I , Harb Omar S , Harper Elizabeth , Helb Danica , Howington Connor , Hu Sufen , Humphrey Jay , Iodice John , Jones Andrew , Judkins John , Kelly Sarah A , Kissinger Jessica C , Kittur Nupur , Kwon Dae Kun , Lamoureux Kristopher , Li Wei , Lodha Disha , MacCallum Robert M , Maslen Gareth , McDowell Mary Ann , Myers Jeremy , Nural Mustafa Veysi , Roos David S , Rund Samuel S C , Shanmugasundram Achchuthan , Sitnik Vasily , Spruill Drew , Starns David , Tomko Sheena Shah , Wang Haiming , Warrenfeltz Susanne , Wieck Robert , Wilkinson Paul A , Zheng Jie 
Published: November 2023

Abstract
The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB, https://veupathdb.org) is a Bioinformatics Resource Center funded by the National Institutes of Health with additional funding from the Wellcome Trust. VEuPathDB supports &gt;600 organisms that comprise invertebrate vectors, eukaryotic pathogens (protists and fungi) and relevant free-living or non-pathogenic species or hosts. Since 2004, VEuPathDB has analyzed omics data from the public domain using contemporary bioinformatic workflows, including orthology predictions via OrthoMCL, and integrated the analysis results with analysis tools, visualizations, and advanced search capabilities. The unique data mining platform coupled with &gt;3000 pre-analyzed data sets facilitates the exploration of pertinent omics data in support of hypothesis driven research. Comparisons are easily made across data sets, data types and organisms. A Galaxy workspace offers the opportunity for the analysis of private large-scale datasets and for porting to VEuPathDB for comparisons with integrated data. The MapVEu tool provides a platform for exploration of spatially resolved data such as vector surveillance and insecticide resistance monitoring. To address the growing body of omics data and advances in laboratory techniques, VEuPathDB has added several new data types, searches and features, improved the Galaxy workspace environment, redesigned the MapVEu interface and updated the infrastructure to accommodate these changes.
Inter-generational nuclear crosstalk links the control of gene expression to programmed genome rearrangement during the Paramecium sexual cycle
Authors: Bazin-Gélis Mélanie , Eleftheriou Evangelia , Zangarelli Coralie , Lelandais Gaëlle , Sperling Linda , Arnaiz Olivier , Bétermier Mireille 
Published: November 2023

Abstract
Multinucleate cells are found in many eukaryotes, but how multiple nuclei coordinate their functions is still poorly understood. In the cytoplasm of the ciliate Paramecium tetraurelia, two micronuclei (MIC) serving sexual reproduction coexist with a somatic macronucleus (MAC) dedicated to gene expression. During sexual processes, the MAC is progressively destroyed while still ensuring transcription, and new MACs develop from copies of the zygotic MIC. Several gene clusters are successively induced and switched off before vegetative growth resumes. Concomitantly, programmed genome rearrangement (PGR) removes transposons and their relics from the new MACs. Development of the new MACs is controlled by the old MAC, since the latter expresses genes involved in PGR, including the PGM gene encoding the essential PiggyMac endonuclease that cleaves the ends of eliminated sequences. Using RNA deep sequencing and transcriptome analysis, we show that impairing PGR upregulates key known PGR genes, together with ∼600 other genes possibly also involved in PGR. Among these genes, 42% are no longer induced when no new MACs are formed, including 180 genes that are co-expressed with PGM under all tested conditions. We propose that bi-directional crosstalk between the two coexisting generations of MACs links gene expression to the progression of MAC development.
KnockTF 2.0: a comprehensive gene expression profile database with knockdown/knockout of transcription (co-)factors in multiple species
Authors: Feng Chenchen , Song Chao , Song Shuang , Zhang Guorui , Yin Mingxue , Zhang Yuexin , Qian Fengcui , Wang Qiuyu , Guo Maozu , Li Chunquan 
Published: November 2023

Abstract
Transcription factors (TFs), transcription co-factors (TcoFs) and their target genes perform essential functions in diseases and biological processes. KnockTF 2.0 (http://www.licpathway.net/KnockTF/index.html) aims to provide comprehensive gene expression profile datasets before/after T(co)F knockdown/knockout across multiple tissue/cell types of different species. Compared with KnockTF 1.0, KnockTF 2.0 has the following improvements: (i) Newly added T(co)F knockdown/knockout datasets in mice, Arabidopsis thaliana and Zea mays and also an expanded scale of datasets in humans. Currently, KnockTF 2.0 stores 1468 manually curated RNA-seq and microarray datasets associated with 612 TFs and 172 TcoFs disrupted by different knockdown/knockout techniques, which are 2.5 times larger than those of KnockTF 1.0. (ii) Newly added (epi)genetic annotations for T(co)F target genes in humans and mice, such as super-enhancers, common SNPs, methylation sites and chromatin interactions. (iii) Newly embedded and updated search and analysis tools, including T(co)F Enrichment (GSEA), Pathway Downstream Analysis and Search by Target Gene (BLAST). KnockTF 2.0 is a comprehensive update of KnockTF 1.0, which provides more T(co)F knockdown/knockout datasets and (epi)genetic annotations across multiple species than KnockTF 1.0. KnockTF 2.0 facilitates not only the identification of functional T(co)Fs and target genes but also the investigation of their roles in the physiological and pathological processes.
SPDB: a comprehensive resource and knowledgebase for proteomic data at the single-cell resolution
Authors: Wang Fang , Liu Chunpu , Li Jiawei , Yang Fan , Song Jiangning , Zang Tianyi , Yao Jianhua , Wang Guohua 
Published: November 2023

Abstract
The single-cell proteomics enables the direct quantification of protein abundance at the single-cell resolution, providing valuable insights into cellular phenotypes beyond what can be inferred from transcriptome analysis alone. However, insufficient large-scale integrated databases hinder researchers from accessing and exploring single-cell proteomics, impeding the advancement of this field. To fill this deficiency, we present a comprehensive database, namely Single-cell Proteomic DataBase (SPDB, https://scproteomicsdb.com/), for general single-cell proteomic data, including antibody-based or mass spectrometry-based single-cell proteomics. Equipped with standardized data process and a user-friendly web interface, SPDB provides unified data formats for convenient interaction with downstream analysis, and offers not only dataset-level but also protein-level data search and exploration capabilities. To enable detailed exhibition of single-cell proteomic data, SPDB also provides a module for visualizing data from the perspectives of cell metadata or protein features. The current version of SPDB encompasses 133 antibody-based single-cell proteomic datasets involving more than 300 million cells and over 800 marker/surface proteins, and 10 mass spectrometry-based single-cell proteomic datasets involving more than 4000 cells and over 7000 proteins. Overall, SPDB is envisioned to be explored as a useful resource that will facilitate the wider research communities by providing detailed insights into proteomics from the single-cell perspective.
standR: spatial transcriptomic analysis for GeoMx DSP data
Authors: Liu Ning , Bhuva Dharmesh D , Mohamed Ahmed , Bokelund Micah , Kulasinghe Arutha , Tan Chin Wee , Davis Melissa J 
Published: November 2023

Abstract
To gain a better understanding of the complexity of gene expression in normal and diseased tissues it is important to account for the spatial context and identity of cells in situ. State-of-the-art spatial profiling technologies, such as the Nanostring GeoMx Digital Spatial Profiler (DSP), now allow quantitative spatially resolved measurement of the transcriptome in tissues. However, the bioinformatics pipelines currently used to analyse GeoMx data often fail to successfully account for the technical variability within the data and the complexity of experimental designs, thus limiting the accuracy and reliability of the subsequent analysis. Carefully designed quality control workflows, that include in-depth experiment-specific investigations into technical variation and appropriate adjustment for such variation can address this issue. Here, we present standR, an R/Bioconductor package that enables an end-to-end analysis of GeoMx DSP data. With four case studies from previously published experiments, we demonstrate how the standR workflow can enhance the statistical power of GeoMx DSP data analysis and how the application of standR enables scientists to develop in-depth insights into the biology of interest.