bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distinguish characters of luminal and glandular epithelium from mouse uterus using a novel enzyme-based separation method
Authors: Xu Qi-Xin , Zhang Wang-Qing , Lu Lei , Wang Ke-Zhi , Su Ren-Wei 
Published: August 2022

AbstractThe uterine luminal epithelium, glandular epithelium, and stromal cells are vital for the establishment of pregnancy. Previously studies have shown various methods to isolate mouse uterine epithelium and stromal cells, including Laser Capture Microdissection (LCM), enzyme digestion, and Immunomagnetic beads. Despite the importance of the endometrial epithelium as the site of implantation and nutritional support for the conceptus, there is no isolated method to separate the luminal epithelium and glandular epithelium. Here, we establish a novel enzyme-based way to separate two types of epithelium and keep their viability. In this article, we analyzed their purity by mRNA level, immunostaining, and transcriptome analysis. Our isolation method revealed several unstudied luminal and glandular epithelial markers in transcriptome analysis. We further demonstrated the viability of the isolated epithelium by 2D and 3D cultures. The results showed that we successfully separated the endometrial luminal epithelium and glandular epithelium. We also provided an experimental model for the following study of the physiological function of the different parts of the uterus and related diseases.
eIF3 mRNA selectivity profiling reveals eIF3k as a cancer-relevant regulator of ribosome content
Authors: Duan Haoran , Zhang Siqiong , Zarai Yoram , Öllinger Rupert , Wu Yanmeng , Sun Li , Hu Cheng , Tian Guiyou , Rad Roland , Cheng Yabin , Tuller Tamir , Wolf Dieter A. 
Published: August 2022

ABSTRACTeIF3, whose subunits are frequently overexpressed in cancer, regulates mRNA translation from initiation to termination, but mRNA-selective functions of individual subunits remain poorly defined. Using multi-omic profiling upon acute depletion of eIF3 subunits, we observed that while eIF3a, b, e, and f markedly differed in their impact on eIF3 holo-complex formation and translation, they were each required for cancer cell proliferation and tumor growth. Remarkably, eIF3k showed the opposite pattern with depletion promoting global translation, cell proliferation, tumor growth, and stress resistance through repressing the synthesis of ribosomal proteins, especially RPS15A. Whereas ectopic expression of RPS15A mimicked the anabolic effects of eIF3k depletion, disruption of eIF3 binding to the 5’-UTR ofRSP15AmRNA negated them. Supported by mathematical modeling, our data uncovers eIF3k-l as a mRNA-specific module which, through controllingRPS15Atranslation, serves as a rheostat of ribosome content to secure spare translational capacity that can be mobilized during stress.
Natural variation in PHY causes differential response to R/FR light following a latitudinal cline in Norway spruce
Authors: Ranade Sonali Sachin , García-Gil María Rosario 
Published: August 2022

AbstractDetection of the genomic basis of local adaptation to environmental conditions is challenging in forest trees. Phytochromes (PHY) and cryptochromes (CRY) perceive the red (R)/far-red (FR) and blue light respectively and, play a fundamental role in regulating the light pathway in plants contributing to plant growth and development. Norway spruce shows an adaptive latitudinal cline for shade (low R:FR or FR-enriched light) tolerance and requirement of FR light for its growth, thus showing differential response to light quality. We analyzed the exome capture data that included a uniquely large data set of 1654 Norway spruce trees sampled from different latitudes across Sweden that differ in exposure to photoperiod and FR light received during the growing season. Statistically significant clinal variation was detected in allele and genotype frequencies of missense mutations in coding regions belonging to well-defined functional domains of PHYO (PAS-B), PHYP2 (PAS fold-2), CRY1 (CCT1) and CRY2 (CCT2) that strongly correlates with the latitudinal gradient in response to variable light quality in Norway spruce. Asn835Ser in PHYO displayed the steepest cline among all other polymorphisms. We propose that these variations represent signs of local adaptation to light quality in Norway spruce.
Screening of genes related to the interaction between Listeria monocytogenes and host cells
Authors: Fan Gao , Jun-xing Pu , Jin-wen Huang 
Published: August 2022

SummaryTo investigate how host cells respond to the hijacking of host cells by Listeria monocytogenes (LM) and affect their gene expression in the process of infection by LM. In this study, three data lines in the GEO database were used for differential expression analysis. The results showed that 34 co-expressed genes (DEGs) were selected from the differential expression analysis of three data lines. Among them, 30 genes were co-up-regulated and 4 genes were co-down-regulated. In the blood test group, 131 genes were up-regulated and 28 genes were down-regulated. In the liver, 132 genes were up-regulated and 18 genes were down-regulated. In the spleen, 142 genes were up-regulated and 11 genes were down-regulated. Among the 30 upregulated IDEGs, GBP3, MB21D1, FPR2, SAMHD1, CXCL10, STAT2, IRF1, and STAT1 genes were involved in the defense response to the virus, type i interferon signaling pathway, and inflammatory response. Functional enrichment analysis revealed that 30 up-regulated genes were enriched in cytoplasmic spermatoproteasome complex, proteasome core complex, and cell membrane lateral signaling pathway, which were involved in the regulation of threonine-type endopeptidase activity and guanosine triphosphate (GTP) signaling process.
Performance efficient macromolecular mechanics via sub-nanometer shape based coarse graining
Authors: Bryer Alexander J. , Perilla Juan R. 
Published: August 2022

AbstractDimensionality reduction via coarse grain modeling has positioned itself as an indispensable tool for decades, particularly for biomolecular simulations where atomic systems encompass hundreds of millions of atoms. While distinct flavors of coarse grain modeling exist, those occupying the coarse end of the spectrum are typically knowledge based, relying on a priori information to parameterize models, thus hindering general predictive capability. Here, we present an algorithmic and transferable approach known as shape based coarse graining (SBCG) which employs unsupervised machine learning via competitive Hebbian adaptation to construct coarse molecules that perfectly represent atomistic topologies. We show how SBCG provides ample control over model granularity, and we provide a quantitative metric for selection thereof. Parameter optimization, inclusion of small molecule species, as well as simulation configuration are discussed in detail. Our method and its implementation is made available as part of the CGBuilder plugin, present in the widely-used visual molecular dynamics (VMD) and nanoscale molecular dynamics (NAMD) software suites. We demonstrate applications of our method with a variety of systems from the inositol hexaphosphate-bound, full-scale HIV-1 capsid to heteromultimeric cofilin-2-bound actin filaments. Overall, we show that SBCG provides a simple yet robust approach to coarse graining that requires minimal user input and lacks any ad hoc interactions between protein domains. Furthermore, because the Hamiltonian employed in SBCG is CHARMM compatible, SBCG takes full advantage of the latest GPU-accelerated NAMD3 yielding molecular sampling of over a microsecond per day for systems that span micrometers.
Human XIRP1 is a macrophage podosome protein utilized by Listeria for actin-based motility
Authors: Urbano Rodolfo , Park Eui-Soon , Tretina Kyle , Tunaru Alexandru , Gaudet Ryan G. , Hu Xiaoyun , Wang Da-Zhi , MacMicking John D. 
Published: August 2022

ABSTRACTActin is integral to eukaryotic physiology as a biomechanical polymer and as a structural barrier for cell-autonomous defense against infection. Some microbial pathogens exploit the actin cytoskeleton, however, to evade cell-autonomous immunity. Subversion of actin to enter host cells and for actin-based motility are often employed by intracellular pathogens to spread from cell-to-cell. Using RNA-sequencing and computational data mining, we identify the host actin-binding protein XIRP1 as commonly induced during infection. XIRP1 is expressed by fibroblasts and macrophages in response to immune cytokines such as interferon-gamma (IFN-γ) and infection with bacteria such as Listeria, Shigella, and Salmonella. Confocal and super-resolution structured illumination microscopy (SIM) found XIRP1 localizes to fibroblast focal adhesions and macrophages podosomes. Within human macrophages, XIRP1 is recruited to cytosolic Listeria monocytogenes in an ActA-dependent manner as it replicates and uses actin-based motility for host cell escape. Chromosomal removal of XIRP1 in mice impaired this dissemination and rendered them more resistant to Listeria infection than C57BL/6NJ wildtype controls in vivo. We propose that professional cytosolic pathogens like Listeria can co-opt XIRP1 to escape the hostile intracellular environment of IFN-γ-activated macrophages as part of the host-pathogen arms race during cell-autonomous immunity.
Graph Neural Networks Ameliorate Potential Impacts of Imprecise Large-Scale Autonomous Immunofluorescence Labeling of Immune Cells on Whole Slide Images
Authors: Reddy Ramya , Reddy Ram , Sharma Cyril , Jackson Christopher , Palisoul Scott , Barney Rachael , Kolling Fred , Salas Lucas , Christensen Brock , Brooks Gabriel , Tsongalis Gregory , Vaickus Louis , Levy Joshua 
Published: August 2022

AbstractThe characteristics of tumor-infiltrating lymphocytes (TIL) are essential in cancer prognostication and treatment through the ability to indicate the tumor’s capacity to evade the immune system (e.g., as evidenced by nodal involvement). Machine learning technologies have demonstrated remarkable success for localizing TILs, though these methods require extensive curation of manual annotations or restaining procedures that can degrade tissue quality, resulting in imprecise annotation. In this study, we co-registered tissue slides stained for both hematoxylin and eosin (H&E) and immunofluorescence (IF) as means to rapidly perform large-scale annotation of nuclei. We integrated the following approaches to improve the prediction of TILs: 1) minimized tissue degradation on same-section tissue restaining, 2) developed a scoring algorithm to improve the selection of patches for machine learning modeling and 3) utilized a graph neural network deep learning approach to identify relevant contextual features for lymphocyte prediction. Our graph neural network approach accounts for surrounding contextual micro/macro-architecture tissue features to facilitate interpretation of registered IF. The graph neural network compares favorably (F1-score=0.9235, AUROC=0.9462) to two alternative modeling approaches. This study brings insight to the importance of contextual information leveraged from within and around neighboring cells in a nuclei classification workflow, as well as elucidate approaches which enable the rapid generation of large-scale annotations of lymphocytes for machine learning approaches for immune phenotyping. Such approaches can help further interrogate the spatial biology of colorectal cancer tumors and tumor metastasis.
Epidermal growth factor receptor signaling protects epithelia from morphogenetic instability and tissue damage in Drosophila
Authors: Yoshida Kentaro , Hayashi Shigeo 
Published: August 2022

AbstractDying cells in the epithelia communicate with neighboring cells to initiate coordinated cell removal to maintain epithelial integrity. Naturally occurring apoptotic cells are mostly extruded basally and engulfed by macrophages. Here, we investigated the role of Epidermal growth factor (EGF) receptor (EGFR) signaling in the maintenance of epithelial homeostasis. In Drosophila embryos, epithelial tissues undergoing groove formation preferentially enhanced extracellular signal-regulated kinases (ERK) signaling. In EGFR mutant embryos at stage 11, sporadic apical cell extrusion in the head initiates a cascade of apical extrusions of apoptotic and non-apoptotic cells that sweeps the entire ventral body wall. Here, we showed that clustered apoptosis, groove formation, and wounding sensitized EGFR mutant epithelia to initiate massive tissue disintegration. We further showed that tissue detachment from the vitelline membrane, which frequently occurs during morphogenetic processes, is a key trigger for the EGFR mutant phenotype. These findings indicate that, in addition to cell survival, EGFR plays a role in maintaining epithelial integrity, which is essential for protecting tissues from transient instability caused by morphogenetic movement and damage.
Validation of saline, PBS and a locally produced VTM at varying storage conditions to detect the SARS-CoV-2 virus by qRT-PCR
Authors: Ngetsa Caroline , Osoti Victor , Okanda Dorcas , Marura Faith , Shah Krupali , Karanja Henry , Mugo Daisy , Gitonga John , Mutunga Martin , Lewa Clement , Orindi Benedict , Bejon Philip , Ochola-Oyier Lynette Isabella 
Published: August 2022

AbstractCoronavirus Disease-2019 tests require a Nasopharyngeal (NP) and/or Oropharyngeal (OP) specimen from the upper airway, from which virus RNA is extracted and detected through quantitative reverse transcription-Polymerase Chain Reaction (qRT-PCR). The viability of the virus is maintained after collection by storing the NP/OP swabs in Viral Transport Media (VTM).We evaluated the performance of four transport media: locally manufactured (“REVITAL”) Viral Transport Media (RVTM), Standard Universal Transport Media (SUTM), PBS and 0.9% (w/v) NaCl (normal saline). We used laboratory cultured virus to evaluate: i) viral recovery and maintaining integrity at different time periods and temperatures; ii) stability in yielding detectable RNA consistently for all time points and conditions; and iii) their overall accuracy.Four vials of SARS-CoV-2 cultured virus (2 high and 2 low concentration samples) and 1 negative control sample were prepared for each media type (SUTM, RVTM, PBS and normal saline) and stored at the following temperatures, -80°C, 4°C, room temperature (25°C) and 37°C for 7 days. Viral Ribonucleic acid (RNA) extractions and qRT-PCR were done on the following days after inoculation with the cultured virus, days 1, 2, 3, 4 and 7 to assess virus stability and viral recovery.CT values fell over time at room temperature, but normal saline, PBS, RVTM and SUTM all showed comparable performance in maintaining virus integrity and stability allowing for the detection of SARS-CoV-2 viral RNA.Overall, this study demonstrated that normal saline, PBS and the locally manufactured VTM can be used for COVID-19 sample collection and testing, thus expanding the range of SARS-CoV-2 viral collection media.
Insurance for climate change and environmental risk: a bibliometric review
Authors: Nobanee Haitham , Dilshad Mehroz Nida , Abu Lamdi Omar , Ballool Bashaier , Al Dhaheri Saeed , AlMheiri Noura , Alyammahi Abdalla , Alhemeiri Sultan Salah 
Published: August 2022

Purpose
This study aims to examine the research output on climate change, environmental risks and insurance from 1986 to 2020, thereby revealing the development of the literature through collaborative networks. The relationship between insurance, climate change and environmental threats has gained research attention. This study describes the interaction between insurance, climate change and environmental risk.

Design/methodology/approach
This study is a bibliometric analysis of the literature and assessed the current state of science. A total of 97 academic papers from top-level journals listed in the Scopus database are shortlisted.

Findings
The understanding of climate change, environmental risks and insurance is shaped and enhanced through the collaborative network maps of researchers. Their reach expands across different networks, core themes and streams, as these topics develop.

Research limitations/implications
Data for this study were generated from English-written journal articles listed in the Scopus database only; subsequently, this study was representative of high-quality papers published in the areas of climate change, environmental risks and insurance.

Practical implications
The results of this study can be useful to academic researchers to aid their understanding of climate change, environmental risks and insurance research development, to identify the current context and to develop a future research agenda.

Social implications
The findings of this study can improve the understanding of industry practitioners about climate change and global warming challenges, and how insurance can be used as a tool to address such challenges.

Originality/value
This study is a novel attempt. To the best of the authors’ knowledge, this is one of the first studies to better understand climate change, environmental risks and insurance as a research topic by examining its evolution in an academic context through visualization, coupling and bibliometric analysis. This bibliometric study is unique in reviewing climate change literature and providing a future research agenda. Using bibliometric data, this study addressed the technical aspects and the value it adds to actual practice. Bibliometric indicators quantitatively and qualitatively evaluate emerging disciplinary progress in this topic.
Bolstering green supply chain integration via big data analytics capability: the moderating role of data-driven decision culture
Authors: Liu Yang , Fang Wei , Feng Taiwen , Gao Na 
Published: August 2022

PurposeBased on organizational information processing theory, this research explores how big data analytics capability (BDAC) contributes to green supply chain integration (GSCI) and the contingency role that data-driven decision culture plays.Design/methodology/approachUsing the two-wave survey data collected from 317 Chinese manufacturing firms, the authors validate the hypotheses.FindingsThe results show that big data managerial capability has positive impacts on three dimensions of GSCI, while big data technical capability has positive impacts on green internal and customer integration. Moreover, green internal integration mediates the impacts of big data technical capability and managerial capability on green supplier and customer integration. Finally, data-driven decision culture alleviates the positive impacts of big data technical and managerial capability on green internal integration.Practical implicationsThe findings suggest that firms can leverage big data technical and managerial capability to enhance information processing capability for achieving a higher degree of GSCI. Further, the critical role of data-driven decision culture in affecting the link between BDAC and GSCI should not be overlooked.Originality/valueThis research contributes to literature on green supply chain management by revealing the role of BDAC in improving GSCI.
Belief perseverance in students’ perceptions of accounting in a distance-learning environment: evidence from a GCC university
Authors: Elsayed Nader 
Published: August 2022

PurposeBy drawing on Belief Perseverance Theory (BPT), this study investigates the pre- and post-perceptions of the First Accounting Course (FAC) differentiating between accounting and non-accounting students in a virtual learning setting at a Gulf Cooperation Council (GCC) university, and explains why students' perceptions have formed.Design/methodology/approachAdopting a case study approach, this study employs quantitative (anonymous questionnaires) and qualitative (semi-structured interviews) methods.FindingsResponses from 142 financial accounting students indicate that non-accounting majors generally changed the students' perceptions significantly at the end of the semester, whereas students' accounting counterparts had relatively stable perceptions. This study also finds that a large number of non-accounting students perceived the benefits of taking the FAC and generally have less negative perceptions of the accounting profession, which supports the notion that non-accounting students evaluated discrediting information to reassess non-accounting students pre-established perceptions.Practical implicationsThis study has several implications as follows: for the accounting education literature on how FAC assists students in changing students' perceptions through the lens of BPT, for professional accounting bodies to find ways to promote accounting careers for students and for educators to increase students’ desire for accounting study and profession.Originality/valueThe findings from this study are expected to contribute to GCC society by providing clarifications towards increasing students’ desire for accounting studies and professions.
Cloud-based accounting information systems usage and its impact on Jordanian SMEs’ performance: the post-COVID-19 perspective
Authors: Al-Okaily Manaf , Alkhwaldi Abeer F. , Abdulmuhsin Amir A. , Alqudah Hamza , Al-Okaily Aws 
Published: August 2022

Purpose
The purpose of this study is to examine the factors influencing the usage of cloud-based accounting information systems (AIS) in the crisis era (i.e. the COVID-19 pandemic) by expanding the unified theory of acceptance and use of technology (UTAUT) with new related critical factors.

Design/methodology/approach
A quantitative research approach based on a cross-sectional online questionnaire was used for collecting empirical data from 438 potential and current users of cloud-based AIS. Structural equation modeling based on analysis of a moment structures 25.0 was applied in the data analysis.

Findings
The outcome of the structural path revealed that performance expectancy, social motivation, COVID-19 risk (COV-19 PR) and trust (TR) were significantly influencing users’ behavioral intention (BI) toward using cloud-based AIS and explained 71% of its variance. While, contrary to what is expected, the impact of effort expectancy and perceived security risk (SEC) on BI was insignificant. In addition, BI was revealed to influence the actual usage behaviors and explained 74% of its variance. The outcome factors: communication quality (CQ) and decision quality (DQ) were significantly influenced by the usage of cloud-based AIS.

Practical implications
The current research would be valuable for small- and medium-sized enterprises officials and policymakers to illustrate the relatively low rates of cloud-based AIS and formulate strategies to boost the acceptance and use of cloud-based AIS by Jordanian users, where cloud-based services are still deemed as an innovation.

Originality/value
To the best of the authors’ knowledge, the current study is the first academic paper that extends the UTAUT by integrating additional factors: TR, SEC and COV-19 PR. In addition to two outcome variables: CQ and DQ, to study the cloud-based AIS in the Jordanian setting beyond the COVID-19 pandemic. The current research contributes to the academic knowledge on information technology information system adoption by considering cloud accounting acceptance and use and integration into the work practices of users through the BIs and actual use of cloud-based AIS in Jordan.