bluuebunny/crossref_metadata_2025_split huggingface dataset:
CD3+T-cell: CD14+monocyte complexes are dynamic and increased with HIV and glucose intolerance
Authors: Obare Laventa M. , Simmons Joshua , Oakes Jared , Zhang Xiuqi , Nochowicz Cindy , Priest Stephen , Bailin Samuel S. , Warren Christopher M. , Mashayekhi Mona , Beasley Heather K. , Shao Jianqiang , Meenderink Leslie M. , Sheng Quanhu , Stolze Joey , Gangula Rama , Absi Tarek , Su Yan Ru , Neikirk Kit , Chopra Abha , Gabriel Curtis L. , Temu Tecla , Pakala Suman , Wilfong Erin M. , Gianella Sara , Phillips Elizabeth J. , Harrison David G. , Hinton Antentor , Kalams Spyros A. , Kirabo Annet , Mallal Simon A. , Koethe John R. , Wanjalla Celestine N. 
Published: April 2023

AbstractAn increased risk of cardiometabolic disease accompanies persistent systemic inflammation. Yet, the innate and adaptive immune system features in persons who develop these conditions remain poorly defined. Doublets, or cell-cell complexes, are routinely eliminated from flow cytometric and other immune phenotyping analyses, which limits our understanding of their relationship to disease states. Using well-characterized clinical cohorts, including participants with controlled HIV as a model for chronic inflammation and increased immune cell interactions, we show that circulating CD14+monocytes complexed to CD3+T cells are dynamic, biologically relevant, and increased in individuals with diabetes after adjusting for confounding factors. The complexes form functional immune synapses with increased expression of proinflammatory cytokines and greater glucose utilization. Furthermore, in persons with HIV, the CD3+T-cell: CD14+monocyte complexes had more HIV copies compared to matched CD14+monocytes or CD4+T cells alone. Our results demonstrate that circulating CD3+T-cell:CD14+monocyte pairs represent dynamic cellular interactions that may contribute to inflammation and cardiometabolic disease pathogenesis and may originate or be maintained, in part, by chronic viral infections. These findings provide a foundation for future studies investigating mechanisms linking T cell-monocyte cell-cell complexes to developing immune-mediated diseases, including HIV and diabetes.Abstract FigureHighlightsCirculating CD3+CD14+T cell-monocyte complexes are higher in individuals with diabetes.CD3+CD14+T cell-monocytes complexes comprise a heterogenous group of functional and dynamic cell-cell interactions.The proportion of CD3+CD14+T cell-monocyte complexes is positively associated with fasting blood glucose and negatively with plasma IL-10 levels and CD4+T regulatory cells.CD3+CD14+T cell-monocyte complexes are metabolically flexible and can utilize both glycolysis and oxidative phosphorylation for their energy requirements.In persons with treated HIV, CD3+CD14+T cell-monocytes have more detectable HIV DNA than circulating CD4+T cells alone.
REVEILLE2Thermosensitive Splicing: A Molecular Basis for the Integration of Nocturnal Temperature Information by the Arabidopsis Circadian Clock
Authors: James Allan B. , Sharples Chantal , Laird Janet , Armstrong Emily May , Guo Wenbin , Tzioutziou Nikoleta , Zhang Runxuan , Brown John W.S. , Nimmo Hugh G. , Jones Matthew A. 
Published: April 2023

SummaryCold stress is one of the major environmental factors that limit growth and yield of plants. However, it is still not fully understood how plants account for daily temperature fluctuations, nor how these temperature changes are integrated with other regulatory systems such as the circadian clock.We demonstrate that REVEILLE2, a MYB-like transcription factor, exhibits a cold-induced alternative splicing switch from a non-translatable isoform at ambient temperature to a translatable isoform upon cold exposure. We explore the biological function ofREVEILLE2using a combination of molecular genetics, transcriptomics, and physiology.Disruption of theREVEILLE2cooling switch alters regulatory gene expression, impairs circadian timing, and improves photosynthetic capacity. Changes in nuclear gene expression are particularly apparent in the initial hours following chilling, with chloroplast gene expression subsequently up-regulated.TheREVEILLE2cold switch extends our understanding of plants immediate response to cooling. We propose that the circadian componentREVEILLE2restricts plants responses to nocturnal reductions in temperature, thereby enabling appropriate responses to daily environmental changes.Plain language summaryPlants need to respond appropriately to temperature, accounting for the expected daily patterns of reduced temperatures that occur every night relative to the day. Here, we show that a gene expressed at night fulfils this function.
The ortholog of human REEP1-4 is required for autophagosomal enclosure of ER-phagy/nucleophagy cargos in fission yeast
Authors: Zou Chen-Xi , Ma Zhu-Hui , Jiang Zhao-Di , Pan Zhao-Qian , Xu Dan-Dan , Suo Fang , Shao Guang-Can , Dong Meng-Qiu , Du Li-Lin 
Published: April 2023

AbstractSelective macroautophagy of the endoplasmic reticulum (ER) and the nucleus, known as ER-phagy and nucleophagy respectively, are processes whose mechanisms remain inadequately understood. Through an imaging-based screen, we find that in the fission yeastSchizosaccharomyces pombe, Yep1 (also known as Hva22 or Rop1), the ortholog of human REEP1-4, is essential for ER-phagy and nucleophagy, but not for bulk autophagy. In the absence of Yep1, the initial phase of ER-phagy and nucleophagy proceeds normally, with the ER-phagy/nucleophagy receptor Epr1 co-assembling with Atg8. However, ER-phagy/nucleophagy cargos fail to reach the vacuole. Instead, nucleus- and cortical-ER-derived membrane structures not enclosed within autophagosomes accumulate in the cytoplasm. Intriguingly, the outer membranes of nucleus-derived structures remain continuous with the nuclear envelope-ER network, suggesting a possible outer membrane fission defect during cargo separation from source compartments. We find that the ER-phagy role of Yep1 relies on its abilities to self-interact and shape membranes, and requires its C-terminal amphipathic helices. Moreover, we show that human REEP1-4 and budding yeast Atg40 can functionally substitute for Yep1 in ER-phagy, and Atg40 is a divergent ortholog of Yep1 and REEP1-4. Our findings uncover an unexpected mechanism governing the autophagosomal enclosure of ER-phagy/nucleophagy cargos and shed new light on the functions and evolution of REEP family proteins.
Spatio-temporal X-linked gene reactivation and site-specific retention of epigenetic silencing in the mouse germline
Authors: Roidor Clara , Syx Laurène , Beyne Emmanuelle , Zielinski Dina , Teissandier Aurélie , Lee Caroline , Walter Marius , Servant Nicolas , Chebli Karim , Bourc’his Déborah , Surani M. Azim , Borensztein Maud 
Published: April 2023

AbstractRandom X-chromosome inactivation (XCI) is a hallmark of female mammalian somatic cells. This epigenetic mechanism, mediated by the long non-coding RNAXist, occurs in the epiblast and is stably maintained to ensure proper dosage compensation of X-linked genes during life. However, this silencing is lost during primordial germ cell (PGC) development. Using a combination of single-cell allele-specific RNA sequencing and low-input chromatin profiling in developingin vivoPGC, we provide unprecedented detailed maps of gene reactivation. We demonstrated that PGC still carry a fully silent X chromosome on embryonic day (E) 9.5, despite the loss ofXistexpression. X-linked genes are then gradually reactivated outside theXistfirst-bound regions. At E12.5, a significant part of the inactive X chromosome (Xi) still resists reactivation, carrying an epigenetic memory of its silencing. Late-reactivated genes are enriched in repressive chromatin marks, including DNA methylation and H3K27me3 marks. Our results define the timing of reactivation of the silent X chromosome a key event in female PGC reprogramming with direct implications for reproduction.
Annelid adult cell type diversity and their pluripotent cellular origins
Authors: Álvarez-Campos Patricia , García-Castro Helena , Emili Elena , Pérez-Posada Alberto , Salamanca-Díaz David A. , Mason Vincent , Metzger Bria , Bely Alexandra E. , Kenny Nathan , Özpolat B. Duygu , Solana Jordi 
Published: April 2023

AbstractAnnelids are a broadly distributed, highly diverse, economically and environmentally important group of animals. Most species can regenerate missing body parts, and many are able to reproduce asexually. Therefore, many annelids can generate all adult cell types in adult stages. However, the putative adult stem cell populations involved in these processes, as well as the diversity of adult cell types generated by them, are still unknown. Here, we recover 75,218 single cell transcriptomes ofPristina leidyi, a highly regenerative and asexually-reproducing freshwater annelid. We characterise all major annelid adult cell types, and validate many of our observations by HCRin situhybridisation. Our results uncover complex patterns of regionally expressed genes in the annelid gut, as well as neuronal, muscle and epidermal specific genes. We also characterise annelid-specific cell types such as the chaetal sacs andglobin+ cells, and novel cell types of enigmatic affinity, including avigilin+ cell type, alumbrokinase+ cell type, and a diverse set of metabolic cells. Moreover, we characterise transcription factors and gene networks that are expressed specifically in these populations. Finally, we uncover a broadly abundant cluster of putative stem cells with a pluripotent signature. This population expresses well-known stem cell markers such asvasa, piwiandnanoshomologues, but also shows heterogeneous expression of differentiated cell markers and their transcription factors. In thesepiwi+ cells, we also find conserved expression of pluripotency regulators, including multiple chromatin remodelling and epigenetic factors. Finally, lineage reconstruction analyses reveal the existence of differentiation trajectories frompiwi+ cells to diverse adult types. Our data reveal the cell type diversity of adult annelids for the first time and serve as a resource for studying annelid cell types and their evolution. On the other hand, our characterisation of apiwi+cell population with a pluripotent stem cell signature will serve as a platform for the study of annelid stem cells and their role in regeneration.
De Novo Design of κ-Opioid Receptor Antagonists Using a Generative Deep Learning Framework
Authors: Salas-Estrada Leslie , Provasi Davide , Qui Xing , Kaniskan H. Ümit , Huang Xi-Ping , DiBerto Jeffrey F. , Ribeiro João Marcelo Lamim , Jin Jian , Roth Bryan L. , Filizola Marta 
Published: April 2023

ABSTRACTLikely effective pharmacological interventions for the treatment of opioid addiction include attempts to attenuate brain reward deficits during periods of abstinence. Pharmacological blockade of the κ-opioid receptor (KOR) has been shown to abolish brain reward deficits in rodents during withdrawal, as well as to reduce the escalation of opioid use in rats with extended access to opioids. Although KOR antagonists represent promising candidates for the treatment of opioid addiction, very few potent selective KOR antagonists are known to date and most of them exhibit significant safety concerns. Here, we used a generative deep learning framework for thede novodesign of chemotypes with putative KOR antagonistic activity. Molecules generated by models trained with this framework were prioritized for chemical synthesis based on their predicted optimal interactions with the receptor. Our models and proposed training protocol were experimentally validated by binding and functional assays.
Genomic characterization of a pandrug-resistantKlebsiella pneumoniaebelonging to the high-risk ST11 in the Brazilian Amazon region
Authors: Fonseca Érica L. , Morgado Sérgio M. , Freitas Fernanda S. , Bighi Nathalia S. , Cipriano Rosângela , Vicente Ana Carolina P. 
Published: April 2023

ABSTRACTPandrug-resistant (PDR)K. pneumoniaehas been reported sporadically in many countries and remains rare in Brazil. The lack of genomic studies limits the comprehension of the determinants mostly involved with the PDR emergence inK. pneumoniae. This study aimed to unravel the main genetic determinants involved with the PDR background of a clinical ST11K. pneumoniaerecovered in the Brazilian Amazon region. The carbapenem-resistant Kp196 was submitted to WGS and its intrinsic and acquired resistome was assessed by CARD and comparison with wild-type genes. Kp196 resistome was composed of acquired resistance determinants and mutations in chromosomal genes. Among the formers,blaCTX-M-15andblaNDM-1,blaOXA-9,blaOXA-1,aadA1, aacA4, strAB, aph(3’)-VI, aac(3)-IId, qnrS1, qnrB1, oqxAB, dfrA14, sul2, catB3were found in the vicinity of mobile genetic elements, which could contribute to their spread. Kp196 colistin resistance was multifactorial and attributed to modifications in ArnT (M114L/V117I/R372K), PhoQ (D150G), and themgrBdisruption by ISKpn25. Besides the presence ofqnrandoqxABgenes, Kp196 also presented altered GyrA (S83I) and ParC (S80I). Anin-blockdeletion in the repressor RamR, contributing toacrABoverexpression, and the presence of an enhanced-function AcrB variant (S966A), probably led to the Kp196 multidrug and tigecycline resistance. Insertions,in-blockdeletion, and missense mutations were involved withompK35-36-37inactivation, also accounting for the Kp196 multidrug resistance, including carbapenems. The Kp196 PDR profile, especially the carbapenem resistance, was due to the accumulation of different mechanisms, in which modifications in housekeeping genes accounted for a more stable resistome.
Intranasal VLP-RBD vaccine adjuvanted with BECC470 confers immunity against Delta SARS-CoV-2 challenge in K18-hACE2-mice
Authors: Lee Katherine S , Rader Nathaniel A , Miller Olivia A , Cooper Melissa , Wong Ting Y , Amin Md. Shahrier , Barbier Mariette , Bevere Justin R , Ernst Robert K , Damron F. Heath 
Published: April 2023

AbstractAs the COVID-19 pandemic transitions to endemic, seasonal boosters are a plausible reality across the globe. We hypothesize that intranasal vaccines can provide better protection against asymptomatic infections and more transmissible variants of SARS-CoV-2. To formulate a protective intranasal vaccine, we utilized a VLP-based platform. Hepatitis B surface antigen- based virus like particles (VLP) linked with receptor binding domain (RBD) antigen were paired with the TLR4-based agonist adjuvant, BECC 470. K18-hACE2 mice were primed and boosted at four-week intervals with either VLP-RBD-BECC or mRNA-1273. Both VLP-RBD-BECC and mRNA-1273 vaccination resulted in production of RBD-specific IgA antibodies in serum. RBD- specific IgA was also detected in the nasal wash and lung supernatants and were highest in VLP-RBD-BECC vaccinated mice. Interestingly, VLP-RBD-BECC vaccinated mice showed slightly lower levels of pre-challenge IgG responses, decreased RBD-ACE2 binding inhibition, and lower neutralizing activityin vitrothan mRNA-1273 vaccinated mice. Both VLP-RBD-BECC and mRNA-1273 vaccinated mice were protected against challenge with a lethal dose of Delta variant SARS-CoV-2. Both vaccines limited viral replication and viral RNA burden in the lungs of mice. CXCL10 is a biomarker of severe SARS-CoV-2 infection and we observed both vaccines limited expression of serum and lung CXCL10. Strikingly, VLP-RBD-BECC when administered intranasally, limited lung inflammation at early timepoints that mRNA-1273 vaccination did not. VLP-RBD-BECC immunization elicited antibodies that do recognize SARS-CoV-2 Omicron variant. However, VLP-RBD-BECC immunized mice were protected from Omicron challenge with low viral burden. Conversely, mRNA-1273 immunized mice had low to no detectable virus in the lungs at day 2. Together, these data suggest that VLP-based vaccines paired with BECC adjuvant can be used to induce protective mucosal and systemic responses against SARS- CoV-2.
The frequency of mutations in thepenA,mtrR,gyrA andparC genes ofNeisseria gonorrhoeae, the presence oftetM gene and antibiotic resistance/susceptibility: a systematic review and meta-analyses
Authors: Mendes Ana Clara , de Souza Renan Pedra , Bahia Diana 
Published: April 2023

ABSTRACTSexually transmitted infections (STIs) are a major global public health problem and among the most common infectious diseases. Gonorrhoea is an STI that affects only humans, caused by the bacteriumNeisseria gonorrhoeae. In 2016, the WHO estimated that there were 86.9 million cases of gonorrhoea worldwide. Gonorrhoea is currently one of the most important STIs due to the increased spread and emergence of multiresistant strains. The main goal of this study was to analyse the relationship between resistance or decreased susceptibility to antibiotics inN. gonorrhoeaeand the presence of mutations in the genespenA,mtrR,tetM,gyrA andparC. Therefore, we conducted a systematic review following the PRISMA guidelines. We selected 19 studies for thepenA gene, 23 forgyrA andparC, 18 formtrR, and 12 fortetM using the Science Direct and PubMed databases. The included studies addressed susceptibility and resistance to antibiotics and mutations in the selected genes. Then, 21 different meta-analyses of the studies were performed. A meta-analysis was conducted when two or more studies were found for the same gene and the same antibiotic. Meta-analyses of isolates resistant to penicillin, cefixime, and ceftriaxone showed that more than 50% of the isolates had mutations in the genespenA andmtrR. Meanwhile, more than 50% of azithromycin-resistant isolates had mutations in themtrR gene, while more than 50% of the isolates resistant and intermediate-resistant to ciprofloxacin had mutations ingyrA. Moreover, less than 50% of isolates with intermediate resistance to ciprofloxacin had mutations inparC. The plasmid containing thetetM gene was found in more than 50% of tetracycline-resistant isolates. Infection monitoring and genetic studies are important to control the spread, which can improve the quality of life of infected individuals and lessen the financial burden on public healthcare systems.
Gender diversity, financial performance, and the moderating effect of CSR: empirical evidence from UK financial institutions
Authors: Ben Fatma Hanen , Chouaibi Jamel 
Published: April 2023

Purpose
This study aims to examine the direct relationship between board gender diversity (BGD) and financial performance and the moderating role of corporate social responsibility (CSR) in the said relationship.

Design/methodology/approach
Using data collected from the Thomson Reuters Eikon ASSET4 database from 42 UK financial institutions listed in the ESG index for the period 2005–2019, this study used multivariate regression analysis on panel data to test the effect of BGD on financial performance and estimate the moderating effect of CSR between them. Moreover, to control the endogeneity problem, the authors conducted an additional analysis by testing the dynamic dimension of the data set through the generalized moment method.

Findings
The empirical results show that BGD is positively related to financial performance and that BGD increases firm performance with the moderating effect of CSR. Regarding the endogeneity problem, the existence of continuity between financial institution performances over time is demonstrated.

Research limitations/implications
The current paper sheds light on the importance of BGD in improving firm performance and the moderating role of CSR in strengthening the relationship between BGD and firm performance, thereby contributing to the agency theory, the resource dependency theory and the stakeholder theory. Therefore, regulators and policymakers in the UK can use the outcomes of this study to enforce the representation of female directors on boards to enhance the financial performance of financial institutions. Moreover, the findings could be useful for regulatory bodies to encourage financial institutions to practice CSR activities and disclose them in their annual reports.

Originality/value
To the best of the authors’ knowledge, this is the first study investigating the moderating role of CSR on the relationship between BGD and financial performance in the context of the financial sector. It is also the first study documenting that CSR reinforces the relationship between gender-diverse boards and financial institutions' performance. This study fills a research gap as it expands the existing literature that has generally focused on the impact of BGD on financial performance and has not reached similar results.
Exploring the topic structure and evolutionary trends of health informatics research in library and information science
Authors: Tian Peilin , Wang Le 
Published: April 2023

Purpose
This study aims to reveal the topic structure and evolutionary trends of health informatics research in library and information science.

Design/methodology/approach
Using publications in Web of Science core collection, this study combines informetrics and content analysis to reveal the topic structure and evolutionary trends of health informatics research in library and information science. The analyses are conducted by Pajek, VOSviewer and Gephi.

Findings
The health informatics research in library and information science can be divided into five subcommunities: health information needs and seeking behavior, application of bibliometrics in medicine, health information literacy, health information in social media and electronic health records. Research on health information literacy and health information in social media is the core of research. Most topics had a clear and continuous evolutionary venation. In the future, health information literacy and health information in social media will tend to be the mainstream. There is room for systematic development of research on health information needs and seeking behavior.

Originality/value
To the best of the authors’ knowledge, this is the first study to analyze the topic structure and evolutionary trends of health informatics research based on the perspective of library and information science. This study helps identify the concerns and contributions of library and information science to health informatics research and provides compelling evidence for researchers to understand the current state of research.
The efficiency measurement of business intelligence systems in the big data-driven economy: a multidimensional model
Authors: Al-Okaily Aws , Teoh Ai Ping , Al-Okaily Manaf , Iranmanesh Mohammad , Al-Betar Mohammed Azmi 
Published: April 2023

PurposeThere is a growing importance of business intelligence systems (BIS) adoption in today’s digital economy age which is characterized by uncertainty and ambiguity considering the magnitude and influence of data-related issues to be solved in contemporary businesses. This study aims to investigate critical success factors that affect business intelligence efficiency based on the DeLone and McLean model in Jordanian banking industry.Design/methodology/approachA quantitative research method through a questionnaire was used to collect data from actual users who depend on business intelligence tools to make operational and strategic decisions in Jordanian banks. The data obtained were tested using the partial least squares–structural equation modeling approach.FindingsThe survey findings attest that system quality, information quality, user quality, user satisfaction and user performance are important factors and contribute to business intelligence efficiency in the Jordanian banking industry.Practical implicationsThe findings gained from this work can help policymakers in Jordanian banks to improve the business intelligence success and organizational performance.Originality/valueTo the best of the authors’ knowledge, this study is the first of its kind to propose a theoretical model to assess drivers of BIS efficiency from the Jordanian banks’ perspective.