bluuebunny/crossref_metadata_2025_split huggingface dataset:
The GEN-ERA toolbox: unified and reproducible workflows for research in microbial genomics
Authors: Cornet Luc , Durieu Benoit , Baert Frederik , D’hooge Elizabet , Colignon David , Meunier Loic , Lupo Valérian , Cleenwerck Ilse , Daniel Heide-Marie , Rigouts Leen , Sirjacobs Damien , Declerck Stéphane , Vandamme Peter , Wilmotte Annick , Baurain Denis , Becker Pierre 
Published: October 2022

AbstractBackgroundMicrobial culture collections play a key role in taxonomy by studying the diversity of their accessions and providing well characterized strains to the scientific community for fundamental and applied research. These microbial resource centers thus need to implement new standards in species delineation, including whole-genome sequencing and phylogenomics. In this context, the genomic needs of the Belgian Coordinated Collections of Microorganisms (BCCM) were studied, resulting in the GEN-ERA toolbox. The latter is a unified cluster of bioinformatic workflows dedicated to both bacteria and small eukaryotes (i.e. yeasts).FindingsThis public toolbox allows researchers without a specific training in bioinformatics to perform robust phylogenetic analyses. Hence, it facilitates all steps from genome downloading and quality assessment, including genomic contamination estimation, to tree reconstruction. It also offers workflows for average nucleotide identity comparisons and metabolic modeling.Technical detailsNextflow workflows are launched by a single command and are available on the GEN-ERA GitHub repository (https://github.com/Lcornet/GENERA). All the workflows are based on Singularity containers to increase reproducibility.TestingThe toolbox was developed for a diversity of microorganisms, including bacteria and fungi. It was further tested on an empirical dataset of 18 (meta)genomes of early-branching Cyanobacteria, providing the most up-to-date phylogenomic analysis of theGloeobacteralesorder, the first group to diverge in the evolutionary tree of Cyanobacteria.ConclusionThe GEN-ERA toolbox can be used to infer completely reproducible comparative genomic and metabolic analyses on prokaryotes and small eukaryotes. Although designed for routine bioinformatics of culture collections, it can also be useful for other applications, as shown by our case study onGloeobacterales.
Integrated assessment of structure and dynamics of solid proteins
Authors: Söldner Benedikt , Grohe Kristof , Neidig Peter , Auch Jelena , Blach Sebastian , Klein Alexander , Vasa Suresh K. , Schäfer Lars V. , Linser Rasmus 
Published: October 2022

AbstractUnderstanding macromolecular function, interactions and stability hinges on detailed assessment of conformational ensembles. For solid proteins, accurate elucidation of the spatial aspects of dynamics at physiological temperatures are limited by the qualitative character or low abundance of solid-state NMR internuclear distance information. Here, we demonstrate access to abundant proton-proton internuclear distances for integrated structural biology and chemistry with unprecedented accuracy. Apart from highest-resolution single-state structures, the exact distances enable molecular dynamics (MD) ensemble simulations orchestrated by a dense network of experimental inter-proton distance boundaries gathered in the context of their physical lattices. This direct embedding of experimental ensemble distances into MD will provide access to representative, atomic-level spatial details of conformational dynamics in supramolecular assemblies, crystalline and lipid-embedded proteins, and beyond.
Naturally occurring Alzheimer’s disease in rhesus monkeys
Authors: Li Zhenhui , He Xiaping , Wu Shihao , Huang Rongyao , Li Hao , Wang Zhengbo , Wang Limin , Qin Dongdong , Kong Yu , Guo Yingqi , Ma Xia , Turck Christoph W. , Xiong Zhiqi , Wang Wenchao , Hu Xintian 
Published: October 2022

AbstractAlzheimer’s disease (AD) is the most common neurodegenerative disease. To date, its cause is unclear and there are no effective treatments or preventive measures. Despite there are accumulating evidences for the existence of AD pathological hallmarks in the brain of aging rhesus monkeys, it remains a mainstream notion that monkeys do not develop AD naturally. This is an important issue because it will determine how we use monkeys in AD studies. To settle down this issue, a group (n=10) of aged rhesus monkeys 26 years old or above went through a systematic AD screening procedure in this study. Three of these monkeys showed severe memory impairments (SMI) after evaluated with a classic working memory test. Further behavioral testing revealed that the SMI monkeys also exhibited apathy-like behavior, which is another core AD clinical symptom. In addition to the cognitive deficits, two of the three SMI monkeys developed all of the three AD pathological hallmarks, including neurofibrillary tangles, senile plaques and neuronal loss. According to the diagnostic criteria of human AD, the two SMI monkeys were clearly naturally occurring AD monkeys. These results suggest that AD is not a uniquely human disease and monkeys have great potential for the development of much needed etiological AD models, which are vital for better understanding of developmental process of AD and the base of identification of early diagnostic biomarkers and effective therapeutic targets of AD.
Short-range interactions between fibrocytes and CD8+T cells in COPD bronchial inflammatory response
Authors: Eyraud Edmée , Maurat Elise , Sac-Epée Jean-Marc , Henrot Pauline , Zysman Maeva , Esteves Pauline , Trian Thomas , Dupuy Jean-William , Leipold Alexander , Saliba Antoine-Emmanuel , Bégueret Hugues , Girodet Pierre-Oliver , Thumerel Matthieu , Hustache-Castaing Romain , Marthan Roger , Levet Florian , Vallois Pierre , Contin-Bordes Cécile , Berger Patrick , Dupin Isabelle 
Published: October 2022

AbstractBronchi of chronic obstructive pulmonary disease (COPD) are the site of extensive cell infiltration, allowing persistent contacts between resident cells and immune cells. Tissue fibrocytes interaction with CD8+T cells and its consequences were investigated using a combination ofin situ,in vitroexperiments and mathematical modeling. We show that fibrocytes and CD8+T cells are found in vicinity in distal airways and that potential interactions are more frequent in tissues from COPD patients compared to those of control subjects. Increased proximity and clusterization between CD8+T cells and fibrocytes are associated with altered lung function. Tissular CD8+T cells from COPD patients promote fibrocyte chemotaxis via the CXCL8-CXCR1/2 axis. Live imaging shows that CD8+T cells establish short-term interactions with fibrocytes, that trigger CD8+T cell proliferation in a CD54– and CD86-dependent manner, pro-inflammatory cytokines production, CD8+T cell cytotoxic activity against bronchial epithelial cells and fibrocyte immunomodulatory properties. We defined a computational model describing these intercellular interactions and calibrated the parameters based on our experimental measurements. We show the model’s ability to reproduce histological ex vivo characteristics, and observe an important contribution of fibrocyte-mediated CD8+T cell proliferation in COPD development. Using the model to test therapeutic scenarios, we predict a recovery time of several years, and the failure of targeting chemotaxis or interacting processes. Altogether, our study reveals that local interactions between fibrocytes and CD8+T cells could jeopardize the balance between protective immunity and chronic inflammation in bronchi of COPD patients.
Genome-wide identification and analysis of analysis of BURP genes inTriticum aestivum
Authors: Zhu Wengen 
Published: October 2022

AbstractPlant-specific BURP genes are involved in most aspects of plant development and in diverse stress responses. However, there has been no comprehensive and systematic research on the wheat (Triticum aestivumL.) BURP gene family. We comprehensively identified 54 BURP genes in wheat and 12, 23, and 32 BURP genes, respectively, in its three progenitor species,Triticum urartu, Aegilops tauschii,andTriticum dicoccoides. By phylogenetic analysis, we classified the wheat BURP genes into five subfamilies: BURP VI, BURP VII, RD22-like, PG1β-like, and the newly defined BURP VIII. BURP genes were distributed unevenly on 20 chromosomes, and 33 (61%) were anchored in the distal chromosome segments. Analysis of gene duplication events showed that segmental duplication was the main contributor to the expansion of this gene family in wheat. Assessment of tissue-specific and stress-induced expression indicated that most BURP members are heavily involved in plant development and responses to various stress conditions. RNA-seq data revealed tenTaBURPgenes expressed specifically in spikes.
Structural and functional basis of the universal transcription factor NusG pro-pausing activity inMycobacterium tuberculosis
Authors: Delbeau Madeleine , Omollo Expery O. , Froom Ruby , Koh Steven , Mooney Rachel A. , Lilic Mirjana , Brewer Joshua J. , Rock Jeremy , Darst Seth A. , Campbell Elizabeth A. , Landick Robert 
Published: October 2022

ABSTRACTTranscriptional pauses mediate regulation of RNA biogenesis. DNA-encoded pause signals trigger elemental pausing by stabilizing a half-translocated (RNA-not-DNA) state and by promoting RNAP swiveling that other factors can enhance. The universal transcription factor NusG (Spt5 in eukaryotes and archaea) N-terminal domain (NGN) modulates pausing through contacts to RNAP and DNA. Pro-pausing NusGs (e.g.,Bacillus subtilis) enhance some pauses whereas anti-pausing NusGs (e.g.,Escherichia coli) suppress some pauses. Little is known about pausing and NusG in the human pathogenMycobacterium tuberculosis (Mtb). Using biochemistry and cryo-electron microscopy, we show thatMtbNusG is a pro-pausing NusG that captures paused, swiveled RNAP by contacts to the RNAP protrusion and to a nontemplate strand–DNA wedge inserted between the NGN and the RNAP gate loop. On the other hand, we find that anti-pausingE. coliNGN contacts the RNAP gate loop to inhibit swiveling and pausing ofMtbRNAP. Using CRISPR-mediated mycobacterial genetics, we show that a pro-pausing NGN is required to support robust mycobacterial growth. Our results define an essential function of NusG in mycobacteria and the structural basis of pro-vs. anti-pausing NusG activity with broad implications for NusG function in all domains of life.
T cell subsets in chronic hepatitis C patients genotype 4 who achieved SVR following DAAs Therapy
Authors: Shiha Gamal , Soliman Reham , Hassan Ayman A , Mikhail Nabiel NH , Nabil Ahmed , Saleh Laila M , Sayed Doaa A , Eslam Mohamed 
Published: October 2022

AbstractBackgroundT cells are the primary effector cells that mediate viral clearance in spontaneous recovery from HCV infection and T cell dysfunction is a hallmark of progression to chronic HCV infection.Material and methodsThis study included 49 well charcterised HCV genotype 4-infected patients at Egyptian Liver Research Institute and Hospital (ELRIAH), Mansoura, Egypt, who were enrolled to receive direct acting antiviral therapy for hepatitis C. Immuno-phenotyping was performed to assess the expression of multiple T cell lineage, activation and inhibitory receptors. This was done before treatment, during treatment, at end of treatment and one year after treatment. 50 patients were also enrolled as control.ResultsOur data showed, significant increase in the percentages of CD8+ cells as compared to control group. The percentages of PD-1 expression on the CD8+ T-cell population were signifecntly elevated in patients before treatment (p<0.001). Significant increase in Treg (CD4+CD25hFoxP3+) subsets was noticed in comparison with control pateints.The expression of the inhibitory and activated markers in CD8+ T-cells was markedly reduced but more obvios in exhausted cytotoxic T cells compared to baseline finding (p<0.001). exhausted (PD1+CD8+) T-cells from HCV+ individuals reduced markedly after 4 weeks of DAA therapy (by 3 folds, p <0.001). Intereatingly it started to increase gradually again at the end of treatment and after 1 year but the increase doesn’t reach levels noticed in healthy control subjects.ConclusionUnderstanding the mechanisms of immune dysfunction and barriers to immune restoration after HCV cure will aid in better understanding of the remaining negative long-term health outcomes for HCV patients and the possibility of HCC development.
Treatment of non-alcoholic steatohepatitis with recombinant Orosomucoid 2, an acute phase protein that attenuates the Erk1/2-PPARγ-Cd36 signaling pathway
Authors: Li Li , Sun Haoming , Chen Jionghao , Ding Cong , Yang Xiaojun , Han Hua , Sun Qingzhu 
Published: October 2022

SummaryTherapeutic administration of recombinant proteins has been used for the treatment of various diseases in multiple studies. Herein, we investigated the function of the acute phase protein Orosomucoid 2 (Orm2), which is mainly secreted by hepatocytes, and evaluated its potential as a therapeutic strategy for non-alcoholic fatty liver disease (NAFLD) and non-alcoholic steatohepatitis (NASH). We here revealed that a high expression of Orm2 protected mice from high-fat diet (HFD)-induced obesity. The pharmacological administration of recombinant ORM2 protein attenuated hepatic steatosis, inflammation, hepatocyte injury, and fibrosis in mouse livers, which suffered NAFLD and NASH under dietary challenge conditions. Orm2 knockout mice spontaneously underwent obese after 16 weeks under normal diet. Orm2 deficiency exacerbated HFD-induced steatosis, steatohepatitis, and fibrosis in mice. Mechanistically, the deletion of Orm2 led to the activation of the Erk1/2-PPARγ-Cd36 signaling pathway, which in turn increased fatty acid uptake and absorption in hepatocytes and mice. Collectively, our results provide Orm2 is an essential factor for preventing NASH and associated NAFLD under obesity.
Cultivation of widespreadBathyarchaeiareveals a novel methyltransferase system utilizing lignin-derived aromatics
Authors: Yu Tiantian , Hu Haining , Zeng Xianhong , Wang Yinzhao , Pan Donald , Wang Fengping 
Published: October 2022

AbstractAnaerobic lignin degradation is a major process in the global carbon cycle that would significantly influence estimates of carbon flux in both terrestrial and marine ecosystems. The ubiquitousBathyarchaeia, one of the most abundant taxa in marine sediments, have been proposed to be key players in this process. However, the mechanism of Bathyarchaeial lignin degradation is unclear due to the lack of cultured strains. Here we report the cultivation of CandidatusMarisediminiarchaeum ligniniphilusDL1YTT001, a Bathyarchaeial representative from nearshore marine sediments that can grow with lignin as the sole organic carbon source under mesophilic and anaerobic conditions. Strain DL1YTT001 possesses and highly expresses a novel and specific methyltransferase system for O-demethylation of lignin-derived methoxylated aromatic compounds (ArOCH3). The key gene, methyltransferase 1 (MtgB), is not homologous to any other lineages. Enzymatic activity was confirmed through the heterologous expression of the MtgB gene, showing O-demethylation activity with guaiacol as the substrate. Considering that Bathyarchaeial lineages carrying this specific methyltransferase system are widely distributed in diverse anoxic environments, especially lignin-rich nearshore sediments,Bathyarchaeia-mediated O-demethylation is likely a key step in global anaerobic lignin remineralization.
Early life low-calorie sweetener consumption impacts energy balance during adulthood
Authors: Hayes Anna M.R. , Tsan Linda , Kao Alicia E. , Schwartz Grace M. , Décarie-Spain Léa , Lauer Logan Tierno , Klug Molly E. , Schier Lindsey A. , Kanoski Scott E. 
Published: October 2022

AbstractChildren frequently consume beverages sweetened with either sugars (sugar-sweetened beverages; SSB) or low-calorie sweeteners (LCS). Here we evaluated the effects of habitual early life consumption of either SSB or LCS on energy balance later during adulthood. Male and female rats were provided with chow, water, and a solution containing either SSB (sucrose), LCS [acesulfame potassium (ACE-K) or stevia], or control (no solution) during the juvenile and adolescent periods (postnatal days 26-70). SSB or LCS consumption was voluntary and restricted within federal recommended daily limits. When subsequently maintained on a cafeteria-style junk food diet (CAF; various high-fat, high-sugar foods) during adulthood, ACE-K-exposed rats demonstrated reduced caloric consumption vs. controls, which contributed to lower body weights in female but not male ACE-K rats. These discrepant intake and body weight effects in male ACE-K rats are likely based on reduced gene expression of thermogenic indicators (UCP1, BMP8B) in brown adipose tissue. Female stevia-exposed rats did not differ from controls in caloric intake or body weight, yet they consumed more SSB during adult CAF exposure. No SSB-exposed rats, neither male nor female, differed from controls in adult total caloric consumption or body weight measures. Collective results reveal that early life LCS consumption alters sugar preference, body weight, and gene expression for markers of thermogenesis during adulthood, with both sex- and sweetener-dependent effects.
Saliva-based COVID-19 Rapid Antigen Test: a practical and accurate alternative mass screening method
Authors: Diawara Idrissa , Ahid Samir , Jeddane Leïla , Kim Soyoun , Nejjari Chakib 
Published: October 2022

ABSTRACTAs SARS-CoV-2 and its variants continue to spread, a reliable and convenient alternative to nasopharyngeal swabbing and RT-PCR testing is needed. To test the usability and performance of saliva sample collection, saliva, nasal and nasopharyngeal swab specimens were collected from a total of 338 individuals consisting of confirmed COVID-19 patients and healthy subjects. To evaluate the diagnostic accuracy of self-collected and performed SARS-CoV-2 rapid antigen test on saliva and nasal swabs specimens, we compared its performance to nasopharyngeal swab specimen RT-PCR as a comparator test. In saliva specimens, the positive percent agreement was 90.14%, and the negative percent agreement was 99.61%, while in nasal swab specimens, the positive percent agreement was 91.55%, and the negative percent agreement was 100%, both meeting the sensitivity and specificity criteria required by the FDA. Therefore, when considering both the reliability and convenience of testing, we found saliva testing to be the better method for large-scale and frequent self-testing.
Quartet protein reference materials and datasets for multi-platform assessment of label-free proteomics
Authors: Tian Sha , Zhan Dongdong , Yu Ying , Liu Mingwei , Wang Yunzhi , Song Lei , Qin Zhaoyu , Li Xianju , Liu Yang , Li Yao , Ji Shuhui , Li Yan , Li Lingling , Wang Shanshan ,   Proteomic Massive Analysis and Quality Control Consortium, Zheng Yuanting , He Fuchu , Qin Jun , Ding Chen 
Published: October 2022

AbstractQuantitative proteomics is an indispensable tool in life science research. However, there is a lack of reference materials for evaluating the reproducibility of label-free liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based measurements among different instruments and laboratories. We developed the Quartet as a proteome reference material with built-in truths, and distributed the same aliquots to 15 laboratories with nine conventional LC-MS/MS platforms across six cities in China. Relative abundance of over 12,000 proteins on 816 MS files were obtained and compared for reproducibility among the instruments and laboratories to ultimately generate proteomics benchmark datasets. There was a wide dynamic range of proteomes spanning ~7 orders of magnitude (101–108copies/cell), and the injection order had marked effects on quantitative instead of qualitative. Overall, the Quartet offers valuable standard materials and data resources for improving the quality control of proteomic analyses as well as the reproducibility and reliability of research findings.
Measuring the current state-of-the-art in lean healthcare literature from the lenses of bibliometric indicators
Authors: Santos Ana Carla de Souza Gomes dos , Reis Augusto da Cunha , Souza Cristina Gomes de , Santos Igor Leão , Ferreira Letícia Ali Figueiredo , Senna Pedro 
Published: October 2022

PurposeLean healthcare (LHC) applies lean philosophy in the healthcare sector to promote a culture of continuous improvement through the elimination of non-value-added activities. Studies on the subject can be classified as conceptual (theoretical) or analytical (applied). Therefore, this research compares bibliometric indicators between conceptual and analytical articles on LHC.Design/methodology/approachFor data collection, the PRISMA Protocol was employed, and 488 articles published from 2009 to 2021, indexed in the Scopus and WoS databases, were retrieved.FindingsThis study reveals how conceptual and analytical LHC studies are organized in terms of the most relevant journals, articles, institutions, countries, the total number of citations, collaboration networks (co-authorship, international collaboration network and institutional collaboration network) and main co-words.Originality/valueOnly four papers conducting bibliometric analysis on LHC studies were identified in the Scopus and Web of Science databases. In addition, none of these papers compared conceptual and analytical bibliometric indicators to reveal the evolution, organization and trends of each category. Therefore, this work is not only the first to make this comparison but also the first to analyze the collaboration between authors, institutions and countries in relation to studies on LHC. The analyses performed in this work allow one new possible understanding, by researchers and health professionals, of the literature behavior in this field of study.
Google SEO score and accessibility rank on the American University Libraries’ websites: one comparative analysis
Authors: Tavosi Maryam , Naghshineh Nader 
Published: October 2022

Purpose
This study aims to present a comparative study of university library websites (in the USA) from the standpoint of “Google SEO” and “Accessibility”. Furthermore, correlation analysis between these two done.

Design/methodology/approach
By opting for a webometric approach, the present study analyzed university library websites in the USA. The Lighthouse add-on for the Google Chrome browser has been used as a data collection tool, by writing and implementing a computer program in Bash language automatically (May 2020). Data analysis tools used were “Libre-Office-Calc”, “SPSS22” and “Excel”.

Findings
In all 81 university library websites in the USA, Google search engine optimization (SEO) scores have been observed the amount higher than 60 (Total Score = 100). The accessibility rank obtained lay between 0.56 and 1 (Total Score = 1). A weak correlation relationship between “SEO score” and “accessibility rank” (P-value = 0.02, Spearman Correlation Coefficient = 0.345) was observed. This weak relationship can be explained due to the impact of several components affecting Google’s SEO score, one of them being having a high “accessibility rank”.

Practical implications
Given the increasing automation of library processes, SEO tools can help libraries in achieving their digital marketing goals.

Originality/value
Accurate measurement of the Google SEO score and accessibility rank for the university library websites (in the USA) were obtained by Lighthouse add-on for Google Chrome browser. Moreover, data extraction by the implementation of one program computer without the direct observation of human resources is the innovation of this study.