bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dysregulation of innate cell types in the hepatic immune microenvironment of alcoholic liver cirrhosis
Authors: Ren Ao , He Wenjing , Rao Jiawei , Ye Dongmei , Cheng Pengrui , Jian Qian , Fu Zongli , Zhang Xuzhi , Deng Ronghai , Gao Yifang , Ma Yi 
Published: February 2023

IntroductionThe risk of alcoholic cirrhosis increases in a dose- and time-dependent manner with alcohol consumption and ethanol metabolism in the liver. Currently, no effective antifibrotic therapies are available. We aimed to obtain a better understanding of the cellular and molecular mechanisms involved in the pathogenesis of liver cirrhosis. MethodsWe performed single-cell RNA-sequencing to analyze immune cells from the liver tissue and peripheral blood form patients with alcoholic cirrhosis and healthy controls to profile the transcriptomes of more than 100,000 single human cells and yield molecular definitions for non-parenchymal cell types. In addition, we performed single-cell RNA-sequencing analysis to reveal the immune microenvironment related to alcoholic liver cirrhosis. Hematoxylin and eosin, Immunofluorescence staining and Flow cytometric analysis were employed to study the difference between tissues and cells with or without alcoholic cirrhosis.ResultsWe identified a fibrosis-associated M1 subpopulation of macrophages that expands in liver fibrosis, differentiates from circulating monocytes, and is pro-fibrogenic. We also define mucosal-associated invariant T (MAIT) cells that expand in alcoholic cirrhosis and are topographically restricted to the fibrotic niche. Multilineage modeling of ligand and receptor interactions between the fibrosis-associated macrophages, MAIT, and NK cells revealed the intra-fibrotic activity of several pro-fibrogenic pathways, including responses to cytokines and antigen processing and presentation, natural killer cell-mediated cytotoxicity, cell adhesion molecules, Th1/Th2/Th17 cell differentiation, IL-17 signaling pathway, and Toll-like receptor signaling pathway.DiscussionOur work dissects unanticipated aspects of the cellular and molecular basis of human organ alcoholic fibrosis at the single-cell level and provides a conceptual framework for the discovery of rational therapeutic targets in liver alcoholic cirrhosis.
An ex vivo test to investigate genetic factors conferring susceptibility to atypical haemolytic uremic syndrome
Authors: Gastoldi Sara , Aiello Sistiana , Galbusera Miriam , Breno Matteo , Alberti Marta , Bresin Elena , Mele Caterina , Piras Rossella , Liguori Lucia , Santarsiero Donata , Benigni Ariela , Remuzzi Giuseppe , Noris Marina 
Published: February 2023

IntroductionComprehensive genetic analysis is essential to clinical care of patients with atypical haemolytic uremic syndrome (aHUS) to reinforce diagnosis, and to guide treatment. However, the characterization of complement gene variants remains challenging owing to the complexity of functional studies with mutant proteins. This study was designed: 1) To identify a tool for rapid functional determination of complement gene variants; 2) To uncover inherited complement dysregulation in aHUS patients who do not carry identified gene variants.MethodsTo address the above goals, we employed an ex-vivo assay of serum-induced C5b-9 formation on ADP-activated endothelial cells in 223 subjects from 60 aHUS pedigrees (66 patients and 157 unaffected relatives).ResultsSera taken from all aHUS patients in remission induced more C5b-9 deposition than control sera, independently from the presence of complement gene abnormalities. To avoid the possible confounding effects of chronic complement dysregulation related to aHUS status, and considering the incomplete penetrance for all aHUS-associated genes, we used serum from unaffected relatives. In control studies, 92.7% of unaffected relatives with known pathogenic variants exhibited positive serum-induced C5b-9 formation test, documenting a high sensitivity of the assay to identify functional variants. The test was also specific, indeed it was negative in all non-carrier relatives and in relatives with variants non-segregating with aHUS. All but one variants in aHUS-associated genes predicted in-silico as likely pathogenic or of uncertain significance (VUS) or likely benign resulted as pathogenic in the C5b-9 assay. At variance, variants in putative candidate genes did not exhibit a functional effect, with the exception of a CFHR5 variant. The C5b-9 assay in relatives was helpful in defining the relative functional effect of rare variants in 6 pedigrees in which the proband carried more than one genetic abnormality. Finally, for 12 patients without identified rare variants, the C5b-9 test in parents unmasked a genetic liability inherited from an unaffected parent.DiscussionIn conclusion, the serum-induced C5b-9 formation test in unaffected relatives of aHUS patients may be a tool for rapid functional evaluation of rare complement gene variants. When combined with exome sequencing the assay might be of help in variant selection, to identify new aHUS-associated genetic factors.
Hydroacoustic survey on fish spatial distribution in the early impoundment stage of Yuwanghe Reservoir in southwest China
Authors: Luo Bin , Zhou Xianjun , Zhang Chaoshuo , Bao Jianghui , Mei Feng , Lian Yuxi , Zhang Dongxu , Hu Shaoqiu , Guo Longgen , Duan Ming 
Published: February 2023

Understanding the fish community structure and spatial distribution characteristics is essential for appropriate reservoir fishery management, especially in the early impoundment stage of the reservoir, which could help in obtaining basic data and performing artificial adjustments to biological communities. On the basis of this concept, we conducted a survey of the fish community and distribution at the newly constructed reservoir in southwest China by using a combination of methods, including hydroacoustic survey and fish sampling. Fish sampling showed a single fish community structure (six species belonging to four families) assembled in the reservoir, and the dominant species was Pseudorasbora parva which accounted for 98.79% of the fish population. In the hydroacoustic survey, the average fish density was 318.7 ± 256.1 individuals/1,000 m2. Irregular distribution of the fish was observed in the horizontal direction. The fish densities in the head area, middle area, and tail area of the reservoir were 168.5 ± 60.1, 306.8 ± 124.7, and 696.4 ± 288.9 individuals/1,000 m2, respectively, which showed a trend of increase in fish density with an increase in distance from the dam. More than 97.3% of the fish in the vertical direction were distributed in the water layer of depth 0 to 12 m. The average total length of fish was 75.4 mm, and the mean fish biomass in the reservoir was approximately 984.8 g/1,000 m2. According to Pearson correlation analysis, the main factors affecting the spatial distribution of fish were water depth, water temperature, dissolved oxygen, total nitrogen, and plankton density. Our results suggested that the fish community structure should be adjusted by releasing native carnivorous fish to control the abundance of small fish. Moreover, filter-feeding fish such as silver carp and bighead carp should be released in the reservoir to control the plankton community; this will enable the maintenance of the reservoir ecosystem in a healthy state while increasing the economic benefits to the local area.
Seasonal variability of nektonic community structure and phylogenetic diversity in Weizhou Island, the Beibu Gulf
Authors: Xu Lei , Du Feiyan , Tang Quehui , Wang Lianggen , Ning Jiajia , Huang Delian , Li Yafang , Liu Shuangshuang , Wang Xuehui 
Published: February 2023

The favorable natural conditions and variety of habitats in the Beibu Gulf provide a basis for harboring a high diversity of marine organisms. Sustainable coastal ecosystem management can be benefited from a comprehensive assessment of species diversity. In this study, we analyzed the seasonal changes in nektonic phylogenetic and community structures in the waters of Weizhou Island in the northern Beibu Gulf. The results showed that both the nektonic phylogenetic diversity and community structure in the northern Beibu Gulf exhibited strong seasonal differences between spring and autumn. The catch density was 291.9 kg per km2 in spring and 1081.1 kg per km2 in autumn. Phylogenetic diversity of nektonic communities obviously increased from spring to autumn, while phylogenetic patterns changed from clustering to overdispersion. The seasonal patterns of nektonic communities were mainly related to the different fishing intensities in spring and autumn. Summer fishing intensity in the Beibu Gulf was effectively controlled by a mid-summer fishing moratorium, during which nektonic diversity and fish stocks rapidly recovered from the larval pool. Our study revealed that fishing intensity had a greater impact on nektonic communities at smaller spatial scales, and even exceeded the effects of environmental factors.
Safety and efficacy of 650 nm invasive laser acupuncture on non-specific chronic low back pain: A protocol for a multicenter randomized placebo-controlled trial
Authors: Kim Jae-Hong , Yang Changsop , Yoo Jaehee , Park Gwang-Cheon , Kang Byoung-Kab , Kim Ae-Ran , Kim Jihye , Nam Dongwoo , Hong Yejin 
Published: February 2023

BackgroundWe aim to obtain clinical trial data regarding the safety, efficacy, and usefulness of invasive laser acupuncture (ILA) for non-specific chronic low back pain (NSCLBP) through a randomized placebo-controlled trial.MethodsOur clinical trial will be an assessor- and patient-blinded, prospective, parallel-arm, multi-center, randomized placebo-controlled clinical trial. One hundred and six participants with NSCLBP will be allocated evenly to the 650 ILA or control group. All participants will receive education on exercise and self-management. The 650 ILA group will undergo 650 nm ILA for 10 min, and the control group will undergo sham ILA for 10 min per visit, twice a week for 4 weeks, at bilateral GB30, BL23, BL24, and BL25. The primary outcome will be the proportion of responders (≥30% reduction in pain visual analogue scale [VAS] without increased use of painkillers) at 3 days after the intervention ends. The secondary outcomes will include changes in the scores of the VAS, European Quality of Life Five Dimension Five Level scale, and Korean version of the Oswestry Disability Index at 3 days after the intervention ends and 8 weeks after the intervention ends.DiscussionsThe results of our study will provide clinical evidence concerning the safety and efficacy of 650 nm ILA for the management of NSCLBP.Clinical trial registrationhttps://cris.nih.go.kr/cris/search/detailSearch.do?search_lang=E&amp;focus=reset_12&amp;search_page=M&amp;pageSize=10&amp;page=undefined&amp;seq=21591&amp;status=5&amp;seq_group=21591, identifier KCT0007167.
Diagnosis and treatment of infectious vaginitis: Proposal for a new algorithm
Authors: Eleutério José , Campaner Adriana Bittencourt , de Carvalho Newton Sergio 
Published: February 2023

BackgroundVaginitis is the most common gynecologic diagnosis in primary care, and most women have at least one episode during their lives. The need for standardized strategies to diagnose and treat vaginitis, both in primary care and among gynecologists, is emphasized. The Brazilian Group for Vaginal Infections (GBIV, acronym in Portuguese) aimed to update the practical approach to affected women by reviewing and discussing recent literature, and developing algorithms for diagnosis and treatment of vaginitis.MethodsA literature search within biomedical databases PubMed and SCieLo was conducted in January 2022. The available literature was evaluated by three experienced researchers, members of the GBIV, to summarize the main data and develop practical algorithms.Results and conclusionDetailed algorithms were developed with the main goal to improve gynecological practice considering different scenarios and access to diagnostic tools, from the simplest to the most complex tests. Different age groups and specific contexts were also considered. The combination of anamnesis, gynecological examination, and complementary tests remains the basis of a proper diagnostic and therapeutic approach. Periodic updates of these algorithms are warranted as new evidence becomes available.
The accelerated waning of immunity and reduced effect of booster in patients treated with bDMARD and tsDMARD after SARS-CoV-2 mRNA vaccination
Authors: Tobudic Selma , Simader Elisabeth , Deimel Thomas , Straub Jennifer , Kartnig Felix , Heinz Leonhard X. , Mandl Peter , Haslacher Helmuth , Perkmann Thomas , Schneider Lisa , Nothnagl Thomas , Radner Helga , Winkler Florian , Burgmann Heinz , Stiasny Karin , Novacek Gottfried , Reinisch Walter , Aletaha Daniel , Winkler Stefan , Blüml Stephan 
Published: February 2023

ObjectivesThis study aimed to assess the duration of humoral responses after two doses of SARS-CoV-2 mRNA vaccines in patients with inflammatory joint diseases and IBD and booster vaccination compared with healthy controls. It also aimed to analyze factors influencing the quantity and quality of the immune response.MethodsWe enrolled 41 patients with rheumatoid arthritis (RA), 35 with seronegative spondyloarthritis (SpA), and 41 suffering from inflammatory bowel disease (IBD), excluding those receiving B-cell-depleting therapies. We assessed total anti-SARS-CoV-2 spike antibodies (Abs) and neutralizing Ab titers 6 months after two and then after three doses of mRNA vaccines compared with healthy controls. We analyzed the influence of therapies on the humoral response.ResultsPatients receiving biological or targeted synthetic disease-modifying antirheumatic drugs (b/tsDMARDs) showed reduced anti-SARS-CoV-2 S Abs and neutralizing Ab titers compared with HC or patients receiving conventional synthetic (cs)DMARDs 6 months after the first two vaccination doses. Anti-SARS-CoV-2 S titers of patients with b/tsDMARDs declined more rapidly, leading to a significant reduction in the duration of vaccination-induced immunity after two doses of SARS-CoV-2 mRNA vaccines. While 23% of HC and 19% of patients receiving csDMARDs were without detectable neutralizing Abs 6 months after the first two vaccination doses, this number was 62% in patients receiving b/tsDMARDs and 52% in patients receiving a combination of csDMARDs and b/tsDMARDs. Booster vaccination led to increased anti-SARS-CoV-2 S Abs in all HC and patients. However, anti-SARS-CoV-2 S Abs after booster vaccination was diminished in patients receiving b/tsDMARDs, either alone or in combination with csDMARDs compared to HC.ConclusionPatients receiving b/tsDMARDs have significantly reduced Abs and neutralizing Ab titers 6 months after mRNA vaccination against SARS-CoV-2. This was due to a faster decline in Ab levels, indicating a significantly reduced duration of vaccination-induced immunity compared with HC or patients receiving csDMARDs. In addition, they display a reduced response to a booster vaccination, warranting earlier booster vaccination strategies in patients under b/tsDMARD therapy, according to their specific Ab levels.
Determinants of patient and physician global assessments of disease activity in anti-neutrophil cytoplasmic antibody-associated vasculitis
Authors: Rohde Marius , Kernder Anna , Acar Hasan , Düsing Christina , Fischer-Betz Rebecca , Haase Isabell , Mucke Johanna , Sander Oliver , Richter Jutta , Filla Tim , Schneider Matthias , Chehab Gamal 
Published: February 2023

ObjectiveTo compare physician and patient assessments of global disease activity in anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV) and to identify associated factors.MethodsGlobal disease activity scores (0–10 points) were retrospectively analyzed from physicians and patients with AAV at each outpatient visit from 2010 to 2020. We compared the scores and performed a linear regression with a random effects to identify associated factors.ResultsPatients (n = 143, 1,291 pairs, 52% female) had a mean 64 (±15) years of age and a mean disease duration of 9 (±7) years. Patients and physicians global disease activity assessments showed a moderate correlation (Pearson R 0.31, CI [0.23–0.52], p &lt; 0.001). Linear regression showed a strong association between the physician-documented disease activity scores and serum CRP levels (β = 0.22, CI [0.18, 0.28]), disease duration (β = −0.022, CI [−0.04,-0.01]) and patients’ assessment of disease activity (β = 0.08, CI [0.04, 0.12]). By contrast, patient assessments were strongly associated with the degree of pain (β = 0.30, CI [0.25, 0.35]), functional limitations in daily living (HAQ, β = 0.49, CI [0.21, 0.78]) and the global physical well-being (NRS, β = 0.39, CI [0.32, 0.46]).ConclusionPatients’ and physicians’ assessments of disease activity correlated. High CRP levels and disease duration were associated with physician-assessed disease activity scores, while subjective limitations were associated with higher patient-assessed disease activity scores. These findings highlight and support the need to develop and evaluate patient-reported outcomes to assess disease activity in patients diagnosed with AAV.
Microbial community structural response to variations in physicochemical features of different aquifers
Authors: Dai Heng , Zhang Yiyu , Fang Wen , Liu Juan , Hong Jun , Zou Chaowang , Zhang Jin 
Published: February 2023

IntroductionThe community structure of groundwater microorganisms has a significant impact on groundwater quality. However, the relationships between the microbial communities and environmental variables in groundwater of different recharge and disturbance types are not fully understood.MethodsIn this study, measurements of groundwater physicochemical parameters and 16S rDNA high-throughput sequencing technology were used to assess the interactions between hydrogeochemical conditions and microbial diversity in Longkou coastal aquifer (LK), Cele arid zone aquifer (CL), and Wuhan riverside hyporheic zone aquifer (WH). Redundancy analysis indicated that the primary chemical parameters affecting the microbial community composition were NO3–, Cl–, and HCO3–.ResultsThe species and quantity of microorganisms in the river–groundwater interaction area were considerably higher than those in areas with high salinity [Shannon: WH (6.28) &gt; LK (4.11) &gt; CL (3.96); Chao1: WH (4,868) &gt; CL (1510) &gt; LK (1,222)]. Molecular ecological network analysis demonstrated that the change in microbial interactions caused by evaporation was less than that caused by seawater invasion under high-salinity conditions [(nodes, links): LK (71,192) &gt; CL (51,198)], whereas the scale and nodes of the microbial network were greatly expanded under low-salinity conditions [(nodes, links): WH (279,694)]. Microbial community analysis revealed that distinct differences existed in the classification levels of the different dominant microorganism species in the three aquifers.DiscussionEnvironmental physical and chemical conditions selected the dominant species according to microbial functions. Gallionellaceae, which is associated with iron oxidation, dominated in the arid zones, while Rhodocyclaceae, which is related to denitrification, led in the coastal zones, and Desulfurivibrio, which is related to sulfur conversion, prevailed in the hyporheic zones. Therefore, dominant local bacterial communities can be used as indicators of local environmental conditions.
Alterations in metabolome and microbiome signatures provide clues to the role of antimicrobial peptide KT2 in ulcerative colitis
Authors: Nan Qiong , Ye Yan , Tao Yan , Jiang Xinyi , Miao Yinglei , Jia Jie , Miao Jiarong 
Published: February 2023

IntroductionUlcerative colitis (UC) is an inflammatory disease of the intestinal tract with unknown etiology. Both genetic and environmental factors are involved in the occurrence and development of UC. Understanding changes in the microbiome and metabolome of the intestinal tract is crucial for the clinical management and treatment of UC.MethodsHere, we performed metabolomic and metagenomic profiling of fecal samples from healthy control mice (HC group), DSS (Dextran Sulfate Sodium Salt) -induced UC mice (DSS group), and KT2-treated UC mice (KT2 group).Results and DiscussionIn total, 51 metabolites were identified after UC induction, enriched in phenylalanine metabolism, while 27 metabolites were identified after KT2 treatment, enriched in histidine metabolism and bile acid biosynthesis. Fecal microbiome analysis revealed significant differences in nine bacterial species associated with the course of UC, including Bacteroides, Odoribacter, and Burkholderiales, which were correlated with aggravated UC, and Anaerotruncus, Lachnospiraceae, which were correlated with alleviated UC. We also identified a disease-associated network connecting the above bacterial species with UC-associated metabolites, including palmitoyl sphingomyelin, deoxycholic acid, biliverdin, and palmitoleic acid. In conclusion, our results indicated that Anaerotruncus, Lachnospiraceae, and Mucispirillum were protective species against DSS-induced UC in mice. The fecal microbiomes and metabolomes differed significantly among the UC mice and KT2-treated and healthy-control mice, providing potential evidence for the discovery of biomarkers of UC.
Effect of deposit chemistry on microbial community structure and activity: Implications for under-deposit microbial corrosion
Authors: Diaz-Mateus Maria A. , Salgar-Chaparro Silvia J. , Machuca Laura L. , Farhat Hanan 
Published: February 2023

IntroductionThe deposition of solid particles carried by production fluids from oil and gas companies in horizontal surfaces of different assets has shown to cause severe localised corrosion. Sand, one of the most common deposits in the energy sector pipelines, is frequently mixed with crude, oil, asphaltenes, corrosion inhibitors, and other organic compounds. For this reason, they might favour the metabolic activity of native microbial communities. This study aimed to determine the impact of sand-deposit chemical composition on the microbial community structure and functional attributes of a multispecies consortium recovered from an oilfield and the resulting risk of under-deposit microbial corrosion of carbon steel.MethodsSand deposits recovered from an oil pipeline were used in their raw form and compared against the same deposits exposed to heat treatment to remove organic compounds. A four-week immersion test in a bioreactor filled with synthetic produced water and a two-centimeter layer of sand was set up to assess corrosion and microbial community changes.ResultsThe raw untreated deposit from the field containing hydrocarbons and treatment chemicals resulted in a more diverse microbial community than its treated counterpart. Moreover, biofilms developed in the raw sand deposit exhibited higher metabolic rates, with functional profile analysis indicating a predominance of genes associated with xenobiotics degradation. Uniform and localized corrosion were more severe in the raw sand deposit compared to the treated sand.DiscussionThe complex chemical composition of the untreated sand might have represented an additional source of energy and nutrients to the microbial consortium, favoring the development of different microbial genera and species. The higher corrosion rate obtained under the untreated sand suggests that MIC occurred due to syntrophic relationships between sulphate reducers or thiosulphate reducers and fermenters identified in the consortium.