bluuebunny/crossref_metadata_2025_split huggingface dataset:
Potential role of fecal microbiota in patients with constipation
Authors: Tian Yan , Zuo Luo , Guo Qin , Li Jun , Hu Zhangyong , Zhao Kui , Li Can , Li Xiaohui , Zhou Jinggang , Zhou Yan , Li Xiao-an 
Published: October 2020

Background We evaluated the safety and efficacy of fecal microbiota transplantation (FMT) for chronic functional constipation (CFC) ineffectively treated by conventional constipation medication. Methods Thirty-four patients with CFC underwent FMT treatment (three rounds, via gastroscopy). Clinical scales, including the Wexner constipation score as the main index of efficiency, were completed at baseline; after each treatment, and at 2 and 3 months of follow up. Secondary evaluation indices included the self-assessment of constipation symptoms, patient assessment constipation quality-of-life questionnaire, Bristol stool form scale, and Zung’s self-rating depression and anxiety scales. Gastrointestinal motility, motilin, gastrin, nitric oxide (NO), and 5-hydroxytryptamine (5-HT) were assessed before and after treatment. Intestinal flora changes were assessed by 16S ribosomal ribonucleic acid (rRNA) sequencing. Results There were no serious adverse reactions. The clinical cure rate was 73.5% (25/34), clinical remission rate was 14.7% (5/34), and the inefficiency rate was 11.8% (4/34). Clinical scale data indicated that the FMT treatment was effective. Furthermore, FMT treatment promoted intestinal peristalsis, increased gastrointestinal motility, and increased serum NO and 5-HT levels. The 16S rRNA sequencing data indicated that high abundances of Bacteroides, Klebsiella, Megamonas, Erysipelotrichaceae and Epulopiscium may be the cause of constipation, and high abundances of Prevotella, Acidaminococcus and Butyricimonas may be the main factors in curing constipation. Conclusion Treatment with FMT regulates the intestinal microflora and changes the abundance of CFC-associated bacterial flora to improve constipation.
CEA and CYFRA 21-1 as prognostic biomarker and as a tool for treatment monitoring in advanced NSCLC treated with immune checkpoint inhibitors
Authors: Dall’Olio Filippo G. , Abbati Francesca , Facchinetti Francesco , Massucci Maria , Melotti Barbara , Squadrilli Anna , Buti Sebastiano , Formica Francesca , Tiseo Marcello , Ardizzoni Andrea 
Published: October 2020

Aims: To assess prognostic value of pre-therapy carcinoembryonic antigen (CEA) and cytokeratin-19 fragments (CYFRA 21-1) blood levels in non-small cell lung cancer (NSCLC) patients treated with immune-checkpoint inhibitors (ICIs) and their early change as predictor of benefit. Materials and methods: This is a retrospective cohort study including patients with stage IIIB–IV NSCLC who received anti PD-1/PD-L1 in first or advanced lines of therapy in two institutions. A control cohort of patients treated only with chemotherapy has been enrolled as well. Results: A total of 133 patients treated with nivolumab or atezolizumab were included in the test set, 74 treated with pembrolizumab first line in the validation set and 89 in the chemotherapy only cohort. CYFRA 21-1 >8 ng/mL was correlated with overall survival (OS) in the test set, validation set and in univariate and multivariate analysis (pooled cohort hazard ratio (HR) 1.90, 95% confidence interval (CI) 1.24–2.93, p 0.003). Early 20% reduction after the third cycle was correlated with OS for CEA (HR 0.12; 95% CI 0.04–0.33; p < 0.001), and for CYFRA 21-1 (HR 0.19; 95% CI 0.07–0.55; p 0.002) Conclusions: CYFRA 21-1 pre-therapy assessment provides clinicians with relevant prognostic information about patients treated with ICI. CEA and CYFRA 21-1 repeated measures could be useful as an early marker of benefit.
Hypothesis generative head-to-head study comparing efficacy of afatinib and osimertinib based on immunological biomarkers in Japanese NSCLC patients with EGFR mutations (Heat on Beat study)
Authors: Morikawa Kei , Tanaka Hisashi , Itani Hidetoshi , Takata Saori , Watanabe Satoshi , Kishi Kazuma , Soejima Kenzo , Kaira Kyoichi , Kagamu Hiroshi , Yoshimura Kenichi , Matsutani Noriyuki , Seki Nobuhiko 
Published: October 2020

Background: In the FLAURA trial, superiority of osimertinib over the standard of care (SOC) was not demonstrated in Asian patients; SOC seemed favorable among Japanese patients (hazard ratio 1.39, 95% confidence interval 0.82–2.33). Three reasons are suggested: since rechallenge with epidermal growth factor receptor tyrosine kinase inhibitor (EGFR-TKI) is covered by health insurance in Japan, EGFR-TKI rechallenge rate was higher in SOC than in the osimertinib group, which resulted in a long-term sequential administration of EGFR-TKIs; treatment discontinuation rate was high in the osimertinib group due to adverse events such as interstitial pneumonia among Japanese patients. EGFR-TKIs enhance tumor antigen-specific cytotoxicity of T cells, especially first- and second-generation EGFR-TKIs, which are more active against various cells with wild-type EGFR, including regulatory T cells. Consequently, subsequent immune checkpoint inhibitor therapy seemed more promising in the SOC group. Therefore, optimal first-line EGFR-TKI for EGFR-mutant advanced lung cancer may not have been identified in Japanese patients. Methods: The Heat on Beat study is a randomized, open-label, multicenter, phase II study to compare OS between initial treatment with afatinib and osimertinib in treatment-naïve patients with advanced or recurrent EGFR-mutant NSCLC. Exploration of immunomonitoring through peripheral blood mononuclear cells will also be performed, before, during, and after treatment. Treatment-naïve EGFR mutation-positive non-small cell lung cancer (NSCLC) patients ( N = 100) will be randomized to two groups in a 1:1 ratio. The co-primary endpoints are 3-year survival rate and characterization of immune environment associated with response to afatinib, osimertinib, or immune checkpoint inhibitors. Enrollment will start in May 2020 at 28 sites in Japan and continue for 1 year, with 3-year follow-up. Discussion: Because there is no clinical trial comparing second- with third-generation EGFR-TKI for advanced EGFR-mutant NSCLC, our study would provide a major impact on clinical practice. Trial registration Japan Registry of Clinical Trials, jRCTs031190221, registered date: 25 February 2020, https://jrct.niph.go.jp/en-latest-detail/jRCTs031190221
Potential of sugi wood diterpenes as an Alzheimer's disease preventive and therapeutic drug by the β-amyloid toxicity reduction effect
Authors: Yamaji Yoshie , Wakabayashi Tokumitsu , Kofujita Hisayoshi 
Published: October 2020

Abstract
Alzheimer's disease is the most common form of dementia, and neurological disorder from beta amyloid (Aβ) peptide is regarded as a cause of Alzheimer's disease. In this study, the authors evaluate Aβ toxicity reduction effects of major diterpenes isolated from sugi wood by bioassay using Caenorhabditis elegans and examined its relationship with the antioxidative activity. Among the six kinds of sugi wood diterpenes: ferruginol, 6,7-dehydroferruginol, sandaracopimarinal, sandaracopimarinol, abietadiene, abietatriene and phyllocladenes, prominent Aβ toxicity reduction effects were found in ferruginol and 6,7-dehydroferruginol, and their activity was almost equivalent to that of the four kinds of anti-Alzheimer active agents that have been reported so far: ginkgolide A, morin, rosmarinic acid and carnosic acid. Antioxidative activity similar to other anti-Alzheimer active agents was found in ferruginol and 6,7-dehydroferruginol in a 1,1-Diphenyl-2-picrylhydrazyl (DPPH) radical scavenging activity test, which suggested that antioxidative activity is concerned with expression of the Aβ toxicity reduction effect of sugi wood diterpenes.
An overview of occupational noise-induced hearing loss among workers: epidemiology, pathogenesis, and preventive measures
Authors: Chen Kou-Huang , Su Shih-Bin , Chen Kow-Tong 
Published: October 2020

Abstract
Occupational noise-induced hearing loss (ONIHL) is the most prevalent occupational disease in the world. The goal of this study was to review the epidemiology, pathogenesis, and preventive measures of ONIHL among workers and provide evidence for the implementation of control measures. Literature studies were identified from the MEDLINE, PubMed, Embase, Web of Science, and Google Scholar using the search terms “noise-induced hearing loss” “prevalence”, “pathogenesis”, and “preventive measures”. The articles reviewed in this report were limited from 2000 to 2020. Articles that were not published in the English language, manuscripts without an abstract, and opinion articles were excluded. After a preliminary screening, all of the articles were reviewed and synthesized to provide an overview of the current status of ONIHL among workers. The mechanism of ONIHL among workers is a complex interaction between environmental and host factors (both genetic and acquired factors). The outcomes of noise exposure are different among individual subjects. Clinical trials are currently underway to evaluate the treatment effect of antioxidants on ONIHL. Noise exposure may contribute to temporary or permanent threshold shifts; however, even temporary threshold shifts may predispose an individual to eventual permanent hearing loss. Noise prevention programs are an important preventive measure in reducing the morbidity of ONIHL among workers.
Flow velocity and nutrients affect CO2 emissions from agricultural drainage channels in the North China Plain
Authors: Leng Peifang , Li Fadong , Du Kun , Li Zhao , Gu Congke , Koschorreck Matthias 
Published: October 2020

Abstract

Background
Groundwater is typically over-saturated in CO2 with respect to atmospheric equilibrium. Irrigation with groundwater is a common agricultural practice in many countries, but little is known about the fate of dissolved inorganic carbon (DIC) in irrigation groundwater and its contribution to the CO2 emission inventory from land to the atmosphere. We performed a mesocosm experiment to study the fate of DIC entering agricultural drainage channels in the North China Plain. Specifically, we aimed to unravel the effect of flow velocity and nutrient on CO2 emissions.

Results
All treatments were emitting CO2. Approximately half of the DIC in the water was consumed by TOC production (1–16%), emitted to the atmosphere (14–20%), or precipitated as calcite (CaCO3) (14–20%). We found that DIC depletion was stimulated by nutrient addition, whereas more CO2 evasion occurred in the treatments without nutrients addition. On the other hand, about 50% of CO2 was emitted within the first 50 h under high flow velocity. Thus, in the short term, high nutrient levels may counteract CO2 emissions from drainage channels, whereas the final fate of the produced biomass (burial versus mineralization to CO2 or even CH4) determines the duration of the effect.

Conclusion
Our study reveals that both hydrology and biological processes affect CO2 emissions from groundwater irrigation channels. The estimated CO2 emission from total groundwater depletion in the North China Plain is up to 0.52 ± 0.07 Mt CO2 year−1. Thus, CO2 emissions from groundwater irrigation should be considered in regional CO2 budgets, especially given that groundwater depletion is expected to acceleration in the future.
Moesin is involved in microglial activation accompanying morphological changes and reorganization of the actin cytoskeleton
Authors: Okazaki Tomonori , Saito Daichi , Inden Masatoshi , Kawaguchi Kotoku , Wakimoto Sayuri , Nakahari Takashi , Asano Shinji 
Published: October 2020

AbstractMoesin is a member of the ezrin, radixin and moesin (ERM) proteins that are involved in the formation and/or maintenance of cortical actin organization through their cross-linking activity between actin filaments and proteins located on the plasma membranes as well as through regulation of small GTPase activities. Microglia, immune cells in the central nervous system, show dynamic reorganization of the actin cytoskeleton in their process elongation and retraction as well as phagocytosis and migration. In microglia, moesin is the predominant ERM protein. Here, we show that microglial activation after systemic lipopolysaccharide application is partly inhibited in moesin knockout (Msn-KO) mice. We prepared primary microglia from wild-type and Msn-KO mice, and studied them to compare their phenotypes accompanying morphological changes and reorganization of the actin cytoskeleton induced by UDP-stimulated phagocytosis and ADP-stimulated migration. The Msn-KO microglia showed higher phagocytotic activity in the absence of UDP, which was not further increased by the treatment with UDP. They also exhibited decreased ADP-stimulated migration activities compared with the wild-type microglia. However, the Msn-KO microglia retained their ability to secrete tumor necrosis factor α and nitric oxide in response to lipopolysaccharide.
Effectiveness of impedance parameters for muscle quality evaluation in healthy men
Authors: Sato Hiroki , Nakamura Takao , Kusuhara Toshimasa , Kenichi Kobara , Kuniyasu Katsushi , Kawashima Takaki , Hanayama Kozo 
Published: October 2020

Abstract
We investigated the relationship between impedance parameters and skeletal muscle function in the lower extremities, as well as the effectiveness of impedance parameters in evaluating muscle quality. Lower extremity impedance of 19 healthy men (aged 23–31 years) measured using the direct segmental multi-frequency bioelectrical impedance analysis were arc-optimized using the Cole–Cole model, following which phase angle (PA), $${R}_{i}/{R}_{e}$$

R
i

/

R
e

, and β were estimated. Skeletal muscle function was assessed by muscle thickness, muscle intensity, and isometric knee extension force (IKEF). IKEF was positively correlated with PA (r = 0.58, p < 0.01) and β (r = 0.34, p < 0.05) was negatively correlated with $${R}_{i}/{R}_{e}$$

R
i

/

R
e

(r = − 0.43, p < 0.01). Stepwise multiple regression analysis results revealed that PA, β, and $${R}_{i}/{R}_{e}$$

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i

/

R
e

were correlated with IKEF independently of muscle thickness. This study suggests that arc-optimized impedance parameters are effective for evaluating muscle quality and prediction of muscle strength.
BIOCOM-PIPE: a new user-friendly metabarcoding pipeline for the characterization of microbial diversity from 16S, 18S and 23S rRNA gene amplicons
Authors: Djemiel Christophe , Dequiedt Samuel , Karimi Battle , Cottin Aurélien , Girier Thibault , El Djoudi Yassin , Wincker Patrick , Lelièvre Mélanie , Mondy Samuel , Chemidlin Prévost-Bouré Nicolas , Maron Pierre-Alain , Ranjard Lionel , Terrat Sébastien 
Published: October 2020

Abstract

Background
The ability to compare samples or studies easily using metabarcoding so as to better interpret microbial ecology results is an upcoming challenge. A growing number of metabarcoding pipelines are available, each with its own benefits and limitations. However, very few have been developed to offer the opportunity to characterize various microbial communities (e.g., archaea, bacteria, fungi, photosynthetic microeukaryotes) with the same tool.

Results
BIOCOM-PIPE is a flexible and independent suite of tools for processing data from high-throughput sequencing technologies, Roche 454 and Illumina platforms, and focused on the diversity of archaeal, bacterial, fungal, and photosynthetic microeukaryote amplicons. Various original methods were implemented in BIOCOM-PIPE to (1) remove chimeras based on read abundance, (2) align sequences with structure-based alignments of RNA homologs using covariance models, and (3) a post-clustering tool (ReClustOR) to improve OTUs consistency based on a reference OTU database. The comparison with two other pipelines (FROGS and mothur) and Amplicon Sequence Variant definition highlighted that BIOCOM-PIPE was better at discriminating land use groups.

Conclusions
The BIOCOM-PIPE pipeline makes it possible to analyze 16S, 18S and 23S rRNA genes in the same packaged tool. The new post-clustering approach defines a biological database from previously analyzed samples and performs post-clustering of reads with this reference database by using open-reference clustering. This makes it easier to compare projects from various sequencing runs, and increased the congruence among results. For all users, the pipeline was developed to allow for adding or modifying the components, the databases and the bioinformatics tools easily, giving high modularity for each analysis.
Directional divergence of Ep300 duplicates in teleosts and its implications
Authors: Wang Xianzong , Yan Junli 
Published: October 2020

AbstractBackgroundEP300 is a conserved protein in vertebrates, which serves as a key mediator of cellular homeostasis. Mutations and dysregulation of EP300 give rise to severe human developmental disorders and malignancy.Danio reriois a promising model organism to study EP300 related diseases and drugs; however, the effect of EP300 duplicates derived from teleost-specific whole genome duplication should not just be neglected.ResultsIn this study, we obtained EP300 protein sequences of representative teleosts, mammals and sauropsids, with which we inferred a highly supported maximum likelihood tree. We observed that Ep300 duplicates (Ep300a and Ep300b) were widely retained in teleosts and universally expressed in a variety of tissues. Consensus sequences of Ep300a and Ep300b had exactly the same distribution of conserved domains, suggesting that their functions should still be largely overlapped. We analyzed the molecular evolution of Ep300 duplicates in teleosts, using branch-site models, clade models and site models. The results showed that both duplicates were subject to strong positive selection; however, for an extant species, generally at most one copy was under positive selection. At the clade level, there were evident positive correlations between evolutionary rates, the number of positively selected sites and gene expression levels. In Ostariophysi, Ep300a were under stronger positive selection than Ep300b; in Neoteleostei, another species-rich teleost clade, the contrary was the case. We also modeled 3D structures of zf-TAZ domain and its flanking regions of Ep300a and Ep300b ofD. rerioandOryzias latipesand found that in either species the faster evolving copy had more short helixes.ConclusionsCollectively, the two copies of Ep300 have undoubtedly experienced directional divergence in main teleost clades. The divergence of EP300 between teleosts and mammals should be greater than the divergence between different teleost clades. Further studies are needed to clarify to what extent the EP300 involved regulatory network has diverged between teleosts and mammals, which would also help explain the huge success of teleosts.
Identification of diverse cell populations in skeletal muscles and biomarkers for intramuscular fat of chicken by single-cell RNA sequencing
Authors: Li Jinghui , Xing Siyuan , Zhao Guiping , Zheng Maiqing , Yang Xinting , Sun Jiahong , Wen Jie , Liu Ranran 
Published: October 2020

Abstract

Background
The development of skeletal muscle is closely related to the efficiency of meat production and meat quality. Chicken skeletal muscle development depends on myogenesis and adipogenesis and occurs in two phases—hyperplasia and hypertrophy. However, cell profiles corresponding to the two-phase muscle development have yet to be determined. Single-cell RNA-sequencing (scRNA-seq) can elucidate the cell subpopulations in tissue and capture the gene expression of individual cells, which can provide new insights into the myogenesis and intramuscular adipogenesis.

Results
Ten cell clusters at the post-hatching developmental stage at Day 5 and seven cell clusters at the late developmental stage at Day 100 were identified in chicken breast muscles by scRNA-seq. Five myocyte-related clusters and two adipocyte clusters were identified at Day 5, and one myocyte cluster and one adipocyte cluster were identified at Day 100. The pattern of cell clustering varied between the two stages. The cell clusters showed clear boundaries at the terminal differentiation stage at Day 100; by contrast, cell differentiation was not complete at Day 5. APOA1 and COL1A1 were selected from up-regulated genes in the adipocyte cluster and found to be co-expressed with the ADIPOQ adipocyte marker gene in breast muscles by RNA in situ hybridization.

Conclusions
This study is the first to describe the heterogeneity of chicken skeletal muscle at two developmental stages. The genes APOA1 and COL1A1 were identified as biomarkers for chicken intramuscular fat cells.
Short chain fatty acids induced the type 1 and type 2 fimbrillin-dependent and fimbrillin-independent initial attachment and colonization of Actinomyces oris monoculture but not coculture with streptococci
Authors: Suzuki Itaru , Shimizu Takehiko , Senpuku Hidenobu 
Published: October 2020

AbstractBackgroundActinomyces orisis an early colonizer and has two types of fimbriae on its cell surface, type 1 fimbriae (FimP and FimQ) and type 2 fimbriae (FimA and FimB), which contribute to the attachment and coaggregation with other bacteria and the formation of biofilm on the tooth surface, respectively. Short-chain fatty acids (SCFAs) are metabolic products of oral bacteria includingA. orisand regulate pH in dental plaques. To clarify the relationship between SCFAs and fimbrillins, effects of SCFAs on the initial attachment and colonization (INAC) assay usingA. oriswild type and fimbriae mutants was investigated. INAC assays usingA. orisMG1 strain cells were performed with SCFAs (acetic, butyric, propionic, valeric and lactic acids) or a mixture of them on human saliva-coated 6-well plates incubated in TSB with 0.25% sucrose for 1 h. The INAC was assessed by staining live and dead cells that were visualized with a confocal microscope.ResultsAmong the SCFAs, acetic, butyric and propionic acids and a mixture of acetic, butyric and propionic acids induced the type 1 and type 2 fimbriae-dependent and independent INAC by liveA. oris, but these cells did not interact with streptococci. The main effects might be dependent on the levels of the non-ionized acid forms of the SCFAs in acidic stress conditions. GroEL was also found to be a contributor to the FimA-independent INAC by liveA. oriscells stimulated with non-ionized acid.ConclusionSCFAs affect the INAC-associated activities of theA. orisfimbrillins and non-fimbrillins during ionized and non-ionized acid formations in the form of co-culturing with other bacteria in the dental plaque but not impact the interaction ofA. oriswith streptococci.