bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessment of Knowledge, Attitude and Practices and the Analysis of Risk Factors regarding Schistosomiasis Among Fishermen and Boatmen in the Dongting Lake Basin, P.R. China
Authors: Guan Zhou , Dai Si-Min , Zhou Jie , Ren Xiao-Bing , Qin Zhi-Qiang , Li Yin-Long , Lv Shan , Li Shi-Zhu , Zhou Xiao-Nong , Xu Jing 
Published: May 2020

Abstract
Background: Fishermen and boatmen are a risk population for contracting schistosomiasis due to their high frequency of water contact in endemic areas of schistosomiasis in the People’s Republic of China (P.R. China). To develop specific interventions towards this population, our present study was designed to assess the knowledge, attitudes and practices (KAPs) towards schistosomiasis of fishermen and boatmen, and to identify the risk factors associated with schistosome infection using molecular technique in the selected area of Hunan Province in P.R. China. Methods: A cross sectional survey was conducted in the Dongting Lake Basin of Yueyang County, Hunan Province, P.R. China. A total of 601 fishermen and boatmen were interviewed between October and November 2017. Information regarding socio-demographic details and KAPs towards schistosomiasis were collected using a standardized questionnaire. Fecal samples of participants were collected and tested by Polymerase Chain Reaction (PCR). Logistic regression analysis was conducted to explore the risk factors related to the positive results of PCR. Results: Of the 601 respondents, over 90% knew schistosomiasis and how the disease was contracted, the intermediate host of schistosomes and preventive methods. The majority of respondents had a positive attitude towards schistosomiasis prevention. However, only 6.66% (40/601) of respondents had installed a latrine on their boats, while 32.61% (196/601) of respondents defecated in the public toilets on shore. In addition, only 4.99% (30/601) respondents protected themselves while exposed to freshwater. The prevalence of schistosomiasis, as determined by PCR, among fishermen and boatmen in Yueyang County was 13.81% (83/601). Age, years of performing the current job, number of times receiving treatment, and whether they were treated in past three years were the main influencing factors of PCR results among this population. Conclusions: Fishermen and boatmen are still at high risk of infection in P.R. China and gaps exist in KAPs towards schistosomiasis in this population group. Chemotherapy, and health education encouraging behavior change in combination with other integrated approaches to decrease the transmission risk in environments should be improved.
Genome-wide identification and characterization of lectin receptor-like kinase gene family in cucumber and expression profiling analysis under different treatments
Authors: Lv Duo , Wang Gang , Xiong Liang-Rong , Sun Jing-Xian , Chen Yue , Guo Chun-Li , Yu Yao , He Huan-Le , Cai Run , Pan Junsong 
Published: May 2020

Abstract
Background Lectin receptor-like kinases (LecRLKs) are a class of membrane proteins found in plants that are involved in diverse functions, including plant development and stress responses. Although LecRLK families have been identified in a variety of plants, a comprehensive analysis has not yet been undertaken in cucumber ( Cucumis sativus L.). Results In this study, 46 putative LecRLK genes were identified in cucumber genome, including 23 G-type, 22 L-type and 1 C-type LecRLK genes. They unequally distributed on all 7 chromosomes with a clustering trendency. Most of the genes in the cucumber LecRLK ( Cs ecRLK ) gene family lacked introns. In addition, there were many regulatory elements associated with phytohormone and stress on these genes’ promoters. Transcriptome data demonstrated that distinct expression patterns of CsLecRLK genes in various tissues. Furthermore, we found that each member of the CsLecRLK family had its own unique expression pattern under hormone and stress treatment by the quantitative real time PCR (qRT-PCR) analysis. Conclusion This study provides a better understanding of the evolution and function of LecRLK gene family in cucumber, and opens the possibility to explore the roles that LecRLK s might play in the life cycle of cucumber.
Effect of Porphyromonas gingivalis infection on gut dysbiosis and arthritis exacerbation in mouse model
Authors: Hamamoto Yuta , Ouhara Kazuhisa , Munenaga Syuichi , Shoji Mikio , Ozawa Tatsuhiko , Hisatsune Jyunzo , Kado Isamu , Kajiya Mikihito , Matsuda Shinji , Kawai Toshihisa , Mizuno Noriyoshi , Fujita Tsuyoshi , Hirata Shintaro , Tanimoto Kotaro , Nakayama Koji , Kishi Hiroyuki , Sugiyama Eiji , Kurihara Hidemi 
Published: May 2020

Abstract
Background: Porphyromonas gingivalis (Pg) infection causes periodontal disease and is involved in the exacerbation of rheumatoid arthritis (RA). Gut microbiota dysbiosis has shown strong associations with systemic diseases, including RA, diabetes mellitus, and inflammatory bowel disease, and inoculation of periodontopathogenic bacteria (i.e. Pg) can alter gut microbiota composition. Therefore, this study investigated dysbiosis-mediated arthritis exacerbation by Pg oral inoculation in an experimental arthritis model mouse.Methods: Pg inoculation in the oral cavity twice a week for 6 weeks was performed to induce periodontitis in SKG mice. Concomitantly, a single intraperitoneal (i.p.) injection of laminarin (LA) was administered to induce experimental arthritis (Pg-LA mouse). Citrullinated protein (CP) and IL-6 levels in periodontal, intestinal, and joint tissues, and serum were measured by ELISA. Gut microbiota composition was determined by sequencing the bacterial 16S rRNA after DNA purification of mouse feces. Fecal microbiota transplantation (FMT) was performed by transferring Pg-RA-derived feces to normal SKG mice. The effect of the Pg peptidylarginine deaminase (PgPAD) on the level of citrullinated proteins and arthritis progression were determined using PgPAD knockout mutant.Results: Periodontal alveolar bone loss and IL-6 in gingival tissue were induced by Pg oral infection, as well as severe joint destruction, increased arthritis scores (AS), and IL-6 and CP production in serum, joint, and intestinal tissues. Distribution of Deferribacteres and S24-7 was decreased, while CP was significantly increased in gingival, joint, and intestinal tissues of Pg-inoculated experimental arthritis mice compared to experimental arthritis mice without Pg inoculation. Further, FMT from Pg-inoculated experimental arthritis mice showed the reproduction of donor gut microbiota and resulted in severe joint destruction with increased IL-6 and CP production in joint and intestinal tissues. The avarage AS of FMT from Pg-inoculated experimental arthritis was much higher than that of donor mouse. However, inoculation of the PgPAD knockout mutant inhibited the elevation of arthritis scores, ACPA level in serum and reduced CP amount in gingival, joint, and intestinal tissues compared to Pg wild type inoculation .Conclusion: Pg oral infection affected gut microbiota dysbiosis and joint destruction via increased CP generation.
Two-by-two factorial randomised study within a trial (SWAT) to evaluate strategies for follow-up in a randomised prevention trial
Authors: Bradshaw Lucy , Montgomery Alan A , Williams Hywel , Chalmers Joanne , Haines Rachel 
Published: May 2020

Abstract
Background Failure to collect outcome data in randomised trials can result in bias and loss of statistical power. Further evaluations of strategies to increase retention are required. We assessed the effectiveness of two strategies for retention in a randomised prevention trial using a two-by-two factorial randomised study within a trial (SWAT). Methods Parents of babies included in the host trial were randomised to (1) Short message service (SMS) notification prior to sending questionnaires at 3, 6, 12 and 18 months versus no SMS notification and (2) £10 voucher sent with the invitation letter for the primary follow up visit at 24 months or given at the visit. The two co-primary outcomes were collection of host trial (1) questionnaire data at interim follow-up times and (2) primary outcome at 24 months during a home/clinic visit with a research nurse. Results Between November 2014 and November 2016, 1394 participants were randomised: 350 to no SMS + voucher at visit, 345 to SMS + voucher at visit, 352 to no SMS + voucher before visit and 347 to SMS + voucher before visit. Overall questionnaire data was collected at interim follow-up times for 75% in both the group allocated to the prior SMS notification and the group allocated to no SMS notification (odds ratio (OR) SMS v. none 1.02, 95% CI 0.83 to 1.25). Host trial primary outcome data was collected at a visit for 557 (80%) allocated to the voucher before the visit in the invitation letter and for 566 (81%) whose parents were allocated to receive the voucher at the visit (OR before v. at visit 0.89, 95% CI 0.69 to 1.17). Conclusion There was no evidence of a difference in retention according to SMS notification or voucher timing. Future synthesis of SWAT results is required to be able to detect small but important incremental effects of retention strategies. Trial registration: Host trial registration: ISRCTN registry; ID: ISRCTN21528841. Registered on 25 July 2014. SWAT Repository Store ID 25
DL-3-n-butylphthalide improves cerebral hypoperfusion in patients with large cerebral atherosclerotic stenosis. A single-center, randomized, double-blind, placebo-controlled study.
Authors: Chen Dawei , Yin Yanwei , Shi Jin , Yang Fen , Wang Kehua , Zhao Faguo , Li Wenping , Li Bin 
Published: May 2020

Abstract
Background: DL-3-n-butylphthalide (NBP) was demonstrated to increase the cerebral blood flow (CBF) in the animal models, but there are no clinic studies to verify this. We aimed to explore the effect of NBP on improving cerebral hypoperfusion caused by cerebral large-vessel stenosis.Methods: In this single-center, randomized, double-blind, placebo-controlled study, 120 patients with severe carotid atherosclerotic stenosis and cerebral hypoperfusion in the ipsilateral middle cerebral artery (MCA) were included and randomly assigned into NBP or placebo group as 1:1 radio. Patients in NBP or placebo group received 200mg or 20mg of NBP capsules three times daily for four weeks respectively. Single photon emission computed tomography (SPECT) was used to assess regional CBF (rCBF) in four regions of interest (ROIs) corresponding to MCA before and 12 weeks after the treatment. After therapy, the rCBF change for every ROI and the whole CBF change in MCA territory for every patient were classified into amelioration, stabilization and deterioration respectively.Results: 48 NBP patients (6 with bilateral stenosis) and 46 placebo patients (8 with bilateral stenosis) completed the trial. Overall, both groups had 54 stenotic carotid arteries and 216 ROIs for rCBF change analysis. After therapy, the rCBF in ROIs increased in NBP group (83.5%±11.4% vs. 85.8%±12.5%, p=0.000), whereas no change was found in placebo group (86.9%±11.6% vs. 87.8%±11.7%, p=0.331). Besides, there was higher percentages of ROIs with rCBF amelioration and stabilization in NBP group than in placebo group (93.1% vs. 79.2%, p=0.000). Furthermore, ordinal regression analysis showed that compared with placebo, NBP independently made more patients to have whole CBF amelioration in ipsilateral MCA (Wald-χ2=5.247, OR=3.31, p=0.022).Conclusions: NBP might improve the cerebral hypoperfusion in the patients with carotid artery atherosclerotic stenosis.Trial registration: Chinese Clinical Trial Registry, ChiCTR1900028005, registered December 8th 2019- Retrospectively registered (http://www.chictr.org.cn/index.aspx).
HiCoP, a simple and robust method for detecting interactions of regulatory regions
Authors: Zhang Yan , Li Zhaoqiang , Bian Shasha , Zhao Hao , Feng Delong , Chen Yanhong , Hou Yuhe , Liu Qifa , Hao Bingtao 
Published: May 2020

Abstract
Background: Chromatin physical interactions provide essential information for understanding the regulation of cis-elements like enhancers, promoters, and insulators in cell development and differentiation. The Hi-C assay is a technique detecting chromatin structures of the whole genome but not sensitive to interactions of regulatory elements. Several methods, like HiChIP, DNase-C, and OCEAN-C, have been developed for enriching interactions of regulatory regions, but all of them have some shortcomings. New simple, efficient, and robust methods are still in need of detecting interactions of regulatory regions. Results: We developed a new, simple, and robust assay called CoP (Column Purified chromatin) for profiling of open chromatin regions by directly purifying fragmentized crosslinked chromatin with a DNA purification column. The accessible chromatin regions, including active enhancers, promoters, and insulators, were significantly enriched in CoP chromatin. The CoP-seq assay can efficiently detect open chromatin regions, especially active promoters, with a high signal-to-noise ratio. We integrated the CoP-seq and Hi-C technique (HiCoP) for the detection of interactions of accessible chromatin regions, which represent active cis-regulatory elements in cells. We observed that the HiCoP captured the peaks in the promoters-associated enhancer regions, and the chromatin features identified by HiCoP were similar to HiChIP of histone H3K27 acetylation rather than Hi-C. HiCoP detected more promoter-enhancer (P-E), promoter-promoter (P-P), and enhancer-enhancer (E-E) interactions within 20kb-5Mb than Hi-C. Most of the loops identified by HiCoP were associated with the expressed genes. Conclusion: CoP assay can efficiently enrich open chromatin regions. When CoP assay was integrated with Hi-C assay, it provides a simple, robust, alternative technique for profiling accessible chromatin regions and chromatin conformation simultaneously.
Circulating metabolites from the choline pathway and acute coronary syndromes in a Chinese case-control study
Authors: Dai Yuxiang , Tian Qianqian , Si Jing , Sun Zhonghan , Shali Shalaimaiti , Xu Lili , Ren Daoyuan , Chang Shufu , Dong Xin , Zhao Hongxia , Mei Zhengdong , Zheng Yan , Ge Junbo 
Published: May 2020

Abstract
Background: Accumulating evidence shows that circulating levels of trimethylamine N-oxide, which is generated from the metabolism of dietary choline, may predict cardiovascular disease among Caucasians. Acute coronary syndrome (ACS), one common presentation of cardiovascular disease, is a spectrum of signs and symptoms due to acute decreased blood flow in the coronary arteries. The relationship between the metabolites from choline pathway and ACS remains unclear. We aimed to assess the associations of circulating metabolites from the choline pathway with ACS among a Chinese population, who consume a different dietary pattern than their Western counterparts. Methods: We recruited 501 participants who were admitted to the Department of Cardiology, Zhongshan Hospital,Shanghai China between March 2017 and June 2018, including 254 ACS cases and 247 controls. Liquid chromatography-tandem mass spectrometry was used to measure circulating concentrations of metabolites in the choline pathway, including betaine, choline, trimethylamine, and trimethylamine N-oxide. A composite metabolite score using a weighted sum of these four metabolites, and the betaine/choline ratio were calculated. Multivariable logistic regressions were applied to estimate the association of metabolites with ACS, with adjustment of age, sex, body mass index, smoking index, history of diseases, and kidney function. Results : After adjusting for traditional risk factors, per 1-standard deviation (SD) increment in choline was positively associated with the odds of ACS [odds ratio (OR), 95% confidence interval (CI), 1.77(1.44-2.18)], and the other metabolites were not associated with ACS at a statistical significance level. Compared with participants in the lowest quartile of the metabolite score, those in the highest quartile had higher odds of ACS [OR (95% CI), 3.18(1.85-5.54), p <0.001 for trend]. Per 1-SD increment in metabolite score was positively associated with higher odds of ACS [OR (95% CI), 1.80 (1.37-2.40)], and per 1-SD increment inthebetaine/choline ratio was inversely associated with the odds of ACS [OR (95% CI), 0.49 (0.39-0.60)]. Conclusions: Among our Chinese participants, trimethylamine N-oxide was not associated with ACS, while a composite metabolite score of metabolites from the choline pathway was associated with increased odds of ACS. The choline pathway metabolites may be related to the pathophysiology of ACS among Chinese.
Novel insights into the Thaumarchaeota in the deepest oceans: their metabolism and potential adaptation mechanisms
Authors: Zhong Haohui , Lehtovirta-Morley Laura , Liu Jiwen , Zheng Yanfen , Lin Heyu , Song Delei , Todd Jonathan D. , Tian Jiwei , Zhang Xiao-Hua 
Published: May 2020

Abstract
Background: Marine Group I (MGI) Thaumarchaeota, which play key roles in the global biogeochemical cycling of nitrogen and carbon (ammonia oxidizers), thrive in the aphotic deep sea with massive populations. Recent studies have revealed that MGI Thaumarchaeota were present in the deepest part of oceans - the hadal zone (depth > 6,000 m, consisting almost entirely of trenches), with the predominant phylotype being distinct from that in the “shallower” deep sea. However, little is known about the metabolism and distribution of these ammonia oxidizers in the hadal water.Results: In this study, metagenomic data were obtained from 0-10,500 m deep seawater samples from the Mariana Trench. The distribution patterns of Thaumarchaeota derived from metagenomics and 16S rRNA gene sequencing were in line with that reported in previous studies: abundance of Thaumarchaeota peaked in bathypelagic zone (depth 1,000 – 4,000 m) and the predominant clade shifted in the hadal zone. Several metagenome-assembled thaumarchaeotal genomes were recovered, including a near-complete one representing the dominant hadal phylotype of MGI. Using comparative genomics we predict that unexpected genes involved in bioenergetics, including two distinct ATP synthase genes (predicted to be coupled with H+ and Na+ respectively), and genes horizontally transferred from other extremophiles, such as those encoding putative di-myo-inositol-phosphate (DIP) synthases, might significantly contribute to the success of this hadal clade under the extreme condition. We also found that hadal MGI have the genetic potential to import a far higher range of organic compounds than their shallower water counterparts. Despite this trait, hadal MDI ammonia oxidation and carbon fixation genes are highly transcribed providing evidence they are likely autotrophic, contributing to the primary production in the aphotic deep sea.Conclusions: Our study reveals potentially novel adaptation mechanisms of deep-sea thaumarchaeotal clades and suggests key functions of deep-sea Thaumarchaeota in carbon and nitrogen cycling.
First month of the epidemic caused by COVID-19 in Italy: current status and real-time outbreak development forecast
Authors: Megna Rosario 
Published: May 2020

Abstract
Background : The first outbreaks of COVID-19 in Italy occurred during the second half of February 2020 in some areas in the North of the country. Due to the high contagiousness of the infection, further spread by asymptomatic people, Italy has become in a few weeks the country with the greatest number of infected people in the World. The large number of severe cases among infected people in Italy led to the hospitalization of thousands of patients, with a heavy burden on the National Health Service. Methods: We analyzed data provided daily by Italian Authorities for the period from 24 February 2020 to 30 March 2020. Considering such information, we developed a forecast model in real-time, based on the cumulative logistic distribution. We then produced an estimate of the overall number of potentially infected individuals and epidemic duration at a national and Regional level, for the most affected Regions. Results: A total of 101,739 infected individuals was confirmed until 30 March 2020, of which 75,528 active cases, 14,620 recovered or discharged, and 11,591 deaths. Until the same date patients quarantined at home were 43,752, whereas hospitalized patients were 31,776, of which 3,981 in intensive care. The forecast model estimated a number of infected persons for Italy of 130,000 about, and a duration of the epidemic greater than 2 months. Conclusions : Once month after the first outbreaks there seems to be the first signs of a decrease in the number of infections, showing that we could be now facing the descending phase of the epidemic. The forecast obtained thanks to our model could be used by decision-makers to implement coordinative and collaborative efforts in order to control the epidemic. The pandemic due to novel Coronavirus must be a warning for all countries worldwide, regarding a rapid and complete dissemination of information, surveillance, health organization, and cooperation among the states.
Artificial Immune Network Clustering Based on a Cultural Algorithm
Authors: Deng Liyuan , Yang Ping , Liu Weidong 
Published: May 2020

Abstract
There are some problems in evolutionary immune network clustering, such as the lack of guidance in the clustering process, the sensitivity of the fuzzy boundary and the difficulty in determining parameters. To solve these problems, an artificial immune network clustering algorithm based on a cultural algorithm is proposed. Three kinds of knowledge are constructed: normative knowledge is used to standardize the spatial scope of population initialization, avoiding blindness; state knowledge is used to distinguish antigens and take immune defense measures to prevent noise and unclear network structure caused by boundary; topology knowledge is used to guide the optimal antibody search. The clone mutation operation of the traditional method is improved, and a compression threshold adaptive determination method is proposed based on the shadow sets theory. The experimental results show that the proposed method can effectively overcome the above problems, and the clustering performance on a synthetic dataset and an actual dataset is satisfactory.