bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association of Alcohol Consumption with the Incidence of Proteinuria and Chronic Kidney Disease: A Retrospective Cohort Study in Japan
Authors: Tanaka Akio , Yamaguchi Makoto , Ishimoto Takuji , Katsuno Takayuki , Nobata Hironobu , Iwagaitsu Shiho , Sugiyama Hirokazu , Kinashi Hiroshi , Banno Shogo , Ando Masahiko , Kubo Yoko , Ito Yasuhiko 
Published: October 2021

Abstract
Background

The difference in the clinical impact of alcohol consumption on kidney function based on sex remains to be elucidated. This study aimed to assess the association between the dose of alcohol consumption and the incidence of proteinuria and chronic kidney disease stratified by sex.
Methods

This retrospective cohort study included 26,788 workers (19,702 men and 7086 women) with normal renal function (estimated glomerular filtration rate ≥60 mL/min/1.73 m2) at annual health examinations between January 2010 and March 2015 in Japan. The main exposure was alcohol consumption. The primary outcomes were the incidence of proteinuria (dipstick urinary protein ≥1) and incidence of chronic kidney disease (an estimated glomerular filtration rate <60 mL/min per 1.73 m2 and a 25% decrease from the baseline estimated glomerular filtration rate).
Results

During a median observational period of 4 years (interquartile range: 2–6), 1993 (10.1%) men and 462 (6.5%) women developed proteinuria, whereas 667 (3.4%) men and 255 (3.6%) women developed chronic kidney disease. After adjustment for clinically relevant factors using a Cox proportional hazards model, alcohol consumption of ≥40 g/day in females was significantly associated with the incidence of proteinuria (hazard ratio, 1.65; 95% confidence interval, 1.09–2.51) and chronic kidney disease (hazard ratio, 1.77; 95% confidence interval, 1.09–2.85). However, no significant association between alcohol consumption and primary outcomes was observed in men.
Conclusions

In conclusion, daily higher alcohol consumption was significantly associated with a higher incidence of proteinuria and chronic kidney disease among women. Women might be prone to high alcohol consumption with kidney dysfunction.
Systematic Proteomics Analysis of Colorectal Cancer: to Recognize Potential Biomarkers and Remedial Target
Authors: Jahromi Noosha Zia , Mandani Amin Mahmoudi , Kaji Nahid Sadeghi Moghadam , Teshnizi Hadis Abbasi , Zamani Atefeh , Fattahi Nasrin , Sazegar Hossein 
Published: October 2021

Abstract
BackgroundColorectal Cancer (CRC) is a high prevalence malignant of the digestive system. Notwithstanding huge investigation, the precise involved mechanisms are still blunted. It emerges that more research is needed to understand the underlying mechanisms of CRC better. In this investigation, a systems biology method was applied to provide a comprehensive insight through making a multilayer network to recognize novel biomarkers and potential drug targets.MethodTo identify the affected proteins in this disease, an existing protein expression profile on CRC was attained from ProteomeXchange. In the first step, the quality of the dataset was assessed, and then differentially expressed proteins (DEPs) were recognized based on FDR<0.05 as the statistically significant threshold. Subsequently, all identified DEPs were subjected to further enrichment analysis for finding the involved biomedical phenomena. In the following action, lncRNAs and miRNAs related to DEPs were predicted as regulatory layers via Cytoscape to make an integrative network.ResultThe empirical findings in this study indicated that the identified DEPs were mainly associated with two biomedical terms, such as “Mitochondrial dysfunction” and “Extracellular matrix organization.” Additionally, several hub molecules were introduced in the constructed multilayer network, hub-DEPs (ITGB1, ACTG1, ...), hub-miRs (miR-16-5p, miR-26b-5p, ...), and hub-lncRNAs (KCNQ1OT1, NEAT1, …) that Can be deemed as a potential biomarker in the pathogenesis of CRC, further research should concentrate on the investigation of their role in CRC development.ConclusionThe attained results of this study may be paving a way to provide a deeper understanding of the vaguely involved mechanisms through an integrative insight into the interaction of proteins with regulatory layers.
Optimization of Enzymatic Fragmentation is Crucial To Maximize Genome Coverage: A Comparison of Library Preparation Methods for Illumina Sequencing
Authors: Ribarska Teodora , Bjørnstad Pål Marius , Sundaram Arvind Y.M. , Gilfillan Gregor D. 
Published: October 2021

Abstract
Background
Novel commercial kits for whole genome library preparation for next-generation sequencing on Illumina platforms promise shorter workflows, lower inputs and cost savings. Time savings are achieved by employing enzymatic DNA fragmentation and by combining end-repair and tailing reactions. Fewer cleanup steps also allow greater DNA input flexibility (1 ng-1 µg), PCR-free options from 100 ng DNA, and lower price as compared to the well-established sonication and tagmentation-based DNA library preparation kits.
Results
We compared the performance of four enzymatic fragmentation-based DNA library preparation kits (from New England Biolabs, Roche, Swift Biosciences and Quantabio) to a tagmentation-based kit (Illumina) using low input DNA amounts (10 ng) and PCR-free reactions with 100 ng DNA. With four technical replicates of each input amount and kit, we compared the kits` fragmentation sequence-bias as well as performance parameters such as sequence coverage and the clinically relevant detection of single nucleotide and indel variants. While all kits produced high quality sequence data and demonstrated similar performance, several enzymatic fragmentation methods produced library insert sizes which deviated from those intended. Libraries with longer insert lengths performed better in terms of coverage, SNV and indel detection. Lower performance of shorter-insert libraries could be explained by loss of sequence coverage to overlapping paired-end reads, exacerbated by the preferential sequencing of shorter fragments on Illumina sequencers. We also observed that libraries prepared with minimal or no PCR performed best with regard to indel detection.
Conclusions
The enzymatic fragmentation-based DNA library preparation kits from NEB, Roche, Swift and Quantabio are good alternatives to the tagmentation based Nextera DNA flex kit from Illumina, offering reproducible results using flexible DNA inputs, quick workflows and lower prices. Libraries with insert DNA fragments longer than the cumulative sum of both read lengths avoid read overlap, thus produce more informative data that leads to strongly improved genome coverage and consequently also increased sensitivity and precision of SNP and indel detection. In order to best utilize such enzymatic fragmentation reagents, researchers should be prepared to invest time to optimize fragmentation conditions for their particular samples.
Direct Cyclodextrin Based Powder Extrusion 3D Printing for One-step Production of the BCS Class II Model Drug Niclosamide
Authors: Pistone Monica , Racaniello Giuseppe Francesco , Arduino Ilaria , Laquintana Valentino , Lopalco Antonio , Cutrignelli Annalisa , Rizzi Rosanna , Franco Massimo , Lopedota Angela , Denora Nunzio 
Published: October 2021

Abstract
Niclosamide (NCS) is a drug that has been used as an anthelmintic and anti-parasitic active principle for about 40 years. Recently, some studies have highlighted its potential in treating various tumors, allowing a repositioning of this drug. Despite its potential, NCS is a Biopharmaceutical Classification System (BCS) Class II drug, and is consequently characterised by low aqueous solubility, poor dissolution rate and reduced bioavailability, which limits its applicability. In this work, we utilize a very novel technique, Direct Powder Extrusion (DPE) 3D printing, which overcomes the limitations of previously used techniques (Fused Deposition Modelling, FDM) to achieve direct extrusion of pharmaceutical grade powder mixtures consisting of NCS, hydroxypropyl methylcellulose (HPMC, Affinisol 15 LV), hydroxypropyl-b-cyclodextrin (HP-β-CD) and polyethylene glycol (PEG) 6000. For the first time, direct printing of powder blends containing HP-β-CD was explored. For all tablets, in vitro dissolution studies showed sustained drug release over 48 hours, but for tablets containing HP-β-CD, the release was faster. Solid-state characterisation studies showed that during extrusion, the drug lost its crystal structure and was evenly distributed within the polymer matrix. All printed tablets exhibited good mechanical and physical features and guarantee stability of the drug content for up to 3 months. This innovative printing technique has demonstrated the possibility to produce personalised pharmaceutical dosage forms starting directly from powders, avoiding the use of filament used by FDM.
Experimental Investigations on the Wall-attached Bubble Growth Process in Water With Supersaturated Total Dissolved Gas
Authors: Lin Lu , Li Ran , Feng Jingjie , Zou Qin , Cheng Xiaolong , Lin Honghui 
Published: October 2021

Abstract
Due to dam discharge, waterfalls, sudden increases in water temperature and oxygen production by photosynthesis, the total dissolved gas (TDG) in water is often supersaturated, which may have serious effects on aquatic ecology. When the atmospheric pressure is lower than the TDG pressure in water, the supersaturated dissolved gas in water will slowly release into air. Wall-attached bubbles were formed during the TDG release process. The generation and departure of wall-attached bubbles influence the release process of TDG in water. To simulate the growth period of the wall-attached bubbles under different pressures, a decompression experimental device was designed to record the supersaturated TDG release process. Based on experimental data and mathematical calculations, the quantitative relationship between the bubble growth rate and environmental pressure was obtained. The supersaturated TDG dissipation rate increases monotonically with increasing relative vacuum degree. Based on the wall-attached bubble growth rate calculation method applied in this paper, a formula of the supersaturated TDG adsorption flux based on wall-attached bubbles was proposed, and a prediction method of the TDG release coefficient was established. The simulation results show that with increasing relative vacuum degree, the TDG coefficient increases correspondingly, and the adsorption mechanism of vegetation surface area can be obviously promoted under lower environmental pressure. This study provides an important theoretical basis for the accurate calculation of the TDG release process and provides a scientific basis for the accurate prediction of the spatial and temporal distribution of supersaturated TDG under different environmental conditions.
Efficacy of tuina, cupping and acupuncture therapy on pain, anxiety, depression and quality of life in patients with neck pain: A protocol for systematic review and network meta-analysis
Authors: Qin Shi-xin , Li An , Zhan Mao-Lin , Wu Yi-Cheng , Zhao Yong-Hua , Lv Zi-Meng , Zhang Yu 
Published: October 2021

Abstract
Background: Neck pain is a common disorder and is more frequent in females than in males worldwide. Recently, more attention is being paid to precautions for and treatment of neck pain. Current therapeutic methods for neck pain include pharmaceutical, complementary and alternative therapies. Tuina, acupuncture and cupping are effective in the treatment of neck pain, which enrich patients’ options. In this study, we aim to evaluate the efficacy of different interventions using randomised controlled trials to identify a prioritised treatment for neck pain.Methods: We will search five English databases (Web of Science, MEDLINE, EMBASE, OVID and Cochrane Library) and four Chinese databases (CNKI, SinoMed, Wanfang Database and VIP) from database inception to December 2020. Two reviewers will independently perform article screening (title, keywords, abstract and full text); data extraction; risk of bias (RoB) assessment and grading of recommendations assessment, development and evaluation. We will use RevMan 5.3 software to carry out statistical analysis of the RoB and risk ratio to analyse the dichotomous data. Finally, we will use GeMTC V.0.8.1 package of R-3.3.2 software for network meta-analysis based on a Bayesian framework.Discussion: We will compare these three interventions to determine the most effective therapy for neck pain in terms of improving pain, anxiety, depression and QoL. In this way, we will provide powerful evidence for future clinical practice guidelines for patients with neck pain who want to receive a suitable treatment.Systematic review registration: PROSPERO CRD42020206853.
Liver enzymes and lipid profile of malaria patients before and after antimalarial drug treatment at Dembia Primary Hospital and Teda Health Center, Northwest, Ethiopia
Authors: Megabiaw Fentahun , Eshetu Tegegne , Kassahun Zeleke , AEMERO MULUGETA 
Published: October 2021

Abstract
Backgroundinfection with malaria in humans involves liver cell destruction, which alters the levels of liver enzymes and lipid profiles. Although a number of studies have been conducted to address the impact of malaria on liver enzymes and lipid profiles, their findings lack consistency and no studies were conducted after antimalarial drug treatment in the Ethiopian context. This study, therefore, is intended to fill this gap. MethodsAn observational cohort study was conducted at Dembia Primary Hospital and Teda Health Center, from June to August 2020. A total of 88 study participants were recruited using random sampling techniques. Socio-demographic data, capillary and venous blood samples were collected from confirmed Plasmodium -infected individuals. Assessment of liver enzymes and lipid profiles was done using Beckman Coulter DC-700 clinical chemistry analyzer. Data were entered using Epi-data and exported to SPSS version 20 software for analysis. One way ANova, independent t-test, and paired t-test were used to compare the mean liver enzymes and lipid profile. A p -value<0.05 was considered statistically significant. RESULTSBefore anti-malaria treatment, among 88 malaria-infected study participants, abnormally elevated AST was observed in 87.5% of them. Similarly, elevated ALT, ALP, and TG were observed among 12.5%, 43.2%, and 17.2% of the study subjects, respectively. A lower level of HDL was observed among 87.5% of the study participants, while LDL and TC levels were within the normal range. After anti-malaria treatment,100% of AST, ALT, HDL, and LDL, and 92% of ALP, 94.3% of TC, and 86.4% of TG results were in the normal range. The mean level of AST (39.70±3.55and 55.35±9.6) and ALT (22.11±11.75, and23.24±16.05) results were increased, whereas HDL (28.88±11.63and22.73±14.26) level decreased from low to higher density parasitaemia. The mean level of AST at posttreatment (33.90±15.15) was significantly lower compared to the pretreatment (47.60±9.65). The mean levels of ALT had not altered during pretreatment(23.53±16.28)and posttreatment (23.49±11.10).Moreover, the mean of HDL, LDL, and TC at posttreatment were found to be increased when compared with pretreatment, though it is statistically insignificant ( P >0.05). CONCLUSIONMalaria parasites could be responsible for increased liver enzymes and certain lipids while decreasing some lipid profiles compared with the normal range. After anti-malaria treatment, these parameters were reversed to normal from 86.4% to 100%. When the mean values are compared, a significant change was observed in AST level while ALT level remains the same. Hence, prompt treatment is important to improve liver enzymes and lipid profile impairment during malaria infection.
Alterations of Thyroid Microbiota Across Different Thyroid Microhabitats in Patients With Thyroid Carcinoma
Authors: Dai Daofeng , Yan Yang , Yang Yong , Dang Tianfeng , Xiao Jiansheng , Wang Weibin , Teng Lisong , Ye Jing , Jiang Hongqun 
Published: October 2021

Abstract
Background: In recent years, the incidence rate of Thyroid carcinoma(TC) has been increasing worldwide. Thus, research on factors of TC carcinogenesis may promote TC prevention and decrease the incidence rate. There are several studies targeting the correlation between gut microbiota and thyroid disease. Carcinogenesis of several malignancies is influenced by microbiota. However, thyroid microbiome of TC has not been revealed. This study investigated thyroid microbiota in different TC microhabitats. Methods: We performed 16s rRNA gene sequencing using tumor tissues and matched peritumor tissues from 30 patients with TC to characterize thyroid microbiota. Results: The richness and diversity of thyroid microbiota were lower in TC tumor samples than in matched peritumor tissues. At the genus level, the core microbiota of thyroid included Sphingomonas, Comamonas, Acinetobacter, Pseudomonas, Microvirgula, and Soonwooa. The abundance of Sphingomonas and Aeromonas was significantly increased in tumor tissues, while the abundance of Comamonas, Acinetobacter, and Peptostreptococcus was significantly enhanced in peritumor tissues. The combination of Comamonas and Sphingomonas could discriminate tumor samples from peritumor samples with an area under the curve (AUC) of 0.981 (95% confidence interval [CI]: 0.949-1.000). The abundance of Sphingomonas was significantly higher in N1 stage than in N0 stage. Sphingomonas could distinguish between N0 and N1 stage with an AUC of 0.964 (95% CI: 0.907-1.000).Conclusions: The microbial diversity and composition were significantly different between peritumor and tumor microhabitats from patients with TC, which may eventually affect TC carcinogenesis and progression. The combination of Comamonas and Sphingomonas could serve as a powerful biomarker for discrimination between tumor and peritumor tissues. Furthermore, the higher abundance of Sphingomonas was correlated with lymph node metastasis, indicating that it may play a role in promoting TC progression.
Determining the Impacts of Educational Intervention based on PLST Extended Care model on Caregiving Methods and Improved Exposure to Challenging Behaviors of People with Dementia (PWD): A mixed-methods study
Authors: Zamani-Alavijeh Fereshteh , Zahed Shakiba , Emami Maryam , Bazargan-Hejazi Shahrzad , Barekatain Majid , Hassanzadeh Akbar , Eslami Ahmad Ali 
Published: October 2021

Abstract
Background: Psychological events in People with Dementia (PWD) lead to behavioral disorders which require targeted planning for caregivers on how to adapt to these behaviors. Progressively lowered stress threshold (PLST) model provides effective interventions for caregivers to adapt to the behaviors of People with Dementia (PWD). Therefore, this study aims to determine the impacts of educational intervention based on the progressively lowered Stress threshold extended (PLSTE) model on the caregiving of People with Dementia (PWD) in Isfahan, Iran. Methods: This exploratory mixed methods study was initially conducted with a qualitative approach to content analysis type from May 2016 to June 2018. Data were collected in a qualitative stage through in-depth non-structured interviews with 29 People with Dementia (PWD)'s caregivers using the "new comment" command in a word and then analyzed. The researcher designed a multi-sectional questionnaire, including demographic characteristics, knowledge measurement, and monitoring the practice of caregivers. The validity of the questionnaire was verified by the panel of experts and its reliability was confirmed using the Cronbach alpha coefficient (knowledge section 0.838 and practice section 0.802). To adjust the intervention program, the educational content based on the PLSTE model was used for 38 caregivers available at two elderly nursing centers in Isfahan. The data were collected immediately and one month after the educational intervention using a questionnaire. Results: According to the results of the qualitative section of this study, the researcher was able to add a cultural and belief class, and then the related Intervention method to the PLST model. In the quantitative part, paired t-test indicated that the mean scores of knowledge, caregiving practice, and exposure to Challenging Behaviors (CB) in all dimensions of practice immediately and one a month after intervention were significantly higher than the mean scores before intervention (P < 0.05).Conclusion: Considering the impacts of this intervention, educating the caregivers with PLST extended the care model is recommended, with a specific focus on cultural and traditional issues of the society, to improve knowledge and practice of caregivers in caregiving skills and appropriate exposure to Challenging Behaviors People with Dementia (CBPWD).
The Management of Lichen Sclerosus Urethral Strictures by 3 Different Techniques: a single-center surgical algorithm based on the evaluation of corpus spongiosum
Authors: Zheng Dachao , Xie Minkai , Wan Xiang , Mao Yuanshen , Yao Haijun , Wang Zhong 
Published: October 2021

Abstract
BackgroundLichen sclerosus (LS) is a chronic, inflammatory disease of unknown cause which occurs in the male genital area and can affect the external genital and the anterior urethra. Nowdays, urethral stricture associated with LS is still a challenge to urologists and different surgical options are employed according to surgeons’ personal preferences. In this study, we report our experience of surgical treatments for genital lichen sclerosus urethral stricture and try to share our surgical algorithm. MethodsBetween March 2013 and March 2018, 55 patients with LS urethral strictures underwent three different surgical techniques including of Kulkarni technique, Bracka technique and perineal urethrostomy (PU). Approaches were chosen according to the evaluation of the degree of spongiofibrosis and patients’ wishes. ResultsThe overall success rate was 74.55%. Kulkarni technique was performed in 37 patients with a success rate of 78.38%. 12 patients who were planned for staged substitution urethroplasty, developed a 50% success rate, including 3 local graft contractures following the first stage, 2 fistulas and 1 dehiscence following the urethroplasty respectively. PU was chosen as the primary treatment in 6 patients and performed as salvage surgery on 4 patients, which resulted a 100% success rate. Comparing to the Kulkarni and Bracka techniques, PU offers the highest degree of success and could be considered as a final salvage for all patients and statistic difference was found between three techniques (P=0.0082). ConclusionThe staged urethroplasty by excising corpus spongiosum consumed more cost of time and money but could not provide similar therapeutic effects as the Kulkarni technique and PU. Therefore, the evaluation of corpus spongiosum is a necessary step in the surgical decision making which can make surgeons avoid unsuitable decisions and improve the success rate.