bluuebunny/crossref_metadata_2025_split huggingface dataset:
How are systematic reviews of prevalence conducted? A methodological study
Authors: Migliavaca Celina Borges , Stein Cinara , Colpani Verônica , Barker Timothy Hugh , Munn Zachary , Falavigna Maicon 
Published: April 2020

Abstract
Background: There is a notable lack of methodological and reporting guidance for systematic reviews of prevalence data. This information void has the potential to result in reviews that are inconsistent and inadequate to inform healthcare policy and decision making. The aim of this meta-epidemiological study is to describe the methodology of recently published prevalence systematic reviews.Methods: We searched MEDLINE (via PubMed) from February 2017 to February 2018 for systematic reviews of prevalence studies. We included systematic reviews assessing the prevalence of any clinical condition using patients as the unit of measurement and we summarized data related to reporting of and methodology of the reviews.Results: A total of 235 systematic reviews of prevalence were analyzed. The median number of authors was 5 (interquartile range [IQR] 4-7), the median number of databases searched was 4 (3-6) and the median of studies included in each review was 24 (IQR 15-41.5). Search strategies were presented for 68% of reviews. Forty five percent of reviews received external funding, and 24% did not provide funding information. Twenty three percent of included reviews had published or registered the systematic review protocol. Reporting guidelines were used in 72% of reviews. The quality of included studies was assessed in 80% of reviews. Nine reviews assessed the overall quality of evidence (4 using GRADE). Meta-analysis was conducted in 65% of reviews; 1% used Bayesian methods. Random effect meta-analysis was used in 94% of reviews; among them, 75% did not report the variance estimator used. Among the reviews with meta-analysis, 70% did not report how data was transformed; 59% percent conducted subgroup analysis, 38% conducted meta-regression and 2% estimated prediction interval; I2 was estimated in 95% of analysis. Publication bias was examined in 48%. The most common software used was STATA (55%).Conclusions: Our results indicate that there are significant inconsistencies regarding how these reviews are conducted. Many of these differences arose in the assessment of methodological quality and the formal synthesis of comparable data. This variability indicates the need for clearer reporting standards and consensus on methodological guidance for systematic reviews of prevalence data.
Development of a novel method for the quantification of tyrosine 39 phosphorylated a- and β-synuclein in human cerebrospinal fluid
Authors: Na Chan Hyun , Sathe Gajanan , Rosenthal Liana S. , Moghekar Abhay R. , Dawson Valina L. , Dawson Ted M. , Pandey Akhilesh 
Published: April 2020

Abstract
Background: Parkinson’s disease (PD) is the second most prevalent neurodegenerative disorder. Biomarkers that can help monitor the progression of PD or response to disease-modifying agents will be invaluable in making appropriate therapeutic decisions. Further, biomarkers that could be used to distinguish PD from other related disorders with PD-like symptoms will be useful for accurate diagnosis and treatment. C-Abl tyrosine kinase is activated in PD resulting in increased phosphorylation of the tyrosine residue at position 39 (Y39) of a-synuclein (a-syn) (pY39 a-syn), which contributes to the death of dopaminergic neurons. Because pY39 a-syn may be pathogenic, monitoring pY39 a-syn could allow us to diagnose presymptomatic PD and help monitor disease progression and response to treatment. We sought to investigate if increased phosphorylation of pY39 a-syn can be detected in the cerebrospinal fluid (CSF) of PD patients by targeted mass spectrometry. Methods: Here, we report a two-step enrichment method in which phosphotyrosine peptides were first enriched with an anti-phosphotyrosine antibody followed by a second round of enrichment by titanium dioxide (TiO2) beads to detect EGVLpYVGSK sequence derived from tyrosine 39 region of α- and β-synuclein (aβ-syn). Accurate quantification was achieved by adding a synthetic heavy version of pY39 aβ-syn peptide before enzymatic digestion. Results: Using the developed enrichment methods and optimized parallel reaction monitoring (PRM) assays, we detected pY39 aβ-syn peptide in human CSF and demonstrated that the ratio of pY39 aβ-syn to Y39 aβ-syn was significantly increased in the CSF of patients with PD.Conclusions: We anticipate that this optimized two-step enrichment-based PRM detection method will help monitor c-Abl activation in PD patients and can also be used to quantify other phosphotyrosine peptides of low abundance in biological samples.
Prospective Randomized Study Evaluating the Usefulness of a Surgical Smoke Evacuation System in Operating Rooms for Breast Surgery
Authors: Tokuda Yutaka , Okamura Takuho , Maruta Miki , Orita Mutsuko , Noguchi Miyuki , Suzuki Toshiyasu , Matsuki Hideaki 
Published: April 2020

Abstract
Background: No prospective evaluation of surgical smoke evacuation systems has yet been conducted anywhere in the world. A prospective randomized study was conducted to clarify the usefulness of a surgical smoke evacuation system in terms of reducing the quantity of environmental pollutants found in operating room air and reducing the occupational exposure of doctors and nurses involved in surgical procedures to surgical smoke, volatile organic compounds, formaldehyde, etc. Methods: Operating room environment conditions with and without the use of a surgical smoke evacuation system were measured, and the personal exposure levels of doctors and nurses involved in surgical procedures were also surveyed. Use of the evacuation system was determined randomly, and the procedures involved were breast-conserving surgery and mastectomy, which were treated as stratification factors. Results: The average total volatile organic compound concentration in the operating room was significantly lower when the evacuation system was used compared with when it was not used. The findings were similar for formaldehyde concentration. Multiple regression analysis for healthcare professionals’ personal exposure levels showed that the evacuation system was a factor that significantly impacted their formaldehyde and acetaldehyde personal exposure levels, which were greatly reduced by the use of the system. Conclusion: This study’s findings demonstrate the effectiveness of the evacuation systems, which should increase awareness that their benefits take priority over the drawbacks. Trial Registration: The study was conducted after explaining to participants that it was a study of operating room environments in which their participation was voluntary and obtaining their consent. The study was also approved by the Tokai University Hospital clinical research review committee (no. 5R-022) and registered with the UMIN registry　(UMIN000029092) on 13, September, 2017-　retrospectively registered, http://www.umin.ac.jp/ctr/UMIN000029092.
The prevalence of domestic violence and its association with family factors: A cross-sectional study among pregnant women in urban communities of Hengyang City, China
Authors: Zheng Baohua , Zhu Xidi , Hu Zhao , Zhou Wensu , Yu Yunhan , Yin Shilin , Xu Huilan 
Published: April 2020

Abstract
Background：With the increased vulnerability during pregnancy, domestic violence (DV) is a serious threat to the physical and mental health of pregnant women, making it a significant issue in public health initiatives. In China, family is of great significance to pregnant women, but few scholars have focused specifically on the relationship between the family factors of pregnant women and DV. This study aimed to explore the prevalence and association between family factors and DV among women in late pregnancy, to provide evidence for the prevention of domestic violence during pregnancy. Methods：A cross-sectional survey was conducted from July-October, 2019 among pregnant women in urban communities of Hengyang City, Hunan Province, China. A total of 813 participants were included by a multi-staged cluster random sampling method. DV was assessed by the Abuse Assessment Screen Questionnaire (AAS). A multivariate binary logistic regression model was used to evaluate the relationship between family factors and DV. Results：Ultimately, 127 (15.62%) participants were identified as victims of DV. After adjustment, the potential risk factors of DV were tensions between their mother-in-law and other family members (OR: 2.85; 95% CI: 1.29 to 6.30 and OR: 3.30; 95% CI: 1.57 to 6.93), medium household debt (OR: 2.17; 95% CI: 1.18 to 4.00), middle and low family APGARI (OR: 2.01; 95% CI: 1.30 to 3.13 and OR: 4.01; 95% CI: 2.09 to 7.69). Conclusions：In summary, women in late pregnancy were at higher risk of DV in the family with tensions, medium household debt and family dysfunction, which may help medical personnel intervene in cases of domestic violence against pregnant women in a reasonable and timely manner.
Did the extended coverage policy contribute to alleviating socioeconomic inequality in untreated dental caries of both children and adolescents in South Korea?
Authors: Shin Bo-Mi , Jung Se-Hwang , Kim Myong-Hee , Ryu Jae-In 
Published: April 2020

Abstract
Background Dental sealants have been covered by the National Health Insurance Service (NHIS) since December 2009 in South Korea. This study aims to determine whether the socioeconomic inequality in untreated dental caries decreased after implementing the extended coverage policy for dental sealant.Methods The data were derived from the fourth (2007–2009) and sixth (2013–2015) waves of the Korean National Health and Nutrition Examination Survey (KNHANES) conducted by the Korea Centers for Disease Control and Prevention (KCDC). Dental caries and sealant experience by income quartiles were tested using the Rao-Scott chi-squared test. In order to examine socioeconomic inequalities and their trends over time, the prevalence ratios (PRs), slope index of inequality (SII), and relative index of inequality (RII) were estimated for each wave and age group. All analyses were conducted using SAS version 9.3.Results The adjusted PRs of untreated dental caries and sealants in the poorest in the aged 6-11 group were significantly higher and lower, respectively, compared to the most affluent quartile group for the fourth wave; however, all significant differences disappeared for the sixth wave, after the sealant coverage. The gap between the lowest and the highest was similar for the aged 12-18 group but it widened in the untreated dental caries even after the sealant coverage. The statistical significance of the PRs was maintained at the sixth wave for both caries and sealants. Children showed decreases in both SII and RII over time so its significance disappeared. The SII among adolescents decreased over time but the RII of untreated dental caries increased.Conclusions This study found that the NHIS coverage expansion of dental care had a positive effect on overall status in dental health among children and adolescents. However, younger children benefited more in terms of inequalities. Our findings indicate that strategies to enhance access to preventive dental services should consider the differential effects for the vulnerable population in terms of socioeconomic status and age from the beginning stage of the policy.
The association between sialolithiasis and smoking, alcohol drinking and obesity in Korea: A nested case-control study
Authors: Jin Young Ju , Han Young Eun , Choi Hyo Geun 
Published: April 2020

Abstract
Background: Smoking and alcohol consumption are the most common social habits in patients with sialolithiasis. Moreover, obesity has been reported to have a significant association with poor oral hygiene, one of the causes of sialolithiasis. The purpose of this study was to evaluate the relationships among tobacco smoking, drinking alcohol, obesity and sialolithiasis in a Korean population.Methods: The Korean National Health Insurance Service-Health Screening Cohort, which includes patients ≥ 40 years old, was assessed from 2002 to 2013. A total of 947 sialolithiasis participants were matched with 3,788 control subjects at a ratio of 1:4 with respect to age group, sex, income group, region of residence, hypertension, diabetes, and dyslipidemia. We analyzed the participants’ previous histories of smoking (current or past smokers compared to nonsmokers) and alcohol consumption (≥ 1 time per week compared to < 1 time per week) in the sialolithiasis and control groups. Obesity was measured using body mass index (BMI, kg/m2), which was categorized as < 18.5 (underweight), ≥ 18.5 and < 23 (normal), ≥ 23 and < 25 (overweight), ≥ 25 and < 30 (obese I), and ≥ 30 (obese II). Crude and adjusted odds ratios (ORs) and 95% confidence intervals (CIs) were calculated using conditional logistic regression analyses.Results: The rate of smoking was higher in the sialolithiasis group (32.4% [307/947]) than in the control group (29.1% [1,103/3,788], P = 0.047). The adjusted OR of smoking for the sialolithiasis group was 1.31 (95% CI = 1.08-1.59, P = 0.006). Alcohol consumption and obesity were not statistically significantly related to sialolithiasis.Conclusion: The odds of smoking were increased in sialolithiasis patients compared with control subjects in the population ≥ 40 years of age.
BAMscale: quantification of next-generation sequencing peaks and generation of scaled coverage tracks
Authors: Pongor Lorinc , Gross Jacob M , Alvarez Roberto Vera , Murai Junko , Jang Sang-Min , Zhang Hongliang , Redon Christophe , Fu Haiqing , Huang Shar-Yin , Thakur Bhushan , Baris Adrian , Marino-Ramirez Leonardo , Landsman David , Aladjem Mirit I , Pommier Yves 
Published: April 2020

Abstract
Background Next-generation sequencing allows genome-wide analysis of changes in chromatin states and gene expression. Data analysis of these increasingly used methods either requires multiple analysis steps, or extensive computational time. We sought to develop a tool for rapid quantification of sequencing peaks from diverse experimental sources and an efficient method to produce coverage tracks for accurate visualization that can be intuitively displayed and interpreted by experimentalists with minimal bioinformatics background. We demonstrate its strength and usability by integrating data from several types of sequencing approaches. Results We have developed BAMscale , a one-step tool that processes a wide set of sequencing datasets. To demonstrate the usefulness of BAMscale , we analyzed multiple sequencing datasets from chromatin immunoprecipitation sequencing data (ChIP-seq), chromatin state change data (Assay for Transposase-Accessible Chromatin using sequencing: ATAC-seq, DNA double-strand break mapping sequencing: END-seq), DNA replication data (Okazaki fragments sequencing: OK-seq, Nascent-strand sequencing: NS-seq, single-cell replication timing sequencing: scRepli-seq) and RNA-seq data. The outputs consist of raw and normalized peak scores (multiple normalizations) in text format and scaled bigWig coverage tracks that are directly accessible to data visualization programs. BAMScale also includes a visualization module facilitating direct, on-demand quantitative peak comparisons that can be used by experimentalists. Our tool can effectively analyze large sequencing datasets (~100Gb size) in minutes, outperforming currently available tools. Conclusions BAMscale accurately quantifies and normalizes identified peaks directly from BAM files, and creates coverage tracks for visualization in genome browsers. BAMScale can be implemented for a wide set of methods for calculating coverage tracks, including ChIP-seq and ATAC-seq, as well as methods that currently require specialized, separate tools for analyses, such as splice aware RNA-seq, END-seq and OK-seq for which no dedicated software is available. BAMscale is freely available on github ( https://github.com/ncbi/BAMscale ).
Non-health outcomes affecting self-care behaviors and medical decision-making preference in patients with type 2 diabetes: a cross-sectional study
Authors: Wang Ming-Jye , Lin Hung-Ming , Hung Li-Chen , Lo Yi-Ting 
Published: April 2020

Abstract
Background: The effects of patient sustained self-care behaviors on glycemic control are even greater than the effects of medical treatment, indicating the value of identifying the factors that influence self-care behaviors. To date, these factors have not been placed in a single model to clarify the critical path affecting self-care behaviors. The aims of this study were to explore the relationships of these factors and the differences in patient preference for medical decision-making.Methods: A cross-sectional study was conducted among outpatients with type 2 diabetes at a regional teaching hospital. Purposive sampling was adopted to recruit 316 eligible patients via self-administered questionnaires. Partial least squares structural equation modeling was used for analysis.Results: Significant direct pathways were identified from health literacy to self-efficacy, patient empowerment, and self-care behaviors; from self-efficacy to self-care behaviors; and from patient empowerment to self-care behaviors. Indirect pathways were from health literacy to self-care behaviors via self-efficacy or patient empowerment. The pathway from health literacy to self-efficacy was significantly stronger in those preferring shared decision-making than in those who preferred physician decision-making. Conclusions: Health literacy is a critical factor in improving self-care behaviors in patients with type 2 diabetes, and the effect of health literacy on self-efficacy was more significant in the shared decision-making than in the physician decision-making. Therefore, developing an effective health strategy to strengthen health literacy awareness and designing friendly, diverse health literacy materials, and application tools is the most important factor to facilitate self-care behaviors in this population.
Evaluation of resistance to pyrethroid and organophosphate adulticides and kdr genotyping in Aedes aegypti populations from Roraima, the Northernmost Brazilian State
Authors: Hayd Ramão Luciano Nogueira , Carrara Luana , Lima Joel de Melo , de Almeida Nathalia Coelho Vargas , Lima José Bento Pereira , Martins Ademir Jesus 
Published: April 2020

Abstract
Background. Roraima, the northernmost State in Brazil, borders Venezuela and Guyana. Although mostly covered by the tropical forests, the urban centers of this State are highly infested with Ae. aegypti and endemic for dengue, Zika and chikungunya. Herein we present the levels of Ae. aegypti infestation and number of arboviruses cases between 2015 and 2018 in the studied localities. We accessed the insecticide resistance status of Ae. aegypti populations from the capital Boa Vista, two cities on international borders (Pacaraima and Bonfim) and Rorainópolis bordering Amazonas State, in order to evaluate the chemical control efficacy in these localities. Methods. Tests with World Health Organization (WHO)-like tubes impregnated with the pyrethroid deltamethrin (0.05 and 0.12%) and the organophosphate malathion (0.7%) were conducted with Ae. aegypti from Boa Vista, Pacaraima, Bonfim and Rorainópolis, collected in 2016 and 2018. Genotyping of kdr mutations, related to resistance to pyrethroids, was performed for the SNP variations in the sites 1016 and 1534 of the voltage gated sodium channel gene (NaV) with a TaqMan qPCR approach. Results. Ae. albopictus was absent in our collections, and therefore only Ae. aegypti was tested. All Ae. aegypti populations were susceptible to 0.7% malathion in 2016, however mortality dropped to under 90% in Bonfim and Pacaraima populations in 2018. All populations were resistant to 0.05% deltamethrin in both years. The time that 50% of females suffered knockdown (KdT50) under exposition to 0.05% deltamethrin was 3.3-5.9 fold longer in mosquitoes from the populations compared to the susceptible strain Rockefeller. Only Pacaraima population (2018) remained resistant to 0.12% deltamethrin. The kdr genotyping revealed the absence of the wild-type NaVS haplotype (1016Val + 1534Phe) in the populations from Roraima, signifying that all tested insects had a genetic background for pyrethroid resistance. The double kdr NaVR2 haplotype (1016Ile + 15434Cys) was present in higher frequencies in all populations except Rorainópolis, where this haplotype seems to have arrived recently. Conclusions. These results are important for the knowledge about insecticide resistance status of Ae. aegypti populations from Roraima and will help to improve vector control strategies that may be applied to diverse localities under similar geographical and urban conditions.
Physiological Effects of Different Recruitment Maneuvers for Improved Lung Inhomogeneity in a Pig Model of ARDS
Authors: Xia Feiping , Pan Chun , Wang Lihui , Liu Ling , Liu Songqiao , Guo Fengmei , Yang Yi , Huang Yingzi 
Published: April 2020

Abstract
Background: In acute respiratory distress syndrome (ARDS), lung recruitment maneuvers can recruit collapsed alveoli in gravity-dependent lung regions, improving the homogeneity of ventilation distribution. This study used electrical impedance tomography (EIT) to investigate the physiological effects of different recruitment maneuvers for alveolar recruitment in a pig model of ARDS. Methods: ARDS was induced in ten healthy male pigs with repeated bronchoalveolar lavage until the arterial partial pressure of oxygen (PaO2)/fraction of inspired oxygen (FiO2) (P/F ratio) was < 100 mmHg and remained stable for 30 minutes (TARDS). ARDS pigs underwent three sequential recruitment maneuvers, including sustained inflation (SI), increments of positive end-expiratory pressure (PEEP) (IP), and pressure-controlled ventilation (PCV) applied in random order, with 30 mins at a PEEP of 5 cmH2O between maneuvers. Respiratory mechanics, hemodynamics, arterial blood gas, and EIT were recorded at baseline, TARDS, and before and after each recruitment maneuver.Results: In all ten pigs, ARDS was successfully induced with a mean 2.8±1.03L (2800±1032.80ml) bronchoalveolar lavages. PaO2, SO2, P/F, and compliance were significantly improved after recruitment with SI, IP or PCV (all p<0.05), and there were no significant differences between maneuvers. Global inhomogeneity (GI) was significantly decreased after recruitment with SI, IP, or PCV. There were no significant differences in GI before or after recruitment with the different maneuvers. The decrease in GI (ΔGI) was significantly greater after recruitment with IP compared to SI (p=0.023), but there was no significant difference in ΔGI between IP and PCV.Conclusion: SI, IP, and PCV increased oxygenation, and regional and global compliance of the respiratory system, and decreased inhomogeneous gas distribution in ARDS pigs. IP significantly improved inhomogeneity of the lung compared to SI.