bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison and development of a metagenomic next-generation sequencing protocol for combined detection of DNA and RNA pathogens in cerebrospinal fluid
Authors: Jiang Hanfang , Xing Zhihao , Liu Xiaorong , Chai Qiang , Xin Zefeng , Zhu Chunqing , Lin Ruihong , Deng Xuwen , Cui Dong , Gao HongDan , Ma Dongli 
Published: April 2022

Abstract
Background
The purpose of this study was to evaluate different pretreatment, extraction, amplification, and library generation methods for metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) and to develop an efficient procedure for the simultaneous detection of DNA and RNA pathogens.

Methods
We generated thirteen mock CSF samples with four representative pathogens of encephalitis. Each sample was subjected to ten different methods by varying sample pretreatment/nucleic acid extraction (microbial DNA, total DNA, total NA, total RNA, Whole Transcriptome Amplification (WTA)) and library generation (Illumina or NEB). Negative extraction controls (NECs) were used for each method variation.

Results
We found that the quality of mNGS sequencing reads was higher from the NEB kit for library generation. Microbial DNA and total RNA increased microbial deposition by depleting the host DNA. Methods total NA and total RNA can detect gram-positive, gram-negative, RNA and DNA pathogens. We applied mNGS, including total NA and NEB library generation, to CSF samples from five patients diagnosed with infectious encephalitis and correctly determined all pathogens identified in clinical etiological tests.

Conclusions
Our findings suggested that total nucleic acid extraction combined with NEB library generation is the most effective mNGS procedure in CSF pathogen detection. The optimization of positive criteria and databases can improve the specificity and sensitivity of mNGS diagnosis.
Trial registration: Chinese Clinical Trial Registry, ChiCTR1800015425 (29/03/2018), https://www.chictr.org.cn/edit.aspx?pid=26292&htm=4.
Diagnostic accuracy of circulating microRNAs for hepatitis C virus-associated hepatocellular carcinoma: a systematic review and meta-analysis
Authors: Huang Yicheng , Chen Yingsha , Tu Sheng , Zhang Jiajie , Qiu Yunqing , Yu Wei 
Published: April 2022

Abstract
Aims
The purpose of this study was to perform an assessment of circulating microRNAs (miRNAs) as promising biomarker for hepatitis C virus (HCV)-associated hepatocellular carcinoma (HCV-HCC) through a meta-analysis.

Methods
A comprehensive literatures search extended up to March 1, 2020 in PubMed, Cochrane library, Embase, Web of Science, Scopus and Ovid databases. The collected data were analyzed by random-effects model, the pooled sensitivity (SEN), specificity (SPE), positive and negative likelihood ratios (PLR and NLR), diagnostic odds ratio (DOR), and area under the curve (AUC) were used to explore the diagnostic performance of circulating miRNAs. Meta-regression and subgroup analysis were further carried out to explore the heterogeneity.

Results
A total of 16 articles including 3606 HCV-HCC patients and 3387 HCV patients without HCC were collected. The pooled estimates indicated miRNAs could distinguish HCC patients from chronic hepatitis C (CHC) and HCV-associated liver cirrhosis (HCV-LC), with a SEN of 0.83 (95% CI, 0.79–0.87), a SPE of 0.77 (95% CI, 0.71–0.82), a DOR of 17 (95% CI, 12–28), and an AUC of 0.87 (95% CI, 0.84–0.90). The combination of miRNAs and AFP showed a better diagnostic accuracy than each alone. Subgroup analysis demonstrated that diagnostic accuracy of miRNAs was better for plasma types, up-regulated miRNAs, and miRNA clusters. There was no evidence of publication bias in Deeks’ funnel plot.

Conclusions
Circulating miRNAs, especially for miRNA clusters, have a relatively high diagnostic value for HCV-HCC from CHC and HCV-LC.
Effects of high frequency rTMS of contralesional dorsal premotor cortex in severe subcortical chronic stroke: protocol of a randomized controlled trial with multimodal neuroimaging assessments
Authors: Li Jiali , Wang Hewei , Yuan Yujian , Fan Yunhui , Liu Fan , Zhu Jingjing , Xu Qing , Chen Lan , Guo Miao , Ji Zhaoying , Chen Yun , Yu Qiurong , Gao Tianhao , Hua Yan , Fan Mingxia , Sun Limin 
Published: April 2022

Abstract
Background
Previous studies have revealed that low frequency repeated transcranial magnetic stimulation (rTMS) on the contralesional primary motor cortex (cM1) is less effective in severe stroke patients with poor neural structural reserve than in patients with highly reserved descending motor pathway. This may be attributed to the fact that secondary motor cortex, especially contralesional dorsal premotor cortex (cPMd), might play an important compensatory role in the motor function recovery of severely affected upper extremity. The main purpose of this study is to compare the effectiveness of low frequency rTMS on cM1 and high frequency rTMS on cPMd in subcortical chronic stroke patients with severe hemiplegia. By longitudinal analysis of multimodal neuroimaging data, we hope to elucidate the possible mechanism of brain reorganization following different treatment regimens of rTMS therapy, and to determine the cut-off of stimulation strategy selection based on the degree of neural structural reserve.

Methods/design
The study will be a single-blinded randomized controlled trial involving a total of 60 subcortical chronic stroke patients with severe upper limb motor impairments. All patients will receive 3 weeks of conventional rehabilitation treatment, while they will be divided into three groups and receive different rTMS treatments: cM1 low frequency rTMS (n = 20), cPMd high frequency rTMS (n = 20), and sham stimulation group (n = 20). Clinical functional assessment, multimodal functional MRI (fMRI) scanning, and electrophysiological measurement will be performed before intervention, 3 weeks after intervention, and 4 weeks after the treatment, respectively.

Discussion
This will be the first study to compare the effects of low-frequency rTMS of cM1 and high-frequency rTMS of cPMd. The outcome of this study will provide a theoretical basis for clarifying the bimodal balance-recovery model of stroke, and provide a strategy for individualized rTMS treatment for stroke in future studies and clinical practice.

Trial registration
Chinese Clinical Trial Registry, ChiCTR1900027399. Registered on 12 Nov 2019, http://www.chictr.org.cn/showproj.aspx?proj=43686.
Use of assessment instruments in forensic evaluations of criminal responsibility in Norway
Authors: Løvgren Pia Jorde , Laake Petter , Reitan Solveig Klæbo , Narud Kjersti 
Published: April 2022

Abstract
Objectives
Assessment instruments are often used to enhance quality and objectivity in therapeutic and legal settings. We aimed to explore the use of instruments in Norwegian reports of forensic evaluations of criminal responsibility; specifically, whether this use was associated with diagnostic and forensic conclusions.

Methods
Our study has an exploratory cross-sectional design. We examined 500 reports filed with the Norwegian Board of Forensic Medicine in 2009–2018 regarding defendants indicted for the most serious violent crimes. The first author coded data from all reports according to a registration form developed for this study. Two co-authors then coded a random sample of 50 reports, and inter-rater reliability measures were calculated. The first author coded 41 reports for calculation of intra-rater reliability. Descriptive statistics are presented for the use of assessment instruments, and a generalized linear mixed model (GLMM) was used to estimate associations between the use of instruments and diagnostic and forensic conclusions.

Results
Instruments were used in 50.0% of reports. The Wechler’s Adult Intelligence Scale (WAIS), Historical Clinical Risk-20 (HCR-20), and the Structured Clinical Interview for DSM disorders (SCID I), were used in 15.8, 13.8, and 9.0% of reports, respectively. The use of instruments increased from 36% in 2009 to 58% in 2015; then decreased to 49% in 2018. Teams of two experts wrote 98.0% of reports, and 43.4% of these teams comprised two psychiatrists. In 20.0% of reports, the diagnostic conclusion was schizophrenia, and in 8.8% it was other psychotic disorders. A conclusion of criminal irresponsibility was given in 25.8% of reports. Instruments were more often used in reports written by teams that comprised both a psychiatrist and a psychologist, compared to reports by two psychiatrists. The use of instruments was strongly associated with both diagnostic and forensic conclusions.

Conclusion
Instruments were used in 50% of reports on forensic evaluations of criminal responsibility in Norway, and their use increased during the study period. Use of instruments was associated with diagnostic and forensic conclusions.
Internalizing symptoms in adolescence are modestly affected by symptoms of anxiety, depression, and neurodevelopmental disorders in childhood
Authors: Doering Sabrina , Larsson Henrik , Halldner Linda , Gillberg Christopher , Kuja-Halkola Ralf , Lundström Sebastian 
Published: April 2022

Abstract
Background
Internalizing disorders, such as anxiety and depressive disorders, are common mental disorders in young people, but a detailed understanding of the symptom continuity from childhood to adolescence that additionally includes a variety of neurodevelopmental disorder (NDD) symptoms is lacking. We therefore aimed to assess the extent to which parent-reported anxiety, depression, and NDD symptoms in childhood predict parent-reported internalizing symptoms in adolescence.

Methods
We used the nation-wide population-based Child and Adolescent Twin Study in Sweden, comprising 4492 twins born in Sweden between 1998 and 2003 that were assessed at age 9, and then again at age 15. Linear regression in a structural equation modelling framework was used to analyze the data.

Results
Overall, our results indicate that 15.9% of the variance in internalizing symptoms at age 15 can be predicted by anxiety, depression, and NDD symptoms at age 9. Anxiety and NDD symptoms in childhood predicted the largest amount of internalizing symptoms in adolescence.

Conclusions
Adolescent internalizing symptoms are modestly affected by childhood symptoms of anxiety, depression, and NDDs, suggesting that they may represent different constructs across age. Future studies should further empirically investigate differences in etiology and trajectories of childhood versus adolescent internalizing symptoms.
Type and intensity distribution of structured and incidental lifestyle physical activity of students and office workers: a retrospective content analysis
Authors: Wallmann-Sperlich Birgit , Düking Peter , Müller Miriam , Froböse Ingo , Sperlich Billy 
Published: April 2022

Abstract
Background
Physical activity (PA) guidelines acknowledge the health benefits of regular moderate-to-vigorous physical activity (MVPA) regardless of bout duration. However, little knowledge exists concerning the type and intensity distribution of structured and incidental lifestyle PA of students and office workers. The present study aimed to i) assess the duration and distribution of intensity of MVPAs during waking hours ≥50% of heart rate reserve (HRR), ii) to identify the type of PA through diary assessment, iii) to assign these activities into structured and lifestyle incidental PA, and iv) to compare this information between students and office workers.

Methods
Twenty-three healthy participants (11 students, 12 office workers) recorded heart rate (HR) with a wrist-worn HR monitor (Polar M600) and filled out a PA diary throughout seven consecutive days (i.e. ≥ 8 waking h/day). Relative HR zones were calculated, and PA diary information was coded using the Compendium of PA. We matched HR data with the reported PA and identified PA bouts during waking time ≥ 50% HRR concerning duration, HRR zone, type of PA, and assigned each activity to incidental and structured PA. Descriptive measures for time spend in different HRR zones and differences between students and office workers were calculated.

Results
In total, we analyzed 276.894 s (76 h 54 min 54 s) of waking time in HRR zones ≥50% and identified 169 different types of PA. The participants spend 31.9 ± 27.1 min/day or 3.9 ± 3.2% of their waking time in zones of ≥50% HRR with no difference between students and office workers (p > 0.01). The proportion of assigned incidental lifestyle PA was 76.9 ± 22.5%.

Conclusions
The present study provides initial insights regarding the type, amount, and distribution of intensity of structured and incidental lifestyle PA ≥ 50% HRR. Findings show a substantial amount of incidental lifestyle PA during waking hours and display the importance of promoting a physically active lifestyle. Future research could employ ambulatory assessments with integrated electronic diaries to detect information on the type and context of MVPA during the day.
Prevalence of suicidal ideation and suicide attempts among refugees: a meta-analysis
Authors: Haase Elisa , Schönfelder Antje , Nesterko Yuriy , Glaesmer Heide 
Published: April 2022

Abstract
Background
Suicidal ideation and attempts are one of the most serious mental health problems affecting refugees. Risk factors such as mental disorders, low socio-economic status, and stressful life events all contribute to making refugees a high-risk group. For this reason, this meta-analysis aims to investigate the prevalence of suicidal ideation and attempts among refugees in non-clinical populations.

Method
We searched PubMed, Web of Science, PubPsych, and PsycInfo for articles reporting (period) prevalence rates of suicidal ideation and attempts. Inclusion criteria were the population of refugees or asylum seekers (aged 16 years and older), assessment of the prevalence of suicidal ideation and attempts in empirical studies in cross-sectional or longitudinal settings, written in English, and published by August 2020. Exclusion criteria were defined as a population of immigrants who have lived in the host country for a long time, studies that examined children and adolescents younger than 16 years, and research in clinical samples. Overall prevalence rates were calculated using Rstudio.

Results
Of 294 matches, 11 publications met the inclusion criteria. The overall period prevalence of suicidal ideation was 20.5% (CI: 0.11–0.32, I2 = 98%, n = 8), 22.3% (CI: 0.10–0.38, I2 = 97%, n = 5) for women, and 27.7% for men (CI: 0.14–0.45, I2 = 93%, n = 3). Suicide attempts had an overall prevalence of 0.57% (CI: 0.00–0.02, I2 = 81%, n = 4).

Conclusion
There is a great lack of epidemiological studies on suicidal ideation and attempts among refugees. The high prevalence of suicidal ideation indicates the existence of heavy psychological burden among this population. The prevalence of suicide attempts is similar to that in non-refugee populations. Because of the large heterogeneity between studies, the pooled prevalence estimates must be interpreted with caution. The results underline the need for systematic and standardized assessment and treatment of suicidal ideation and attempts.
The ROX index as a predictor of high-flow nasal cannula outcome in pneumonia patients with acute hypoxemic respiratory failure: a systematic review and meta-analysis
Authors: Zhou Xiaoyang , Liu Jiequan , Pan Jianneng , Xu Zhaojun , Xu Jianfei 
Published: April 2022

Abstract
Background
The respiratory rate-oxygenation (ROX) index has been increasingly applied to predict the outcome of high-flow nasal cannula (HFNC) in pneumonia patients with acute hypoxemic respiratory failure (AHRF). However, its diagnostic accuracy for the HFNC outcome has not yet been systematically assessed. This meta-analysis sought to evaluate the predictive performance of the ROC index for the successful weaning from HFNC in pneumonia patients with AHRF.

Methods
A literature search was conducted on electronic databases through February 12, 2022, to retrieve studies that investigated the diagnostic accuracy of the ROC index for the outcome of HFNC application in pneumonia patients with AHRF. The area under the hierarchical summary receiver operating characteristic curve (AUHSROC) was estimated as the primary measure of diagnostic accuracy due to the varied cutoff values of the index. We observed the distribution of the cutoff values and estimated the optimal threshold with corresponding 95% confidential interval (CI).

Results
Thirteen observational studies comprising 1751 patients were included, of whom 1003 (57.3%) successfully weaned from HFNC. The ROC index exhibits good performance for predicting the successful weaning from HFNC in pneumonia patients with AHRF, with an AUHSROC of 0.81 (95% CI 0.77–0.84), a pooled sensitivity of 0.71 (95% CI 0.64–0.78), and a pooled specificity of 0.78 (95% CI 0.70–0.84). The cutoff values of the ROX index were nearly conically symmetrically distributed; most data were centered between 4.5 and 6.0, and the mean and median values were 4.8 (95% CI 4.2–5.4) and 5.3 (95% CI 4.2–5.5), respectively. Moreover, the AUHSROC in the subgroup of measurement within 6 h after commencing HFNC was comparable to that in the subgroup of measurement during 6–12 h. The stratified analyses also suggested that the ROC index was a reliable predictor of HFNC success in pneumonia patients with coronavirus disease 2019.

Conclusions
In pneumonia patients with AHRF, the ROX index measured within 12 h after HFNC initiation is a good predictor of successful weaning from HFNC. The range of 4.2–5.4 may represent the optimal confidence interval for the prediction of HFNC outcome.
Dentists’ situation and their needs during the COVID-19 pandemic in Nepal: an online questionnaire survey
Authors: Harada Yuriko , Iwashita Hanako , Prajapati Dilip , Sugishita Tomohiko 
Published: April 2022

Abstract
Background
During the coronavirus disease (COVID-19) pandemic, ordinary dental services were sustained in Nepal. Because a dental practice is considered to involve a high risk of infection, the needs of dentists should be identified, and demand-driven support should be provided. The purpose of this study was to investigate the situation and needs of dentists during the COVID-19 pandemic in order to guide demand-driven support. First, we investigated how the situation of Nepali dentists differed according to their types of practices between private clinics and university/government hospitals. Second, we assessed the characteristics of dentists demanding four types of support: financial, material, technical, and guidelines/guidance support.

Methods
A cross-sectional online questionnaire survey was conducted between July 28th and August 7th 2020. Closed-ended questions were prepared regarding behavior, material availability, economic and psychological impacts, training, and the main support dentists wanted to receive. The situation of dentists between private clinics and university/government hospitals was determined using a chi-squared test for each variable. To examine the association between the characteristics of dentists and four types of support, multivariable logistic regression analyses were used to estimate adjusted odds ratios (ORs) with a 95% confidence interval (CI) for each variable.

Results
There were 352 dentists (137 males and 215 females) included in the analysis. Private clinic dentists experienced a bigger economic impact and demanded financial support that 45.5% of them did not receive a salary, compared to 18.9% in university/government hospitals. On the contrary, university/government hospitals experienced lack of PPE and demanded material support that 79.8% had personal protective equipment, compared to 92.5% in private clinics. Financial support was demanded significantly more by male than female dentists (ORs = 5.56; 95% CI = 2.96–10.45). Material support was demanded significantly more by dentists who received training regarding COVID-19 management (ORs = 1.96; 95% CI = 1.01–3.81). Technical support was demanded significantly less by male dentists (ORs = 0.44; 95% CI = 0.23–0.83). Guideline/guidance support was demanded significantly more by dentists who answered that Nepal Dental Association provided appropriate support (ORs = 2.21; 95% CI = 1.25–3.91).

Conclusion
This study articulated the diverse needs of Nepali dentists during the COVID-19 pandemic. Demand-driven support should be provided in the future.
Assessing changes in the quality of quantitative health educations research: a perspective from communities of practice
Authors: Wright Katherine M. , Gruppen Larry D. , Kuo Kevin W. , Muzyk Andrew , Nahmias Jeffry , Reed Darcy A. , Sandhu Gurjit , Shelgikar Anita V. , Stojan Jennifer N. , Uchida Toshiko L. , Wallihan Rebecca , Hurtubise Larry 
Published: April 2022

Abstract
Background
As a community of practice (CoP), medical education depends on its research literature to communicate new knowledge, examine alternative perspectives, and share methodological innovations. As a key route of communication, the medical education CoP must be concerned about the rigor and validity of its research literature, but prior studies have suggested the need to improve medical education research quality. Of concern in the present study is the question of how responsive the medical education research literature is to changes in the CoP. We examine the nature and extent of changes in the quality of medical education research over a decade, using a widely cited study of research quality in the medical education research literature as a benchmark to compare more recent quality indicators.

Methods
A bibliometric analysis was conducted to examine the methodologic quality of quantitative medical education research studies published in 13 selected journals from September 2013 to December 2014. Quality scores were calculated for 482 medical education studies using a 10-item Medical Education Research Study Quality Instrument (MERSQI) that has demonstrated strong validity evidence. These data were compared with data from the original study for the same journals in the period September 2002 to December 2003. Eleven investigators representing 6 academic medical centers reviewed and scored the research studies that met inclusion and exclusion criteria. Primary outcome measures include MERSQI quality indicators for 6 domains: study design, sampling, type of data, validity, data analysis, and outcomes.

Results
There were statistically significant improvements in four sub-domain measures: study design, type of data, validity and outcomes. There were no changes in sampling quality or the appropriateness of data analysis methods. There was a small but significant increase in the use of patient outcomes in these studies.

Conclusions
Overall, we judge this as equivocal evidence for the responsiveness of the research literature to changes in the medical education CoP. This study identified areas of strength as well as opportunities for continued development of medical education research.