bluuebunny/crossref_metadata_2025_split huggingface dataset:
A programmable CRISPR/Cas9-based phage defense system for Escherichia coli BL21(DE3)
Authors: Liu Li , Zhao Dongdong , Ye Lijun , Zhan Tao , Xiong Bin , Hu Muzi , Bi Changhao , Zhang Xueli 
Published: January 2020

Abstract
Escherichia coli BL21 is arguably the most popular host for industrial production of proteins, and industrial fermentations are often plagued by phage infections. The CRISPR/Cas system is guided by a gRNA to cleave a specific DNA cassette, which can be developed into a highly efficient programable phage defense system. In this work, we constructed a CRISPR/Cas system targeting multiple positions on the genome of T7 phage and found that it increased the ability of BL21 to defend against phage infection. Furthermore, the targeted loci played a critical role. For better control of expression of CRISPR/Cas9, various modes were tested, and the OD of the optimized strain BL21(pT7cas9, pT7-3gRNA, prfp) after 4 hours of phage infection was significantly improved, reaching 2.0, which was similar to the control culture without phage infection. The viable cell count of the engineered strain in the presence of phage was only one order of magnitude lower than that of the strain with no infection, which further demonstrated the effectiveness of the CRISPR/Cas9 phage defense system. Finally, the engineered BL21 strain under phage attack expressed RFP protein at about 60% the rate of the un-infected control, which was significantly higher than the parent BL21. We successfully constructed a programable CRISPR/Cas9 system to increase the ability of E. coli BL21’s to defend against phage infection, and created a resistant protein expression host. This work provides a simple and feasible strategy for protecting industrial E. coli strains against phage infection.
Social support and subjective well-being among elderly Chinese empty-nester: Self-worth as a Mediator and self-reported health as a Moderator
Authors: Su Hong , Zhou Yuqiu , Cao Jianqin , Wang Haina 
Published: January 2020

Abstract
Purpose This study aimed to explore the relationship between social support, self-worth, self-reported health, and subjective well-being among the Chinese rural empty nest elderly, and whether self-worth and self-reported health affect these associations.Methods This cross-sectional study was performed from May 2017 to April 2018, the participants were 365 empty-nest elderly adults from rural areas of Chifeng City in Inner Mongolia. Data were collected with the General information questionnaire, Self-worth questionnaire for adults, Social Support Scale and Memorial University of New Found land Scale of Happiness. Structural equation modeling was used to test the mediation hypothesis. Bootstrapping was performed to confirm the mediation effect. Hayes’s SPSS-PROCESS was used for testing the moderating eﬀects.Results Self-worth showed significant correlations with social support, self-reported health and subjective well-being (all P<0.01).Bootstrapping indicated that the mediating role of self-worth was statistically significant. And self-reported health moderated the social support and subjective well-being association.Conclusions Self-worth and self-reported health are important targets for prevention and intervention for improving the subjective well-being of the rural empty-nest elderly.
Does Balancing Site Characteristics Result in Balanced Population Characteristics in a Cluster-Randomized Controlled Trial?
Authors: Stolzmann Kelly , Lew Robert , Miller Christopher J , Kim Bo , Wu Hongsheng , Bauer Mark S 
Published: January 2020

Abstract
BackgroundIntervention trials with nested designs seek to balance sites randomized regarding key site characteristics. Among the goals of such site-level balancing is to accrue patient-level equivalence among treatment arms. We investigated patient-level equivalence in a cluster randomized controlled trial, which balanced study waves on site-level characteristics.Methods The Behavioral Health Interdisciplinary Program - Collaborative Chronic Care Model project utilized a stepped wedge design to stagger implementation of an evidence-based team-oriented mental health patient management system at 9 Veteran Affairs Medical Centers. Study sites were balanced on eight site-level characteristics over time (3 balanced waves [consecutive time periods] with 3 sites per wave) to minimize trend. Sites were balanced on selected site-level characteristics but not on patient-level variables. We explored internal differences in patient demographics across the three study waves. Eligible patients had at least two visits to a participating mental health clinic in the prior year and did not have a diagnosis of dementia (n=5,596).Results We found modest but statistically significant inter-site differences in age, marital status, ethnicity, service-related disability, mental health hospitalizations, and selected diagnoses by study wave. Although many of the differences in patient demographics by study wave were statistically significant, only a few results were practically meaningful as measured by effect size. A bipolar diagnosis (49.0%, 21.0%, 17.0% in waves 1-3, respectively; Cramer’s V=.3124) and Hispanic ethnicity (2.9%, 29.6%, 2.0% in waves 1-3, respectively; Cramer’s V=.3949) resulted in differences that were considered a ‘moderate’ effect size. The number of patient characteristics that were both statistically and meaningfully different by study wave among all possible site assignments was comparable to the 34 most balanced site assignments identified in our balancing algorithm.Conclusions Using a balancing algorithm to reduce imbalance among site characteristics across time periods did not appear to negatively affect the balance of patient characteristics across sites over time. A site-level balancing algorithm that includes characteristics with a direct relationship to relevant patient-level factors may improve the overall balance across key elements of the study, and aide in the interpretation of results.
Association of Genetic Polymorphisms in Tumour Necrosis Factor-alpha (TNF-α-308G/A) and Interleukin-6 (IL-6-174G/C and IL-6-634C/G) with lung cancer risk: a meta-analysis
Authors: Guo Yibo , Wang Xinshuai , Yuan Xiang , Liu Yiwen , Sun Wei , Gao Shegan 
Published: January 2020

Abstract
Background: Several studies have indicated an association between tumor necrosis factor-alpha (TNF-α) or interleukin(IL)-6 gene polymorphisms and the risk of lung cancer. However, the conclusions remain controversial. The aim of this study is to examine the association of tumour necrosis factor-alpha (TNF-α) and interleukin-6（IL-6） gene polymorphisms with the risk of developing lung cancer. Methods: We searched several electronic databases, including PubMed and Excerpt Medica Database (EMBASE). The effects of three polymorphisms, TNF-α-308G/A, IL-6-174G/C and IL-6-634C/G, were evaluated. The pooled odds ratio (OR) with 95% confidence interval (CI) was calculated by RevMan software. Heterogeneity was also assessed. Results: For a total of 17 studies involving 4,094 cases and 4,988 controls, were identified in this meta-analysis. Based on our results, we found an association between the TNF-α-308G/A polymorphism and lung cancer risk under the dominant model (GG+GA vs. AA, OR = 0.60, 95% CI: 0.40 to 0.89). For the IL-6-174G/C polymorphisms, the pooled ORs (95% CI) of GG/GC vs. CC, GG vs. GC/CC, GC vs. CC, and GG vs. CC were 1.22 (1.02 to 1.46), 1.22 (1.01 to 1.48), 1.22 (1.01 to 1.48), and 1.12 (0.87 to 1.44), respectively. For the IL-6-634C/G polymorphisms, the pooled ORs (95% CI) of CC/CG vs. GG, CC vs. CG/GG, and C vs. G were 1.04 (0.68 to 1.58), 0.69 (0.57 to 0.85), and 0.79 (0.67 to 0.93) respectively. Conclusions: The results of our analysis of these IL-6 polymorphisms revealed an association between IL-6 and lung cancer risk. This association, however, was not as strong as the association between TNF-α-308G/A polymorphisms and lung cancer risk. Because the current study was limited in sample size, further studies are needed to reveal more precise associations.
Mental health and psychosocial support for families of missing persons in Sri Lanka: a retrospective cohort study
Authors: Andersen Ida , Poudyal Bhava , Abeypala Arundathi , Uriarte Carla , Rossi Rodolfo 
Published: January 2020

Abstract
BackgroundThe International Committee of the Red Cross (ICRC) has developed its ‘Accompaniment model’ to address the multi-faceted needs of relatives of people who go missing during armed conflict. In Sri Lanka an Accompaniment Programme was launched in 2015 for the relatives of the more than 16,000 missing persons who remain unaccounted for. Method1,783 relatives who took part in the mental health and psychosocial support (MHPSS) component of the ICRC’s Accompaniment Programme in Sri Lanka between April 2016 and August 2017 were offered eight peer-support group sessions, individual home visits, referrals to local services, and commemoration events to pay tribute to their missing relatives. Symptoms of anxiety and depression (using the HADS scale), somatic distress (using the BSI scale) and daily functioning (ICRC scale) were assessed before and after the MHPSS intervention. ResultsPrior to receiving support, Tamil and Muslim ethnicity, ≥60 years of age and civilian status were predictors of severe symptoms of anxiety; Tamil ethnicity, ≥50 years of age and being the mother of a missing person were predictors of severe symptoms of depression; and ≥50 years of age and severe symptoms of anxiety and depression were predictors of severe somatic pain. After receiving support, the vast majority of the relatives of missing persons showed reduced levels of anxiety (81%), depression (79%) and somatic pain (77%), as well as increased functioning (75%). Predictors of improvement following support were severe levels of distress at baseline and Tamil and Muslim ethnicity. In addition, attending at least three group sessions was a predictor of decreased anxiety, age group 51-60 was a predictor of decreased depression, female gender was a predictor of decreased somatic distress, and referrals were a predictor of increased functioning. ConclusionThe MHPSS component of the ICRC’s Accompaniment Programme is a promising approach to helping families to cope with not knowing the fate and whereabouts of their missing relatives, to reduce distress, to break their social isolation and to resume more functional lives. However, further research is needed, possibly through a controlled trial, to better establish the effectiveness of this approach.
Unraveling city-specific signature and identifying sample origin locations for the data from CAMDA MetaSUB challenge
Authors: Zhang Runzhi , Walker Alejandro R. , Datta Susmita 
Published: January 2020

Abstract
BackgroundComposition of microbial communities can be location specific, and the different abundance of taxon within location could help us to unravel city-specific signature and predict the sample origin locations accurately. In this study, the whole genome shotgun (WGS) metagenomics data from samples across 16 cities around the world and samples from another 8 cities were provided as the main and mystery datasets respectively as the part of the CAMDA 2019 MetaSUB “Forensic Challenge”. The feature selection, normalization, three methods of machine learning, PCoA (Principal Coordinates Analysis) and ANCOM (Analysis of composition of microbiomes) were conducted for both the main and mystery datasets.ResultsFeature selection, combined with the machines learning methods, revealed that the combination of the common features was effective for predicting the origin of the samples. The average error rates of 11.6% and 30.0% of three machine learning methods were obtained for main and mystery datasets respectively. Using the samples from main dataset to predict the labels of samples from mystery dataset, nearly 89.98% of the test samples could be correctly labeled as “mystery” samples. PCoA showed that nearly 60% of the total variability of the data could be explained by the first two PCoA axes. Although many cities overlapped, the separation of some cities was found in PCoA. The results of ANCOM, combined with importance score from the Random Forest, indicated that the common “family”, “order” of the main-dataset and the common “order” of the mystery dataset provided the most efficient information for prediction respectively.ConclusionsThe results of the classification suggested that the composition of the microbiomes was distinctive across the cities, which was also supported by the results from ANCOM and importance score from the RF. The analysis utilized in this study can be of great help in field of forensic science to efficiently predict the origin of the samples. And the accurate of the prediction could be improved by more samples and better sequencing depth.
Sarcopenic is associated with hypertension in older adults: a systematic review and meta-analysis
Authors: Bai Tingting , Fang Fang , Li Feika , Ren Yan , Hu Jiaan , Cao Jiumei 
Published: January 2020

Abstract
BackgroundBoth sarcopenia and handgrip strength have been observed association with hypertension. However, the results in different studies were inconsistent. In the current study, we conducted a systematic review and meta-analysis to reveal the association between sarcopenia, handgrip strength, and hypertension in older adults.MethodsPubMed, MEDLINE, Cochrane Library, and EMBASE databases were searched from inception to 15 November, 2019for original research studies. The studies that addressed the association between sarcopenia, handgrip strength, and hypertension were included and summarized.Results19 studies met the inclusion criteria and a total of 21301 were included in the meta-analysis. Eight eligible studiesreported the odd ratios (ORs) of hypertension and the ORs ranged from 0.41 to 4.38. When pooled the ORs together, the summarized ORs was 1.29 [95% confidence interval (CI) =1.00-1.67]. The summarized ORs for the Asian group 1.50 (95% CI=1.35-1.67) was significantly higher than that of Caucasian group 1.08 (95% CI=0.39-2.97). Eleven studies provided the data on association between handgrip strength and hypertension. The overall ORs and 95% CI was 0.99 (95% CI=0.80-1.23), showing no association.ConclusionSarcopenia was associated with hypertension but no correlation was found between handgrip strength and hypertension in older adults.
Multiplex tests for respiratory tract infections, direct utility of FilmArray respiratory panel in the emergency department
Authors: Yang Siyuan , Li Hui , Tang Yunxia , Yu Fengting , Ma Chengjie , Zhang Huimin , Pang Lin , Hongxin Zhao , Wang Linghang 
Published: January 2020

Abstract
BackgroundThe FilmArray respiratory panel with 20 targets for viral and atypical pathogens aimed at point of care tests, as multiplex tests for respiratory tract infections it has been widely used and verified in various clinical trials. The FilmArray respiratory panel (FilmArray RP) seems to be a reliable and rapid tool in special tests settings such as clinical laboratory, and it’s necessary to evaluate the panel’s performance in point of care directly with non-specific tests settings. MethodsIn this single-centre, open, observational study, we enrolled outpatients with respiratory tract infection from emergency department during 2016-2017 winter season, specimens from participants were detected using FilmArray RP. All steps including recruitment, collection of specimens and testing were performed by our clinical staff. The results of pathogens detected, clinical and demographic data were collected and analyzed. ResultsBetween October 2016 and May 2017, we enrolled 271 eligible patients, FilmArray RP was successful used in 270 patients: 196 (72.6 %) patients had been detected with one or more pathogens, 74 (27.4) patients got negative results; in the analysis of signal pathogen detected, influenza A virus had the highest rate of detection, and the rate in group ≤ 16 years, 16-49 years and ≥ 50 years was 22.8 %, 32.4 %, 31.1 % respectively; 45 (16.7 %) patients were co-detected with two or more respiratory pathogens, most multiplex pathogens were rhinovirus/enterovirus co-detected with Bordetella. pertussis (17.8 %). The outcomes provided by FilmArray RP had impact on the prescriptions of antimicrobials, there were difference in the rates of antibiotic prescriptions and anti-influenza prescriptions among patients with Flu A/B virus detected, non-Flu A/B virus pathogen detected and non-pathogen.ConclusionsThe performance of FilmArray RP using by clinical staffs was successfully implemented in emergency department for which is the first time in China. The multiplex diagnostic system significantly increased the rate of respiratory pathogens detected in diagnostic methods limited hospital. Despite this, FilmArray RP has a potential use as a tool for point of care testing in non-specific setting and operated by clinical staffs not in a laboratory.
Nosocomial outbreak of Aeromonas hydrophila surgical site infections after spinal surgery: Identification and control
Authors: Xiao Xiumei , Jiang Yu , Yang Xu , Zheng Jiajia , Guo Zhaoqing , Qi Qiang , Zeng Yan , Sun Chuiguo , Chen Zhongqiang , Cui Liyan , Li Weishi 
Published: January 2020

Abstract
Background: Aeromonas hydrophila surgical site infections (SSIs) were diagnosed in April 2017 in four patients who had received spinal surgery. We launched an outbreak investigation to identify the source, and accordingly, preventive and control measures were implemented. Methods: Environmental samples and samples from the healthcare providers were collected for microbiological analysis. The clonal relatedness of A. hydrophila strains was determined by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Whole genome sequencing (WGS) of one clinical A. hydrophila isolate (AE456) was performed using an Illumina NovaSeq PE150. Results: We identified eight case patients with SSIs due to A. hydrophila in orthopaedic ward 2 (three males; median age, 58 years). Strict infection control measures were adopted, particularly contact precautions and unit disinfection. We also identified A. hydrophila from water in a fish tank. PFGE and MLST revealed identical patterns and STs among the 10 clinical A. hydrophila strains (clone A, ST 517), which were different from those of the strains from the fish tank (clone B, ST518). WGS of isolate AE456 revealed the presence of cepS, cphA and blaOXA-12 genes encoding resistance to β-lactams. All patients recovered after antimicrobial therapy and/or surgical debridement. After removal of the fish tank, no new case occurred, and the outbreak was stopped.Conclusions: Aeromonas hydrophila is rare, but severe, pathogen in surgical infections and caused long hospital stay and physical suffering. Strict measures, including environmental disinfection and contact precautions, are needed to prevent infection outbreak after surgery.
Extreme Gradient Boosting for Parkinson’s Disease Diagnosis from Voice Recordings
Authors: Karabayir Ibrahim , Pappu Suguna , Goldman Samuel , Akbilgic Oguz 
Published: January 2020

Abstract
Background : Parkinson’s Disease (PD) is a clinically diagnosed neurodegenerative disorder that affects both motor and non-motor neural circuits. Speech deterioration (hypokinetic dysarthria) is a common symptom, which often presents early in the disease course. Machine learning can help movement disorders specialists improve their diagnostic accuracy using non-invasive and inexpensive voice recordings. Method : We used “Parkinson Dataset with Replicated Acoustic Features Data Set” from the UCI-Machine Learning repository. The dataset included 45 features including sex and 44 speech test based acoustic features from 40 patients with Parkinson’s disease and 40 controls. We analyzed the data using various machine learning algorithms including tree-based ensemble approaches such as random forest and extreme gradient boosting. We also implemented a variable importance analysis to identify important variables classifying patients with PD. Results : The cohort included total of 80 subjects; 40 patients with PD (55% men) and 40 controls (67.5% men). PD patients showed at least two of the three symptoms; resting tremor, bradykinesia, or rigidity. All patients were over 50 years old and the mean age for PD subjects and controls were 69.6 (SD 7.8) and 66.4 (SD 8.4), respectively. Our final model provided an AUC of 0.940 with 95% confidence interval 0.935-0.945in 4-folds cross validation using only six acoustic features including Delta3 (Run2), Delta0 (Run 3), MFCC4 (Run 2), Delta10 (Run 2/Run 3), MFCC10 (Run 2) and Jitter_Rap (Run 1/Run 2). Conclusions : Machine learning can accurately detect Parkinson’s disease using an inexpensive and non-invasive voice recording. Such technologies can be deployed into smartphones for screening of large patient populations for Parkinson’s disease.
Pre-application of dentin bonding agent prevents discoloration by mineral trioxide aggregate
Authors: Choi Yoo-Lim , Jang Young-Eun , Kim Bom Sahn , Kim Jin-Woo , Kim Yemi 
Published: January 2020

Abstract
Background: To evaluate tooth discoloration by newly developed calcium silicate-based materials, and to examine the pre-application of dentin bonding agent (DBA) for preventing discoloration caused by mineral trioxide aggregate (MTA). Methods: The roots of 50 premolars were randomly divided into five groups (n=10) and cavities were prepared from resected root surfaces. MTA was placed in the cavities of teeth belonging to the ProRoot MTA (Pr) and RetroMTA (Rt) groups. For teeth belonging to the DBA + ProRoot MTA (B-Pr) and DBA + RetroMTA (B-Rt) groups, DBA was first applied to the cavities prior to the addition of MTA. Teeth in the control group were restored with composite resin only (i.e., without MTA). After 12 weeks, MTA was removed from the Pr and Rt teeth and bleaching agents were applied for 3 additional weeks. Color assessments were recorded at baseline, and 1, 4, and 12 weeks, as well as after bleaching. Results: Following 12 weeks of MTA treatment, there was a significant difference between the discoloration in the Pr and B-Pr groups. However, no significant difference was observed between the Rt and B-Rt groups. Following bleaching, the color changes (ΔE values) of the Pr group were not significantly different from those of the B-Pr group. The difference of ΔE between the Rt group after internal bleaching and the B-Rt group also was not significant. Conclusions: RetroMTA caused significantly less discoloration than ProRoot MTA. Pre-application of DBA prevented discoloration by ProRoot MTA. MTA discoloration was improved equally well between DBA pre-application and post-bleaching. Clinical Relevance Tooth discoloration by mineral trioxide aggregate (MTA) limits its use in esthetic region. The pre-application of dentin bonding agent (DBA) and the newly developed RetroMTA prevented discoloration caused by MTA, thus expanding its use in esthetic applications.