bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of a new Rapid Antimicrobial Susceptibility system for Gram-negative and Gram-positive bloodstream infections: Speed and accuracy of Alfred 60 AST
Authors: Anton-Vazquez Vanesa , Samuel Adjepong , Cristina Suarez , Timothy Planche 
Published: November 2019

Abstract
Background: Blood stream infections (BSIs) are a major cause of morbidity and mortality. The time from taking blood cultures to obtain results of antibiotic sensitivity can be up to five days which impacts patient care. The Alfred 60 AST™ can reduce laboratory time from positive culture bottle to susceptibility results from 16-25 hours to 5-6 hours, transforming patient care. To evaluate the diagnostic accuracy of a rapid antimicrobial susceptibility system, the Alfred 60 AST™, in clinical isolates from patients with BSIs and confirm time to results. 301 Gram-negative and 86 Gram-positive isolates were analysed directly from positive blood culture bottles following Gram staining. Antimicrobial susceptibility results and time-to-results obtained by rapid Alfred 60 AST system and BD Phoenix were compared . Results: A total of 2,196 antimicrobial susceptibility test results (AST) were performed: 1,863 Gram-negative and 333 Gram-positive. AST categorical agreement (CA) for Alfred 60 AST™ was 95% (1772/1863) for Gram-negative and 89% (295/333) for Gram-positive isolates. Gram-negative CA: ampicillin 96% (290/301); ciprofloxacin 95% (283/297); ceftriaxone 96% (75/78); meropenem 97% (288/297); piperacillin-tazobactam 95% (280/295); gentamicin 94% (279/297) and amikacin 93% (277/298). The median time to susceptibility results from blood culture flagging positive was 6.3 h vs 20 h (p<0.01) for Alfred system vs BD Phoenix™. Conclusion: Alfred 60 AST system greatly reduced time to antimicrobial susceptibility results in Gram-negative and Gram-positive BSIs with good performance and cost, particularly for Gram-negative bacteraemia. Keywords: Rapid diagnostics. Bloodstream infection. Bacteraemia. Antimicrobial susceptibility testing. Gram-negative bacteria. Gram-positive bacteria
Genome-wide identification and comparison of differentially expressed profiles of miRNAs and lncRNAs with associated ceRNA networks in the gonads of Chinese soft-shelled turtle, Pelodiscus sinensis
Authors: Ma Xiao , Cen Shuangshuang , Wang Luming , Zhang Chao , Wu Limin , Tian Xue , Wu Qisheng , Li Xuejun , Wang Xiaoqing 
Published: November 2019

Abstract
Background: The gonad is the major factor affecting animal reproduction. The regulatory mechanism of the expression of protein-coding genes involved in reproduction still remains to be elucidated. Increasing evidence has shown that ncRNAs play key regulatory roles in gene expression in many life processes. The roles of microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) in reproduction have been investigated in some species. However, the regulatory patterns of miRNA and lncRNA in the sex biased expression of protein coding genes remains to be elucidated. In this study, we performed an integrated analysis of miRNA, messenger RNA (mRNA), and lncRNA expression profiles to explore their regulatory patterns in the female ovary and male testis of the soft-shelled turtle, Pelodiscus sinensis. Results: We identified 10 446 mature miRNAs, 20 414 mRNAs and 28 500 lncRNAs in the ovaries and testes, and 633 miRNAs, 11 319 mRNAs, and 10 495 lncRNAs showed different expression. A total of 2 814 target genes were identified for miRNAs. The predicted target genes of these differentially expressed (DE) miRNAs and lncRNAs included abundant genes related to reproductive regulation. Furthermore, we found that 189 DE miRNAs and 5 408 DElncRNAs showed sex-specific expression. Of these, 3 DEmiRNAs and 917 DElncRNAs were testis specific and 186 DEmiRNAs and 4 491 DElncRNAs were ovary specific. We further constructed compete endogenous lncRNA-miRNA-mRNA networks using bioinformatics, including 103 DEmiRNAs, 636 DEmRNAs, and 1 622 DElncRNAs. The target genes for the differentially expressed miRNAs and lncRNAs included abundant genes involved in gonadal development, including Wt1, Creb3l2, Gata4, Wnt2, Nr5a1, Hsd17, Igf2r, H2afz, Lin52, Trim71, Zar1, and Jazf1. Conclusions: In animals, miRNA and lncRNA as master regulators regulate reproductive processes by controlling the expression of mRNAs. Considering their importance, the identified miRNAs, lncRNAs, and their targets in P. sinensis might be useful for studying the molecular processes involved in sexual reproduction and genome editing to produce higher quality aquaculture animals. A thorough understanding of ncRNA-based cellular regulatory networks will aid in the improvement of P. sinensis reproductive traits for aquaculture.
HIV-1 CRF01_AE subtype and HIV-1 DNA level among patients with chronic HIV-1 infection: a correlation study
Authors: Lyu Tingxia , Yue Yongsong , Evelyn Hsieh , Han Yang , Zhu Ting , Song Xiaojing , Cao Wei , Lyu Wei , Wang Jianhua , Li Taisheng 
Published: November 2019

Abstract
Background: The impact of HIV-1 subtype (CRF01_AE and non-CRF01_AE) on HIV-1 DNA levels in HIV-1 chronically infected patients with suppressive antiretroviral therapy (ART) remains poorly understood. To evaluate the correlation of HIV-1 subtype with DNA level, and identify baseline predictors of HIV-1 DNA decay. Methods: ART-naïve HIV-1-infected patients from two large multi-center studies in China were classified into CRF01_AE and non-CRF01_AE subtype groups. Peripheral blood samples were collected at baseline and week 12, 24, 48 and 96 after ART initiation and total HIV-1 DNA levels were quantified by real-time PCR. HIV-1 DNA levels at week 96 were categorized into high, moderate, and low levels, reflecting HIV-1 DNA ≥ 3, 2–3, ≤ 2 log10 copies/106 PBMCs, respectively, and the corresponding proportion of CRF01_AE and non-CRF01_AE subtype were compared. The baseline predictors of low HIV-1 total DNA levels (≤ 2 log10 copies/106 PBMCs) at week 96 were evaluated using a logistic regression model. Results: Compared to the non-CRF01_AE subtypes (n=185), patients with CRF01_AE subtype (n=188) harboured a higher level of HIV-1 DNA (median: 3.19 vs. 2.95 log10 copies/106 PBMCs, P < 0.001) prior to treatment. After 96 weeks of ART, HIV-1 DNA levels remained higher in the CRF01_AE subtype group (median: 2.63 vs. 2.39 log10 copies/106 PBMCs, P = 0.002). There was no significant difference in the proportion of patients achieving high (22.3% vs. 14.6%, P = 0.054), moderate (59.6% vs. 60.5%, P = 0.849) and low levels (18.1% vs 24.9%, P = 0.111) between CRF01_AE and non-CRF01_AE groups. In the multivariable analysis, baseline HIV-1 DNA level and CD4+ T cell count but not the subtype were independent risk factors for achieving HIV-1 DNA level ≤ 2 log10 copies/106 PBMCs. Conclusion: HIV-1 CRF01_AE subtype is neither correlated with HIV-1 DNA reservoir decline nor a prognostic factor for achieving lower HIV-1 DNA levels (≤ 2 log10 copies/106 PBMCs) after ART. However, higher HIV-1 DNA level in HIV-1 CRF01_AE patients should be aroused much attention and strengthen surveillance during ART.
Social Determinants of Psychological Wellness for Children and Adolescents in Rural NSW
Authors: Peters Ingrid , Handley Tonelle , Oakley Karen , Lutkin Sarah , Perkins David 
Published: November 2019

Abstract
Background: The mental wellness of children and adolescents in rural Australia is under researched and key to understanding the long-term mental health outcomes for rural communities. This study used data from the Australian Rural Mental Health Study (ARMHS), particularly the parent report Strengths and Difficulties Questionnaire (SDQ) measure for children under 18 years old and their reporting parent’s demographic information to compare this sample’s mental wellness scores to the Australian norms and to identify what personal, family, community and rurality factors contribute to child mental wellness as pertaining to the SDQ total and subdomain scores. Method: 539 children from 294 families from rural NSW were included. SDQ scores for each child as well as personal factors (sex and age), family factors (employment status, household income and sense of community of responding parent), community SES (IRSAD) and rurality (ASCG) were examined. Results: Children and adolescents from rural areas had poorer mental wellness when compared to a normative Australian sample. Further, personal and family factors were significant predictors of the psychological wellness of children and adolescents, while after controlling for other factors, community SES and level of rurality did not contribute significantly. Conclusions: Early intervention for children and families living in rural and remote communities is warranted particularly for low income families. There is a growing need for affordable, universal and accessible services provided in a timely way to balance the discrepancy of mental wellness scores between rural and urban communities.
Motor Intervention With And Without Nintendo® Wii For Children With Developmental Coordination Disorder: Protocol For A Randomized Clinical Trial
Authors: NETO JORGE Lopes CAVALCANTE , Steenbergen Bert , Tudella Eloisa 
Published: November 2019

Abstract
Background: Despite the benefits highlighted by motor interventions based on virtual reality for children with Developmental Coordination Disorder (DCD), there are still doubts whether these are greater than those obtained with conventional interventions due to the absence of systematized protocols and lack of evidence. Here we present a protocol to systematically compare the effects of two motor training programs (one Nintendo® Wii based and the other no-Wii motor activities) on the motor learning in children with DCD. Methods/Design: Two intervention protocols (one based on Nintendo® Wii and the other no-Wii motor activities) will be carried out, with interventions occurring twice a week in 60-minute sessions, with a minimum of 12 and a maximum of 16 sessions per child. The protocols were developed based on the domains of the Movement Assessment Battery for Children – Second Edition (MABC-2) (Manual dexterity, aiming & catching, balance), with two activities for each of the MABC -2 domains. The study will include children aged 7 to 10 with total MABC-2 score ≤16, and Developmental Coordination Disorder Questionnaire (DCDQ) score <46 (age of 7 years), score <55 (age group of 8 to 9 years and 11 months), or score <57 (age of 10 years) as scored by the parents. Children will be randomly allocated by draw in one of the two intervention protocols. MABC-2 and DCDQ will be applied before and after intervention to evaluate the effects of the interventions on motor performance and parents’ perception respectively. Motor learning will be assessed by means of the scores obtained in the games. Evaluators and therapists will be trained and evaluators will be blind about the data of the children in the study. Discussion: Owing to its motivating aspects, training with Nintendo® Wii may be particularly beneficial for children with DCD. The results of this study protocol will help researchers and therapists to better understand the benefits of Nintendo® Wii based motor intervention over those obtained with no-Wii interventions in children with DCD. It will also create references about more systematized protocols for replication in clinical practice, seeking the improvement of the motor components of these children. Trial registration: http://www.ensaiosclinicos.gov.br/rg/RBR-89ydgj/
PS4DR: a multimodal workflow for identification and prioritization of drugs based on pathway signatures
Authors: Emon Mhammad Asif , Domingo-Fernández Daniel , Hoyt Charles Tapley , Hofmann-Apitius Martin 
Published: November 2019

Abstract
Background: During the last decade, there has been a surge towards computational drug repositioning owing to constantly increasing -omics data in the biomedical research field. While numerous existing methods focus on the integration of heterogeneous data to propose candidate drugs, it is still challenging to substantiate their results with mechanistic insights of these candidate drugs. Therefore, there is an unmet need for more innovative and efficient methods which can enable better integration of the data and knowledge for drug repositioning.
Results: Here, we present a customizable workflow (PS4DR) which not only integrates high-throughput data such as genome-wide association study (GWAS) data and gene expression signatures from disease and drug perturbations but also takes pathway knowledge into consideration to predict drug candidates for repositioning. We have collected and integrated publicly available GWAS data and gene expression signatures for several diseases and hundreds of FDA-approved drugs or those under clinical trial in this study. Additionally, different pathway databases were used for mechanistic knowledge integration in the workflow. Using this systematic consolidation of data and knowledge, the workflow computes pathway signatures that assist in the prediction of new indications for approved and investigational drugs.
Conclusion: We showcase PS4DR with applications on how this tool can be used for repurposing drugs as well as to propose drugs that can simulate disease dysregulations. We were able to validate our workflow by demonstrating its capability to predict FDA-approved drugs for their approved indications for several diseases. Further, PS4DR returned many potential drug candidates for repositioning that were backed up by epidemiological evidence extracted from the scientific literature. Source code is freely available at https://github.com/ps4dr/ps4dr.
Bio-Plex phosphoprotein assay using spinal cords and skeletal muscles of mice
Authors: Iida Madoka , Katsuno Masahisa 
Published: November 2019

Abstract
Bio-Plex phosphoprotein assays are magnetic bead-based immunoassays for the detection of intracellular phosphoproteins in cell and tissue lysates. The assay can be readily multiplexed to simultaneously examine the expression levels of numerous phosphorylated proteins.
Inequity in healthcare needs, health service use and financial burden of medical expenditures in China: results from a consecutive household monitoring study in Jiangsu Province
Authors: Jiang Weixi , Xu Xiaolin , Tang Shenglan , Xu Ling , Zhang Yaoguang , Elbers Chris , Cobelens Frank , Yan Lijing 
Published: November 2019

Abstract
Background: Although public medical insurance covers over 95% of the population in China, disparities in health service use and out-of-pocket (OOP) health expenditure across income groups are still widely observed. This study aims to investigate the socio-economic disparities in perceived healthcare needs, informal care, formal care and payment for healthcare and explore their equity implication.

Methods: We assessed healthcare needs, service use and payment in 400 households in rural and urban areas in Jiangsu, China, and included only the adult sample (N=925). One baseline survey and 10 follow-up surveys were conducted during the 7-month monitoring period, and the Affordability Ladder Program (ALP) framework was adopted for data analysis. Negative binomial/zero-inflated negative binomial and logit regression models were used to explore factors associated with perceived needs of care and with the use of self-treatment, outpatient and inpatient care respectively. Two-part model and logit regression modeling were conducted to explore factors associated with OOP health expenditure and with the likelihood of incurring catastrophic health expenditure (CHE).

Results : After adjusting for covariates, rural residence was significantly associated with more perceived healthcare needs, more self-treatment, higher probability of using outpatient and inpatient service, more OOP health expenditure and higher likelihood of incurring catastrophic expenditure ( P <0.05). Compared to the Urban Employee Basic Medical Insurance (UEBMI), enrollment in the New Rural Cooperative Medical Scheme (NRCMS) or in the Urban Resident Basic Medical Insurance (URBMI) was correlated with lower probability of ever using outpatient services, but with more outpatient visits when people were at risk of using outpatient service ( P <0.05). NRCMS/URBMI enrollment was also associated with higher likelihood of incurring CHE compared to UEBMI enrollment (OR=2.02, P <0.05); in stratified analysis of the rural and urban sample this effect was only significant for the rural population.

Conclusions: The rural population in Jiangsu perceived more healthcare needs, had a higher probability of using both informal and formal healthcare services, and had more OOP health expenditure and a higher likelihood of incurring CHE. The inequity mainly exists in health care financing, and may be partially addressed through improving the benefit packages of NRCMS/URBMI.
TOPK Promotes Metastasis of Esophageal Squamous Cell Carcinoma by Activating the Src/GSK3β/STAT3 Signaling Pathway via γ-Catenin
Authors: Jiang Yanan , Zhang Jing , Zhao Jimin , Li Zhenzhen , Chen Hanyong , Qiao Yan , Chen Xinhuan , liu kangdong , Dong Ziming 
Published: November 2019

Abstract
Background Esophageal squamous cell carcinoma (ESCC) is a fatal disease with poor prognosis. The predominant reason for ESCC-related death is distal metastasis. A comprehensive understanding of the molecular mechanism underlying metastasis is needed for improving patient prognosis. T-LAK cell-originated protein kinase (TOPK) is a MAPKK-like kinase, which plays a vital role in various physiological and pathophysiological processes. However, the role of TOPK in ESCC metastasis is unclear. Methods Tissue array was used to evaluate the correlation between TOPK expression and ESCC lymph node metastasis. Wound healing assay, transwell assay, and lung metastasis mice model were used to examine the role of TOPK in the migration of ESCC cells in vitro and in vivo. Protein kinase array, mass spectrometry (MS), and molecular modeling were used to examine the pathways and direct target proteins of TOPK that are involved in ESCC metastasis. Additionally, immunofluorescence and western blotting analyses were performed to verify these findings. Results The enhanced expression of TOPK was correlated with lymph node metastasis in the ESCC tissues. TOPK knockdown or treatment with the TOPK inhibitor (HI-TOPK-032) decreased the invasion and migration of ESCC cells in vitro. HI-TOPK-032 also inhibited the lung metastasis in ESCC cell xenograft in vivo model. Moreover, TOPK promoted the invasion of ESCC cells by activating the Src/GSK3β/STAT3 and ERK signaling pathways via γ-catenin. Conclusion The findings of this study reveal that TOPK is involved in ESCC metastasis and promoted the ESCC cell mobility by activating the Src/GSK3β/STAT3 and ERK signaling pathways. This indicated that TOPK may be a potential molecular therapeutic target for ESCC metastasis. Keywords esophageal squamous cell carcinoma; TOPK; tumor metastasis; Src/GSK3β/STAT3; γ-catenin
Biodegradation of Endocrine Disruptor Bisphenol A by Pseudomonas putida Strain YC-AE1 Isolated from Polluted Soil, Guangdong, China
Authors: Eltoukhy Adel Aly Esmail , Jia Yang , Nahurira Ruth , Abo-Kadoum M. A. , Khokhar Ibatsam , Wang Junhuan , Yan Yanchun 
Published: November 2019

Abstract
Background
Bisphenol A is an important organic chemical as an intermediate, final and inert ingredient in manufacturing of many important products like polycarbonate plastics, epoxy resins, flame retardants, food–drink packaging coating, and other. BPA is an endocrine disruptor compound that mimics the function of estrogen causing damage to reproductive organs. Bacterial degradation has been consider as a cost effective and eco-friendly method for BPA degradation compared with physical and chemical methods. This study aimed to isolate and identify bacterial strain capable to degrade and tolerate high concentrations of this pollutant, studying the factors affecting the degradation process and study the degradation mechanism of this strain.
Results
YC-AE1 is a Gram negative bacterial strain isolated from soil and identified as Pseudomonas putida by 16S rRNA gene sequence and BIOLOG identification system. This strain found to have a high capacity to degrade the endocrine disruptor Bisphenol A (BPA). Response surface methodology using central composite design was used to statistically optimize the environmental factors during BPA degradation and the results obtained by significant model were 7.2, 30 oC and 2.5 % for optimum initial pH, temperature and inoculum size, respectively. Prolonged incubation period with low NaCl concentration improve the biodegradation of BPA. Analysis of variance (ANOVA) showed high coefficient of determination, R2 and Adj-R2 which were 0.9979 and 0.9935, respectively. Substrate analysis found that, strain YC-AE1 could degrade a wide variety of bisphenol A-related pollutants such as bisphenol B, bisphenol F, bisphenol S, Dibutyl phthalate, Diethylhexyl phthalate and Diethyl phthalate in varying proportion. Pseudomonas putida YC-AE1 showed high ability to degrade a wide range of BPA concentrations (0.5-1000 mg l−1) with completely degradation for 500 mg l−1 within 72 hours. Metabolic intermediates detected in this study by HPLC-MS were identified as 4,4-dihydroxy-alpha-methylstilbene, p-hydroxybenzaldeyde, p-hydroxyacetophenone, 4-hydroxyphenylacetate, 4-hydroxyphenacyl alcohol, 2,2-bis(4-hydroxyphenyl)-1-propanol, 1,2-bis(4-hydroxyphenyl)-2-propanol and 2,2-bis(4-hydroxyphenyl) propanoate.
Conclusions
This study reports Pseudomonas putida YC-AE1 as BPA biodegrader with high performance in degradation and tolerance to high BPA concentration. It exhibited strong degradation capacity and prominent adaptability towards a wide range of environmental conditions. Moreover, it degrades BPA in a short time via two different degradation pathways.
Comprehensive 5-P framework for active ageing through ecological approach: an iterative systematic review
Authors: Lak Azadeh , Rashidghalam Parichehr , Myint Phyo K , Bradaran Hamid R 
Published: November 2019

Abstract
Background "Active Ageing" is an inclusive term thus has been defined from a variety of aspects in different domains throughout the literature. The aim of this review is to identify the aspects which play significant roles in building this concept in an ecological approach.Methods We searched seven online database s, JSTOR, Pub-Med, Web of Science, Google Scholar, ProQuest, EBSCO, and Scopus, from 2002 to 2018 (from introducing this concept by WHO) for both qualitative and quantitative articles in only English language. Two reviewers independently found the related articles using the search terms “active ageing” and “built environment” and included both “ageing” and “aging”.Results Of 1337 records which passed the screening, 86 were eligible for the inclusion for the review purpose. A total of 15 themes were derived: Personal characteristic, Behavioral attitude, Land- use, Access, Physical form, Cityscape/City Image, Public open spaces, Housing, Social Environment, Cultural Environment, Economic Environment, Good Governance, Physical Health, Mental Health, and Social Health. Ecological themes of active ageing can be defined as the 5P model: Person, Processes, Place and Policy- Making based on the Prime aspect of health.Conclusions This study sheds light on the aspects of "Active Ageing" through ecological model while offering the significance of the multidimensional nature of active ageing micro (person), meso-(process) and macro-system (place and policy-making) based on health (prime) environments according to the relationships between person and environment at the individual, interpersonal and environmental levels for the future research and population ageing policies.