bluuebunny/crossref_metadata_2025_split huggingface dataset:
Risk factors of nosocomial infection after cardiac surgery in children with congenital heart disease
Authors: Yu Xindi , Chen Maolin , Liu Xu , Chen Yiwei , Hao Zedong , Zhang Haibo , Wang Wei 
Published: December 2019

Abstract
Background: The aim of our study was to analyze the risk factors of nosocomial infection after cardiac surgery in children with congenital heart disease (CHD).
Methods: We performed a retrospective cohort study, and children with CHD who underwent open-heart surgeries at Shanghai Children’s Medical Center from January 1, 2012 to December 31, 2018 were included. The baseline characteristics of these patients of different ages, including neonates (0-1 months old), infants (1-12 months old) and children (1-10 years old), were analyzed, and the association of risk factors with postoperative nosocomial infection were assessed.
Results: A total of 11651 subjects were included in the study. The overall nosocomial infection rate was 10.8%. Nosocomial infection rates in neonates, infants, and children with congenital heart disease were 32.9%, 15.4%, and 5.2%, respectively. Multivariate logistic regression analysis found age (OR 0798, 95%CI: 0.769-0.829; P<0.001), STS risk grade (OR 1.267, 95%CI: 1.159-1.385; P<0.001), body mass index (BMI) <5th percentile (OR 1.295, 95%CI: 1.023-1.639; P=0.032), BMI ＞95th percentile (OR 0.792, 95%CI: 0.647-0.969; P=0.023), cardiopulmonary bypass (CPB) time (OR 1.008, 95%CI: 1.003-1.012; P<0.001) and aortic clamping time （OR 1.009, 1.002-1.015; P = 0.008）were significantly associated with nosocomial infection in CHD infants. After adjusted for confounding factors, we found STS risk grade (OR 1.38, 95%CI: 1.167-1.633; P<0.001), BMI<5th percentile (OR 1.934, 95%CI: 1.377-2.715; P<0.001), CPB time (OR 1.018, 95%CI: 1.015-1.022; P<0.001), lymphocyte/WBC ratio﹤cut off value (OR 3.818, 95%CI: 1.529-9.533; P=0.004) and AST＞cut off value (OR 1.546, 95%CI: 1.119-2.136; P=0.008) were significantly associated with nosocomial infection in CHD children.

Conclusion:
Our study suggested STS risk grade, BMI, CPB duration, low lymphocyte/WBC or high neutrophil/WBC ratio were independently associated with nosocomial infection in CHD infant and children after cardiac surgery.
A novel predictive model based on inflammatory markers to assess the prognosis of patients with HBV-related acute-on-chronic liver failure:a retrospective cohort study
Authors: Qiang Li , Qin Jiao , Sun Changfeng , Sheng Yunjian , Chen Wen , Qiu Bangdong , Chen Xin , Chen Yuanfang , Liu Fei , Wu Gang 
Published: December 2019

Abstract
Background: Systemic inflammatory response is closely related to the development and prognosis of liver failure. This study aimed to establish a new model combing the inflammatory markers including neutrophil/lymphocyte ratio (NLR) and red blood cell distribution width (RDW) with several hematological testing indicators to assess the prognosis of patients with hepatitis B virus-related acute-on-chronic liver failure (HBV-ACLF). Methods: A derivation cohort with 421 patients and a validation cohort with 156 patients were recruited from three hospitals. Retrospectively collecting their clinical data and laboratory testing indicators. Medcalc-15.10 software was employed for Data analyses. Results: Multivariate analysis indicated that RDW, NLR, INR, TBIL and Cr were risk factors for 90-day mortality in patients with HBV-ACLF. The risk assessment model is COXRNTIC=0.053×RDW+0.027×NLR+0.003×TBIL+0.317×INR+0.003×Cr (RNTIC) with a cut-off value of 3.08 (sensitivity: 77.89%, specificity: 86.04%). The area under the receiver operating characteristics curve (AUC) of the RNTIC was 0.873 [95%CI(0.837–0.903)], better than the predictive value of MELD score [0.732, 95%CI(0.687–0.774)], MELD-Na [0.714, 95%CI(0.668-0.757)], CTP[0.703, 95%CI(0.657-0.747)], CLIF-SOFA[0.709, 95%CI(0.663-0.752)]. In the validation cohort, RNTIC also performed a better prediction value than MELD score, MELD-Na, CTP and CLIF-SOFA with the AUC of [0.845, 95%CI(0.778-0.898)], [0.768, 95%CI (0.694-0.832)], [0.759, 95%CI(0.684-0.824)], [0.718, 95%CI(0.641-0.787)]and [0.717, 95%CI(0.639-0.786)] respectively. Conclusions: The inflammatory markers RDW and NLR could be used as independent predictors of 90-day mortality in patients with HBV-ACLF. Compared with MELD score, RNTIC had a more powerful predictive value for prognosis of patients with HBV-ACLF.
BMC NeurologyFactors determining recurrence in transient global amnesia
Authors: Tynas Rebecca , Panegyres Peter K 
Published: December 2019

Abstract
Aetiology of transient global amnesia (TGA) remains uncertain, though many have been proposed, including ischaemic, migrainous or epileptic pathologies. We attempted to determine risk factors for TGA, as well as prognostic factors that may cause recurrence. We evaluated clinical history, family history and magnetic resonance diffusion-weighted imaging (DWI) studies of 93 prospective patients with TGA. Patients were followed from 2004-2016. Fifteen of 93 (16%) patients experienced a recurrence of TGA. Among precipitating events, physical activities inducing Valsalva-like manoeuvres were most common, followed by emotional stress. Eighty-four patients had possible comorbidities or risk factors for TGA, though no single risk factor was ubiquitous. Risk factors associated with recurrence were head injury (isolated vs. recurrent, 16.7% vs. 53.5%, p < 0.01), depression (isolated vs. recurrent, 15.4% vs 46.7%, p = 0.01) and family history of dementia (isolated vs. recurrent, 20.5% vs. 46.7%, p = 0.03). Of 15 patients with confirmed recurrent TGA, two developed dementia and four subjective memory impairment. DWI lesions were observed in 24 patients and were located anywhere within the hippocampus. DWI lesions were not significantly associated with outcomes (recurrence, subjective memory impairment, dementia). We have found that depression, previous head injury and family history of dementia may predict TGA recurrence.
What impact do chronic disease self-management support interventions have on health inequity gaps related to socioeconomic status: A Systematic Review
Authors: Hardman Ruth , Begg Stephen , Spelten Evelien 
Published: December 2019

Abstract
Background: The social gradient in chronic disease (CD) is well-documented, and the ability to effectively self-manage is crucial to reducing morbidity and mortality from CD. This systematic review aimed to assess the moderating effect of socioeconomic status on self-management support (SMS) interventions in relation to participation, retention and post-intervention outcomes. Methods: Six databases were searched for studies of any design published until December 2018. Eligible studies reported on outcomes from SMS interventions for adults with chronic disease, where socioeconomic status was recorded and a between-groups comparison on SES was made. Possible outcomes were participation rates, retention rates and clinical or behavioural post-intervention results. Results: Nineteen studies were retrieved, including five studies on participation, five on attrition and nine studies reporting on outcomes following SMS intervention. All participation studies reported reduced engagement in low SES cohorts. Studies assessing retention and post-intervention outcomes had variable results, related to the diversity of interventions. A reduction in health disparity was seen in longer interventions that were individually tailored. Most studies did not provide a theoretical justification for the intervention being investigated, although four studies referred to Bandura’s concept of self-efficacy. Conclusions: The limited research suggests that socioeconomic status does moderate the efficacy of SMS interventions, such that without careful tailoring and direct targeting of barriers to self-management, SMS may exacerbate the social gradient in chronic disease outcomes. Screening for patient disadvantage or workload, rather than simply recording SES, may increase the chances of tailored interventions being directed to those most likely to benefit from them. Future interventions for low SES populations should consider focussing more on treatment burden and patient capacity. Trial registration: PROSPERO registration CRD42019124760 Keywords: Self-management, socioeconomic status, health inequity, patient capacity, chronic disease
Addressing the deprived: Need and access of Sexual reproductive health services to street adolescents in Ethiopia: The case of Nekemte Town: Mixed methods study.
Authors: Ababor Abdo Abazinab , Tesso Desalegn Wirtu , Cheme Melese Chego 
Published: December 2019

Abstract
Objectives

Research knowledge gap exists in addressing sexual reproductive health services to street adolescents globally. The intensity of SRH problem is high in the settings like Ethiopia where there is limited access and integration of services in the way it responds to the needs of the street adolescents and this study aimed at exploring risky sexual behaviors; needs and barriers of SRH services utilization among street adolescents in Nekemte town. Community based Cross-sectional study design with mixed approaches was used on sample size of 219 street adolescents. Supplementary qualitative data of 24 in-depth interviews were collected from the street adolescents and SRH service providers. Time-location sampling or venue sampling technique (VDT) was used for quantitative study. Quantitative data was analyzed by SPSS version 24.0.Results

About 93% of street adolescents reported difficulty of accessing contraceptives. Behavioral change and sustainable access of SRH services is lacking among street adolescents; but, Knowledge gap is more evident in early adolescents (10-13) period than the other classes. Generally, street adolescents are deprived in terms of access of sexual reproductive health services. Mobile and flexible access of contraceptive should be designed targeting street adolescents.
Composite genome sequence of Bacillus clausii, a probiotic commercially available as Enterogermina®, and insights into its probiotic properties
Authors: Khatri Indu , Sharma Gaurav , Subramanian Srikrishna 
Published: December 2019

Abstract
Background: Some of the spore-forming strains of Bacillus probiotics are marketed commercially as they survive harsh gastrointestinal conditions and bestow health benefits to the host.
Results: We report the composite genome of Bacillus clausii ENTPro from a commercially available probiotic Enterogermina® and compare it with the genomes of other Bacillus probiotics. We find that the members of B. clausii species harbor high heterogeneity at the species as well as genus level. The genes conferring resistance to chloramphenicol, streptomycin, rifampicin, and tetracycline in the B. clausii ENTPro strain could be identified. The genes coding for the bacteriocin gallidermin, which prevents biofilm formation in the pathogens S. aureus and S. epidermidis, were also identified. KEGG Pathway analysis suggested that the folate biosynthesis pathway, which depicts one of the important roles of probiotics in the host, is conserved completely in B. subtilis and minimally in Bacillus clausii and other probiotics.
Conclusions: We identified various antibiotic resistance, bacteriocins, stress-related, and adhesion-related domains, and industrially-relevant pathways, in the genomes of these probiotic bacteria that are likely to help them survive in the harsh gastrointestinal tract, facilitating adhesion to host epithelial cells, persistence during antibiotic treatment and combating bacterial infections.
Vitamin D Deficiency in Non-Autoimmune Hypothyroidism: A case-control study
Authors: Ahi Salma , Dehdar Mohammad Reza , Hatami Naser 
Published: December 2019

Abstract
Objectives: Although in many studies, the relationship between autoimmune hypothyroidism (Hashimoto) and Vitamin D deficiency was shown, no research has been performed on the role of vitamin D in non-autoimmune hypothyroidism. Design: This was a Retrospective case–control study in Endocrinology clinic of Jahrom (south of Iran). The patients with Hashimoto (n=633) and non-Hashimoto hypothyroidism (n=305), along with a control group (n=200) were evaluated. 25(OH)D level, T3 and T4 levels were studied and Anti TPO and Anti TG tests were performed. The results of vitamin D level were analyzed and interpreted using SPSS in terms of the cause of hypothyroidism (immune and non-immune). Results: The results of the study showed a significantly lower level of vitamin D in both immune and non-immune Hashimoto’s thyroiditis (HT) in comparison to healthy controls (P<0.05). We observed a significant inverse correlation between the vitamin D and TGAb level (p=0.001, r=-0.261) and a direct correlation of vitamin D with TSH level (p=0.008, r=0.108) in HT patients. Conclusion: Finally, the results indicated that non-autoimmune hypothyroidism, as well as HT, is associated with vitamin D deficiency. The role of vitamin D deficiency in HT was thought to be in the association of higher autoantibody (TGAb) level; while, there should be further studies determining vitamin D deficiency's role in non-immune hypothyroidism.
Evaluating a digital tool for supporting breast cancer patients: a randomised controlled trial protocol (ADAPT)
Authors: Lidington Emma , McGrath Sophie , Noble Jillian , Stanway Susannah , Lucas Amanda , Mohammed Kabir , Graaf Winette van der , Husson Olga 
Published: December 2019

Abstract
Background: There is a growing number of mHealth tools for breast cancer patients but a lack of scientific evidence for their effects. Recent studies have shown a mix of positive and negative impacts on users. Here we will assess the impact of OWise Breast Cancer, a mobile application for self-monitoring symptoms and managing care, on the process of self-management. Methods: This randomised controlled trial with early-stage breast cancer patients will assess the effect of OWise use on patient activation at 3 months from diagnosis measured by the PAM-13 questionnaire. We will also assess differences in changes in health-related quality of life, psychological distress, health status and NHS health resource utilisation over the first year from diagnosis. Participants will be randomly allocated (1:1) to standard care or standard care plus OWise. Participants will complete questionnaires before starting anti-cancer treatment and at 3 months, 6 months and 12 months from diagnosis. Clinical and patient-reported outcome data will be linked to health resource utilisation data from Discover, an integrated care record of primary, secondary and social care in North West London. We will measure contamination in the control group and adjust the sample size to mitigate the dilution of effect estimates. A per protocol analysis will be conducted as a sensitivity analysis to assess robustness of the primary results. Discussion: This study aims to generate evidence for the effectiveness of OWise at improving patient activation for women with early-stage breast cancer. The results will show the impact of using the tool at the patient level and the NHS health system level. The outcomes of the study will have implications for the application of OWise across the NHS for breast cancer patients and expansion into other tumour types. Assessing publicly available mHealth tools poses a challenge to trialists due to the risk of contamination. Here we apply various methods to measure, mitigate and assess the effects of contamination.
Whole genome sequencing of Borrelia miyamotoi isolate Izh-4: reference for a complex bacterial genome
Authors: Kuleshov Konstantin V. , Margos Gabriele , Fingerle Volker , Koetsveld Joris , Goptar Irina A. , Markelov Mikhail L. , Kolyasnikova Nadezhda M. , Sarksyan Denis S. , Kirdyashkina Nina P. , Shipulin German A. , Hovius Joppe W. , Platonov Alexander E. 
Published: December 2019

Abstract
Background: The genus Borrelia comprises spirochaetal bacteria maintained in natural transmission cycles by tick vectors and vertebrate reservoir hosts. The main groups are represented by a species complex including the causative agents of Lyme borreliosis and relapsing fever group Borrelia. Borrelia miyamotoi belongs to the relapsing-fever group of spirochetes and forms distinct populations in North America, Asia, and Europe. As all Borrelia species B. miyamotoi possess an unusual and complex genome consisting of a linear chromosome and a number of linear and circular plasmids. The species is considered an emerging human pathogen and an increasing number of human cases are being described in the Northern hemisphere. The aim of this study was to produce a high quality reference genome that will facilitate future studies into genetic differences between different populations and the genome plasticity of B. miyamotoi.
Results: We used multiple available sequencing methods, including Pacific Bioscience single-molecule real-time technology (SMRT) and Oxford Nanopore technology (ONT) supplemented with highly accurate Illumina sequences, to explore the suitability for whole genome assembly of the Russian B. miyamotoi isolate, Izh-4. Plasmids were typed according to their potential plasmid partitioning genes (PF32, 49, 50, 57/62). Comparing and combining results of both long-read (SMRT and ONT) and short-read methods (Illumina), we determined that the genome of the isolate Izh-4 consisted of one linear chromosome, 12 linear and two circular plasmids. Whilst the majority of plasmids had corresponding contigs in the Asian B. miyamotoi isolate FR64b, there were only four that matched plasmids of the North American isolate CT13-2396, indicating differences between B. miyamotoi populations. Several plasmids, e.g. lp41, lp29, lp23, and lp24, were found to carry variable major proteins. Amongst those were variable large proteins (Vlp) subtype Vlp-α, Vlp-γ, Vlp-δ and also Vlp-β. Phylogenetic analysis of common plasmids types showed the uniqueness in Russian/Asian isolates of B. miyamotoi compared to other isolates.
Conclusions: We here describe the genome of a Russian B. miyamotoi clinical isolate, providing a solid basis for future comparative genomics of B. miyamotoi isolates. This will be a great impetus for further basic, molecular and epidemiological research on this emerging tick-borne pathogen.
Different transcriptional response between susceptible and resistant common carp (Cyprinus carpio) fish hints on the mechanism of CyHV-3 disease resistance
Authors: Tadmor-Levi Roni , Doron-Faigenboim Adi , Marcos-Haddad Jenny , Petit Jules , Hulata Gideon , Forlenza Maria , Wiegertjes Geert F. , David Lior 
Published: December 2019

Abstract
Background Infectious disease outbreaks form major setbacks to aquaculture production and to further development of this important sector. Cyprinid herpes virus-3 (CyHV-3) is a dsDNA virus widely hampering production of common carp (Cyprinus carpio), one of the most farmed fish species worldwide. Genetically disease resistant strains are highly sought after as a sustainable solution to this problem. To study the genetic basis and cellular pathways underlying disease resistance, RNA-Seq was used to characterize transcriptional responses of susceptible and resistant fish at day 4 after CyHV-3 infection. Results In susceptible fish, over four times more differentially expressed genes were up-regulated between day 0 and 4 compared to resistant fish. Susceptible and resistant fish responded distinctively to infection as only 55 (9%) of the up-regulated genes were shared by these two fish types. Susceptible fish elicited a typical anti-viral response, involving interferon and interferon responsive genes, earlier than resistant fish did. Furthermore, chemokine profiles indicated that the two fish types elicited different cellular immunity responses. A comparative phylogenetic approach assisted in chemokine copies annotation pointing to different orthologous copies common to bony-fishes and even carp-specific paralogs that were differentially regulated and contributed to the different response of these two fish types. Susceptible fish up-regulated more ccl19 chemokines, which attract T-cells and macrophages, the anti-viral role of which is established, whereas resistant fish up-regulated more cxcl8/il8 chemokines, which attract neutrophils, the antiviral role of which is unfamiliar. Conclusions Taken together, by pointing out transcriptional differences between susceptible and resistant fish in response to CyHV-3 infection, this study unraveled possible genes and pathways that take part in disease resistance mechanisms in fish and thus, enhances our understanding of fish immunogenetics and supports the development of sustainable and safe aquaculture.
The true panel of Cystic Fibrosis mutations in the Sicilian population
Authors: chamayou sandrine , SICALI Maria , LOMBARDO Debora , MAGLIA Elena , LIPRINO Annalisa , CARDEA Clementina , FICHERA Michele , VENTI Ermanno , GUGLIELMINO Antonino 
Published: December 2019

Abstract
Background: the aim was to establish the true risk of having an affected child with Cystic Fibrosis (CF) in the Sicilian infertile population.
Methods: a longitudinal CFTR screening of 1,279 Sicilian infertile patients for all CFTR mutations sequencing the entire gene by Next Generation Sequencing (NGS) was performed from patient’s blood.
Results: one patient out of 16 was a carrier of a CFTR mutation. Twenty-four mutations were found. Theoretically one couple out of 256 was at risk of CF transmission.
Conclusions: the risk of CF transmission is unexpectedly high in Sicily and with a high heterogeneity. Sequencing an entire and long gene such as CFTR makes accessible the true panel of mutations in a specific population and helps better to understand the true risk of having an affected child.
Deep learning improves the ability of sgRNA off-target propensity prediction
Authors: Liu Qiaoyue , Cheng Xiang , Liu Gan , Li Bohao , Liu Xiuqin 
Published: December 2019

Abstract
Background CRISPR/Cas9 system, as the third-generation genome editing technology, has been widely applied in target gene repair and gene expression regulation. Selection of appropriate sgRNA can improve the on-target knockout efficacy of CRISPR/Cas9 system with high sensitivity and specificity. However, when CRISPR/Cas9 system is operating, unexpected cleavage may occur at some sites, known as off-target. Presently, a number of prediction methods have been developed to predict the off-target propensity of sgRNA at specific DNA fragment. Most of them use artificial feature extraction operations and machine learning techniques to obtain off-target scores. With the rapid expansion of off-target data and the rapid development of deep learning theory, the existing prediction methods can no longer satisfy the prediction accuracy at the clinical level. Results Here, we propose a prediction method named CnnCrispr to predict the off-target propensity of sgRNA at specific DNA fragments. CnnCrispr automatically trains the sequence features of sgRNA-DNA pairs with GloVe model, and embeds the trained word vector matrix into the deep learning model including biLSTM and CNN with five hidden layers. We conducted performance verification on the data set provided by DeepCrispr, and found that the auROC and auPRC in the "leave-one-sgRNA-out" cross validation could reach 0.957 and 0.429 respectively (the pearson value and spearman value could reach 0.495 and 0.151 respectively under the same settings). Conclusion Our results show that CnnCrispr has better classification and regression performance than the existing states-of-art models.