bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of different doses of magnesium sulfate on pneumoperitoneum-related hemodynamic changes in patients undergoing gastrointestinal laparoscopy: a randomized, double-blind, controlled trial
Authors: Tan Wei , Qian Dong-chen , Zheng Meng-meng , Lu Xuan , Han Yuan , Qi Dun-yi 
Published: December 2019

AbstractBackgroundThe infusion of magnesium sulfate is well known to reduce arterial pressure and attenuate hemodynamic response to pneumoperitoneum. This study aimed to investigate whether different doses of magnesium sulfate can effectively attenuate the pneumoperitoneum-related hemodynamic changes and the release of vasopressin in patients undergoing laparoscopic gastrointestinal surgery.MethodsSixty-nine patients undergoing laparoscopic partial gastrectomy were randomized into three groups: group L received magnesium sulfate 30 mg/kg loading dose and 15 mg/kg/h continuous maintenance infusion for 1 h; group H received magnesium sulfate 50 mg/kg followed by 30 mg/kg/h for 1 h; and group S (control group) received same volume 0.9% saline infusion, immediately before the induction of pneumoperitoneum. Systemic vascular resistance (SVR), cardiac output (CO), mean arterial pressure (MAP), heart rate (HR), central venous pressure (CVP), serum vasopressin and magnesium concentrations were measured. The extubation time, visual analogue scale were also assessed. The primary outcome is the difference in SVR between different groups. The secondary outcome is the differences of other indicators between groups, such as CO, MAP, HR, CVP, vasopressin and postoperative pain score.ResultsPneumoperitoneum instantly resulted in a significant reduction of cardiac output and an increase in mean arterial pressure, systemic vascular resistance, central venous pressure and heart rate in the control group (P <  0.01). The mean arterial pressure (T2 – T4),systemic vascular resistance (T2 – T3), central venous pressure(T3-T5) and the level of serum vasopressin were significantly lower (P <  0.05) and the cardiac output (T2 – T3) was significantly higher (P <  0.05) in group H than those in the control group. The mean arterial pressure (T4), systemic vascular resistance (T2), and central venous pressure(T3-T4) were significantly lower in group H than those in group L (P <  0.05). Furthermore, the visual analog scales at 5 min and 20 min, the level of vasopressin, and the dose of remifentanil were significantly decreased in group H compared to the control group and group L (P <  0.01).ConclusionMagnesium sulfate could safely and effectively attenuate the pneumoperitoneum-related hemodynamic instability during gastrointestinal laparoscopy and improve postoperative pain at serum magnesium concentrations above 2 mmol/L.Trial registrationThe study was retrospectively registered at Chinese Clinical Trial Registry; the registration number isChiCTR-IPD-17011145, principal investigator: D.Y. Q., date of registration: April 13, 2017.
What rationale do GPs use to choose a particular antibiotic for a specific clinical situation?
Authors: Krishnakumar Jegatha , Tsopra Rosy 
Published: December 2019

Abstract
Background
Many studies have investigated the ways in which physicians decide whether to prescribe antibiotics, but very few studies have focused on the reasons for which general practitioners (GPs) choose to prescribe a particular antibiotic in a specific clinical situation. Improvements in our understanding of the rationale behind GPs’ decisions would provide insight into the reasons for which GPs do not always prescribe the antibiotic recommended in clinical practice guidelines and facilitate the development of appropriate interventions to improve antibiotic prescription.
The objective of the study was to understand the rationale used by GPs to decide which antibiotic to prescribe in a specific clinical situation, and to propose a model representing this rationale.

Methods
We used a three-step process. First, data were collected from interviews with 20 GPs, and analysed according to the grounded theory approach. Second, data were collected from publications exploring the factors used by GPs to choose an antibiotic. Third, data were used to develop a comprehensive model of the rationale used by GPs to decide which antibiotic to prescribe.

Results
The GPs considered various factors when choosing antibiotics: factors relating to microbiology (bacterial resistance), pharmacology (adverse effects, efficacy, practicality of the administration protocol, antibiotic class, drug cost), clinical conditions (patient profile and comorbid conditions, symptoms, progression of infection, history of antibiotic treatment, preference), and personal factors (GP’s experience, knowledge, emotion, preference).

Conclusions
Various interventions, targeting all the factors underlying antibiotic choice, are required to improve antibiotic prescription. GP-related factors could be improved through interventions aiming to improve the GPs’ knowledge of antibiotics (e.g. continuing medical education). Factors relating to microbiology, pharmacology and clinical conditions could be targeted through the use of clinical decision support systems in everyday clinical practice.
Improved cell composition deconvolution method of bulk gene expression profiles to quantify subsets of immune cells
Authors: Chiu Yen-Jung , Hsieh Yi-Hsuan , Huang Yen-Hua 
Published: December 2019

Abstract
Background
To facilitate the investigation of the pathogenic roles played by various immune cells in complex tissues such as tumors, a few computational methods for deconvoluting bulk gene expression profiles to predict cell composition have been created. However, available methods were usually developed along with a set of reference gene expression profiles consisting of imbalanced replicates across different cell types. Therefore, the objective of this study was to create a new deconvolution method equipped with a new set of reference gene expression profiles that incorporate more microarray replicates of the immune cells that have been frequently implicated in the poor prognosis of cancers, such as T helper cells, regulatory T cells and macrophage M1/M2 cells.

Methods
Our deconvolution method was developed by choosing ε-support vector regression (ε-SVR) as the core algorithm assigned with a loss function subject to the L1-norm penalty. To construct the reference gene expression signature matrix for regression, a subset of differentially expressed genes were chosen from 148 microarray-based gene expression profiles for 9 types of immune cells by using ANOVA and minimizing condition number. Agreement analyses including mean absolute percentage errors and Bland-Altman plots were carried out to compare the performances of our method and CIBERSORT.

Results
In silico cell mixtures, simulated bulk tissues, and real human samples with known immune-cell fractions were used as the test datasets for benchmarking. Our method outperformed CIBERSORT in the benchmarks using in silico breast tissue-immune cell mixtures in the proportions of 30:70 and 50:50, and in the benchmark using 164 human PBMC samples. Our results suggest that the performance of our method was at least comparable to that of a state-of-the-art tool, CIBERSORT.

Conclusions
We developed a new cell composition deconvolution method and the implementation was entirely based on the publicly available R and Python packages. In addition, we compiled a new set of reference gene expression profiles, which might allow for a more robust prediction of the immune cell fractions from the expression profiles of cell mixtures. The source code of our method could be downloaded from https://github.com/holiday01/deconvolution-to-estimate-immune-cell-subsets.
GTX.Digest.VCF: an online NGS data interpretation system based on intelligent gene ranking and large-scale text mining
Authors: Jiang Yanhuang , Wu Chengkun , Zhang Yanghui , Zhang Shaowei , Yu Shuojun , Lei Peng , Lu Qin , Xi Yanwei , Wang Hua , Song Zhuo 
Published: December 2019

Abstract
Background
An important task in the interpretation of sequencing data is to highlight pathogenic genes (or detrimental variants) in the field of Mendelian diseases. It is still challenging despite the recent rapid development of genomics and bioinformatics. A typical interpretation workflow includes annotation, filtration, manual inspection and literature review. Those steps are time-consuming and error-prone in the absence of systematic support. Therefore, we developed GTX.Digest.VCF, an online DNA sequencing interpretation system, which prioritizes genes and variants for novel disease-gene relation discovery and integrates text mining results to provide literature evidence for the discovery. Its phenotype-driven ranking and biological data mining approach significantly speed up the whole interpretation process.

Results
The GTX.Digest.VCF system is freely available as a web portal at http://vcf.gtxlab.com for academic research. Evaluation on the DDD project dataset demonstrates an accuracy of 77% (235 out of 305 cases) for top-50 genes and an accuracy of 41.6% (127 out of 305 cases) for top-5 genes.

Conclusions
GTX.Digest.VCF provides an intelligent web portal for genomics data interpretation via the integration of bioinformatics tools, distributed parallel computing, biomedical text mining. It can facilitate the application of genomic analytics in clinical research and practices.
BrightFocus Alzheimer’s Fast Track 2019
Authors: Whitaker Keith W. , LaFerla Frank M. , Steinbusch Harry W. M. , Lemere Cynthia A. , Bovenkamp Diane E. 
Published: December 2019

AbstractThe 3 day workshop “Alzheimer’s Fast Track” is a unique opportunity for graduate students, postdoctoral fellows, or other early-career scientists, focused on Alzheimer’s disease research, to gain new knowledge and become an expert in where this emerging scientific field is moving. In addition, it is not only about receiving a good overview, but also learning to write and defend a successful application for securing funding for Alzheimer’s disease research projects.
PIRCh-seq: functional classification of non-coding RNAs associated with distinct histone modifications
Authors: Fang Jingwen , Ma Qing , Chu Ci , Huang Beibei , Li Lingjie , Cai Pengfei , Batista Pedro J. , Tolentino Karen Erisse Martin , Xu Jin , Li Rui , Du Pengcheng , Qu Kun , Chang Howard Y. 
Published: December 2019

AbstractWe develop PIRCh-seq, a method which enables a comprehensive survey of chromatin-associated RNAs in a histone modification-specific manner. We identify hundreds of chromatin-associated RNAs in several cell types with substantially less contamination by nascent transcripts. Non-coding RNAs are found enriched on chromatin and are classified into functional groups based on the patterns of their association with specific histone modifications. We find single-stranded RNA bases are more chromatin-associated, and we discover hundreds of allele-specific RNA-chromatin interactions. These results provide a unique resource to globally study the functions of chromatin-associated lncRNAs and elucidate the basic mechanisms of chromatin-RNA interactions.
Neck paraganglioma and follicular lymphoma: a case report
Authors: Marchetti Lara , Perrucci Luca , D’Ercole Francesca , Zatelli Maria Chiara , Ambrosio Maria Rosaria , Giganti Melchiore , Carnevale Aldo 
Published: December 2019

Abstract
Background
Paragangliomas and pheochromocytomas are sympathetic or parasympathetic tumors derived from the paraganglia and the adrenal medulla, respectively. Paragangliomas and pheochromocytomas can be sporadic or familial, the latter frequently being multifocal and possibly due to succinate dehydrogenase complex genes mutations. In addition, 12% of sporadic paragangliomas are related to covered succinate dehydrogenase complex mutations. The importance of identifying succinate dehydrogenase complex mutations is related to the risk for these patients of developing multiple tumors, including non-endocrine ones, showing an aggressive clinical presentation.

Case presentation
We report the case of a 45-year-old Caucasian man with an indolent mass in his neck. Ultrasound of his neck, magnetic resonance imaging, and 1,4,7,10-tetraazacyclododecane-N(I),N(II),N(III),N(IIII)-tetraacetic acid(D)-Phe(1)-thy(3)-octreotide (68Ga-DOTATOC) positron emission tomography-computed tomography and endocrine work-up were consistent with a carotid body paraganglioma with concomitant nodal enlargement in several body regions, which turned out to be a follicular lymphoma at histology. He was found to carry a germline Succinate dehydrogenase subunit B gene (SDHB) mutation.

Conclusion
It is crucial to look for a second malignancy in the case of a paraganglioma demonstrating succinate dehydrogenase complex germline mutations.
Comparative profiling of the synaptic proteome from Alzheimer’s disease patients with focus on the APOE genotype
Authors: Hesse Raphael , Hurtado Maica Llavero , Jackson Rosemary J. , Eaton Samantha L. , Herrmann Abigail G. , Colom-Cadena Marti , Tzioras Makis , King Declan , Rose Jamie , Tulloch Jane , McKenzie Chris-Anne , Smith Colin , Henstridge Christopher M. , Lamont Douglas , Wishart Thomas M. , Spires-Jones Tara L. 
Published: December 2019

AbstractDegeneration of synapses in Alzheimer’s disease (AD) strongly correlates with cognitive decline, and synaptic pathology contributes to disease pathophysiology. We recently observed that the strongest genetic risk factor for sporadic AD, apolipoprotein E epsilon 4 (APOE4), is associated with exacerbated synapse loss and synaptic accumulation of oligomeric amyloid beta in human AD brain. To begin to understand the molecular cascades involved in synapse loss in AD and how this is mediated by APOE, and to generate a resource of knowledge of changes in the synaptic proteome in AD, we conducted a proteomic screen and systematic in silico analysis of synaptoneurosome preparations from temporal and occipital cortices of human AD and control subjects with known APOE gene status. We examined brain tissue from 33 subjects (7–10 per group). We pooled tissue from all subjects in each group for unbiased proteomic analyses followed by validation with individual case samples. Our analysis identified over 5500 proteins in human synaptoneurosomes and highlighted disease, brain region, and APOE-associated changes in multiple molecular pathways including a decreased abundance in AD of proteins important for synaptic and mitochondrial function and an increased abundance of proteins involved in neuroimmune interactions and intracellular signaling.
Using stakeholder input to inform scenario content: an example from physiotherapy
Authors: Edwards Sandy , Tuttle Neil 
Published: December 2019

Abstract
Background
Simulated learning environments (SLEs) are being embraced as effective, though potentially costly tools, by health educators in a variety of contexts. The selection of scenarios, however, can be arbitrary and idiosyncratic.

Methods
We conducted a stakeholder audit to determine priorities for student learning which would inform scenario design. The process consisted of (1) the identification of stakeholders, (2) consultation with stakeholders to identify their priorities, (3) determination of priorities that could be addressed in the SLE being developed, and (4) incorporating these priorities into scenarios.

Results
The identified stakeholders were the funding body, educational institution and discipline, regulatory agency, accreditation agency, external clinical placement providers, employers of new graduates, patients, and learners. Stakeholder input included a combination of surveys, consultation of online resources, and semi-structured interviews. Identified areas where student learning could be improved included (1) all students not having experience of all populations or ‘essential’ conditions, (2) situations where adverse events had occurred, (3) working with people from diverse backgrounds or those with psychosocial issues including those in chronic pain, (4) communication, (5) situation awareness, and (6) ethical issues.

Conclusions
Ten scenarios were developed considering the stakeholder input. Facilitator notes were written to ensure all facilitators addressed the areas that had been identified. Where possible, simulated patients, with diverse backgrounds, were hired to portray roles even though such areas of diversity were not explicitly written into the scenarios. Whilst the example concerns physiotherapy students within Australia, the principles may be applicable across a range of health disciplines.
Interprofessional simulation in a student community clinic: insights from an educational framework and contact theory
Authors: Waller Susan , Nestel Debra 
Published: December 2019

Abstract
Introduction
Simulation in community care is a relatively understudied area. In this paper, we report a qualitative evaluation of the Simulated Client Interprofessional Education (SCIPE) program in a community clinic for undergraduate health and social care students in a rural setting. We sought to explore the stakeholders’ perceptions and experiences of training for, and conduct of, a simulated client-based activity to support the development of collaborative practice of students. We used an educational framework (presage, process, product–3P) and contact theory to analyse the evaluation data and suggest improvement strategies.

Methods
Data on professional characteristics was collected from facilitators, simulated client and students. Facilitators and simulated clients received training. Written evaluations were collected after training and after the simulated clinics. Purposively sampled facilitators, students and community partner agencies participated in individual semi-structured interviews to gain deeper insights into experiences.

Results
Fourteen clinics involved 5 facilitators, 12 simulated clients and 40 students. Fifteen interviews were conducted. The SCIPE program led to perceived improvements in students’ communication and awareness of interprofessional collaboration. Participation in the program enabled students to experience a holistic approach to client interviewing and development of competency in collaborative goal setting. Further attention to presage and ability of facilitators to build positive contact conditions was identified. Coordination from a central site facilitated exchange and quality assurance for all elements of the program. Scoping of conditions of positive contact enabled a greater understanding of students’ and facilitators’ evaluation of the experience and constraints which would be modifiable for future improvement and sustainability.

Discussion
Although the SCIPE program benefited students, the need for more explicit organisational engagement and support was revealed in interviews. The use of 3P and contact theory was helpful in identifying elements of the program for maintenance and development. Future research could follow students into practice to see if the behaviours are sustained and translated. Strengths included broad stakeholder involvement and immediate feedback. The key limitation was that the activity lacked explicit institutional support, facilitators required further training in briefing and the outcomes largely refer to participants’ perceptions and may not translate to practice.
Online teaching in response to student protests and campus shutdowns: academics’ perspectives
Authors: Czerniewicz Laura , Trotter Henry , Haupt Genevieve 
Published: December 2019

AbstractDuring the period 2015–2017, student protests and university shutdowns rocked the higher education sector in South Africa, with key issues being raised regarding student exclusion based on financial, epistemological and cultural grounds. In this highly politicised and contested environment, some universities decided to use blended and online delivery as a strategy to enable the academic year to be completed and all curriculum to be covered, despite the disruptions. This was a controversial decision politically and a challenging one practically. From the perspective of the academics at the University of Cape Town (UCT), this paper draws on interviews with educators in three broad disciplinary areas to explore their views, practices, and experiences regarding the use of online materials in these unique circumstances. Activity Theory provides a framework to consider the issues systemically and to identify the tensions and contradictions in the system.
Pre-activation affects the effect of stretch-shortening cycle by modulating fascicle behavior
Authors: Fukutani Atsuki , Shimoho Kento , Isaka Tadao 
Published: December 2019

ABSTRACTThe torque attained during active shortening is enhanced after an active stretch (stretch-shortening cycle, SSC). This study examined the influence of pre-activation on fascicle behavior and the SSC effect. Subjects exhibited the following three conditions by electrically induced plantar flexions. In the isometric-concentric (ISO-CON) condition, subjects exhibited active shortening from dorsiflexion of 15° to 0° after isometric pre-activation. In the eccentric-concentric (ECC-CON) condition, subjects exhibited the above active shortening immediately after the eccentric pre-activation. In the isometric-eccentric-concentric (ISO-ECC-CON) condition, isometric pre-activation was conducted before exhibiting the ECC-CON maneuver. Joint torque and fascicle length of the medial gastrocnemius were compared. The joint torque at the onset and end of shortening was larger in the ISO-ECC-CON than in the ISO-CON or ECC-CON conditions, while no differences were found between ISO-CON and ECC-CON conditions. The magnitude of fascicle elongation attained during the active stretch was larger in the ISO-ECC-CON than in the ECC-CON condition. This could be caused by the shorter fascicle length at the onset of active stretch due to isometric pre-activation. This shorter fascicle length could lead to larger fascicle elongation during the subsequent active stretch, which should emphasize the effect of active stretch-induced force enhancement mechanism.
Norovirus genogroup correlation with acute diarrhea severity in Indonesian pediatric patients aged 1-60 months: a cross-sectional study
Authors: Fardah Athiyyah Alpha , Shigemura Katsumi , Kitagawa Koichi , Agustina Nazara , Darma Andy , Ranuh Reza , Raharjo Dadik , Shirakawa Toshiro , Fujisawa Masato , Marto Sudarmo Subijanto 
Published: December 2019

Background: The objective of this study was to investigate the correlation between norovirus genogroup and severity of acute diarrhea in pediatric patients at the Dr. Soetomo Hospital, Surabaya, Indonesia. Methods: This cross-sectional study involved 31 participants aged 1-60 months admitted to the hospital with acute diarrhea from April 2012 to March 2013. Norovirus genogroups (GI and II) were identified from patient stool using reverse transcription polymerase chain reaction (RT-PCR). Severity was measured using the Ruuska and Vesikari scoring system. Results: In total, 91 stool samples were obtained, of which 31 (19%) were norovirus positive. Norovirus GI was found in one sample with mild diarrhea. Norovirus GII was found in 30 samples (96.8%); one sample with mild diarrhea (3.3%), 20 samples with moderate diarrhea (66.7%), and nine samples with severe diarrhea (30%). Conclusion: Norovirus GII was the most prevalent cause of acute diarrhea and 30% of the cases manifested as severe diarrhea.