bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of thiazide diuretics for the prevention of recurrent kidney calculi: a systematic review and meta-analysis
Authors: Li Dan-feng , Gao Yu-lu , Liu Hong-chao , Huang Xiao-chen , Zhu Rui-fang , Zhu Chang-tai 
Published: February 2020

Abstract
Background
Thiazide diuretics reduce the risk of recurrent kidney calculi in patients with kidney calculi or hypercalciuria. However, whether thiazide diuretics can definitely prevent recurrent kidney calculi remains unclear. We aimed to evaluate the effect and safety of thiazide diuretics on recurrent kidney calculi.

Methods
The PubMed, Cochrane Library, and EMBASE databases were systematically searched using the keywords thiazide diuretics and kidney calculi to identify randomized controlled trials (RCTs). The primary outcome was the incidence of recurrent kidney calculi, and the secondary outcome was the 24-h urinary calcium level. The pooled risk ratio (RR), risk difference (RD), standardized mean difference (SMD), and 95% confidence interval (CI) were calculated. The evidence quality was graded using the GRADE criteria, and recommendations for recurrent kidney calculus prevention using thiazide diuretics were reassessed.

Results
Eight RCTs involving 571 patients were included. The pooled RR for the incidence of kidney calculi in the thiazide diuretic groups was 0.44 (95% CI 0.33–0.58, P < 0.0001) compared to that in the placebo and untreated groups; the pooled RD was − 0.23 (95% CI − 0.30 to − 0.16, P < 0.0001). The pooled SMD for the 24-h urinary calcium level was − 18.59 (95% CI − 25.11 to − 12.08, P < 0.0001). The thiazide diuretic groups had a high incidence of adverse reactions and low tolerance. The evidence quality for decrease in kidney calculus incidence using thiazide diuretics was low, while that for the 24-h urinary calcium level decrease among those with recurrent kidney calculi was moderate, and that for the decrease in kidney calculus incidence using short-acting and long-acting thiazide diuretics was low. The overall strength of recommendation for prevention of recurrent renal calculi using thiazide diuretics was not recommended. The subgroup and sensitivity analysis findings were robust.

Conclusions
Long-term use of thiazide diuretics reduces the incidence of recurrent renal calculi and 24-h urinary calcium level. However, the benefits are insufficient, and the evidence quality is low. Considering the adverse effects, poor patient compliance, and economic burden of long-term medication, their use in preventing recurrent kidney calculi is not recommended.
Episodes of violence suffered by migrants transiting through Libya: a cross-sectional study in “Médecins du Monde’s” reception and healthcare centre in Seine-Saint-Denis, France
Authors: Reques L. , Aranda-Fernandez E. , Rolland C. , Grippon A. , Fallet N. , Reboul C. , Godard N. , Luhmann N. 
Published: February 2020

Abstract
Introduction
The Central Mediterranean Route, passing through Libya, is one of the most dangerous for migrants. Episodes of violence have been documented but have not been accurately quantified. The objective of the study was to estimate the prevalence of episodes of violence suffered in Libya by migrants consulting the Médecins du Monde reception and healthcare centre in Seine-Saint-Denis (Ile-de-France).

Methodology
A monocentric cross-sectional study was conducted from February to May 2019 including migrants over the age of 18 years who had passed through Libya and arrived in Europe from 2017. The presence of emotional distress was considered as exclusion criterion. The proportion, frequency and factors associated to physical, deprivation and sexual violence in Libya were estimated through a bespoke questionnaire, as well as healthcare access in Libya and psychosocial support needs.

Results
Ninety eight people were recruited and 72 were interviewed (17 refused to participate and 9 were excluded). 76.4% were men, with a mean age of 31.9 years, 76.4% had low educational level, 66.7% came from Ivory Coast and 59.7% had left their country for security reasons. The median length of stay in Libya was 180 days. The overall proportion of participants having suffered from violence was 96.4% among men and 88.2% among women. The prevalence of physical, deprivation and sexual violence for men and women were 94.2, 81.7 and 18% and 80.0, 86.7 and 53.3%, respectively. Access to healthcare in Libya was 2.8 and 63.9% of participants were oriented to psychosocial support after the interview.

Conclusions
The vast majority of migrants reported having been victims of violence during their transit through Libya. Women were at particular risk of sexual violence. Access to health care in Libya was almost non-existent. Psychosocial support for this population is urgent.
Novel CDKL5 mutations were found in patients in China: retrospective investigation in cases of CDKL5-related disorders
Authors: Yan Yumei , He Dake , Wu Jing , Hou Ruolin , Sun Kun , Li Ling 
Published: February 2020

Abstract
Objective
CDKL5-related disorders (CDD) is an epileptic encephalopathy resulted of gene mutations of CDKL5. This study aimed to explore the development process of CDD and to expand its mutation spectrum.

Methods
Clinic datawas collected about three infantile epileptic encephalopathy cases diagnosed at Xinhua Hospital Affiliated to Shanghai Jiaotong University, School of Medicine. Next generation sequencing technology was used to find three de novo mutations of CDKL5. We searched published literatures about CDKL5 in pubmed and made an analysis about our clinic data and the related literatures.

Results
The three patients were all girls. Their average onset age of seizures was around 2 months, and all of them have intractable epileptic seizures, severe intellectual disability, and hypotension. Among them, two presented infantile spasm and high arrhythmia in EEG, and the other manifested clonic seizure and broad epileptiform discharge in EEG. Extracerebral space widening in cranial MRIs was demonstrated in two cases. Visual evoked potential was abnormal in two cases. Seizures were resistant to all kinds of antiepileptic drugs (AEDs). Gene tests showed three de novo mutations of CDKL5: one was a truncated mutation (c.2254A > T,P.R752X, stop279), which was pathogenic according to the ACMG guide, the other two were missense mutations (c.377G > T,p.Cys126Phe) and a frameshift mutation (c.362-362insG(p.Ala122GlyfsTer7), which were likely pathogenic according to the ACMG.

Conclusions
All three de novo mutations are first reported. Based on the combined related literature and the manifestations observed, we diagnosed the three children as CDKL5-related disorders, and concluded that the de novo CDKL5 mutations are the reason for their epilepsy.
Impact of protocolized diuresis for de-resuscitation in the intensive care unit
Authors: Bissell Brittany D. , Laine Melanie E. , Thompson Bastin Melissa L. , Flannery Alexander H. , Kelly Andrew , Riser Jeremy , Neyra Javier A. , Potter Jordan , Morris Peter E. 
Published: February 2020

Abstract
Objective
Administration of diuretics has been shown to assist fluid management and improve clinical outcomes in the critically ill post-shock resolution. Current guidelines have not yet included standardization or guidance for diuretic-based de-resuscitation in critically ill patients. This study aimed to evaluate the impact of a multi-disciplinary protocol for diuresis-guided de-resuscitation in the critically ill.

Methods
This was a pre-post single-center pilot study within the medical intensive care unit (ICU) of a large academic medical center. Adult patients admitted to the Medical ICU receiving mechanical ventilation with either (1) clinical signs of volume overload via chest radiography or physical exam or (2) any cumulative fluid balance ≥ 0 mL since hospital admission were eligible for inclusion. Patients received diuresis per clinician discretion for a 2-year period (historical control) followed by a diuresis protocol for 1 year (intervention). Patients within the intervention group were matched in a 1:3 ratio with those from the historical cohort who met the study inclusion and exclusion criteria.

Results
A total of 364 patients were included, 91 in the protocol group and 273 receiving standard care. Protocolized diuresis was associated with a significant decrease in 72-h post-shock cumulative fluid balance [median, IQR − 2257 (− 5676–920) mL vs 265 (− 2283–3025) mL; p < 0.0001]. In-hospital mortality in the intervention group was lower compared to the historical group (5.5% vs 16.1%; p = 0.008) and higher ICU-free days (p = 0.03). However, no statistically significant difference was found in ventilator-free days, and increased rates of hypernatremia and hypokalemia were demonstrated.

Conclusions
This study showed that a protocol for diuresis for de-resuscitation can significantly improve 72-h post-shock fluid balance with potential benefit on clinical outcomes.
Scaling up Quality Improvement for Surgical Teams (QIST) – avoiding surgical site infection and anaemia at the time of surgery: protocol for a cluster randomised controlled trial
Authors: Scrimshire Ashley B , Booth Alison , Fairhurst Caroline , Reed Mike , Tadd Win , Laverty Annie , Corbacho Belen , Torgerson David , McDaid Catriona 
Published: February 2020

Abstract
Background
Measures shown to improve outcomes for patients often fail to be adopted into routine practice in the NHS. The Institute for Health Improvement Breakthrough Series Collaborative (BSC) model is designed to support implementation at scale. This trial aims to assess the effectiveness and cost-effectiveness of quality improvement collaboratives (QICs) based on the BSC method for introducing service improvements at scale in the NHS.

Methods
Forty Trusts will be randomised (1:1) to introduce one of two protocols already shown to improve outcomes in patients undergoing elective total hip and knee replacement surgery.
The intervention is improvement collaboratives based on the BSC model, a learning system that brings together a large number of teams to seek improvement focussed on a proven intervention. Collaboratives aim to deliver at scale, maximise local engagement and leadership and are designed to build capacity, enable learning and prepare for sustainability. Collaboratives involve Learning Sessions, Action Periods, and a summative congress.
Trusts will be supported to introduce either: decolonisation for Methicillin Sensitive Staphylococcus aureus (MSSA) to reduce post-operative infection (QIST: Infection), or an anaemia optimisation programme to reduce peri-operative blood transfusions (QIST: Anaemia). Trusts will continue with their usual practice for whichever protocol they are not introducing. Anonymised data related to both infection and anaemia outcomes for patients undergoing hip or knee arthroplasty at all sites will mean that the two groups act as controls for each other.
The primary outcome for the QIST: Infection collaborative is deep MSSA surgical site infection within 90 days of surgery, and for the QIST: Anaemia collaborative is blood transfusion within 7 days of surgery. Patient-level secondary outcomes include length of hospital stay and readmission, which will also inform the economic costings. Qualitative interviews will evaluate the support provided to teams.

Discussion
The scale of this trial brings considerable challenges and potential barriers to delivery. Anticipated challenges relate to recruiting and sustaining up to 40 organisations, each with its own culture and context. This complex project with multiple stakeholders across a large geographical area will be managed by experienced senior-level project leaders with a proven track record in advanced project management. The team should ensure effective project governance and communications.

Trial registration
ISRCTN, ISRCTN11085475. Prospectively registered on 15 February 2018.
Large-scale kinetic metabolic models of Pseudomonas putida KT2440 for consistent design of metabolic engineering strategies
Authors: Tokic Milenko , Hatzimanikatis Vassily , Miskovic Ljubisa 
Published: February 2020

AbstractBackgroundPseudomonas putidais a promising candidate for the industrial production of biofuels and biochemicals because of its high tolerance to toxic compounds and its ability to grow on a wide variety of substrates. Engineering this organism for improved performances and predicting metabolic responses upon genetic perturbations requires reliable descriptions of its metabolism in the form of stoichiometric and kinetic models.ResultsIn this work, we developed kinetic models ofP. putidato predict the metabolic phenotypes and design metabolic engineering interventions for the production of biochemicals. The developed kinetic models contain 775 reactions and 245 metabolites. Furthermore, we introduce here a novel set of constraints within thermodynamics-based flux analysis that allow for considering concentrations of metabolites that exist in several compartments as separate entities. We started by a gap-filling and thermodynamic curation of iJN1411, the genome-scale model ofP. putidaKT2440. We then systematically reduced the curated iJN1411 model, and we created three core stoichiometric models of different complexity that describe the central carbon metabolism ofP. putida. Using the medium complexity core model as a scaffold, we generated populations of large-scale kinetic models for two studies. In the first study, the developed kinetic models successfully captured the experimentally observed metabolic responses to several single-gene knockouts of a wild-type strain ofP. putidaKT2440 growing on glucose. In the second study, we used the developed models to propose metabolic engineering interventions for improved robustness of this organism to the stress condition of increased ATP demand.ConclusionsThe study demonstrates the potential and predictive capabilities of the kinetic models that allow for rational design and optimization of recombinantP. putidastrains for improved production of biofuels and biochemicals. The curated genome-scale model ofP. putidatogether with the developed large-scale stoichiometric and kinetic models represents a significant resource for researchers in industry and academia.
Whole-cell biocatalysis for hydrogen storage and syngas conversion to formate using a thermophilic acetogen
Authors: Schwarz Fabian M. , Müller Volker 
Published: February 2020

Abstract
Background
In times of global climate change, the conversion and capturing of inorganic CO2 have gained increased attention because of its great potential as sustainable feedstock in the production of biofuels and biochemicals. CO2 is not only the substrate for the production of value-added chemicals in CO2-based bioprocesses, it can also be directly hydrated to formic acid, a so-called liquid organic hydrogen carrier (LOHC), by chemical and biological catalysts. Recently, a new group of enzymes were discovered in the two acetogenic bacteria Acetobacterium woodii and Thermoanaerobacter kivui which catalyze the direct hydrogenation of CO2 to formic acid with exceptional high rates, the hydrogen-dependent CO2 reductases (HDCRs). Since these enzymes are promising biocatalysts for the capturing of CO2 and the storage of molecular hydrogen in form of formic acid, we designed a whole-cell approach for T. kivui to take advantage of using whole cells from a thermophilic organism as H2/CO2 storage platform. Additionally, T. kivui cells were used as microbial cell factories for the production of formic acid from syngas.

Results
This study demonstrates the efficient whole-cell biocatalysis for the conversion of H2 + CO2 to formic acid in the presence of bicarbonate by T. kivui. Interestingly, the addition of KHCO3 not only stimulated formate formation dramatically but it also completely abolished unwanted side product formation (acetate) under these conditions and bicarbonate was shown to inhibit the membrane-bound ATP synthase. Cell suspensions reached specific formate production rates of 234 mmol gprotein−1 h−1 (152 mmol gCDW−1 h−1), the highest rates ever reported in closed-batch conditions. The volumetric formate production rate was 270 mmol L−1 h−1 at 4 mg mL−1. Additionally, this study is the first demonstration that syngas can be converted exclusively to formate using an acetogenic bacterium and high titers up to 130 mM of formate were reached.

Conclusions
The thermophilic acetogenic bacterium T. kivui is an efficient biocatalyst which makes this organism a promising candidate for future biotechnological applications in hydrogen storage, CO2 capturing and syngas conversion to formate.
A reference profile-free deconvolution method to infer cancer cell-intrinsic subtypes and tumor-type-specific stromal profiles
Authors: Wang Li , Sebra Robert P. , Sfakianos John P. , Allette Kimaada , Wang Wenhui , Yoo Seungyeul , Bhardwaj Nina , Schadt Eric E. , Yao Xin , Galsky Matthew D. , Zhu Jun 
Published: February 2020

Abstract
Background
Patient stratification based on molecular subtypes is an important strategy for cancer precision medicine. Deriving clinically informative cancer molecular subtypes from transcriptomic data generated on whole tumor tissue samples is a non-trivial task, especially given the various non-cancer cellular elements intertwined with cancer cells in the tumor microenvironment.

Methods
We developed a computational deconvolution method, DeClust, that stratifies patients into subtypes based on cancer cell-intrinsic signals identified by distinguishing cancer-type-specific signals from non-cancer signals in bulk tumor transcriptomic data. DeClust differs from most existing methods by directly incorporating molecular subtyping of solid tumors into the deconvolution process and outputting molecular subtype-specific tumor reference profiles for the cohort rather than individual tumor profiles. In addition, DeClust does not require reference expression profiles or signature matrices as inputs and estimates cancer-type-specific microenvironment signals from bulk tumor transcriptomic data.

Results
DeClust was evaluated on both simulated data and 13 solid tumor datasets from The Cancer Genome Atlas (TCGA). DeClust performed among the best, relative to existing methods, for estimation of cellular composition. Compared to molecular subtypes reported by TCGA or other similar approaches, the subtypes generated by DeClust had higher correlations with cancer-intrinsic genomic alterations (e.g., somatic mutations and copy number variations) and lower correlations with tumor purity. While DeClust-identified subtypes were not more significantly associated with survival in general, DeClust identified a poor prognosis subtype of clear cell renal cancer, papillary renal cancer, and lung adenocarcinoma, all of which were characterized by CDKN2A deletions. As a reference profile-free deconvolution method, the tumor-type-specific stromal profiles and cancer cell-intrinsic subtypes generated by DeClust were supported by single-cell RNA sequencing data.

Conclusions
DeClust is a useful tool for cancer cell-intrinsic molecular subtyping of solid tumors. DeClust subtypes, together with the tumor-type-specific stromal profiles generated by this pan-cancer study, may lead to mechanistic and clinical insights across multiple tumor types.
Billing I-AIM: a novel framework for ultrasound billing
Authors: Hughes Daralee , Corrado Michelle M. , Mynatt Irene , Prats Michael , Royall Nelson A. , Boulger Creagh , Bahner David P. 
Published: February 2020

Abstract
Background
Point-of-care ultrasound (POCUS) has an ever-growing footprint in medicine. With this growth POCUS billing and reimbursement has become an area gaining quite a bit of attention as a means of funding and sustaining quality and education programs. Standardization across providers is needed to improve the financial viability of POCUS.

Results
We created an institutional collaborative which developed a framework to identify critical POCUS billing and reimbursement checkpoints. The framework, Billing I-AIM, provides a feasible structure to enhance provider-based reimbursement and perform quality improvement efforts across variable POCUS environments.

Conclusions
POCUS billing using the Billing I-AIM technique allows administrative oversight, quality assurance, and educational functions as well. A discussion of the framework and respective application is provided.
Transcriptome differences in adipose stromal cells derived from pre- and postmenopausal women
Authors: Xie Yun , Fang Bin , Liu Wenhui , Li Guangshuai , Huang Ru-Lin , Zhang Lu , He Jiahao , Zhou Shuangbai , Liu Kai , Li Qingfeng 
Published: February 2020

AbstractBackgroundAs the population ages, an increasing number of postmenopausal women are donors of adipose stromal cells (ASCs) and may benefit from autologous ASC-related treatments. However, the effect of menopausal status on ASCs has not been investigated.MethodsRNA sequencing data were downloaded, and differentially expressed genes (DEGs) were identified. Hierarchical clustering, Gene Ontology, and pathway analyses were applied to the DEGs. Two gene coexpression network analysis approaches were applied to the DEGs to provide a holistic view and preserve gene interactions. Hub genes of the gene coexpression network were identified, and their expression profiles were examined with clinical samples. ASCs from pre- and postmenopausal women were co-cultured with monocytes and T cells to determine their immunoregulatory role.ResultsIn total, 2299 DEGs were identified and presented distinct expression profiles between pre- and postmenopausal women. Gene Ontology and pathway analyses revealed some fertility-, sex hormone-, immune-, aging-, and angiogenesis-related terms and pathways. Gene coexpression networks were constructed, and the top hub genes, including TIE1, ANGPT2, RNASE1, PLVAP, CA2, and MPZL2, were consistent between the two approaches. Expression profiles of hub genes from the RNA sequencing data and clinical samples were consistent. ASCs from postmenopausal women elicit M1 polarization, while their counterparts facilitate CD3/4+ T cell proliferation.ConclusionsThe present study reveals the transcriptome differences in ASCs derived from pre- and postmenopausal women and provides holistic views by preserving gene interactions via gene coexpression network analysis. The top hub genes identified by this study could serve as potential targets to enhance the therapeutic potential of ASCs.
Impulsive quantum $(p,q)$-difference equations
Authors: Nuntigrangjana Thana , Putjuso Sasitorn , Ntouyas Sotiris K. , Tariboon Jessada 
Published: February 2020

AbstractIn this paper we study quantum $(p,q)$(p,q)-difference equations with impulse and initial or boundary conditions. We consider first order impulsive $(p,q)$(p,q)-difference boundary value problems and second order impulsive $(p,q)$(p,q)-difference initial value problems. Existence and uniqueness results are proved via Banach’s fixed point theorem.