bluuebunny/crossref_metadata_2025_split huggingface dataset:
Can Freehand Elastosonography Be an Alternative to Renal Scintigraphy in Pediatric Vesicoureteral Reflux Cases?
Authors: Karabulut Bilge , Bayram Gulsah , Oztorun Can Ihsan , Ozcift Burak , Tiryaki Tuğrul Hüseyin 
Published: October 2018

Introduction Detecting renal scar is important in pediatric patients with vesicoureteral reflux (VUR) for deciding on treatment option. The aim of this study is to detect whether freehand elastosonography technique could be an alternative to dimercaptosuccinic acid (DMSA) scan in determining renal scar formation.
Materials and Methods Between November 2015 and April 2016, 25 VUR patients, age ranging from 3 to 17 years admitted to our clinic, had urinary ultrasound and elastosonography, and data of approximately 147 renal region were recorded. Data were upper, middle, and lower pole renal parenchymal thickness and echogenicities obtained by ultrasound and these poles strain target (ST), strain reference (SR), and strain index (SI) values obtained by freehand elastosonography. DMSA scan data (differential function and upper, middle, and lower pole parenchymal scar formation) were recorded.
Results Scar formation and more than 10% reduction in differential function in renal scan were statistically higher in renal regions in which parenchymal thinning and echogenicity increase was detected by ultrasound. There was no elastosonographic data difference between renal units with and without differential function decrease. Also, there was no elastosonographic data difference between renal units with and without scar formation.
Conclusion In this study, we could not find any significant difference in term of tissue tension values (ST and SI) measured by freehand elastosonography between renal units with and without scar formation in renal scan.
Trial Characteristics That Affect Parental Consent in Neonatal Drug Trials
Authors: Hanvey I. Blaire , Aliaga Sofia , Laughon Matthew M. , Testoni Daniela , Smith P. Brian , Bauserman Melissa 
Published: October 2018

Objective The main purpose of this article is to determine parental consent rates in neonatal drug trials and describe trial characteristics associated with higher rates.
Study Design We included neonatal drug trials published between 2009 and 2014 and compared parental consent rates among the following characteristics: phase type, gestational age, randomization type, drug administration route, drug dosing frequency, blood sampling, control type, length of study, funding source, and length of treatment. We compared characteristics using chi-square, Fisher's exact, one-way analysis of variance or Kruskal–Wallis tests.
Results We identified 52 trials: 38 trials (73%) reported data of parental consent. Median percentage (interquartile range) of parental consent was 79% (62, 89). Higher rates were observed in studies that used active comparators (87%) and shorter study lengths (81% for studies <24 hours).
Conclusion Parental consent rates for neonatal drug trials varied by study characteristics. Information on proportion of parents consented is valuable to assess generalizability of trial results and for preparing trial protocols.
Single versus Double-Balloon Transcervical Catheter for Labor Induction: A Systematic Review and Meta-Analysis
Authors: de los Reyes Samantha X. , Sheffield Jeanne S. , Eke Ahizechukwu C. 
Published: October 2018

Objective To evaluate for difference in outcomes between single- and double-balloon catheters for labor induction.
Study Design We searched CINAHL, Embase, Cochrane Register, MEDLINE, ISI Web of Sciences, LILACs, and Google Scholar and retrieved studies through May 2017. Selection criteria included randomized controlled trials comparing single- versus double-balloon catheters. The primary outcome was time from catheter insertion to delivery. Heterogeneity of the results among studies was tested with the quantity I2
. For I2
values ≥50%, a random effects model was used to pool data across studies. Summary measures were reported as adjusted odds ratios (aORs) or as a mean difference (MD) with 95% confidence interval (CI).
Results Four trials including a total of 682 patients were included: 340 patients were randomized to induction with a single-balloon catheter and 342 to induction with a double-balloon catheter. There was no significant difference between groups with respect to time to delivery (18.8 vs. 19.6 hours; MD: 0.40; 95% CI: –1.56 to 0.76), vaginal delivery rate (65.3 vs. 62.3%; aOR: 1.04; 95% CI: 0.56–1.92), cesarean delivery rate (25.6 vs. 27.5%; aOR: 0.98; 95% CI: 0.55–1.73), or epidural use (58.4 vs. 62%; aOR: 0.81; 95% CI: 0.56–1.18).
Conclusion Double-balloon catheters have no apparent advantage over single-balloon catheters for labor induction.
Automating a Manual Sepsis Screening Tool in a Pediatric Emergency Department
Authors: Lloyd Julia , Ahrens Erin , Clark Donnie , Dachenhaus Terri , Nuss Kathryn 
Published: October 2018

Objective This article describes the method of integrating a manual pediatric emergency department sepsis screening process into the electronic health record that leverages existing clinical documentation and keeps providers in their current, routine clinical workflows.
Methods Criteria in the manual pediatric emergency department sepsis screening tool were mapped to standard documentation routinely entered in the electronic health record. Data elements were extracted and scored from the medical history, medication record, vital signs, and physical assessments. Scores that met a predefined sepsis risk threshold triggered interruptive system alerts which notified emergency department staff to perform sepsis huddles and consider appropriate interventions. Statistical comparison of the new electronic tool to the manual process was completed by a two-tail paired t-test.
Results The performance of the pediatric electronic sepsis screening tool was evaluated by comparing flowsheet row documentation of the manual, sepsis alert process against the interruptive system alert instance of the electronic sepsis screening tool. In an 8-week testing period, the automated pediatric electronic sepsis screening tool identified 100% of patients flagged by the manual process (n = 29), on average, 68 minutes earlier.
Conclusion Integrating a manual sepsis screening tool into the electronic health record automated identification of pediatric sepsis screening in a busy emergency department. The electronic sepsis screening tool is as accurate as a manual process and would alert bedside clinicians significantly earlier in the emergency department course. Deployment of this electronic tool has the capability to improve timely sepsis detection and management of patients at risk for sepsis without requiring additional documentation by providers.
Risk of Neonatal and Infant Mortality in Twins and Singletons by Gestational Age
Authors: Chen Han-Yang , Chauhan Suneet P. 
Published: October 2018

Objective To compare neonatal and infant mortality rates stratified by gestational age (GA) between singletons and twins and examine the three leading causes of death among them.
Study Design This was a retrospective cohort study using the U.S. vital statistics datasets. The study was restricted to nonanomalous live births at 24 to 40 weeks delivered in 2005 to 2014. We used multivariable Poisson regression models with robust error variance to examine the association between birth plurality (singleton vs. twin) and mortality outcomes within each GA, while adjusting for confounders. The results were presented as adjusted risk ratios (aRRs) with 95% confidence intervals (CIs).
Results Of 26,292,747 live births, 96.6% were singletons and 3.4% were twins. At 29 to 36 weeks of GA, compared with singletons, twins had a lower risk of neonatal mortality (aRR: 0.37–0.78) and infant mortality (aRR: 0.54–0.86). When examined by GA, the three leading causes of neonatal and infant mortality varied between singletons and twins.
Conclusion When stratified by GA, the risk of neonatal and infant mortality was lower at 29 to 36 weeks in twins than in singletons, though the cause of death varied.
Buccal versus Vaginal Misoprostol for Term Induction of Labor: A Retrospective Cohort Study
Authors: Dorr Meredith L. , Pierson Rebecca C. , Daggy Joanne , Quinney Sara K. , Haas David M. 
Published: October 2018

Objective To compare the efficacy of similar buccal and vaginal misoprostol doses for induction of labor.
Study Design Retrospective chart review of 207 consecutive women undergoing term induction of labor with misoprostol. Misoprostol route and dosing were collected. Time to delivery and other labor outcomes (e.g., vaginal delivery less than 24 hours) were compared between women receiving buccal and vaginal misoprostol.
Results There was no significant difference in time to delivery for women receiving buccal (median 18.2 hour, 95% confidence interval [CI] = [14.9, 21.5]) versus vaginal (median 18.3 hour, 95% CI = [15.0, 20.4]) misoprostol (p = 0.428); even after adjusting for covariates (p = 0.381). Women who presented with premature rupture of membranes were more likely to receive buccal misoprostol (92.7% received buccal vs. 7.3% received vaginal, p < 0.001). A similar number of women delivered vaginally in the buccal group (88.2%) and vaginal misoprostol group (86.8%, p = 0.835). The proportion of women who experienced uterine tachysystole or chorioamnionitis did not significantly differ by route of administration.
Conclusion We found no significant differences in time to delivery or other labor outcomes between buccal or vaginal dosing of misoprostol in women undergoing labor induction at term.
Effects of Preeclampsia on Maternal and Pediatric Health at 11 Years Postpartum
Authors: Chan Stephanie E. , Pudwell Jessica , Smith Graeme N. 
Published: October 2018

Objective To determine the association of preeclampsia (PE) with the presence of cardiovascular risk (CVR) factors at approximately 11 years postpartum and to assess the longer term effect of PE on childhood development.
Study Design A mail-out survey was sent to all women who were previously recruited into the Kingston arm of the Pre-Eclampsia New Emerging Team's prospective cohort (n = 112 PE and n = 150 control). Physical and biochemical CVR markers were compared between the two groups. Physical, social, and cognitive development of the children involved in the pregnancies was evaluated using the Vineland-3 Domain-Level Parent/Caregiver Form.
Results Thirteen PE women and 28 control women returned the study questionnaire. Based on the 2017 American Heart Association High Blood Pressure Clinical Practice Guidelines, 9/13 (69.2%) of the PE women, compared with 6/28 (21.4%) of the control women, have hypertension (p < 0.01). The median percentile rank for overall adaptive functioning was 58 (interquartile range [IQR: 21–73]) in the PE children and 81 (IQR: 61–94) in the control children (p < 0.05).
Conclusion The development of PE leads to longer term changes in CVR markers and in childhood development at approximately 11 years postpartum. Pregnancy and the postpartum provide an early window of opportunity for early maternal and child screening and intervention for health preservation and disease prevention.
The Effect of Early Active Mobilization on Union Rate after Ulnar Shortening Osteotomy
Authors: Saqib Rukhtam , Rooker Jemma , Baumann Andreas , Amirfeyz Rouin , Blackburn Julia 
Published: October 2018

Background Ulnocarpal impaction occurs when there is excessive loading between the ulnar carpus and the distal ulna. Ulnar shortening osteotomies (USOs) decompress the ulnocarpal joint. Many studies have evaluated USO but none have considered the effect of early active mobilization on union rate.
Questions Does early active mobilization affect rate of union following USO? Does early active mobilization affect rate of complications following USO?
Patients and Methods We performed a retrospective review of 15 consecutive patients that underwent 16 USOs between 2011 and 2015. There were seven males and eight females. Median age at time of shortening osteotomy was 47 years (range: 11–63 years). The median time of the procedure was 62 minutes (range: 45–105 minutes) and the median change in ulnar variance was 5.5 mm (range: 0–10.5 mm). Six patients were initially immobilized in incomplete plaster casts postoperatively, while the remainder had only wool and crepe dressings. Early active mobilization commenced after the first postoperative visit at 12 days.
Results There was a 100% union rate in our series and 12 patients were pain-free at final follow-up. However, three of the patients with the longest times to union were smokers. Additionally, some patients may have achieved union between follow-up clinic visits.
Conclusion Early active mobilization after USO does not affect union rate. Prospective, randomized studies are required to investigate the effect of early active mobilization in light of factors known to increase time to union, such as smoking.
Level of Evidence This is a Level IV, case series.
A Rare Case of Pre-Existing Deep Venous Thrombosis in the Peroneal Vein of a Free Osteocutaneous Fibula Flap
Authors: Hayashi Satoshi , Kawamura Kenji , Maegawa Naoki , Nakanishi Akito , Mizutani Yasushi , Okuda Akinori , Kurata Shinpei , Shimizu Takamasa , Kira Tsutomu , Omokawa Shohei , Tanaka Yasuhito 
Published: October 2018

Background Deep venous thrombosis (DVT) of the lower leg is a widespread medical problem and is associated with hypercoagulable states. Although spontaneous thrombosis of the peroneal vein of a fibula flap is theoretically possible, few cases of asymptomatic DVT of the peroneal vein encountered during fibula flap harvest have been reported.
Case Report A 45-year-old man presented with segmental bone defects of the tibia resulting from a fall. Treatment with a free vascularized osteocutaneous fibula flap from the contralateral lower leg was scheduled. Intraoperatively, diffuse thrombi were found in the peroneal venous system. After removal of thrombi, the fibula was grafted with anastomosis of the peroneal vessels to the recipient posterior tibial vessels. The skin paddle of the flap became congested after surgery; exsanguination of the skin paddle was performed with multiple skin incisions to relieve congestion. Despite treatment, the skin paddle became partially necrotic and additional skin grafting was performed. Bone union of the grafted fibula was achieved 5 months after initial surgery.
Conclusions To the best of our knowledge, only six cases of pre-existing DVT in the peroneal vein of a free osteocutaneous fibula flap have been reported. In three of these cases, the fibula flap was successfully grafted. Although successful free osteocutaneous fibula flap surgery might be possible in patients with peroneal venous thrombosis, careful preoperative evaluation is recommended for high-risk patients.
Cell engineering with microfluidic squeezing preserves functionality of primary immune cells in vivo
Authors: DiTommaso Tia , Cole Julie M. , Cassereau Luke , Buggé Joshua A. , Hanson Jacquelyn L. Sikora , Bridgen Devin T. , Stokes Brittany D. , Loughhead Scott M. , Beutel Bruce A. , Gilbert Jonathan B. , Nussbaum Kathrin , Sorrentino Antonio , Toggweiler Janine , Schmidt Tobias , Gyuelveszi Gabor , Bernstein Howard , Sharei Armon 
Published: October 2018

Significance
Ex vivo manipulation of primary cells is critical to the success of this emerging generation of cell-based therapies, such as chimeric antigen receptor T cells for the treatment of cancer and CRISPR for the correction of developmental diseases. However, the limitations of existing delivery approaches may dramatically restrict the impact of genetic engineering to study and treat disease. In this paper, we compared electroporation to a microfluidic membrane deformation technique termed “squeezing” and found that squeezed cells had dramatically fewer side effects than electroporation and gene expression profiles similar to those of unmanipulated cells. The significant differences in outcomes from the two techniques underscores the importance of understanding the impact of intracellular delivery methods on cell function for research and clinical applications.
Universality of jamming of nonspherical particles
Authors: Brito Carolina , Ikeda Harukuni , Urbani Pierfrancesco , Wyart Matthieu , Zamponi Francesco 
Published: October 2018

Significance
The jamming transition is a key property of granular materials, including sand and dense suspensions. In the generic situation of nonspherical particles, its scaling properties are not completely understood. Previous empirical and theoretical work in ellipsoids and spherocylinders indicates that both structural and vibrational properties are fundamentally affected by shape. Here we explain these observations using a combination of marginal stability arguments and the replica method. We unravel a universality class for particles with internal degrees of freedom and derive how the structure of packings and their vibrations scale as the particles evolve toward spheres.
Cow's milk as a post‐exercise recovery drink: implications for performance and health
Authors: James Lewis J. , Stevenson Emma J. , Rumbold Penny L. S. , Hulston Carl J. 
Published: October 2018

AbstractPost‐exercise recovery is a multi‐facetted process that will vary depending on the nature of the exercise, the time between exercise sessions and the goals of the exerciser. From a nutritional perspective, the main considerations are: (1) optimisation of muscle protein turnover; (2) glycogen resynthesis; (3) rehydration; (4) management of muscle soreness; (5) appropriate management of energy balance. Milk is approximately isotonic (osmolality of 280–290 mosmol/kg), and the mixture of high quality protein, carbohydrate, water and micronutrients (particularly sodium) make it uniquely suitable as a post‐exercise recovery drink in many exercise scenarios. Research has shown that ingestion of milk post‐exercise has the potential to beneficially impact both acute recovery and chronic training adaptation. Milk augments post‐exercise muscle protein synthesis and rehydration, can contribute to post‐exercise glycogen resynthesis, and attenuates post‐exercise muscle soreness/function losses. For these aspects of recovery, milk is at least comparable and often out performs most commercially available recovery drinks, but is available at a fraction of the cost, making it a cheap and easy option to facilitate post‐exercise recovery. Milk ingestion post‐exercise has also been shown to attenuate subsequent energy intake and may lead to more favourable body composition changes with exercise training. This means that those exercising for weight management purposes might be able to beneficially influence post‐exercise recovery, whilst maintaining the energy deficit created by exercise.
DrugThatGene: integrative analysis to streamline the identification of druggable genes, pathways and protein complexes from CRISPR screens
Authors: Canver Matthew C , Bauer Daniel E , Maeda Takahiro , Pinello Luca 
Published: October 2018

AbstractMotivationThe clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) nuclease system has allowed for high-throughput, large scale pooled screens for functional genomic studies. To aid in the translation of functional genomics to therapeutics, we developed DrugThatGene (DTG) as a web-based application that streamlines analysis of potential therapeutic targets identified from functional genetic screens.ResultsStarting from a gene list as input, DTG offers automated identification of small molecules along with supporting information from human genetic and other relevant databases. Furthermore, DTG aids in the identification of common biological pathways and protein complexes in conjunction with associated small molecule inhibitors. Taken together, DTG aims to expedite the identification of small molecules from the abundance of functional genetic data generated from CRISPR screens.Availability and implementationDTG is an open-source and free software available as a website at http://drugthatgene.pinellolab.org. Source code is available at: https://github.com/pinellolab/DrugThatGene, which can be downloaded in order to run DTG locally.
Bastion3: a two-layer ensemble predictor of type III secreted effectors
Authors: Wang Jiawei , Li Jiahui , Yang Bingjiao , Xie Ruopeng , Marquez-Lago Tatiana T , Leier André , Hayashida Morihiro , Akutsu Tatsuya , Zhang Yanju , Chou Kuo-Chen , Selkrig Joel , Zhou Tieli , Song Jiangning , Lithgow Trevor 
Published: October 2018

Abstract

Motivation
Type III secreted effectors (T3SEs) can be injected into host cell cytoplasm via type III secretion systems (T3SSs) to modulate interactions between Gram-negative bacterial pathogens and their hosts. Due to their relevance in pathogen–host interactions, significant computational efforts have been put toward identification of T3SEs and these in turn have stimulated new T3SE discoveries. However, as T3SEs with new characteristics are discovered, these existing computational tools reveal important limitations: (i) most of the trained machine learning models are based on the N-terminus (or incorporating also the C-terminus) instead of the proteins’ complete sequences, and (ii) the underlying models (trained with classic algorithms) employed only few features, most of which were extracted based on sequence-information alone. To achieve better T3SE prediction, we must identify more powerful, informative features and investigate how to effectively integrate these into a comprehensive model.

Results
In this work, we present Bastion3, a two-layer ensemble predictor developed to accurately identify type III secreted effectors from protein sequence data. In contrast with existing methods that employ single models with few features, Bastion3 explores a wide range of features, from various types, trains single models based on these features and finally integrates these models through ensemble learning. We trained the models using a new gradient boosting machine, LightGBM and further boosted the models’ performances through a novel genetic algorithm (GA) based two-step parameter optimization strategy. Our benchmark test demonstrates that Bastion3 achieves a much better performance compared to commonly used methods, with an ACC value of 0.959, F-value of 0.958, MCC value of 0.917 and AUC value of 0.956, which comprehensively outperformed all other toolkits by more than 5.6% in ACC value, 5.7% in F-value, 12.4% in MCC value and 5.8% in AUC value. Based on our proposed two-layer ensemble model, we further developed a user-friendly online toolkit, maximizing convenience for experimental scientists toward T3SE prediction. With its design to ease future discoveries of novel T3SEs and improved performance, Bastion3 is poised to become a widely used, state-of-the-art toolkit for T3SE prediction.

Availability and implementation
http://bastion3.erc.monash.edu/

Contact
selkrig@embl.de or wyztli@163.com or or trevor.lithgow@monash.edu

Supplementary information
Supplementary data are available at Bioinformatics online.