bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prognostic value of pretreatment lymphocyte-to-monocyte ratio in patients with urologic tumors
Authors: Li Jialin , Cheng Yusheng , Ji Zhigang 
Published: January 2019

Abstract

Background:
The prognostic value of pretreatment lymphocyte to monocyte ratio (LMR) in patients with urologic tumors remains controversial. Therefore, we herein conducted a meta-analysis to systematically assess the prognostic value of LMR in patients with urologic tumors.

Methods:
We comprehensively searched PubMed, EMBASE and Web of Science to identify eligible studies. Hazard ratios (HRs) and their 95% confidence intervals (CIs) were used to assess the prognostic value of LMR in patients with urologic tumors. This meta-analysis was registered in PROSPERO (CRD42018108959).

Results:
A total of 20 studies were included in this meta-analysis. Our synthesized analysis showed that low LMR was significantly correlated with poor overall survival (OS) and progression-free survival (PFS) in patients with upper tract urothelial cancer (UTUC). We also found that renal cell cancer (RCC) patients with low LMR had poor OS, PFS and cancer-specific survival (CSS). Besides, it was observed that low LMR predicted poor OS, RFS and CSS in patients with bladder cancer (BC).

Conclusion:
This meta-analysis demonstrated that pretreatment LMR is associated with survival, and may be a useful prognostic parameter in urologic tumors. Nevertheless, more prospective and heterogeneous studies with large samples are required to further confirm our findings before it is applied for daily clinical decision making.
Comparison of keyhole endoscopy and craniotomy for the treatment of patients with hypertensive cerebral hemorrhage
Authors: Sun Guoqing , Li Xiaolong , Chen Xiangtao , Zhang Yuhai , Xu Zhen 
Published: January 2019

Abstract
By comparing the intraoperative and postoperative conditions under different surgical methods, namely, keyhole endoscopy and craniotomy, we aim to provide more reasonable surgical treatment for patients with hypertensive cerebral hemorrhage.
Eighty-nine patients with cerebral hemorrhage at Rizhao People's Hospital between January 2015 and December 2016 were analyzed retrospectively. Patients were assigned to the keyhole endoscopy group and the craniotomy group. The intraoperative (the duration of operation, operative blood transfusion and loss, and hematoma clearance rate) and the postoperative parameters (death rate, rebleeding rate, edema, and postoperative activity of daily living [ADL] scores) of the 2 groups were compared.
Compared with the craniotomy group, the keyhole endoscopy group exhibited decreases in mean blood loss (P < .05, 180 ± 13.6 mL vs 812 ± 35.2 mL), blood transfusion (P < .05, 0 mL vs 480 ± 13.6 mL), the average surgical duration of operation (P < .05, 113 ± 14.3 minutes vs 231 ± 26.1 minutes), and the severe edema rate (P < .05, 10.9% vs 72.1%) and increases in the average hematoma clearance rate (P < .05, 95.6% vs 82.3%) and postoperative ADL scores (P < .05, 85.2% vs 39.0%). Neither the death rate (P > .05, 4.3% vs 4.7%) nor rebleeding rate (P > .05, 2.2% vs 2.3%) showed any obvious changes.
Keyhole endoscopy for the treatment of hypertensive intracerebral hemorrhage has the advantages of minimal trauma with good effects, and its main reason for short operation time, reduced bleeding, and high hematoma clearance rate is the “brain-hematoma” pressure gradient. Use of the intraoperative micropull technique and removal of intracerebral hematoma in the shortest time possible are critical factors contributing to the high ADL scores in the keyhole endoscopy group. However, further validation on a larger sample size is required.
Diagnostic and Therapeutic Approach in Paediatric Inflammatory Bowel Diseases
Authors: Bronsky Jiri , de Ridder Lissy , Ruemmele Frank M. , Griffiths Anne , Buderus Stephan , Hradsky Ondrej , Hauer Almuthe Christina 
Published: January 2019

ABSTRACTObjectives:Despite existence of international guidelines for diagnosis and management of inflammatory bowel diseases (IBD) in children, there might be differences in the clinical approach.Methods:A survey on clinical practice in paediatric IBD was performed among members of the ESPGHAN Porto IBD working group and interest group, PIBD‐NET, and IBD networks in Canada and German‐speaking countries (CIDsCANN, GPGE), using a web‐based questionnaire. Responses to 63 questions from 106 paediatric IBD centres were collected.Results:Eighty‐four percentage of centres reported to fulfil the revised Porto criteria in the majority of patients. In luminal Crohn disease (CD), exclusive enteral nutrition is used as a first‐line induction therapy and immunomodulators (IMM) are used since diagnosis in the majority of patients. Infliximab (IFX) is mostly considered as first‐line biological. Sixty percentage of centres have experience with vedolizumab and/or ustekinumab and 40% use biosimilars. In the majority of ulcerative colitis (UC) patients 5‐aminosalicylates are continued as concomitant therapy to IMM (usually azathioprine [AZA]/6‐MP). After ileocaecal resection (ICR) in CD patients without postoperative residual disease, AZA monotherapy is the preferred treatment.Conclusions:A majority of centres follows both the Porto diagnostic criteria as well as paediatric (ESPGHAN/ECCO) guidelines on medical and surgical IBD management. This reflects the value of international societal guidelines. However, potentially desirable answers might have been given instead of what is true daily practice, and the most highly motivated people might have answered, leading to some bias.
Impact of Immunosuppression on Executive Functioning After Pediatric Liver Transplantation
Authors: Goldschmidt Imeke , van Dick Rolf , Jacobi Christoph , Junge Norman , Pfister Eva , Richter Nico , Baumann Ulrich 
Published: January 2019

ABSTRACTObjectives:Children after liver transplantation show increased rates of impaired cognitive functioning. We aimed to assess the potential effects of immunosuppressive therapy on executive functioning measured by the Children's Color Trail Test and the cognitive functioning module of the PedsQL (cogPedsQL) in liver transplanted children to explore potential targets for intervention to improve executive functioning.Methods:We performed a cross‐sectional study in 155 children (78 girls) aged 10.4 (2–18) years at 5.0 (0.1–17) years after liver transplantation, with follow‐up at 6 months in n = 114. Executive functioning was assessed by Children's Color Trail Test (ages 8–16) and by patients and parent‐proxy cogPedsQL (ages 5–18/2–18, respectively). Results were correlated with clinical parameters. Stability of results over time was compared between n = 23 patients who for clinical reasons switched from twice daily calcineurin inhibitor (CNI) to once‐daily slow‐release tacrolimus (Tac) during the study period, and patients with unchanged CNI.Results:Worse executive functioning was associated with longer stay in the intensive care unit and longer time elapsed since transplantation. No difference was found between users of cyclosporine and Tac. Children on once‐daily slow‐release Tac performed better than children on twice‐daily Tac. In children who switched from twice‐daily CNI to once‐daily Tac, parent‐proxy cogPedsQL improved significantly compared to stable results in the nonswitch group.Conclusions:In addition to a strong impact of disease burden around transplantation, executive functioning appears to deteriorate over time. Although there is no clear‐cut advantage of any CNI, once‐daily Tac appears to be advantageous compared to twice‐daily Tac.
Pediatric Endoscopy and High‐risk Patients
Authors: Lightdale Jenifer R. , Liu Quin Y. , Sahn Benjamin , Troendle David M. , Thomson Mike , Fishman Douglas S. ,   NASPGHAN Endoscopy and Procedures Committee
Published: January 2019

ABSTRACTPediatric gastrointestinal endoscopy has been established as safe and effective for diagnosis and management of many pediatric gastrointestinal diseases. Nevertheless, certain patient and procedure factors should be recognized that increase the risk of intra‐ and/or postprocedural adverse events (AEs). AEs associated with endoscopic procedures can broadly be categorized as involving sedation‐related physiological changes, bleeding, perforation, and infection. Factors which may increase patient risk for such AEs include but are not limited to, cardiopulmonary diseases, anatomical airway or craniofacial abnormalities, compromised intestinal luminal wall integrity, coagulopathies, and compromised immune systems. Examples of high‐risk patients include patients with congenital heart disease, craniofacial abnormalities, connective tissues diseases, inflammatory bowel disease, and children undergoing treatment for cancer. This clinical report is intended to help guide clinicians stratify patient risks and employ clinical practices that may minimize AEs during and after endoscopy. These include use of CO2 insufflation, endoscopic techniques for maneuvers such as biopsies, and endoscope loop‐reduction to mitigate the risk of such complications such as bleeding and intestinal perforation. Endoscopic infection risk and guidance regarding periprocedural antibiotics are also discussed.
Synchronization of sensory gamma oscillations promotes multisensory communication
Authors: Misselhorn Jonas , Schwab Bettina C. , Schneider Till R. , Engel Andreas K. 
Published: January 2019

AbstractRhythmic neuronal activity in the gamma range is a signature of active cortical processing and its synchronization across distant sites has been proposed as a fundamental mechanism of network communication. While this has been shown within sensory modalities, we tested whether crosstalk between the senses relies on similar mechanisms. In two consecutive experiments, we used a task in which human participants (male and female) matched amplitude changes of concurrent visual, auditory and tactile stimuli. In this task, matching of congruent stimuli was associated with a behavioral benefit compared to matching of incongruent stimuli. In the first experiment, we used source-level analysis of high-density electroencephalography (EEG) and observed that cross-modal matching of congruent inputs was associated with relatively weaker coherence between gamma oscillations in early sensory regions. Next, we used bifocal high-definition transcranial alternating current stimulation (hd-tACS) to manipulate the strength of coupling between sensory cortices. Here, we used a lateralized version of the task in which hd-tACS was applied either ipsilateral or contralateral to the hemisphere receiving sensory stimuli. Ipsilateral gamma, but not alpha stimulation slowed responses to congruent trials whereas responding to incongruent trials was not changed by tACS. We speculate that fast responding to congruent stimuli involves decoupling of sensory gamma oscillations, which was prevented by tACS. These results indicate that synchronization of gamma oscillations promotes direct communication between sensory modalities. The framework of coupled gamma oscillations underlying cortical communication might thus be generalizable from processing within sensory streams to interactions between sensory networks.Significance statementCortical gamma oscillations structure segregated neural activity and were suggested to represent a fundamental mechanism of network communication. While there is ample evidence for the role of long-range gamma synchronization in unisensory processing, its significance in multisensory networks is still unclear. We show that direct interactions between sensory cortices rely on synchronization of gamma band activity. To that end, we carried out two consecutive experiments using state-of-the-art high-density electroencephalography (EEG) and high-definition transcranial alternating current stimulation (hd-tACS). By complementing an observational with an interventional method, we provide novel evidence for the role of synchronized gamma oscillations in multisensory communication.
DisCVR: Rapid viral diagnosis from high-throughput sequencing data
Authors: Maabar Maha , Davison Andrew J. , Palmarini Massimo , Hughes Joseph 
Published: January 2019

AbstractHigh-throughput sequencing (HTS) enables most pathogens in a clinical sample to be detected from a single analysis, thereby providing novel opportunities for diagnosis, surveillance and epidemiology. However, this powerful technology is difficult to apply in diagnostic laboratories because of its computational and bioinformatic demands. We have developed DisCVR, which detects known human viruses in clinical samples by matching sample k-mers (22 nucleotide sequences) to k-mers from taxonomically labelled viral genomes. DisCVR was validated using published HTS data for 89 clinical samples from adults with upper respiratory tract infections. These samples had been tested for viruses metagenomically and also by real-time polymerase chain reaction assay, which is the standard diagnostic method. DisCVR detected human viruses with high sensitivity (79%) and specificity (100%), and was able to detect mixed infections. Moreover, it produced results comparable to those in a published metagenomic analysis of 177 blood samples from patients in Nigeria. DisCVR has been designed as a user-friendly tool for detecting human viruses from HTS data using computers with limited RAM and processing power, and includes a graphical user interface to help users interpret and validate the output. It is written in Java and is publicly available from http://bioinformatics.cvr.ac.uk/discvr.php.Issue SectionResources
Mice adaptively generate choice variability in a deterministic task
Authors: Belkaid Marwen , Bousseyrol Elise , Cuttoli Romain Durand-de , Dongelmans Malou , Duranté Etienne K. , Yahia Tarek Ahmed , Didienne Steve , Hanesse Bernadette , Come Maxime , Mourot Alex , Naudé Jérémie , Sigaud Olivier , Faure Philippe 
Published: January 2019

AbstractCan our choices just be driven by chance? To investigate this question, we designed a deterministic setting in which mice reinforce non-repetitive choice sequences, and modeled it using reinforcement learning. Mice progressively increased their choice variability using a memory-free, pseudo-random selection, rather than by learning complex sequences. Our results demonstrate that a decision-making process can self-generate variability and randomness even when the rules governing reward delivery are not stochastic.
Mechanical feedback enables catch bonds to selectively stabilize scanning microvilli at T-cell surfaces
Authors: Pullen Robert H. , Abel Steven M. 
Published: January 2019

AbstractT cells use microvilli to search the surfaces of antigen-presenting cells for antigenic ligands. The active motion of scanning microvilli provides a force-generating mechanism that is intriguing in light of single-molecule experiments showing that applied forces on stimulatory receptor-ligand bonds increase their lifetimes (catch-bond behavior). In this work, we introduce a theoretical framework to explore the motion of a microvillus tip above an antigen-presenting surface when receptors on the tip stochastically bind to ligands on the surface and dissociate from them in a force-dependent manner. Forces on receptor-ligand bonds impact the motion of the microvillus, leading to feedback between binding and microvillar motion. We use computer simulations to show that the average microvillus velocity varies in a ligand-dependent manner, that catch bonds generate responses in which some microvilli almost completely stop while others move with a broad distribution of velocities, and that the frequency of stopping depends on the concentration of stimulatory ligands. Typically, a small number of catch bonds initially immobilize the microvillus, after which additional bonds accumulate and increase the cumulative receptor-engagement time. Our results demonstrate that catch bonds can selectively slow and stabilize scanning microvilli, suggesting a physical mechanism that may contribute to antigen discrimination by T cells.
High-throughput phenotyping with deep learning gives insight into the genetic architecture of flowering time in wheat
Authors: Wang Xu , Xuan Hong , Evers Byron , Shrestha Sandesh , Pless Robert , Poland Jesse 
Published: January 2019

ABSTRACTBackgroundPrecise measurement of plant traits with precision and speed on large populations has emerged as a critical bottleneck in connecting genotype to phenotype in genetics and breeding. This bottleneck limits advancements in understanding plant genomes and the development of improved, high-yielding crop varieties.ResultsHere we demonstrate the application of deep learning on proximal imaging from a mobile field vehicle to directly score plant morphology and developmental stages in wheat under field conditions. We developed and trained a convolutional neural network with image datasets labeled from expert visual scores and used this ‘breeder-trained’ network to directly score wheat morphology and developmental stages. For both morphological (awned) and phenological (flowering time) traits, we demonstrate high heritability and extremely high accuracy against the ‘ground-truth’ values from visual scoring. Using the traits scored by the network, we tested genotype-to-phenotype association using the deep learning phenotypes and uncovered novel epistatic interactions for flowering time. Enabled by the time-series high-throughput phenotyping, we describe a new phenotype as the rate of flowering and show heritable genetic control.ConclusionsWe demonstrated a field-based high-throughput phenotyping approach using deep learning that can directly score morphological and developmental phenotypes in genetic populations. Most powerfully, the deep learning approach presented here gives a conceptual advancement in high-throughput plant phenotyping as it can potentially score any trait in any plant species through leveraging expert knowledge from breeders, geneticist, pathologists and physiologists.
Cryo-EM structures reveal a conformational change of SOPA1 during mitochondrial inner membrane fusion
Authors: Zhang Danyang , Zhang Yan , Ma Jun , Niu Tongxin , Chen Wenbo , Pang Xiaoyun , Zhai Yujia , Sun Fei 
Published: January 2019

ABSTRACTMammalian mitochondrial inner membrane fusion is mediated by OPA1(optic atrophy 1). Under physiological condition, OPA1 undergoes proteolytic processing to form a membrane-anchored long isoform (LOPA1) and a soluble short isoform (SOPA1). A combination of LOPA1 and SOPA1 are required for membrane fusion, however, the relevant mechanism is not well understood. In this study, we investigate the cryo-EM structures of SOPA1 coated liposome tube at nucleotide-free and GTPγS bound states. SOPA1 exhibits a general structure of dynamin family and can assemble onto membrane in a helical array with a building block of dimer and thus induce membrane tubulation. A predicted amphipathic helix is discovered to mediate the tubulation activity of SOPA1. The binding of GTPγS causes a conformational rotation between GTPase domain and stalk region, and then induces a rearrangement of the helical array and an expansion of the tube, which is opposite to the behavior of other dynamin proteins, suggesting a unique role of SOPA1 in the fusion of mitochondrial inner membrane.
Sex differences in brain correlates of STEM anxiety
Authors: Gonzalez Ariel A. , Bottenhorn Katherine L. , Bartley Jessica E. , Hayes Timothy , Riedel Michael C. , Salo Taylor , Bravo Elsa I. , Odean Rosalie , Nazareth Alina , Laird Robert W. , Sutherland Matthew T. , Brewe Eric , Pruden Shannon M. , Laird Angela R. 
Published: January 2019

ABSTRACTAnxiety is known to dysregulate the salience, default mode, and central executive networks of the human brain, yet this phenomenon has not been fully explored across the STEM learning experience, where anxiety can impact negatively academic performance. Here, we evaluated anxiety and large-scale brain connectivity in 101 undergraduate physics students. We found sex differences in STEM-related but not clinical anxiety, with longitudinal increases in science anxiety observed for both female and male students. Sex-specific impacts of STEM anxiety on brain connectivity emerged, with male students exhibiting distinct inter-network connectivity for STEM and clinical anxiety and female students demonstrating no significant within-sex correlations. Anxiety was negatively correlated with academic performance in sex-specific ways at both pre-and post-instruction. Moreover, math anxiety in male students mediated the relation between default mode-salience connectivity and course grade. Together, these results reveal complex sex differences in the neural mechanisms driving how anxiety impacts STEM learning.
Genome-scale model of Rhodotorula toruloides metabolism
Authors: Tiukova Ievgeniia A , Prigent Sylvain , Nielsen Jens , Sandgren Mats , Kerkhoven Eduard J 
Published: January 2019

AbstractThe basidiomycete red yeast Rhodotorula toruloides is a promising platform organism for production of biooils. We present rhto-GEM, the first genome-scale model of R. toruloides metabolism, that was largely reconstructed using RAVEN toolbox. The model includes 4869 genes, 897 reactions, and 3334 metabolites. Lipid metabolism was described using the SLIMEr formalism, which allows direct integration of lipid class and acyl chain experimental distribution data. The simulation results confirmed that the R. toruloides model provides valid growth predictions on glucose, xylose and glycerol, while prediction of genetic engineering targets to increase production of linolenic acid and triacylglycerols highlighted genes that have previously been successfully used to increase lipid production. This renders rtho-GEM useful for future studies to improve the production of other industrially important oleochemicals including both value-added fatty acids and carotenoids, while it will also be valuable tool for system-wide omics-data analysis in R. toruloides. Expanding the portfolio of GEMs for lipid accumulating fungi contributes to both understanding of metabolic mechanisms of the oleaginous phenotype but also uncover particularities of lipid production machinery in R. toruloides.