bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical Guidelines in Pediatric Hearing Loss: Systemic Review Using the Appraisal of Guidelines for Research and Evaluation II Instrument
Authors: Kanabur Pratik , Hubbard Caleb , Jeyakumar Anita 
Published: December 2018

ObjectivesDespite the importance, impact, and prevalence of pediatric hearing loss (HL), there are very few published clinical practice guidelines (CPG) supporting the evaluation and management of pediatric patients with HL. Our objective was to appraise existing CPGs to ensure safe and effective practices.MethodsA literature search was conducted in PubMed, Google Scholar, EBSCO, as well as a manual Google search. Three independent assessors using the Appraisal of Guidelines for Research and Evaluation II (AGREE II) instrument evaluated CPGs related to HL in children. Standardized domain scores were calculated for each guideline.ResultsA total of four guidelines met the inclusion criteria and were appraised. Scope and purpose achieved a high median score of 83%. Stakeholder involvement, clarity of presentation, and editorial independence achieved intermediate scores of 67%, 54%, and 50%, respectively. The areas that required most improvement and achieved low scores were rigor of development and applicability, with scores of 22% and 38%, respectively. Based on the AGREE II measures, the four guidelines had domain scores less than 60% for each domain, and without modification no guideline could be recommended.ConclusionsBased on the AGREE II, the qualities of CPGs for pediatric HL have several shortcomings, and the need for a comprehensive CPG remains. Rigor of development and applicability present the greatest opportunities for improvement of these CPGs. Laryngoscope, 130:212–216, 2020
Simultaneous cosegmentation of tumors in PET‐CT images using deep fully convolutional networks
Authors: Zhong Zisha , Kim Yusung , Plichta Kristin , Allen Bryan G. , Zhou Leixin , Buatti John , Wu Xiaodong 
Published: December 2018

PurposeTo investigate the use and efficiency of 3‐D deep learning, fully convolutional networks (DFCN) for simultaneous tumor cosegmentation on dual‐modality nonsmall cell lung cancer (NSCLC) and positron emission tomography (PET)‐computed tomography (CT) images.MethodsWe used DFCN cosegmentation for NSCLC tumors in PET‐CT images, considering both the CT and PET information. The proposed DFCN‐based cosegmentation method consists of two coupled three‐dimensional (3D)‐UNets with an encoder‐decoder architecture, which can communicate with the other in order to share complementary information between PET and CT. The weighted average sensitivity and positive predictive values denoted as Scores, dice similarity coefficients (DSCs), and the average symmetric surface distances were used to assess the performance of the proposed approach on 60 pairs of PET/CTs. A Simultaneous Truth and Performance Level Estimation Algorithm (STAPLE) of 3 expert physicians’ delineations were used as a reference. The proposed DFCN framework was compared to 3 graph‐based cosegmentation methods.ResultsStrong agreement was observed when using the STAPLE references for the proposed DFCN cosegmentation on the PET‐CT images. The average DSCs on CT and PET are 0.861 ± 0.037 and 0.828 ± 0.087, respectively, using DFCN, compared to 0.638 ± 0.165 and 0.643 ± 0.141, respectively, when using the graph‐based cosegmentation method. The proposed DFCN cosegmentation using both PET and CT also outperforms the deep learning method using either PET or CT alone.ConclusionsThe proposed DFCN cosegmentation is able to outperform existing graph‐based segmentation methods. The proposed DFCN cosegmentation shows promise for further integration with quantitative multimodality imaging tools in clinical trials.
Validation and investigation of reactive species yields of Geant4‐DNA chemistry models
Authors: Peukert Dylan , Incerti Sebastien , Kempson Ivan , Douglass Michael , Karamitros Mathieu , Baldacchino Gérard , Bezak Eva 
Published: December 2018

PurposeIndirect biological damage due to reactive species produced in water radiolysis reactions is responsible for the majority of biological effect for low linear energy transfer (LET) radiation. Modeling water radiolysis and the subsequent interactions of reactive species, as well as track structures, is essential to model radiobiology on the microscale. Recently, chemistry models have been developed for Geant4‐DNA to be used in combination with the comprehensive existing physics models. In the current work, the first detailed, independent, in silico validation of all species yields with published experimental observations and comparison with other radiobiological simulations is presented. Additionally, the effect of LET of protons and heavier ions on reactive species yield in the model was examined, as well as the completeness of the chemical reactions following the radiolysis within the time after physical interactions simulated in the model.MethodsYields over time of reactive species were simulated for water radiolysis by incident electrons, protons, alpha particles, and ions with various LETs using Geant4 and RITRACKS simulation tools. Water dissociation and recombination was simulated using Geant4 to determine the completeness of chemical reactions at the end of the simulation. Yield validation was performed by comparing yields simulated using Geant4 with experimental observations and other simulations. Validation was performed for all species for low LET radiation and the solvated electron and hydroxyl radical for high LET ions.ResultsIt was found that the Geant4‐DNA chemistry yields were generally in good agreement with experimental observations and other simulations. However, the Geant4‐DNA yields for the hydroxyl radical and hydrogen peroxide at the end of the chemistry stage were found to be respectively considerably higher and lower than the experimentally observed yields. Increasing the LET of incident hadrons increased the yield of secondary species and decreased the yield of primary species. The effect of LET on the yield of the hydroxyl radical at 100 ns simulated with Geant4 was in good agreement with experimental measurements. Additionally, by the end of the simulation only 40% of dissociated water molecules had been recombined and the rate of recombination was slowing.ConclusionsThe yields simulated using Geant4 are within reasonable agreement with experimental observations. Higher LET radiation corresponds with increased yields of secondary species and decreased yields of primary species. These trends combined with the LET having similar effects on the 100 ns hydroxyl radical yield for Geant4 and experimental measurements indicate that Geant4 accurately models the effect of LET on radiolysis yields. The limited recombination within the modeled chemistry stage and the slowing rate of recombination at the end of the stage indicate potential long‐range indirect biological damage.
Robust kidney perfusion mapping in pediatric chronic kidney disease using single‐shot 3D‐GRASE ASL with optimized retrospective motion correction
Authors: Nery Fabio , De Vita Enrico , Clark Chris A. , Gordon Isky , Thomas David L. 
Published: December 2018

PurposeTo develop a robust renal arterial spin labeling (ASL) acquisition and processing strategy for mapping renal blood flow (RBF) in a pediatric cohort with severe kidney disease.MethodsA single‐shot background‐suppressed 3D gradient and spin‐echo (GRASE) flow‐sensitive alternating inversion recovery (FAIR) ASL acquisition method was used to perform 2 studies. First, an evaluation of the feasibility of single‐shot 3D‐GRASE and retrospective noise reduction methods was performed in healthy volunteers. Second, a pediatric cohort with severe chronic kidney disease underwent single‐shot 3D‐GRASE FAIR ASL and RBF was quantified following several retrospective motion correction pipelines, including image registration and threshold‐free weighted averaging. The effect of motion correction on the fit errors of saturation recovery (SR) images (required for RBF quantification) and on the perfusion‐weighted image (PWI) temporal signal‐to‐noise ratio (tSNR) was evaluated, as well as the intra‐ and inter‐session repeatability of renal longitudinal relaxation time (T1) and RBF.ResultsThe mean cortical and/or functional renal parenchyma RBF in healthy volunteers and CKD patients was 295 ± 97 and 95 ± 47 mL/100 g/min, respectively. Motion‐correction reduced image artefacts in both T1 and RBF maps, significantly reduced SR fit errors, significantly increased the PWI tSNR and improved the improved the repeatability of T1 and RBF in the pediatric patient cohort.ConclusionSingle‐shot 3D‐GRASE ASL combined with retrospective motion correction enabled repeatable non‐invasive RBF mapping in the first pediatric cohort with severe kidney disease undergoing ASL scans.
Neuromuscular transmission defects in myopathies: Rare but worth searching for
Authors: Elahi Behzad , Laughlin Ruple S. , Litchy William J. , Milone Margherita , Liewluck Teerin 
Published: December 2018

ABSTRACTIntroduction: Decremental responses in repetitive nerve stimulation have been reported in a few hereditary myopathies. We examined the frequency of decrement in a cohort of myopathy patients. Methods: We reviewed all patients referred for myopathy who underwent repetitive nerve stimulation between January 2007 and May 2017. We included patients with decrement (>10%) and either a pathological or molecular diagnosis of myopathy. Results: Among 157 patients with myopathies, 4 patients had decrement (2 hydroxychloroquine‐associated vacuolar myopathy, 1 centronuclear myopathy, and 1 distal myopathy). One hydroxychloroquine‐associated vacuolar myopathy patient also had inflammatory myopathy. Pyridostigmine improved weakness in the centronuclear myopathy patient, but not in the distal myopathy patient. No patient with an acquired myopathy received pyridostigmine. Conclusions: Despite the rare occurrence of decrement in myopathy, its presence may urge consideration of pharmacological intervention. Muscle Nerve 59:475–478, 2019
BICD2 mutational analysis in hereditary spastic paraplegia and hereditary motor and sensory neuropathy
Authors: Kropatsch Regina , Schmidt Helena M. , Buttkereit Pia , Epplen Jörg T. , Hoffjan Sabine 
Published: December 2018

ABSTRACTIntroduction: Mutations in the BICD2 gene are causative for an autosomal dominant form of spinal muscular atrophy (SMALED2). Further, BICD2 mutations have been implicated in hereditary spastic paraplegia (HSP), but only very few such patients have been described. In this report we aimed to investigate the frequency of BICD2 mutations in patients with HSP and hereditary motor and sensory neuropathy (HMSN) who were negative for the most common known genetic causes. Methods: The cohorts comprised 171 HSP and 189 HMSN patients. Mutational analysis was performed with high‐resolution melting analysis followed by Sanger sequencing. Results: In both cohorts, we found no known or likely pathogenic mutations in the BICD2 gene. Discussion:
BICD2 mutations appear rather unlikely to cause a phenotype of HMSN and are a very rare cause of the HSP phenotype. Muscle Nerve 59:484–486, 2019
Complexity of edge coloring with minimum reload/changeover costs
Authors: Gözüpek Didem , Shalom Mordechai 
Published: December 2018

AbstractIn an edge‐colored graph, a traversal cost occurs along a path when consecutive edges with different colors are traversed. The value of the traversal cost depends only on the colors of the edges. Two related global cost measures, namely the reload cost and the changeover cost with applications in telecommunications, transportation networks, and energy distribution networks have been studied in the literature. Previous work focused on problems with an edge‐colored graph being part of the input. In this paper, we formulate problems that aim to find an edge coloring of a graph minimizing the reload and changeover costs. One pair of problems aims to find a proper edge coloring to minimize the reload/changeover cost of a set of paths. Another pair of problems aim to find a proper edge coloring and a spanning tree to minimize the reload/changeover cost. We present several hardness results and polynomial‐time solvable special cases.
Fibroblast‐specific integrin‐alpha V differentially regulates type 17 and type 2 driven inflammation and fibrosis
Authors: Sciurba Joshua C , Gieseck Richard L , Jiwrajka Nikhil , White Sandra D , Karmele Erik P , Redes Jamie , Vannella Kevin M , Henderson Neil C , Wynn Thomas A , Hart Kevin M 
Published: December 2018

AbstractFibroproliferative diseases affect a significant proportion of the world's population. Despite this, core mechanisms driving organ fibrosis of diverse etiologies remain ill defined. Recent studies suggest that integrin‐alpha V serves as a master driver of fibrosis in multiple organs. Although diverse mechanisms contribute to the progression of fibrosis, TGF‐β and IL‐13 have emerged as central mediators of fibrosis during type 1/type 17, and type 2 polarized inflammatory responses, respectively. To investigate if integrin‐alpha V interactions or signaling is critical to the development of type 2 fibrosis, we analyzed fibroblast‐specific integrin‐alpha V knockout mice in three type 2‐driven inflammatory disease models. While we confirmed a role for integrin‐alpha V in type 17‐associated fibrosis, integrin‐alpha V was not critical to the development of type 2‐driven fibrosis. Additionally, our studies support a novel mechanism through which fibroblasts, via integrin‐alpha V expression, are capable of regulating immune polarization. We show that when integrin‐alpha V is deleted on fibroblasts, initiation of type 17 inflammation is inhibited leading to a deregulation of type 2 inflammation. This mechanism is most evident in a model of severe asthma, which is characterized by a mixed type 2/type 17 inflammatory response. Together, these findings suggest dual targeting of integrin‐alpha V and type 2 pathways may be needed to ameliorate fibrosis and prevent rebound of opposing pro‐fibrotic and inflammatory mechanisms. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
TLR9 rs352139 Genetic Variant Promotes Tacrolimus Elimination in Chinese Liver Transplant Patients During the Early Posttransplantation Period
Authors: Ou Baochi , Liu Yuan , Zhang Tao , Sun Yahuang , Chen Jiayi , Peng Zhihai 
Published: December 2018

BackgroundThere are limited markers that could facilitate individualized tacrolimus treatment in the early posttransplantation period. Genetic factors have been found to play critical roles in determining tacrolimus pharmacokinetics.ObjectiveWe aimed to examine the association of donor and recipient Toll‐like receptor (TLR) polymorphisms with tacrolimus elimination and the potential mechanism for TLR gene polymorphism–mediated tacrolimus metabolism.MethodsTwo independent cohorts including 297 patients receiving liver transplantation (LT) were enrolled in this study (cohort A was composed of 200 patients; cohort B included 97 patients and served as a validation set). Toll‐like receptors polymorphisms were genotyped using TaqMan single nucleotide polymorphisms (SNPs) assays. The protein expressions were detected by Western blotting. The metabolism assay was used to quantify tacrolimus elimination. The activity of nuclear factor‐kB (NF‐kB) was evaluated by luciferase reporter assay.ResultsTacrolimus dose‐adjusted trough blood concentrations (C/D) ratios were significantly lower for donor TLR9 rs352139 AG/GG carriers than AA carriers at weeks 1, 2, and 3 after LT. In multivariate analysis, donor and recipient CYP3A5 rs776746 and donor TLR9 rs352139 were independent predictors of tacrolimus C/D ratios in the early period after transplantation in both cohorts. When investigating the combined effects of donor CYP3A5 rs776746 and donor TLR9 rs352139 genotypes, the C/D ratios were remarkably significant at all time points during the first month after LT within the four groups. Furthermore, CYP3A5 mRNA expression in liver tissue was significantly higher for AG/GG patients than AA carriers after LT. In addition, we demonstrated that the TLR9 rs352139 genetic variant promotes tacrolimus metabolism of liver cells via upregulation of CYP3A5, which is dependent on the repression of NF‐κB/pregnane X receptor (PXR) signaling.ConclusionsDonor TLR9 rs352139 genetic variant facilitated tacrolimus elimination during the early stage after LT in Chinese patients, which might be related to the upregulation of CYP3A5 enzyme via the NF‐kB/PXR signaling pathway.
A Combination of Proteomic Approaches Identifies A Panel of Circulating Extracellular Vesicle Proteins Related to the Risk of Suffering Cardiovascular Disease in Obese Patients
Authors: Barrachina María N. , Sueiro Aurelio M. , Casas Vanessa , Izquierdo Irene , Hermida‐Nogueira Lidia , Guitián Esteban , Casanueva Felipe F. , Abián Joaquín , Carrascal Montserrat , Pardo María , García Ángel 
Published: December 2018

AbstractPlasma‐derived extracellular vesicles (EVs) have been extensively described as putative biomarkers in different diseases. Interestingly, increased levels of EVs subpopulations are well known to associate with obesity. The goal of this study is to identify EVs‐derived biomarkers in plasma from obese patients in order to predict the development of pathological events associated with obesity. Samples are obtained from 22 obese patients and their lean‐matched controls are divided into two cohorts: one for a 2D fluorescence difference gel electrophoresis (2D‐DIGE)‐based study, and the other one for a label free LC–MS/MS‐based approach. EVs are isolated following a serial ultracentrifugation protocol. Twenty‐two and 23 differentially regulated features are detected from 2D‐DIGE and label free LC–MS/MS, respectively; most of them involve in the coagulation and complement cascades. Remarkably, there is an upregulation of complement C4, complement C3, and fibrinogen in obese patients following both approaches, the latter two also validated by 2D‐western‐blotting in an independent cohort. These results correlate with a proinflammatory and prothrombotic state of those individuals. On the other hand, a downregulation of adiponectin leading to an increased risk of suffering cardiovascular diseases has been shown. The results suggest the relevance of plasma‐derived‐EVs proteins as a source of potential biomarkers for the development of atherothrombotic events in obesity.
Scavager: A Versatile Postsearch Validation Algorithm for Shotgun Proteomics Based on Gradient Boosting
Authors: Ivanov Mark V. , Levitsky Lev I. , Bubis Julia A. , Gorshkov Mikhail V. 
Published: December 2018

AbstractShotgun proteomics workflows for database protein identification typically include a combination of search engines and postsearch validation software based mostly on machine learning algorithms. Here, a new postsearch validation tool called Scavager employing CatBoost, an open‐source gradient boosting library, which shows improved efficiency compared with the other popular algorithms, such as Percolator, PeptideProphet, and Q‐ranker, is presented. The comparison is done using multiple data sets and search engines, including MSGF+, MSFragger, X!Tandem, Comet, and recently introduced IdentiPy. Implemented in Python programming language, Scavager is open‐source and freely available at https://bitbucket.org/markmipt/scavager.
A model for charge transport in semicrystalline polymer thin films
Authors: Raj Mohan S. , Singh Manoranjan P. , Joshi M. P. 
Published: December 2018

ABSTRACTA model for simulating the charge transport properties of semicrystalline polymer (SCrP) using Monte Carlo simulation is reinvented. The model is validated by reproducing the experimentally observed field and temperature dependence of mobility in Poly(3‐hexylthiophene‐2,5‐diyl) (P3HT) thin films. This study also provides a new physical insight to the origin of much debated negative field dependence of mobility (NFDM) observed at low electric field strengths in P3HT thin films. The observed NFDM, which is not explainable with the mechanisms proposed earlier, is attributed to the weak dependence of transit time on the applied electric field strengths. In the semicrystalline films, the charge transport takes place mostly through the crystalline regions, in which the charge transport is weakly dependent on the strength of the applied electric field. In addition, a possible explanation for the origin of Arrhenius temperature dependence of mobility (lnμ ∝ 1/T) commonly observed in SCrP thin films is also proposed. © 2018 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2019, 57, 137–141
Hydrostatic vertical velocity and incompressibility in the Northern Hemisphere
Authors: Egger Joseph , Hoinka Klaus‐Peter 
Published: December 2018

The vertical velocity w is evaluated for the Northern Hemisphere from reanalysis data and two forms of the Richardson equation. This equation is based on the hydrostatic assumption and the thermodynamic energy equation. The standard form of the Richardson equation allows one to quantify the contributions to the vertical velocity of the horizontal divergence δ, the vertical pressure velocity ω and heating, and to test the incompressibility assumption underlying many dynamic models and theories. However, there are cancellations between two important terms. This shortcoming is substantially reduced in a further version of this equation where one term dominates. This version is the backbone of the data evaluation.The vertical velocities resulting from the Richardson equation in the troposphere are in good agreement with those obtained directly from the reanalysis data. It is found that the assumption of incompressibility provides a good estimate for w in the mid troposphere, even above Greenland and the Tibetan Plateau, both for the annual mean and the standard deviation of w, but is less acceptable in the upper troposphere and almost useless in the lower stratosphere. The contribution of heating to w is small.
Vector field analysis for surface registration in computer‐assisted ENT surgery
Authors: Diakov Georgi , Freysinger Wolfgang 
Published: December 2018

AbstractBackgroundManual paired‐point registration for navigated ENT‐surgery is prone to human errors; automatic surface registration is often caught in local minima.MethodsAnatomical features of the human occiput are integrated into an algorithm for surface registration. A vector force field is defined between the patient and operating room datasets; registration is facilitated through gradient‐based vector field analysis optimization of an energy function. The method is validated exemplarily on patient surface data provided by a mechanically positioned A‐mode ultrasound sensor.ResultsSuccessful registrations were achieved within the entire parameter space, as well as from positions of local minima that were found by the Gaussian fields algorithm for surface registration. Sub‐millimetric registration error was measured in clinically relevant anatomical areas on the anterior skull and within the generally accepted margin of 1.5 mm for the entire head.ConclusionThe satisfactory behavior of this approach potentially suggests a wider clinical integration.