bluuebunny/crossref_metadata_2025_split huggingface dataset:
Perioperative Complications in Neonatal Surgery: Biliary Atresia and Choledochal Malformations
Authors: Wilde Jim , Calinescu Ana , Wildhaber Barbara 
Published: March 2018

AbstractBiliary atresia (BA) and congenital choledochal malformations (CCM) are rare. Both pathologies must (BA) or may (CCM) be operated during the neonatal period or early infancy. We briefly describe the classical operative techniques for both pathologies, followed by the most common and severe perioperative complications encountered during and up to 30 days after surgery in children operated for BA and CCM early in life. For patients with BA, intestinal complications represent the most common and hazardous perioperative surgical complications. Cholangitis is the most frequently encountered medical complication post hepato-porto-enterostomy. For CCM, it seems that neonates encounter little perioperative complications; however, reports are scarce; bile leak and/or cholangitis are the most reported. Overall, for patients with CCM, the literature is ambivalent whether more perioperative complications occur in the younger or in the older patient, and whether these occur more frequently in those symptomatic or asymptomatic at operation. It is difficult to give clear advice for when children with asymptomatic CCM should be operated, and benefits and risks must be carefully counterbalanced. Perioperative mortality for both BA and CCM is low and is reported to be around 1 to 2%.
In Vitro Studies on Physiological and Chemical Stability of New LE404-Derivatives with Extended Half-Life
Authors: Zergiebel Stephanie , Seeling Andreas 
Published: March 2018

AbstractDibenzoazecines are a class of potential neuroleptics with high affinity to dopamine and serotonin receptors. The efficacy and high therapeutic range has already been demonstrated in vivo with the lead structure 7-methyl-5,6,7,8,9,14-hexahydrodibenzo[d,g]azecin-3-ol (LE404) and selected derivatives. There is a variety of new synthesized structurally different dibenzoazecine derivatives with the aim to improve pharmacokinetic parameters, all of which contain the lead structure LE404. For a multitude of these substances is still a lack of information, inclusive of stability, physicochemical parameters, pharmacokinetics and metabolism. Therefore, the present study investigated the stability properties of 17 new azecine derivatives, including esterase cleavage, stability in simulated gastrointestinal fluid, stability at different pH-values and determination of octanol/water-partition coefficients. These findings, in correlation to the properties and efficacy of the already in vivo tested substances, will be useful for safety and efficacy in further in vivo tests.
Optimizing a Sensor Network with Data from Hazard Mapping Demonstrated in a Heavy-Vehicle Manufacturing Facility
Authors: Berman Jesse D , Peters Thomas M , Koehler Kirsten A 
Published: March 2018

AbstractObjectivesTo design a method that uses preliminary hazard mapping data to optimize the number and location of sensors within a network for a long-term assessment of occupational concentrations, while preserving temporal variability, accuracy, and precision of predicted hazards.MethodsParticle number concentrations (PNCs) and respirable mass concentrations (RMCs) were measured with direct-reading instruments in a large heavy-vehicle manufacturing facility at 80–82 locations during 7 mapping events, stratified by day and season. Using kriged hazard mapping, a statistical approach identified optimal orders for removing locations to capture temporal variability and high prediction precision of PNC and RMC concentrations. We compared optimal-removal, random-removal, and least-optimal-removal orders to bound prediction performance.ResultsThe temporal variability of PNC was found to be higher than RMC with low correlation between the two particulate metrics (ρ = 0.30). Optimal-removal orders resulted in more accurate PNC kriged estimates (root mean square error [RMSE] = 49.2) at sample locations compared with random-removal order (RMSE = 55.7). For estimates at locations having concentrations in the upper 10th percentile, the optimal-removal order preserved average estimated concentrations better than random- or least-optimal-removal orders (P &lt; 0.01). However, estimated average concentrations using an optimal-removal were not statistically different than random-removal when averaged over the entire facility. No statistical difference was observed for optimal- and random-removal methods for RMCs that were less variable in time and space than PNCs.ConclusionsOptimized removal performed better than random-removal in preserving high temporal variability and accuracy of hazard map for PNC, but not for the more spatially homogeneous RMC. These results can be used to reduce the number of locations used in a network of static sensors for long-term monitoring of hazards in the workplace, without sacrificing prediction performance.
GOLabeler: improving sequence-based large-scale protein function prediction by learning to rank
Authors: You Ronghui , Zhang Zihan , Xiong Yi , Sun Fengzhu , Mamitsuka Hiroshi , Zhu Shanfeng 
Published: March 2018

AbstractMotivationGene Ontology (GO) has been widely used to annotate functions of proteins and understand their biological roles. Currently only &lt;1% of &gt;70 million proteins in UniProtKB have experimental GO annotations, implying the strong necessity of automated function prediction (AFP) of proteins, where AFP is a hard multilabel classification problem due to one protein with a diverse number of GO terms. Most of these proteins have only sequences as input information, indicating the importance of sequence-based AFP (SAFP: sequences are the only input). Furthermore, homology-based SAFP tools are competitive in AFP competitions, while they do not necessarily work well for so-called difficult proteins, which have &lt;60% sequence identity to proteins with annotations already. Thus, the vital and challenging problem now is how to develop a method for SAFP, particularly for difficult proteins.MethodsThe key of this method is to extract not only homology information but also diverse, deep-rooted information/evidence from sequence inputs and integrate them into a predictor in a both effective and efficient manner. We propose GOLabeler, which integrates five component classifiers, trained from different features, including GO term frequency, sequence alignment, amino acid trigram, domains and motifs, and biophysical properties, etc., in the framework of learning to rank (LTR), a paradigm of machine learning, especially powerful for multilabel classification.ResultsThe empirical results obtained by examining GOLabeler extensively and thoroughly by using large-scale datasets revealed numerous favorable aspects of GOLabeler, including significant performance advantage over state-of-the-art AFP methods.Availability and implementationhttp://datamining-iip.fudan.edu.cn/golabeler.Supplementary informationSupplementary data are available at Bioinformatics online.
AnaCoDa: analyzing codon data with Bayesian mixture models
Authors: Landerer Cedric , Cope Alexander , Zaretzki Russell , Gilchrist Michael A 
Published: March 2018

Abstract

Summary
AnaCoDa is an R package for estimating biologically relevant parameters of mixture models, such as selection against translation inefficiency, non-sense errors and ribosome pausing time, from genomic and high throughput datasets. AnaCoDa provides an adaptive Bayesian MCMC algorithm, fully implemented in C++ for high performance with an ergonomic R interface to improve usability. AnaCoDa employs a generic object-oriented design to allow users to extend the framework and implement their own models. Current models implemented in AnaCoDa can accurately estimate biologically relevant parameters given either protein coding sequences or ribosome foot-printing data. Optionally, AnaCoDa can utilize additional data sources, such as gene expression measurements, to aid model fitting and parameter estimation. By utilizing a hierarchical object structure, some parameters can vary between sets of genes while others can be shared. Genes may be assigned to clusters or membership may be estimated by AnaCoDa. This flexibility allows users to estimate the same model parameter under different biological conditions and categorize genes into different sets based on shared model properties embedded within the data. AnaCoDa also allows users to generate simulated data which can be used to aid model development and model analysis as well as evaluate model adequacy. Finally, AnaCoDa contains a set of visualization routines and the ability to revisit or re-initiate previous model fitting, providing researchers with a well rounded easy to use framework to analyze genome scale data.

Availability and implementation
AnaCoDa is freely available under the Mozilla Public License 2.0 on CRAN (https://cran.r-project.org/web/packages/AnaCoDa/).
Optimality and identification of dynamic models in systems biology: an inverse optimal control framework
Authors: Tsiantis Nikolaos , Balsa-Canto Eva , Banga Julio R 
Published: March 2018

Abstract

Motivation
Optimality principles have been used to explain many biological processes and systems. However, the functions being optimized are in general unknown a priori. Here we present an inverse optimal control framework for modeling dynamics in systems biology. The objective is to identify the underlying optimality principle from observed time-series data and simultaneously estimate unmeasured time-dependent inputs and time-invariant model parameters. As a special case, we also consider the problem of optimal simultaneous estimation of inputs and parameters from noisy data. After presenting a general statement of the inverse optimal control problem, and discussing special cases of interest, we outline numerical strategies which are scalable and robust.

Results
We discuss the existence, relevance and implications of identifiability issues in the above problems. We present a robust computational approach based on regularized cost functions and the use of suitable direct numerical methods based on the control-vector parameterization approach. To avoid convergence to local solutions, we make use of hybrid global-local methods. We illustrate the performance and capabilities of this approach with several challenging case studies, including simulated and real data. We pay particular attention to the computational scalability of our approach (with the objective of considering large numbers of inputs and states). We provide a software implementation of both the methods and the case studies.

Availability and implementation
The code used to obtain the results reported here is available at https://zenodo.org/record/1009541.

Supplementary information
Supplementary data are available at Bioinformatics online.
esATAC: an easy-to-use systematic pipeline for ATAC-seq data analysis
Authors: Wei Zheng , Zhang Wei , Fang Huan , Li Yanda , Wang Xiaowo 
Published: March 2018

Abstract

Summary
ATAC-seq is rapidly emerging as one of the major experimental approaches to probe chromatin accessibility genome-wide. Here, we present ‘esATAC’, a highly integrated easy-to-use R/Bioconductor package, for systematic ATAC-seq data analysis. It covers essential steps for full analyzing procedure, including raw data processing, quality control and downstream statistical analysis such as peak calling, enrichment analysis and transcription factor footprinting. esATAC supports one command line execution for preset pipelines and provides flexible interfaces for building customized pipelines.

Availability and implementation
esATAC package is open source under the GPL-3.0 license. It is implemented in R and C++. Source code and binaries for Linux, MAC OS X and Windows are available through Bioconductor (https://www.bioconductor.org/packages/release/bioc/html/esATAC.html).

Supplementary information
Supplementary data are available at Bioinformatics online.
Modelled salmon lice dispersion and infestation patterns in a sub-arctic fjord
Authors: Skarðhamar Jofrid , Albretsen Jon , Sandvik Anne D , Lien Vidar S , Myksvoll Mari S , Johnsen Ingrid A , Asplin Lars , Ådlandsvik Bjørn , Halttunen Elina , Bjørn Pål Arne 
Published: March 2018

Abstract
Salmon lice infestation is a major challenge for the aquaculture industry in Norway, threatening wild salmonid populations and causing welfare problems for farmed salmon. Lice dispersion and infestation patterns are simulated by combining a high-resolution hydrodynamic model for the Norwegian coast and fjords with an individual-based model for salmon lice. We here present results from Altafjorden, a sub-arctic fjord with large stocks of wild salmonids, where the inner part is protected as a National Salmon Fjord. The outer part of the fjord hosts several fish farms, and our simulations demonstrate how ocean currents can disperse lice between farms as well as into the protected part of the fjord. The relative contributions from the farms in the different parts of the fjord depends on their locations relative to the currents and circulation patterns in the fjord. Knowledge of how the highly variable water currents disperse salmon lice within fjord systems is necessary for managing farm locations and production quotas, if the goal is to minimize infestation pressure on wild salmonids and between fish farms.
Mid-infrared multi-wavelength imaging of Ophiuchus IRS 48 transitional disk
Authors: Honda Mitsuhiko , Okada Kazushi , Miyata Takashi , Mulders Gijs D , Swearingen Jeremy R , Kamizuka Takashi , Ohsawa Ryou , Fujiyoshi Takuya , Fujiwara Hideaki , Uchiyama Mizuho , Yamashita Takuya , Onaka Takashi 
Published: March 2018

Abstract
Transitional disks around the Herbig Ae/Be stars are fascinating targets in the contexts of disk evolution and planet formation. Oph IRS 48 is one of such Herbig Ae stars, which shows an inner dust cavity and azimuthally lopsided large dust distribution. We present new images of Oph IRS 48 at eight mid-infrared (MIR) wavelengths from 8.59 to 24.6 μm taken with COMICS mounted on the 8.2 m Subaru Telescope. The N-band (7 to 13 μm) images show that the flux distribution is centrally peaked with a slight spatial extent, while the Q-band (17 to 25 μm) images show asymmetric double peaks (east and west). Using 18.8- and 24.6 μm images, we derived the dust temperature at both east and west peaks to be 135 ±  22 K. Thus, the asymmetry may not be attributed to a difference in the temperature. Comparing our results with previous modeling works, we conclude that the inner disk is aligned to the outer disk. A shadow cast by the optically thick inner disk has a great influence on the morphology of MIR thermal emission from the outer disk.
Revision ACL Reconstruction in Children and Adolescents
Authors: Christino Melissa A. , Tepolt Frances A. , Sugimoto Dai , Micheli Lyle J. , Kocher Mininder S. 
Published: March 2018

Background:
Revision anterior cruciate ligament (ACL) reconstruction in pediatric patients has not been well studied. The purpose of this study was to assess the demographics, technique, and results of ACL revision surgery in children and adolescents.

Methods:
This was a retrospective case series with outcomes assessment of patients 18 years old and younger who underwent revision ACL surgery over a 16-year period at a single institution. Medical records were reviewed for demographics, clinical and operative data, and patients were contacted for outcomes at a minimum of 1 year after revision surgery.

Results:
Ninety revision ACL reconstructions were performed by 7 surgeons in 88 patients (44 male, 44 female). Average patient age at the time of revision was 16.6 years (SD, 1.7), and 28.8% of patients were skeletally immature. Time to failure after primary ACL reconstruction was 1.28 years (SD, 1.1) and revision surgery was performed 1.56 years (SD, 1) after the index procedure. Revision graft type included allograft (61.1%), patellar tendon (21.1%), hamstring (16.7%), and iliotibial band (1.1%). There was a 20% graft reinjury rate. Subsequent surgical procedures after revision were required in 25.5% of knees. Twenty percent of revision reconstructions had contralateral ACL injuries, and this percentage was higher (33%) among those who went on to injure their revision graft. Median outcome scores collected from 44 patients (50%) at a mean of 5.1 years following surgery (SD, 3.4) were: Pedi-IKDC 79.9, Lysholm 84.5, and Tegner 9.0. Sixty-nine percent of patients reported returning to sports, however, only 55.2% of these reported being able to return to the same level of play.

Conclusions:
Revision ACL reconstruction in pediatric patients was associated with suboptimal patient-reported outcomes, high complication rates, relatively high graft retear rates, high risk of contralateral ACL injury, and compromised return to sports rates.

Level of Evidence:
Level IV.
Using the Medial and Lateral Humeral Lines as an Adjunct to Intraoperative Elbow Arthrography to Guide Intraoperative Reduction and Fixation of Distal Humerus Physeal Separations Reduces the Incidence of Postoperative Cubitus Varus
Authors: Chou Andrew Chia Chen , Wong Ho Yin Kevin , Kumar Sumanth , Mahadev Arjandas 
Published: March 2018

Background:
Distal humerus physeal separations are rare pediatric elbow fractures that are often misdiagnosed and difficult to treat. Adequate reduction is often technically challenging and up to 71% of children develop postoperative cubitus varus. We propose using the medial and lateral humeral lines as an adjunct to elbow arthrography in order to guide intraoperative fixation of distal humerus physeal separations to reduce the incidence of postoperative cubitus varus.

Methods:
From 2009 to 2014, all pediatric patients under the age of 3 diagnosed with a distal humerus physeal separation and treated surgically at our institution were included for analysis. Two senior pediatric orthopaedic surgeons separately reviewed the preoperative, intraoperative, and postoperative images of all patients and measured the position of the ulnar axis relative to the medial and lateral humeral lines. The medial and lateral humeral shafts were defined as parallel lines drawn along the medial and lateral humeral diaphysis. Adequate reduction was defined by reduction of the ulnar axis within the boundaries of the medial and lateral humeral lines. Patients were assessed at latest follow-up for cubitus varus and any other surgical complications.

Results:
Thirteen patients fulfilled the inclusion criteria and were on average 1.70 years old, ranging from 0.62 to 3 years old. Intraoperatively and immediately postoperatively, all 13 patients (100%) were noted to have adequate reduction of the ulnar axis within the boundaries medial and lateral humeral lines. None of the patients required intraoperative arthrography (0%). At the date of latest follow-up, 12 patients (92.3%) had no angular deformities compared with the contralateral limb and 1 patient (7.7%) had developed cubitus varus. No surgical complications were noted (0%).

Conclusion:
Intraoperative reduction of the ulnar axis within the boundaries of the medial and lateral humeral lines is associated with a lower incidence of postoperative cubitus varus in the treatment of distal humerus physeal separations in children.

Level of Evidence:
Level IV.
Flexion-Relaxation Phenomenon in Children and Adolescents With and Without Nonspecific Chronic Low Back Pain
Authors: Tabard-Fougère Anne , Dayer Romain , Armand Stéphane , Vuillerme Nicolas 
Published: March 2018

Study Design.
A cross-sectional comparative study.

Objective.
This study aimed to investigate the flexion-relaxation phenomenon (FRP), in standing trunk flexion and slumped sitting tasks, by comparing children and adolescents suffering from nonspecific chronic low back pain (NSCLBP) with controls (CTRL).

Summary of Background Data.
The absence of the FRP can accurately discriminate adults with NSCLBP from those without during standing trunk flexion and slumped sitting tasks. Even if the FRP has been extensively studied in adults with NSCLBP, only one study has evaluated the FRP in adolescents, during a slumped sitting task, and this suggested that the FRP was also present in adolescents with NSCLBP.

Methods.
Thirty-seven children and adolescents with NSCLBP and 23 CTRL performed standing trunk flexion and slumped sitting tasks. All participants were equipped with surface electromyography (EMG) electrodes on the erector spinae longissimus (ESL) and multifidus (M) muscles and reflective markers on the spinous processes of C7, L1, and S1. Global (C7-S1), thoracic (C7-L1), and lumbar (L1-S1) trunk flexion absolute angle were measured. The FRP was reported using visual inspection and a flexion-relaxation ratio (FRR). A self-reference threshold was used to identify the time of FRP onset. Repeated-measures analysis of variance (ANOVA) was used to determine the main and interaction effects of task, group and muscle on FRR, and the relative maximal angle at FRP onset of the global trunk (C7-S1).

Results.
Results showed three main findings: (1) the FRP's low sensitivity in discriminating between NSCLBP and CTRL participants in groups, tasks, or muscles; (2) similar observed maximal flexion angles in both groups during flexion tasks; and (3) similar observed relative maximal global trunk flexion angles at FRP onset in groups, tasks, and muscles.

Conclusion.
These results are not consistent with the literature on adults and could lead to modified therapeutic management of NSCLBP in children and adolescents.

Level of Evidence: 3
Renal Blood Flow, Glomerular Filtration Rate, and Renal Oxygenation in Early Clinical Septic Shock*
Authors: Skytte Larsson Jenny , Krumbholz Vitus , Enskog Anders , Bragadottir Gudrun , Redfors Bengt , Ricksten Sven-Erik 
Published: March 2018

Objective:
Data on renal hemodynamics, function, and oxygenation in early clinical septic shock are lacking. We therefore measured renal blood flow, glomerular filtration rate, renal oxygen consumption, and oxygenation in patients with early septic shock.

Design:
Prospective comparative study.

Setting:
General and cardiothoracic ICUs.

Patients:
Patients with norepinephrine-dependent early septic shock (n = 8) were studied within 24 hours after arrival in the ICU and compared with postcardiac surgery patients without acute kidney injury (comparator group, n = 58).

Interventions:
None.

Measurements and Main Results:
Data on systemic hemodynamics and renal variables were obtained during two 30-minute periods. Renal blood flow was measured by the infusion clearance of para-aminohippuric acid, corrected for renal extraction of para-aminohippuric acid. Renal filtration fraction was measured by renal extraction of chromium-51 labeled EDTA. Renal oxygenation was estimated from renal oxygen extraction. Renal oxygen delivery (–24%; p = 0.037) and the renal blood flow-to-cardiac index ratio (–21%; p = 0.018) were lower, renal vascular resistance was higher (26%; p = 0.027), whereas renal blood flow tended to be lower (–19%; p = 0.068) in the septic group. Glomerular filtration rate (–32%; p = 0.006) and renal sodium reabsorption (–29%; p = 0.014) were both lower in the septic group. Neither renal filtration fraction nor renal oxygen consumption differed significantly between groups. Renal oxygen extraction was significantly higher in the septic group (28%; p = 0.022). In the septic group, markers of tubular injury were elevated.

Conclusions:
In early clinical septic shock, renal function was lower, which was accompanied by renal vasoconstriction, a lower renal oxygen delivery, impaired renal oxygenation, and tubular sodium reabsorption at a high oxygen cost compared with controls.