bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prenatal immune programming of the sex-dependent risk for major depression
Authors: Gilman S E , Cherkerzian S , Buka S L , Hahn J , Hornig M , Goldstein J M 
Published: May 2016

AbstractMaternal immune functioning during pregnancy contributes to sex-dependent deficits in neurodevelopment and to behaviors associated with affective traits in preclinical studies, and has been indirectly associated with offspring depression in epidemiologic studies. We therefore investigated the association between immune activity during pregnancy and the risk of depression among male and female offspring. We conducted a case–control study of depression (n=484 cases and n=774 controls) using data from the New England Family Study, a pregnancy cohort enrolled between 1959 and 1966 that assessed psychiatric outcomes in adult offspring (mean age=39.7 years). We assayed concentrations of three pro-inflammatory cytokines, interleukin (IL)-1β, IL-6 and tumor necrosis factor (TNF)-α, and the anti-inflammatory cytokine, IL-10, in maternal serum collected at the end of the second and beginning of the third trimesters. High maternal TNF-α was associated with reduced odds of depression among both male and female offspring (odds ratio (OR)=0.68; confidence interval (CI)=0.48, 0.98). However, when considering the TNF-α to IL-10 ratio, a measure of the ratio of pro- to anti-inflammatory loading, maternal immune effects on offspring depression differed significantly by sex (χ2=13.9, degrees of freedom=4, P=0.008). Among females, higher maternal TNF-α:IL-10 was associated with reduced odds of depression (OR=0.51; CI=0.32, 0.81), whereas, among males, high maternal TNF-α:IL-10 was associated with elevated odds of depression (OR=1.86; CI=1.02, 3.39). Thus, the balance between TNF-α and IL-10 in maternal prenatal serum was associated with depression in a sex-dependent manner. These findings are consistent with the role of TNF-α in the maturation of the sexually dimorphic fetal brain circuitry that regulates stress and affective responses, and support a prenatal stress-immune model of depression pathogenesis.
The effects of a probiotic formulation (Lactobacillus rhamnosus and L. helveticus) on developmental trajectories of emotional learning in stressed infant rats
Authors: Cowan C S M , Callaghan B L , Richardson R 
Published: May 2016

AbstractRecently, scientific interest in the brain–gut axis has grown dramatically, particularly with respect to the link between gastrointestinal and psychiatric dysfunction. However, the role of gut function in early emotional dysregulation is yet to be examined, despite the prevalence and treatment resistance of early-onset psychiatric disorders. The present studies utilized a developmental rodent model of early-life stress (ELS) to explore this gap. Rats were exposed to maternal separation (MS) on postnatal days 2–14. Throughout MS, dams received either vehicle or a probiotic formulation (previously shown to reduce gastrointestinal dysfunction) in their drinking water. Replicating past research, untreated MS infants exhibited an adult-like profile of long-lasting fear memories and fear relapse following extinction. In contrast, probiotic-exposed MS infants exhibited age-appropriate infantile amnesia and resistance to relapse. These effects were not mediated by changes in pups’ or dams’ anxiety at the time of training, nor by maternal responsiveness. Overall, probiotics acted as an effective and non-invasive treatment to restore normal developmental trajectories of emotion-related behaviors in infant rats exposed to ELS. These results provide promising initial evidence for this novel approach to reduce the risk of mental health problems in vulnerable individuals. Future studies are needed to test this treatment in humans exposed to ELS and to elucidate mechanisms for the observed behavioral changes.
Broadband RCS reduction using a novel double layer chessboard AMC surface
Authors: Mighani M. , Dadashzadeh G. 
Published: May 2016

A novel broadband chessboard surfaces with double layer structure to reduce the radar cross‐section (RCS) of an object is presented. By combining two artificial magnetic conductor (AMC) cells and a novel structure, 73% frequency bandwidth of −10 dB RCS reduction compared with a metallic plate has been obtained. In order to increase the bandwidth in chessboard structures, boards with high thickness are required, cheaper boards’ thickness are limited. An RO4003 board on an air substrate has been used. This technique, in addition to accommodating the designer with a new parameter, decreases the costs and increases the bandwidth greatly and also simulation results and measurements are in good correspondence.
methylFlow: cell-specific methylation pattern reconstruction from high-throughput bisulfite-converted DNA sequencing
Authors: Dorri Faezeh , Mendelowitz Lee , Corrada Bravo Héctor 
Published: May 2016

Abstract
Motivation: DNA methylation aberrations are now known to, almost universally, accompany the initiation and progression of cancers. In particular, the colon cancer epigenome contains specific genomic regions that, along with differences in methylation levels with respect to normal colon tissue, also show increased epigenetic and gene expression heterogeneity at the population level, i.e. across tumor samples, in comparison with other regions in the genome. Tumors are highly heterogeneous at the clonal level as well, and the relationship between clonal and population heterogeneity is poorly understood.
Results: We present an approach that uses sequencing reads from high-throughput sequencing of bisulfite-converted DNA to reconstruct heterogeneous cell populations by assembling cell-specific methylation patterns. Our methodology is based on the solution of a specific class of minimum cost network flow problems. We use our methods to analyze the relationship between clonal heterogeneity and population heterogeneity in high-coverage data from multiple samples of colon tumor and matched normal tissues.
Availability and implementation: http://github.com/hcorrada/methylFlow.
Contact: hcorrada@umiacs.umd.edu
Supplementary information: Supplementary information is available at Bioinformatics online.
Radiation therapy for nasopharyngeal carcinoma: the predictive value of interim survival assessment
Authors: Toya Ryo , Murakami Ryuji , Saito Tetsuo , Murakami Daizo , Matsuyama Tomohiko , Baba Yuji , Nishimura Ryuichi , Hirai Toshinori , Semba Akiko , Yumoto Eiji , Yamashita Yasuyuki , Oya Natsuo 
Published: May 2016

Abstract
Pretreatment characteristics are suggested as predictive and/or prognostic factors for nasopharyngeal carcinoma (NPC); however, individual tumor radiosensitivities have previously not been considered. As boost planning is recommended for NPC, we performed interim assessments of magnetic resonance (MR) images for boost planning and retrospectively evaluated their predictive value for the survival of NPC patients. Radiation therapy via elective nodal irradiation (median dose: 39.6 Gy) with/without chemotherapy was used to treat 63 NPC patients. Boost irradiation (median total dose: 70 Gy) was performed based on the interim assessment. The largest lymph node (LN) was measured on MR images acquired at the time of interim assessment. The site of first failure was local in 8 (12.7%), regional in 7 (11.1%), and distant in 12 patients (19.0%). All 7 patients with regional failure harbored LNs ≥15 mm at interim assessment. We divided the 63 patients into two groups based on LN size [large (≥15 mm), n = 10 and small (&lt;15 mm), n = 53]. Univariate analysis showed that 5-year overall survival (OS) and cause-specific survival (CSS) rates for large LNs were significantly lower than for small LNs (OS: 12.5% vs 70.5%, P &lt; 0.001 and CSS: 25.0% vs 80.0%, P &lt; 0.001). Multivariate analysis showed that large LNs were a significantly unfavorable factor for both OS (hazard ratio = 4.543, P = 0.002) and CSS (hazard ratio = 6.020, P = 0.001). The results suggest that LN size at interim assessment could predict survival in NPC patients.
Evaluation of Effective Dose from CT Scans for Overweight and Obese Adult Patients Using the VirtualDose Software
Authors: Liang Baohui , Gao Yiming , Chen Zhi , Xu X. George 
Published: May 2016

Abstract
This paper evaluates effective dose (ED) of overweight and obese patients who undergo body computed tomography (CT) examinations. ED calculations were based on tissue weight factors in the International Commission on Radiological Protection Publication 103 (ICRP 103). ED per unit dose length product (DLP) are reported as a function of the tube voltage, body mass index (BMI) of patient. The VirtualDose software was used to calculate ED for male and female obese phantoms representing normal weight, overweight, obese 1, obese 2 and obese 3 patients. Five anatomic regions (chest, abdomen, pelvis, abdomen/pelvis and chest/abdomen/pelvis) were investigated for each phantom. The conversion factors were computed from the DLP, and then compared with data previously reported by other groups. It was observed that tube voltage and BMI are the major factors that influence conversion factors of obese patients, and that ED computed using ICRP 103 tissue weight factors were 24% higher for a CT chest examination and 21% lower for a CT pelvis examination than the ED using ICRP 60 factors. For body CT scans, increasing the tube voltage from 80 to 140 kVp would increase the conversion factors by as much as 19–54% depending on the patient's BMI. Conversion factor of female patients was ~7% higher than the factors of male patients. DLP and conversion factors were used to estimate ED, where conversion factors depended on tube voltage, sex, BMI and tissue weight factors. With increasing number of obese individuals, using size-dependence conversion factors will improve accuracy, in estimating patient radiation dose.
Hierarchical analysis of the degradation of fibre-reinforced polymers under the presence of void imperfections
Authors: Liebig Wilfried V. , Schulte Karl , Fiedler Bodo 
Published: May 2016

The subject of this work is the investigation of the influence of voids on the mechanical properties of fibre-reinforced polymers (FRPs) under compression loading. To specify the damage accumulation of FRPs in the presence of voids, the complex three-dimensional structure of the composite including voids was analysed and a reduced mechanical model composite was derived. The hierarchical analysis of the model composite on a micro-scale level implies the description of the stress and strain behaviour of the matrix using the photoelasticity technique and digital image correlation technology. These studies are presented along with an analytical examination of the stability of a single fibre. As a result of the experimental and analytical studies, the stiffness of the matrix and fibre as well as their bonding, the initial fibre orientation and the fibre diameter have the highest impact on the failure initiation. All these facts lead to a premature fibre–matrix debonding with ongoing loss of stability of the fibre and followed by kink-band formation. Additional studies on the meso-scale of transparent glass FRPs including a unique void showed that the experiments carried out on the model composites could be transferred to real composites.
This article is part of the themed issue ‘Multiscale modelling of the structural integrity of composite materials’.
The role of interlayer adhesion in graphene oxide upon its reinforcement of nanocomposites
Authors: Li Zheling , Kinloch Ian A. , Young Robert J. 
Published: May 2016

Graphene oxide (GO) has become a well-established reinforcement for polymer-based nanocomposites. It provides stronger interfacial interaction with the matrix when compared with that of graphene, but its intrinsic stiffness and strength are somewhat compromised because of the presence of functional groups damaging the graphene lattice and increasing its thickness, and its tendency to adopt a crumpled structure. Although the micromechanics of graphene reinforcement in nanocomposites has been studied widely, the corresponding micromechanics investigations on GO have not been undertaken in such detail. In this work, it is shown that the deformation micromechanics of GO can be followed using Raman spectroscopy and the observed behaviour can be analysed with continuum mechanics. Furthermore, it is shown that the reinforcement efficiency of GO is independent of its number of layers and stacking configurations, indicating that it is not necessary to ensure a high degree of exfoliation of GO in the polymer matrix. It also demonstrates the possibility of increasing the concentration of GO in nanocomposites without sacrificing mechanical reinforcement efficiency.
This article is part of the themed issue ‘Multiscale modelling of the structural integrity of composite materials’.
Modelling of stiffness degradation due to cracking in laminates subjected to multi-axial loading
Authors: Kashtalyan M. , Soutis C. 
Published: May 2016

The paper presents an analytical approach to predicting the effect of intra- and interlaminar cracking on residual stiffness properties of the laminate, which can be used in the post-initial failure analysis, taking full account of damage mode interaction. The approach is based on a two-dimensional shear lag stress analysis and the equivalent constraint model of the laminate with multiple damaged plies. The application of the approach to predicting degraded stiffness properties of multidirectional laminates under multi-axial loading is demonstrated on cross-ply glass/epoxy and carbon/epoxy laminates with transverse and longitudinal matrix cracks and crack-induced transverse and longitudinal delaminations.This article is part of the themed issue ‘Multiscale modelling of the structural integrity of composite materials’.
Structural integrity of engineering composite materials: a cracking good yarn
Authors: Beaumont Peter W. R. , Soutis Costas 
Published: May 2016

Predicting precisely where a crack will develop in a material under stress and exactly when in time catastrophic fracture of the component will occur is one the oldest unsolved mysteries in the design and building of large-scale engineering structures. Where human life depends upon engineering ingenuity, the burden of testing to prove a ‘fracture safe design’ is immense. Fitness considerations for long-life implementation of large composite structures include understanding phenomena such as impact, fatigue, creep and stress corrosion cracking that affect reliability, life expectancy and durability of structure. Structural integrity analysis treats the design, the materials used, and figures out how best components and parts can be joined, and takes service duty into account. However, there are conflicting aims in the complete design process of designing simultaneously for high efficiency and safety assurance throughout an economically viable lifetime with an acceptable level of risk.
This article is part of the themed issue ‘Multiscale modelling of the structural integrity of composite materials’.
Measurement uncertainty matters: ecological management using POMDPs
Authors: Memarzadeh Milad , Boettiger Carl 
Published: May 2016

AbstractOver the past 30 years, researchers have used various approximations to address the impact of measurement uncertainty on optimal management policy.This literature has consistently suggested the counter-intuitive proposition that increasing harvest levels in the presence of measurement error is often optimal. Here, we use state-of-the art algorithms for Partially Observed Markov Decision Processes (POMDPs) to provide the first complete solution to this classic problem, and demonstrate that contrary to previous work, the resulting policy is usually more conservative than without measurement error. We demonstrate that management which underestimates the measurement error results in both low economic returns and high frequency of stock collapses, while overestimating the role of measurement error can still result in nearly-optimal economic performance while avoiding stock collapse.
GutCyc: a Multi-Study Collection of Human Gut Microbiome Metabolic Models
Authors: Hahn Aria S. , Altman Tomer , Konwar Kishori M. , Hanson Niels W. , Kim Dongjae , Relman David A. , Dill David L. , Hallam Steven J. 
Published: May 2016

AbstractAdvances in high-throughput sequencing are reshaping how we perceive microbial communities inhabiting the human body, with implications for therapeutic interventions. Several large-scale datasets derived from hundreds of human microbiome samples sourced from multiple studies are now publicly available. However, idiosyncratic data processing methods between studies introduce systematic differences that confound comparative analyses. To overcome these challenges, we developed GUTCYC, a compendium of environmental pathway genome databases constructed from 418 assembled human microbiome datasets using METAPATHWAYS, enabling reproducible functional metagenomic annotation. We also generated metabolic network reconstructions for each metagenome using the PATHWAYTOOLSsoftware, empowering researchers and clinicians interested in visualizing and interpreting metabolic pathways encoded by the human gut microbiome. For the first time, GUTCYCprovides consistent annotations and metabolic pathway predictions, making possible comparative community analyses between health and disease states in inflammatory bowel disease, Crohn’s disease, and type 2 diabetes. GUTCYCdata products are searchable online, or may be downloaded and explored locally using METAPATHWAYSand PATHWAYTOOLS.
A large field of view two-photon mesoscope with subcellular resolution for in vivo imaging
Authors: Sofroniew N. J. , Flickinger D. , King J. , Svoboda K. 
Published: May 2016

AbstractImaging is used to map activity across populations of neurons. Microscopes with cellular resolution have small (< 1 millimeter) fields of view and cannot simultaneously image activity distributed across multiple brain areas. Typical large field of view microscopes do not resolve single cells, especially in the axial dimension. We developed a 2-photon random access mesoscope (2p-RAM) that allows high-resolution imaging anywhere within a volume spanning multiple brain areas (Ø 5 mm × 1 mm cylinder). 2p-RAM resolution is near diffraction limited (lateral, 0.66 μm, axial 4.09 μm at the center; excitation wavelength = 970 nm; numerical aperture = 0.6) over a large range of excitation wavelengths. A fast threedimensional scanning system allows efficient sampling of neural activity in arbitrary regions of interest across the entire imaging volume. We illustrate the use of the 2p-RAM by imaging neural activity in multiple, non-contiguous brain areas in transgenic mice expressing protein calcium sensors.
JuPOETs: A Constrained Multiobjective Optimization Approach to Estimate Biochemical Model Ensembles in the Julia Programming Language
Authors: Bassen David , Vilkhovoy Michael , Minot Mason , Butcher Jonathan T , Varner Jeffrey D. 
Published: May 2016

AbstractEnsemble modeling is a well established approach for obtaining robust predictions and for simulating course grained population behavior in deterministic mathematical models. In this study, we present a multiobjective based technique to estimate model ensembles, the Pareto Optimal Ensemble Technique in the Julia programming language (JuPOETs). JuPOETs integrates simulated annealing with Pareto optimality to estimate parameter ensembles on or near the optimal tradeoff surface between competing training objectives. We demonstrated JuPOETs on a suite of multiobjective problems, including test functions with parameter bounds and system constraints as well as for the identification of a proof-of-concept biochemical model with four conflicting training objectives. JuPOETs identified optimal or near optimal solutions approximately six-fold faster than a corresponding implementation in Octave for the suite of test functions. For the proof-of-concept biochemical model, JuPOETs produced an ensemble of parameters that gave both the mean of the training data for conflicting data sets, while simultaneously estimating parameter sets that performed well on each of the individual objective functions. JuPOETs can be adapted to solve many problem types, including mixed binary and continuous variable types, bilevel optimization problems and constrained problems without altering the base algorithm. JuPOETs can be installed using the Julia package manager from the JuPOETs GitHub repository athttps://github.com/varnerlab/POETs.jl.
Detailed dendritic excitatory/inhibitory balance through heterosynaptic spike-timing-dependent plasticity
Authors: Hiratani Naoki , Fukai Tomoki 
Published: May 2016

AbstractBalance between excitatory and inhibitory inputs is a key feature of cortical dynamics. Such balance is arguably preserved in dendritic branches, yet its underlying mechanism and functional roles remain unknown. Here, by considering computational models of heterosynaptic spike-timing-dependent plasticity (STDP), we show that the detailed excitatory/inhibitory balance on dendritic branch is robustly achieved through heterosynaptic interaction between excitatory and inhibitory synapses. The model well reproduces experimental results on heterosynaptic STDP, and provides analytical insights. Furthermore, heterosynaptic STDP explains how maturation of inhibitory neurons modulates selectivity of excitatory neurons in critical period plasticity of binocular matching. Our results propose heterosynaptic STDP as a critical factor in synaptic organization and resultant dendritic computation.Significance statementRecent experimental studies have revealed that relative spike timings among neighboring Glutamatergic and GABAergic synapses on a dendritic branch significantly influences changes in synaptic efficiency of these synapses. This heterosynaptic form of spike-timing-dependent plasticity (STDP) is potentially important for shaping the synaptic organization and computation of neurons, but its functional role remains elusive. Here, through computational modeling, we show that heterosynaptic plasticity causes the detailed balance between excitatory and inhibitory inputs on the dendrite, at the parameter regime where previous experimental results are well reproduced. Our result reveals a potential principle of GABA-driven neural circuit formation.