bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis and Visualization of Dynamic Networks Using the DyNet App for Cytoscape
Authors: Salamon John , Goenawan Ivan H. , Lynn David J. 
Published: August 2018

AbstractBiological processes are regulated at a cellular level by tightly controlled molecular interaction networks, which are collectively known as the interactome. The interactome is not a static entity, but instead is dynamically reorganized or “rewired” under varying temporal, spatial, and environmental conditions. Most network analysis and visualization tools have, to date, been developed for static representations of molecular interaction data. Here, we describe a protocol that provides a step‐by‐step guide to DyNet, a Cytoscape 3 application that facilitates the visualization and analysis of dynamic molecular interaction networks. DyNet represents a dynamic network as a set of state graphs that are synchronized in their layout. This synchronization is managed in real time and is automatically updated when a graph is manipulated by a user (e.g., dragging, zooming, moving a node). DyNet also provides several statistical tools enabling users to quickly identify and analyze the most ‘rewired’ nodes across many network states. © 2018 by John Wiley & Sons, Inc.
Use of a constrained hierarchical optimization dataset enhances knowledge‐based planning as a quality assurance tool for prostate bed irradiation
Authors: Lin Yen Hwa , Hong Linda X. , Hunt Margie A. , Berry Sean L. 
Published: August 2018

PurposeTo investigate whether building a knowledge‐based planning (KBP) model with prostate bed plans constructed from constrained hierarchical optimization (CHO) would result in more efficient model construction with more consistent output than a model built using plans from a traditional, trial‐and‐error‐based optimization (TEO) technique.MethodsThree KBP models were constructed from plans from subsets of 58 post‐prostatectomy patients treated with intensity‐modulated radiation therapy. TEO54 was built from 54 TEO plans, selected to represent typical clinical variations in target and organ‐at‐risk sizes and shapes. CHO30 and TEO30 were built from the same 30 patients populated with CHO and TEO plans, respectively. The three models were each applied to a new set of 18 patient scans and dose–volume histogram estimates (DVHEs) were generated for rectal and bladder walls and compared for each patient.ResultsCHO30 resulted in a significantly tighter range in DVHEs (P < 0.01) for both the rectal and bladder walls compared with either of the TEO models, indicating less uncertainty in the dose estimation. Plans resulting from KBP optimization using each model were very similar.ConclusionPopulating a KBP model with CHO data resulted in a high quality model. Since CHO plans can be generated automatically offline in a process that necessitates little to no user interaction, a CHO‐KBP model can quickly adapt to changes in plan evaluation criteria or planning techniques without the need to wait to accrue sufficient numbers of clinical TEO plans. This may facilitate the use of KBP approaches for initial or ongoing quality assurance procedures and plan quality audits.
Precursors for Atmospheric Plasma‐Enhanced Sintering: Low‐Temperature Inkjet Printing of Conductive Copper
Authors: Knapp Caroline E. , Metcalf Elizabeth A. , Mrig Shreya , Sanchez‐Perez Clara , Douglas Samuel. P. , Choquet Patrick , Boscher Nicolas D. 
Published: August 2018

AbstractBidentate diamine and amino‐alcohol ligands have been used to form solid, water‐soluble, and air‐stable monomeric copper complexes of the type [Cu(NH2CH2CH(R)Y)2(NO3)2] (1, R=H, Y=NH2;2, R=H, Y=OH;3, R=Me, Y=OH). The complexes were characterized by elemental analysis, mass spectrometry, infrared spectroscopy, thermal gravimetric analysis, and single‐crystal X‐ray diffraction. Irrespective of their decomposition temperature, precursors1–3yield highly conductive copper features [1.5×10−6 Ω m (±5×10−7 Ω m)] upon atmospheric‐pressure plasma‐enhanced sintering.
Community-Based Preventive and Remedial Measures to Prevent Violent Extremism: A Human Security Approach to Help Transform Conflicts, Improve Social Cohesion and Improve Local Security
Authors:   Human Security Collective (HSC)
Published: August 2018

AbstractThis article, presented as part of a panel on “Community-based preventive and remedial measures” at a conference on Responses to Female Migration to ISIS, is on ways in which local communities are able to strengthen social cohesion and prevent growing polarization, especially in areas where radicalization to violent extremism takes place. The analysis is based on the Human Security Collective (HSC)’s work in Palestine, Libya, Tunisia and the Netherlands where we support local communities and the professionals who work with them on addressing systemic causes that lead to exclusion, alienation and possibly radicalization leading to violent extremism. We have learnt that approaches to prevent the attraction to violent extremism networks require methods and processes akin to those developed for conflict transformation. Some of the characteristics of this approach include the inclusion of different stakeholders, local ownership in defining problems and seeking solutions, the building of trusted relationships, the mentoring of young women and men who take on a peer-model role, and the development of innovative small-scale community activities that can then be taken up by the wider community. HSC and its partners connect these local community initiatives to policymakers at municipal, national and international levels. Through the process of facilitated dialogue we aim to create “safe spaces” where persons from different backgrounds and with different interests are able to meet and exchange practices and policies. In this way, policies are validated by lived realities and citizens become aware of the way that policies that influence local security are developed and executed. This dialogue leads to a mutual understanding of and improvement in security-related policies.
Modeling Cutaneous Radiation Injury from Fallout
Authors: Adams Grace , Yeddanapudi Neelima , Clay Matthew , Asher Jason , Appler Jessica , Casagrande Rocco 
Published: August 2018

ABSTRACTObjectiveBeta radiation from nuclear weapons fallout could pose a risk of cutaneous radiation injury (CRI) to evacuating populations but has been investigated only cursorily. This work examines 2 components of CRI necessary for estimating the potential public health consequences of exposure to fallout: dose protraction and depth of dose.MethodsDose protraction for dry and moist desquamation was examined by adapting the biological effective dose (BED) calculation to a hazard function calculation similar to those recommended by the National Council on Radiation Protection and Measurements for other acute radiation injuries. Depth of burn was examined using Monte Carlo neutral Particle version 5 to model the penetration of beta radiation from fallout to different skin tissues.ResultsNonlinear least squares analysis of the BED calculation estimated the hazard function parameter θ1 (dose rate effectiveness factors) as 25.5 and 74.5 (Gy-eq)2 h−1 for dry and moist desquamation, respectively. Depth of dose models revealed that beta radiation is primarily absorbed in the dead skin layers and basal layer and that dose to underlying tissues is small (<5% of dose to basal layer).ConclusionsThe low relative dose to tissues below the basal layer suggests that radiation-induced necrosis or deep skin burns are unlikely from direct skin contamination with fallout. These results enable future modeling studies to better examine CRI risk and facilitate effectively managing and treating populations with specialized injuries from a nuclear detonation. (Disaster Med Public Health Preparedness. 2019;13:463-469)
THE CURVED A∞-COALGEBRA OF THE KOSZUL CODUAL OF A FILTERED DG ALGEBRA
Authors: HERSCOVICH ESTANISLAO 
Published: August 2018

AbstractThe goal of this article is to study the coaugmented curvedA∞-coalgebra structure of the Koszul codual of a filtered dg algebra over a fieldk. More precisely, we first extend one result of B. Keller that allowed to compute theA∞-coalgebra structure of the Koszul codual of a nonnegatively graded connected algebra to the case of any unitary dg algebra provided with a nonnegative increasing filtration whose zeroth term isk. We then show how to compute the coaugmented curvedA∞-coalgebra structure of the Koszul codual of a Poincaré-Birkhoff-Witt (PBW) deformation of anN-Koszul algebra.
Collimated proton beams from magnetized near-critical plasmas
Authors: Kuri Deep Kumar , Das Nilakshi , Patel Kartik 
Published: August 2018

AbstractGeneration of collimated proton beams by linearly and circularly polarized (CP) lasers from magnetized near-critical plasmas has been investigated with the help of three-dimensional (3D) particle-in-cell (PIC) simulations. Due to cyclotron effects, the transverse proton momentum gets significantly reduced in the presence of an axial magnetic field which leads to an enhancement in collimation. Collimation is observed to be highest in case of a linearly polarized (LP) laser in the presence of magnetic field. However, protons accelerated by a right CP laser in the presence of magnetic field are not only highly collimated but are also more energetic than those accelerated by the LP laser. Although, the presence of an axial magnetic field enhances the collimation by reducing the transverse proton momentum, the maximum proton energy gets reduced since the transverse proton momentum has a significant contribution towards proton energy.
Birds of different feather flock together - genetic structure of Taiga Bean Goose in Central Scandinavia
Authors: DE JONG ADRIAAN , KLEVEN ODDMUND , ØSTNES JAN EIVIND , KROGLUND ROLF TERJE , VAHLSTRÖM ISAK , NILSSON JAN , SPONG GÖRAN 
Published: August 2018

SummaryDuring their flightless summer moult, Taiga Bean GeeseAnser fabalis fabalisgather at communal moulting sites. Individuals from the Nord-Trøndelag breeding area in Norway have been observed to join with local individuals on moulting sites in Vilhelmina Municipality, Sweden. These two groups show distinct features in breeding habitat and migratory behaviour, but are they also genetically distinct? We used 12 microsatellite loci for genotyping 109 blood, feather and faecal samples from three sampling areas (Røyrvik in Norway and Stalon and Nästansjö in Sweden) to examine genetic diversity and structure. Clustering and Principal Coordinate analyses of all samples unveiled at least two distinct clusters, which were unevenly distributed over the sampling sites. Grouped by sampling sites, AMOVA and FSTanalyses showed that samples from the three sites differed genetically. These differences were larger between Røyrvik and Nästansjö than between Stalon and the other two. Relatedness was high among the Røyrvik samples. From our results we conclude that one of the clusters describes the Røyrvik breeding subpopulation, while the other(s) breed mainly in Sweden. Although these subpopulations simultaneously use the same moulting area in Vilhelmina, they appear to be ecologically, behaviourally and genetically distinct, in particular the Røyrvik sub-population. For goose conservation and management, we suggest that the Nord-Trøndelag (Røyrvik) subpopulation is considered a separate flyway management unit. Unravelling the Swedish sub-populations will need further study. For bird conservation is general, we suggest active genetic sampling for detailed population structure analyses and subsequent differentiated conservation and/or management schemes.
Variation in Personality States as Predicted by Interpersonal Context
Authors: Churchyard Jamie S. , Pine Karen J. , Sharma Shivani , Fletcher Ben (C) 
Published: August 2018

Abstract. Diary studies of personality have shown that personality is variable, and can help the person deal appropriately with the different interpersonal demands they encounter. This study aims to demonstrate how interpersonal context predicts personality states. Thirty-six participants (9 male, 27 female, Mage = 24.72, SD = 7.11) kept an online diary for one month. The diary recorded measurements of HEXACO personality states, momentary interpersonal factors including current interpersonal role (with friend, family member, partner, as employee/student, alone), and social goal orientation (socializing with others, avoidance of others, asserting yourself, personal/work achievement), and dispositional anxiety and depression. Individuals’ personality states were found to vary considerably across measurements in a normal distribution. Multilevel modelling analyses showed that interpersonal factors did predict within subject personality variation. Social goal orientations had a greater relative impact than interpersonal roles. Depression had a significant effect on between subject variance in state emotionality. These findings highlight the importance of interpersonal context in predicting stable personality variation.
Coronary stents with inducible VEGF/HGF-secreting UCB-MSCs reduced restenosis and increased re-endothelialization in a swine model
Authors: Chang Hyun-Kyung , Kim Pyung-Hwan , Kim Dong Wook , Cho Hyun-Min , Jeong Mi Jin , Kim Dea Han , Joung Yoon Ki , Lim Kyung Seob , Kim Han Byul , Lim Han Cheol , Han Dong Keun , Hong Young Joon , Cho Je-Yoel 
Published: August 2018

AbstractAtherosclerotic plaques within the vasculature may eventually lead to heart failure. Currently, cardiac stenting is the most effective and least invasive approach to treat this disease. However, in-stent restenosis is a complex chronic side effect of stenting treatment. This study used coronary stents coated with stem cells secreting angiogenic growth factors via an inducible genome-editing system to reduce stent restenosis and induce re-endothelialization within the artery. The characteristics of the cells and their adhesion properties on the stents were confirmed, and the stents were transplanted into a swine model to evaluate restenosis and the potential therapeutic use of stents with stem cells. Restenosis was evaluated using optical coherence tomography (OCT), microcomputed tomography (mCT) and angiography, and re-endothelialization was evaluated by immunostaining after cardiac stent treatment. Compared to a bare metal stent (BMS) or a parental umbilical cord blood-derived mesenchymal stem cell (UCB-MSC)-coated stent, the stents with stem cells capable of the controlled release of hepatocyte growth factor (HGF) and vascular endothelial growth factor (VEGF) successfully reduced restenosis within the stent and induced natural re-endothelialization. Furthermore, UCB-MSCs exhibited the ability to differentiate into endothelial cells in Matrigel, and HGF and VEGF improved this differentiation. Our study indicates that stents coated with UCB-MSCs secreting VEGF/HGF reduce the restenosis side effects of cardiac stenting with improved re-endothelialization.
Polygenic risk score analyses of symptoms and treatment response in an antipsychotic-naive first episode of psychosis cohort
Authors: Santoro Marcos Leite , Ota Vanessa , de Jong Simone , Noto Cristiano , Spindola Leticia M. , Talarico Fernanda , Gouvea Eduardo , Lee Sang Hyuck , Moretti Patricia , Curtis Charles , Patel Hamel , Newhouse Stephen , Carvalho Carolina Muniz , Gadelha Ary , Cordeiro Quirino , Bressan Rodrigo Affonseca , Belangero Sintia Iole , Breen Gerome 
Published: August 2018

AbstractIn this study, we aimed to test if the schizophrenia (SCZ) polygenic risk score (PRS) was associated with clinical symptoms in (a) the first episode of psychosis pre-treatment (FEP), (b) at nine weeks after initiation of risperidone treatment (FEP-9W) and (c) with the response to risperidone. We performed a detailed clinical assessment of 60 FEP patients who were antipsychotic-naive and, again, after nine weeks of standardized treatment with risperidone. After blood collection and DNA isolation, the samples were genotyped using the Illumina PsychArrayChip and then imputed. To calculate PRS, we used the latest available GWAS summary statistics from the Psychiatric Genomics Consortium wave-2 SCZ group as a training set. We used Poisson regression to test association between PRS and clinical measurements correcting for the four principal components (genotyping). We considered a p-value < 0.0014 (Bonferroni correction) as significant. First, we verified that the schizophrenia PRS was also able to distinguish cases from controls in this south-eastern Brazilian sample, with a similar variance explained to that seen in Northern European populations. In addition, within-cases analyses, we found that PRS is significantly correlated with baseline (pre-treatment) symptoms, as measured by lower clinical global assessment of functioning (−GAF), higher depressive symptoms and higher scores on a derived excitement factor. After standardized treatment for nine weeks, the correlation with GAF and the excitement factor disappeared while depressive symptoms became negatively associated with PRS. We conclude that drug (and other treatments) may confound attempts to understand the aetiological influence on symptomatology of polygenic risk scores. These results highlight the importance of studying schizophrenia, and other disorders, pre-treatment to understand the relationship between polygenic risk and phenotypic features.
The recombinase Rad51 plays a key role in events of genetic exchange in Trypanosoma cruzi
Authors: Alves Ceres Luciana , Repolês Bruno Marçal , da Silva Marcelo Santos , Mendes Isabela Cecília , Marin Paula Andrea , Aguiar Pedro Henrique Nascimento , Santos Selma da Silva , Franco Glória Regina , Macedo Andréa Mara , Pena Sérgio Danilo Junho , Andrade Luciana de Oliveira , Guarneri Alessandra Aparecida , Tahara Erich Birelli , Elias Maria Carolina , Machado Carlos Renato 
Published: August 2018

AbstractDetection of genetic exchange has been a limiting factor to deepen the knowledge on the mechanisms by which Trypanosoma cruzi is able to generate progeny and genetic diversity. Here we show that incorporation of halogenated thymidine analogues, followed by immunostaining, is a reliable method not only to detect T. cruzi fused-cell hybrids, but also to quantify their percentage in populations of this parasite. Through this approach, we were able to detect and quantify fused-cell hybrids of T. cruzi clones CL Brener and Y. Given the increased detection of fused-cell hybrids in naturally-occurring hybrid CL Brener strain, which displays increased levels of RAD51 and BRCA2 transcripts, we further investigated the role of Rad51 – a recombinase involved in homologous recombination – in the process of genetic exchange. We also verified that the detection of fused-cell hybrids in T. cruzi overexpressing RAD51 is increased when compared to wild-type cells, suggesting a key role for Rad51 either in the formation or in the stabilization of fused-cell hybrids in this organism.
Dampening of Submesoscale Currents by Air-Sea Stress Coupling in the Californian Upwelling System
Authors: Renault Lionel , McWilliams James C. , Gula Jonathan 
Published: August 2018

AbstractOceanic submesoscale currents (SMCs) occur on an scale of 0.1–10 km horizontally and have a large influence on the oceanic variability and on ecosystems. At the mesoscale (10–250 km), oceanic thermal and current feedbacks are known to have a significant influence on the atmosphere and on oceanic dynamics. However, air-sea interactions at the submesoscale are not well known because the small size of SMCs presents observational and simulation barriers. Using high-resolution coupled oceanic and atmospheric models for the Central California region during the upwelling season, we show that the current feedback acting through the surface stress dominates the thermal feedback effect on the ocean and dampens the SMC variability by ≈17% ± 4%. As for the mesoscale, the current feedback induces an ocean sink of energy at the SMCs and a source of atmospheric energy that is related to induced Ekman pumping velocities. However, those additional vertical velocities also cause an increase of the injection of energy by baroclinic conversion into the SMCs, partially counteracting the sink of energy by the stress coupling. These stress coupling effects have important implications in understanding SMC variability and its links with the atmosphere and should be tested in other regions.
Ag/MnO2 Composite Sheath-Core Structured Yarn Supercapacitors
Authors: Kim Ji Hwan , Choi Changsoon , Lee Jae Myeong , de Andrade Mônica Jung , Baughman Ray H. , Kim Seon Jeong 
Published: August 2018

AbstractOne-dimensional (1D) yarn or fiber-based supercapacitors that have small diameter, volume and high mechanical strength are needed due to the demands on power source for wearable electronics, micro-devices, and implantable medical devices. The composite sheath is fabricated on a commercially available CNT yarn substrate by alternating depositions of MnO2 and Ag layers. Synergistic effect of high loading level of pseudocapacitive MnO2 and reasonably improved rate-capability are achieved. In the composite sheath, the interconnected networks provide electrical contact between MnO2 aggregates and adjacent Ag layer. The conductive Ag inter layers shorten the solid-state charge diffusion length in the MnO2. Moreover, generated electrons during the charge/discharge process can be collected rapidly by the adjacent Ag layer, therefore, the great extents of MnO2 could be loaded onto the surface of CNT core fiber electrode without a significant rate-capability degradation. Due to the high MnO2 loading level, the composite sheath-core yarn supercapacitor showed excellent specific areal capacitance (322.2 mF/cm2) and according energy density (18.3 µWh/cm2).
The emerging sub-genotype C2 of CoxsackievirusA10 Associated with Hand, Foot and Mouth Disease extensively circulating in mainland of China
Authors: Ji Tianjiao , Guo Yue , Huang Wei , Shi Yong , Xu Yi , Tong Wenbin , Yao Wenqing , Tan Zhaolin , Zeng Hanri , Ma Jiangtao , Zhao Hua , Han Taoli , Zhang Yong , Yan Dongmei , Yang Qian , Zhu Shuangli , Zhang Yan , Xu Wenbo 
Published: August 2018

AbstractCoxsackievirus A10 (CV-A10) associated with Hand, foot, and mouth disease (HFMD) cases emerged increasingly in recent years. In this study, the samples from nation-wide HFMD surveillance, including 27 out of 31 provinces in China were investigated, and the continuous and extensive virological surveillance, covered 13 years, were conducted to provide a comprehensive molecular characterization analysis of CV-A10. 855 CV-A10 viruses (33 severe cases included), were isolated from HFMD children patients during 2009 to 2016 in China. 164 representative sequences from theseviruses, together with 117 CV-A10 sequences downloaded from GenBank based on entire VP1 were recruited in this study. Two new genotypes (F and G) and two sub-genotypes (C1 and C2) were identified.Among 264 Chinese sequences, 9 of them were genotype B, 8 of them were C1, and the other (247) were C2, the predominant sub-genotype in China since 2012. Chinese C2 viruses showed obvious temporal characteristics and can be divided into 3 clusters (cluster 1~3). Cluster 3 viruses was circulating extensively during 2014 and 2016 with more severe cases.It is very necessary and important to continuously conduct the extensive virological surveillance for CV-A10, and further evolutionary studies will provide more evidence on its evolution and virulence.