bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unraveling low-resolution structural data of large biomolecules by constructing atomic models with experiment-targeted parallel cascade selection simulations
Authors: Peng Junhui , Zhang Zhiyong 
Published: July 2016

AbstractVarious low-resolution experimental techniques have gained more and more popularity in obtaining structural information of large biomolecules. In order to interpret the low-resolution structural data properly, one may need to construct an atomic model of the biomolecule by fitting the data using computer simulations. Here we develop, to our knowledge, a new computational tool for such integrative modeling by taking the advantage of an efficient sampling technique called parallel cascade selection (PaCS) simulation. For given low-resolution structural data, this PaCS-Fit method converts it into a scoring function. After an initial simulation starting from a known structure of the biomolecule, the scoring function is used to pick conformations for next cycle of multiple independent simulations. By this iterative screening-after-sampling strategy, the biomolecule may be driven towards a conformation that fits well with the low-resolution data. Our method has been validated using three proteins with small-angle X-ray scattering data and two proteins with electron microscopy data. In all benchmark tests, high-quality atomic models, with generally 1–3 Å from the target structures, are obtained. Since our tool does not need to add any biasing potential in the simulations to deform the structure, any type of low-resolution data can be implemented conveniently.
RIP3 induces ischemic neuronal DNA degradation and programmed necrosis in rat via AIF
Authors: Xu Yang , Wang Jingye , Song Xinghui , Qu Lindi , Wei Ruili , He Fangping , Wang Kai , Luo Benyan 
Published: July 2016

AbstractWe have reported that nuclear translocation of Receptor-interacting protein 3 (RIP3) involves in neuronal programmed necrosis after 20-min global cerebral ischemia/reperfusion (I/R) injury. Herein, the underlying mechanisms and the nuclear role of RIP3 were investigated further. The necroptosis inhibitor necrostatin-1 (Nec-1), the autophagy inhibitor 3-methyladenine (3-MA) and the caspase-3 inhibitor acetyl-L-aspartyl-L-methionyl-L-glutaminyl-L-aspart-1-al (Ac-DMQD-CHO) were administered intracerebroventricularly 1 h before ischemia. Protein expression, location and interaction was determined by western blot, immunofluorescence or immunoprecipitation. Most CA1 neuronal death induced by 20-min global cerebral I/R injury was TUNEL-positive. Neuronal death and rat mortality rates were greatly inhibited by Nec-1 and 3-MA pre-treatment, but not by Ac-DMQD-CHO. And no activation of caspase-3 was detected after I/R injury. Caspase-8 was expressed richly in GFAP-positive astrocytes and Iba-1-positive microglia, but was not detected in Neun-positive neurons. The nuclear translocation and co-localization of RIP3 and AIF and their interaction were detected after I/R injury. These processes were inhibited by Nec-1 and 3-MA pre-treatment, but not by Ac-DMQD-CHO. The formation of an RIP3-AIF complex and its nuclear translocation are critical to ischemic neuronal DNA degradation and programmed necrosis. Neurons are more likely to enter the programmed necrosis signal pathway for the loss of caspase-8 suppression.
Self-Assembly of Amphiphilic Dendrimers: The Role of Generation and Alkyl Chain Length in siRNA Interaction
Authors: Márquez-Miranda Valeria , Araya-Durán Ingrid , Camarada María Belén , Comer Jeffrey , Valencia-Gallegos Jesús A. , González-Nilo Fernando Danilo 
Published: July 2016

AbstractAn ideal nucleic-acid transfection system should combine the physical and chemical characteristics of cationic lipids and linear polymers to decrease cytotoxicity and uptake limitations. Previous research described new types of carriers termed amphiphilic dendrimers (ADs), which are based on polyamidoamine dendrimers (PAMAM). These ADs display the cell membrane affinity advantage of lipids and preserve the high affinity for DNA possessed by cationic dendrimers. These lipid/dendrimer hybrids consist of a low-generation, hydrophilic dendron (G2, G1, or G0) bonded to a hydrophobic tail. The G2-18C AD was reported to be an efficient siRNA vector with significant gene silencing. However, shorter tail ADs (G2-15C and G2-13C) and lower generation (G0 and G1) dendrimers failed as transfection carriers. To date, the self-assembly phenomenon of this class of amphiphilic dendrimers has not been molecularly explored using molecular simulation methods. To gain insight into these systems, the present study used coarse-grained molecular dynamics simulations to describe how ADs are able to self-assemble into an aggregate, and, specifically, how tail length and generation play a key role in this event. Finally, explanations are given for the better efficiency of G2/18-C as gene carrier in terms of binding of siRNA. This knowledge could be relevant for the design of novel, safer ADs with well-optimized affinity for siRNA.
Conditional ablation of TGF-β signaling inhibits tumor progression and invasion in an induced mouse bladder cancer model
Authors: Liang Yu , Zhu Fengyu , Zhang Haojie , Chen Demeng , Zhang Xiuhong , Gao Qian , Li Yang 
Published: July 2016

AbstractThe role of transforming growth factor-β (TGF-β) signaling in cancer progression is still under debate. To determine the function of TGF-β signaling in bladder cancer progression, we conditionally knocked out the Tgfbr2 in mouse model after a N-butyl-N-4-hydroxybutyl Nitrosamine induced bladder carcinogenesis. We found the ablation of TGF-β signaling could inhibit the cancer cell proliferation, cancer stem cell population and EMT, hence suppressed the invasive cancer progression, which is similar with the result of TGF-β receptor I inhibitor treatment. These findings recognize the roles and mechanisms of TGF-β signaling in bladder cancer progression in vivo for the first time.
What remains of history? Historical epistemology and historical understanding in Scotland's Curriculum for Excellence
Authors: Smith Joseph 
Published: July 2016

ABSTRACTThis paper critically examines the framing of historical knowledge in the primary and ‘broad general education’ phases (ages 4–14) of Scotland's Curriculum for Excellence. The paper focuses on curriculum documentation, particularly the curriculum's aims and ‘Experiences and Outcomes’ and evaluates these in light of recent research on children's historical understanding. It is argued that the decision to frame historical understanding as ‘People, Past Events and Societies’ within the context of a ‘social studies’ curriculum area has been motivated by a misunderstanding of history's unique disciplinary identity. It is argued that history curricula must take account of the unique ontological and epistemological challenges posed by investigating the past and that by failing to do this, ‘Curriculum for Excellence’ offers children in Scotland a problematic representation of what it means to study the past. The paper challenges the curriculum in both epistemic and pedagogical terms, before suggesting that a rigorous study of history as a discipline can make a valuable contribution to children's personal and social development.
Effects of load mass carried in a backpack upon respiratory muscle fatigue
Authors: Faghy Mark , Blacker Sam , Brown Peter I. 
Published: July 2016

AbstractPurpose: The purpose of this study was to investigate whether loads carried in a backpack, with a load mass ranging from 0 to 20 kg, causes respiratory muscle fatigue. Methods: Eight males performed four randomised load carriage (LC) trials comprising 60 min walking at 6.5 km h−1 wearing a backpack of either 0 (LC0), 10 (LC10), 15 (LC15) or 20 kg (LC20). Inspiratory (PImax) and expiratory (PEmax) mouth pressures were assessed prior to and immediately following each trial. Pulmonary gas exchange, heart rate (HR), blood lactate and glucose concentration and perceptual responses were recorded during the first and final 60 s of each trial. Results: Group mean PImax and PEmax were unchanged following 60‐min load carriage in all conditions (p > .05). There was an increase over time in pulmonary gas exchange, HR and perceptions of effort relative to baseline measures during each trial (p < .05) with changes not different between trials (p > .05). Conclusions: These findings indicate that sub‐maximal walking with no load or carrying 10, 15 or 20 kg in a backpack for up to 60 min does not cause respiratory muscle fatigue despite causing an increase in physiological, metabolic and perceptual parameters.
Final report of CCQM-K129 Measurement of Mole Fractions of Cu, In, Ga and Se in Cu(In,Ga)Se2 Films
Authors: Kim K J , Kim A S , Jang J S , Suh J K , Wirth T , Unger W , Hodoroaba V-D , Araujo J R , Archanjo B S , Galhardo C E , Damasceno J , Achete C A , Wang H , Wang M , Bennett J , Simon D , Kurokawa A , Terauchi S , Fujimoto T , Streeck C , Beckhoff B , Spencer S , Shard A 
Published: July 2016

CCQM key comparison K-129 for the quantitative analysis of Cu(In,Ga)Se2 (CIGS) films has been performed by the Surface Analysis Working Group (SAWG) of the Consultative Committee for Amount of Substance (CCQM). The objective of this key comparison is to compare the equivalency of the National Metrology Institutes (NMIs) and Designated Institutes (DIs) for the measurement of mole fractions of Cu, In, Ga and Se in a thin CIGS film. The measurand of this key comparison is the average mole fractions of Cu, In, Ga and Se of a test CIGS alloy film in the unit of mole fraction (mol/mol). Mole fraction with the metrological unit of % mol/mol can be practically converted to atomic fraction with the unit of at %.
In this key comparison, a CIGS film with certified mole fractions was supplied as a reference specimen to determine the relative sensitivity factors (RSFs) of Cu, In, Ga and Se. The mole fractions of the reference specimen were certified by isotope dilution - inductively coupled plasma/mass spectrometry (ID-ICP/MS). A total number counting (TNC) method was recommended as a method to determine the signal intensities of the constituent elements acquired in the depth profiles by Secondary Ion Mass Spectrometry (SIMS), X-ray Photoelectron Spectroscopy (XPS) and Auger Electron Spectroscopy (AES). Seven NMIs and one DI participated in this key comparison. The mole fractions of the CIGS films were measured by depth profiling based-SIMS, AES and XPS.
In this key comparison, the average degrees of equivalence uncertainties for Cu, In, Ga and Se are 0.0093 mol/mol, 0.0123 mol/mol, 0.0047 mol/mol and 0.0228 mol/mol, respectively.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.
The final report has been peer-reviewed and approved for publication by the CCQM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Hexagonal boron nitride hollow capsules with collapsed surfaces: Chemical vapor deposition with single-source precursor ammonium fluoroborate*
Authors: Li Xiaopeng , Zhang Jun , Yu Chao , Liu Xiaoxi , Abbas Saleem , Li Jie , Xue Yanming , Tang Chengchun 
Published: July 2016

Abstract
SBA-15 (mesoporous SiO2) is used to stabilize and transfer F− in the NH4BF4 CVD reaction for the first time, and a large-scale crystalline h-BN phase can be prepared. We successfully fabricate hollow h-BN capsules with collapsed surfaces in our designed NH4BF4 CVD system. Optimum temperature conditions are obtained, and a detailed formation mechanism is further proposed. The successful SBA-15-assisted NH4BF4 CVD route is of importance and enriches the engineering technology in the h-BN single-source CVD reaction.
Savannas: A Very Short Introduction
Authors: Furley Peter A. 
Published: July 2016

Abstract
Savannas form one of the largest and most important of the world’s ecological zones. Covering one-fifth of the Earth’s land surface, they are home to some of the world’s most iconic animals and form an extremely important global resource for plants and wildlife. Savannas: A Very Short Introduction considers savannas as landscapes and explains the variety of the vegetation, wildlife, and environments. Discussing their origin, topography, and global distribution, it explores the dynamic nature of savannas and illustrates how they have shaped human evolution and movements. It goes on to discuss the unrelenting pressures that confront conservation and management, and considers the future for savannas.
TwoPhaseInd: an R package for estimating gene–treatment interactions and discovering predictive markers in randomized clinical trials
Authors: Wang Xiaoyu , Dai James Y. 
Published: July 2016

Abstract
Summary: In randomized clinical trials, identifying baseline genetic or genomic markers for predicting subgroup treatment effects is of rising interest. Outcome-dependent sampling is often employed for measuring markers. The R package TwoPhaseInd implements a number of efficient statistical methods we developed for estimating subgroup treatment effects and gene–treatment interactions, exploiting the gene–treatment independence dictated by randomization, including the case-only estimator, the maximum estimated likelihood estimator and the semiparametric maximum likelihood estimator for parameters in a logistic model. For rare failure events subject to censoring, we have proposed efficient augmented case-only designs, a variation of the case–cohort design, to estimate genetic associations and subgroup treatment effects in a Cox regression model. The R package is computationally scalable to genome-wide studies, as illustrated by an example from Women’s Health Initiative.
Availability and Implementation: The R package TwoPhaseInd is available from http://cran.r-project.org/web/packages .
Contact: jdai@fredhutch.org
MetaPred2CS: a sequence-based meta-predictor for protein–protein interactions of prokaryotic two-component system proteins
Authors: Kara Altan , Vickers Martin , Swain Martin , Whitworth David E. , Fernandez-Fuentes Narcis 
Published: July 2016

Abstract
Motivation: Two-component systems (TCS) are the main signalling pathways of prokaryotes, and control a wide range of biological phenomena. Their functioning depends on interactions between TCS proteins, the specificity of which is poorly understood.
Results: The MetaPred2CS web-server interfaces a sequence-based meta-predictor specifically designed to predict pairing of the histidine kinase and response-regulator proteins forming TCSs. MetaPred2CS integrates six sequence-based methods using a support vector machine classifier and has been intensively tested under different benchmarking conditions: (i) species specific gene sets; (ii) neighbouring versus orphan pairs; and (iii) k-fold cross validation on experimentally validated datasets.
Availability and Implementation: Web server at: http://metapred2cs.ibers.aber.ac.uk/ , Source code: https://github.com/martinjvickers/MetaPred2CS or implemented as Virtual Machine at: http://metapred2cs.ibers.aber.ac.uk/download
Contact: naf4@aber.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
An empirical Bayes method for genotyping and SNP detection using multi-sample next-generation sequencing data
Authors: Huang Gongyi , Wang Shaoli , Wang Xueqin , You Na 
Published: July 2016

Abstract
Motivation: The development of next generation sequencing technology provides an efficient and powerful approach to rare variant detection. To identify genetic variations, the essential question is how to quantity the sequencing error rate in the data. Because of the advantage of easy implementation and the ability to integrate data from different sources, the empirical Bayes method is popularly employed to estimate the sequencing error rate for SNP detection.
Results: We propose a novel statistical model to fit the observed non-reference allele frequency data, and utilize the empirical Bayes method for both genotyping and SNP detection, where an ECM algorithm is implemented to estimate the model parameters. The performance of our proposed method is investigated via simulations and real data analysis. It is shown that our method makes less genotype-call errors, and with the parameter estimates from the ECM algorithm, it attains high detection power with FDR being well controlled.
Availability and implementation : The proposed algorithm is wrapped in the R package ebGenotyping, which can be downloaded from http://cran.r-project.org/web/packages/ebGenotyping/ .
Contact: youn@mail.sysu.edu.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
Carbon-ion pencil beam scanning for thoracic treatment – initiation report and dose metrics evaluation
Authors: Karube Masataka , Mori Shinichiro , Tsuji Hiroshi , Yamamoto Naoyoshi , Nakajima Mio , Nakagawa Keiichi , Kamada Tadashi 
Published: July 2016

Abstract
Carbon-ion beam scanning has not previously been used for moving tumor treatments. We have commenced respiratory-gated carbon-ion radiotherapy (CIRT) in the thoracic and abdominal regions under free-breathing conditions as a clinical trial. This study aimed to investigate this treatment in the lungs in comparison with passive scattering CIRT. Five patients had thoracic tumors treated with carbon-ion scanned beams using respiratory gating. We analyzed the actual treatments and calculated passive scattering treatment plans based on the same planning CT. We evaluated tumor size until 3 months post treatment and each treatment plan regarding dose delivered to 95% of the clinical target volume (CTV-D95), mean lung dose, percentage of lung receiving at least 5 Gy (RBE) (Lung-V5), Lung-V10, Lung-V20, heart maximum dose (Dmax), esophagus Dmax, cord Dmax and skin Dmax. Obvious tumor deterioration was not observed up to 3 months post treatment. The dose evaluation metrics were similar item by item between respiratory-gated scanned CIRT and passive scattering CIRT. In conclusion, scanned beam CIRT provided treatments equivalent to passive scattering CIRT for thoracic tumors. Increased sample numbers and longer-term observation are needed.
Evaluation of a Systems Analysis and Improvement Approach to Optimize Prevention of Mother-To-Child Transmission of HIV Using the Consolidated Framework for Implementation Research
Authors: Gimbel Sarah , Rustagi Alison S. , Robinson Julia , Kouyate Seydou , Coutinho Joana , Nduati Ruth , Pfeiffer James , Gloyd Stephen , Sherr Kenneth ,   with input from the SAIA study team, Granato S. Adam , Kone Ahoua , Cruz Emilia , Manuel Joao Luis , Zucule Justina , Napua Manuel , Mbatia Grace , Wariua Grace , Maina Martin 
Published: July 2016

Background:
Despite large investments to prevent mother-to-child-transmission (PMTCT), pediatric HIV elimination goals are not on track in many countries. The Systems Analysis and Improvement Approach (SAIA) study was a cluster randomized trial to test whether a package of systems engineering tools could strengthen PMTCT programs. We sought to (1) define core and adaptable components of the SAIA intervention, and (2) explain the heterogeneity in SAIA's success between facilities.

Methods:
The Consolidated Framework for Implementation Research (CFIR) guided all data collection efforts. CFIR constructs were assessed in focus group discussions and interviews with study and facility staff in 6 health facilities (1 high-performing and 1 low-performing site per country, identified by study staff) in December 2014 at the end of the intervention period. SAIA staff identified the intervention's core and adaptable components at an end-of-study meeting in August 2015. Two independent analysts used CFIR constructs to code transcripts before reaching consensus.

Results:
Flow mapping and continuous quality improvement were the core to the SAIA in all settings, whereas the PMTCT cascade analysis tool was the core in high HIV prevalence settings. Five CFIR constructs distinguished strongly between high and low performers: 2 in inner setting (networks and communication, available resources) and 3 in process (external change agents, executing, reflecting and evaluating).

Discussion:
The CFIR is a valuable tool to categorize elements of an intervention as core versus adaptable, and to understand heterogeneity in study implementation. Future intervention studies should apply evidence-based implementation science frameworks, like the CFIR, to provide salient data to expand implementation to other settings.
Optimizing Antiretroviral Therapy (ART) for Maternal and Child Health (MCH): Rationale and Design of the MCH-ART Study
Authors: Myer Landon , Phillips Tamsin K. , Zerbe Allison , Ronan Agnes , Hsiao Nei-Yuan , Mellins Claude A. , Remien Robert H. , Le Roux Stanzi M. , Brittain Kirsty , Ciaranello Andrea , Petro Greg , McIntyre James A. , Abrams Elaine J. 
Published: July 2016

Background:
Prevention of mother-to-child transmission of HIV implementation faces significant challenges globally, particularly in the context of universal lifelong antiretroviral therapy (ART) for all HIV-infected pregnant women.

Methods:
We describe the rationale and methods of the Maternal and Child Health-Antiretroviral Therapy (MCH-ART) study, an implementation science project examining strategies for providing HIV care and treatment to HIV-infected women who initiate ART during pregnancy and their HIV-exposed infants.

Results:
MCH-ART is composed of 3 interrelated study designs across the antenatal and postnatal periods. Phase 1 is a cross-sectional evaluation of consecutive HIV-infected pregnant women seeking antenatal care; phase 2 is an observational cohort of all women from phase 1 who are eligible for initiation of ART following local guidelines; and phase 3 is a randomized trial of strategies for delivering ART to breastfeeding women from phase 2 during the postpartum period. During each phase, a set of study measurement visits is carried out separately from antenatal care and ART services; a maximum of 9 visits takes place from the beginning of antenatal care through 12 months postpartum. In parallel, in-depth interviews are used to examine issues of ART adherence and retention qualitatively, and costs and cost-effectiveness of models of care are examined. Separate substudies examine health outcomes in HIV-uninfected women and their HIV-unexposed infants, and the role of the adherence club model for long-term adherence and retention.

Discussion:
Combining observational and experimental components, the MCH-ART study presents a novel approach to understand and optimize ART delivery for MCH.