bluuebunny/crossref_metadata_2025_split huggingface dataset:
Disparities in breast cancer care and research: report from a Breast Cancer Research Foundation sponsored workshop, 9–10 October 2014
Authors: Canin Beverly , Freund Karen M , Ganz Patricia A , Hershman Dawn L , Paskett Electra D ,   on behalf of the workshop participants
Published: October 2015

AbstractThe purpose of this workshop was to bring together diverse stakeholders from the breast cancer research community to discuss critical issues related to disparities in breast cancer care and to identify potential strategies for reducing disparities and inequities in care through research. The workshop format included a series of formal content presentations, participation in break out groups that focused on specific topics highlighted in the content presentations, reporting back of findings and a facilitated discussion that focused on shaping a research agenda. The workshop members concluded that numerous groups of women are at increased risk for disparities in breast cancer care: many patients and survivors suffer disproportionately from inadequate access to high-quality diagnosis and treatment, resulting in more frequent and severe adverse outcomes from the disease. Research on breast cancer disparities provides a major opportunity for reducing the burden of breast cancer. Thus, it is important for the Breast Cancer Research Foundation and other research funders to consider how to best promote research focused on ensuring breast cancer health equity.
Determining Associations between Human Diseases and non-coding RNAs with Critical Roles in Network Control
Authors: Kagami Haruna , Akutsu Tatsuya , Maegawa Shingo , Hosokawa Hiroshi , Nacher Jose C. 
Published: October 2015

AbstractDeciphering the association between life molecules and human diseases is currently an important task in systems biology. Research over the past decade has unveiled that the human genome is almost entirely transcribed, producing a vast number of non-protein-coding RNAs (ncRNAs) with potential regulatory functions. More recent findings suggest that many diseases may not be exclusively linked to mutations in protein-coding genes. The combination of these arguments poses the question of whether ncRNAs that play a critical role in network control are also enriched with disease-associated ncRNAs. To address this question, we mapped the available annotated information of more than 350 human disorders to the largest collection of human ncRNA-protein interactions, which define a bipartite network of almost 93,000 interactions. Using a novel algorithmic-based controllability framework applied to the constructed bipartite network, we found that ncRNAs engaged in critical network control are also statistically linked to human disorders (P-value of P = 9.8 × 10−109). Taken together, these findings suggest that the addition of those genes that encode optimized subsets of ncRNAs engaged in critical control within the pool of candidate genes could aid disease gene prioritization studies.
Neonicotinoid pesticides severely affect honey bee queens
Authors: Williams Geoffrey R. , Troxler Aline , Retschnig Gina , Roth Kaspar , Yañez Orlando , Shutler Dave , Neumann Peter , Gauthier Laurent 
Published: October 2015

AbstractQueen health is crucial to colony survival of social bees. Recently, queen failure has been proposed to be a major driver of managed honey bee colony losses, yet few data exist concerning effects of environmental stressors on queens. Here we demonstrate for the first time that exposure to field-realistic concentrations of neonicotinoid pesticides during development can severely affect queens of western honey bees (Apis mellifera). In pesticide-exposed queens, reproductive anatomy (ovaries) and physiology (spermathecal-stored sperm quality and quantity), rather than flight behaviour, were compromised and likely corresponded to reduced queen success (alive and producing worker offspring). This study highlights the detriments of neonicotinoids to queens of environmentally and economically important social bees and further strengthens the need for stringent risk assessments to safeguard biodiversity and ecosystem services that are vulnerable to these substances.
Computational analysis of stochastic heterogeneity in PCR amplification efficiency revealed by single molecule barcoding
Authors: Best Katharine , Oakes Theres , Heather James M. , Shawe-Taylor John , Chain Benny 
Published: October 2015

AbstractThe polymerase chain reaction (PCR) is one of the most widely used techniques in molecular biology. In combination with High Throughput Sequencing (HTS), PCR is widely used to quantify transcript abundance for RNA-seq and in the context of analysis of T and B cell receptor repertoires. In this study, we combine DNA barcoding with HTS to quantify PCR output from individual target molecules. We develop computational tools that simulate both the PCR branching process itself and the subsequent subsampling which typically occurs during HTS sequencing. We explore the influence of different types of heterogeneity on sequencing output and compare them to experimental results where the efficiency of amplification is measured by barcodes uniquely identifying each molecule of starting template. Our results demonstrate that the PCR process introduces substantial amplification heterogeneity, independent of primer sequence and bulk experimental conditions. This heterogeneity can be attributed both to inherited differences between different template DNA molecules and the inherent stochasticity of the PCR process. The results demonstrate that PCR heterogeneity arises even when reaction and substrate conditions are kept as constant as possible and therefore single molecule barcoding is essential in order to derive reproducible quantitative results from any protocol combining PCR with HTS.
Extracellular microvesicles and invadopodia mediate non-overlapping modes of tumor cell invasion
Authors: Sedgwick Alanna E. , Clancy James W. , Olivia Balmert M. , D’Souza-Schorey Crislyn 
Published: October 2015

AbstractTumor cell invasion requires the molecular and physical adaptation of both the cell and its microenvironment. Here we show that tumor cells are able to switch between the use of microvesicles and invadopodia to facilitate invasion through the extracellular matrix. Invadopodia formation accompanies the mesenchymal mode of migration on firm matrices and is facilitated by Rac1 activation. On the other hand, during invasion through compliant and deformable environments, tumor cells adopt an amoeboid phenotype and release microvesicles. Notably, firm matrices do not support microvesicle release, whereas compliant matrices are not conducive to invadopodia biogenesis. Furthermore, Rac1 activation is required for invadopodia function, while its inactivation promotes RhoA activation and actomyosin contractility required for microvesicle shedding. Suppression of RhoA signaling blocks microvesicle formation but enhances the formation of invadopodia. Finally, we describe Rho-mediated pathways involved in microvesicle biogenesis through the regulation of myosin light chain phosphatase. Our findings suggest that the ability of tumor cells to switch between the aforementioned qualitatively distinct modes of invasion may allow for dissemination across different microenvironments.
Towards the Knittability of Graphene Oxide Fibres
Authors: Seyedin Shayan , Romano Mark S. , Minett Andrew I. , Razal Joselito M. 
Published: October 2015

AbstractRecent developments in graphene oxide fibre (GO) processing include exciting demonstrations of hand woven textile structures. However, it is uncertain whether the fibres produced can meet the processing requirements of conventional textile manufacturing. This work reports for the first time the production of highly flexible and tough GO fibres that can be knitted using textile machinery. The GO fibres are made by using a dry-jet wet-spinning method, which allows drawing of the spinning solution (the GO dispersion) in several stages of the fibre spinning process. The coagulation composition and spinning conditions are evaluated in detail, which led to the production of densely packed fibres with near-circular cross-sections and highly ordered GO domains. The results are knittable GO fibres with Young’s modulus of ~7.9 GPa, tensile strength of ~135.8 MPa, breaking strain of ~5.9% and toughness of ~5.7 MJ m−3. The combination of suitable spinning method, coagulation composition and spinning conditions led to GO fibres with remarkable toughness; the key factor in their successful knitting. This work highlights important progress in realising the full potential of GO fibres as a new class of textile.
Prioritization Of Nonsynonymous Single Nucleotide Variants For Exome Sequencing Studies Via Integrative Learning On Multiple Genomic Data
Authors: Wu Mengmeng , Wu Jiaxin , Chen Ting , Jiang Rui 
Published: October 2015

AbstractThe rapid advancement of next generation sequencing technology has greatly accelerated the progress for understanding human inherited diseases via such innovations as exome sequencing. Nevertheless, the identification of causative variants from sequencing data remains a great challenge. Traditional statistical genetics approaches such as linkage analysis and association studies have limited power in analyzing exome sequencing data, while relying on simply filtration strategies and predicted functional implications of mutations to pinpoint pathogenic variants are prone to produce false positives. To overcome these limitations, we herein propose a supervised learning approach, termed snvForest, to prioritize candidate nonsynonymous single nucleotide variants for a specific type of disease by integrating 11 functional scores at the variant level and 8 association scores at the gene level. We conduct a series of large-scale in silico validation experiments, demonstrating the effectiveness of snvForest across 2,511 diseases of different inheritance styles and the superiority of our approach over two state-of-the-art methods. We further apply snvForest to three real exome sequencing data sets of epileptic encephalophathies and intellectual disability to show the ability of our approach to identify causative de novo mutations for these complex diseases. The online service and standalone software of snvForest are found at http://bioinfo.au.tsinghua.edu.cn/jianglab/snvforest.
The eQTL-missense polymorphisms of APOBEC3H are associated with lung cancer risk in a Han Chinese population
Authors: Zhu Meng , Wang Yuzhuo , Wang Cheng , Shen Wei , Liu Jia , Geng Liguo , Cheng Yang , Dai Juncheng , Jin Guangfu , Ma Hongxia , Hu Zhibin , Shen Hongbing 
Published: October 2015

AbstractAPOBEC (Apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like) enzymes may involve in mutagenic processes in multiple cancer types, including lung cancer. APOBEC family of cytidine deaminases induces base substitutions with a stringent TCW motif, which is widespread in multiple human cancers. We hypothesized that common missense variants in coding regions of APOBEC genes might damage the structure of proteins and modify lung cancer risk. To test this hypothesis, we systematically screened predicted deleterious polymorphisms in the exon regions of 10 APOBEC core genes (APOBEC1, APOBEC2, APOBEC3A, APOBEC3B, APOBEC3C, APOBEC3D, APOBEC3F, APOBEC3G, APOBEC3H and APOBEC4) and evaluated them with a case-control study including 1200 cases and 1253 controls. We found that the T allele of rs139293 in exon 2 of APOBEC3H was significantly associated with decreased risk of lung cancer (odds ratio = 0.76, 95% confidence interval: 0.63–0.91). Similar inverse association of this variant was observed in subgroups. Further study showed that the T allele of rs139293 was associated with the altered expression of APOBEC3H and APOBEC3C and that the two genes were co-expressed in both tumor and adjacent normal tissues. These results indicate that genetic variants in APOBEC3H may contribute to lung cancer susceptibility in Chinese population.
Junb controls lymphatic vascular development in zebrafish via miR-182
Authors: Kiesow Kristin , Bennewitz Katrin , Miranda Laura Gutierrez , Stoll Sandra J. , Hartenstein Bettina , Angel Peter , Kroll Jens , Schorpp-Kistner Marina 
Published: October 2015

AbstractJUNB, a subunit of the AP-1 transcription factor complex, mediates gene regulation in response to a plethora of extracellular stimuli. Previously, JUNB was shown to act as a critical positive regulator of blood vessel development and homeostasis as well as a negative regulator of proliferation, inflammation and tumour growth. Here, we demonstrate that the oncogenic miR-182 is a novel JUNB target. Loss-of-function studies by morpholino-mediated knockdown and the CRISPR/Cas9 technology identify a novel function for both JUNB and its target miR-182 in lymphatic vascular development in zebrafish. Furthermore, we show that miR-182 attenuates foxo1 expression indicating that strictly balanced Foxo1 levels are required for proper lymphatic vascular development in zebrafish. In conclusion, our findings uncover with the Junb/miR-182/Foxo1 regulatory axis a novel key player in governing lymphatic vascular morphogenesis in zebrafish.
Rapid DNA detection of Mycobacterium tuberculosis-towards single cell sensitivity in point-of-care diagnosis
Authors: Ng Benjamin Y.C. , Wee Eugene J.H. , West Nicholas P. , Trau Matt 
Published: October 2015

AbstractAlthough there have been many recent advances in Tuberculosis (TB) detection technologies, there still remains a major need to develop simpler point-of-care techniques. In an effort towards such a diagnostic test for resource-poor settings, we have designed a bioassay based on detecting amplified DNA via bridging flocculation. The assay is cheap, with a sensitivity approaching a single cell of Mycobacterium tuberculosis and the potential for translation into broader applications.
The folate-coupled enzyme MTHFD2 is a nuclear protein and promotes cell proliferation
Authors: Gustafsson Sheppard Nina , Jarl Lisa , Mahadessian Diana , Strittmatter Laura , Schmidt Angelika , Madhusudan Nikhil , Tegnér Jesper , Lundberg Emma K. , Asplund Anna , Jain Mohit , Nilsson Roland 
Published: October 2015

AbstractFolate metabolism is central to cell proliferation and a target of commonly used cancer chemotherapeutics. In particular, the mitochondrial folate-coupled metabolism is thought to be important for proliferating cancer cells. The enzyme MTHFD2 in this pathway is highly expressed in human tumors and broadly required for survival of cancer cells. Although the enzymatic activity of the MTHFD2 protein is well understood, little is known about its larger role in cancer cell biology. We here report that MTHFD2 is co-expressed with two distinct gene sets, representing amino acid metabolism and cell proliferation, respectively. Consistent with a role for MTHFD2 in cell proliferation, MTHFD2 expression was repressed in cells rendered quiescent by deprivation of growth signals (serum) and rapidly re-induced by serum stimulation. Overexpression of MTHFD2 alone was sufficient to promote cell proliferation independent of its dehydrogenase activity, even during growth restriction. In addition to its known mitochondrial localization, we found MTHFD2 to have a nuclear localization and co-localize with DNA replication sites. These findings suggest a previously unknown role for MTHFD2 in cancer cell proliferation, adding to its known function in mitochondrial folate metabolism.
Interface designed MoS2/GaAs heterostructure solar cell with sandwich stacked hexagonal boron nitride
Authors: Lin Shisheng , Li Xiaoqiang , Wang Peng , Xu Zhijuan , Zhang Shengjiao , Zhong Huikai , Wu Zhiqian , Xu Wenli , Chen Hongsheng 
Published: October 2015

AbstractMoS2 is a layered two-dimensional semiconductor with a direct band gap of 1.8 eV. The MoS2/bulk semiconductor system offers a new platform for solar cell device design. Different from the conventional bulk p-n junctions, in the MoS2/bulk semiconductor heterostructure, static charge transfer shifts the Fermi level of MoS2 toward that of bulk semiconductor, lowering the barrier height of the formed junction. Herein, we introduce hexagonal boron nitride (h-BN) into MoS2/GaAs heterostructure to suppress the static charge transfer and the obtained MoS2/h-BN/GaAs solar cell exhibits an improved power conversion efficiency of 5.42%. More importantly, the sandwiched h-BN makes the Fermi level tuning of MoS2 more effective. By employing chemical doping and electrical gating into the solar cell device, PCE of 9.03% is achieved, which is the highest among all the reported monolayer transition metal dichalcogenide based solar cells.
Lateral prefrontal model-based signatures are reduced in healthy individuals with high trait impulsivity
Authors: Deserno L , Wilbertz T , Reiter A , Horstmann A , Neumann J , Villringer A , Heinze H-J , Schlagenhauf F 
Published: October 2015

AbstractHigh impulsivity is an important risk factor for addiction with evidence from endophenotype studies. In addiction, behavioral control is shifted toward the habitual end. Habitual control can be described by retrospective updating of reward expectations in ‘model-free’ temporal-difference algorithms. Goal-directed control relies on the prospective consideration of actions and their outcomes, which can be captured by forward-planning ‘model-based’ algorithms. So far, no studies have examined behavioral and neural signatures of model-free and model-based control in healthy high-impulsive individuals. Fifty healthy participants were drawn from the upper and lower ends of 452 individuals, completing the Barratt Impulsiveness Scale. All participants performed a sequential decision-making task during functional magnetic resonance imaging (fMRI) and underwent structural MRI. Behavioral and fMRI data were analyzed by means of computational algorithms reflecting model-free and model-based control. Both groups did not differ regarding the balance of model-free and model-based control, but high-impulsive individuals showed a subtle but significant accentuation of model-free control alone. Right lateral prefrontal model-based signatures were reduced in high-impulsive individuals. Effects of smoking, drinking, general cognition or gray matter density did not account for the findings. Irrespectively of impulsivity, gray matter density in the left dorsolateral prefrontal cortex was positively associated with model-based control. The present study supports the idea that high levels of impulsivity are accompanied by behavioral and neural signatures in favor of model-free behavioral control. Behavioral results in healthy high-impulsive individuals were qualitatively different to findings in patients with the same task. The predictive relevance of these results remains an important target for future longitudinal studies.
The effect of “Jelly” CdTe QD uptake on RAW264.7 monocytes: immune responses and cell fate study
Authors: Gladkovskaya O. , Loudon A. , Nosov M. , Gun'ko Y. K. , O'Connor G. M. , Rochev Y. 
Published: October 2015

Abstract
Encapsulation of Quantum Dots (QDs) has become an essential factor which regulates particles cytotoxicity, as well as physical and chemical stability. Negatively charged cellular membranes have a great affinity to nanoparticles with surface molecules carrying positive charge, hence creating perfect conditions for fast and aggressive intracellular penetration. The preference for non-charged outer shells is topical in QD design and various applications. In the current paper we develop gelatination as a prominent coating approach to create neutrally passivated QDs with improved biocompatibility. We have revealed the trends in particle's uptake, accumulation, intracellular localisation and retaining time as well as RAW264.7 monocyte cell fate and immune responses. Also the difference in particle endocytosis kinetics and dynamics has been shown to depend on the QD core size. The intracellular QD content along with cell responses at the population level was quantified by flow cytometry.
Transconductance improvement technique for bulk‐driven OTA in nanometre CMOS process
Authors: Zhao Xiao , Fang Huajun , Ling Tong , Xu Jun 
Published: October 2015

A transconductance improvement technique for a bulk‐driven operational transconductance amplifier (OTA) working in the weak inversion region is presented. Using the quasi‐floating gate method, the proposed technique achieves larger transconductance improvement than conventional approaches with the CMOS technologies scaling. Moreover, its enhanced performance is at no expense of the power budget. Simulated on UMC 180 nm technology, the results demonstrate that the proposed bulk‐driven OTA achieves more than two times gain–bandwidth improvement than that of the traditional counterpart with the same power.
Frequency tunable antenna using coupling patterns for mobile terminals
Authors: Lee Won‐Woo , Cho Yong‐Sang 
Published: October 2015

A frequency‐reconfigurable antenna based on aperture tuning using a coupled aperture structure on which a digital variable capacitor (DVC) is connected is presented. The coupled aperture structure is used to avoid electrical contact between the antenna radiator and the DVC in order to reduce antenna efficiency degradation due to ohmic losses at the DVC. The operating frequency is 700 MHz where the antenna efficiency is sensitive to the ohmic loss in the DVC. Analysis based on measurements and simulation confirm the benefits of using the coupled aperture structure over the conventional aperture tuning. It is shown that the coupled aperture plays a key role in reducing the impact of the equivalent series resistance of the DVC component on the antenna efficiency at 700 MHz.
Ohmic contacts to n‐type GaN layer using ECR‐sputtered AlN interfacial layer
Authors: Terano A. , Takei A. , Tanaka S. , Tsuchiya T. 
Published: October 2015

Ohmic contacts to an n‐type GaN layer using an electron cyclotron resonance (ECR)‐sputtered AlN (thickness of 3 nm)/Ti/Pt/Au electrode without an Al metal layer were investigated. Ohmic characteristics were achieved when annealed at a temperature of 400°C or more. Contact resistance reached a minimum (7.67 × 10−1 Ω‐mm) at an annealing temperature of 500°C.
Three‐phase resistive capacitor switching transient limiter for mitigating power capacitor switching transients
Authors: Ghanbari Teymoor , Farjah Ebrahim , Naseri Farshid 
Published: October 2015

This study presents a new resistive capacitor switching transient limiter (RCSTL) for mitigating power capacitor switching transients. The RCSTL is composed of three limiting resistors, a three‐phase full bridge diode rectifier, a thyristor and a three‐phase coupling transformer. The limiting resistors are connected in series with the capacitor bank and the thyristor is installed at the DC side of the diode rectifier. During the capacitor bank energising, the thyristor remains off and hence, the secondary side of the coupling transformer acts as open circuit. Consequently, high impedance including the transformer's magnetic reactance in parallel with the limiting resistors is inserted in series with the capacitor bank. Under such circumstance, the limiting resistors restrain the capacitor switching transients. In the steady‐state, the control system triggers the thyristor and the coupling transformer acts as short circuit. As a result, the limiting resistors are bypassed by the coupling transformer and thus, the RCSTL has no significant effect on the circuit. Analytical analysis is performed to describe different operation modes of the proposed RCSTL. A single stage of a three‐phase wye‐connected capacitor bank with 25 kVAR is energised and the performance of the proposed limiter is investigated. Both the simulation and experimental results confirm the effectiveness of the RCSTL.