bluuebunny/crossref_metadata_2025_split huggingface dataset:
Loss of ARID1A expression predicts poor survival prognosis in gastric cancer: a systematic meta-analysis from 14 studies
Authors: Yang Lin , Wei Sheng , Zhao Rongxian , Wu Yingxing , Qiu Hong , Xiong Huihua 
Published: June 2016

AbstractThe chromatin remodeling gene, AT-rich interactive domain 1A gene (ARID1A), frequently mutates inactively in gastric cancer (GC). However, its prognostic value remains controversial. To address this issue, a comprehensive meta-analysis was performed. Studies published until March 2016 were systematically searched. A total of 15 cohorts from 14 literatures involving 3183 patients were subjected to this meta-analysis. The pooled data showed that ARID1A expression loss predicted poor overall survival (OS) in GC (Hazard Ratio (HR) = 1.60; 95% Confidence Interval (CI) = 1.40–1.81; P < 0.001), with low heterogeneity among these studies (I2 = 21.5%; P = 0.214). Stratification analyses revealed that ARID1A expression loss was associated with poor OS in Asians (HR = 1.65, 95% CI = 1.44–1.89), proportion of proximal disease ≤30% subgroup (HR = 1.80, 95% CI = 1.36–2.38) and Epstein-Barr virus (EBV) (+) > 5% subgroup (HR = 1.59, 95% CI = 1.18–2.15). The robust results were suggested by sensitivity analyses and no evidence of significant publication bias was detected. This study demonstrated a significant relationship between deletion of ARID1A expression and poor OS in GC. Moreover, ethnicity, tumor location and EBV infection status might be potential key factors influencing this correlation.
A Broadband Terahertz Waveguide T-Junction Variable Power Splitter
Authors: Reichel Kimberly S. , Mendis Rajind , Mittleman Daniel M. 
Published: June 2016

AbstractIn order for the promise of terahertz (THz) wireless communications to become a reality, many new devices need to be developed, such as those for routing THz waves. We demonstrate a power splitting router based on a parallel-plate waveguide (PPWG) T-junction excited by the TE1 waveguide mode. By integrating a small triangular septum into the waveguide plate, we are able to direct the THz light down either one of the two output channels with precise control over the ratio between waveguide outputs. We find good agreement between experiment and simulation in both amplitude and phase. We show that the ratio between waveguide outputs varies exponentially with septum translation offset and that nearly 100% transmission can be achieved. The splitter operates over almost the entire range in which the waveguide is single mode, providing a sensitive and broadband method for THz power splitting.
Cargo binding promotes KDEL receptor clustering at the mammalian cell surface
Authors: Becker Björn , Shaebani M. Reza , Rammo Domenik , Bubel Tobias , Santen Ludger , Schmitt Manfred J. 
Published: June 2016

AbstractTransmembrane receptor clustering is a ubiquitous phenomenon in pro- and eukaryotic cells to physically sense receptor/ligand interactions and subsequently translate an exogenous signal into a cellular response. Despite that receptor cluster formation has been described for a wide variety of receptors, ranging from chemotactic receptors in bacteria to growth factor and neurotransmitter receptors in mammalian cells, a mechanistic understanding of the underlying molecular processes is still puzzling. In an attempt to fill this gap we followed a combined experimental and theoretical approach by dissecting and modulating cargo binding, internalization and cellular response mediated by KDEL receptors (KDELRs) at the mammalian cell surface after interaction with a model cargo/ligand. Using a fluorescent variant of ricin toxin A chain as KDELR-ligand (eGFP-RTAH/KDEL), we demonstrate that cargo binding induces dose-dependent receptor cluster formation at and subsequent internalization from the membrane which is associated and counteracted by anterograde and microtubule-assisted receptor transport to preferred docking sites at the plasma membrane. By means of analytical arguments and extensive numerical simulations we show that cargo-synchronized receptor transport from and to the membrane is causative for KDELR/cargo cluster formation at the mammalian cell surface.
Identification and expression profiles of neuropeptides and their G protein-coupled receptors in the rice stem borer Chilo suppressalis
Authors: Xu Gang , Gu Gui-Xiang , Teng Zi-Wen , Wu Shun-Fan , Huang Jia , Song Qi-Sheng , Ye Gong-Yin , Fang Qi 
Published: June 2016

AbstractIn insects, neuropeptides play important roles in the regulation of multiple physiological processes by binding to their corresponding receptors, which are primarily G protein-coupled receptors (GPCRs). The genes encoding neuropeptides and their associated GPCRs in the rice stem borerChilo suppressaliswere identified by a transcriptomic analysis and were used to identify potential targets for the disruption of physiological processes and the protection of crops. Forty-three candidate genes were found to encode the neuropeptide precursors for all known insect neuropeptides except for arginine-vasopressin-like peptide (AVLP), CNMamide, neuropeptide-like precursors 2-4 (NPLP2-4) and proctolin. In addition, novel alternative splicing variants of three neuropeptide genes (allatostatin CC, CCHamide 1 and short neuropeptide F) are reported for the first time and 51 putative neuropeptide GPCRs were identified. Phylogenetic analyses demonstrated that 44 of these GPCRs belong to the A-family (or rhodopsin-like), 5 belong to the B-family (or secretin-like) and 2 are leucine-rich repeat-containing GPCRs. These GPCRs and their likely ligands were also described. qRT-PCR analyses revealed the expression profiles of the neuropeptide precursors and GPCR genes in various tissues ofC. suppressalis. Our study provides fundamental information that may further our understanding of neuropeptidergic signaling systems in Lepidoptera and aid in the design of peptidomimetics, pseudopeptides or small molecules capable of disrupting the physiological processes regulated by these signaling molecules and their receptors.
Discovery and identification of candidate genes from the chitinase gene family for Verticillium dahliae resistance in cotton
Authors: Xu Jun , Xu Xiaoyang , Tian Liangliang , Wang Guilin , Zhang Xueying , Wang Xinyu , Guo Wangzhen 
Published: June 2016

AbstractVerticillium dahliae, a destructive and soil-borne fungal pathogen, causes massive losses in cotton yields. However, the resistance mechanism to V. dahilae in cotton is still poorly understood. Accumulating evidence indicates that chitinases are crucial hydrolytic enzymes, which attack fungal pathogens by catalyzing the fungal cell wall degradation. As a large gene family, to date, the chitinase genes (Chis) have not been systematically analyzed and effectively utilized in cotton. Here, we identified 47, 49, 92 and 116 Chis from four sequenced cotton species, diploid Gossypium raimondii (D5), G. arboreum (A2), tetraploid G. hirsutum acc. TM-1 (AD1) and G. barbadense acc. 3–79 (AD2), respectively. The orthologous genes were not one-to-one correspondence in the diploid and tetraploid cotton species, implying changes in the number of Chis in different cotton species during the evolution of Gossypium. Phylogenetic classification indicated that these Chis could be classified into six groups, with distinguishable structural characteristics. The expression patterns of Chis indicated their various expressions in different organs and tissues and in the V. dahliae response. Silencing of Chi23, Chi32, or Chi47 in cotton significantly impaired the resistance to V. dahliae, suggesting these genes might act as positive regulators in disease resistance to V. dahliae.
Efficient production of multi-modified pigs for xenotransplantation by ‘combineering’, gene stacking and gene editing
Authors: Fischer Konrad , Kraner-Scheiber Simone , Petersen Björn , Rieblinger Beate , Buermann Anna , Flisikowska Tatiana , Flisikowski Krzysztof , Christan Susanne , Edlinger Marlene , Baars Wiebke , Kurome Mayuko , Zakhartchenko Valeri , Kessler Barbara , Plotzki Elena , Szczerbal Izabela , Switonski Marek , Denner Joachim , Wolf Eckhard , Schwinzer Reinhard , Niemann Heiner , Kind Alexander , Schnieke Angelika 
Published: June 2016

AbstractXenotransplantation from pigs could alleviate the shortage of human tissues and organs for transplantation. Means have been identified to overcome hyperacute rejection and acute vascular rejection mechanisms mounted by the recipient. The challenge is to combine multiple genetic modifications to enable normal animal breeding and meet the demand for transplants. We used two methods to colocate xenoprotective transgenes at one locus, sequential targeted transgene placement - ‘gene stacking’ and cointegration of multiple engineered large vectors - ‘combineering’, to generate pigs carrying modifications considered necessary to inhibit short to mid-term xenograft rejection. Pigs were generated by serial nuclear transfer and analysed at intermediate stages. Human complement inhibitors CD46, CD55 and CD59 were abundantly expressed in all tissues examined, human HO1 and human A20 were widely expressed. ZFN or CRISPR/Cas9 mediated homozygous GGTA1 and CMAH knockout abolished α-Gal and Neu5Gc epitopes. Cells from multi-transgenic piglets showed complete protection against human complement-mediated lysis, even before GGTA1 knockout. Blockade of endothelial activation reduced TNFα-induced E-selectin expression, IFNγ-induced MHC class-II upregulation and TNFα/cycloheximide caspase induction. Microbial analysis found no PERV-C, PCMV or 13 other infectious agents. These animals are a major advance towards clinical porcine xenotransplantation and demonstrate that livestock engineering has come of age.
Zonulin Regulates Intestinal Permeability and Facilitates Enteric Bacteria Permeation in Coronary Artery Disease
Authors: Li Chuanwei , Gao Min , Zhang Wen , Chen Caiyu , Zhou Faying , Hu Zhangxu , Zeng Chunyu 
Published: June 2016

AbstractSeveral studies have reported an association between enteric bacteria and atherosclerosis. Bacterial 16S ribosomal RNA (rRNA) gene belong to Enterobacteriaceae have been detected in atherosclerotic plaques. How intestinal bacteria go into blood is not known. Zonulin reversibly modulate intestinal permeability (IP), the circulating zonulin levels were increased in diabetes, obesity, all of which are risk factors for atherosclerosis. It is unclear whether the circulating zonulin levels were changed in coronary artery disease (CAD) patients and modulate IP. The 16S rRNA gene of bacteria in blood sample was checked by 454 pyrosequencing. The zonulin levels were determined by enzyme-linked immunosorbent assay (ELISA) methods. The distribution of zonulin was detected by confocal immunofluorescence microscopy. Bacteria and Caco-2 cell surface micro-structure were checked by transmission electron microscopy. A high diversity of bacterial 16S rRNA gene can be detected in samples from CAD patients, most of them (99.4%) belong to Enterobacteriaceaes, eg. Rahnella. The plasma zonulin levels were significantly higher in CAD patients. Pseudomonas fluorescens exposure significantly increased zonulin expression and decreased IP in a time dependent manner. The elevated zonulin increase IP and may facilitate enteric translocation by disassembling the tight junctions, which might explain the observed high diversity of bacterial 16S rRNA genes in blood samples.
Computational imaging with a balanced detector
Authors: Soldevila F. , Clemente P. , Tajahuerce E. , Uribe-Patarroyo N. , Andrés P. , Lancis J. 
Published: June 2016

AbstractSingle-pixel cameras allow to obtain images in a wide range of challenging scenarios, including broad regions of the electromagnetic spectrum and through scattering media. However, there still exist several drawbacks that single-pixel architectures must address, such as acquisition speed and imaging in the presence of ambient light. In this work we introduce balanced detection in combination with simultaneous complementary illumination in a single-pixel camera. This approach enables to acquire information even when the power of the parasite signal is higher than the signal itself. Furthermore, this novel detection scheme increases both the frame rate and the signal-to-noise ratio of the system. By means of a fast digital micromirror device together with a low numerical aperture collecting system, we are able to produce a live-feed video with a resolution of 64 × 64 pixels at 5 Hz. With advanced undersampling techniques, such as compressive sensing, we can acquire information at rates of 25 Hz. By using this strategy, we foresee real-time biological imaging with large area detectors in conditions where array sensors are unable to operate properly, such as infrared imaging and dealing with objects embedded in turbid media.
Design of wideband filtering power divider with high selectivity and good isolation
Authors: Wang Xuedao , Wang Jianpeng , Zhang Gang 
Published: June 2016

A new microstrip wideband filtering power divider (FPD) is presented. By selecting proper coupling topology between a λ/4 short‐ended microstrip transmission line and two multimode resonators, a wideband FPD is initially constructed. Meanwhile, by wisely introducing an isolation resistor between the resonators, good port‐to‐port isolation of the FPD is obtained. For validation, one prototype wideband FPD operating at 2.24 GHz with the fractional bandwidth of 32.1% is designed, fabricated, and measured. Results indicate that the presented FPD exhibits not only a high‐frequency selectivity performance with the help of two out‐of‐band transmission zeros, but also better than 22.5 dB isolation within the entire operation band.
Physiological role for amyloid precursor protein in adult experience-dependent plasticity
Authors: Marik Sally A. , Olsen Olav , Tessier-Lavigne Marc , Gilbert Charles D. 
Published: June 2016

Significance
Amyloid precursor protein (APP) has long been implicated in Alzheimer’s disease, but its normal physiological role has only recently come to light. Here we demonstrate that APP plays a key role in axonal pruning after experience-dependent plasticity in the adult. Furthermore, we show that APP operates in a cell-autonomous fashion in the cortex to induce axonal pruning after sensory loss. APP is therefore important for the normal process of adult cortical plasticity through its role in the sculpting of axonal arbors.
Air pollutant emissions from Chinese households: A major and underappreciated ambient pollution source
Authors: Liu Jun , Mauzerall Denise L. , Chen Qi , Zhang Qiang , Song Yu , Peng Wei , Klimont Zbigniew , Qiu Xinghua , Zhang Shiqiu , Hu Min , Lin Weili , Smith Kirk R. , Zhu Tong 
Published: June 2016

Significance
China suffers from severe outdoor air pollution and associated public health impacts. In response, the government has imposed restrictions on major pollution sources such as vehicles and power plants. We show that due to uncontrolled and inefficient combustion of solid fuels in household devices, emission reductions from the residential sector may have greater air quality benefits in the North China Plain, including Beijing than reductions from other sectors. These benefits would be largest in the winter heating season when severe air pollution occurs. Household emissions, mostly from space heating and cooking with solid fuels, are an important and generally unrecognized source of ambient air pollution in China and other developing countries. Alternative fuels and other ways of reducing emissions would have large benefits.
Nanofluid of graphene-based amphiphilic Janus nanosheets for tertiary or enhanced oil recovery: High performance at low concentration
Authors: Luo Dan , Wang Feng , Zhu Jingyi , Cao Feng , Liu Yuan , Li Xiaogang , Willson Richard C. , Yang Zhaozhong , Chu Ching-Wu , Ren Zhifeng 
Published: June 2016

Significance
Improving crude oil recovery by 1% worldwide would result in a huge amount of crude oil resources becoming available. However, the economic and environmental concerns are too serious to ignore when chemical methods (surfactants or polymers flooding, etc.) are used for an average 10–20% enhancement for tertiary oil recovery. Simple nanofluid (containing only nanoparticles) flooding at low concentration (0.01 wt % or less) is a promising alternative, but the efficiency is below 5% in a saline environment (2 wt % or higher NaCl content). We report a simple nanofluid of graphene-based Janus amphiphilic nanosheets for enhanced oil recovery with efficiency of about 15.2%, comparable to chemical methods, which is both economically and environmentally beneficial to the petroleum industry.
The effects of neutron radiation on nickel-based alloys
Authors: Stopher M. A. 
Published: June 2016

The effects of neutron radiation on nickel-based alloys in thermal reactors are defying predictions that were made based upon accelerated testing in fast reactors. As nickel-based alloy components face significant doses in aging thermal reactors and their role in Gen-IV reactor designs becomes prominent, the literature on the effects of radiation on such alloys must be reviewed to enable better structural integrity assessments for relevant components and optimise alloys with respect to irradiation embrittlement resistance. This paper reviews the available data on the effects of radiation, notably neutron radiation, on nickel-based alloys and discusses the possible mitigation strategies and design opportunities for radiation embrittlement-resistant alloys based on recent developments in alloy computational design. This review was submitted as part of the 2016 Materials Literature Review Prize of the Institute of Materials, Minerals and Mining run by the Editorial Board of MST. Sponsorship of the prize by TWI Ltd is gratefully acknowledged.
Review of tailoring ZnO for optoelectronics through atomic layer deposition experimental variables
Authors: Burgess C. H. 
Published: June 2016

Atomic layer deposition (ALD) is an increasingly popular thin film deposition technique which offers unique large area capability combined with excellent conformality, thus ALD will likely be important in the development of next generation optoelectronic devices. Such device platforms include solar cells, thin film transistors and light emitting diodes, and in all of these technologies one material is frequently used – zinc oxide (ZnO) – owing to its excellent electrical and optical properties combined with earth abundance. The approaches and achievements in tailoring the properties of ALD ZnO are discussed. Key process variables include deposition temperature and purge times as well dopant incorporation, with particular attention paid to tuning band alignment and carrier concentrations (focusing on lower carrier concentration applications). This review was submitted as part of the 2016 Materials Literature Review Prize of the Institute of Materials, Minerals and Mining run by the Editorial Board of MST. Sponsorship of the prize by TWI Ltd is gratefully acknowledged.
Functional characterization of selective exosite-binding inhibitors of matrix metalloproteinase-13 (MMP-13) – experimental validation in human breast and colon cancer
Authors: Kothapalli Roopa , Sivaraman Siveen Kodappully , Tan Tuan Zea , Thiery Jean Paul , Kumar Alan Prem , Sethi Gautam , Swaminathan Kunchithapadam 
Published: June 2016

Abstract
Considering the pathological significance of MMP-13 in breast and colon cancers, exosite-based inhibition of the C-terminal hemopexin (Hpx) domain could serve as an alternative strategy to develop selective inhibitors for MMP-13.Two of six lead compounds, compound 5 (2,3-dihydro-1,4-benzodioxine-5-carboxylic acid) and compound 6 (1-acetyl-4-hydroxypyrrolidine-2-carboxylic acid) exhibited considerable inhibitory activity against MMP-13. Complementing to this study, we have also shown the gene expression levels of MMP-13 within the subtypes of colon and breast cancers classified from patients’ tissue samples to provide a better understanding on which subtype of breast cancer patients would get benefited by MMP-13 inhibitors.Our current results show that compounds 5 and 6 could effectively inhibit MMP-13 and provide specific therapeutic possibilities in the treatment of inflammatory disorders and cancers. The characterization of these lead compounds would provide a better mechanistic understanding of exosite-based inhibition of MMP-13, which could overcome the challenges in the identification of other MMP catalytic domain-specific inhibitors.
A probabilistic approach for collective similarity-based drug–drug interaction prediction
Authors: Sridhar Dhanya , Fakhraei Shobeir , Getoor Lise 
Published: June 2016

Abstract
Motivation: As concurrent use of multiple medications becomes ubiquitous among patients, it is crucial to characterize both adverse and synergistic interactions between drugs. Statistical methods for prediction of putative drug–drug interactions (DDIs) can guide in vitro testing and cut down significant cost and effort. With the abundance of experimental data characterizing drugs and their associated targets, such methods must effectively fuse multiple sources of information and perform inference over the network of drugs.
Results: We propose a probabilistic approach for jointly inferring unknown DDIs from a network of multiple drug-based similarities and known interactions. We use the highly scalable and easily extensible probabilistic programming framework Probabilistic Soft Logic. We compare against two methods including a state-of-the-art DDI prediction system across three experiments and show best performing improvements of more than 50% in AUPR over both baselines. We find five novel interactions validated by external sources among the top-ranked predictions of our model.
Availability and implementation: Final versions of all datasets and implementations will be made publicly available.
Contact: dsridhar@ucsc.edu
Abnormal right ventricular-pulmonary artery coupling with exercise in heart failure with preserved ejection fraction
Authors: Borlaug Barry A. , Kane Garvan C. , Melenovsky Vojtech , Olson Thomas P. 
Published: June 2016

Background
Exercise intolerance is common in people with heart failure and preserved ejection fraction (HFpEF). Right ventricular (RV) dysfunction has been shown at rest in HFpEF but little data are available regarding dynamic RV-pulmonary artery (PA) coupling during exercise.

Methods and results
Subjects with HFpEF (n = 50) and controls (n = 24) prospectively underwent invasive cardiopulmonary exercise testing using high-fidelity micromanometer catheters along with simultaneous assessment of RV and left ventricular (LV) mechanics by echocardiography. Compared with controls at rest, subjects with HFpEF displayed preserved RV systolic and diastolic mechanics (RV s′ and e′), impaired LV s′ and e′, higher biventricular filling pressures, and higher pulmonary artery pressures. On exercise, subjects with HFpEF displayed less increase in stroke volume, heart rate, and cardiac output (CO), with blunted increase in CO relative to O2 consumption (VO2). Enhancement in RV systolic and diastolic function on exercise was impaired in HFpEF compared with controls. Exercise-induced PA vasodilation was reduced in HFpEF in correlation with greater venous hypoxia. Elevations in biventricular filling pressures and limitations in CO reserve were strongly correlated with abnormal enhancement in ventricular mechanics in the RV and LV during stress.

Conclusions
In addition to limited LV reserve, patients with HFpEF display impaired RV reserve during exercise that is associated with high filling pressures and inadequate CO responses. These findings highlight the importance of biventricular dysfunction in HFpEF and suggest that novel therapies targeting myocardial reserve in both the left and right heart may be effective to improve clinical status.