bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrative topological analysis of mass spectrometry data reveals molecular features with clinical relevance in esophageal squamous cell carcinoma
Authors: Gao She-Gan , Liu Rui-Min , Zhao Yun-Gang , Wang Pei , Ward Douglas G. , Wang Guang-Chao , Guo Xiang-Qian , Gu Juan , Niu Wan-Bin , Zhang Tian , Martin Ashley , Guo Zhi-Peng , Feng Xiao-Shan , Qi Yi-Jun , Ma Yuan-Fang 
Published: February 2016

AbstractCombining MS-based proteomic data with network and topological features of such network would identify more clinically relevant molecules and meaningfully expand the repertoire of proteins derived from MS analysis. The integrative topological indexes representing 95.96% information of seven individual topological measures of node proteins were calculated within a protein-protein interaction (PPI) network, built using 244 differentially expressed proteins (DEPs) identified by iTRAQ 2D-LC-MS/MS. Compared with DEPs, differentially expressed genes (DEGs) and comprehensive features (CFs), structurally dominant nodes (SDNs) based on integrative topological index distribution produced comparable classification performance in three different clinical settings using five independent gene expression data sets. The signature molecules of SDN-based classifier for distinction of early from late clinical TNM stages were enriched in biological traits of protein synthesis, intracellular localization and ribosome biogenesis, which suggests that ribosome biogenesis represents a promising therapeutic target for treating ESCC. In addition, ITGB1 expression selected exclusively by integrative topological measures correlated with clinical stages and prognosis, which was further validated with two independent cohorts of ESCC samples. Thus the integrative topological analysis of PPI networks proposed in this study provides an alternative approach to identify potential biomarkers and therapeutic targets from MS/MS data with functional insights in ESCC.
Substituent Effects on the Photodeprotection Reactions of Selected Ketoprofen Derivatives in Phosphate Buffered Aqueous Solutions
Authors: Liu Mingyue , Li Ming-De , Huang Jinqing , Li Tianlu , Liu Han , Li Xuechen , Phillips David Lee 
Published: February 2016

AbstractPhotodeprotection is an important reaction that has been attracting broad interest for use in a variety of applications. Recent advances in ultrafast and vibrational time-resolved spectroscopies can facilitate obtaining data to help unravel the reaction mechanisms involving in the photochemical reactions of interest. The kinetics and reaction mechanisms for the photodeprotection reactions of ketoprofen derivatives containing three different substituents (ibuprofen, Br and I) were investigated by femtosecond transient absorption (fs-TA) and nanosecond time-resolved resonance Raman (ns-TR3) spectroscopy methods in phosphate buffered solutions (PBS). Fs-TA allows us to detect the decay kinetics of the triplet species as the key precursor for formation of a carbanion species for three different substituents attached to ketoprofen. To characterize the structural and electronic properties of the corresponding carbanion and triplet intermediates, TR3 spectroscopic experiments were conducted. The transient spectroscopy work reveals that the different substituents affect the photodecarboxylation reaction to produce carbon dioxide which in turn influences the generation of the carbanion species which determines the rate of the photorelease of the functional groups attached on the ketoprofen parent molecule. The fingerprint TR3 spectroscopy results suggest that ketoprofen derivatives may be deactivated to produce a triplet carbanion when increasing the atom mass of the halogen atoms.
High-throughput proteomics reveal alarmins as amplifiers of tissue pathology and inflammation after spinal cord injury
Authors: Didangelos Athanasios , Puglia Michele , Iberl Michaela , Sanchez-Bellot Candela , Roschitzki Bernd , Bradbury Elizabeth J. 
Published: February 2016

AbstractSpinal cord injury is characterized by acute cellular and axonal damage followed by aggressive inflammation and pathological tissue remodelling. The biological mediators underlying these processes are still largely unknown. Here we apply an innovative proteomics approach targeting the enriched extracellular proteome after spinal cord injury for the first time. Proteomics revealed multiple matrix proteins not previously associated with injured spinal tissue, including small proteoglycans involved in cell-matrix adhesion and collagen fibrillogenesis. Network analysis of transcriptomics and proteomics datasets uncovered persistent overexpression of extracellular alarmins that can trigger inflammation via pattern recognition receptors. In mechanistic experiments, inhibition of toll-like receptor-4 (TLR4) and the receptor for advanced glycation end-products (RAGE) revealed the involvement of alarmins in inflammatory gene expression, which was found to be dominated by IL1 and NFκΒ signalling. Extracellular high-mobility group box-1 (HMGB1) was identified as the likely endogenous regulator of IL1 expression after injury. These data reveal a novel tissue remodelling signature and identify endogenous alarmins as amplifiers of the inflammatory response that promotes tissue pathology and impedes neuronal repair after spinal cord injury.
Burning and graphitization of optically levitated nanodiamonds in vacuum
Authors: Rahman A. T. M. A. , Frangeskou A. C. , Kim M. S. , Bose S. , Morley G. W. , Barker P. F. 
Published: February 2016

AbstractA nitrogen-vacancy (NV−) centre in a nanodiamond, levitated in high vacuum, has recently been proposed as a probe for demonstrating mesoscopic centre-of-mass superpositions and for testing quantum gravity. Here, we study the behaviour of optically levitated nanodiamonds containing NV− centres at sub-atmospheric pressures and show that while they burn in air, this can be prevented by replacing the air with nitrogen. However, in nitrogen the nanodiamonds graphitize below ≈10 mB. Exploiting the Brownian motion of a levitated nanodiamond, we extract its internal temperature (Ti) and find that it would be detrimental to the NV− centre’s spin coherence time. These values of Ti make it clear that the diamond is not melting, contradicting a recent suggestion. Additionally, using the measured damping rate of a levitated nanoparticle at a given pressure, we propose a new way of determining its size.
A pilot-scale forward osmosis membrane system for concentrating low-strength municipal wastewater: performance and implications
Authors: Wang Zhiwei , Zheng Junjian , Tang Jixu , Wang Xinhua , Wu Zhichao 
Published: February 2016

AbstractRecovery of nutrients and energy from municipal wastewater has attracted much attention in recent years; however, its efficiency is significantly limited by the low-strength properties of municipal wastewater. Herein, we report a pilot-scale forward osmosis (FO) system using a spiral-wound membrane module to concentrate real municipal wastewater. Under active layer facing feed solution mode, the critical concentration factor (CCF) of this FO system was determined to be 8 with 0.5 M NaCl as draw solution. During long-term operation at a concentration factor of 5, (99.8 ± 0.6)% of chemical oxygen demand and (99.7 ± 0.5)% of total phosphorus rejection rates could be achieved at a flux of 6 L/(m2 h) on average. In comparison, only (48.1 ± 10.5)% and (67.8 ± 7.3)% rejection of ammonium and total nitrogen were observed. Cake enhanced concentration polarization is a major contributor to the decrease of water fluxes. The fouling also led to the occurrence of a cake reduced concentration polarization effect, improving ammonium rejection rate with the increase of operation time in each cycle. This work demonstrates the applicability of using FO process for wastewater concentrating and also limitations in ammonium recovery that need further improvement in future.
Non-ionizing radiofrequency electromagnetic waves traversing the head can be used to detect cerebrovascular autoregulation responses
Authors: Oziel M. , Hjouj M. , Gonzalez C. A. , Lavee J. , Rubinsky B. 
Published: February 2016

AbstractMonitoring changes in non-ionizing radiofrequency electromagnetic waves as they traverse the brain can detect the effects of stimuli employed in cerebrovascular autoregulation (CVA) tests on the brain, without contact and in real time. CVA is a physiological phenomenon of importance to health, used for diagnosis of a number of diseases of the brain with a vascular component. The technology described here is being developed for use in diagnosis of injuries and diseases of the brain in rural and economically underdeveloped parts of the world. A group of nine subjects participated in this pilot clinical evaluation of the technology. Substantial research remains to be done on correlating the measurements with physiology and anatomy.
An ecological method to understand agricultural standardization in peach orchard ecosystems
Authors: Wan Nian-Feng , Zhang Ming-Yi , Jiang Jie-Xian , Ji Xiang-Yun , Hao-Zhang  
Published: February 2016

AbstractWhile the worldwide standardization of agricultural production has been advocated and recommended, relatively little research has focused on the ecological significance of such a shift. The ecological concerns stemming from the standardization of agricultural production may require new methodology. In this study, we concentrated on how ecological two-sidedness and ecological processes affect the standardization of agricultural production which was divided into three phrases (pre-, mid- and post-production), considering both the positive and negative effects of agricultural processes. We constructed evaluation indicator systems for the pre-, mid- and post-production phases and here we presented a Standardization of Green Production Index (SGPI) based on the Full Permutation Polygon Synthetic Indicator (FPPSI) method which we used to assess the superiority of three methods of standardized production for peaches. The values of SGPI for pre-, mid- and post-production were 0.121 (Level IV, “Excellent” standard), 0.379 (Level III, “Good” standard), and 0.769 × 10−2 (Level IV, “Excellent” standard), respectively. Here we aimed to explore the integrated application of ecological two-sidedness and ecological process in agricultural production. Our results are of use to decision-makers and ecologists focusing on eco-agriculture and those farmers who hope to implement standardized agricultural production practices.
Xeno-sensing activity of the aryl hydrocarbon receptor in human pluripotent stem cell-derived hepatocyte-like cells
Authors: Kim Hye-Min , Kim Ji-Woo , Choi Youngjun , Chun Hang-Suk , Im Ilkyun , Han Yong-Mahn , Song Chang-Woo , Yoon Seokjoo , Park Han-Jin 
Published: February 2016

AbstractAlthough hepatocyte-like cells derived from human pluripotent stem cells (hPSC-HLCs) are considered a promising model for predicting hepatotoxicity, their application has been restricted because of the low activity of drug metabolizing enzymes (DMEs). Here we found that the low expression of xenobiotic receptors (constitutive androstane receptor, CAR; and pregnane X receptor, PXR) contributes to the low activity of DMEs in hPSC-HLCs. Most CAR- and PXR-regulated DMEs and transporters were transcriptionally down-regulated in hPSC-HLC. Transcriptional expression of CAR and PXR was highly repressed in hPSC-HLCs, whereas mRNA levels of aryl hydrocarbon receptor (AHR) were comparable to those of adult liver. Furthermore, ligand-induced transcriptional activation was observed only at AHR in hPSC-HLCs. Bisulfite sequencing analysis demonstrated that promoter hypermethylation of CAR and PXR was associated with diminished transcriptional activity in hPSC-HLCs. Treatment with AHR-selective ligands increased the transcription of AHR-dependent target genes by direct AHR-DNA binding at the xenobiotic response element. In addition, an antagonist of AHR significantly inhibited AHR-dependent target gene expression. Thus, AHR may function intrinsically as a xenosensor as well as a ligand-dependent transcription factor in hPSC-HLCs. Our results indicate that hPSC-HLCs can be used to screen toxic substances related to AHR signaling and to identify potential AHR-targeted therapeutics.
Bifurcation-based adiabatic quantum computation with a nonlinear oscillator network
Authors: Goto Hayato 
Published: February 2016

AbstractThe dynamics of nonlinear systems qualitatively change depending on their parameters, which is called bifurcation. A quantum-mechanical nonlinear oscillator can yield a quantum superposition of two oscillation states, known as a Schrödinger cat state, via quantum adiabatic evolution through its bifurcation point. Here we propose a quantum computer comprising such quantum nonlinear oscillators, instead of quantum bits, to solve hard combinatorial optimization problems. The nonlinear oscillator network finds optimal solutions via quantum adiabatic evolution, where nonlinear terms are increased slowly, in contrast to conventional adiabatic quantum computation or quantum annealing, where quantum fluctuation terms are decreased slowly. As a result of numerical simulations, it is concluded that quantum superposition and quantum fluctuation work effectively to find optimal solutions. It is also notable that the present computer is analogous to neural computers, which are also networks of nonlinear components. Thus, the present scheme will open new possibilities for quantum computation, nonlinear science and artificial intelligence.
Placental Transfer of Perfluoroalkyl Substances and Associations with Thyroid Hormones: Beijing Prenatal Exposure Study
Authors: Yang Lin , Li Jingguang , Lai Jianqiang , Luan Hemi , Cai Zongwei , Wang Yibaina , Zhao Yunfeng , Wu Yongning 
Published: February 2016

AbstractPerfluoroalkyl substances (PFASs) have been detected in wildlife and human samples worldwide. Toxicology research showed that PFASs could interfere with thyroid hormone homeostasis. In this study, eight PFASs, fifteen PFAS precursors and five thyroid hormones were analyzed in 157 paired maternal and cord serum samples collected in Beijing around delivery. Seven PFASs and two precursors were detected in both maternal and cord sera with significant maternal-fetal correlations (r = 0.336 to 0.806, all P < 0.001). The median ratios of major PFASs concentrations in fetal versus maternal serum were from 0.25:1 (perfluorodecanoic acid, PFDA) to 0.65:1 (perfluorooctanoic acid, PFOA). Spearman partial correlation test showed that maternal thyroid stimulating hormone (TSH) was negatively correlated with most maternal PFASs (r = −0.261 to −0.170, all P < 0.05). Maternal triiodothyronin (T3) and free T3 (FT3) showed negative correlations with most fetal PFASs (r = −0.229 to −0.165 for T3; r = −0.293 to −0.169 for FT3, all P < 0.05). Our results suggest prenatal exposure of fetus to PFASs and potential associations between PFASs and thyroid hormone homeostasis in humans.
Modulation of E-cadherin expression promotes migration ability of esophageal cancer cells
Authors: Li Shujun , Qin Xuebo , Chai Song , Qu Changbao , Wang Xiaolu , Zhang Helin 
Published: February 2016

AbstractLosing the E-cadherin plays an important role in the metastasis of cancer. The regulation of the expression of E-cadherin is unclear. Circadian rhythm alteration is associated with the pathogenesis of a number of cancers. This study aims to investigate the role of one of the circadian proteins, period-2 (Per2) in repressing the expression of E-cadherin in esophageal cancer (esophageal cancer). We observed that the levels of circadian protein Per2 were significantly increased and E-cadherin was significantly decreased in the tissue of human esophageal cancer with metastasis as compared with non-metastatic esophageal cancer. Overexpression of Per2 in the esophageal cancer cells markedly repressed the expression of E-cadherin. The pHDAC1 was detected in human esophageal cancer with metastasis, which was much less in the esophageal cancer tissue without metastasis. Overexpression of Per2 increased the levels of pHDAC1 as well as the E-cadherin repressors at the E-cadherin promoter locus. Overexpression of Per2 markedly increased the migratory capacity of esophageal cancer cells, which was abolished by the inhibition of HDAC1. We conclude that Per-2 plays an important role in the esophageal cancer cell metastasis, which may be a novel therapeutic target for the treatment of esophageal cancer.
Memantine Improves Attentional Processes in Fragile X-Associated Tremor/Ataxia Syndrome: Electrophysiological Evidence from a Randomized Controlled Trial
Authors: Yang Jin-Chen , Rodriguez Annette , Royston Ashley , Niu Yu-Qiong , Avar Merve , Brill Ryan , Simon Christa , Grigsby Jim , Hagerman Randi J. , Olichney John M. 
Published: February 2016

AbstractProgressive cognitive deficits are common in patients with fragile X-associated tremor/ataxia syndrome (FXTAS), with no targeted treatment yet established. In this substudy of the first randomized controlled trial for FXTAS, we examined the effects of NMDA antagonist memantine on attention and working memory. Data were analyzed for patients (24 in each arm) who completed both the primary memantine trial and two EEG recordings (at baseline and follow-up) using an auditory “oddball” task. Results demonstrated significantly improved attention/working memory performance after one year only for the memantine group. The event-related potential P2 amplitude elicited by non-targets was significantly enhanced in the treated group, indicating memantine-associated improvement in attentional processes at the stimulus identification/discrimination level. P2 amplitude increase was positively correlated with improvement on the behavioral measure of attention/working memory during target detection. Analysis also revealed that memantine treatment normalized the P2 habituation effect at the follow-up visit. These findings indicate that memantine may benefit attentional processes that represent fundamental components of executive function/dysfunction, thought to comprise the core cognitive deficit in FXTAS. The results provide evidence of target engagement of memantine, as well as therapeutically relevant information that could further the development of specific cognitive or disease-modifying therapies for FXTAS.
The shear band controlled deformation in metallic glass: a perspective from fracture
Authors: Yang G. N. , Shao Y. , Yao K. F. 
Published: February 2016

AbstractDifferent from the homogenous deformation in conventional crystalline alloys, metallic glasses and other work-softening materials deform discontinuously by localized plastic strain in shear bands. Here by three-point bending test on a typical ductile Pd-Cu-Si metallic glass, we found that the plastic deformed region during fracture didn’t follow the yielding stress distribution as the conventional material mechanics expected. We speculated that such special behavior was because the shear bands in metallic glasses could propagate easily along local shear stress direction once nucleated. Based on a 3D notch tip stress field simulation, we considered a new fracture process in a framework of multiple shear band deformation mechanism instead of conventional materials mechanics, and successfully reproduced the as-observed complicate shear band morphologies. This work clarifies many common misunderstandings on metallic glasses fracture, and might also provide a new insight to the shear band controlled deformation. It suggests that the deformation of metallic glasses is sensitive to local stress condition, and therefore their mechanical properties would depend on not only the material, but also other external factors on stress condition. We hope that start from this work, new methods, criteria, or definitions could be proposed to further study these work-softening materials, especially for metallic glasses.
Long 5′ untranslated regions regulate the RNA stability of the deep-sea filamentous phage SW1
Authors: Jian Huahua , Xiong Lei , Xu Guanpeng , Xiao Xiang , Wang Fengping 
Published: February 2016

AbstractVirus production in the deep-sea environment has been found to be high, and viruses have been suggested to play significant roles in the overall functioning of this ecosystem. Nevertheless, little is known about these viruses, including the mechanisms that control their production, which makes them one of the least understood biological entities on Earth. Previously, we isolated the filamentous phage SW1, whose virus production and gene transcription were found to be active at low temperatures, from a deep-sea bacterium, Shewanella piezotolerans WP3. In this study, the operon structure of phage SW1 is presented, which shows two operons with exceptionally long 5′ and 3′ untranslated regions (UTRs). In addition, the 5′UTR was confirmed to significantly influence the RNA stability of the SW1 transcripts. Our study revealed novel regulation of the operon and led us to propose a unique regulatory mechanism for Inoviruses. This type of RNA-based regulation may represent a mechanism for significant viral production in the cold deep biosphere.
Effect of diabetic duration on hemorheological properties and platelet aggregation in streptozotocin-induced diabetic rats
Authors: Yeom Eunseop , Byeon Hyeokjun , Lee Sang Joon 
Published: February 2016

AbstractDiabetes mellitus with abnormal glucose concentration is associated with changes in hemorheological properties, endothelial function and platelets hyperactivity. Disturbances may significantly be responsible for diabetes-related vascular complications. In this study, hemorheological and hemodynamic properties were measured according to diabetic duration after streptozotocin treatment in rats. For ex vivo measurements, an extracorporeal model was adopted. Flow rate and blood viscosity were measured using a microfluidic device. Erythrocyte aggregation and morphological parameters of erythrocytes were measured by modified erythrocyte sedimentation rate and the phase-contrast holography under in vitro conditions. The platelet aggregation and mean pressure in the femoral artery were estimated under ex vivo conditions. Hemorheological properties including blood viscosity, erythrocyte aggregation and shape parameters for the control group are significantly different with those for diabetic groups. The changes with respect to diabetic duration were relatively unnoticeable. However, the platelet aggregation is strongly dependent on the diabetic duration. Based on these results, hyperglycemia exposure may induce hemorheological variations in early stages of diabetes mellitus. High platelet aggregation may become more pronounced according to the diabetic duration caused by variations in hemorheological properties resulting in endothelial dysfunction. This study would be helpful in understanding the effects of diabetic duration on biophysical properties.
High rate lithium-sulfur battery enabled by sandwiched single ion conducting polymer electrolyte
Authors: Sun Yubao , Li Gai , Lai Yuanchu , Zeng Danli , Cheng Hansong 
Published: February 2016

AbstractLithium-sulfur batteries are highly promising for electric energy storage with high energy density, abundant resources and low cost. However, the battery technologies have often suffered from a short cycle life and poor rate stability arising from the well-known “polysulfide shuttle” effect. Here, we report a novel cell design by sandwiching a sp3 boron based single ion conducting polymer electrolyte film between two carbon films to fabricate a composite separator for lithium-sulfur batteries. The dense negative charges uniformly distributed in the electrolyte membrane inherently prohibit transport of polysulfide anions formed in the cathode inside the polymer matrix and effectively blocks polysulfide shuttling. A battery assembled with the composite separator exhibits a remarkably long cycle life at high charge/discharge rates.