bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reactivity of disulfide bonds is markedly affected by structure and environment: implications for protein modification and stability
Authors: Karimi Maryam , Ignasiak Marta T. , Chan Bun , Croft Anna K. , Radom Leo , Schiesser Carl H. , Pattison David I. , Davies Michael J. 
Published: December 2016

AbstractDisulfide bonds play a key role in stabilizing protein structures, with disruption strongly associated with loss of protein function and activity. Previous data have suggested that disulfides show only modest reactivity with oxidants. In the current study, we report kinetic data indicating that selected disulfides react extremely rapidly, with a variation of 104in rate constants. Five-membered ring disulfides are particularly reactive compared with acyclic (linear) disulfides or six-membered rings. Particular disulfides in proteins also show enhanced reactivity. This variation occurs with multiple oxidants and is shown to arise from favorable electrostatic stabilization of the incipient positive charge on the sulfur reaction center by remote groups, or by the neighboring sulfur for conformations in which the orbitals are suitably aligned. Controlling these factors should allow the design of efficient scavengers and high-stability proteins. These data are consistent with selective oxidative damage to particular disulfides, including those in some proteins.
Stochastic quantum Zeno-based detection of noise correlations
Authors: Müller Matthias M. , Gherardini Stefano , Caruso Filippo 
Published: December 2016

AbstractA system under constant observation is practically freezed to the measurement subspace. If the system driving is a random classical field, the survival probability of the system in the subspace becomes a random variable described by the Stochastic Quantum Zeno Dynamics (SQZD) formalism. Here, we study the time and ensemble average of this random survival probability and demonstrate how time correlations in the noisy environment determine whether the two averages do coincide or not. These environment time correlations can potentially generate non-Markovian dynamics of the quantum system depending on the structure and energy scale of the system Hamiltonian. We thus propose a way to detect time correlations of the environment by coupling a quantum probe system to it and observing the survival probability of the quantum probe in a measurement subspace. This will further contribute to the development of new schemes for quantum sensing technologies, where nanodevices may be exploited to image external structures or biological molecules via the surface field they generate.
Tunable reflecting terahertz filter based on chirped metamaterial structure
Authors: Yang Jing , Gong Cheng , Sun Lu , Chen Ping , Lin Lie , Liu Weiwei 
Published: December 2016

AbstractTunable reflecting terahertz bandstop filter based on chirped metamaterial structure is demonstrated by numerical simulation. In the metamaterial, the metal bars are concatenated to silicon bars with different lengths. By varying the conductivity of the silicon bars, the reflectivity, central frequency and bandwidth of the metamaterial could be tuned. Light illumination could be introduced to change the conductivity of the silicon bars. Numerical simulations also show that the chirped metamaterial structure is insensitive to the incident angle and polarization-dependent. The proposed chirped metamaterial structure can be operated as a tunable bandstop filter whose modulation depth, bandwidth, shape factor and center frequency can be controlled by light pumping.
Enhancing radiosensitization in EphB4 receptor-expressing Head and Neck Squamous Cell Carcinomas
Authors: Bhatia Shilpa , Hirsch Kellen , Sharma Jaspreet , Oweida Ayman , Griego Anastacia , Keysar Stephen , Jimeno Antonio , Raben David , Krasnoperov Valery , Gill Parkash S. , Pasquale Elena B. , Wang Xiao-Jing , Karam Sana D. 
Published: December 2016

AbstractMembers of the Eph family of receptor tyrosine kinases have been implicated in a wide array of human cancers. The EphB4 receptor is ubiquitously expressed in head and neck squamous cell carcinoma (HNSCC) and has been shown to impart tumorigenic and invasive characteristics to these cancers. In this study, we investigated whether EphB4 receptor targeting can enhance the radiosensitization of HNSCC. Our data show that EphB4 is expressed at high to moderate levels in HNSCC cell lines and patient-derived xenograft (PDX) tumors. We observed decreased survival fractions in HNSCC cells following EphB4 knockdown in clonogenic assays. An enhanced G2 cell cycle arrest with activation of DNA damage response pathway and increased apoptosis was evident in HNSCC cells following combined EphB4 downregulation and radiation compared to EphB4 knockdown and radiation alone. Data using HNSCC PDX models showed significant reduction in tumor volume and enhanced delay in tumor regrowth following sEphB4-HSA administration with radiation compared to single agent treatment. sEphB4-HSA is a protein known to block the interaction between the EphB4 receptor and its ephrin-B2 ligand. Overall, our findings emphasize the therapeutic relevance of EphB4 targeting as a radiosensitizer that can be exploited for the treatment of human head and neck carcinomas.
Molecular mechanism for sphingosine-induced Pseudomonas ceramidase expression through the transcriptional regulator SphR
Authors: Okino Nozomu , Ito Makoto 
Published: December 2016

AbstractPseudomonas aeruginosa,an opportunistic, but serious multidrug-resistant pathogen, secretes a ceramidase capable of cleaving theN-acyl linkage of ceramide to generate fatty acids and sphingosine. We previously reported that the secretion ofP. aeruginosaceramidase was induced by host-derived sphingolipids, through which phospholipase C-induced hemolysis was significantly enhanced. We herein investigated the gene(s) regulating sphingolipid-induced ceramidase expression and identified SphR, which encodes a putative AraC family transcriptional regulator. Disruption of thesphRgene inP. aeruginosamarkedly decreased the sphingomyelin-induced secretion of ceramidase, reduced hemolytic activity, and resulted in the loss of sphingomyelin-induced ceramidase expression. A microarray analysis confirmed that sphingomyelin significantly induced ceramidase expression inP. aeruginosa. Furthermore, an electrophoretic mobility shift assay revealed that SphR specifically bound free sphingoid bases such as sphingosine, dihydrosphingosine, and phytosphingosine, but not sphingomyelin or ceramide. A β-galactosidase-assisted promoter assay showed that sphingosine activated ceramidase expression through SphR at a concentration of 100 nM. Collectively, these results demonstrated that sphingosine induces the secretion of ceramidase by promoting the mRNA expression of ceramidase through SphR, thereby enhancing hemolytic phospholipase C-induced cytotoxicity. These results facilitate understanding of the physiological role of bacterial ceramidase in host cells.
Metastatic lymph node ratio demonstrates better prognostic stratification than pN staging in patients with esophageal squamous cell carcinoma after esophagectomy
Authors: Zhang Hongdian , Liang Huagang , Gao Yongyin , Shang Xiaobin , Gong Lei , Ma Zhao , Sun Ke , Tang Peng , Yu Zhentao 
Published: December 2016

AbstractThis study aimed to evaluate the prognostic significance of lymph node ratio (LNR) by establishing a hypothetical tumor-ratio-metastasis (TRM) staging system in patients with esophageal squamous cell carcinoma (ESCC). The records of 387 ESCC patients receiving curative esophagectomy were retrospectively investigated. The optimal cut-point for LNR was assessed via the best cut-off approach. Potential prognostic parameters were identified through univariate and multivariate analyses. A novel LNR-based TRM stage was proposed. The prognostic discriminatory ability and prediction accuracy of each system were determined using hazard ratio (HR), Akaike information criterion (AIC), concordance index (C-index), and area under the receiver operating characteristic curve (AUC). The optimal cut-points of LNR were set at 0, 0~0.2, 0.2~0.4, and 0.4~1.0. Multivariate Cox analysis indicated that the LNR category was an independent risk factor of overall survival (P < 0.001). The calibration curves for the probability of 3- and 5-year survival showed good consistency between nomogram prediction and actual observation. The LNR category and TRM stage yielded a larger HR, a smaller AIC, a larger C-index, and a larger AUC than the N category and TNM stage did. In summary, the proposed LNR category was superior to the conventional N category in predicting the prognosis of ESCC patients.
Coexistence of Write Once Read Many Memory and Memristor in blend of Poly(3,4-ethylenedioxythiophene): polystyrene sulfonate and Polyvinyl Alcohol
Authors: Nguyen Viet Cuong , Lee Pooi See 
Published: December 2016

AbstractIn this work, the coexistence of Write Once Read Many Memory (WORM) and memristor can be achieved in a single device of Poly(3,4-ethylenedioxythiophene): polystyrene sulfonate (PEDOT: PSS) and Polyvinyl Alcohol (PVA) blend organic memory system. In memristor mode, the bistable resistance states of the device can be cycled for more than 1000 times. Once a large negative bias of −8V was applied to the device, it was switched to permanent high resistance state that cannot be restored back to lower resistance states. The mechanism of the memristor effect can be attributed to the charge trapping behaviour in PVA while the WORM effect can be explained as the electrochemical characteristic of PEDOT: PSS which harnesses the percolative conduction pathways. The results may facilitate multipurpose memory device with active tunability.
Profiling bacterial communities associated with sediment-based aquaculture bioremediation systems under contrasting redox regimes
Authors: Robinson Georgina , Caldwell Gary S. , Wade Matthew J. , Free Andrew , Jones Clifford L. W. , Stead Selina M. 
Published: December 2016

AbstractDeposit-feeding invertebrates are proposed bioremediators in microbial-driven sediment-based aquaculture effluent treatment systems. We elucidate the role of the sediment reduction-oxidation (redox) regime in structuring benthic bacterial communities, having direct implications for bioremediation potential and deposit-feeder nutrition. The sea cucumber Holothuria scabra was cultured on sediments under contrasting redox regimes; fully oxygenated (oxic) and redox stratified (oxic-anoxic). Taxonomically, metabolically and functionally distinct bacterial communities developed between the redox treatments with the oxic treatment supporting the greater diversity; redox regime and dissolved oxygen levels were the main environmental drivers. Oxic sediments were colonised by nitrifying bacteria with the potential to remediate nitrogenous wastes. Percolation of oxygenated water prevented the proliferation of anaerobic sulphate-reducing bacteria, which were prevalent in the oxic-anoxic sediments. At the predictive functional level, bacteria within the oxic treatment were enriched with genes associated with xenobiotics metabolism. Oxic sediments showed the greater bioremediation potential; however, the oxic-anoxic sediments supported a greater sea cucumber biomass. Overall, the results indicate that bacterial communities present in fully oxic sediments may enhance the metabolic capacity and bioremediation potential of deposit-feeder microbial systems. This study highlights the benefits of incorporating deposit-feeding invertebrates into effluent treatment systems, particularly when the sediment is oxygenated.
Using deep belief network modelling to characterize differences in brain morphometry in schizophrenia
Authors: Pinaya Walter H. L. , Gadelha Ary , Doyle Orla M. , Noto Cristiano , Zugman André , Cordeiro Quirino , Jackowski Andrea P. , Bressan Rodrigo A. , Sato João R. 
Published: December 2016

AbstractNeuroimaging-based models contribute to increasing our understanding of schizophrenia pathophysiology and can reveal the underlying characteristics of this and other clinical conditions. However, the considerable variability in reported neuroimaging results mirrors the heterogeneity of the disorder. Machine learning methods capable of representing invariant features could circumvent this problem. In this structural MRI study, we trained a deep learning model known as deep belief network (DBN) to extract features from brain morphometry data and investigated its performance in discriminating between healthy controls (N = 83) and patients with schizophrenia (N = 143). We further analysed performance in classifying patients with a first-episode psychosis (N = 32). The DBN highlighted differences between classes, especially in the frontal, temporal, parietal, and insular cortices, and in some subcortical regions, including the corpus callosum, putamen, and cerebellum. The DBN was slightly more accurate as a classifier (accuracy = 73.6%) than the support vector machine (accuracy = 68.1%). Finally, the error rate of the DBN in classifying first-episode patients was 56.3%, indicating that the representations learned from patients with schizophrenia and healthy controls were not suitable to define these patients. Our data suggest that deep learning could improve our understanding of psychiatric disorders such as schizophrenia by improving neuromorphometric analyses.
Exploration of the Optimal Minimum Lymph Node Count after Colon Cancer Resection for Patients Aged 80 Years and Older
Authors: Guan Xu , Chen Wei , Jiang Zheng , Liu Zheng , Miao Dazhuang , Hu Hanqing , Zhao Zhixun , Yang Runkun , Wang Xishan 
Published: December 2016

AbstractThe elderly colon cancer (CC) patients are increasing and represent a heterogeneous patient group. The objectives of this study were to identify the features of lymph node examination and to explore the optimal minimum lymph node count after CC resection for patients aged ≥80. Using the Surveillance, Epidemiology, and End Results (SEER) database, we identified 65719 CC patients in stage I-III between 2004 and 2012, 26.0% of patients were aged ≥80. The median node count decreased with increasing age, which were 25.5, 20.2, 17.8 and 16.9 for patients aged 20–39, 40–59, 60–79, and ≥80. The rate of ≥12 nodes and the rate of node positivity for patients aged ≥80 were obviously lower than younger patients. Using X-tile analysis, we determined 9 nodes as the optimal node count for patients aged ≥80. Then, we compared the 5-year cancer specific survival (CSS) between patients with ≥9 nodes and <9 nodes. The results showed the 5-year CSSs were improved for patients with ≥9 nodes. Furthermore, the rate of node positivity and survival under the 9-node measure were equal to 12-node measure. Therefore, the lymph node examination should be discriminately evaluated for elder patients, and 9-node measure was available for patients aged ≥80.
A novel approach to quantify different iron forms in ex-vivo human brain tissue
Authors: Kumar Pravin , Bulk Marjolein , Webb Andrew , van der Weerd Louise , Oosterkamp Tjerk H. , Huber Martina , Bossoni Lucia 
Published: December 2016

AbstractWe propose a novel combination of methods to study the physical properties of ferric ions and iron-oxide nanoparticles inpost-mortemhuman brain, based on the combination of Electron Paramagnetic Resonance (EPR) and SQUID magnetometry. By means of EPR, we derive the concentration of the low molecular weight iron pool, as well as the product of its electron spin relaxation times. Additionally, by SQUID magnetometry we identify iron mineralization products ascribable to a magnetite/maghemite phase and a ferrihydrite (ferritin) phase. We further derive the concentration of magnetite/maghemite and of ferritin nanoparticles. To test out the new combined methodology, we studied brain tissue of an Alzheimer’s patient and a healthy control. Finally, we estimate that the size of the magnetite/maghemite nanoparticles, whose magnetic moments are blocked at room temperature, exceeds 40–50 nm, which is not compatible with the ferritin protein, the core of which is typically 6–8 nm. We believe that this methodology could be beneficial in the study of neurodegenerative diseases such as Alzheimer’s Disease which are characterized by abnormal iron accumulation in the brain.
Association of Bicipital Peritendinous Effusion with Subacromial Impingement: A Dynamic Ultrasonographic Study of 337 Shoulders
Authors: Chang Ke-Vin , Wu Wei-Ting , Özçakar Levent 
Published: December 2016

AbstractBicipital peritendinous effusion (BPE) is the most common biceps tendon abnormality and can be related to various shoulder ultrasonographic findings. Since the association of BPE with subacromial impingement is unclear, our study aimed to explore its association with the dynamic subacromial impingement test during ultrasound (US) imaging. We included 337 shoulders referred for US examinations and quantified the amount of BPE. Effusion more than 1 mm in thickness was considered a positive finding. A comparison of three grades of subacromial impingement, adjusted by patient demographics, static sonographic shoulder pathology, and physical findings, by using multivariate regression models revealed that the odds ratio of subacromial impingement (with 95% confidence intervals) in the presence of BPE was 6.54 (3.21–13.32) in grade 1, 6.93 (3.05–15.76) in grade 2 and 3.18 (1.48–6.80) in grade 3. An increase in age, subdeltoid bursitis, full-thickness supraspinatus tendon tear, and shoulder stiffness were also associated with BPE. Since our study demonstrated a positive association of BPE with all grades of impingement, a US dynamic subacromial impingement test is suggested when BPE is present. Future prospective studies are needed to identify changes in BPE after treatment.
Fast Quantum Rabi Model with Trapped Ions
Authors: Moya-Cessa Héctor M. 
Published: December 2016

AbstractWe show how to produce a fast quantum Rabi model with trapped ions. Its importance resides not only in the acceleration of the phenomena that may be achieved with these systems, from quantum gates to the generation of nonclassical states of the vibrational motion of the ion, but also in reducing unwanted effects such as the decay of coherences that may appear in such systems.
The concept of entropic rectifier facing experiments
Authors: Lairez D. , Clochard M.-C. , Wegrowe J.-E. 
Published: December 2016

AbstractThe transport of molecules in confined media is subject to entropic barriers. So theoretically, asymmetry of the confinement length may lead to molecular ratchets with entropy as the only driving force for the biased transport. We address experimentally this question by performing alternative ionic current measurements on electrolytes confined in neutral conical nanopores. In case anions and cations widely differ in size, we show that rectification of ionic current can be obtained that depends on ions size and cycle frequency, consistently with the entropic ratchet mechanism.
Antibacterial and anticancer PDMS surface for mammalian cell growth using the Chinese herb extract paeonol(4-methoxy-2-hydroxyacetophenone)
Authors: Jiao Jiajia , Sun Lili , Guo Zaiyu , Hou Sen , Holyst Robert , Lu Yun , Feng Xizeng 
Published: December 2016

AbstractPolydimethylsiloxane (PDMS) is widely used as a cell culture platform to produce micro- and nano-technology based microdevices. However, the native PDMS surface is not suitable for cell adhesion and is always subject to bacterial pollution and cancer cell invasion. Coating the PDMS surface with antibacterial or anticancer materials often causes considerable harm to the non-cancer mammalian cells on it. We have developed a method to fabricate a biocompatible PDMS surface which not only promotes non-cancer mammalian cell growth but also has antibacterial and anticancer activities, by coating the PDMS surface with a Chinese herb extract, paeonol. Coating changes the wettability and the elemental composition of the PDMS surface. Molecular dynamic simulation indicates that the absorption of paeonol onto the PDMS surface is an energy favourable process. The paeonol-coated PDMS surface exhibits good antibacterial activity against both Gram-positive and Gram-negative bacteria. Moreover considerable antibacterial activity is maintained after the coated surface is rinsed or incubated in water. The coated PDMS surface inhibits bacterial growth on the contact surface and promotes non-cancer mammalian cell growth with low cell toxicity; meanwhile the growth of cancer cells is significantly inhibited. Our study will potentially guide PDMS surface modification approaches to produce biomedical devices.
LncRNAs expression profiling in normal ovary, benign ovarian cyst and malignant epithelial ovarian cancer
Authors: Wang Huan , Fu Ziyi , Dai Chencheng , Cao Jian , Liu Xiaoguang , Xu Juan , Lv Mingming , Gu Yun , Zhang Jingmin , Hua Xiangdong , Jia Genmei , Xu Sujuan , Jia Xuemei , Xu Pengfei 
Published: December 2016

AbstractLong noncoding RNA (lncRNA) has been recognized as a regulator of gene expression, and the dysregulation of lncRNAs is involved in the progression of many types of cancer, including epithelial ovarian cancer (EOC). To explore the potential roles of lncRNAs in EOC, we performed lncRNA and mRNA microarray profiling in malignant EOC, benign ovarian cyst and healthy control tissues. In this study, 663 transcripts of lncRNAs were found to be differentially expressed in malignant EOC compared with benign and normal control tissues. We also selected 18 altered lncRNAs to confirm the validity of the microarray analysis using quantitative real-time PCR (qPCR). Pathway and Gene Ontology (GO) analyses demonstrated that these altered transcripts were involved in multiple biological processes, especially the cell cycle. Furthermore, Series Test of Cluster (STC) and lncRNA-mRNA co-expression network analyses were conducted to predict lncRNA expression trends and the potential target genes of lncRNAs. We also determined that two antisense lncRNAs (RP11-597D13.9 and ADAMTS9-AS1) were associated with their nearby coding genes (FAM198B, ADAMTS9), which participated in cancer progression. This study offers helpful information to understand the initiation and development mechanisms of EOC.
Single‐fed broadband circularly polarised dipole antenna with simple structure
Authors: Xue Hai‐Gao , Yang Xue‐Xia , Ma Zhewang , Wang Yan 
Published: December 2016

A new designed single‐fed broadband circularly polarised dipole antenna with simple structure is presented. The antenna is composed of a horizontal electric dipole and an equivalent magnetic dipole realised by two vertical patches quarter‐wave shorted at the bottom. The electric dipole and equivalent magnetic dipole are positioned along the same axis to excite the orthogonal radiation fields with the same amplitude and 90° phase difference for circular polarisation. A broad impedance bandwidth of 69% (|S11| < −10 dB) from 1.6 to 3.2 GHz is achieved, which covers the whole 3 dB axial ratio bandwidth of 42.7% from 2.0 to 3.1 GHz. In this operation frequency band, the measured gain is above 6.4 dBi and the peak value is 8.4 dBi.