bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deterministic error correction for nonlocal spatial-polarization hyperentanglement
Authors: Li Tao , Wang Guan-Yu , Deng Fu-Guo , Long Gui-Lu 
Published: February 2016

AbstractHyperentanglement is an effective quantum source for quantum communication network due to its high capacity, low loss rate and its unusual character in teleportation of quantum particle fully. Here we present a deterministic error-correction scheme for nonlocal spatial-polarization hyperentangled photon pairs over collective-noise channels. In our scheme, the spatial-polarization hyperentanglement is first encoded into a spatial-defined time-bin entanglement with identical polarization before it is transmitted over collective-noise channels, which leads to the error rejection of the spatial entanglement during the transmission. The polarization noise affecting the polarization entanglement can be corrected with a proper one-step decoding procedure. The two parties in quantum communication can, in principle, obtain a nonlocal maximally entangled spatial-polarization hyperentanglement in a deterministic way, which makes our protocol more convenient than others in long-distance quantum communication.
Prediction of Immunomodulatory potential of an RNA sequence for designing non-toxic siRNAs and RNA-based vaccine adjuvants
Authors: Chaudhary Kumardeep , Nagpal Gandharva , Dhanda Sandeep Kumar , Raghava Gajendra P. S. 
Published: February 2016

AbstractOur innate immune system recognizes a foreign RNA sequence of a pathogen and activates the immune system to eliminate the pathogen from our body. This immunomodulatory potential of RNA can be used to design RNA-based immunotherapy and vaccine adjuvants. In case of siRNA-based therapy, the immunomodulatory effect of an RNA sequence is unwanted as it may cause immunotoxicity. Thus, we developed a method for designing a single-stranded RNA (ssRNA) sequence with desired immunomodulatory potentials, for designing RNA-based therapeutics, immunotherapy and vaccine adjuvants. The dataset used for training and testing our models consists of 602 experimentally verified immunomodulatory oligoribonucleotides (IMORNs) that are ssRNA sequences of length 17 to 27 nucleotides and 520 circulating miRNAs as non-immunomodulatory sequences. We developed prediction models using various features that include composition-based features, binary profile, selected features and hybrid features. All models were evaluated using five-fold cross-validation and external validation techniques; achieving a maximum mean Matthews Correlation Coefficient (MCC) of 0.86 with 93% accuracy. We identified motifs using MERCI software and observed the abundance of adenine (A) in motifs. Based on the above study, we developed a web server, imRNA, comprising of various modules important for designing RNA-based therapeutics (http://crdd.osdd.net/raghava/imrna/).
Tumour-induced neoneurogenesis and perineural tumour growth: a mathematical approach
Authors: Lolas Georgios , Bianchi Arianna , Syrigos Konstantinos N. 
Published: February 2016

AbstractIt is well-known that tumours induce the formation of a lymphatic and a blood vasculature around themselves. A similar but far less studied process occurs in relation to the nervous system and is referred to as neoneurogenesis. The relationship between tumour progression and the nervous system is still poorly understood and is likely to involve a multitude of factors. It is therefore relevant to study tumour-nerve interactions through mathematical modelling: this may reveal the most significant factors of the plethora of interacting elements regulating neoneurogenesis. The present work is a first attempt to model the neurobiological aspect of cancer development through a system of differential equations. The model confirms the experimental observations that a tumour is able to promote nerve formation/elongation around itself, and that high levels of nerve growth factor and axon guidance molecules are recorded in the presence of a tumour. Our results also reflect the observation that high stress levels (represented by higher norepinephrine release by sympathetic nerves) contribute to tumour development and spread, indicating a mutually beneficial relationship between tumour cells and neurons. The model predictions suggest novel therapeutic strategies, aimed at blocking the stress effects on tumour growth and dissemination.
Quorum sensing activity of Citrobacter amalonaticus L8A, a bacterium isolated from dental plaque
Authors: Goh Share-Yuan , Khan Saad Ahmed , Tee Kok Keng , Abu Kasim Noor Hayaty , Yin Wai-Fong , Chan Kok-Gan 
Published: February 2016

AbstractCell-cell communication is also known as quorum sensing (QS) that happens in the bacterial cells with the aim to regulate their genes expression in response to increased cell density. In this study, a bacterium (L8A) isolated from dental plaque biofilm was identified as Citrobacter amalonaticus by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS). Its N-acylhomoserine-lactone (AHL) production was screened by using two types of AHL biosensors namely Chromobacterium violaceum CV026 and Escherichia coli [pSB401]. Citrobacter amalonaticus strain L8A was identified and confirmed producing numerous types of AHL namely N-butyryl-L-homoserine lactone (C4-HSL), N-hexanoyl-L-homoserine lactone (C6-HSL), N-octanoyl-L-homoserine lactone (C8-HSL) and N-hexadecanoyl-L-homoserine lactone (C16-HSL). We performed the whole genome sequence analysis of this oral isolate where its genome sequence reveals the presence of QS signal synthase gene and our work will pave the ways to study the function of the related QS genes in this bacterium.
The role of Xpert MTB/RIF in diagnosing pulmonary tuberculosis in post-mortem tissues
Authors: García-Basteiro Alberto L. , Ismail Mamudo R. , Carrilho Carla , Ussene Esperança , Castillo Paola , Chitsungo Dércio , Rodríguez Cristina , Lovane Lucília , Vergara Andrea , López-Varela Elisa , Mandomando Inacio , Lorenzoni Cesaltina , Ordi Jaume , Menéndez Clara , Bassat Quique , Martínez Miguel J. 
Published: February 2016

AbstractThe extent to which the Xpert MTB/RIF (Gene Xpert) contributes to tuberculosis (TB) diagnosis in samples other than sputum and cerebrospinal fluid remains uncertain. We aimed to assess the role of Xpert MTB/RIF for detecting M. tuberculosis in post-mortem tissues. We conducted a study among 30 complete diagnostic autopsies (CDA) performed at the Maputo Central Hospital (Mozambique). Lung tissues were screened for TB in all cases. In addition other tissues were tested when compatible lesions were identified in the histological exam. We used in-house real time PCR and LAMP assays to confirm the presence of M. tuberculosis DNA. The diagnosis of tuberculosis at death was established based on microbiological and histopathological results. Eight out of 30 cases (26.7%) were diagnosed of tuberculosis. Xpert had a sensitivity to detect TB in lung tissue of 87.5% (95% CI 47.3–99.7) and a specificity of 95.7% (95% CI: 78.1–99.9). In-house DNA amplification methods and Xpert showed 93.6% concordance for lung tissue and 100% concordance for brain and liver tissues. The final cause of death was attributable to tuberculosis in four cases. Xpert MTB/RIF may represent a valuable, easy-to perform technique for post-mortem TB diagnosis.
Add-on unidirectional elastic metamaterial plate cloak
Authors: Lee Min Kyung , Kim Yoon Young 
Published: February 2016

AbstractMetamaterial cloaks control the propagation of waves to make an object invisible or insensible. To manipulate elastic waves in space, a metamaterial cloak is typically embedded in a base system that includes or surrounds a target object. The embedding is undesirable because it structurally weakens or permanently alters the base system. In this study, we propose a new add-on metamaterial elastic cloak that can be placed over and mechanically coupled with a base structure without embedding. We designed an add-on type annular metamaterial plate cloak through conformal mapping, fabricated it and performed cloaking experiments in a thin-plate with a hole. Experiments were performed in a thin plate by using the lowest symmetric Lamb wave centered at 100 kHz. As a means to check the cloaking performance of the add-on elastic plate cloak, possibly as a temporary stress reliever or a so-called “stress bandage”, the degree of stress concentration mitigation and the recovery from the perturbed wave field due to a hole were investigated.
Determination of Scrub typhus Suggests a New Epidemic Focus in the Anhui Province of China
Authors: Cao Min , Che Li , Zhang Jinhai , Hu Jianli , Srinivas Swaminath , Xu Ruiyao , Guo Henbing , Zhang Yun , Wang Changjun , Feng Youjun 
Published: February 2016

AbstractIn 2007, 19 cases of a scrub typhus epidemic occurred within a week at a sports school in Mingguang County, Anhui Province, where no previous incidence of this mite borne disease had been reported. Sero-surveillance in 2009 indicated that 10 of the 100 school students possessed anti-Orientia tsutsugamushi antibodies. From 2009 to 2013, 60 small animals and 2250 mites were collected in the vicinity of the school. 5 of the Apodemus agrarius samples and 1 group of Leptotrombidium linhuaikongense tested positive via PCR for O. tsutsugamushi. Two strains of O. tsutsugamushi were identified by injecting Kun Ming (KM) mice peritoneally with the organs of either Apodemus agrarius or Leptotrombidium linhuaikongense. Apart from sharing 98% homology with the O. tsutsugamushi Yongworl strain, genes encoding the membrane protein from the two O. tsutsugamushi isolates shared >99% sequence homology with each other, reflecting the consistency of the pathogen in both the vector and the host. In addition, we also characterized a chronic scrub typhus infection in a local patient. The membrane protein gene fragment from the patient’s blood shared 99% homology with O. tsutsugamushi Gilliam strain, suggesting that more than one O. tsutsugamushi strain is present at this location.
Near-field engineering of Fano resonances in a plasmonic assembly for maximizing CARS enhancements
Authors: He Jinna , Fan Chunzhen , Ding Pei , Zhu Shuangmei , Liang Erjun 
Published: February 2016

AbstractSurface enhanced coherent anti-Stokes Raman scattering (SECARS) is a sensitive tool and promising for single molecular detection and chemical selective imaging. However, the enhancement factors (EF) were only 10~100 for colloidal silver and gold nanoparticles usually used as SECARS substrates. In this paper, we present a design of SECARS substrate consisting of three asymmetric gold disks and strategies for maximizing the EF by engineering near-field properties of the plasmonic Fano nanoassembly. It is found that the E-field “hot spots” corresponding to three different frequencies involved in SECARS process can be brought to the same spatial locations by tuning incident orientations, giving rise to highly confined SECARS “hot spots” with the EF reaching single-molecule sensitivity. Besides, an even higher EF of SECARS is achieved by introducing double Fano resonances in this plasmonic nanoassembly via further enlarging the sizes of the constituent disks. These findings put an important step forward to the plasmonic substrate design for SECARS as well as for other nonlinear optical processes.
Ankyrin Repeat Domain 1 is Up-regulated During Hepatitis C Virus Infection and Regulates Hepatitis C Virus Entry
Authors: Than Thoa T. , Tran Giao V. Q. , Son Kidong , Park Eun-Mee , Kim Seungtaek , Lim Yun-Sook , Hwang Soon B. 
Published: February 2016

AbstractHepatitis C virus (HCV) is highly dependent on host proteins for its own propagation. By transcriptome sequencing (RNA-Seq) analysis, we identified 30 host genes that were significantly differentially expressed in cell culture-grown HCV (HCVcc)-infected cells. Of these candidate genes, we selected and characterized ankyrin repeat domain 1 (ANKRD1). Here, we showed that protein expression of ANKRD1 was up-regulated in HCVcc-infected cells. We further showed that protein expression level of ANKRD1 was increased by nonstructural 5A (NS5A) protein. ANKRD1 specifically interacted with NS5A both in vitro and coimmunoprecipitation assays. Protein interaction was mediated through the domain II of NS5A and the C-terminal region of ANKRD1. Promoter activity of ANKRD1 was also increased by NS5A protein. Moreover, up-regulation of ANKRD1 expression was mediated through alteration in intracellular calcium homeostasis and ER stress in HCVcc-infected cells. We showed that silencing of ANKRD1 impaired HCV propagation without affecting HCV replication. By using HCV-like infectious particle (HCV-LP), we demonstrated that HCV single-cycle infection was drastically impaired in ANKRD1 knockdown cells. Finally, we verified that ANKRD1 was required for HCV entry. These data suggest that HCV coopts ANKRD1 for its own propagation and up-regulation of ANKRD1 may contribute to HCV-mediated liver pathogenesis.
Luminescence- and nanoparticle-mediated increase of light absorption by photoreceptor cells: Converting UV light to visible light
Authors: Li Lei , Sahi Sunil K. , Peng Mingying , Lee Eric B. , Ma Lun , Wojtowicz Jennifer L. , Malin John H. , Chen Wei 
Published: February 2016

AbstractWe developed new optic devices – singly-doped luminescence glasses and nanoparticle-coated lenses that convert UV light to visible light – for improvement of visual system functions. Tb3+ or Eu3+ singly-doped borate glasses or CdS-quantum dot (CdS-QD) coated lenses efficiently convert UV light to 542 nm or 613 nm wavelength narrow-band green or red light, or wide-spectrum white light and thereby provide extra visible light to the eye. In zebrafish (wild-type larvae and adult control animals, retinal degeneration mutants and light-induced photoreceptor cell degeneration models), the use of Tb3+ or Eu3+ doped luminescence glass or CdS-QD coated glass lenses provide additional visible light to the rod and cone photoreceptor cells and thereby improve the visual system functions. The data provide proof-of-concept for the future development of optic devices for improvement of visual system functions in patients who suffer from photoreceptor cell degeneration or related retinal diseases.
Associations of 6p21.3 Region with Age-related Macular Degeneration and Polypoidal Choroidal Vasculopathy
Authors: Ye Zimeng , Shuai Ping , Zhai Yaru , Li Fang , Jiang Lingxi , Lu Fang , Wen Feng , Huang Lulin , Zhang Dingding , Liu Xiaoqi , Lin Ying , Luo Huaichao , Zhang Houbin , Zhu Xianjun , Wu Zhengzheng , Yang Zhenglin , Gong Bo , Shi Yi 
Published: February 2016

AbstractNeovascular age-related macular degeneration (AMD) and polypoidal choroidal vasculopathy (PCV) are leading causes of blindness in aging populations. This study was conducted to investigate the associations of chromosome 6p21.3 region, includingCFB-SKIV2L-TNXB-FKBPL-NOTCH4genes, with both neovascular AMD and PCV. Six single nucleotide polymorphisms (SNPs) in this region and two known AMD-associated SNPs inCFH(rs800292) andHTRA1(rs11200638) were genotyped in a Han Chinese cohort composed of 490 neovascular AMD patients, 419 PCV patients and 1316 controls. Among the SNPs,TNXBrs12153855 andFKBPLrs9391734 conferred an increased susceptibility to neovascular AMD (P = 2.8 × 10−4and 0.001, OR = 1.80 and 1.76, respectively), whileSKIV2Lexerted a protective effect on neovascular AMD (P = 2.2 × 10−4, OR = 0.49). Rs12153855C and rs9391734A alleles could further increase the susceptibility to AMD in subjects with rs800292, rs11200638 and rs429608 risk alleles. However, only the association ofSKIV2Lrs429608 remained significant after adjusting for rs800292, rs11200638 and the other 5 SNPs. The protective haplotype AATGAG exhibited significant association with neovascular AMD (permutationP = 0.015, OR = 0.34). None of the SNPs in this region was associated with PCV. Association profiles of 6p21.3 region showed discrepancy between neovascular AMD and PCV, indicating possible molecular and pathological differences between these two retinal disorders.
Co-transfection of decorin and interleukin-10 modulates pro-fibrotic extracellular matrix gene expression in human tenocyte culture
Authors: Abbah Sunny A. , Thomas Dilip , Browne Shane , O’Brien Timothy , Pandit Abhay , Zeugolis Dimitrios I. 
Published: February 2016

AbstractExtracellular matrix synthesis and remodelling are driven by increased activity of transforming growth factor beta 1 (TGF-β1). In tendon tissue repair, increased activity of TGF-β1 leads to progressive fibrosis. Decorin (DCN) and interleukin 10 (IL-10) antagonise pathological collagen synthesis by exerting a neutralising effect via downregulation of TGF-β1. Herein, we report that the delivery of DCN and IL-10 transgenes from a collagen hydrogel system supresses the constitutive expression of TGF-β1 and a range of pro-fibrotic extracellular matrix genes.
Defining Core and Penumbra in Ischemic Stroke: A Voxel- and Volume-Based Analysis of Whole Brain CT Perfusion
Authors: Yu Yannan , Han Quan , Ding Xinfa , Chen Qingmeng , Ye Keqi , Zhang Sheng , Yan Shenqiang , Campbell Bruce C. V. , Parsons Mark W. , Wang Shaoshi , Lou Min 
Published: February 2016

AbstractWhole brain computed tomography perfusion (CTP) has the potential to select eligible patients for reperfusion therapy. We aimed to find the optimal thresholds on baseline CTP for ischemic core and penumbra in acute ischemic stroke. We reviewed patients with acute ischemic stroke in the anterior circulation, who underwent baseline whole brain CTP, followed by intravenous thrombolysis and perfusion imaging at 24 hours. Patients were divided into those with major reperfusion (to define the ischemic core) and minimal reperfusion (to define the extent of penumbra). Receiver operating characteristic (ROC) analysis and volumetric consistency analysis were performed separately to determine the optimal threshold by Youden’s Index and mean magnitude of volume difference, respectively. From a series of 103 patients, 22 patients with minimal-reperfusion and 47 with major reperfusion were included. Analysis revealed delay time ≥ 3 s most accurately defined penumbra (AUC = 0.813; 95% CI, 0.812-0.814, mean magnitude of volume difference = 29.1 ml). The optimal threshold for ischemic core was rCBF ≤ 30% within delay time ≥ 3 s (AUC = 0.758; 95% CI, 0.757-0.760, mean magnitude of volume difference = 10.8 ml). In conclusion, delay time ≥ 3 s and rCBF ≤ 30% within delay time ≥ 3 s are the optimal thresholds for penumbra and core, respectively. These results may allow the application of the mismatch on CTP to reperfusion therapy.
Retrogradation enthalpy does not always reflect the retrogradation behavior of gelatinized starch
Authors: Wang Shujun , Li Caili , Zhang Xiu , Copeland Les , Wang Shuo 
Published: February 2016

AbstractStarch retrogradation is a term used to define the process in which gelatinized starch undergoes a disorder-to-order transition. A thorough understanding of starch retrogradation behavior plays an important role in maintaining the quality of starchy foods during storage. By means of DSC, we have demonstrated for the first time that at low water contents, the enthalpy change of retrograded starch is higher than that of native starch. In terms of FTIR and Raman spectroscopic results, we showed that the molecular order of reheated retrograded starch samples is lower than that of DSC gelatinized starch. These findings have led us to conclude that enthalpy change of retrograded starch at low water contents involves the melting of recrystallized starch during storage and residual starch crystallites after DSC gelatinization and that the endothermic transition of retrograded starch gels at low water contents does not fully represent the retrogradation behavior of starch. Very low or high water contents do not favor the occurrence of starch retrogradation.
Silicene nanomeshes: bandgap opening by bond symmetry breaking and uniaxial strain
Authors: Jia Tian-Tian , Fan Xin-Yu , Zheng Meng-Meng , Chen Gang 
Published: February 2016

AbstractBased on the first-principles calculations, we have investigated in detail the bandgap opening of silicene nanomeshes. Different to the mechanism of bandgap opening induced by the sublattice equivalence breaking, the method of degenerate perturbation through breaking the bond symmetry could split the π-like bands in the inversion symmetry preserved silicene nanomeshes, resulting into the πa1 − πa2and πz1 − πz2band sets with sizable energy intervals. Besides the bandgap opening in the nanomeshes with Dirac point being folded to Γ point, the split energy intervals are however apart away from Fermi level to leave the semimetal nature unchanged for the other nanomeshes with Dirac points located at opposite sides of Γ point as opposite pseudo spin wave valleys. A mass bandgap could be then opened at the aid of uniaxial strain to transfer the nanomesh to be semiconducting, whose width could be continuously enlarged until reaching its maximum Emax. Moreover, the Emaxcould also be tuned by controlling the defect density in silicene nanomeshes. These studies could contribute to the understanding of the bandgap engineering of silicene-based nanomaterials to call for further investigations on both theory and experiment.
Suhuang antitussive capsule at lower doses attenuates airway hyperresponsiveness, inflammation and remodeling in a murine model of chronic asthma
Authors: Zhang Chao , Zhang Lan-Hong , Wu Yin-Fang , Lai Tian-Wen , Wang Hai-Sheng , Xiao Hui , Che Luan-Qing , Ying Song-Min , Li Wen , Chen Zhi-Hua , Shen Hua-Hao 
Published: February 2016

AbstractSuhuang antitussive capsule (Suhuang), a traditional Chinese medication, is found effective in treating chronic cough and cough variant asthma (CVA). This study aimed to determine the possible effects and underlying mechanisms of Suhuang on chronic ovalbumin (OVA)-induced airway hyperresponsiveness (AHR), inflammation and remodeling in mice. Mice were randomly assigned to six experimental groups: control, OVA model with or without Suhuang (low dose: 3.5 g/kg, middle dose: 7.0 g/kg, high dose: 14.0 g/kg), or dexamethasone (2.5 mg/kg). AHR, inflammatory cells, cytokines in bronchoalveolar lavage fluid (BALF), lung pathology, mucus production and airway remodeling were examined. We found Suhuang treated at lower doses effectively inhibited OVA-induced AHR, airway inflammation, mucus production and collagen deposition around the airway. High dose of Suhuang reduced most of the inflammatory hallmarks while exerted inconsiderable effects on the number of macrophages in BALF and AHR. At all doses, Suhuang significantly reduced the levels of interlukin (IL) -13 and transforming growth factor (TGF)-β1, but had little effects on IL-4, IL-5, IL-17A and interferon (IFN)-γ. Thus, Suhuang administration alleviates the pathological changes of chronic asthma likely through inhibition of IL-13 and TGF-β1. Suhuang might be a promising therapy for patients with allergic asthma in the future.