bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimation of nonclassical independent Gaussian processes by classical interferometry
Authors: Ruppert László , Filip Radim 
Published: January 2017

AbstractWe propose classical interferometry with low-intensity thermal radiation for the estimation of nonclassical independent Gaussian processes in material samples. We generally determine the mean square error of the phase-independent parameters of an unknown Gaussian process, considering a noisy source of radiation the phase of which is not locked to the pump of the process. We verify the sufficiency of passive optical elements in the interferometer, active optical elements do not improve the quality of the estimation. We also prove the robustness of the method against the noise and loss in both interferometric channels and the sample. The proposed method is suitable even for the case when a source of radiation sufficient for homodyne detection is not available.
Promotion of natural tooth repair by small molecule GSK3 antagonists
Authors: Neves Vitor C. M. , Babb Rebecca , Chandrasekaran Dhivya , Sharpe Paul T. 
Published: January 2017

AbstractThe restoration of dentine lost in deep caries lesions in teeth is a routine and common treatment that involves the use of inorganic cements based on calcium or silicon-based mineral aggregates. Such cements remain in the tooth and fail to degrade and thus normal mineral volume is never completely restored. Here we describe a novel, biological approach to dentine restoration that stimulates the natural formation of reparative dentine via the mobilisation of resident stem cells in the tooth pulp. Biodegradable, clinically-approved collagen sponges are used to deliver low doses of small molecule glycogen synthase kinase (GSK-3) antagonists that promote the natural processes of reparative dentine formation to completely restore dentine. Since the carrier sponge is degraded over time, dentine replaces the degraded sponge leading to a complete, effective natural repair. This simple, rapid natural tooth repair process could thus potentially provide a new approach to clinical tooth restoration.
Superconductivity Bordering Rashba Type Topological Transition
Authors: Jin M. L. , Sun F. , Xing L. Y. , Zhang S. J. , Feng S. M. , Kong P. P. , Li W. M. , Wang X. C. , Zhu J. L. , Long Y. W. , Bai H. Y. , Gu C. Z. , Yu R. C. , Yang W. G. , Shen G. Y. , Zhao Y. S. , Mao H. K. , Jin C. Q. 
Published: January 2017

AbstractStrong spin orbital interaction (SOI) can induce unique quantum phenomena such as topological insulators, the Rashba effect, or p-wave superconductivity. Combining these three quantum phenomena into a single compound has important scientific implications. Here we report experimental observations of consecutive quantum phase transitions from a Rashba type topological trivial phase to topological insulator state then further proceeding to superconductivity in a SOI compound BiTeI tuned via pressures. The electrical resistivity measurement with V shape change signals the transition from a Rashba type topological trivial to a topological insulator phase at 2 GPa, which is caused by an energy gap close then reopen with band inverse. Superconducting transition appears at 8 GPa with a critical temperature TC of 5.3 K. Structure refinements indicate that the consecutive phase transitions are correlated to the changes in the Bi–Te bond and bond angle as function of pressures. The Hall Effect measurements reveal an intimate relationship between superconductivity and the unusual change in carrier density that points to possible unconventional superconductivity.
Identification of small RNAs in extracellular vesicles from the commensal yeast Malassezia sympodialis
Authors: Rayner Simon , Bruhn Sören , Vallhov Helen , Andersson Anna , Billmyre R. Blake , Scheynius Annika 
Published: January 2017

AbstractMalassezia is the dominant fungus in the human skin mycobiome and is associated with common skin disorders including atopic eczema (AE)/dermatitis. Recently, it was found that Malassezia sympodialis secretes nanosized exosome-like vesicles, designated MalaEx, that carry allergens and can induce inflammatory cytokine responses. Extracellular vesicles from different cell-types including fungi have been found to deliver functional RNAs to recipient cells. In this study we assessed the presence of small RNAs in MalaEx and addressed if the levels of these RNAs differ when M. sympodialis is cultured at normal human skin pH versus the elevated pH present on the skin of patients with AE. The total number and the protein concentration of the released MalaEx harvested after 48 h culture did not differ significantly between the two pH conditions nor did the size of the vesicles. From small RNA sequence data, we identified a set of reads with well-defined start and stop positions, in a length range of 16 to 22 nucleotides consistently present in the MalaEx. The levels of small RNAs were not significantly differentially expressed between the two different pH conditions indicating that they are not influenced by the elevated pH level observed on the AE skin.
The histone 3 lysine 9 methyltransferase inhibitor chaetocin improves prognosis in a rat model of high salt diet-induced heart failure
Authors: Ono Tomohiko , Kamimura Naomi , Matsuhashi Tomohiro , Nagai Toshihiro , Nishiyama Takahiko , Endo Jin , Hishiki Takako , Nakanishi Tsuyoshi , Shimizu Noriaki , Tanaka Hirotoshi , Ohta Shigeo , Suematsu Makoto , Ieda Masaki , Sano Motoaki , Fukuda Keiichi , Kaneda Ruri 
Published: January 2017

AbstractHistone acetylation has been linked to cardiac hypertrophy and heart failure. However, the pathological implications of changes in histone methylation and the effects of interventions with histone methyltransferase inhibitors for heart failure have not been fully clarified. Here, we focused on H3K9me3 status in the heart and investigated the effects of the histone H3K9 methyltransferase inhibitor chaetocin on prognoses in Dahl salt-sensitive rats, an animal model of chronic heart failure. Chaetocin prolonged survival and restored mitochondrial dysfunction. ChIP-seq analysis demonstrated that chronic stress to the heart induced H3K9me3 elevation in thousands of repetitive elements, including intronic regions of mitochondria-related genes, such as the gene encoding peroxisome proliferator-activated receptor-gamma coactivator 1 alpha. Furthermore, chaetocin reversed this effect on these repetitive loci. These data suggested that excessive heterochromatinization of repetitive elements of mitochondrial genes in the failing heart may lead to the silencing of genes and impair heart function. Thus, chaetocin may be a potential therapeutic agent for chronic heart failure.
Production of itaconate by whole-cell bioconversion of citrate mediated by expression of multiple cis-aconitate decarboxylase (cadA) genes in Escherichia coli
Authors: Kim Junyoung , Seo Hyung-Min , Bhatia Shashi Kant , Song Hun-Seok , Kim Jung-Ho , Jeon Jong-Min , Choi Kwon-Young , Kim Wooseong , Yoon Jeong-Jun , Kim Yun-Gon , Yang Yung-Hun 
Published: January 2017

AbstractItaconate, a C5 unsaturated dicarboxylic acid, is an important chemical building block that is used in manufacturing high-value products, such as latex and superabsorbent polymers. Itaconate is produced by fermentation of sugars by the filamentous fungus Aspergillus terreus. However, fermentation by A. terreus involves a long fermentation period and the formation of various byproducts, resulting in high production costs. E. coli has been developed as an alternative for producing itaconate. However, fermentation of glucose gives low conversion yields and low productivity. Here, we report the whole-cell bioconversion of citrate to itaconate with enhanced aconitase and cis-aconitate decarboxylase activities by controlling the expression of multiple cadA genes. In addition, this bioconversion system does not require the use of buffers, which reduces the production cost and the byproducts released during purification. Using this whole-cell bioconversion system, we were able to catalyze the conversion of 319.8 mM of itaconate (41.6 g/L) from 500 mM citrate without any buffer system or additional cofactors, with 64.0% conversion in 19 h and a productivity of 2.19 g/L/h. Our bioconversion system suggests very high productivity for itaconate production.
U24 from Roseolovirus interacts strongly with Nedd4 WW Domains
Authors: Sang Yurou , Zhang Rui , Scott Walter R. P. , Creagh A. Louise , Haynes Charles A. , Straus Suzana K. 
Published: January 2017

AbstractU24 is a protein found in both roseoloviruses Human Herpes Virus type 6 and 7 (HHV-6 and HHV-7), with an N-terminus that is rich in prolines (PY motif in both HHV-6A and 7; PxxP motif in HHV-6A). Previous work has shown that the interaction between U24 and WW domains is important for endocytic recycling of T-cell receptors, but a cognate ligand was never identified. In this contribution, data was obtained from pull-downs, ITC, NMR and molecular dynamics simulations to show that a specific interaction exists between U24 and Nedd4 WW domains. ITC experiments were also carried out for U24 from HHV-6A phosphorylated at Thr6 (pU24-6A) and a peptide containing the PY motif from Nogo-A, a protein implicated in both the initial inflammatory and the neurodegenerative phases of multiple sclerosis (MS). The results suggest that phosphorylation of U24 from HHV-6A may be crucial for its potential role in MS.
Validation of suitable normalizers for miR expression patterns analysis covering tumour heterogeneity
Authors: Morata-Tarifa C. , Picon-Ruiz M. , Griñan-Lison C. , Boulaiz H. , Perán M. , Garcia M. A. , Marchal J. A. 
Published: January 2017

AbstractOncogenic microRNAs (miRs) have emerged as diagnostic biomarkers and novel molecular targets for anti-cancer drug therapies. Real-time quantitative PCR (qPCR) is one of the most powerful techniques for analyzing miRs; however, the use of unsuitable normalizers might bias the results. Tumour heterogeneity makes even more difficult the selection of an adequate endogenous normalizer control. Here, we have evaluated five potential referenced small RNAs (U6, rRNA5s, SNORD44, SNORD24andhsa-miR-24c-3p) using RedFinder algorisms to perform a stability expression analysis in i) normal colon cells, ii) colon and breast cancer cell lines and iii) cancer stem-like cell subpopulations. We identifiedSNORD44as a suitable housekeeping gene for qPCR analysis comparing normal and cancer cells. However, this small nucleolar RNA was not a useful normalizer for cancer stem-like cell subpopulations versus subpopulations without stemness properties. In addition, we show for the first time thathsa-miR-24c-3pis the most stable normalizer for comparing these two subpopulations. Also, we have identified by bioinformatic and qPCR analysis, different miR expression patterns in colon cancer versus non tumour cells using the previously selected suitable normalizers. Our results emphasize the importance of select suitable normalizers to ensure the robustness and reliability of qPCR data for analyzing miR expression.
Mechanically Controlled Electron Transfer in a Single-Polypeptide Transistor
Authors: Sheu Sheh-Yi , Yang Dah-Yen 
Published: January 2017

AbstractProteins are of interest in nano-bio electronic devices due to their versatile structures, exquisite functionality and specificity. However, quantum transport measurements produce conflicting results due to technical limitations whereby it is difficult to precisely determine molecular orientation, the nature of the moieties, the presence of the surroundings and the temperature; in such circumstances a better understanding of the protein electron transfer (ET) pathway and the mechanism remains a considerable challenge. Here, we report an approach to mechanically drive polypeptide flip-flop motion to achieve a logic gate with ON and OFF states during protein ET. We have calculated the transmission spectra of the peptide-based molecular junctions and observed the hallmarks of electrical current and conductance. The results indicate that peptide ET follows an NC asymmetric process and depends on the amino acid chirality and α-helical handedness. Electron transmission decreases as the number of water molecules increases, and the ET efficiency and its pathway depend on the type of water-bridged H-bonds. Our results provide a rational mechanism for peptide ET and new perspectives on polypeptides as potential candidates in logic nano devices.
Topological transformations in proteins: effects of heating and proximity of an interface
Authors: Zhao Yani , Chwastyk Mateusz , Cieplak Marek 
Published: January 2017

AbstractUsing a structure-based coarse-grained model of proteins, we study the mechanism of unfolding of knotted proteins through heating. We find that the dominant mechanisms of unfolding depend on the temperature applied and are generally distinct from those identified for folding at its optimal temperature. In particular, for shallowly knotted proteins, folding usually involves formation of two loops whereas unfolding through high-temperature heating is dominated by untying of single loops. Untying the knots is found to generally precede unfolding unless the protein is deeply knotted and the heating temperature exceeds a threshold value. We then use a phenomenological model of the air-water interface to show that such an interface can untie shallow knots, but it can also make knots in proteins that are natively unknotted.
Determining the migration duration of rice leaf folder (Cnaphalocrocis medinalis (Guenée)) moths using a trajectory analytical approach
Authors: Wang Feng-Ying , Yang Fan , Lu Ming-Hong , Luo Shan-Yu , Zhai Bao-Ping , Lim Ka-Sing , McInerney Caitríona E. , Hu Gao 
Published: January 2017

AbstractMany moths finish their long distance migration after consecutive nights, but little is known about migration duration and distance. This information is key to predicting migration pathways and understanding their evolution. Tethered flight experiments have shown that ovarian development of rice leaf folder (Cnaphalocrocis medinalis [Guenée]) moths was accelerated and synchronized by flight in the first three nights, whereby most females were then matured for mating and reproduction. Thus, it was supposed that this moth might fly three nights to complete its migration. To test this hypothesis, 9 year’s field data for C. medinalis was collected from Nanning, Guangxi Autonomous Region in China. Forward trajectories indicated that most moths arrived at suitable breeding areas after three nights’ flight. Thus, for C. medinalis this migration duration and distance was a reasonable adaptation to the geographic distribution of suitable habitat. The development of female moth ovaries after three consecutive night flights appears to be a well-balanced survival strategy for this species to strike between migration and reproduction benefits. Hence, an optimum solution of migration-reproduction trade-offs in energy allocation evolved in response to the natural selection on migration route and physiological traits.
Reconstruction of Rift Valley fever transmission dynamics in Madagascar: estimation of force of infection from seroprevalence surveys using Bayesian modelling
Authors: Olive Marie-Marie , Grosbois Vladimir , Tran Annelise , Nomenjanahary Lalaina Arivony , Rakotoarinoro Mihaja , Andriamandimby Soa-Fy , Rogier Christophe , Heraud Jean-Michel , Chevalier Veronique 
Published: January 2017

AbstractThe force of infection (FOI) is one of the key parameters describing the dynamics of transmission of vector-borne diseases. Following the occurrence of two major outbreaks of Rift Valley fever (RVF) in Madagascar in 1990–91 and 2008–09, recent studies suggest that the pattern of RVF virus (RVFV) transmission differed among the four main eco-regions (East, Highlands, North-West and South-West). Using Bayesian hierarchical models fitted to serological data from cattle of known age collected during two surveys (2008 and 2014), we estimated RVF FOI and described its variations over time and space in Madagascar. We show that the patterns of RVFV transmission strongly differed among the eco-regions. In the North-West and Highlands regions, these patterns were synchronous with a high intensity in mid-2007/mid-2008. In the East and South-West, the peaks of transmission were later, between mid-2008 and mid-2010. In the warm and humid northwestern eco-region favorable to mosquito populations, RVFV is probably transmitted all year-long at low-level during inter-epizootic period allowing its maintenance and being regularly introduced in the Highlands through ruminant trade. The RVF surveillance of animals of the northwestern region could be used as an early warning indicator of an increased risk of RVF outbreak in Madagascar.
The metastasis suppressor RARRES3 as an endogenous inhibitor of the immunoproteasome expression in breast cancer cells
Authors: Anderson Alison M. , Kalimutho Murugan , Harten Sarah , Nanayakkara Devathri M. , Khanna Kum Kum , Ragan Mark A. 
Published: January 2017

AbstractIn breast cancer metastasis, the dynamic continuum involving pro- and anti-inflammatory regulators can become compromised. Over 600 genes have been implicated in metastasis to bone, lung or brain but how these genes might contribute to perturbation of immune function is poorly understood. To gain insight, we adopted a gene co-expression network approach that draws on the functional parallels between naturally occurring bone marrow-derived mesenchymal stem cells (BM-MSCs) and cancer stem cells (CSCs). Our network analyses indicate a key role for metastasis suppressor RARRES3, including potential to regulate the immunoproteasome (IP), a specialized proteasome induced under inflammatory conditions. Knockdown of RARRES3 in near-normal mammary epithelial and breast cancer cell lines increases overall transcript and protein levels of the IP subunits, but not of their constitutively expressed counterparts. RARRES3 mRNA expression is controlled by interferon regulatory factor IRF1, an inducer of the IP, and is sensitive to depletion of the retinoid-related receptor RORA that regulates various physiological processes including immunity through modulation of gene expression. Collectively, these findings identify a novel regulatory role for RARRES3 as an endogenous inhibitor of IP expression, and contribute to our evolving understanding of potential pathways underlying breast cancer driven immune modulation.
Therapeutic Effects of Human Umbilical Cord-Derived Mesenchymal Stem Cells in Acute Lung Injury Mice
Authors: Zhu Hua , Xiong Yi , Xia Yunqiu , Zhang Rong , Tian Daiyin , Wang Ting , Dai Jihong , Wang Lijia , Yao Hongbing , Jiang Hong , Yang Ke , Liu Enmei , Shi Yujun , Fu Zhou , Gao Li , Zou Lin 
Published: January 2017

AbstractThe incidence and mortality of acute lung injury (ALI)/acute respiratory distress syndrome (ARDS) are still very high, but stem cells show some promise for its treatment. Here we found that intratracheal administration of human umbilical cord-mesenchymal stem cells (UC-MSCs) significantly improved survival and attenuated the lung inflammation in lipopolysaccharide (LPS)-induced ALI mice. We also used the proteins-chip and bioinformatics to analyze interactions between UC-MSCs treatment and immune-response alternations of ALI mice. Then we demonstrated that UC-MSCs could inhibit the inflammatory response of mouse macrophage in ALI mice, as well as enhance its IL-10 expression. We provide data to support the concept that the therapeutic capacity of UC-MSCs for ALI was primarily through paracrine secretion, particularly of prostaglandin-E2 (PGE2). Furthermore, we showed that UC-MSCs might secrete a panel of factors including GM-CSF, IL-6 and IL-13 to ameliorate ALI. Our study suggested that UC-MSCs could protect LPS-induced ALI model by immune regulation and paracrine factors, indicating that UC-MSCs should be a promising strategy for ALI/ARDS.
Controlled generation of high-intensity optical rogue waves by induced modulation instability
Authors: Zhao Saili , Yang Hua , Chen Nengsong , Zhao Chujun 
Published: January 2017

AbstractOptical rogue waves are featured as the generation of high amplitude events at low probability in optical systems. Moreover, the formation of optical rogue waves is unpredictable and transient in photonic crystal fibers. In this paper, we put forward a method to generate high-intensity optical rogue waves in a more controlled way based on induced modulation instability, which can suppress the noise effect and hence play a leading role in the process of pulse evolution. Our numerical simulations indicate that the generation of rogue wave can be controlled when seeding at the optimal modulation frequency and the intensity of rogue wave can be enhanced with appropriate modulation depth. Further, high-intensity rogue wave can also be ejected in the fiber with a shorter propagation length by regulating the modulation depth. These results all provide a better understanding of optical rogue wave, which can contribute to the generation of tunable long-wavelength spectral components and selective excitation of mid-infrared supercontinuum.
Association of regular physical activity with total and cause-specific mortality among middle-aged and older Chinese: a prospective cohort study
Authors: Zhou Yun , Zhang Runbo , Liu Yuewei , Guo Yanjun , Wang Dongming , He Meian , Yuan Jing , Liang Yuan , Zhang Xiaomin , Wang Youjie , Guo Huan , Wei Sheng , Miao Xiaoping , Yao Ping , Wu Tangchun , Chen Weihong 
Published: January 2017

AbstractAssociation between physical activity and mortality has rarely been investigated among the Chinese population. Furthermore, the most appropriate amount of physical activity for longevity benefits remains unclear. We used data from the Dongfeng-Tongji cohort, including 24,606 middle-aged and older retired adults in 2008 and followed to 2013, to quantify linear and non-linear dose-response relationships between regular physical activity and mortality risks by Cox proportional hazards model. Compared with participants who did not engage in regular physical activity, those performing regular physical activity had significantly 46%, 56%, and 49% decreased risks of mortality from all causes, circulatory, and respiratory diseases, respectively. Each one-SD increase in regular physical activity was associated with 32% decrease of respiratory disease mortality. There were significant nonlinear dose-response associations between regular physical activity and mortality from all causes and circulatory diseases. Mortality risks decreased monotonically with increased regular physical activity amount, and appeared to reach a threshold at around 100 MET-hours/week. More mortality benefits were found among non-smokers than that among current and former smokers. Our results suggest that middle-aged and older Chinese adults can achieve mortality benefits from regular physical activity at the WHO recommended minimum, and the benefit threshold appears at approximately 100 MET hours/week.