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  • 1
    Electronic Resource
    Electronic Resource
    Amsterdam : Elsevier
    Physics Letters B 294 (1992), S. 466-478 
    ISSN: 0370-2693
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Physics
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    Amsterdam : Elsevier
    Physics Letters B 317 (1993), S. 474-484 
    ISSN: 0370-2693
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Physics
    Type of Medium: Electronic Resource
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  • 3
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    MDPI Publishing
    Publication Date: 2018-04-03
    Description: Sustainability, Vol. 10, Pages 1043: Network Analysis on Green Technology in National Research and Development Projects in Korea Sustainability doi: 10.3390/su10041043 Authors: Jae Jeong Inje Kang Ki Choi Byeong-Hee Lee This study examined how green technology (GT) has evolved recently in the domain of national research and development (R&D) in Korea. The analysis considered social network analysis by using keywords of national R&D projects in environmentally benign (‘green’ in this paper) technologies. Data for analysis were collected from the R&D database of the National Science and Technology Information Service (NTIS). By selecting the official GT category in the NTIS’s database, we gathered 53,896 GT R&D projects from 2011 to 2016 inclusive. By constructing a co-occurrence matrix with keywords, we conducted a centrality analysis (including degree, closeness, betweenness centrality) and visualized the network matrix to display a cluster map. This study presents the following findings: (1) the chronical trends of GT R&D, (2) focused fields of GT R&D, (3) the relations between keywords and GTs, and (4) the characteristics and problems in GT R&D. The paper ends with suggested policy implications to boost national GT R&D and to develop GTs in the future.
    Electronic ISSN: 2071-1050
    Topics: Energy, Environment Protection, Nuclear Power Engineering
    Published by MDPI Publishing
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  • 4
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    Elsevier
    Publication Date: 2018-04-03
    Description: Publication date: 1 June 2018 Source: Topology and its Applications, Volume 241 Author(s): Ziemowit Kostana Let ( X , + ) denote ( R , + ) or ( 2 ω , + 2 ) . We prove that for any meagre set F ⊆ X there exists a subgroup G ≤ X without the Baire property, disjoint with some translation of F . We point out several consequences of this fact and indicate why analogous result for the measure cannot be established in ZFC. We extend proof techniques from [1] .
    Print ISSN: 0166-8641
    Electronic ISSN: 1879-3207
    Topics: Mathematics
    Published by Elsevier
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  • 5
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    MDPI Publishing
    Publication Date: 2018-04-03
    Description: Symmetry, Vol. 10, Pages 92: Applying Genetic Programming with Similar Bug Fix Information to Automatic Fault Repair Symmetry doi: 10.3390/sym10040092 Authors: Geunseok Yang Youngjun Jeong Kyeongsic Min Jung-won Lee Byungjeong Lee Owing to the high complexity of recent software products, developers cannot avoid major/minor mistakes, and software bugs are generated during the software development process. When developers manually modify a program source code using bug descriptions to fix bugs, their daily workloads and costs increase. Therefore, we need a way to reduce their workloads and costs. In this paper, we propose a novel automatic fault repair method by using similar bug fix information based on genetic programming (GP). First, we searched for similar buggy source codes related to the new given buggy code, and then we searched for a fixed the buggy code related to the most similar source code. Next, we transformed the fixed code into abstract syntax trees for applying GP and generated the candidate program patches. In this step, we verified the candidate patches by using a fitness function based on given test cases to determine whether the patch was valid or not. Finally, we produced program patches to fix the new given buggy code.
    Electronic ISSN: 2073-8994
    Topics: Mathematics , Physics
    Published by MDPI Publishing
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  • 6
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    MDPI Publishing
    Publication Date: 2018-04-03
    Description: Symmetry, Vol. 10, Pages 93: Big Data Analysis for Personalized Health Activities: Machine Learning Processing for Automatic Keyword Extraction Approach Symmetry doi: 10.3390/sym10040093 Authors: Jun-Ho Huh The obese population is increasing rapidly due to the change of lifestyle and diet habits. Obesity can cause various complications and is becoming a social disease. Nonetheless, many obese patients are unaware of the medical treatments that are right for them. Although a variety of online and offline obesity management services have been introduced, they are still not enough to attract the attention of users and are not much of help to solve the problem. Obesity healthcare and personalized health activities are the important factors. Since obesity is related to lifestyle habits, eating habits, and interests, I concluded that the big data analysis of these factors could deduce the problem. Therefore, I collected big data by applying the machine learning and crawling method to the unstructured citizen health data in Korea and the search data of Naver, which is a Korean portal company, and Google for keyword analysis for personalized health activities. It visualized the big data using text mining and word cloud. This study collected and analyzed the data concerning the interests related to obesity, change of interest on obesity, and treatment articles. The analysis showed a wide range of seasonal factors according to spring, summer, fall, and winter. It also visualized and completed the process of extracting the keywords appropriate for treatment of abdominal obesity and lower body obesity. The keyword big data analysis technique for personalized health activities proposed in this paper is based on individual’s interests, level of interest, and body type. Also, the user interface (UI) that visualizes the big data compatible with Android and Apple iOS. The users can see the data on the app screen. Many graphs and pictures can be seen via menu, and the significant data values are visualized through machine learning. Therefore, I expect that the big data analysis using various keywords specific to a person will result in measures for personalized treatment and health activities.
    Electronic ISSN: 2073-8994
    Topics: Mathematics , Physics
    Published by MDPI Publishing
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  • 7
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    MDPI Publishing
    In: Water
    Publication Date: 2018-04-03
    Description: Water, Vol. 10, Pages 417: The Suitability of Pozzolan as Admixing Aggregate for Fe0-Based Filters Water doi: 10.3390/w10040417 Authors: Arnaud Ndé-Tchoupé Suzanne Makota Achille Nassi Hu Rui Chicgoua Noubactep Continuous gravity-fed column experiments using the methylene blue (MB) discoloration method were performed to characterize the suitability of a pozzolan (PZ) specimen as alternative admixing aggregate for metallic iron filters (Fe0-filters). Investigated systems were: (i) pure sand, (ii) pure PZ, (iii) pure Fe0, (iv) Fe0/sand, (v) Fe0/PZ, and (vi) Fe0/sand/PZ. The volumetric proportion of Fe0 was 25%. The volumetric proportions of the Fe0/sand/PZ system was 25/45/30. The initial MB concentration was 2.0 mg·L−1, 6.0 g of Fe0 was used, and the experiments lasted for 46 days. The individual systems were fed with 3.9 to 8.4 L (7.80 to 16.69 mg of MB) and were characterized by the time-dependent changes of: (i) the pH value, (ii) the iron breakthrough, (iii) the MB breakthrough, and (iv) the hydraulic conductivity. Results showed that the Fe0/sand/PZ system was the most efficient. This ternary system was also the most permeable and therefore the most sustainable. The suitability of MB as a powerful operative indicator for the characterization of processes in the Fe0/H2O system was confirmed. The tested PZ is recommended as an alternative material for efficient but sustainable Fe0 filters.
    Electronic ISSN: 2073-4441
    Topics: Energy, Environment Protection, Nuclear Power Engineering
    Published by MDPI Publishing
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  • 8
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    MDPI Publishing
    In: Water
    Publication Date: 2018-04-03
    Description: Water, Vol. 10, Pages 416: A Hybrid Model for Annual Runoff Time Series Forecasting Using Elman Neural Network with Ensemble Empirical Mode Decomposition Water doi: 10.3390/w10040416 Authors: Xike Zhang Qiuwen Zhang Gui Zhang Zhiping Nie Zifan Gui Because of the complex nonstationary and nonlinear characteristics of annual runoff time series, it is difficult to achieve good prediction accuracy. In this paper, ensemble empirical mode decomposition (EEMD) coupled with Elman neural network (ENN)—namely the EEMD-ENN model—is proposed to reduce the difficulty of modeling and to improve prediction accuracy. The annual runoff time series from four hydrological stations in the lower reaches of the four main rivers in the Dongting Lake basin, and one at the outlet of the lake, are used as a case study to test this new hybrid model. First, the nonstationary and nonlinear original annual runoff time series are decomposed to several relatively stable intrinsic mode functions (IMFs) by using EEMD. Then, each IMF is predicted by using ENN. Next, the predicted results of each IMF are aggregated as the final prediction results for the original annual runoff time series. Finally, five statistical indices are adopted to measure the performance of the proposed hybrid model compared with a back propagation (BP) neural network, EEMD-BP, and ENN models—mean absolute error (MAE), mean absolute percentage error (MAPE), root mean square error (RMSE), Pearson correlation coefficient (R) and Nash–Sutcliffe coefficient of efficiency (NSCE). The performance comparison results show that the proposed hybrid model performs better than the BP, EEMD-BP or ENN models. In short, the developed hybrid model can provide a significant improvement in annual runoff time series forecasting.
    Electronic ISSN: 2073-4441
    Topics: Energy, Environment Protection, Nuclear Power Engineering
    Published by MDPI Publishing
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  • 9
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    MDPI Publishing
    In: Water
    Publication Date: 2018-04-03
    Description: Water, Vol. 10, Pages 415: Planning Water Resources in an Agroforest Ecosystem for Improvement of Regional Ecological Function Under Uncertainties Water doi: 10.3390/w10040415 Authors: Xueting Zeng Cong Chen Yinan Sheng Chunjiang An Xiangming Kong Shan Zhao Guohe Huang In this study, an agroforestry ecosystem project (AEP) is developed for confronting the conflict between agricultural development and forest protection. A fuzzy stochastic programming with Laplace scenario analysis (FSL) is proposed for planning water resources in an AEP issue under uncertainties. FSL can not only deal with spatial and temporal variations of hydrologic elements and meteorological conditions; but also handle uncertainties that are expressed in terms of probability, possibility distributions and fuzzy sets; meanwhile, policy scenario analysis with Laplace’s criterion (PSL) is introduced to handle probability of each scenario occurrence under the supposition of no data available. The developed FSL can be applied to an AEP issue in Xixian county, located in north of China. The result of ecological effects, water allocation patterns, pollution mitigation schemes and system benefits under various scenarios are obtained, which can support policymakers adjusting current strategy to improve regional ecological function with cost-effective and sustainable manners. Meanwhile, it can support generating a robust water plan for regional sustainability in an AEP issue under uncertainties.
    Electronic ISSN: 2073-4441
    Topics: Energy, Environment Protection, Nuclear Power Engineering
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  • 10
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    MDPI Publishing
    In: Forests
    Publication Date: 2018-04-04
    Description: Forests, Vol. 9, Pages 182: Ortet Age and Clonal Effects on Growth and Market Value of Fraser Fir (Abies fraseri) Grafts as Christmas Trees Forests doi: 10.3390/f9040182 Authors: Eric Hinesley John Frampton Buddy Deal Earl Deal Grafting provides a means to clonally produce Fraser fir (Abies fraseri (Pursh) Poir.) Christmas trees that have desirable traits such as faster growth, greater crown density, increased pest resistance, or more desirable foliage attributes than seedling stock. Grafting Fraser fir to disease resistant rootstocks also provides a means to ameliorate the impact of root rot, predominantly caused by Phytophthora cinnamomi Rands. The influence of ortet age on growth and market value of grafts has not been studied for Fraser fir Christmas tree production. A field trial was established in 2004 near Independence, Virginia (USA), with the objectives of assessing (1) the effect of ortet age (stock plants = 6 to 8, 10 to 12, and 18 to 20 years) and (2) shearing regimes (fixed leader length versus variable leader length) on growth, quality, and market value of Fraser fir Christmas trees. Commercial height, Christmas tree grade (based on U. S. Dept. of Agric. standards), and net present value (US dollars) were assessed at the time of harvest. Cone damage to quality was rated after 8 years in the field. Scions from Fraser fir Christmas trees 2 m or taller produced grafts that expressed maturation, resulting in lower tree quality, heavier cone damage, and decreased market value compared to seedling stock. In contrast, the quality and market value of grafts was similar to that of seedlings when scions were collected from young Fraser fir Christmas trees. For Christmas tree production, scions should be collected from the upper whorls of trees no older than 2 to 3 years in the field (6 to 8 years from seed). The effect of age on Fraser fir clones varies so that pre-screening might identify some older selections suitable for use as scion donors. Fixed versus variable shearing regimes had little effect on tree value, although some individual clones responded better to one regime or the other.
    Electronic ISSN: 1999-4907
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by MDPI Publishing
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  • 11
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    MDPI Publishing
    In: Forests
    Publication Date: 2018-04-04
    Description: Forests, Vol. 9, Pages 181: Traffic-Induced Changes and Processes in Forest Road Aggregate Particle-Size Distributions Forests doi: 10.3390/f9040181 Authors: Hakjun Rhee James Fridley Deborah Page-Dumroese Traffic can alter forest road aggregate material in various ways, such as by crushing, mixing it with subgrade material, and sweeping large-size, loose particles (gravel) toward the outside of the road. Understanding the changes and physical processes of the aggregate is essential to mitigate sediment production from forest roads and reduce road maintenance efforts. We compared the particle-size distributions of forest road aggregate from the Clearwater National Forest in Idaho, USA in three vertical layers (upper, middle, and bottom of the road aggregate), three horizontal locations (tire track, shoulder, and half-way between them), and three traffic uses (none, light (no logging vehicles), and heavy (logging vehicles and equipment)) using Tukey’s multiple comparison test. Light traffic appears to cause aggregate crushing where vehicle tires passed and caused sweeping on the road surface. Heavy traffic caused aggregate crushing at all vertical and horizontal locations, and subgrade mixing with the bottom layer at the shoulder location. Logging vehicles and heavy equipment with wide axles drove on the shoulder and exerted enough stress to cause subgrade mixing. These results can help identify the sediment source and define adequate mitigation measures to reduce sediment production from forest roads and reduce road maintenance efforts by providing information for best management practices.
    Electronic ISSN: 1999-4907
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
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  • 12
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    MDPI Publishing
    In: Forests
    Publication Date: 2018-04-04
    Description: Forests, Vol. 9, Pages 180: Tamarix microRNA Profiling Reveals New Insight into Salt Tolerance Forests doi: 10.3390/f9040180 Authors: Jianwen Wang Meng Xu Zhiting Li Youju Ye Hao Rong Li-an Xu The halophyte tamarisk (Tamarix) is extremely salt tolerant, making it an ideal material for salt tolerance-related studies. Although many salt-responsive genes of Tamarix were identified in previous studies, there are no reports on the role of post-transcriptional regulation in its salt tolerance. We constructed six small RNA libraries of Tamarix chinensis roots with NaCl treatments. High-throughput sequencing of the six libraries was performed and microRNA expression profiles were constructed. We investigated salt-responsive microRNAs to uncover the microRNA-mediated genes regulation. From these analyses, 251 conserved and 18 novel microRNA were identified from all small RNAs. From 191 differentially expressed microRNAs, 74 co-expressed microRNAs were identified as salt-responsive candidate microRNAs. The most enriched GO (gene ontology) terms for the 157 genes targeted by differentially expressed microRNAs suggested that transcriptions factors were highly active. Two hub microRNAs (miR414, miR5658), which connected by several target genes into an organic microRNA regulatory network, appeared to be the key regulators of post-transcriptional salt-stress responses. As the first survey on the tamarisk small RNAome, this study improves the understanding of tamarisk salt-tolerance mechanisms and will contribute to the molecular-assisted resistance breeding.
    Electronic ISSN: 1999-4907
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
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  • 13
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    Elsevier
    Publication Date: 2018-04-04
    Description: Publication date: Available online 3 April 2018 Source: Geodesy and Geodynamics Author(s): C. Braitenberg, G. Rossi, J. Bogusz, L. Crescentini, D. Crossley, R.S. Gross, K. Heki, J. Hinderer, T. Jahr, B. Meurers, H. Schuh
    Print ISSN: 1674-9847
    Topics: Architecture, Civil Engineering, Surveying , Geosciences
    Published by Elsevier
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  • 14
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    Molecular Diversity Preservation International (MDPI)
    In: Genes
    Publication Date: 2018-04-04
    Description: Genes, Vol. 9, Pages 191: Genomic Signatures of Reinforcement Genes doi: 10.3390/genes9040191 Authors: Austin Garner Benjamin Goulet Matthew Farnitano Y. Molina-Henao Robin Hopkins Reinforcement is the process by which selection against hybridization increases reproductive isolation between taxa. Much research has focused on demonstrating the existence of reinforcement, yet relatively little is known about the genetic basis of reinforcement or the evolutionary conditions under which reinforcement can occur. Inspired by reinforcement’s characteristic phenotypic pattern of reproductive trait divergence in sympatry but not in allopatry, we discuss whether reinforcement also leaves a distinct genomic pattern. First, we describe three patterns of genetic variation we expect as a consequence of reinforcement. Then, we discuss a set of alternative processes and complicating factors that may make the identification of reinforcement at the genomic level difficult. Finally, we consider how genomic analyses can be leveraged to inform if and to what extent reinforcement evolved in the face of gene flow between sympatric lineages and between allopatric and sympatric populations of the same lineage. Our major goals are to understand if genome scans for particular patterns of genetic variation could identify reinforcement, isolate the genetic basis of reinforcement, or infer the conditions under which reinforcement evolved.
    Electronic ISSN: 2073-4425
    Topics: Biology
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  • 15
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    Molecular Diversity Preservation International (MDPI)
    In: Genes
    Publication Date: 2018-04-04
    Description: Genes, Vol. 9, Pages 192: Exposure to Formaldehyde Perturbs the Mouse Gut Microbiome Genes doi: 10.3390/genes9040192 Authors: Junhui Guo Yun Zhao Xingpeng Jiang Rui Li Hao Xie Leixin Ge Bo Xie Xu Yang Luoping Zhang Exposure to Formaldehyde (FA) results in many pathophysiological symptoms, however the underlying mechanisms are not well understood. Given the complicated modulatory role of intestinal microbiota on human health, we hypothesized that interactions between FA and the gut microbiome may account for FA’s toxicity. Balb/c mice were allocated randomly to three groups: a control group, a methanol group (0.1 and 0.3 ng/mL MeOH subgroups), and an FA group (1 and 3 ng/mL FA subgroups). Groups of either three or six mice were used for the control or experiment. We applied high-throughput sequencing of 16S ribosomal RNA (rRNA) gene approaches and investigated possible alterations in the composition of mouse gut microbiota induced by FA. Changes in bacterial genera induced by FA exposure were identified. By analyzing KEGG metabolic pathways predicted by PICRUSt software, we also explored the potential metabolic changes, such as alpha-Linolenic acid metabolism and pathways in cancer, associated with FA exposure in mice. To the best of our knowledge, this preliminary study is the first to identify changes in the mouse gut microbiome after FA exposure, and to analyze the relevant potential metabolisms. The limitation of this study: this study is relatively small and needs to be further confirmed through a larger study.
    Electronic ISSN: 2073-4425
    Topics: Biology
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  • 16
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    Elsevier
    Publication Date: 2018-04-04
    Description: Publication date: Available online 3 April 2018 Source: Geoscience Frontiers Author(s): Du YongSheng, Fan QiShun, Gao DongLin, Wei HaiCheng, Shan FaShou, Li BinKai, Zhang XiangRu, Yuan Qin, Qin ZhanJie, Ren QianHui, Teng XueMing In this study, nineteen brine samples from the Qarhan Salt Lake (QSL) in western China were collected and analyzed for boron (B) and chlorine (Cl) concentrations, total dissolved solids (TDS), pH values and stable B isotopic compositions. The B concentrations and δ 11 B values of brines in the QSL range from 51.6 to 138.4 mg/L, and from +9.32 to +13.08‰, respectively. By comparison of B concentrations and TDS of brines in QSL with evaporation paths of brackish water, we found that B enrichment of brines primarily results from strong evaporation and concentration of Qarhan lake water. Combining with comparisons of B concentrations, TDS, pH values and δ 11 B values of brines, previously elemental ratios (K/Cl, Mg/Cl, Ca/Cl, B/Cl) and δ 11 B values of halite from a sediment core (ISL1A), we observe good correlations between B concentrations and TDS, TDS and pH values, pH and δ 11 B values of brines, which demonstrate that higher B concentrations and more positive δ 11 B values of halite indicate higher salinity of the Qarhan paleolake water as well as drier paleoclimatic conditions. Based on this interpretation of the δ 11 B values of halite in core ISL1A, higher salinity of the Qarhan paleolake occurred during two intervals, around 46-34 ka and 26-9 ka, which are almost coincident with the upper and lower halite-dominated salt layers in core ISL1A, drier climate phases documented from the δ 18 O record of carbonate in core ISL1A and the paleomoisture record in monsoonal central Asia, and a higher solar insolation at 30°N. These results demonstrate that the δ 11 B values of halite in the arid Qaidam Basin could be regarded as a new proxy for reconstructing the salinity record of paleolake water as well as paleoclimate conditions. Graphical abstract
    Print ISSN: 1674-9871
    Topics: Geosciences
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  • 17
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    Royal Society of Chemistry (RSC)
    Publication Date: 2018-04-04
    Description: Green Chem. , 2018, Accepted Manuscript DOI : 10.1039/C7GC03743K, Communication Louis Monsigny, Elias Feghali, Jean-Claude Berthet, Thibault Cantat Although millions of tons of lignin preparations are produced every year, primarily from the pulp and paper industry, 〉97 % of this resource is utilized as a low quality fuel... The content of this RSS Feed (c) The Royal Society of Chemistry
    Print ISSN: 1463-9262
    Electronic ISSN: 1463-9270
    Topics: Chemistry and Pharmacology
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  • 18
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    Elsevier
    Publication Date: 2018-04-04
    Description: Publication date: Available online 3 April 2018 Source: Geoscience Frontiers Author(s): Beyene G. Haile, Urszula Czarniecka, Ke-Lai Xi, Aleksandra Smyrak-Sikora, Jens Jahren, Alvar Braathen, Helge Hellevang Sedimentary basins containing igneous intrusions within sedimentary reservoir units represent an important risk in petroleum exploration. The Upper Triassic to Lower Jurassic sediments at Wilhelmøya (Svalbard) contains reservoir heterogeneity as a result of sill emplacement and represent a unique case study to better understand the effect of magmatic intrusions on the general burial diagenesis of siliciclastic sediments. Sills develop contact metamorphic aureoles by conduction as presented in many earlier studies. However, there is significant impact of localized hydrothermal circulation systems affecting reservoir sediments at considerable distance from the sill intrusions. Dolerite sill intrusions in the studied area are of limited vertical extent (∼12 m thick), but created localized hydrothermal convection cells affecting sediments at considerable distance (more than five times the thickness of the sill) from the intrusions. We present evidence that the sedimentary sequence can be divided into two units: (1) the bulk poorly lithified sediment with a maximum burial temperature much lower than 60–70°C, and (2) thinner intervals outside the contact zone that have experienced hydrothermal temperatures (around 140°C). The main diagenetic alteration associated with normal burial diagenesis is minor mechanical plastic deformation of ductile grains such as mica. Mineral grain contacts show no evidence of pressure dissolution and the vitrinite reflectance suggests a maximum temperature of ∼40 ºC. Contrary to this, part of the sediment, preferentially along calcite cemented flow baffles, show evidence of hydrothermal alteration. These hydrothermally altered sediment sections are characterized by recrystallized carbonate cemented intervals. Further, the hydrothermal solutions have resulted in localized sericitization (illitization) of feldspars, albitization of both K-feldspar and plagioclase and the formation of fibrous illite nucleated on kaolinite. These observations suggest hydrothermal alteration at T > 120–140 °C at distances considerably further away than expected from sill heat dissipation by conduction only, which commonly affect sediments about twice the thickness of the sill intrusion. We propose that carbonate-cemented sections acted as flow baffles already during the hydrothermal fluid mobility and controlled the migration pathways of the buoyant hot fluids. Significant hydrothermally induced diagenetic alterations affecting the porosity and hence reservoir quality was not noted in the noncarbonate-cemented reservoir intervals. Graphical abstract
    Print ISSN: 1674-9871
    Topics: Geosciences
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  • 19
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    Royal Society of Chemistry (RSC)
    Publication Date: 2018-04-04
    Description: Green Chem. , 2018, Accepted Manuscript DOI : 10.1039/C8GC00482J, Critical Review Hanno C. Christian Erythropel, Julie Zimmerman, Tamara de Winter, Laurene Petitjean, Fjodor Melnikov, Chun Ho Lam, Amanda Lounsbury, Karolina Mellor, Nina Jankovica, Qingshi Tu, Lauren Pincus, Mark Falinski, Wenbo Shi, Philip Coish, Desiree Plata, Paul Anastas The field of Green Chemistry has seen many scientific discoveries and inventions during the twenty years since the 12 Principles were first published. Inspired by tree diagrams that illustrate diversity... The content of this RSS Feed (c) The Royal Society of Chemistry
    Print ISSN: 1463-9262
    Electronic ISSN: 1463-9270
    Topics: Chemistry and Pharmacology
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  • 20
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    MDPI Publishing
    Publication Date: 2018-04-04
    Description: Geosciences, Vol. 8, Pages 120: Geology and Isotope Systematics of the Jianchaling Au Deposit, Shaanxi Province, China: Implications for Mineral Genesis Geosciences doi: 10.3390/geosciences8040120 Authors: Su-Wei Yue Deng-Feng Li Leon Bagas Jing Fang Zhen-Wen Lin The giant Jianchaling Au (52 t Au) deposit is located in the Mian-Lue-Yang Terrane in the southern part of the Qinling Orogen of central China and is hosted by metamorphosed carbonate rocks of the Late Neoproterozoic Duantouya Formation. The deposit consists of multiple generations of mineralised quartz(-carbonate) veins in WNW-trending extensional ductile-brittle shear zones. Based on the mineral assemblages and cross-cutting relationships between the quartz(-carbonate) veins, the paragenesis is characterised by an early coarse-grained pyrite-pyrrhotite-pentlandite-dolomite-quartz assemblage (I), followed by pyrite-sphalerite-galena-carbonate-arsenopyrite-fuchsite-carbonate-quartz containing gold (II), and fine-grained pyrite-dolomite-calcite-quartz-realgar (As2S2)-orpiment (As2S3) (III). The H-O-C isotope systematics for the three vein sets indicate that the mineralising fluid is probably sourced from the metamorphic dehydration of carbonate rocks in the Duantouya Formation, and gradually mixed with meteoric water during the emplacement of the third vein set. The δ34S values for sulfides (6.3–16.6‰) from the second auriferous vein set are greater than zero, indicating sulfates reduction from the Neoproterozoic metamorphic rocks (Duantouya Fm). The (206Pb/204Pb)i ratios from pyrite (17.521–18.477) from each of the vein sets overlap those of the ultramafic rocks (18.324–18.717) and the Bikou Group (17.399–18.417), indicating that the units are possible sources for the sulfides in the mineralisation. Both εNd(t) and Isr(t) of sulfide overlap with the meta-ultramafic field and Duantouya formation and dominated with mature Sr-Nd character, which indicated that the Duantouya may play an important role during the ore formation and there may exist a minor ultramafic source that is involved in the ore fluid. The S-Pb-Sr-Nd isotopic ratios are closely related to those of the Bikou Group and Duantouya Formation, which indicates that the mineralised fluid has interacted with both units. Combining the previously published data with data from this study on the mineralised area, we surmise that Jianchaling is characteristic of an orogenic-type gold deposit related to the Triassic Qinling Orogeny associated with continental collision.
    Electronic ISSN: 2076-3263
    Topics: Geosciences
    Published by MDPI Publishing
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  • 21
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    Royal Society of Chemistry (RSC)
    Publication Date: 2018-04-04
    Description: Green Chem. , 2018, Accepted Manuscript DOI : 10.1039/C8GC00435H, Paper Paul Korner, Dennis Jung, Andrea Kruse The hydrothermal dehydration of fructose to 5-hydroxymethylfurfural (HMF), a promising platform chemical from renewable resources, is commonly known to be Bronsted acid catalysed. Despite, it was not clear, if the... The content of this RSS Feed (c) The Royal Society of Chemistry
    Print ISSN: 1463-9262
    Electronic ISSN: 1463-9270
    Topics: Chemistry and Pharmacology
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  • 22
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    Royal Society of Chemistry (RSC)
    Publication Date: 2018-04-04
    Description: Green Chem. , 2018, Accepted Manuscript DOI : 10.1039/C8GC00358K, Paper Iris KM Yu, Dan CW Tsang, Alex Yip, Andrew J Hunt, James Sherwood, Jin Shang, H. C. Song, Yong Sik Ok, Chi Sun Poon Two green solvents, namely propylene carbonate (PC) and [gamma]-valerolactone (GVL), were examined as co-solvents in the conversion of bread waste to hydroxymethylfurfural (HMF) over SnCl4 as the catalyst under microwave... The content of this RSS Feed (c) The Royal Society of Chemistry
    Print ISSN: 1463-9262
    Electronic ISSN: 1463-9270
    Topics: Chemistry and Pharmacology
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    Royal Society of Chemistry (RSC)
    Publication Date: 2018-04-04
    Description: Green Chem. , 2018, Advance Article DOI : 10.1039/C8GC00423D, Paper Dennis Pingen, Julia Zimmerer, Nele Klinkenberg, Stefan Mecking A two-step one-pot synthesis of benzene from the five-fold unsaturated fatty acid eicosapentaenoic acid (EPA), a component of microalgae oils, is presented. Simultaneously to the dehydrogenation, hydrogenation of the by-products to the desirable sebacic acid and octanoic acid is performed. To cite this article before page numbers are assigned, use the DOI form of citation above. The content of this RSS Feed (c) The Royal Society of Chemistry
    Print ISSN: 1463-9262
    Electronic ISSN: 1463-9270
    Topics: Chemistry and Pharmacology
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  • 24
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    Royal Society of Chemistry (RSC)
    Publication Date: 2018-04-04
    Description: Green Chem. , 2018, Accepted Manuscript DOI : 10.1039/C8GC00205C, Critical Review Diego M. Nascimento, Yana L. Nunes, Maria C.B. Figueiredo, Henriette Azeredo, Fauze A. Aouada, Judith Pessoa Andrade Feitosa, Morsyleide F. Rosa, Alain Dufresne Over the last decade, nanocellulose-based nanocomposite hydrogels have emerged as promising materials in different fields of application such as medicine, food, and agriculture. The present review addresses advances in the... The content of this RSS Feed (c) The Royal Society of Chemistry
    Print ISSN: 1463-9262
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  • 25
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    Royal Society of Chemistry (RSC)
    Publication Date: 2018-04-04
    Description: Green Chem. , 2018, Advance Article DOI : 10.1039/C8GC00008E, Communication Open Access   This article is licensed under a Creative Commons Attribution 3.0 Unported Licence. Katharina Plasch, Gerhard Hofer, Walter Keller, Sam Hay, Derren J. Heyes, Alexander Dennig, Silvia M. Glueck, Kurt Faber Utilization of gaseous carbon dioxide as a C 1 -building block in the biocatalytic ortho -carboxylation of a phenol. To cite this article before page numbers are assigned, use the DOI form of citation above. The content of this RSS Feed (c) The Royal Society of Chemistry
    Print ISSN: 1463-9262
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  • 26
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    Institute of Electrical and Electronics Engineers (IEEE)
    Publication Date: 2018-04-04
    Description: Presents the front cover for this issue of the publication.
    Print ISSN: 2168-6831
    Topics: Architecture, Civil Engineering, Surveying , Electrical Engineering, Measurement and Control Technology , Geosciences , Computer Science
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  • 27
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    Nature Publishing Group (NPG)
    Publication Date: 2018-05-03
    Description: In-situ visualization of solute-driven phase coexistence within individual nanorods In-situ visualization of solute-driven phase coexistence within individual nanorods, Published online: 02 May 2018; doi:10.1038/s41467-018-04021-1 Compared to thin films and other geometries, nanorods can exhibit particularly high performance in solute-intercalation-based energy and information storage devices. Here, the authors use in situ electron microscopy and spectroscopy to study the hydrogenation of palladium nanorods, revealing relationships between nanorod structure and device cyclability and capacity.
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
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  • 28
    Publication Date: 2018-05-03
    Description: Systematic mapping of contact sites reveals tethers and a function for the peroxisome-mitochondria contact Systematic mapping of contact sites reveals tethers and a function for the peroxisome-mitochondria contact, Published online: 02 May 2018; doi:10.1038/s41467-018-03957-8 The internal organization of the cell has been enriched by the discovery that organelles establish membrane contact sites, however the entire repertoire of these contacts is still being explored. Here the authors systematically identify the landscape of cellular contact sites in yeast, discovering four potential novel contact sites and two tether proteins for the peroxisome-mitochondria contact site.
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
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  • 29
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    Institute of Physics (IOP)
    Publication Date: 2018-05-03
    Description: Ultracold quantum gases provide a unique setting for studying and understanding the properties of interacting quantum systems. Here, we investigate a multi-component system of 87 Rb– 39 K Bose–Einstein condensates (BECs) with tunable interactions both theoretically and experimentally. Such multi-component systems can be characterized by their miscibility, where miscible components lead to a mixed ground state and immiscible components form a phase-separated state. Here we perform the first full simulation of the dynamical expansion of this system including both BECs and thermal clouds, which allows for a detailed comparison with experimental results. In particular we show that striking features emerge in time-of-flight (TOF) for BECs with strong interspecies repulsion, even for systems which were separated in situ by a large gravitational sag. An analysis of the centre of mass positions of the BECs after expansion yields qualitative agreement with the h...
    Electronic ISSN: 1367-2630
    Topics: Physics
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  • 30
    Publication Date: 2018-05-03
    Description: We report on the determination of the spin Hall angle in ultra-clean, defect-reduced epitaxial Pt films. By applying vector network analyzer ferromagnetic resonance spectroscopy to a series of single crystalline Fe (12 nm) /Pt ( t Pt ) bilayers we determine the real part of the spin mixing conductance (4.4 ± 0.2) × 10 19 m −2 and reveal a very small spin diffusion length in the epitaxial Pt (1.1 ± 0.1) nm film. We investigate the spin pumping and ISHE in a stripe microstucture excited by a microwave coplanar waveguide antenna. By using their different angular dependencies, we distinguish between spin rectification effects and the inverse spin Hall effect. The relatively large value of the spin Hall angle (5.7 ± 1.4)% shows that ultra-clean e-beam evaporated non-magnetic materials can also have a comparable spin-to-charge current conversion efficiency as sputtered high resistivity layers.
    Electronic ISSN: 1367-2630
    Topics: Physics
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  • 31
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    Institute of Physics (IOP)
    Publication Date: 2018-05-03
    Description: Helical liquids have been experimentally realized in both nanowires and ultracold atomic chains as the result of strong spin–orbit interactions. In both cases the inner degrees of freedom can be considered as an additional space dimension, providing an interpretation of these systems as chiral synthetic ladders, with artificial magnetic fluxes determined by the spin–orbit terms. In this work, we characterize the helical state which appears at filling ν = 1/2: this state is generated by a gap arising in the spin sector of the corresponding Luttinger liquid and it can be interpreted as the one-dimensional (1D) limit of a fractional quantum Hall state of bosonic pairs of fermions. We study its main features, focusing on entanglement properties and correlation functions. The techniques developed here provide a key example for the study of similar quasi-1D systems beyond the semiclassical approximation commonly adopted in the description of the Laughlin-like states.
    Electronic ISSN: 1367-2630
    Topics: Physics
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  • 32
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    Institute of Physics (IOP)
    Publication Date: 2018-05-03
    Description: Non-conventional topology of elastic waves arises from breaking symmetry of phononic structures either intrinsically through internal resonances or extrinsically via application of external stimuli. We develop a spacetime representation based on twistor theory of an intrinsic topological elastic structure composed of a harmonic chain attached to a rigid substrate. Elastic waves in this structure obey the Klein–Gordon and Dirac equations and possesses spinorial character. We demonstrate the mapping between straight line trajectories of these elastic waves in spacetime and the twistor complex space. The twistor representation of these Dirac phonons is related to their topological and fermion-like properties. The second topological phononic structure is an extrinsic structure composed of a one-dimensional elastic medium subjected to a moving superlattice. We report an analogy between the elastic behavior of this time-dependent superlattice, the scalar quantum field theory and gener...
    Electronic ISSN: 1367-2630
    Topics: Physics
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  • 33
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    Institute of Physics (IOP)
    Publication Date: 2018-05-03
    Description: Deterministic port-based teleportation (dPBT) protocol is a scheme where a quantum state is guaranteed to be transferred to another system without unitary correction. We characterise the best achievable performance of the dPBT when both the resource state and the measurement is optimised. Surprisingly, the best possible fidelity for an arbitrary number of ports and dimension of the teleported state is given by the largest eigenvalue of a particular matrix—Teleportation Matrix. It encodes the relationship between a certain set of Young diagrams and emerges as the optimal solution to the relevant semidefinite programme.
    Electronic ISSN: 1367-2630
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  • 34
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    Institute of Electrical and Electronics Engineers (IEEE)
    Publication Date: 2018-04-04
    Description: The Constellation of Small Satellites for the Mediterranean Basin Observation (COSMO)-SkyMed Second Generation (CSG) ground segment (GS) is based on an interoperable and multimission design that provides CSG functionalities to external partners and access through the CSG to services belonging to other Earth observation (EO) partners. Moreover, the CSG GS design supports such cooperation by expansion through replication of user GSs (UGSs) in different ways. In this manner, the CSG GS is able to manage EO foreign missions by providing centralized and multimission access in an integrated environment, thus offering valuable technological solutions to the defense and civilian communities. This article provides an indepth description of the CSG system access portfolio, focusing on the architectural details of the GS that allow the provisioning and exploitation of the CSG's interoperability, expandability, and multisensor/multimission (IEM) features.
    Print ISSN: 2168-6831
    Topics: Architecture, Civil Engineering, Surveying , Electrical Engineering, Measurement and Control Technology , Geosciences , Computer Science
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  • 35
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    American Physical Society (APS)
    In: Physics
    Publication Date: 2018-05-03
    Description: Experiments involving a magnetic quantum Newton’s cradle provide insights into how interacting quantum particles achieve thermal equilibrium. [Physics] Published Wed May 02, 2018
    Electronic ISSN: 1539-0748
    Topics: Physics
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  • 36
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    American Physical Society (APS)
    Publication Date: 2018-05-03
    Description: Author(s): Yijun Tang, Wil Kao, Kuan-Yu Li, Sangwon Seo, Krishnanand Mallayya, Marcos Rigol, Sarang Gopalakrishnan, and Benjamin L. Lev Experiments involving a magnetic quantum Newton’s cradle provide insights into how interacting quantum particles achieve thermal equilibrium. [Phys. Rev. X 8, 021030] Published Wed May 02, 2018
    Electronic ISSN: 2160-3308
    Topics: Physics
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  • 37
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    Institute of Physics (IOP)
    Publication Date: 2018-05-03
    Description: We describe a compact, robust and versatile system for studying the macroscopic spin dynamics in a spinor Bose–Einstein condensate. Condensates of ##IMG## [http://ej.iop.org/images/1367-2630/20/5/053008/njpaab2a0ieqn1.gif] {${}^{87}\mathrm{Rb}$} are produced by all-optical evaporation in a 1560 nm optical dipole trap, using a non-standard loading sequence that employs an ancillary 1529 nm beam for partial compensation of the strong differential light-shift induced by the dipole trap itself. We use near-resonant Faraday rotation probing to non-destructively track the condensate magnetization, and demonstrate few-Larmor-cycle tracking with no detectable degradation of the spin polarization. In the ferromagnetic F = 1 ground state, we observe the spin orientation between atoms in the condensate is preserved, such that they precess all together like one large spin in the presence of a magnetic field. We characterize this dynamics in terms of the single-s...
    Electronic ISSN: 1367-2630
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  • 38
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    Public Library of Science (PLoS)
    Publication Date: 2018-05-03
    Description: by The PLOS Neglected Tropical Diseases Staff
    Print ISSN: 1935-2727
    Electronic ISSN: 1935-2735
    Topics: Medicine
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  • 39
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    Public Library of Science (PLoS)
    Publication Date: 2018-05-03
    Description: by Ari Prayitno, Anne-Frieda Taurel, Joshua Nealon, Hindra Irawan Satari, Mulya Rahma Karyanti, Rini Sekartini, Soedjatmiko Soedjatmiko, Hartono Gunardi, Bernie Endyarni Medise, R. Tedjo Sasmono, James Mark Simmerman, Alain Bouckenooghe, Sri Rezeki Hadinegoro
    Print ISSN: 1935-2727
    Electronic ISSN: 1935-2735
    Topics: Medicine
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  • 40
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    Public Library of Science (PLoS)
    Publication Date: 2018-05-03
    Description: by Kohei Kitami, Megumi Kitami, Masaru Kaku, Bin Wang, Yoshihiro Komatsu Craniofacial abnormalities, including facial skeletal defects, comprise approximately one-third of all birth defects in humans. Since most bones in the face derive from cranial neural crest cells (CNCCs), which are multipotent stem cells, craniofacial bone disorders are largely attributed to defects in CNCCs. However, it remains unclear how the niche of CNCCs is coordinated by multiple gene regulatory networks essential for craniofacial bone development. Here we report that tumor suppressors breast cancer 1 (BRCA1) and breast cancer 2 (BRCA2) are required for craniofacial bone development in mice. Disruption of Brca1 in CNCC-derived mesenchymal cells, but not in epithelial-derived cells, resulted in craniofacial skeletal defects. Whereas osteogenic differentiation was normal, both osteogenic proliferation and survival were severely attenuated in Brca1 mutants. Brca1 -deficient craniofacial skeletogenic precursors displayed increased DNA damage and enhanced cell apoptosis. Importantly, the craniofacial skeletal defects were sufficiently rescued by superimposing p53 null alleles in a neural crest-specific manner in vivo , indicating that BRCA1 deficiency induced DNA damage, cell apoptosis, and that the pathogenesis of craniofacial bone defects can be compensated by inactivation of p53. Mice lacking Brca2 in CNCCs, but not in epithelial-derived cells, also displayed abnormalities resembling the craniofacial skeletal malformations observed in Brca1 mutants. Our data shed light on the importance of BRCA1/BRCA2 function in CNCCs during craniofacial skeletal formation.
    Print ISSN: 1553-7390
    Electronic ISSN: 1553-7404
    Topics: Biology
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  • 41
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    Public Library of Science (PLoS)
    Publication Date: 2018-05-03
    Description: by Shoichiro Yamaguchi, Honda Naoki, Muneki Ikeda, Yuki Tsukada, Shunji Nakano, Ikue Mori, Shin Ishii Animals are able to reach a desired state in an environment by controlling various behavioral patterns. Identification of the behavioral strategy used for this control is important for understanding animals’ decision-making and is fundamental to dissect information processing done by the nervous system. However, methods for quantifying such behavioral strategies have not been fully established. In this study, we developed an inverse reinforcement-learning (IRL) framework to identify an animal’s behavioral strategy from behavioral time-series data. We applied this framework to C . elegans thermotactic behavior; after cultivation at a constant temperature with or without food, fed worms prefer, while starved worms avoid the cultivation temperature on a thermal gradient. Our IRL approach revealed that the fed worms used both the absolute temperature and its temporal derivative and that their behavior involved two strategies: directed migration (DM) and isothermal migration (IM). With DM, worms efficiently reached specific temperatures, which explains their thermotactic behavior when fed. With IM, worms moved along a constant temperature, which reflects isothermal tracking, well-observed in previous studies. In contrast to fed animals, starved worms escaped the cultivation temperature using only the absolute, but not the temporal derivative of temperature. We also investigated the neural basis underlying these strategies, by applying our method to thermosensory neuron-deficient worms. Thus, our IRL-based approach is useful in identifying animal strategies from behavioral time-series data and could be applied to a wide range of behavioral studies, including decision-making, in other organisms.
    Print ISSN: 1553-734X
    Electronic ISSN: 1553-7358
    Topics: Biology , Computer Science
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  • 42
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    Public Library of Science (PLoS)
    Publication Date: 2018-05-03
    Description: by Magdalena Circu, James Cardelli, Martin P. Barr, Kenneth O’Byrne, Glenn Mills, Hazem El-Osta
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 43
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    Public Library of Science (PLoS)
    Publication Date: 2018-05-03
    Description: by Xinyu Feng, Shuisen Zhou, Jingwen Wang, Wei Hu Mosquitoes are incriminated as vectors for many crippling diseases, including malaria, West Nile fever, Dengue fever, and other neglected tropical diseases (NTDs). microRNAs (miRNAs) can interact with multiple target genes to elicit biological functions in the mosquitoes. However, characterization and function of individual miRNAs and their potential targets have not been fully determined to date. We conducted a systematic review of published literature following PRISMA guidelines. We summarize the information about miRNAs in mosquitoes to better understand their metabolism, development, and responses to microorganisms. Depending on the study, we found that miRNAs were dysregulated in a species-, sex-, stage-, and tissue/organ-specific manner. Aberrant miRNA expressions were observed in development, metabolism, host-pathogen interactions, and insecticide resistance. Of note, many miRNAs were down-regulated upon pathogen infection. The experimental studies have expanded the identification of miRNA target from the 3′ untranslated regions (UTRs) of mRNAs of mosquitoes to the 5′ UTRs of mRNAs of the virus. In addition, we discuss current trends in mosquito miRNA research and offer suggestions for future studies.
    Print ISSN: 1935-2727
    Electronic ISSN: 1935-2735
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  • 44
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    Public Library of Science (PLoS)
    Publication Date: 2018-05-03
    Description: by Elisa Sicuri, Azucena Bardají, Sergi Sanz, Sergi Alonso, Silke Fernandes, Kara Hanson, Myriam Arevalo-Herrera, Clara Menendez Malaria in pregnancy threatens birth outcomes and the health of women and their newborns. This is also the case in low transmission areas, such as Colombia, where Plasmodium vivax is the dominant parasite species. Within the Colombian health system, which underwent major reforms in the ‘90s, malaria treatment is provided free of charge to patients. However, patients still incur costs, such as transportation and value of time lost due to the disease. We estimated such costs among 40 pregnant women with clinical malaria (30% Plasmodium falciparum , 70% Plasmodium vivax ) in the municipality of Tierralta, Northern Colombia. In a cross-sectional study, women were interviewed after an outpatient or inpatient laboratory confirmed malaria episode. Women were asked to report all types of cost incurred before (including prevention), during and immediately after the contact with the health facility. Median total cost was over 16US$ for an outpatient visit, rising to nearly 30US$ if other treatments were sought before reaching the health facility. Median total inpatient cost was 26US$ or 54US$ depending on whether costs incurred prior to admission were excluded or included. For both outpatients and inpatients, direct costs were largely due to transportation and indirect costs constituted the largest share of total costs. Estimated costs are likely to represent only one of the constraints that women face when seeking treatment in an area characterized, at the time of the study, by armed conflict, displacement, and high vulnerability of indigenous women, the group at highest risk of malaria. Importantly, the Colombian peace process, which culminated with the cease-fire in August 2016, may have a positive impact on achieving universal access to healthcare in conflict areas. The current study can inform malaria elimination initiatives in Colombia.
    Print ISSN: 1935-2727
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  • 45
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    Public Library of Science (PLoS)
    Publication Date: 2018-05-03
    Description: by Ling Lu, Derrick A. Bennett, Iona Y. Millwood, Sarah Parish, Mark I. McCarthy, Anubha Mahajan, Xu Lin, Fiona Bragg, Yu Guo, Michael V. Holmes, Shoaib Afzal, Børge G. Nordestgaard, Zheng Bian, Michael Hill, Robin G. Walters, Liming Li, Zhengming Chen, Robert Clarke Background Observational studies have reported that higher plasma 25-hydroxyvitamin D (25[OH]D) concentrations are associated with lower risks of diabetes, but it is unclear if these associations are causal. The aim of this study was to test the relevance of 25(OH)D for type 2 diabetes using genetically instrumented differences in plasma 25(OH)D concentrations. Methods and findings Data were available on four 25(OH)D single nucleotide polymorphisms (SNPs; n = 82,464), plasma 25(OH)D concentrations ( n = 13,565), and cases with diabetes ( n = 5,565) in the China Kadoorie Biobank (CKB). The effects on risk of diabetes were assessed by a genetic score using two 25(OH)D synthesis SNPs ( DHCR7 -rs12785878 and CYP2R1 -rs10741657), with and without the addition of SNPs affecting the transport ( GC/DBP -rs2282679) and catabolism ( CYP24A1 -rs6013897) of 25(OH)D. The CKB results were combined in a meta-analysis of 10 studies for the 2 synthesis SNPs ( n = 58,312 cases) and 7 studies for all 4 SNPs ( n = 32,796 cases). Mean (SD) 25(OH)D concentration was 62 (20) nmol/l in CKB, and the per allele effects of genetic scores on 25(OH)D were 2.87 (SE 0.39) for the synthesis SNPs and 3.54 (SE 0.32) for all SNPs. A 25-nmol/l higher biochemically measured 25(OH)D was associated with a 9% (95% CI: 0%–18%) lower risk of diabetes in CKB. In a meta-analysis of all studies, a 25-nmol/l higher genetically instrumented 25(OH)D concentration was associated with a 14% (95% CI: 3%–23%) lower risk of diabetes ( p = 0.01) using the 2 synthesis SNPs. An equivalent difference in 25(OH)D using a genetic score with 4 SNPs was not significantly associated with diabetes (odds ratio 8%, 95% CI: −1% to 16%, lower risk, p = 0.07), but had some evidence of pleiotropy. A limitation of the meta-analysis was the access only to study level rather than individual level data. Conclusions The concordant risks of diabetes for biochemically measured and genetically instrumented differences in 25(OH)D using synthesis SNPs provide evidence for a causal effect of higher 25(OH)D for prevention of diabetes.
    Print ISSN: 1549-1277
    Electronic ISSN: 1549-1676
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    Public Library of Science (PLoS)
    Publication Date: 2018-05-03
    Description: by Inês Bártolo, Ana Rita Diniz, Pedro Borrego, João Pedro Ferreira, Maria Rosário Bronze, Helena Barroso, Rui Pinto, Carlos Cardoso, João F. Pinto, Rafael Ceña Diaz, Pilar Garcia Broncano, Maria Angel Muñoz-Fernández, Nuno Taveira
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 47
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    Public Library of Science (PLoS)
    Publication Date: 2018-05-03
    Description: by The PLOS ONE Staff
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 48
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    Public Library of Science (PLoS)
    Publication Date: 2018-05-03
    Description: by The PLOS ONE Staff
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 49
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    Public Library of Science (PLoS)
    Publication Date: 2018-05-03
    Description: by Folashade Otegbeye, Evelyn Ojo, Stephen Moreton, Nathan Mackowski, Dean A. Lee, Marcos de Lima, David N. Wald
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 50
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    Public Library of Science (PLoS)
    Publication Date: 2018-05-03
    Description: by Ana Kasradze, Diana Echeverria, Khatuna Zakhashvili, Christian Bautista, Nicholas Heyer, Paata Imnadze, Veriko Mirtskhulava
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 51
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    Public Library of Science (PLoS)
    Publication Date: 2018-05-03
    Description: by Ahmed S. Abdel-Moneim, Mohammad E. Mahfouz, Dalia M. Zytouni
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 52
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    Public Library of Science (PLoS)
    Publication Date: 2018-05-03
    Description: by Naoto Fujita, Saki Aono, Kohei Karasaki, Fumi Sera, Tomoyuki Kurose, Hidemi Fujino, Susumu Urakawa Although exercise is effective in improving obesity and hyperinsulinemia, the exact influence of exercise on the capillary density of skeletal muscles remains unknown. The aim of this study was to investigate the effects of low-intensity exercise training on metabolism in obesity with hyperinsulinemia, focusing specifically on the capillary density within the skeletal muscle. Otsuka Long-Evans Tokushima fatty (OLETF) rats were used as animal models of obesity with hyperinsulinemia, whereas Long-Evans Tokushima Otsuka (LETO) rats served as controls (no obesity, no hyperinsulinemia). The animals were randomly assigned to either non-exercise or exercise groups (treadmill running for 60 min/day, for 4 weeks). The exercise groups were further divided into subgroups according to training mode: single bout (60 min, daily) vs. multiple bout (three bouts of 20 min, daily). Fasting insulin levels were significantly higher in OLETF than in LETO rats. Among OLETF rats, there were no significant differences in fasting glucose levels between the exercise and the non-exercise groups, but the fasting insulin levels were significantly lower in the exercise group. Body weight and triacylglycerol levels in the liver were significantly higher in OLETF than in LETO rats; however, among OLETF rats, these levels were significantly lower in the exercise than in the non-exercise group. The capillary-to-fiber ratio of the soleus muscle was significantly higher in OLETF than in LETO rats; however, among OLETF rats, the ratio was lower in the exercise group than in the non-exercise group. No significant differences in any of the studied parameters were noted between the single-bout and multiple-bout exercise training modes among either OLETF or LETO rats. These results suggest that low-intensity exercise training improves insulin sensitivity and fatty liver. Additionally, the fact that attenuation of excessive capillarization in the skeletal muscle of OLETF rats was accompanied by improvement in increased body weight.
    Electronic ISSN: 1932-6203
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  • 53
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    Institute of Electrical and Electronics Engineers (IEEE)
    Publication Date: 2018-04-04
    Description: Advertisement.
    Print ISSN: 1540-7977
    Electronic ISSN: 1558-4216
    Topics: Electrical Engineering, Measurement and Control Technology
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  • 54
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    Institute of Electrical and Electronics Engineers (IEEE)
    Publication Date: 2018-04-04
    Description: Advertisement.
    Print ISSN: 1540-7977
    Electronic ISSN: 1558-4216
    Topics: Electrical Engineering, Measurement and Control Technology
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    Institute of Electrical and Electronics Engineers (IEEE)
    Publication Date: 2018-04-04
    Description: Advertisement.
    Print ISSN: 1540-7977
    Electronic ISSN: 1558-4216
    Topics: Electrical Engineering, Measurement and Control Technology
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    Publication Date: 2018-04-04
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    Publication Date: 2018-04-04
    Description: We are motivated by the need for a generic object proposal generation algorithm which achieves good balance between object detection recall, proposal localization quality and computational efficiency. We propose a novel object proposal algorithm, BING++ , which inherits the virtue of good computational efficiency of BING [1] but significantly improves its proposal localization quality. At high level we formulate the problem of object proposal generation from a novel probabilistic perspective, based on which our BING++ manages to improve the localization quality by employing edges and segments to estimate object boundaries and update the proposals sequentially. We propose learning the parameters efficiently by searching for approximate solutions in a quantized parameter space for complexity reduction. We demonstrate the generalization of BING++ with the same fixed parameters across different object classes and datasets. Empirically our BING++ can run at half speed of BING on CPU, but significantly improve the localization quality by 18.5 and 16.7 percent on both VOC2007 and Microhsoft COCO datasets, respectively. Compared with other state-of-the-art approaches, BING++ can achieve comparable performance, but run significantly faster.
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    Publication Date: 2018-04-04
    Description: In the early days, content-based image retrieval (CBIR) was studied with global features. Since 2003, image retrieval based on local descriptors ( de facto SIFT) has been extensively studied for over a decade due to the advantage of SIFT in dealing with image transformations. Recently, image representations based on the convolutional neural network (CNN) have attracted increasing interest in the community and demonstrated impressive performance. Given this time of rapid evolution, this article provides a comprehensive survey of instance retrieval over the last decade. Two broad categories, SIFT-based and CNN-based methods, are presented. For the former, according to the codebook size, we organize the literature into using large/medium-sized/small codebooks. For the latter, we discuss three lines of methods, i.e., using pre-trained or fine-tuned CNN models, and hybrid methods. The first two perform a single-pass of an image to the network, while the last category employs a patch-based feature extraction scheme. This survey presents milestones in modern instance retrieval, reviews a broad selection of previous works in different categories, and provides insights on the connection between SIFT and CNN-based methods. After analyzing and comparing retrieval performance of different categories on several datasets, we discuss promising directions towards generic and specialized instance retrieval.
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    Publication Date: 2018-04-04
    Description: The goal of this paper is to perform 3D object detection in the context of autonomous driving. Our method aims at generating a set of high-quality 3D object proposals by exploiting stereo imagery. We formulate the problem as minimizing an energy function that encodes object size priors, placement of objects on the ground plane as well as several depth informed features that reason about free space, point cloud densities and distance to the ground. We then exploit a CNN on top of these proposals to perform object detection. In particular, we employ a convolutional neural net (CNN) that exploits context and depth information to jointly regress to 3D bounding box coordinates and object pose. Our experiments show significant performance gains over existing RGB and RGB-D object proposal methods on the challenging KITTI benchmark. When combined with the CNN, our approach outperforms all existing results in object detection and orientation estimation tasks for all three KITTI object classes. Furthermore, we experiment also with the setting where LIDAR information is available, and show that using both LIDAR and stereo leads to the best result.
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    Publication Date: 2018-04-04
    Description: Recent years have witnessed the success of deep neural networks in dealing with a plenty of practical problems. Dropout has played an essential role in many successful deep neural networks, by inducing regularization in the model training. In this paper, we present a new regularized training approach: Shakeout. Instead of randomly discarding units as Dropout does at the training stage, Shakeout randomly chooses to enhance or reverse each unit's contribution to the next layer. This minor modification of Dropout has the statistical trait: the regularizer induced by Shakeout adaptively combines $L_{0}$ , $L_{1}$ and $L_{2}$ regularization terms. Our classification experiments with representative deep architectures on image datasets MNIST, CIFAR-10 and ImageNet show that Shakeout deals with over-fitting effectively and outperforms Dropout. We empirically demonstrate that Shakeout leads to sparser weights under both unsupervised and supervised settings. Shakeout also leads to the grouping effect of the input units in a layer. Considering the weights in reflecting the importance of connections, Shakeout is superior to Dropout, which is valuable for the deep model compression. Moreover, we demonstrate that Shakeout can effectively reduce the instability of the training process of the deep architecture.
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    Institute of Electrical and Electronics Engineers (IEEE)
    Publication Date: 2018-04-04
    Description: This paper introduces a fast and efficient segmentation technique for 2D images and 3D point clouds of building facades. Facades of buildings are highly structured and consequently most methods that have been proposed for this problem aim to make use of this strong prior information. Contrary to most prior work, we are describing a system that is almost domain independent and consists of standard segmentation methods. We train a sequence of boosted decision trees using auto-context features. This is learned using stacked generalization. We find that this technique performs better, or comparable with all previous published methods and present empirical results on all available 2D and 3D facade benchmark datasets. The proposed method is simple to implement, easy to extend, and very efficient at test-time inference.
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    MDPI Publishing
    Publication Date: 2018-05-04
    Description: IJERPH, Vol. 15, Pages 909: Identification of Depression and Screening for Work Disabilities among Long-Term Unemployed People International Journal of Environmental Research and Public Health doi: 10.3390/ijerph15050909 Authors: Kirsti Nurmela Aino Mattila Virpi Heikkinen Jukka Uitti Aarne Ylinen Pekka Virtanen The study explores whether clinical screening targeted at work disabilities among long-term unemployed people reveals eligible individuals for a disability pension and the importance of depression in granting the disability pensions. A total of 364 participants of the screening project were considered as eligible to apply for disability pension. Among them, 188 were diagnosed as clinically depressed. They were classified into those with earlier depression diagnosis (n = 85), those whose depression had not been diagnosed earlier (n = 103), and those without diagnosed depression (n = 176). The association of this ‘Depression identification pattern’ with being granted a disability pension was explored by logistic regression analyses. Compared to those with earlier diagnosis, those whose depression had not been diagnosed earlier were granted disability pension more commonly (72% vs. 54% OR 2.2, p = 0.012). Corresponding figures of the undepressed were 73%, OR 2.3, p = 0.002. The adjustments did not affect the results. Clinical examination of the long-term unemployed people in terms of work disability seems to be worthwhile. In particular, the examination reveals new depression diagnoses, which contribute more to the award of disability pension than depression diagnosed earlier by regular health care. Novel ways to detect depression among the unemployed should be implemented in the health and employment services.
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    MDPI Publishing
    Publication Date: 2018-05-04
    Description: IJERPH, Vol. 15, Pages 910: Suicide Prevention Guideline Implementation in Specialist Mental Healthcare Institutions in The Netherlands International Journal of Environmental Research and Public Health doi: 10.3390/ijerph15050910 Authors: Jan Mokkenstorm Gerdien Franx Renske Gilissen Ad Kerkhof Johannes Smit In The Netherlands, on average 40% of all suicides concern patients treated by mental healthcare institutions (MHIs). Recent evidence indicates that implemented guideline recommendations significantly reduce the odds for patients to die by suicide. Implementation of the multidisciplinary guideline for diagnosis and treatment of suicidal behaviors is a main objective of the Dutch National Suicide Prevention Strategy. To this end, 24 MHIs that collectively reported 73% of patient suicides in 2015 received an educational outreach intervention offered by the national center of expertise. Aim: To investigate changes in levels of implementation of guideline recommendations; and to assess the degree of variation on suicide prevention policies and practices between MHIs. Methods: Implementation study with a prospective cohort design studying change over time on all domains of a Suicide Prevention Monitor, a guideline-based instrument assessing suicide prevention policies and practices within MHIs. Data were collected in six-month intervals between 2015 and 2017. Results: MHIs improved significantly on four out of ten domains: the development of an organizational suicide prevention policy; monitoring and trend-analysis of suicides numbers; evaluations after suicide; and clinician training. No improvement was measured on the domains pertaining to multi-annual training policies; collaborative care with external partners; recording and evaluation of suicide attempts; routine assessment of suicidality in all patients; safety planning and involving next of kin and carers. Furthermore, marked practice variation between MHIs was found which did not decrease over time. Conclusion: This study shows significant improvement in the implementation of four out of ten guideline-based suicide prevention policies in 24 specialist mental healthcare institutions in The Netherlands. The implementation level of suicide prevention policies and practices still appears to vary significantly between MHIs in The Netherlands.
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    MDPI Publishing
    Publication Date: 2018-05-04
    Description: IJERPH, Vol. 15, Pages 908: Factors Associated with Physical Activity and Sedentary Behavior in Older Adults from Six Low- and Middle-Income Countries International Journal of Environmental Research and Public Health doi: 10.3390/ijerph15050908 Authors: Cadeyrn J. Gaskin Liliana Orellana Rising life expectancy in low- and middle-income countries (LMIC), coupled with the increasing burden of non-communicable diseases, accentuates the importance of generating information to support public health strategies. With this aim in mind, the purpose of this study was to identify correlates of physical activity and sedentary behavior in LMIC. We analyzed Wave 1 data (collected 2007–2010) from the World Health Organization’s longitudinal Study on global AGEing and adult health (SAGE), which focuses on nationally representative samples of adults aged 50 years and older from six countries (China, n = 13,157; India, n = 6560; Mexico, n = 2301; Russian Federation, n = 3763; South Africa, n = 3836; and Ghana, n = 4305). Associations of physical activity (operationalized as meeting physical activity guidelines of ≥150 min/week of moderate-to-vigorous physical activity or not) and sedentary behavior (≥4 h/day versus <4 h/day) with demographic, health and health risk, functional, interpersonal, and environmental factors were assessed using multivariate logistic models. Across the six countries, we found fairly consistent and reasonably strong associations between both physical activity and sedentary behavior and several demographic factors (age and employment, in particular), self-reported health, instrumental activities of daily living, factors relating to socializing, and household location. Correlates of physical activity and sedentary behavior in LMIC appear to be similar to those found in high-income countries.
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    Publication Date: 2018-05-04
    Description: IJERPH, Vol. 15, Pages 907: The Relationship between Diabetes Mellitus and Respiratory Function in Patients Eligible for Coronary Artery Bypass Grafting International Journal of Environmental Research and Public Health doi: 10.3390/ijerph15050907 Authors: Aleksandra Szylińska Mariusz Listewnik Żaneta Ciosek Magdalena Ptak Anna Mikołajczyk Wioletta Pawlukowska Iwona Rotter Introduction: Spirometry performed prior to surgery provides information on the types of lung disorders in patients. The purpose of this study was to look for a relationship between the prevalence of diabetes and spirometry parameters. Material and Methods: The study was conducted in patients with coronary artery disease who were eligible for an isolated coronary artery bypass graft in 2013. The study group included 367 patients (287 men and 80 women) aged 68.7 ± 8.4 years. They were divided into those with diagnosed diabetes (group I, n = 138, 37.6%) and without diabetes (group II, n = 229, 62.4%). Spirometry tests were performed on the day of admission to the hospital. Results: Patients with diabetes (group I) had a significantly higher body mass index than those without diabetes (group II). Spirometry tests also showed that patients with diabetes had statistically significantly lower forced vital capacity (FVC) and forced expiratory volume in 1 s (FEV1.0). Both FVC and FEV1.0 were also statistically significantly lower for overweight and obese individuals in group I than those in group II. Conclusion: Patients with diabetes eligible for coronary artery bypass grafting with concurrent overweight or obesity are more likely to have lower spirometry parameters than those without diabetes.
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    Publication Date: 2018-05-04
    Description: IJERPH, Vol. 15, Pages 904: Seroprevalence of Hepatitis E Virus in Roma Settlements: A Comparison with the General Population in Slovakia International Journal of Environmental Research and Public Health doi: 10.3390/ijerph15050904 Authors: Monika Halánová Eduard Veseliny Zuzana Kalinová Peter Jarčuška Martin Janičko Ingrid Urbančíková Daniel Pella Sylvia Dražilová Ingrid Babinská HepaMeta Team Hepatitis E infection is one of the most frequent causes of acute hepatitis in the world. Currently five human genotypes with different geographical distributions and distinct epidemiologic patterns are identified. In Slovakia, only rare cases of hepatitis E have been reported in past years. Because the most important risk factors associated with HEV infection include consumption of contaminated pork meat and poor hygienic standards, the aim of the study was to evaluate the prevalence of anti-HEV total antibodies and the main risk factors for HEV in the population living in separated and segregated Roma settlements (n = 195), which represent places with increased risk of infection in Slovakia and to compare it with the prevalence in the general population (n = 69). Of 264 respondents included in the study, 47 (17.8%) showed positivity for anti-HEV antibodies, 42 of whom were Roma (21.5%, n = 195) and 5 (7.2%, n = 69) non-Roma. The population living in Roma settlements lives in poorer conditions and are at higher risk of HEV in comparison to the general population. However, differences in living conditions within the settlements do not contributed to lower risk of HEV antibody prevalence between Roma living in settlements.
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    Publication Date: 2018-04-04
    Description: In this paper, we consider the inference problem for a wide class of time-series models, referred to as multistate autoregressive models. The time series that we consider are composed of multiple epochs, each modeled by an autoregressive process. The number of epochs is unknown, and the transitions of states follow a Markov process of an unknown order. We propose an inference strategy that enables reliable and efficient offline analysis of this class of time series. The inference is carried out through a three-step approach: detecting the structural changes of the time series using a recently proposed multiwindow algorithm, identifying each segment as a state and selecting the most appropriate number of states, and estimating the Markov source based upon the symbolic sequence obtained from previous steps. We provide theoretical results and algorithms in order to facilitate the inference procedure described above. We demonstrate the accuracy, efficiency, and wide applicability of the proposed algorithms via an array of experiments using synthetic and real-world data.
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    Publication Date: 2018-04-04
    Description: Recent papers have formulated the problem of learning graphs from data as an inverse covariance estimation problem with graph Laplacian constraints. While such problems are convex, existing methods cannot guarantee that solutions will have specific graph topology properties (e.g., being a tree), which are desirable for some applications. The problem of learning a graph with topology properties is in general non-convex. In this paper, we propose an approach to solve these problems by decomposing them into two sub-problems for which efficient solutions are known. Specifically, a graph topology inference (GTI) step is employed to select a feasible graph topology. Then, a graph weight estimation (GWE) step is performed by solving a generalized graph Laplacian estimation problem, where edges are constrained by the topology found in the GTI step. Our main result is a bound on the error of the GWE step as a function of the error in the GTI step. This error bound indicates that the GTI step should be solved using an algorithm that approximates the data similarity matrix by another matrix whose entries have been thresholded to zero to have the desired type of graph topology. The GTI stage can leverage existing methods, which are typically based on minimizing the total weight of removed edges. Since the GWE stage is an inverse covariance estimation problem with linear constraints, it can be solved using existing convex optimization methods. We demonstrate that our approach can achieve good results for both synthetic and texture image data.
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    Publication Date: 2018-04-04
    Description: This special section of the IEEE/ACM Transactions on Computational Biology and Bioinformatics contains extended versions of the best papers presented at the First International Conference on Algorithms for Computational Biology (AlCoB 2014). Out of 39 submissions to the conference, only four papers representing the current state-of-the-art in their respective domains were accepted to this special section.
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    Publication Date: 2018-04-04
    Description: In this paper, we study the feasibility of an opportunistic radar, which exploits the probing signals transmitted during the sector level sweep of the IEEE 802.11ad beamforming training protocol. Several solutions are presented to detect the presence of prospective obstacles and estimate their position, radial velocity, and backscattered signal amplitude, which differ in the amount of prior information as to the transmitted signal and the channel fluctuation. Also, we derive the Cramér–Rao bound as a benchmark for the proposed estimators: The derivation of these bounds is per se relevant, as it generalizes classical results to the case where the echo is not entirely contained in the observation window. Numerical examples are provided to assess performance of the proposed solutions. The results indicate that the close-to-one detection probability is achievable up to 90 m with a probability of false alarm of 1e-4 and Swerling-I target fluctuation; in this region, the target delay is estimated with an accuracy smaller than the symbol interval (corresponding to a range resolution smaller than 10 cm) with probability close to one, while the velocity estimate is generally quite poor as a consequence of the very short duration of the probing signal.
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    Publication Date: 2018-04-04
    Description: This paper studies resilient multiagent distributed estimation of an unknown vector parameter when a subset of the agents is adversarial. We present and analyze a flag raising distributed estimator ( $mathcal {FRDE}$ ) that allows the agents under attack to perform accurate parameter estimation and detect the adversarial agents. The $mathcal {FRDE}$ algorithm is a consensus+innovations estimator in which agents combine estimates of neighboring agents (consensus) with local sensing information (innovations). We establish that, under $mathcal {FRDE}$ , either the uncompromised agents' estimates are almost surely consistent, or the uncompromised agents detect compromised agents (with arbitrarily small false alarm probability) if and only if the network of uncompromised agents is connected and globally observable. Numerical examples illustrate the performance of $mathcal {FRDE}$ .
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    Publication Date: 2018-04-04
    Description: Genome Rearrangements are large-scale mutational events that affect genomes during the evolutionary process. Therefore, these mutations differ from punctual mutations. They can move genes from one place to the other, change the orientation of some genes, or even change the number of chromosomes. In this work, we deal with inversion events which occur when a segment of DNA sequence in the genome is reversed. In our model, each inversion costs the number of elements in the reversed segment. We present a new algorithm for this problem based on the metaheuristic called Greedy Randomized Adaptive Search Procedure (GRASP) that has been routinely used to find solutions for combinatorial optimization problems. In essence, we implemented an iterative process in which each iteration receives a feasible solution whose neighborhood is investigated. Our analysis shows that we outperform any other approach by significant margin. We also use our algorithm to build phylogenetic trees for a subset of species in the Yersinia genus and we compared our trees to other results in the literature.
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    Publication Date: 2018-04-04
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    Publication Date: 2018-04-04
    Description: Read trimming is a fundamental first step of the analysis of next generation sequencing (NGS) data. Traditionally, it is performed heuristically, and algorithmic work in this area has been neglected. Here, we address this topic and formulate three optimization problems for block-based trimming (truncating the same low-quality positions at both ends for all reads and removing low-quality truncated reads). We find that all problems are NP-hard. Hence, we investigate the approximability of the problems. Two of them are NP-hard to approximate. However, the non-random distribution of quality scores in NGS data sets makes it tempting to speculate that quality constraints for read positions are typically satisfied by fulfilling quality constraints for reads. Thus, we propose three relaxed problems and develop efficient polynomial-time algorithms for them including heuristic speed-up techniques and parallelizations. We apply these optimized block trimming algorithms to 12 data sets from three species, four sequencers, and read lengths ranging from 36 to 101 bp and find that (i) the omitted constraints are indeed almost always satisfied, (ii) the optimized read trimming algorithms typically yield a higher number of untrimmed bases than traditional heuristics, and (iii) these results can be generalized to alternative objective functions beyond counting the number of untrimmed bases.
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    Publication Date: 2018-04-04
    Description: The endoplasmic reticulum (ER) is an intricate network that pervades the entire cortex of plant cells and its geometric shape undergoes drastic changes. This paper proposes a mathematical model to reconstruct geometric network dynamics by combining the node movements within the network and topological changes engendered by these nodes. The network topology in the model is determined by a modified optimization procedure from the work (Lemarchand, et al. 2014) which minimizes the total length taking into account both degree and angle constraints, beyond the conditions of connectedness and planarity. A novel feature for solving our optimization problem is the use of “lifted” angle constraints, which allows one to considerably reduce the solution runtimes. Using this optimization technique and a Langevin approach for the branching node movement, the simulated network dynamics represent the ER network dynamics observed under latrunculin B treated condition and recaptures features such as the appearance/disappearance of loops within the ER under the native condition. The proposed modeling approach allows quantitative comparison of networks between the model and experimental data based on topological changes induced by node dynamics. An increased temporal resolution of experimental data will allow a more detailed comparison of network dynamics using this modeling approach.
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    Publication Date: 2018-04-04
    Description: Network component analysis (NCA) is an important method for inferring transcriptional regulatory networks (TRNs) and recovering transcription factor activities (TFAs) using gene expression data, and the prior information about the connectivity matrix. The algorithms currently available crucially depend on the completeness of this prior information. However, inaccuracies in the measurement process may render incompleteness in the available knowledge about the connectivity matrix. Hence, computationally efficient algorithms are needed to overcome the possible incompleteness in the available data. We present a sparse network component analysis algorithm (sparseNCA), which incorporates the effect of incompleteness in the estimation of TRNs by imposing an additional sparsity constraint using the $ell _1$ norm, which results in a greater estimation accuracy. In order to improve the computational efficiency, an iterative re-weighted $ell _2$ method is proposed for the NCA problem which not only promotes sparsity but is hundreds of times faster than the $ell _1$ norm based solution. The performance of sparseNCA is rigorously compared to that of FastNCA and NINCA using synthetic data as well as real data. It is shown that sparseNCA outperforms the existing state-of-the-art algorithms both in terms of estimation accuracy and consistency with the added advantage of low computational complexity. The performance of sparseNCA compared to its predecessors is particularly pronounced in case of incomplete prior info- mation about the sparsity of the network. Subnetwork analysis is performed on the E.coli data which reiterates the superior consistency of the proposed algorithm.
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    Publication Date: 2018-04-04
    Description: Phylogenetic tree reconciliation is an important technique for reconstructing the evolutionary histories of species and genes and other dependent entities. Reconciliation is typically performed in a maximum parsimony framework and the number of optimal reconciliations can grow exponentially with the size of the trees, making it difficult to understand the solution space. This paper demonstrates how a small number of reconciliations can be found that collectively contain the most highly supported events in the solution space. While we show that the formal problem is NP-complete, we give a $1-frac{1}{e}$ approximation algorithm, experimental results that indicate its effectiveness, and the new DTL-RnB software tool that uses our algorithms to summarize the space of optimal reconciliations ( www.cs.hmc.edu/dtlrnb ).
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    Topics: Biology , Computer Science
    Published by Institute of Electrical and Electronics Engineers (IEEE) on behalf of The IEEE Computational Intelligence Society ; The IEEE Computer Society ; The IEEE Control Systems Society ; The IEEE Engineering in Medicine and Biology Society ; The Association for Computing Machinery.
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    Institute of Electrical and Electronics Engineers (IEEE)
    Publication Date: 2018-04-04
    Description: A minimum hybridization network is a rooted phylogenetic network that displays two given rooted phylogenetic trees using a minimum number of reticulations. Previous mathematical work on their calculation has usually assumed the input trees to be bifurcating, correctly rooted, or that they both contain the same taxa. These assumptions do not hold in biological studies and “realistic” trees have multifurcations, are difficult to root, and rarely contain the same taxa. We present a new algorithm for computing minimum hybridization networks for a given pair of “realistic” rooted phylogenetic trees. We also describe how the algorithm might be used to improve the rooting of the input trees. We introduce the concept of “autumn trees”, a nice framework for the formulation of algorithms based on the mathematics of “maximum acyclic agreement forests”. While the main computational problem is hard, the run-time depends mainly on how different the given input trees are. In biological studies, where the trees are reasonably similar, our parallel implementation performs well in practice. The algorithm is available in our open source program Dendroscope 3, providing a platform for biologists to explore rooted phylogenetic networks. We demonstrate the utility of the algorithm using several previously studied data sets.
    Print ISSN: 1545-5963
    Electronic ISSN: 1557-9964
    Topics: Biology , Computer Science
    Published by Institute of Electrical and Electronics Engineers (IEEE) on behalf of The IEEE Computational Intelligence Society ; The IEEE Computer Society ; The IEEE Control Systems Society ; The IEEE Engineering in Medicine and Biology Society ; The Association for Computing Machinery.
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  • 83
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    Institute of Electrical and Electronics Engineers (IEEE)
    Publication Date: 2018-04-04
    Description: Reconstruction of ancestral relationships among genera, species, and populations is a core task in evolutionary biology. At the population level, pedigrees have been commonly used. Reconstruction of pedigree is required in practice due to legal or medical reasons. Pedigrees are very important to geneticists for inferring haplotype segments, recombination, and allele sharing status with which disease loci can be identified. Evaluating reconstruction methods requires comparing the inferred pedigree and the known pedigrees. Moreover, comparison of pedigrees is required in studying relationships among crops such as maize, wheat and barley, etc. In this paper, we discuss three models for comparison of pedigrees, the maximum pedigree isomorphism problem, the maximum paternal-path-preserved mapping problem, and the minimum edge-cutting mapping problem. For the maximum pedigree isomorphism problem, we prove that the problem is NP-hard and give a fixed-parameter algorithm for the problem. For the maximum paternal-path-preserved mapping problem, we give a dynamic-programming algorithm to find the mapping that preserves the maximum number of paternal paths between the two input pedigrees. For the minimum edge-cutting mapping problem, we prove that the problem is NP-hard and give a fixed-parameter algorithm with running time $O(n(1+sqrt{2})^k)$ , where $n$ is the number of vertices in the two input pedigrees and $k$ is the number of edges to be cut. This algorithm is useful in practice when comparing two similar pedigrees.
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