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  • BioMed Central  (10,457)
  • Public Library of Science (PLoS)  (10,371)
  • MDPI Publishing
  • 2015-2019  (28,258)
  • 2005-2009
  • 2015  (28,258)
  • 1
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    Insights into transcriptional changes that accompany organelle sequestration from the stolen nucleus of Mesodinium rubrum (2015)
    BioMed Central
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Genomics 16 (2015): 805, doi:10.1186/s12864-015-2052-9.
    Description: Organelle retention is a form of mixotrophy that allows organisms to reap metabolic benefits similar to those of photoautotrophs through capture of algal prey and sequestration of their plastids. Mesodinium rubrum is an abundant and broadly distributed photosynthetic marine ciliate that steals organelles from cryptophyte algae, such as Geminigera cryophila. M. rubrum is unique from most other acquired phototrophs because it also steals a functional nucleus that facilitates genetic control of sequestered plastids and other organelles. We analyzed changes in G. cryophila nuclear gene expression and transcript abundance after its incorporation into the cellular architecture of M. rubrum as an initial step towards understanding this complex system. We compared Illumina-generated transcriptomes of the cryptophyte Geminigera cryophila as a free-living cell and as a sequestered nucleus in M. rubrum to identify changes in protein abundance and gene expression. After KEGG annotation, proteins were clustered by functional categories, which were evaluated for over- or under-representation in the sequestered nucleus. Similarly, coding sequences were grouped by KEGG categories/pathways, which were then evaluated for over- or under-expression via read count strategies. At the time of sampling, the global transcriptome of M. rubrum was dominated (~58–62 %) by transcription from its stolen nucleus. A comparison of transcriptomes from free-living G. cryophila cells to those of the sequestered nucleus revealed a decrease in gene expression and transcript abundance for most functional protein categories within the ciliate. However, genes coding for proteins involved in photosynthesis, oxidative stress reduction, and several other metabolic pathways revealed striking exceptions to this general decline. Major changes in G. cryophila transcript expression after sequestration by M. rubrum and the ciliate’s success as a photoautotroph imply some level of control or gene regulation by the ciliate and at the very least reflect a degree of coordination between host and foreign organelles. Intriguingly, cryptophyte genes involved in protein transport are significantly under-expressed in M. rubrum, implicating a role for the ciliate’s endomembrane system in targeting cryptophyte proteins to plastid complexes. Collectively, this initial portrait of an acquired transcriptome within a dynamic and ecologically successful ciliate highlights the remarkable cellular and metabolic chimerism of this system.
    Description: The authors wish to acknowledge the support of NSF award 1354773.
    Keywords: Mesodinium rubrum ; Geminigera cryophila ; Karyoklepty ; Acquired phototrophy ; Transcriptome ; Differential gene expression ; Chimeric metabolism ; Organelle retention ; Mixotrophy
    Repository Name: Woods Hole Open Access Server
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    Athletic equipment microbiota are shaped by interactions with human skin (2015)
    BioMed Central
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Microbiome 3 (2015): 25, doi:10.1186/s40168-015-0088-3.
    Description: Americans spend the vast majority of their lives in built environments. Even traditionally outdoor pursuits, such as exercising, are often now performed indoors. Bacteria that colonize these indoor ecosystems are primarily derived from the human microbiome. The modes of human interaction with indoor surfaces and the physical conditions associated with each surface type determine the steady-state ecology of the microbial community. Bacterial assemblages associated with different surfaces in three athletic facilities, including floors, mats, benches, free weights, and elliptical handles, were sampled every other hour (8 am to 6 pm) for 2 days. Surface and equipment type had a stronger influence on bacterial community composition than the facility in which they were housed. Surfaces that were primarily in contact with human skin exhibited highly dynamic bacterial community composition and non-random co-occurrence patterns, suggesting that different host microbiomes—shaped by selective forces—were being deposited on these surfaces through time. However, bacterial assemblages found on the floors and mats changed less over time, and species co-occurrence patterns appeared random, suggesting more neutral community assembly. These longitudinal patterns highlight the dramatic turnover of microbial communities on surfaces in regular contact with human skin. By uncovering these longitudinal patterns, this study promotes a better understanding of microbe-human interactions within the built environment.
    Description: MW was supported by a Weinberg College of Arts and Sciences Summer Grant from Northwestern University. This work was supported in part by the U.S. Dept. of Energy under Contract DE-AC02-06CH11357. This work was also supported by the Alfred P Sloan Foundation’s Microbiology of the Built Environment research program. SMG was supported by an EPA STAR Graduate Fellowship and the National Institutes of Health Training Grant 5 T-32 EB-009412.
    Keywords: Gym microbiome ; Athletic equipment ; Microbiology ; Niche communities ; Next-generation sequencing
    Repository Name: Woods Hole Open Access Server
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    Forensic analysis of the microbiome of phones and shoes (2015)
    BioMed Central
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Microbiome 3 (2015): 21, doi:10.1186/s40168-015-0082-9.
    Description: Microbial interaction between human-associated objects and the environments we inhabit may have forensic implications, and the extent to which microbes are shared between individuals inhabiting the same space may be relevant to human health and disease transmission. In this study, two participants sampled the front and back of their cell phones, four different locations on the soles of their shoes, and the floor beneath them every waking hour over a 2-day period. A further 89 participants took individual samples of their shoes and phones at three different scientific conferences. Samples taken from different surface types maintained significantly different microbial community structures. The impact of the floor microbial community on that of the shoe environments was strong and immediate, as evidenced by Procrustes analysis of shoe replicates and significant correlation between shoe and floor samples taken at the same time point. Supervised learning was highly effective at determining which participant had taken a given shoe or phone sample, and a Bayesian method was able to determine which participant had taken each shoe sample based entirely on its similarity to the floor samples. Both shoe and phone samples taken by conference participants clustered into distinct groups based on location, though much more so when an unweighted distance metric was used, suggesting sharing of low-abundance microbial taxa between individuals inhabiting the same space. Correlations between microbial community sources and sinks allow for inference of the interactions between humans and their environment.
    Description: This work was enabled by the generous support of the Alfred P Sloan foundation. This work was supported in part by the U.S. Dept. of Energy under Contract DE-AC02-06CH11357. S.M.G. was supported by an EPA STAR Graduate Fellowship and by a National Institutes of Health Training Grant 5 T-32 EB-009412.
    Keywords: Forensic microbiology ; Source-sink dynamics ; Shoe microbiome ; Phone microbiome ; Microbial time series
    Repository Name: Woods Hole Open Access Server
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    The ocean sampling day consortium (2015)
    BioMed Central
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    Publication Date: 2022-10-18
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in GigaScience 4 (2015): 27, doi:10.1186/s13742-015-0066-5.
    Description: Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits.
    Description: This work was supported by the Micro B3 project, which is funded from the European Union’s Seventh Framework Programme (FP7; Joint Call OCEAN.2011‐2: Marine microbial diversity – new insights into marine ecosystems functioning and its biotechnological potential) under the grant agreement no 287589.
    Keywords: Ocean sampling day ; OSD ; Biodiversity ; Genomics ; Health index ; Bacteria ; Microorganism ; Metagenomics ; Marine ; Micro B3 ; Standards
    Repository Name: Woods Hole Open Access Server
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    Transcriptional profiling of reproductive development, lipid storage and molting throughout the last juvenile stage of the marine copepod Calanus finmarchicus (2015)
    BioMed Central
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Zoology 11 (2014): 91, doi:10.1186/s12983-014-0091-8.
    Description: Calanus finmarchicus, a highly abundant copepod that is an important primary consumer in North Atlantic ecosystems, has a flexible life history in which copepods in the last juvenile developmental stage (fifth copepodid, C5) may either delay maturation and enter diapause or molt directly into adults. The factors that regulate this developmental plasticity are poorly understood, and few tools have been developed to assess the physiological condition of individual copepods. We sampled a cultured population of C. finmarchicus copepods daily throughout the C5 stage and assessed molt stage progression, gonad development and lipid storage. We used high-throughput sequencing to identify genes that were differentially expressed during progression through the molt stage and then used qPCR to profile daily expression of individual genes. Based on expression profiles of twelve genes, samples were statistically clustered into three groups: (1) an early period occurring prior to separation of the cuticle from the epidermis (apolysis) when expression of genes associated with lipid synthesis and transport (FABP and ELOV) and two nuclear receptors (ERR and HR78) was highest, (2) a middle period of rapid change in both gene expression and physiological condition, including local minima and maxima in several nuclear receptors (FTZ-F1, HR38b, and EcR), and (3) a late period when gonads were differentiated and expression of genes associated with molting (Torso-like, HR38a) peaked. The ratio of Torso-like to HR38b strongly differentiated the early and late groups. This study provides the first dynamic profiles of gene expression anchored with morphological markers of lipid accumulation, development and gonad maturation throughout a copepod molt cycle. Transcriptomic profiling revealed significant changes over the molt cycle in genes with presumed roles in lipid synthesis, molt regulation and gonad development, suggestive of a coupling of these processes in Calanus finmarchicus. Finally, we identified gene expression profiles that strongly differentiate between early and late development within the C5 copepodid stage. We anticipate that these findings and continued development of robust gene expression biomarkers that distinguish between diapause preparation and continuous development will ultimately enable novel studies of the intrinsic and extrinsic factors that govern diapause initiation in Calanus finmarchicus.
    Description: This work was supported by grant number OCE-1132567 from the National Science Foundation to MFB and AMT. Additional supported was provided by WHOI Early Career Scientist Awards provided to MFB and AMT.
    Keywords: Arthropod ; Crustacean ; Gene expression ; Molt cycle ; Transcriptomics
    Repository Name: Woods Hole Open Access Server
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    Unique patterns of transcript and miRNA expression in the South American strong voltage electric eel (Electrophorus electricus) (2015)
    BioMed Central
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Genomics 16 (2015): 243, doi:10.1186/s12864-015-1288-8.
    Description: With its unique ability to produce high-voltage electric discharges in excess of 600 volts, the South American strong voltage electric eel (Electrophorus electricus) has played an important role in the history of science. Remarkably little is understood about the molecular nature of its electric organs. We present an in-depth analysis of the genome of E. electricus, including the transcriptomes of eight mature tissues: brain, spinal cord, kidney, heart, skeletal muscle, Sachs’ electric organ, main electric organ, and Hunter’s electric organ. A gene set enrichment analysis based on gene ontology reveals enriched functions in all three electric organs related to transmembrane transport, androgen binding, and signaling. This study also represents the first analysis of miRNA in electric fish. It identified a number of miRNAs displaying electric organ-specific expression patterns, including one novel miRNA highly over-expressed in all three electric organs of E. electricus. All three electric organ tissues also express three conserved miRNAs that have been reported to inhibit muscle development in mammals, suggesting that miRNA-dependent regulation of gene expression might play an important role in specifying an electric organ identity from its muscle precursor. These miRNA data were supported using another complete miRNA profile from muscle and electric organ tissues of a second gymnotiform species. Our work on the E. electricus genome and eight tissue-specific gene expression profiles will greatly facilitate future research on determining the coding and regulatory sequences that specify the function, development, and evolution of electric organs. Moreover, these data and future studies will be informed by the first comprehensive analysis of miRNA expression in an electric fish presented here.
    Description: This project has been funded in part by NSF Grant MCB No. 1144012 (MRS), NSF Grant DEB No. 0741450 (JSA), NSF Grant CNS No. 1248109 (GAU), W.M. Keck Foundation Distinguished Young Scholars in Medical Research (CDN), NIH R01 GM084879 (HZ), NIH grant R01 GM088670 (RA), NIH grant 1SC1GM092297-01A1 (GAU), the Morgridge Graduate Fellowship (JDV and LLT), University of Wisconsin Genetics NIH Graduate Training Grant (LLT); and the Cornell University Center for Vertebrate Genomics (JRG).
    Keywords: Electric eel ; Genome ; Transcriptome ; miRNA ; Gene ontology
    Repository Name: Woods Hole Open Access Server
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    Evolution of hematophagous habit in Triatominae (Heteroptera: Reduviidae) (2015)
    BioMed Central
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    Publication Date: 2015-02-19
    Print ISSN: 0716-078X
    Electronic ISSN: 0717-6317
    Topics: Biology , Geosciences
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    Prosopis tamarugo Phil.: a native tree from the Atacama Desert groundwater table depth thresholds for conservation (2015)
    BioMed Central
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    Publication Date: 2015-12-01
    Print ISSN: 0716-078X
    Electronic ISSN: 0717-6317
    Topics: Biology , Geosciences
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    Differentiation and characterization of burrows of two species of armadillos in the Brazilian Cerrado (2015)
    BioMed Central
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    Publication Date: 2015-12-01
    Print ISSN: 0716-078X
    Electronic ISSN: 0717-6317
    Topics: Biology , Geosciences
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    The presence of the marsupial Dromiciops gliroides in Parque Nacional Los Alerces, Chubut, Southern Argentina, after the synchronous maturation and flowering of native bamboo and subsequent rodent irruption (2015)
    BioMed Central
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    Publication Date: 2015-10-15
    Print ISSN: 0716-078X
    Electronic ISSN: 0717-6317
    Topics: Biology , Geosciences
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    Oak canopy arthropod communities: which factors shape its structure? (2015)
    BioMed Central
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    Publication Date: 2015-08-18
    Print ISSN: 0716-078X
    Electronic ISSN: 0717-6317
    Topics: Biology , Geosciences
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    Morphological variation of Cosmos bipinnatus (Asteraceae) and its relation to abiotic variables in central Mexico (2015)
    BioMed Central
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    Publication Date: 2015-08-18
    Print ISSN: 0716-078X
    Electronic ISSN: 0717-6317
    Topics: Biology , Geosciences
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    Rapid changes in tree composition and biodiversity: consequences of dams on dry seasonal forests (2015)
    BioMed Central
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    Publication Date: 2015-06-05
    Print ISSN: 0716-078X
    Electronic ISSN: 0717-6317
    Topics: Biology , Geosciences
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    Effect of host-plant genetic diversity on oak canopy arthropod community structure in central Mexico (2015)
    BioMed Central
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    Publication Date: 2015-05-12
    Print ISSN: 0716-078X
    Electronic ISSN: 0717-6317
    Topics: Biology , Geosciences
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    Spatial distribution pattern of Mytilus chilensis beds in the Reloncaví fjord: hypothesis on associated processes (2015)
    BioMed Central
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    Publication Date: 2015-05-01
    Print ISSN: 0716-078X
    Electronic ISSN: 0717-6317
    Topics: Biology , Geosciences
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    Assessment of the efficiency in trapping North American mink (Neovison vison) for population control in Patagonia (2015)
    BioMed Central
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    Publication Date: 2015-04-16
    Print ISSN: 0716-078X
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    Topics: Biology , Geosciences
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    Influence of forest type and host plant genetic relatedness on the canopy arthropod community structure of Quercus crassifolia (2015)
    BioMed Central
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    Publication Date: 2015-03-24
    Print ISSN: 0716-078X
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    Topics: Biology , Geosciences
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    Evidence that the house finch (Carpodacus mexicanus) uses scent to avoid omnivore mammals (2015)
    BioMed Central
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    Publication Date: 2015-02-24
    Print ISSN: 0716-078X
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    Topics: Biology , Geosciences
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    Suaeda foliosa Moq. (Caryophyllales: Amaranthaceae) first record of the genus and species for Valparaíso Region, Chile (2015)
    BioMed Central
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    Publication Date: 2015-01-30
    Print ISSN: 0716-078X
    Electronic ISSN: 0717-6317
    Topics: Biology , Geosciences
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    Invasion of North American beaver (Castor canadensis) in the province of Magallanes, Southern Chile: comparison between dating sites through interviews with the local community and dendrochronology (2015)
    BioMed Central
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    Publication Date: 2015-02-05
    Print ISSN: 0716-078X
    Electronic ISSN: 0717-6317
    Topics: Biology , Geosciences
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  • 21
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    Tail autotomy effects on the escape behavior of the lizard Gonatodes albogularis (Squamata: Sphaerodactylidae), from Córdoba, Colombia (2015)
    BioMed Central
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    Publication Date: 2015-01-07
    Print ISSN: 0716-078X
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    Topics: Biology , Geosciences
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    Germination, seedling performance, and root production after simulated partial seed predation of a threatened Atacama Desert shrub (2015)
    BioMed Central
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    Publication Date: 2015-04-21
    Print ISSN: 0716-078X
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    Topics: Biology , Geosciences
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  • 23
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    Evaluating taxonomic homogenization of freshwater fish assemblages in Chile (2015)
    BioMed Central
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    Publication Date: 2015-09-17
    Print ISSN: 0716-078X
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    Topics: Biology , Geosciences
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    Entropy, Vol. 17, Pages 5729-5751: Deformed Algebras and Generalizations of Independence on Deformed Exponential Families (2015)
    MDPI Publishing
    In: Entropy
    Details
    Publication Date: 2015-08-11
    Description: A deformed exponential family is a generalization of exponential families. Since the useful classes of power law tailed distributions are described by the deformed exponential families, they are important objects in the theory of complex systems. Though the deformed exponential families are defined by deformed exponential functions, these functions do not satisfy the law of exponents in general. The deformed algebras have been introduced based on the deformed exponential functions. In this paper, after summarizing such deformed algebraic structures, it is clarified how deformed algebras work on deformed exponential families. In fact, deformed algebras cause generalization of expectations. The three kinds of expectations for random variables are introduced in this paper, and it is discussed why these generalized expectations are natural from the viewpoint of information geometry. In addition, deformed algebras cause generalization of independences. Whereas it is difficult to check the well-definedness of deformed independence in general, the κ-independence is always well-defined on κ-exponential families. This is one of advantages of κ-exponential families in complex systems. Consequently, we can well generalize the maximum likelihood method for the κ-exponential family from the viewpoint of information geometry.
    Electronic ISSN: 1099-4300
    Topics: Chemistry and Pharmacology , Physics
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    Entropy, Vol. 17, Pages 5752-5770: Consistency of Learning Bayesian Network Structures with Continuous Variables: An Information Theoretic Approach (2015)
    MDPI Publishing
    In: Entropy
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    Publication Date: 2015-08-11
    Description: We consider the problem of learning a Bayesian network structure given n examples and the prior probability based on maximizing the posterior probability. We propose an algorithm that runs in O(n log n) time and that addresses continuous variables and discrete variables without assuming any class of distribution. We prove that the decision is strongly consistent, i.e., correct with probability one as n ! 1. To date, consistency has only been obtained for discrete variables for this class of problem, and many authors have attempted to prove consistency when continuous variables are present. Furthermore, we prove that the “log n” term that appears in the penalty term of the description length can be replaced by 2(1+ε) log log n to obtain strong consistency, where ε > 0 is arbitrary, which implies that the Hannan–Quinn proposition holds.
    Electronic ISSN: 1099-4300
    Topics: Chemistry and Pharmacology , Physics
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    IJERPH, Vol. 12, Pages 9330-9341: The Willingness-to-Pay for General Practitioners in Contractual Service and Influencing Factors among Empty Nesters in Chongqing, China (2015)
    MDPI Publishing
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    Publication Date: 2015-08-11
    Description: Background: In 2012, a pilot health policy of contractual service relations between general practitioners and patients was implemented in China. Due to the decline in body and cognitive function, as well as the lack of family care and narrow social support networks, the demand of health services among the elderly is much higher than that among the general population. This study aims to probe into the empty nesters’ willingness-to-pay for general practitioners using a contractual service policy, investigating empty nesters’ payment levels for the service, and analyze the main factors affecting the willingness of empty-nesters’ general practitioners using contractual service supply cost. Methods: This cross-sectional study adopted a multistage stratified sampling method to survey 865, city empty nesters (six communities in three districts of one city) aged 60–85 years. A condition value method was used to infer the distribution of the willingness-to-pay; Cox’s proportional hazards regression model was used to analyze the influencing factors of willingness-to-pay. Results: More than seventy percent (76.6%) of the empty nesters in this city were willing to pay general practitioners using contract service in Chongqing. The level of willingness-to-pay for the surveyed empty nesters was 34.1 yuan per year. The median value was 22.1 yuan per year, which was below the Chongqing urban and rural cooperative medical insurance individual funding level (60 yuan per year) in 2013. Cox’s proportional hazards regression model analysis showed that the higher the education level was, the worse the self-reported health status would be, accompanied by higher family per capita income, higher satisfaction of community health service, and higher willingness-to-pay empty nesters using a contract service. Women had a higher willingness-to-pay than men. Conclusions: The willingness-to-pay for general practitioners by contractual service is high among city empty nesters in Chongqing, thus, individual financing is feasible. However, people are willing to pay less than half of the current personal financing of cooperative medical insurance of urban and rural residents. Education level, family per capita income, and self-reported health status are the main factors affecting the cost sharing intention for general practitioners using contract service supply. According to the existing situation of different empty nesters, it is important to perfect the design of general practitioners using a contractual service policy system, according to differentiated personal financing levels.
    Print ISSN: 1661-7827
    Electronic ISSN: 1660-4601
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Medicine
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    Fibrinogen production is enhanced in an in-vitro model of non-alcoholic fatty liver disease: an isolated risk factor for cardiovascular events? (2015)
    BioMed Central
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    Publication Date: 2015-08-11
    Description: Background: Cardiovascular disease (CVD) remains the major cause of excess mortality in patients with non-alcoholic fatty liver disease (NAFLD). The aim of this study was to investigate the individual contribution of NAFLD to CVD risk factors in the absence of pathogenic influences from other comorbidities often found in NAFLD patients, by using an established in-vitro model of hepatic steatosis. Methods: Histopathological events in non-alcoholic fatty liver disease were recapitulated by focused metabolic nutrient overload of hepatoblastoma C3A cells, using oleate-treated-cells and untreated controls for comparison. Microarray and proteomic data from cell culture experiments were integrated into a custom-built systems biology database and proteogenomics analysis performed. Candidate genes with significant dysregulation and concomitant changes in protein abundance were identified and STRING association and enrichment analysis performed to identify putative pathogenic pathways. Results: The search strategy yielded 3 candidate genes that were specifically and significantly up-regulated in nutrient-overloaded cells compared to untreated controls: fibrinogen alpha chain (2.2 fold), fibrinogen beta chain (2.3 fold) and fibrinogen gamma chain (2.1 fold) (all rank products pfp
    Electronic ISSN: 1476-511X
    Topics: Biology
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    Materials, Vol. 8, Pages 5138-5153: A Unified Model for the Prediction of Yield Strength in Particulate-Reinforced Metal Matrix Nanocomposites (2015)
    MDPI Publishing
    In: Materials
    Details
    Publication Date: 2015-08-11
    Description: Lightweighting in the transportation industry is today recognized as one of the most important strategies to improve fuel efficiency and reduce anthropogenic climate-changing, environment-damaging, and human death-causing emissions. However, the structural applications of lightweight alloys are often limited by some inherent deficiencies such as low stiffness, high wear rate and inferior strength. These properties could be effectively enhanced by the addition of stronger and stiffer reinforcements, especially nano-sized particles, into metal matrix to form composites. In most cases three common strengthening mechanisms (load-bearing effect, mismatch of coefficients of thermal expansion, and Orowan strengthening) have been considered to predict the yield strength of metal matrix nanocomposites (MMNCs). This study was aimed at developing a unified model by taking into account the matrix grain size and porosity (which is unavoidable in the materials processing such as casting and powder metallurgy) in the prediction of the yield strength of MMNCs. The Zener pinning effect of grain boundaries by the nano-sized particles has also been integrated. The model was validated using the experimental data of magnesium- and titanium-based nanocomposites containing different types of nano-sized particles (namely, Al2O3, Y2O3, and carbon nanotubes). The predicted results were observed to be in good agreement with the experimental data reported in the literature.
    Electronic ISSN: 1996-1944
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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    Energies, Vol. 8, Pages 8431-8446: A New Adsorbent Composite Material Based on Metal Fiber Technology and Its Application in Adsorption Heat Exchangers (2015)
    MDPI Publishing
    In: Energies
    Details
    Publication Date: 2015-08-11
    Description: In order to achieve process intensification for adsorption chillers and heat pumps, a new composite material was developed based on sintered aluminum fibers from a melt-extraction process and a dense layer of silico-aluminophosphate (SAPO-34) on the fiber surfaces. The SAPO-34 layer was obtained through a partial support transformation (PST) process. Preparation of a composite sample is described and its characteristic pore size distribution and heat conductivity are presented. Water adsorption data obtained under conditions of a large pressure jump are given. In the next step, preparation of the composite was scaled up to larger samples which were fixed on a small adsorption heat exchanger. Adsorption measurements on this heat exchanger element that confirm the achieved process intensification are presented. The specific cooling power for the adsorption step per volume of composite is found to exceed 500 kW/m3 under specified conditions.
    Electronic ISSN: 1996-1073
    Topics: Energy, Environment Protection, Nuclear Power Engineering
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    What defines an adaptive radiation? Macroevolutionary diversification dynamics of an exceptionally species-rich continental lizard radiation (2015)
    BioMed Central
    Details
    Publication Date: 2015-08-08
    Description: Background: Adaptive radiation theory posits that ecological opportunity promotes rapid proliferation of phylogenetic and ecological diversity. Given that adaptive radiation proceeds via occupation of available niche space in newly accessed ecological zones, theory predicts that: (i) evolutionary diversification follows an ‘early-burst’ process, i.e., it accelerates early in the history of a clade (when available niche space facilitates speciation), and subsequently slows down as niche space becomes saturated by new species; and (ii) phylogenetic branching is accompanied by diversification of ecologically relevant phenotypic traits among newly evolving species. Here, we employ macroevolutionary phylogenetic model-selection analyses to address these two predictions about evolutionary diversification using one of the most exceptionally species-rich and ecologically diverse lineages of living vertebrates, the South American lizard genus Liolaemus. Results: Our phylogenetic analyses lend support to a density-dependent lineage diversification model. However, the lineage through-time diversification curve does not provide strong support for an early burst. In contrast, the evolution of phenotypic (body size) relative disparity is high, significantly different from a Brownian model during approximately the last 5 million years of Liolaemus evolution. Model-fitting analyses also reject the ‘early-burst’ model of phenotypic evolution, and instead favour stabilizing selection (Ornstein-Uhlenbeck, with three peaks identified) as the best model for body size diversification. Finally, diversification rates tend to increase with smaller body size. Conclusions: Liolaemus have diversified under a density-dependent process with slightly pronounced apparent episodic pulses of lineage accumulation, which are compatible with the expected episodic ecological opportunity created by gradual uplifts of the Andes over the last ~25My. We argue that ecological opportunity can be strong and a crucial driver of adaptive radiations in continents, but may emerge less frequently (compared to islands) when major events (e.g., climatic, geographic) significantly modify environments. In contrast, body size diversification conforms to an Ornstein-Uhlenbeck model with multiple trait optima. Despite this asymmetric diversification between both lineages and phenotype, links are expected to exist between the two processes, as shown by our trait-dependent analyses of diversification. We finally suggest that the definition of adaptive radiation should not be conditioned by the existence of early-bursts of diversification, and should instead be generalized to lineages in which species and ecological diversity have evolved from a single ancestor.
    Electronic ISSN: 1471-2148
    Topics: Biology
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    Confident difference criterion: a new Bayesian differentially expressed gene selection algorithm with applications (2015)
    BioMed Central
    Details
    Publication Date: 2015-08-08
    Description: Background: Recently, the Bayesian method becomes more popular for analyzing high dimensional gene expression data as it allows us to borrow information across different genes and provides powerful estimators for evaluating gene expression levels. It is crucial to develop a simple but efficient gene selection algorithm for detecting differentially expressed (DE) genes based on the Bayesian estimators. Results: In this paper, by extending the two-criterion idea of Chen et al. (Chen M-H, Ibrahim JG, Chi Y-Y. A new class of mixture models for differential gene expression in DNA microarray data. J Stat Plan Inference. 2008;138:387–404), we propose two new gene selection algorithms for general Bayesian models and name these new methods as the confident difference criterion methods. One is based on the standardized differences between two mean expression values among genes; the other adds the differences between two variances to it. The proposed confident difference criterion methods first evaluate the posterior probability of a gene having different gene expressions between competitive samples and then declare a gene to be DE if the posterior probability is large. The theoretical connection between the proposed first method based on the means and the Bayes factor approach proposed by Yu et al. (Yu F, Chen M-H, Kuo L. Detecting differentially expressed genes using alibrated Bayes factors. Statistica Sinica. 2008;18:783–802) is established under the normal-normal-model with equal variances between two samples. The empirical performance of the proposed methods is examined and compared to those of several existing methods via several simulations. The results from these simulation studies show that the proposed confident difference criterion methods outperform the existing methods when comparing gene expressions across different conditions for both microarray studies and sequence-based high-throughput studies. A real dataset is used to further demonstrate the proposed methodology. In the real data application, the confident difference criterion methods successfully identified more clinically important DE genes than the other methods. Conclusion: The confident difference criterion method proposed in this paper provides a new efficient approach for both microarray studies and sequence-based high-throughput studies to identify differentially expressed genes.
    Electronic ISSN: 1471-2105
    Topics: Biology , Computer Science
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    Putative type 1 thymidylate synthase and dihydrofolate reductase as signature genes of a novel bastille-like group of phages in the subfamily Spounavirinae (2015)
    BioMed Central
    Details
    Publication Date: 2015-08-08
    Description: Background: Spounavirinae viruses have received an increasing interest as tools for the control of harmful bacteria due to their relatively broad host range and strictly virulent phenotype. Results: In this study, we collected and analyzed the complete genome sequences of 61 published phages, either ICTV-classified or candidate members of the Spounavirinae subfamily of the Myoviridae. A set of comparative analyses identified a distinct, recently proposed Bastille-like phage group within the Spounavirinae. More importantly, type 1 thymidylate synthase (TS1) and dihydrofolate reductase (DHFR) genes were shown to be unique for the members of the proposed Bastille-like phage group, and are suitable as molecular markers. We also show that the members of this group encode beta-lactamase and/or sporulation-related SpoIIIE homologs, possibly questioning their suitability as biocontrol agents. Conclusions: We confirm the creation of a new genus—the “Bastille-like group”—in Spounavirinae, and propose that the presence of TS1- and DHFR-encoding genes could serve as signatures for the new Bastille-like group. In addition, the presence of metallo-beta-lactamase and/or SpoIIIE homologs in all members of Bastille-like group phages makes questionable their suitability for use in biocontrol.
    Electronic ISSN: 1471-2164
    Topics: Biology
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    A global analysis of the complex landscape of isoforms and regulatory networks of p63 in human cells and tissues (2015)
    BioMed Central
    Details
    Publication Date: 2015-08-08
    Description: Background: The transcription factor p63 belongs to the p53/p63/p73 family and plays key functional roles during normal epithelial development and differentiation and in pathological states such as squamous cell carcinomas. The human TP63 gene, located on chromosome 3q28 is driven by two promoters that generate the full-length transactivating (TA) and N-terminal truncated (ΔN) isoforms. Furthermore alternative splicing at the C-terminus gives rise to additional α, β, γ and likely several other minor variants. Teasing out the expression and biological function of each p63 variant has been both the focus of, and a cause for contention in the p63 field. Results: Here we have taken advantage of a burgeoning RNA-Seq based genomic data-sets to examine the global expression profiles of p63 isoforms across commonly utilized human cell-lines and major tissues and organs. Consistent with earlier studies, we find ΔNp63 transcripts, primarily that of the ΔNp63α isoforms, to be expressed in most cells of epithelial origin such as those of skin and oral tissues, mammary glands and squamous cell carcinomas. In contrast, TAp63 is not expressed in the majority of normal cell-types and tissues; rather it is selectively expressed at moderate to high levels in a subset of Burkitt’s and diffuse large B-cell lymphoma cell lines. We verify this differential expression pattern of p63 isoforms by Western blot analysis, using newly developed ΔN and TA specific antibodies. Furthermore using unsupervised clustering of human cell lines, tissues and organs, we show that ΔNp63 and TAp63 driven transcriptional networks involve very distinct sets of molecular players, which may underlie their different biological functions. Conclusions: In this study we report comprehensive and global expression profiles of p63 isoforms and their relationship to p53/p73 and other potential transcriptional co-regulators. We curate publicly available data generated in part by consortiums such as ENCODE, FANTOM and Human Protein Atlas to delineate the vastly different transcriptomic landscapes of ΔNp63 and TAp63. Our studies help not only in dispelling prevailing myths and controversies on p63 expression in commonly used human cell lines but also augur new isoform- and cell type-specific activities of p63.
    Electronic ISSN: 1471-2164
    Topics: Biology
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    Genetic signatures of adaptation revealed from transcriptome sequencing of Arctic and red foxes (2015)
    BioMed Central
    Details
    Publication Date: 2015-08-08
    Description: Background: The genus Vulpes (true foxes) comprises numerous species that inhabit a wide range of habitats and climatic conditions, including one species, the Arctic fox (Vulpes lagopus) which is adapted to the arctic region. A close relative to the Arctic fox, the red fox (Vulpes vulpes), occurs in subarctic to subtropical habitats. To study the genetic basis of their adaptations to different environments, transcriptome sequences from two Arctic foxes and one red fox individual were generated and analyzed for signatures of positive selection. In addition, the data allowed for a phylogenetic analysis and divergence time estimate between the two fox species. Results: The de novo assembly of reads resulted in more than 160,000 contigs/transcripts per individual. Approximately 17,000 homologous genes were identified using human and the non-redundant databases. Positive selection analyses revealed several genes involved in various metabolic and molecular processes such as energy metabolism, cardiac gene regulation, apoptosis and blood coagulation to be under positive selection in foxes. Branch site tests identified four genes to be under positive selection in the Arctic fox transcriptome, two of which are fat metabolism genes. In the red fox transcriptome eight genes are under positive selection, including molecular process genes, notably genes involved in ATP metabolism. Analysis of the three transcriptomes and five Sanger re-sequenced genes in additional individuals identified a lower genetic variability within Arctic foxes compared to red foxes, which is consistent with distribution range differences and demographic responses to past climatic fluctuations. A phylogenomic analysis estimated that the Arctic and red fox lineages diverged about three million years ago. Conclusions: Transcriptome data are an economic way to generate genomic resources for evolutionary studies. Despite not representing an entire genome, this transcriptome analysis identified numerous genes that are relevant to arctic adaptation in foxes. Similar to polar bears, fat metabolism seems to play a central role in adaptation of Arctic foxes to the cold climate, as has been identified in the polar bear, another arctic specialist.
    Electronic ISSN: 1471-2164
    Topics: Biology
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    Sensors, Vol. 15, Pages 19393-19415: Ultrasonic Technique for Density Measurement of Liquids in Extreme Conditions (2015)
    MDPI Publishing
    In: Sensors
    Details
    Publication Date: 2015-08-08
    Description: An ultrasonic technique, invariant to temperature changes, for a density measurement of different liquids under in situ extreme conditions is presented. The influence of geometry and material parameters of the measurement system (transducer, waveguide, matching layer) on measurement accuracy and reliability is analyzed theoretically along with experimental results. The proposed method is based on measurement of the amplitude of the ultrasonic wave, reflected from the interface of the solid/liquid medium under investigation. In order to enhance sensitivity, the use of a quarter wavelength acoustic matching layer is proposed. Therefore, the sensitivity of the measurement system increases significantly. Density measurements quite often must be performed in extreme conditions at high temperature (up to 220 °C) and high pressure. In this case, metal waveguides between piezoelectric transducer and the measured liquid are used in order to protect the conventional transducer from the influence of high temperature and to avoid depolarization. The presented ultrasonic density measurement technique is suitable for density measurement in different materials, including liquids and polymer melts in extreme conditions. A new calibration algorithm was proposed. The metrological evaluation of the measurement method was performed. The expanded measurement uncertainty Uρ = 7.4 × 10−3 g/cm3 (1%).
    Electronic ISSN: 1424-8220
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
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    Sustainability, Vol. 7, Pages 10837-10853: Diversity and Abundance of Soil Animals as Influenced by Long-Term Fertilization in Grey Desert Soil, China (2015)
    MDPI Publishing
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    Publication Date: 2015-08-08
    Description: The relationship between soil fauna and different fertilizer management practices is of growing concern. The aim of this research was to investigate the response of soil fauna to fertilization regimes, to explore the relationships among the community of soil animals, soil moisture and crop yields. The application of organic fertilizers (i.e., sheep manure or crop residues) increased crop yields and promoted the number of individuals and species of soil fauna owing to the exogenous organic matter that fertilizers provided for the survival and development of soil fauna. Furthermore, the treatments that applied sheep manure (i.e., sheep manure only or nitrogen, phosphorus, potassium and sheep manure plus) were significantly beneficial for increasing crop yields and diversity of soil fauna compared to treatments with crop residues returned (i.e., crop residues returned only or nitrogen, phosphorus, potassium and crop residues returned to the field) (p 〈 0.05) due to the response of soil fauna to diverse exogenous nutrients and the effect of soil fertility. Therefore, the finding that soil fauna abundance is significantly positively correlated with soil moisture and crop yield may mean the effects of fertilizer applications on soil animals were partly masked by the soil moisture and crop yield.
    Electronic ISSN: 2071-1050
    Topics: Energy, Environment Protection, Nuclear Power Engineering
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    The Role of Liver in Determining Serum Colon-Derived Uremic Solutes (2015)
    Public Library of Science (PLoS)
    In: PLoS ONE
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    Publication Date: 2015-08-11
    Description: by Cheng-Jui Lin, Tai-Cherng Liou, Chi-Feng Pan, Pei-Chen Wu, Fang-Ju Sun, Hsuan-Liang Liu, Han-Hsiang Chen, Chih-Jen Wu Evidence has shown that indoxyl sulfate (IS) and p-cresyl sulfate (PCS) may be alternative predictors of clinical outcomes in chronic kidney disease (CKD). Both toxins are derived from the gastrointestinal tract and metabolised in the liver. However, it is unclear whether the liver affects the production of IS and PCS. Here, we explore the association between IS and PCS levels in liver cirrhosis and a CKD-based cohort (N = 115). Liver and kidney function was assessed and classified by a Child-Pugh score (child A–C) and a modified version of the Modification of Diet in Renal Disease (MDRD) equation (Stages 1–4), respectively. An animal model was also used to confirm the two toxin levels in a case of liver fibrosis. In patients with early liver cirrhosis (child A), IS and PCS were significantly associated with CKD stages. In contrast, serum IS and PCS did not significantly change in advanced liver cirrhosis (child C). A stepwise multiple linear regression analysis also showed that T-PCS was significantly associated with stages of liver cirrhosis after adjusting for other confounding factors (B = -2.29, p = 0.012). Moreover, the serum and urine levels of T-PCS and T-IS were significantly lower in rats with liver failure than in those without ( p
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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    Trends in genome dynamics among major orders of insects revealed through variations in protein families (2015)
    BioMed Central
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    Publication Date: 2015-08-08
    Description: Background: Insects belong to a class that accounts for the majority of animals on earth. With over one million identified species, insects display a huge diversity and occupy extreme environments. At present, there are dozens of fully sequenced insect genomes that cover a range of habitats, social behavior and morphologies. In view of such diverse collection of genomes, revealing evolutionary trends and charting functional relationships of proteins remain challenging. Results: We analyzed the relatedness of 17 complete proteomes representative of proteomes from insects including louse, bee, beetle, ants, flies and mosquitoes, as well as an out-group from the crustaceans. The analyzed proteomes mostly represented the orders of Hymenoptera and Diptera. The 287,405 protein sequences from the 18 proteomes were automatically clustered into 20,933 families, including 799 singletons. A comprehensive analysis based on statistical considerations identified the families that were significantly expanded or reduced in any of the studied organisms. Among all the tested species, ants are characterized by an exceptionally high rate of family gain and loss. By assigning annotations to hundreds of species-specific families, the functional diversity among species and between the major clades (Diptera and Hymenoptera) is revealed. We found that many species-specific families are associated with receptor signaling, stress-related functions and proteases. The highest variability among insects associates with the function of transposition and nucleic acids processes (collectively coined TNAP). Specifically, the wasp and ants have an order of magnitude more TNAP families and proteins relative to species that belong to Diptera (mosquitoes and flies). Conclusions: An unsupervised clustering methodology combined with a comparative functional analysis unveiled proteomic signatures in the major clades of winged insects. We propose that the expansion of TNAP families in Hymenoptera potentially contributes to the accelerated genome dynamics that characterize the wasp and ants.
    Electronic ISSN: 1471-2164
    Topics: Biology
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    MicroRNA and Transcription Factor Mediated Regulatory Network Analysis Reveals Critical Regulators and Regulatory Modules in Myocardial Infarction (2015)
    Public Library of Science (PLoS)
    In: PLoS ONE
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    Publication Date: 2015-08-11
    Description: by Guangde Zhang, Hongbo Shi, Lin Wang, Meng Zhou, Zhenzhen Wang, Xiaoxia Liu, Liang Cheng, Weimin Li, Xueqi Li Myocardial infarction (MI) is a severe coronary artery disease and a leading cause of mortality and morbidity worldwide. However, the molecular mechanisms of MI have yet to be fully elucidated. In this study, we compiled MI-related genes, MI-related microRNAs (miRNAs) and known human transcription factors (TFs), and we then identified 1,232 feed-forward loops (FFLs) among these miRNAs, TFs and their co-regulated target genes through integrating target prediction. By merging these FFLs, the first miRNA and TF mediated regulatory network for MI was constructed, from which four regulators (SP1, ESR1, miR-21-5p and miR-155-5p) and three regulatory modules that might play crucial roles in MI were then identified. Furthermore, based on the miRNA and TF mediated regulatory network and literature survey, we proposed a pathway model for miR-21-5p, the miR-29 family and SP1 to demonstrate their potential co-regulatory mechanisms in cardiac fibrosis, apoptosis and angiogenesis. The majority of the regulatory relations in the model were confirmed by previous studies, which demonstrated the reliability and validity of this miRNA and TF mediated regulatory network. Our study will aid in deciphering the complex regulatory mechanisms involved in MI and provide putative therapeutic targets for MI.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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    Genome-scale metabolic model of Rhodococcus jostii RHA1 ( i MT1174) to study the accumulation of storage compounds during nitrogen-limited condition (2015)
    BioMed Central
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    Publication Date: 2015-08-08
    Description: Background: Rhodococcus jostii RHA1 growing on different substrates is capable of accumulating simultaneously three types of carbon storage compounds: glycogen, polyhydroxyalkanoates (PHA), and triacylglycerols (TAG). Under nitrogen-limited (N-limited) condition, the level of storage increases as is commonly observed for other bacteria. The proportion of each storage compound changes with substrate, but it remains unclear what modelling approach should be adopted to predict the relative composition of the mixture of the storage compounds. We analyzed the growth of R. jostii RHA1 under N-limited conditions using a genome-scale metabolic modelling approach to determine which global metabolic objective function could be used for the prediction. Results: The R. jostii RHA1 model (iMT1174) produced during this study contains 1,243 balanced metabolites, 1,935 unique reactions, and 1,174 open reading frames (ORFs).Seven objective functions used with flux balance analysis (FBA) were compared for their capacity to predict the mixture of storage compounds accumulated after the sudden onset of N-limitation. Predictive abilities were determined using a Bayesian approach. Experimental data on storage accumulation mixture (glycogen, polyhydroxyalkanoates, and triacylglycerols) were obtained for batch cultures grown on glucose or acetate. The best FBA simulation results were obtained using a novel objective function for the N-limited condition which combined the maximization of the storage fluxes and the minimization of metabolic adjustments (MOMA) with the preceding non-limited conditions (max storage + environmental MOMA). The FBA solutions for the non-limited growth conditions were simply constrained by the objective function of growth rate maximization. Measurement of central metabolic fluxes by 13 C-labelling experiments of amino acids further supported the application of the environmental MOMA principle in the context of changing environment. Finally, it was found that the quantitative predictions of the storage mixture during N-limited storage accumulation were fairly sensitive to the biomass composition, as expected. Conclusions: The genome-scale metabolic model analysis of R. jostii RHA1 cultures suggested that the intracellular reaction flux profile immediately after the onset of N-limited condition are impacted by the values of the same fluxes during the period of non-limited growth. PHA turned out to be the main storage pool of the mixture in R. jostii RHA1.
    Electronic ISSN: 1752-0509
    Topics: Biology
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    CD73 Activity is Dispensable for the Polarization of M2 Macrophages (2015)
    Public Library of Science (PLoS)
    In: PLoS ONE
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    Publication Date: 2015-08-11
    Description: by Dominik Eichin, Juha P. Laurila, Sirpa Jalkanen, Marko Salmi The ectoenzyme CD73 catalyzes the hydrolysis of AMP, and is one of the most important producers of extracellular adenosine. On regulatory T cells, CD73 is necessary for immunosuppressive functions, and on Th17 cells CD73-generated adenosine exerts anti-inflammatory effects. However, the expression and function of CD73 in pro-inflammatory M1 and in immunosuppressive M2 macrophages is largely unknown. Here we show that CD73 expression and enzyme activity were induced in in vitro polarized pro-inflammatory human M(LPS+TNF) monocytes/macrophages, while CD73 was absent from immunosuppressive M(IL-4+M-CSF)-polarized macrophages. Inhibition of CD73 activity with the inhibitor AMPCP did not affect the polarization of human monocytes. In mice, CD73 was present on resident peritoneal macrophages. In striking contrast, elicited peritoneal macrophages remained CD73 negative regardless of their polarization towards either a pro-inflammatory M(LPS) or anti-inflammatory M(IL-4c) direction. Finally, the ability of peritoneal macrophages to polarize to pro- and anti-inflammatory cells was perfectly normal in CD73-deficient mice in vivo . These data indicate that, in contrast to other major leukocyte subpopulations, CD73 activity on macrophages does not play a major role in their polarization and that in mice host CD73 on any cell type is not required in vivo for peritoneal macrophage polarization towards either a pro- or an anti-inflammatory direction.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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    DNA Tetrominoes: The Construction of DNA Nanostructures Using Self-Organised Heterogeneous Deoxyribonucleic Acids Shapes (2015)
    Public Library of Science (PLoS)
    In: PLoS ONE
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    Publication Date: 2015-08-11
    Description: by Hui San Ong, Mohd Syafiq Rahim, Mohd Firdaus-Raih, Effirul Ikhwan Ramlan The unique programmability of nucleic acids offers alternative in constructing excitable and functional nanostructures. This work introduces an autonomous protocol to construct DNA Tetris shapes (L-Shape, B-Shape, T-Shape and I-Shape) using modular DNA blocks. The protocol exploits the rich number of sequence combinations available from the nucleic acid alphabets, thus allowing for diversity to be applied in designing various DNA nanostructures. Instead of a deterministic set of sequences corresponding to a particular design, the protocol promotes a large pool of DNA shapes that can assemble to conform to any desired structures. By utilising evolutionary programming in the design stage, DNA blocks are subjected to processes such as sequence insertion, deletion and base shifting in order to enrich the diversity of the resulting shapes based on a set of cascading filters. The optimisation algorithm allows mutation to be exerted indefinitely on the candidate sequences until these sequences complied with all the four fitness criteria. Generated candidates from the protocol are in agreement with the filter cascades and thermodynamic simulation. Further validation using gel electrophoresis indicated the formation of the designed shapes. Thus, supporting the plausibility of constructing DNA nanostructures in a more hierarchical, modular, and interchangeable manner.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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    The Influence of Diabetic Peripheral Neuropathy on Local Postural Muscle and Central Sensory Feedback Balance Control (2015)
    Public Library of Science (PLoS)
    In: PLoS ONE
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    Publication Date: 2015-08-11
    Description: by Nima Toosizadeh, Jane Mohler, David G. Armstrong, Talal K. Talal, Bijan Najafi Poor balance control and increased fall risk have been reported in people with diabetic peripheral neuropathy (DPN). Traditional body sway measures are unable to describe underlying postural control mechanism. In the current study, we used stabilogram diffusion analysis to examine the mechanism under which balance is altered in DPN patients under local-control (postural muscle control) and central-control (postural control using sensory cueing). DPN patients and healthy age-matched adults over 55 years performed two 15-second Romberg balance trials. Center of gravity sway was measured using a motion tracker system based on wearable inertial sensors, and used to derive body sway and local/central control balance parameters. Eighteen DPN patients (age = 65.4±7.6 years; BMI = 29.3±5.3 kg/m 2 ) and 18 age-matched healthy controls (age = 69.8±2.9; BMI = 27.0±4.1 kg/m 2 ) with no major mobility disorder were recruited. The rate of sway within local-control was significantly higher in the DPN group by 49% (healthy local-control slope = 1.23±1.06×10 -2 cm 2 /sec, P
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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    Collective Attention and Stock Prices: Evidence from Google Trends Data on Standard and Poor's 100 (2015)
    Public Library of Science (PLoS)
    In: PLoS ONE
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    Publication Date: 2015-08-11
    Description: by Raphael H. Heiberger Today´s connected world allows people to gather information in shorter intervals than ever before, widely monitored by massive online data sources. As a dramatic economic event, recent financial crisis increased public interest for large companies considerably. In this paper, we exploit this change in information gathering behavior by utilizing Google query volumes as a "bad news" indicator for each corporation listed in the Standard and Poor´s 100 index. Our results provide not only an investment strategy that gains particularly in times of financial turmoil and extensive losses by other market participants, but reveal new sectoral patterns between mass online behavior and (bearish) stock market movements. Based on collective attention shifts in search queries for individual companies, hence, these findings can help to identify early warning signs of financial systemic risk. However, our disaggregated data also illustrate the need for further efforts to understand the influence of collective attention shifts on financial behavior in times of regular market activities with less tremendous changes in search volumes.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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    Automated interpretation of 3D laserscanned point clouds for plant organ segmentation (2015)
    BioMed Central
    Details
    Publication Date: 2015-08-09
    Description: Background: Plant organ segmentation from 3D point clouds is a relevant task for plant phenotyping and plant growth observation. Automated solutions are required to increase the efficiency of recent high-throughput plant phenotyping pipelines. However, plant geometrical properties vary with time, among observation scales and different plant types. The main objective of the present research is to develop a fully automated, fast and reliable data driven approach for plant organ segmentation. Results: The automated segmentation of plant organs using unsupervised, clustering methods is crucial in cases where the goal is to get fast insights into the data or no labeled data is available or costly to achieve. For this we propose and compare data driven approaches that are easy-to-realize and make the use of standard algorithms possible. Since normalized histograms, acquired from 3D point clouds, can be seen as samples from a probability simplex, we propose to map the data from the simplex space into Euclidean space using Aitchisons log ratio transformation, or into the positive quadrant of the unit sphere using square root transformation. This, in turn, paves the way to a wide range of commonly used analysis techniques that are based on measuring the similarities between data points using Euclidean distance. We investigate the performance of the resulting approaches in the practical context of grouping 3D point clouds and demonstrate empirically that they lead to clustering results with high accuracy for monocotyledonous and dicotyledonous plant species with diverse shoot architecture. Conclusion: An automated segmentation of 3D point clouds is demonstrated in the present work. Within seconds first insights into plant data can be deviated – even from non-labelled data. This approach is applicable to different plant species with high accuracy. The analysis cascade can be implemented in future high-throughput phenotyping scenarios and will support the evaluation of the performance of different plant genotypes exposed to stress or in different environmental scenarios.
    Electronic ISSN: 1471-2105
    Topics: Biology , Computer Science
    Published by BioMed Central
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    Pursuing the impossible: an interview with Tim Hunt (2015)
    BioMed Central
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    Publication Date: 2015-08-09
    Description: Tim Hunt took an undergraduate degree in Natural Sciences at Cambridge in 1964, and his PhD and subsequent work focussed on the control of protein synthesis until 1982, when his adventitious discovery of the central cell cycle regulator cyclin, while he was teaching at the Marine Biological Laboratory in Woods Hole, redirected him to the study of cell cycle regulation. From 1990 to his retirement Tim worked in the Clare Hall Laboratories of Cancer Research UK. He shared the Nobel Prize in Physiology and Medicine with Lee Hartwell and Paul Nurse in 2001, and talked to us about the series of coincidences that led him to the prizewinning discovery.
    Electronic ISSN: 1741-7007
    Topics: Biology
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    Targeted Intracellular Delivery of Resveratrol to Glioblastoma Cells Using Apolipoprotein E-Containing Reconstituted HDL as a Nanovehicle (2015)
    Public Library of Science (PLoS)
    In: PLoS ONE
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    Publication Date: 2015-08-11
    Description: by Sea H. Kim, Birendra Babu Adhikari, Siobanth Cruz, Michael P. Schramm, Joe A. Vinson, Vasanthy Narayanaswami The objective of this study is to transport and deliver resveratrol to intracellular sites using apolipoprotein E3 (apoE3). Reconstituted high-density lipoprotein (rHDL) bearing resveratrol (rHDL/res) was prepared using phospholipids and the low-density lipoprotein receptor (LDLr)-binding domain of apoE3. Biophysical characterization revealed that resveratrol was partitioned into the phospholipid bilayer of discoidal rHDL/res particles (~19 nm diameter). Co-immunoprecipitation studies indicated that the LDLr-binding ability of apoE3 was retained. Cellular uptake of resveratrol to intracellular sites was evaluated in glioblastoma A-172 cells by direct fluorescence using chemically synthesized NBD-labeled resveratrol (res/NBD) embedded in rHDL/res. Competition and inhibition studies indicate that the uptake is by receptor mediated endocytosis via the LDLr, with co-localization of apoE3 and res/NBD in late endosomes/lysosomes. We propose that rHDL provides an ideal hydrophobic milieu to sequester resveratrol and that rHDL containing apoE3 serves as an effective “nanovehicle” to transport and deliver resveratrol to targeted intracellular sites.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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    Remote Sensing, Vol. 7, Pages 10143-10163: Mapping US Urban Extents from MODIS Data Using One-Class Classification Method (2015)
    MDPI Publishing
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    Publication Date: 2015-08-11
    Description: Urban areas are one of the most important components of human society. Their extents have been continuously growing during the last few decades. Accurate and timely measurements of the extents of urban areas can help in analyzing population densities and urban sprawls and in studying environmental issues related to urbanization. Urban extents detected from remotely sensed data are usually a by-product of land use classification results, and their interpretation requires a full understanding of land cover types. In this study, for the first time, we mapped urban extents in the continental United States using a novel one-class classification method, i.e., positive and unlabeled learning (PUL), with multi-temporal Moderate Resolution Imaging Spectroradiometer (MODIS) data for the year 2010. The Defense Meteorological Satellite Program Operational Linescan System (DMSP-OLS) night stable light data were used to calibrate the urban extents obtained from the one-class classification scheme. Our results demonstrated the effectiveness of the use of the PUL algorithm in mapping large-scale urban areas from coarse remote-sensing images, for the first time. The total accuracy of mapped urban areas was 92.9% and the kappa coefficient was 0.85. The use of DMSP-OLS night stable light data can significantly reduce false detection rates from bare land and cropland far from cities. Compared with traditional supervised classification methods, the one-class classification scheme can greatly reduce the effort involved in collecting training datasets, without losing predictive accuracy.
    Electronic ISSN: 2072-4292
    Topics: Architecture, Civil Engineering, Surveying , Geography
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    Combined Oral Administration of Bovine Collagen Peptides with Calcium Citrate Inhibits Bone Loss in Ovariectomized Rats (2015)
    Public Library of Science (PLoS)
    In: PLoS ONE
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    Publication Date: 2015-08-11
    Description: by JunLi Liu, YiHu Wang, ShuJun Song, XiJie Wang, YaYa Qin, ShaoYan Si, YanChuan Guo Purpose Collagen peptides (CPs) and calcium citrate are commonly used as bone health supplements for treating osteoporosis. However, it remains unknown whether the combination of oral bovine CPs with calcium citrate is more effective than administration of either agent alone. Methods Forty 12-week-old Sprague-Dawley rats were randomly divided into five groups ( n = 8) for once-daily intragastric administration of different treatments for 3 months at 3 months after ovariectomy (OVX) as follows: sham + vehicle; OVX + vehicle; OVX + 750 mg/kg CP; OVX + CP-calcium citrate (75 mg/kg); OVX + calcium citrate (75 mg/kg). After euthanasia, the femurs were removed and analyzed by dual energy X-ray absorptiometry and micro-computed tomography, and serum samples were analyzed for bone metabolic markers. Results OVX rats supplemented with CPs or CP-calcium citrate showed osteoprotective effects, with reductions in the OVX-induced decreases in their femoral bone mineral density. Moreover, CP-calcium citrate prevented trabecular bone loss, improved the microarchitecture of the distal femur, and significantly inhibited bone loss with increased bone volume, connectivity density, and trabecular number compared with OVX control rats. CP or CP-calcium citrate administration significantly increased serum procollagen type I N-terminal propeptide levels and reduced serum bone-specific alkaline phosphatase, osteocalcin, and C-telopeptide of type I collagen levels. Conclusions Our data indicate that combined oral administration of bovine CPs with calcium citrate inhibits bone loss in OVX rats. The present findings suggest that combined oral administration of bovine CPs with calcium citrate is a promising alternative for reducing bone loss in osteopenic postmenopausal women.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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    Remote Sensing, Vol. 7, Pages 10164-10183: Effects of Precipitation Intensity and Temperature on NDVI-Based Grass Change over Northern China during the Period from 1982 to 2011 (2015)
    MDPI Publishing
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    Publication Date: 2015-08-11
    Description: The knowledge about impacts of changes in precipitation regimes on terrestrial ecosystems is fundamental to improve our understanding of global environment change, particularly in the context that heavy precipitation is expected to increase according to the 5th Intergovernmental Panel on Climate Change (IPCC) assessment. Based on observed climate data and the Advanced Very High Resolution Radiometer (AVHRR) Global Inventory Modeling and Mapping Studies (GIMMS) satellite-derived normalized difference vegetation index (NDVI), here we analyzed the spatio-temporal changes in grassland NDVI, covering 1.64 × 106 km2, in northern China and their linkages to changes in precipitation and temperature during the period 1982–2011. We found that mean growing season (April–October) grass NDVI is more sensitive to heavy precipitation than to moderate or light precipitation in both relatively arid areas (RAA) and relatively humid areas (RHA), whereas the sensitivities of grass NDVI to temperature are comparable to total precipitation in RHA. Heavy precipitation showed the strongest impacts in more than half of northern China (56%), whereas impacts of light precipitation on grass NDVI were stronger in some areas (21%), mainly distributed in northwestern China, a typical arid and semi-arid area. Our findings suggest that responses of grasslands are divergent with respect to changes in precipitation intensities.
    Electronic ISSN: 2072-4292
    Topics: Architecture, Civil Engineering, Surveying , Geography
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    Timeframe of speciation inferred from secondary contact zones in the European tree frog radiation ( Hyla arborea group) (2015)
    BioMed Central
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    Publication Date: 2015-08-09
    Description: Background: Hybridization between incipient species is expected to become progressively limited as their genetic divergence increases and reproductive isolation proceeds. Amphibian radiations and their secondary contact zones are useful models to infer the timeframes of speciation, but empirical data from natural systems remains extremely scarce. Here we follow this approach in the European radiation of tree frogs (Hyla arborea group). We investigated a natural hybrid zone between two lineages (Hyla arborea and Hyla orientalis) of Mio-Pliocene divergence (~5 My) for comparison with other hybrid systems from this group. Results: We found concordant geographic distributions of nuclear and mitochondrial gene pools, and replicated narrow transitions (~30 km) across two independent transects, indicating an advanced state of reproductive isolation and potential local barriers to dispersal. This result parallels the situation between H. arborea and H. intermedia, which share the same amount of divergence with H. orientalis. In contrast, younger lineages show much stronger admixture at secondary contacts. Conclusions: Our findings corroborate the negative relationship between hybridizability and divergence time in European tree frogs, where 5 My are necessary to achieve almost complete reproductive isolation. Speciation seems to progress homogeneously in this radiation, and might thus be driven by gradual genome-wide changes rather than single speciation genes. However, the timescale differs greatly from that of other well-studied amphibians. General assumptions on the time necessary for speciation based on evidence from unrelated taxa may thus be unreliable. In contrast, comparative hybrid zone analyses within single radiations such as our case study are useful to appreciate the advance of speciation in space and time.
    Electronic ISSN: 1471-2148
    Topics: Biology
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    IJGI, Vol. 4, Pages 1346-1365: Q-SOS—A Sensor Observation Service for Accessing Quality Descriptions of Environmental Data (2015)
    MDPI Publishing
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    Publication Date: 2015-08-11
    Description: The worldwide Sensor Web comprises observation data from diverse sources. Each data provider may process and assess datasets differently before making them available online. This information is often invisible to end users. Therefore, publishing observation data with quality descriptions is vital as it helps users to assess the suitability of data for their applications. It is also important to capture contextual information concerning data quality such as provenance to trace back incorrect data to its origins. In the Open Geospatial Consortium (OGC)’s Sensor Web Enablement (SWE) framework, there is no sufficiently and practically applicable approach how these aspects can be systematically represented and made accessible. This paper presents Q-SOS—an extension of the OGC’s Sensor Observation Service (SOS) that supports retrieval of observation data together with quality descriptions. These descriptions are represented in an observation data model covering various aspects of data quality assessment. The service and the data model have been developed based on open standards and open source tools, and are productively being used to share observation data from the TERENO observatory infrastructure. We discuss the advantages of deploying the presented solutions from data provider and consumer viewpoints. Enhancements applied to the related open-source developments are also introduced.
    Electronic ISSN: 2220-9964
    Topics: Architecture, Civil Engineering, Surveying , Geosciences
    Published by MDPI Publishing on behalf of International Society for Photogrammetry and Remote Sensing (ISPRS).
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    Sensors, Vol. 15, Pages 19507-19540: A Scalable Context-Aware Objective Function (SCAOF) of Routing Protocol for Agricultural Low-Power and Lossy Networks (RPAL) (2015)
    MDPI Publishing
    In: Sensors
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    Publication Date: 2015-08-11
    Description: In recent years, IoT (Internet of Things) technologies have seen great advances, particularly, the IPv6 Routing Protocol for Low-power and Lossy Networks (RPL), which provides a powerful and flexible routing framework that can be applied in a variety of application scenarios. In this context, as an important role of IoT, Wireless Sensor Networks (WSNs) can utilize RPL to design efficient routing protocols for a specific application to increase the ubiquity of networks with resource-constrained WSN nodes that are low-cost and easy to deploy. In this article, our work starts with the description of Agricultural Low-power and Lossy Networks (A-LLNs) complying with the LLN framework, and to clarify the requirements of this application-oriented routing solution. After a brief review of existing optimization techniques for RPL, our contribution is dedicated to a Scalable Context-Aware Objective Function (SCAOF) that can adapt RPL to the environmental monitoring of A-LLNs, through combining energy-aware, reliability-aware, robustness-aware and resource-aware contexts according to the composite routing metrics approach. The correct behavior of this enhanced RPL version (RPAL) was verified by performance evaluations on both simulation and field tests. The obtained experimental results confirm that SCAOF can deliver the desired advantages on network lifetime extension, and high reliability and efficiency in different simulation scenarios and hardware testbeds.
    Electronic ISSN: 1424-8220
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
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    Sensors, Vol. 15, Pages 19583-19596: Multi-Sensor Approach for the Monitoring of Halitosis Treatment via Lactobacillus brevis (CD2)—Containing Lozenges—A Randomized, Double-Blind Placebo-Controlled Clinical Trial (2015)
    MDPI Publishing
    In: Sensors
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    Publication Date: 2015-08-11
    Description: The aim of this randomized clinical trial was to evaluate whether a recently described multi-sensor approach called BIONOTE® is accurate enough to verify the efficacy of treatment of patients with halitosis. A treatment with Lactobacillus brevis (CD2)–containing lozenges, compared with placebo was tested. The BIONOTE® was compared with traditional techniques used to detect halitosis: OralChroma™ and two calibrated odor judges enrolled for the organoleptic assessments. Twenty patients (10 treated and 10 placebo), suffering from active phase halitosis were included in the study. Treatment consisted of Lactobacillus brevis (CD2)—containing lozenges or placebo, 4 tablets/day for 14 days. t0 was before the beginning of the study; t1 was day 7 and t2 was day 14. The effectiveness of treatment was assessed through: (1) Rosenberg score; (2) Winkel tongue coating index (WTCI) anterior and posterior; (2) OralChroma™; (3) the new developed multi-sensor approach, called BIONOTE® (test technique). Only the WTCI anterior revealed statistically significant changes between t0 and t2 data (p = 0.014) in the treated group. Except for the WTCI anterior, all diagnostic methods revealed the lack of effectiveness for halitosis of a 14-days treatment with Lactobacillus brevis (CD2)–containing lozenges. The BIONOTE® multisensor system seems accurate in addition to OralChroma™ to assess the initial condition of halitosis and its mitigation during treatment.
    Electronic ISSN: 1424-8220
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
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    Algorithms, Vol. 8, Pages 621-631: One-Bit Quantization and Distributed Detection with an Unknown Scale Parameter (2015)
    MDPI Publishing
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    Publication Date: 2015-08-12
    Description: We examine a distributed detection problem in a wireless sensor network, where sensor nodes collaborate to detect a Gaussian signal with an unknown change of power, i.e., a scale parameter. Due to power/bandwidth constraints, we consider the case where each sensor quantizes its observation into a binary digit. The binary data are then transmitted through error-prone wireless links to a fusion center, where a generalized likelihood ratio test (GLRT) detector is employed to perform a global decision. We study the design of a binary quantizer based on an asymptotic analysis of the GLRT. Interestingly, the quantization threshold of the quantizer is independent of the unknown scale parameter. Numerical results are included to illustrate the performance of the proposed quantizer and GLRT in binary symmetric channels (BSCs).
    Electronic ISSN: 1999-4893
    Topics: Computer Science
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    Sensors, Vol. 15, Pages 19495-19506: Distributed Wireless Monitoring System for Ullage and Temperature in Wine Barrels (2015)
    MDPI Publishing
    In: Sensors
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    Publication Date: 2015-08-11
    Description: This paper presents a multipurpose and low cost sensor for the simultaneous monitoring of temperature and ullage of wine in barrels in two of the most important stages of winemaking, that being fermentation and maturation. The distributed sensor subsystem is imbedded within the bung of the barrel and runs on battery for a period of at least 12 months and costs around $27 AUD for all parts. In addition, software was designed which allows for the remote transmission and easy visual interpretation of the data for the winemaker. Early warning signals can be sent when the temperature or ullage deviates from a winemakers expectations so remedial action can be taken, such as when topping is required or the movement of the barrels to a cooler cellar location. Such knowledge of a wine’s properties or storage conditions allows for a more precise control of the final wine quality.
    Electronic ISSN: 1424-8220
    Topics: Chemistry and Pharmacology , Electrical Engineering, Measurement and Control Technology
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    Two novel genetic variants in the mineralocorticoid receptor gene associated with spontaneous preterm birth (2015)
    BioMed Central
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    Publication Date: 2015-08-12
    Description: Background: Preterm birth is the leading cause of mortality and morbidity in newborn infants. Its etiology is multifactorial with genes and environmental factors, including chronic maternal stress, contributing to its risk. Our objective was to investigate whether single nucleotide polymorphisms (SNPs) in genes involved in the stress response are associated with spontaneous preterm birth using a candidate gene approach. Methods: A total of 210 cases (singleton spontaneous preterm birth at
    Electronic ISSN: 1471-2350
    Topics: Biology , Medicine
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    Materials, Vol. 8, Pages 5154-5193: Smart Dressings Based on Nanostructured Fibers Containing Natural Origin Antimicrobial, Anti-Inflammatory, and Regenerative Compounds (2015)
    MDPI Publishing
    In: Materials
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    Publication Date: 2015-08-12
    Description: A fast and effective wound healing process would substantially decrease medical costs, wound care supplies, and hospitalization significantly improving the patients’ quality of life. The search for effective therapeutic approaches seems to be imperative in order to avoid the aggravation of chronic wounds. In spite of all the efforts that have been made during the recent years towards the development of artificial wound dressings, none of the currently available options combine all the requirements necessary for quick and optimal cutaneous regeneration. Therefore, technological advances in the area of temporary and permanent smart dressings for wound care are required. The development of nanoscience and nanotechnology can improve the materials and designs used in topical wound care in order to efficiently release antimicrobial, anti-inflammatory and regenerative compounds speeding up the endogenous healing process. Nanostructured dressings can overcome the limitations of the current coverings and, separately, natural origin components can also overcome the drawbacks of current antibiotics and antiseptics (mainly cytotoxicity, antibiotic resistance, and allergies). The combination of natural origin components with demonstrated antibiotic, regenerative, or anti-inflammatory properties together with nanostructured materials is a promising approach to fulfil all the requirements needed for the next generation of bioactive wound dressings. Microbially compromised wounds have been treated with different essential oils, honey, cationic peptides, aloe vera, plant extracts, and other natural origin occurring antimicrobial, anti-inflammatory, and regenerative components but the available evidence is limited and insufficient to be able to draw reliable conclusions and to extrapolate those findings to the clinical practice. The evidence and some promising preliminary results indicate that future comparative studies are justified but instead of talking about the beneficial or inert effects of those natural origin occurring materials, the scientific community leads towards the identification of the main active components involved and their mechanism of action during the corresponding healing, antimicrobial, or regenerative processes and in carrying out systematic and comparative controlled tests. Once those natural origin components have been identified and their efficacy validated through solid clinical trials, their combination within nanostructured dressings can open up new avenues in the fabrication of bioactive dressings with outstanding characteristics for wound care. The motivation of this work is to analyze the state of the art in the use of different essential oils, honey, cationic peptides, aloe vera, plant extracts, and other natural origin occurring materials as antimicrobial, anti-inflammatory and regenerative components with the aim of clarifying their potential clinical use in bioactive dressings. We conclude that, for those natural occurring materials, more clinical trials are needed to reach a sufficient level of evidence as therapeutic agents for wound healing management.
    Electronic ISSN: 1996-1944
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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    Viewing Complex, Dynamic Scenes “Through the Eyes” of Another Person: The Gaze-Replay Paradigm (2015)
    Public Library of Science (PLoS)
    In: PLoS ONE
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    Publication Date: 2015-08-09
    Description: by Jennifer Choe Bush, Peter Christopher Pantelis, Xavier Morin Duchesne, Sebastian Alexander Kagemann, Daniel Patrick Kennedy We present a novel “Gaze-Replay” paradigm that allows the experimenter to directly test how particular patterns of visual input—generated from people’s actual gaze patterns—influence the interpretation of the visual scene. Although this paradigm can potentially be applied across domains, here we applied it specifically to social comprehension. Participants viewed complex, dynamic scenes through a small window displaying only the foveal gaze pattern of a gaze “donor.” This was intended to simulate the donor’s visual selection, such that a participant could effectively view scenes “through the eyes” of another person. Throughout the presentation of scenes presented in this manner, participants completed a social comprehension task, assessing their abilities to recognize complex emotions. The primary aim of the study was to assess the viability of this novel approach by examining whether these Gaze-Replay windowed stimuli contain sufficient and meaningful social information for the viewer to complete this social perceptual and cognitive task. The results of the study suggested this to be the case; participants performed better in the Gaze-Replay condition compared to a temporally disrupted control condition, and compared to when they were provided with no visual input. This approach has great future potential for the exploration of experimental questions aiming to unpack the relationship between visual selection, perception, and cognition.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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    Oral Migalastat HCl Leads to Greater Systemic Exposure and Tissue Levels of Active α-Galactosidase A in Fabry Patients when Co-Administered with Infused Agalsidase (2015)
    Public Library of Science (PLoS)
    In: PLoS ONE
    Details
    Publication Date: 2015-08-09
    Description: by David G. Warnock, Daniel G. Bichet, Myrl Holida, Ozlem Goker-Alpan, Kathy Nicholls, Mark Thomas, Francois Eyskens, Suma Shankar, Mathews Adera, Sheela Sitaraman, Richie Khanna, John J. Flanagan, Brandon A. Wustman, Jay Barth, Carrolee Barlow, Kenneth J. Valenzano, David J. Lockhart, Pol Boudes, Franklin K. Johnson Trial Registration ClinicalTrials.gov NCT01196871
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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    LTBP-2 Has a Single High-Affinity Binding Site for FGF-2 and Blocks FGF-2-Induced Cell Proliferation (2015)
    Public Library of Science (PLoS)
    In: PLoS ONE
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    Publication Date: 2015-08-12
    Description: by Clementine Menz, Mahroo K. Parsi, Julian R. J. Adams, Mohamed A. Sideek, Zlatko Kopecki, Allison J. Cowin, Mark A. Gibson Latent transforming growth factor-beta-1 binding protein-2 (LTBP-2) belongs to the fibrillin-LTBP superfamily of extracellular matrix proteins. LTBPs and fibrillins are involved in the sequestration and storage of latent growth factors, particularly transforming growth factor β (TGF-β), in tissues. Unlike other LTBPs, LTBP-2 does not covalently bind TGF-β, and its molecular functions remain unclear. We are screening LTBP-2 for binding to other growth factors and have found very strong saturable binding to fibroblast growth factor-2 (FGF-2) (Kd = 1.1 nM). Using a series of recombinant LTBP-2 fragments a single binding site for FGF-2 was identified in a central region of LTBP-2 consisting of six tandem epidermal growth factor-like (EGF-like) motifs (EGFs 9–14). This region was also shown to contain a heparin/heparan sulphate-binding site. FGF-2 stimulation of fibroblast proliferation was completely negated by the addition of 5-fold molar excess of LTBP-2 to the assay. Confocal microscopy showed strong co-localisation of LTBP-2 and FGF-2 in fibrotic keloid tissue suggesting that the two proteins may interact in vivo. Overall the study indicates that LTBP-2 is a potent inhibitor of FGF-2 that may influence FGF-2 bioactivity during wound repair particularly in fibrotic tissues.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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    Promoter Hypomethylation of Maspin Inhibits Migration and Invasion of Extravillous Trophoblast Cells during Placentation (2015)
    Public Library of Science (PLoS)
    In: PLoS ONE
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    Publication Date: 2015-08-12
    Description: by Xinwei Shi, Hao Liu, Jing Cao, Qing Liu, Guiju Tang, Wanlu Liu, Haiyi Liu, Dongrui Deng, Fuyuan Qiao, Yuanyuan Wu Objective Extravillous trophoblast (EVT) cells invade the endometrium and the maternal spiral arterioles during the first trimester. Mammary Serine Protease Inhibitor (Maspin, SERPINB5) plays a putative role in regulating the invasive activity of cytotrophoblasts. The maspin gene is silenced in various cancers by an epigenetic mechanism that involves aberrant cytosine methylation. We investigated the effect of the methylation status of the maspin promoter on the maspin expression and the aggressiveness of EVT cells. Methods Western blotting was used to detect the maspin protein expression in EVT cells upon hypoxia. The proliferative ability, the apoptosis rate and the migration and invasiveness were measured with Cell Counting Kit-8 assay, Flow Cytometry technology and Transwell methods. Subsequently, we treated cells with recombinant maspin protein. The methylation degree of maspin promoter region upon hypoxia/ decitabine was detected by bisulfite sequencing PCR and methylation-specific PCR. Finally, we explored the effects of decitabine on maspin protein expression and the aggressiveness of EVT cells. Results Hypoxia effectively increased maspin protein expression in EVT cells and significantly inhibited their aggressiveness. The addition of recombinant maspin protein inhibited this aggressiveness. Decitabine reduced the methylation in the maspin promoter region and effectively increased the maspin protein expression, which significantly weakened the migration and invasiveness of EVT cells. Discussion The methylation status of the maspin promoter is an important factor that affects the migration and invasion of EVT cells during early pregnancy. A decrease in the methylation status can inhibit the migration and invasion of EVT cells to affect placentation and can result in the ischemia and hypoxia of placenta.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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    Extracellular Matrix Stiffness Regulates Osteogenic Differentiation through MAPK Activation (2015)
    Public Library of Science (PLoS)
    In: PLoS ONE
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    Publication Date: 2015-08-12
    Description: by Jun-Ha Hwang, Mi Ran Byun, A. Rum Kim, Kyung Min Kim, Hang Jun Cho, Yo Han Lee, Juwon Kim, Mi Gyeong Jeong, Eun Sook Hwang, Jeong-Ho Hong Mesenchymal stem cell (MSC) differentiation is regulated by the extracellular matrix (ECM) through activation of intracellular signaling mediators. The stiffness of the ECM was shown to be an important regulatory factor for MSC differentiation, and transcriptional coactivator with PDZ-binding motif (TAZ) was identified as an effector protein for MSC differentiation. However, the detailed underlying mechanism regarding the role of ECM stiffness and TAZ in MSC differentiation is not yet fully understood. In this report, we showed that ECM stiffness regulates MSC fate through ERK or JNK activation. Specifically, a stiff hydrogel matrix stimulates osteogenic differentiation concomitant with increased nuclear localization of TAZ, but inhibits adipogenic differentiation. ERK and JNK activity was significantly increased in cells cultured on a stiff hydrogel. TAZ activation was induced by ERK or JNK activation on a stiff hydrogel because exposure to an ERK or JNK inhibitor significantly decreased the nuclear localization of TAZ, indicating that ECM stiffness-induced ERK or JNK activation is important for TAZ-driven osteogenic differentiation. Taken together, these results suggest that ECM stiffness regulates MSC differentiation through ERK or JNK activation.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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    120 Years of U.S. Residential Housing Stock and Floor Space (2015)
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    In: PLoS ONE
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    Publication Date: 2015-08-12
    Description: by Maria Cecilia P. Moura, Steven J. Smith, David B. Belzer Residential buildings are a key driver of energy consumption and also impact transportation and land-use. Energy consumption in the residential sector accounts for one-fifth of total U.S. energy consumption and energy-related CO 2 emissions, with floor space a major driver of building energy demands. In this work a consistent, vintage-disaggregated, annual long-term series of U.S. housing stock and residential floor space for 1891–2010 is presented. An attempt was made to minimize the effects of the incompleteness and inconsistencies present in the national housing survey data. Over the 1891–2010 period, floor space increased almost tenfold, from approximately 24,700 to 235,150 million square feet, corresponding to a doubling of floor space per capita from approximately 400 to 800 square feet. While population increased five times over the period, a 50% decrease in household size contributed towards a tenfold increase in the number of housing units and floor space, while average floor space per unit remains surprisingly constant, as a result of housing retirement dynamics. In the last 30 years, however, these trends appear to be changing, as household size shows signs of leveling off, or even increasing again, while average floor space per unit has been increasing. GDP and total floor space show a remarkably constant growth trend over the period and total residential sector primary energy consumption and floor space show a similar growth trend over the last 60 years, decoupling only within the last decade.
    Electronic ISSN: 1932-6203
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    Efficient Generation of Plasmacytoid Dendritic Cell from Common Lymphoid Progenitors by Flt3 Ligand (2015)
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    In: PLoS ONE
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    Publication Date: 2015-08-12
    Description: by Yi-Ling Chen, Shiun Chang, Ting-Ting Chen, Chien-Kuo Lee Dendritic cells (DCs), including conventional DCs (cDCs) and plasmacytoid DCs (pDCs) are critical for initiating and controlling the immune response. However, study of DC, particularly pDC, function is hampered by their low frequency in lymphoid organs, and existing methods for in vitro DC generation preferentially favor the production of cDCs over pDCs. Here, we demonstrated that pDCs could be efficiently generated in vitro from common lymphoid progenitors (CLPs) using Flt3 ligand (FL) in three different culture systems, namely feeder-free, BM-feeder and AC-6-feeder. This was in stark contrast to common DC progenitors (CDPs), in which cDCs were prominently generated under the same conditions. Moreover, the efficiency and function of pDCs generated from these three systems varied. While AC-6 system showed the greatest ability to support pDC development from CLPs, BM-feeder system was able to develop pDCs with better functionality. pDCs could also be expanded in vivo using hydrodynamic gene transfer of FL, which was further enhanced by the combined treatment of FL and IFN-α. Interestingly, IFN-α selectively promoted the proliferation of CLPs and not CDPs, which might contribute to enhanced pDC development. Together, we have defined conditions for in vitro and in vivo generation of pDCs, which may be useful for investigating the biology of pDCs.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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    A Haptic Feedback Scheme to Accurately Position a Virtual Wrist Prosthesis Using a Three-Node Tactor Array (2015)
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    In: PLoS ONE
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    Publication Date: 2015-08-12
    Description: by Andrew Erwin, Frank C. Sup In this paper, a novel haptic feedback scheme, used for accurately positioning a 1DOF virtual wrist prosthesis through sensory substitution, is presented. The scheme employs a three-node tactor array and discretely and selectively modulates the stimulation frequency of each tactor to relay 11 discrete haptic stimuli to the user. Able-bodied participants were able to move the virtual wrist prosthesis via a surface electromyography based controller. The participants evaluated the feedback scheme without visual or audio feedback and relied solely on the haptic feedback alone to correctly position the hand. The scheme was evaluated through both normal (perpendicular) and shear (lateral) stimulations applied on the forearm. Normal stimulations were applied through a prototype device previously developed by the authors while shear stimulations were generated using an ubiquitous coin motor vibrotactor. Trials with no feedback served as a baseline to compare results within the study and to the literature. The results indicated that using normal and shear stimulations resulted in accurately positioning the virtual wrist, but were not significantly different. Using haptic feedback was substantially better than no feedback. The results found in this study are significant since the feedback scheme allows for using relatively few tactors to relay rich haptic information to the user and can be learned easily despite a relatively short amount of training. Additionally, the results are important for the haptic community since they contradict the common conception in the literature that normal stimulation is inferior to shear. From an ergonomic perspective normal stimulation has the potential to benefit upper limb amputees since it can operate at lower frequencies than shear-based vibrotactors while also generating less noise. Through further tuning of the novel haptic feedback scheme and normal stimulation device, a compact and comfortable sensory substitution device for upper limb amputees might be created.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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    Anti-Retroviral Lectins Have Modest Effects on Adherence of Trichomonas vaginalis to Epithelial Cells In Vitro and on Recovery of Tritrichomonas foetus in a Mouse Vaginal Model (2015)
    Public Library of Science (PLoS)
    In: PLoS ONE
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    Publication Date: 2015-08-09
    Description: by Aparajita Chatterjee, Daniel M. Ratner, Christopher M. Ryan, Patricia J. Johnson, Barry R. O’Keefe, W. Evan Secor, Deborah J. Anderson, Phillips W. Robbins, John Samuelson Trichomonas vaginalis causes vaginitis and increases the risk of HIV transmission by heterosexual sex, while Tritrichomonas foetus causes premature abortion in cattle. Our goals were to determine the effects, if any, of anti-retroviral lectins, which are designed to prevent heterosexual transmission of HIV, on adherence of Trichomonas to ectocervical cells and on Tritrichomonas infections in a mouse model. We show that Trichomonas Asn-linked glycans ( N -glycans), like those of HIV, bind the mannose-binding lectin (MBL) that is part of the innate immune system. N -glycans of Trichomonas and Tritrichomonas bind anti-retroviral lectins (cyanovirin-N and griffithsin) and the 2G12 monoclonal antibody, each of which binds HIV N -glycans. Binding of cyanovirin-N appears to be independent of susceptibility to metronidazole, the major drug used to treat Trichomonas . Anti-retroviral lectins, MBL, and galectin-1 cause Trichomonas to self-aggregate and precipitate. The anti-retroviral lectins also increase adherence of ricin-resistant mutants, which are less adherent than parent cells, to ectocervical cell monolayers and to organotypic EpiVaginal tissue cells. Topical application of either anti-retroviral lectins or yeast N -glycans decreases by 40 to 70% the recovery of Tritrichomonas from the mouse vagina. These results, which are explained by a few simple models, suggest that the anti-retroviral lectins have a modest potential for preventing or treating human infections with Trichomonas .
    Electronic ISSN: 1932-6203
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    Educational Inequalities in Exit from Paid Employment among Dutch Workers: The Influence of Health, Lifestyle and Work (2015)
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    In: PLoS ONE
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    Publication Date: 2015-08-09
    Description: by Suzan J. W. Robroek, Anne Rongen, Coos H. Arts, Ferdy W. H. Otten, Alex Burdorf, Merel Schuring Background Individuals with lower socioeconomic status are at increased risk of involuntary exit from paid employment. To give sound advice for primary prevention in the workforce, insight is needed into the role of mediating factors between socioeconomic status and labour force participation. Therefore, it is aimed to investigate the influence of health status, lifestyle-related factors and work characteristics on educational differences in exit from paid employment. Methods 14,708 Dutch employees participated in a ten-year follow-up study during 1999–2008. At baseline, education, self-perceived health, lifestyle (smoking, alcohol, sports, BMI) and psychosocial (demands, control, rewards) and physical work characteristics were measured by questionnaire. Employment status was ascertained monthly based on tax records. The relation between education, health, lifestyle, work-characteristics and exit from paid employment through disability benefits, unemployment, early retirement and economic inactivity was investigated by competing risks regression analyses. The mediating effects of these factors on educational differences in exit from paid employment were tested using a stepwise approach. Results Lower educated workers were more likely to exit paid employment through disability benefits (SHR:1.84), unemployment (SHR:1.74), and economic inactivity (SHR:1.53) but not due to early retirement (SHR:0.92). Poor or moderate health, an unhealthy lifestyle, and unfavourable work characteristics were associated with disability benefits and unemployment, and an unhealthy lifestyle with economic inactivity. Educational differences in disability benefits were explained for 40% by health, 31% by lifestyle, and 12% by work characteristics. For economic inactivity and unemployment, up to 14% and 21% of the educational differences could be explained, particularly by lifestyle-related factors. Conclusions There are educational differences in exit from paid employment, which are partly mediated by health, lifestyle and work characteristics, particularly for disability benefits. Health promotion and improving working conditions seem important measures to maintain a productive workforce, particularly among workers with a low education.
    Electronic ISSN: 1932-6203
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    Security Analysis and Improvement of ‘a More Secure Anonymous User Authentication Scheme for the Integrated EPR Information System’ (2015)
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    In: PLoS ONE
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    Publication Date: 2015-08-12
    Description: by SK Hafizul Islam, Muhammad Khurram Khan, Xiong Li Over the past few years, secure and privacy-preserving user authentication scheme has become an integral part of the applications of the healthcare systems. Recently, Wen has designed an improved user authentication system over the Lee et al.’s scheme for integrated electronic patient record (EPR) information system, which has been analyzed in this study. We have found that Wen’s scheme still has the following inefficiencies: (1) the correctness of identity and password are not verified during the login and password change phases; (2) it is vulnerable to impersonation attack and privileged-insider attack; (3) it is designed without the revocation of lost/stolen smart card; (4) the explicit key confirmation and the no key control properties are absent, and (5) user cannot update his/her password without the help of server and secure channel. Then we aimed to propose an enhanced two-factor user authentication system based on the intractable assumption of the quadratic residue problem (QRP) in the multiplicative group. Our scheme bears more securities and functionalities than other schemes found in the literature.
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    GDSCalc: A Web-Based Application for Evaluating Discrete Graph Dynamical Systems (2015)
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    In: PLoS ONE
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    Publication Date: 2015-08-12
    Description: by Sherif H. Elmeligy Abdelhamid, Chris J. Kuhlman, Madhav V. Marathe, Henning S. Mortveit, S. S. Ravi Discrete dynamical systems are used to model various realistic systems in network science, from social unrest in human populations to regulation in biological networks. A common approach is to model the agents of a system as vertices of a graph, and the pairwise interactions between agents as edges. Agents are in one of a finite set of states at each discrete time step and are assigned functions that describe how their states change based on neighborhood relations. Full characterization of state transitions of one system can give insights into fundamental behaviors of other dynamical systems. In this paper, we describe a discrete graph dynamical systems (GDSs) application called GDSCalc for computing and characterizing system dynamics. It is an open access system that is used through a web interface. We provide an overview of GDS theory. This theory is the basis of the web application; i.e., an understanding of GDS provides an understanding of the software features, while abstracting away implementation details. We present a set of illustrative examples to demonstrate its use in education and research. Finally, we compare GDSCalc with other discrete dynamical system software tools. Our perspective is that no single software tool will perform all computations that may be required by all users; tools typically have particular features that are more suitable for some tasks. We situate GDSCalc within this space of software tools.
    Electronic ISSN: 1932-6203
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    Depth-Dependent Mineral Soil CO2 Production Processes: Sensitivity to Harvesting-Induced Changes in Soil Climate (2015)
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    In: PLoS ONE
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    Publication Date: 2015-08-12
    Description: by Lisa Kellman, Amy Myette, Hugo Beltrami Forest harvesting induces a step change in the climatic variables (temperature and moisture), that control carbon dioxide ( CO 2 ) production arising from soil organic matter decomposition within soils. Efforts to examine these vertically complex relationships in situ within soil profiles are lacking. In this study we examined how the climatic controls on CO 2 production change within vertically distinct layers of the soil profile in intact and clearcut forest soils of a humid temperate forest system of Atlantic Canada. We measured mineral soil temperature (0, 5, 10, 20, 50 and 100 cm depth) and moisture (0–15 cm and 30–60 cm depth), along with CO 2 surface efflux and subsurface concentrations (0, 2.5, 5, 10, 20, 35, 50, 75 and 100 cm depth) in 1 m deep soil pits at 4 sites represented by two forest-clearcut pairs over a complete annual cycle. We examined relationships between surface efflux at each site, and soil heat, moisture, and mineral soil CO 2 production. Following clearcut harvesting we observed increases in temperature through depth (1–2°C annually; often in excess of 4°C in summer and spring), alongside increases in soil moisture (30%). We observed a systematic breakdown in the expected exponential relationship between CO 2 production and heat with mineral soil depth, consistent with an increase in the role moisture plays in constraining CO 2 production. These findings should be considered in efforts to model and characterize mineral soil organic matter decomposition in harvested forest soils.
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    Protective Effect of Sevoflurane Postconditioning against Cardiac Ischemia/Reperfusion Injury via Ameliorating Mitochondrial Impairment, Oxidative Stress and Rescuing Autophagic Clearance (2015)
    Public Library of Science (PLoS)
    In: PLoS ONE
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    Publication Date: 2015-08-12
    Description: by Peng Yu, Jing Zhang, Shuchun Yu, Zhenzhong Luo, Fuzhou Hua, Linhui Yuan, Zhidong Zhou, Qin Liu, Xiaohong Du, Sisi Chen, Lieliang Zhang, Guohai Xu Background and Purpose Myocardial infarction leads to heart failure. Autophagy is excessively activated in myocardial ischemia/reperfusion (I/R) in rats. The aim of this study is to investigate whether the protection of sevoflurane postconditioning (SPC) in myocardial I/R is through restored impaired autophagic flux. Methods Except for the sham control (SHAM) group, each rat underwent 30 min occlusion of the left anterior descending coronary (LAD) followed by 2 h reperfusion. Cardiac infarction was determined by 2,3,5-triphenyltetrazolium chloride triazole (TTC) staining. Cardiac function was examined by hemodynamics and echocardiography. The activation of autophagy was evaluated by autophagosome accumulation, LC3 conversion and p62 degradation. Potential molecular mechanisms were investigated by immunoblotting, real-time PCR and immunofluorescence staining. Results SPC improved the hemodynamic parameters, cardiac dysfunction, histopathological and ultrastructural damages, and decreased myocardial infarction size after myocardial I/R injury ( P 〈 0.05 vs. I/R group). Compared with the cases in I/R group, myocardial ATP and NAD + content, mitochondrial function related genes and proteins, and the expressions of SOD2 and HO-1 were increased, while the expressions of ROS and Vimentin were decreased in the SPC group ( P 〈 0.05 vs. I/R group). SPC significantly activated Akt/mTOR signaling, and inhibited the formation of Vps34/Beclin1 complex via increasing expression of Bcl2 protein ( P 〈 0.05 vs. I/R group). SPC suppressed elevated expressions of LC3 II/I ratio, Beclin1, Atg5 and Atg7 in I/R rat, which indicated that SPC inhibited over-activation of autophagy, and promoted autophagosome clearance. Meanwhile, SPC significantly suppressed the decline of Opa1 and increases of Drp1 and Parkin induced by I/R injury ( P 〈 0.05 vs. I/R group). Moreover, SPC maintained the contents of ATP by reducing impaired mitochondria. Conclusion SPC protects rat hearts against I/R injury via ameliorating mitochondrial impairment, oxidative stress and rescuing autophagic clearance.
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    Influential Factors on the Relative Age Effect in Alpine Ski Racing (2015)
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    In: PLoS ONE
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    Publication Date: 2015-08-09
    Description: by Lisa Müller, Erich Müller, Carolin Hildebrandt, Elmar Kornexl, Christian Raschner The relative age effect (RAE), which refers to an over-representation of selected athletes born early in the selection year, was proven to be present in alpine ski racing in all age categories at both national and international levels. However, the influential factors on, or the causal mechanisms of, the RAE are still unknown. Therefore, the aim of the present study was to examine three possible influential factors on the relative age effect in alpine skiing: physical performance, anthropometric characteristics and biological maturational status. The study included the investigation of 282 elite Austrian youth ski racers and 413 non-athletes (comparison group) of the same age (10–13 years) and region. Six physical performance tests were performed, body mass and height were assessed, and the age at peak height velocity (APHV) was calculated. A significant RAE was present in the ski racers. No differences were shown in the physical performance characteristics or in the calculated APHV between the relative age quarters. These results suggest that ski racers born in the last quarter can counteract the relative age disadvantages if they already present the same level of physical performance and maturational status as those born at the beginning of the year. The height and weight of ski racers born at the beginning of the year were significantly higher compared to the non-athletes, and ski racers born in relative age quarter 1 were taller and heavier compared to the ski racers of the other quarters. This indicates that the anthropometric characteristics influence the selection process in alpine ski racing, and that relatively older athletes are more likely to be selected if they exhibit advanced anthropometric characteristics.
    Electronic ISSN: 1932-6203
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    Intrinsic Functional Connectivity in Salience and Default Mode Networks and Aberrant Social Processes in Youth at Ultra-High Risk for Psychosis (2015)
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    In: PLoS ONE
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    Publication Date: 2015-08-09
    Description: by Andrea Pelletier-Baldelli, Jessica A. Bernard, Vijay A. Mittal Social processes are key to navigating the world, and investigating their underlying mechanisms and cognitive architecture can aid in understanding disease states such as schizophrenia, where social processes are highly impacted. Evidence suggests that social processes are impaired in individuals at ultra high-risk for the development of psychosis (UHR). Understanding these phenomena in UHR youth may clarify disease etiology and social processes in a period that is characterized by significantly fewer confounds than schizophrenia. Furthermore, understanding social processing deficits in this population will help explain these processes in healthy individuals. The current study examined resting state connectivity of the salience (SN) and default mode networks (DMN) in association with facial emotion recognition (FER), an integral aspect of social processes, as well as broader social functioning (SF) in UHR individuals and healthy controls. Consistent with the existing literature, UHR youth were impaired in FER and SF when compared with controls. In the UHR group, we found increased connectivity between the SN and the medial prefrontal cortex, an area of the DMN relative to controls. In UHR youth, the DMN exhibited both positive and negative correlations with the somatosensory cortex/cerebellum and precuneus, respectively, which was linked with better FER performance. For SF, results showed that sensory processing links with the SN might be important in allowing for better SF for both groups, but especially in controls where sensory processing is likely to be unimpaired. These findings clarify how social processing deficits may manifest in psychosis, and underscore the importance of SN and DMN connectivity for social processing more generally.
    Electronic ISSN: 1932-6203
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    Remote Sensing, Vol. 7, Pages 10184-10226: Multiple Stable States and Catastrophic Shifts in Coastal Wetlands: Progress, Challenges, and Opportunities in Validating Theory Using Remote Sensing and Other Methods (2015)
    MDPI Publishing
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    Publication Date: 2015-08-12
    Description: Multiple stable states are established in coastal tidal wetlands (marshes, mangroves, deltas, seagrasses) by ecological, hydrological, and geomorphological feedbacks. Catastrophic shifts between states can be induced by gradual environmental change or by disturbance events. These feedbacks and outcomes are key to the sustainability and resilience of vegetated coastlines, especially as modulated by human activity, sea level rise, and climate change. Whereas multiple stable state theory has been invoked to model salt marsh responses to sediment supply and sea level change, there has been comparatively little empirical verification of the theory for salt marshes or other coastal wetlands. Especially lacking is long-term evidence documenting if or how stable states are established and maintained at ecosystem scales. Laboratory and field-plot studies are informative, but of necessarily limited spatial and temporal scope. For the purposes of long-term, coastal-scale monitoring, remote sensing is the best viable option. This review summarizes the above topics and highlights the emerging promise and challenges of using remote sensing-based analyses to validate coastal wetland dynamic state theories. This significant opportunity is further framed by a proposed list of scientific advances needed to more thoroughly develop the field.
    Electronic ISSN: 2072-4292
    Topics: Architecture, Civil Engineering, Surveying , Geography
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    Future Internet, Vol. 7, Pages 294-306: Enhancing Educational Opportunities with Computer-Mediated Assessment Feedback (2015)
    MDPI Publishing
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    Publication Date: 2015-08-12
    Description: As internet technologies make their way into developing areas, so too does the possibility of education and training being delivered to the people living in those previously unserved areas. The growing catalogue of free, high quality courseware, when combined with the newly acquired means of delivery, creates the potential for millions of people in the developing world to acquire a good education. Yet a good education obviously requires more than simply delivering information; students must also receive high quality feedback on their assessments. They must be told how their performance compares with the ideal, and be shown how to close the gap between the two. However, delivering high quality feedback is labor-intensive, and therefore expensive, and has long been recognized as a problematic issue by educators. This paper outlines a case study that uses a Learning Management System (LMS) to efficiently deliver detailed feedback that is informed by the principles of best practice. We make the case that the efficiencies of this method allow for large-scale courses with thousands of enrolments that are accessible to developing and developed areas alike. We explore the question; is computer-mediated feedback delivery efficient and effective and might it be applied to large-scale courses at low-cost?
    Electronic ISSN: 1999-5903
    Topics: Computer Science
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    Sustainability, Vol. 7, Pages 10854-10875: Review of Display Technologies Focusing on Power Consumption (2015)
    MDPI Publishing
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    Publication Date: 2015-08-12
    Description: This paper provides an overview of the main manufacturing technologies of displays, focusing on those with low and ultra-low levels of power consumption, which make them suitable for current societal needs. Considering the typified value obtained from the manufacturer’s specifications, four technologies—Liquid Crystal Displays, electronic paper, Organic Light-Emitting Display and Electroluminescent Displays—were selected in a first iteration. For each of them, several features, including size and brightness, were assessed in order to ascertain possible proportional relationships with the rate of consumption. To normalize the comparison between different display types, relative units such as the surface power density and the display frontal intensity efficiency were proposed. Organic light-emitting display had the best results in terms of power density for small display sizes. For larger sizes, it performs less satisfactorily than Liquid Crystal Displays in terms of energy efficiency.
    Electronic ISSN: 2071-1050
    Topics: Energy, Environment Protection, Nuclear Power Engineering
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    IJERPH, Vol. 12, Pages 9391-9407: Model Averaging for Improving Inference from Causal Diagrams (2015)
    MDPI Publishing
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    Publication Date: 2015-08-12
    Description: Model selection is an integral, yet contentious, component of epidemiologic research. Unfortunately, there remains no consensus on how to identify a single, best model among multiple candidate models. Researchers may be prone to selecting the model that best supports their a priori, preferred result; a phenomenon referred to as “wish bias”. Directed acyclic graphs (DAGs), based on background causal and substantive knowledge, are a useful tool for specifying a subset of adjustment variables to obtain a causal effect estimate. In many cases, however, a DAG will support multiple, sufficient or minimally-sufficient adjustment sets. Even though all of these may theoretically produce unbiased effect estimates they may, in practice, yield somewhat distinct values, and the need to select between these models once again makes the research enterprise vulnerable to wish bias. In this work, we suggest combining adjustment sets with model averaging techniques to obtain causal estimates based on multiple, theoretically-unbiased models. We use three techniques for averaging the results among multiple candidate models: information criteria weighting, inverse variance weighting, and bootstrapping. We illustrate these approaches with an example from the Pregnancy, Infection, and Nutrition (PIN) study. We show that each averaging technique returns similar, model averaged causal estimates. An a priori strategy of model averaging provides a means of integrating uncertainty in selection among candidate, causal models, while also avoiding the temptation to report the most attractive estimate from a suite of equally valid alternatives.
    Print ISSN: 1661-7827
    Electronic ISSN: 1660-4601
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Medicine
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    IJERPH, Vol. 12, Pages 9375-9390: Evidence of Coal-Fly-Ash Toxic Chemical Geoengineering in the Troposphere: Consequences for Public Health (2015)
    MDPI Publishing
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    Publication Date: 2015-08-12
    Description: The widespread, intentional and increasingly frequent chemical emplacement in the troposphere has gone unidentified and unremarked in the scientific literature for years. The author presents evidence that toxic coal combustion fly ash is the most likely aerosolized particulate sprayed by tanker-jets for geoengineering, weather-modification and climate-modification purposes and describes some of the multifold consequences on public health. Two methods are employed: (1) Comparison of 8 elements analyzed in rainwater, leached from aerosolized particulates, with corresponding elements leached into water from coal fly ash in published laboratory experiments, and (2) Comparison of 14 elements analyzed in dust collected outdoors on a high-efficiency particulate air (HEPA) filter with corresponding elements analyzed in un-leached coal fly ash material. The results show: (1) the assemblage of elements in rainwater and in the corresponding experimental leachate are essentially identical. At a 99% confidence interval, they have identical means (T-test) and identical variances (F-test); and (2) the assemblage of elements in the HEPA dust and in the corresponding average un-leached coal fly ash are likewise essentially identical. The consequences on public health are profound, including exposure to a variety of toxic heavy metals, radioactive elements, and neurologically-implicated chemically mobile aluminum released by body moisture in situ after inhalation or through transdermal induction.
    Print ISSN: 1661-7827
    Electronic ISSN: 1660-4601
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Medicine
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    IJERPH, Vol. 12, Pages 9342-9356: Climate Change and Health on the U.S. Gulf Coast: Public Health Adaptation is Needed to Address Future Risks (2015)
    MDPI Publishing
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    Publication Date: 2015-08-12
    Description: The impacts of climate change on human health have been documented globally and in the United States. Numerous studies project greater morbidity and mortality as a result of extreme weather events and other climate-sensitive hazards. Public health impacts on the U.S. Gulf Coast may be severe as the region is expected to experience increases in extreme temperatures, sea level rise, and possibly fewer but more intense hurricanes. Through myriad pathways, climate change is likely to make the Gulf Coast less hospitable and more dangerous for its residents, and may prompt substantial migration from and into the region. Public health impacts may be further exacerbated by the concentration of people and infrastructure, as well as the region’s coastal geography. Vulnerable populations, including the very young, elderly, and socioeconomically disadvantaged may face particularly high threats to their health and well-being. This paper provides an overview of potential public health impacts of climate variability and change on the Gulf Coast, with a focus on the region’s unique vulnerabilities, and outlines recommendations for improving the region’s ability to minimize the impacts of climate-sensitive hazards. Public health adaptation aimed at improving individual, public health system, and infrastructure resilience is urgently needed to meet the challenges climate change may pose to the Gulf Coast in the coming decades.
    Print ISSN: 1661-7827
    Electronic ISSN: 1660-4601
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Medicine
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    Sustainability, Vol. 7, Pages 10876-10894: Reforming China’s Pension Scheme for Urban Workers: Liquidity Gap and Policies’ Effects Forecasting (2015)
    MDPI Publishing
    Details
    Publication Date: 2015-08-12
    Description: This study forecasts the liquidity gap in China’s pension scheme for urban workers in the context of an ageing population and the possible effects of recent governmental policies by constructing a basic pension model, including “old people”, “middle people” and “new people” and a simulation method. We find, firstly, that China’s liquidity gap of pension will reach its peak of approximately 13.11 trillion yuan in 2038. Subsequently, this gap will gradually decrease with growth in the mortality rate. Secondly, reasonable intervals for the replacement and contribution rates should be set at [0.417, 0.604] and [0.189, 0.262], respectively, to sustain China’s pension system. Thirdly, compared to increasing fiscal subsidies, an income doubling plan, raising the contribution rate, lowering the replacement rate and delaying the retirement age can significantly reduce the liquidity gap, although the policy costs are relatively high. A policy permitting families to have two children will increase the rate of reduction of the liquidity gap, but it cannot effectively narrow the gap at the peak moment.
    Electronic ISSN: 2071-1050
    Topics: Energy, Environment Protection, Nuclear Power Engineering
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    Algorithms, Vol. 8, Pages 632-644: Data Fusion Modeling for an RT3102 and Dewetron System Application in Hybrid Vehicle Stability Testing (2015)
    MDPI Publishing
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    Publication Date: 2015-08-13
    Description: More and more hybrid electric vehicles are driven since they offer such advantages as energy savings and better active safety performance. Hybrid vehicles have two or more power driving systems and frequently switch working condition, so controlling stability is very important. In this work, a two-stage Kalman algorithm method is used to fuse data in hybrid vehicle stability testing. First, the RT3102 navigation system and Dewetron system are introduced. Second, a modeling of data fusion is proposed based on the Kalman filter. Then, this modeling is simulated and tested on a sample vehicle, using Carsim and Simulink software to test the results. The results showed the merits of this modeling.
    Electronic ISSN: 1999-4893
    Topics: Computer Science
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    Atmosphere, Vol. 6, Pages 1154-1174: The Impact of Selected Parameters on Visibility: First Results from a Long-Term Campaign in Warsaw, Poland (2015)
    MDPI Publishing
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    Publication Date: 2015-08-13
    Description: The aim of this study was to investigate how atmospheric air pollutants and meteorological conditions affected atmospheric visibility in the largest Polish agglomeration. The correlation analysis, principal component analysis (PCA) and generalized regression models (GRMs) were used to accomplish this objective. The meteorological parameters (temperature, relative humidity, precipitation, wind speed and insolation) and concentrations of the air pollutants (PM10, SO2, NO2, CO and O3) were recorded in 2004–2013. The data came from the Ursynów-SGGW, MzWarszUrsynów and Okęcie monitoring stations, located in the south of Warsaw (Poland). It was shown that the PM10 concentration was the most important parameter affecting the visibility in Warsaw. The concentration, and indirectly the visibility, was mainly affected by the pollutant emission from the flat/building heating (combustion of various fuels). It changed intensively during the research period. There were also periods in which this emission type did not have a great influence on the pollutant concentrations (mainly PM10) and visibility. In such seasons, the research revealed the influence of the traffic emission and secondary aerosol formation processes on the visibility.
    Electronic ISSN: 2073-4433
    Topics: Geosciences
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    Informative gene network for chemotherapy-induced peripheral neuropathy (2015)
    BioMed Central
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    Publication Date: 2015-08-13
    Description: Background: Host genetic variability has been implicated in chemotherapy-induced peripheral neuropathy (CIPN). A dose-limiting toxicity for chemotherapy agents, CIPN is also a debilitating condition that may progress to chronic neuropathic pain. We utilized a bioinformatics approach, which captures the complexity of intracellular and intercellular interactions, to identify genes for CIPN. Methods: Using genes pooled from the literature as a starting point, we used Ingenuity Pathway Analysis (IPA) to generate gene networks for CIPN. Results: We performed IPA core analysis for genes associated with platinum-, taxane- and platinum-taxane–induced neuropathy. We found that IL6, TNF, CXCL8, IL1B and ERK1/2 were the top genes in terms of the number of connections in platinum-induced neuropathy and TP53, MYC, PARP1, P38 MAPK and TNF for combined taxane-platinum–induced neuropathy. Conclusion: Neurotoxicity is common in cancer patients treated with platinum compounds and anti-microtubule agents and CIPN is one of the debilitating sequela. The bioinformatic approach helped identify genes associated with CIPN in cancer patients.
    Electronic ISSN: 1756-0381
    Topics: Biology , Computer Science
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    Design of symmetric TIM barrel proteins from first principles (2015)
    BioMed Central
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    Publication Date: 2015-08-13
    Description: Background: Computational protein design is a rapidly maturing field within structural biology, with the goal of designing proteins with custom structures and functions. Such proteins could find widespread medical and industrial applications. Here, we have adapted algorithms from the Rosetta software suite to design much larger proteins, based on ideal geometric and topological criteria. Furthermore, we have developed techniques to incorporate symmetry into designed structures. For our first design attempt, we targeted the (α/β) 8 TIM barrel scaffold. We gained novel insights into TIM barrel folding mechanisms from studying natural TIM barrel structures, and from analyzing previous TIM barrel design attempts. Methods: Computational protein design and analysis was performed using the Rosetta software suite and custom scripts. Genes encoding all designed proteins were synthesized and cloned on the pET20-b vector. Standard circular dichroism and gel chromatographic experiments were performed to determine protein biophysical characteristics. 1D NMR and 2D HSQC experiments were performed to determine protein structural characteristics. Results: Extensive protein design simulations coupled with ab initio modeling yielded several all-atom models of ideal, 4-fold symmetric TIM barrels. Four such models were experimentally characterized. The best designed structure (Symmetrin-1) contained a polar, histidine-rich pore, forming an extensive hydrogen bonding network. Symmetrin-1 was easily expressed and readily soluble. It showed circular dichroism spectra characteristic of well-folded alpha/beta proteins. Temperature melting experiments revealed cooperative and reversible unfolding, with a T m of 44 °C and a Gibbs free energy of unfolding (ΔG°) of 8.0 kJ/mol. Urea denaturing experiments confirmed these observations, revealing a C m of 1.6 M and a ΔG° of 8.3 kJ/mol. Symmetrin-1 adopted a monomeric conformation, with an apparent molecular weight of 32.12 kDa, and displayed well resolved 1D-NMR spectra. However, the HSQC spectrum revealed somewhat molten characteristics. Conclusions: Despite the detection of molten characteristics, the creation of a soluble, cooperatively folding protein represents an advancement over previous attempts at TIM barrel design. Strategies to further improve Symmetrin-1 are elaborated. Our techniques may be used to create other large, internally symmetric proteins.
    Electronic ISSN: 1471-2091
    Topics: Chemistry and Pharmacology
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    A simplicial complex-based approach to unmixing tumor progression data (2015)
    BioMed Central
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    Publication Date: 2015-08-13
    Description: Background: Tumorigenesis is an evolutionary process by which tumor cells acquire mutations through successive diversification and differentiation. There is much interest in reconstructing this process of evolution due to its relevance to identifying drivers of mutation and predicting future prognosis and drug response. Efforts are challenged by high tumor heterogeneity, though, both within and among patients. In prior work, we showed that this heterogeneity could be turned into an advantage by computationally reconstructing models of cell populations mixed to different degrees in distinct tumors. Such mixed membership model approaches, however, are still limited in their ability to dissect more than a few well-conserved cell populations across a tumor data set. Results: We present a method to improve on current mixed membership model approaches by better accounting for conserved progression pathways between subsets of cancers, which imply a structure to the data that has not previously been exploited. We extend our prior methods, which use an interpretation of the mixture problem as that of reconstructing simple geometric objects called simplices, to instead search for structured unions of simplices called simplicial complexes that one would expect to emerge from mixture processes describing branches along an evolutionary tree. We further improve on the prior work with a novel objective function to better identify mixtures corresponding to parsimonious evolutionary tree models. We demonstrate that this approach improves on our ability to accurately resolve mixtures on simulated data sets and demonstrate its practical applicability on a large RNASeq tumor data set. Conclusions: Better exploiting the expected geometric structure for mixed membership models produced from common evolutionary trees allows us to quickly and accurately reconstruct models of cell populations sampled from those trees. In the process, we hope to develop a better understanding of tumor evolution as well as other biological problems that involve interpreting genomic data gathered from heterogeneous populations of cells.
    Electronic ISSN: 1471-2105
    Topics: Biology , Computer Science
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    MultiSETTER: web server for multiple RNA structure comparison (2015)
    BioMed Central
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    Publication Date: 2015-08-13
    Description: Background: Understanding the architecture and function of RNA molecules requires methods for comparing and analyzing their tertiary and quaternary structures. While structural superposition of short RNAs is achievable in a reasonable time, large structures represent much bigger challenge. Therefore, we have developed a fast and accurate algorithm for RNA pairwise structure superposition called SETTER and implemented it in the SETTER web server. However, though biological relationships can be inferred by a pairwise structure alignment, key features preserved by evolution can be identified only from a multiple structure alignment. Thus, we extended the SETTER algorithm to the alignment of multiple RNA structures and developed the MultiSETTER algorithm. Results: In this paper, we present the updated version of the SETTER web server that implements a user friendly interface to the MultiSETTER algorithm. The server accepts RNA structures either as the list of PDB IDs or as user-defined PDB files. After the superposition is computed, structures are visualized in 3D and several reports and statistics are generated. Conclusion: To the best of our knowledge, the MultiSETTER web server is the first publicly available tool for a multiple RNA structure alignment. The MultiSETTER server offers the visual inspection of an alignment in 3D space which may reveal structural and functional relationships not captured by other multiple alignment methods based either on a sequence or on secondary structure motifs.
    Electronic ISSN: 1471-2105
    Topics: Biology , Computer Science
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    ImmunExplorer (IMEX): a software framework for diversity and clonality analyses of immunoglobulins and T cell receptors on the basis of IMGT/HighV-QUEST preprocessed NGS data (2015)
    BioMed Central
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    Publication Date: 2015-08-13
    Description: Background: Today’s modern research of B and T cell antigen receptors (the immunoglobulins (IG) or antibodies and T cell receptors (TR)) forms the basis for detailed analyses of the human adaptive immune system. For instance, insights in the state of the adaptive immune system provide information that is essentially important in monitoring transplantation processes and the regulation of immune suppressiva. In this context, algorithms and tools are necessary for analyzing the IG and TR diversity on nucleotide as well as on amino acid sequence level, identifying highly proliferated clonotypes, determining the diversity of the cell repertoire found in a sample, comparing different states of the human immune system, and visualizing all relevant information. Results: We here present IMEX, a software framework for the detailed characterization and visualization of the state of human IG and TR repertoires. IMEX offers a broad range of algorithms for statistical analysis of IG and TR data, CDR and V-(D)-J analysis, diversity analysis by calculating the distribution of IG and TR, calculating primer efficiency, and comparing multiple data sets. We use a mathematical model that is able to describe the number of unique clonotypes in a sample taking into account the true number of unique sequences and read errors; we heuristically optimize the parameters of this model. IMEX uses IMGT/HighV-QUEST analysis outputs and includes methods for splitting and merging to enable the submission to this portal and to combine the outputs results, respectively. All calculation results can be visualized and exported. Conclusion: IMEX is an user-friendly and flexible framework for performing clonality experiments based on CDR and V-(D)-J rearranged regions, diversity analysis, primer efficiency, and various different visualization experiments. Using IMEX, various immunological reactions and alterations can be investigated in detail. IMEX is freely available for Windows and Unix platforms at http://bioinformatics.fh-hagenberg.at/immunexplorer/.
    Electronic ISSN: 1471-2105
    Topics: Biology , Computer Science
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    Accurate chromosome segregation by probabilistic self-organisation (2015)
    BioMed Central
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    Publication Date: 2015-08-13
    Description: Background: For faithful chromosome segregation during cell division, correct attachments must be established between sister chromosomes and microtubules from opposite spindle poles through kinetochores (chromosome bi-orientation). Incorrect attachments of kinetochore microtubules (kMTs) lead to chromosome mis-segregation and aneuploidy, which is often associated with developmental abnormalities such as Down syndrome and diseases including cancer. The interaction between kinetochores and microtubules is highly dynamic with frequent attachments and detachments. However, it remains unclear how chromosome bi-orientation is achieved with such accuracy in such a dynamic process. Results: To gain new insight into this essential process, we have developed a simple mathematical model of kinetochore–microtubule interactions during cell division in general, i.e. both mitosis and meiosis. Firstly, the model reveals that the balance between attachment and detachment probabilities of kMTs is crucial for correct chromosome bi-orientation. With the right balance, incorrect attachments are resolved spontaneously into correct bi-oriented conformations while an imbalance leads to persistent errors. In addition, the model explains why errors are more commonly found in the first meiotic division (meiosis I) than in mitosis and how a faulty conformation can evade the spindle assembly checkpoint, which may lead to a chromosome loss. Conclusions: The proposed model, despite its simplicity, helps us understand one of the primary causes of chromosomal instability—aberrant kinetochore–microtubule interactions. The model reveals that chromosome bi-orientation is a probabilistic self-organisation, rather than a sophisticated process of error detection and correction.
    Electronic ISSN: 1741-7007
    Topics: Biology
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    Machine learning classifiers provide insight into the relationship between microbial communities and bacterial vaginosis (2015)
    BioMed Central
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    Publication Date: 2015-08-13
    Description: Background: Bacterial vaginosis (BV) is a disease associated with the vagina microbiome. It is highly prevalent and is characterized by symptoms including odor, discharge and irritation. No single microbe has been found to cause BV. In this paper we use random forests and logistic regression classifiers to model the relationship between the microbial community and BV. We use subsets of the microbial community features in order to determine which features are important to the classification models. Results: We find that models generated using logistic regression and random forests perform nearly identically and identify largely similar important features. Only a few features are necessary to obtain high BV classification accuracy. Additionally, there appears to be substantial redundancy between the microbial community features. Conclusions: These results are in contrast to a previous study in which the important features identified by the classifiers were dissimilar. This difference appears to be the result of using different feature importance measures. It is not clear whether machine learning classifiers are capturing patterns different from simple correlations.
    Electronic ISSN: 1756-0381
    Topics: Biology , Computer Science
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    Length-Based Assessment of Coral Reef Fish Populations in the Main and Northwestern Hawaiian Islands (2015)
    Public Library of Science (PLoS)
    In: PLoS ONE
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    Publication Date: 2015-08-13
    Description: by Marc O. Nadon, Jerald S. Ault, Ivor D. Williams, Steven G. Smith, Gerard T. DiNardo The coral reef fish community of Hawaii is composed of hundreds of species, supports a multimillion dollar fishing and tourism industry, and is of great cultural importance to the local population. However, a major stock assessment of Hawaiian coral reef fish populations has not yet been conducted. Here we used the robust indicator variable “average length in the exploited phase of the population (L¯)”, estimated from size composition data from commercial fisheries trip reports and fishery-independent diver surveys, to evaluate exploitation rates for 19 Hawaiian reef fishes. By and large, the average lengths obtained from diver surveys agreed well with those from commercial data. We used the estimated exploitation rates coupled with life history parameters synthesized from the literature to parameterize a numerical population model and generate stock sustainability metrics such as spawning potential ratios (SPR). We found good agreement between predicted average lengths in an unfished population (from our population model) and those observed from diver surveys in the largely unexploited Northwestern Hawaiian Islands. Of 19 exploited reef fish species assessed in the main Hawaiian Islands, 9 had SPRs close to or below the 30% overfishing threshold. In general, longer-lived species such as surgeonfishes, the redlip parrotfish ( Scarus rubroviolaceus ), and the gray snapper ( Aprion virescens ) had the lowest SPRs, while short-lived species such as goatfishes and jacks, as well as two invasive species ( Lutjanus kasmira and Cephalopholis argus ), had SPRs above the 30% threshold.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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    Performance of Dutch Children on the Bayley III: A Comparison Study of US and Dutch Norms (2015)
    Public Library of Science (PLoS)
    In: PLoS ONE
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    Publication Date: 2015-08-13
    Description: by Leonie J. P. Steenis, Marjolein Verhoeven, Dave J. Hessen, Anneloes L. van Baar Background The Bayley Scales of Infant and Toddler Development-third edition (Bayley-III) are frequently used to assess early child development worldwide. However, the original standardization only included US children, and it is still unclear whether or not these norms are adequate for use in other populations. Recently, norms for the Dutch version of the Bayley-III (The Bayley-III-NL) were made. Scores based on Dutch and US norms were compared to study the need for population-specific norms. Methods Scaled scores based on Dutch and US norms were compared for 1912 children between 14 days and 42 months 14 days. Next, the proportions of children scoring 〈 1-SD and 〈 -2 SD based on the two norms were compared, to identify over- or under-referral for developmental delay resulting from non-population-based norms. Results Scaled scores based on Dutch norms fluctuated around values based on US norms on all subtests. The extent of the deviations differed across ages and subtests. Differences in means were significant across all five subtests (p 〈 .01) with small to large effect sizes ( η p 2 ) ranging from .03 to .26). Using the US instead of Dutch norms resulted in over-referral regarding gross motor skills, and under-referral regarding cognitive, receptive communication, expressive communication, and fine motor skills. Conclusions The Dutch norms differ from the US norms for all subtests and these differences are clinically relevant. Population specific norms are needed to identify children with low scores for referral and intervention, and to facilitate international comparisons of population data.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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    A Pilot Study on Clinical and Neuroimaging Characteristics of Chinese Posterior Cortical Atrophy: Comparison with Typical Alzheimer’s Disease (2015)
    Public Library of Science (PLoS)
    In: PLoS ONE
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    Publication Date: 2015-08-13
    Description: by Xiao-Dan Wang, Hui Lu, Zhihong Shi, Li Cai, Shuai Liu, Shuling Liu, Tong Han, Ying Wang, Yuying Zhou, Xinping Wang, Shuo Gao, Yong Ji Posterior cortical atrophy (PCA) is a clinicoradiologic neurodegenerative syndrome characterized by predominant impairment of higher visual functions. Neuroimaging and neuropathological studies show that PCA is probably an atypical presentation of Alzheimer’s disease. However, in China PCA has rarely been studied and remains largely unknown. Our study therefore aimed to analyze the clinical manifestations and patterns of cerebral atrophy, amyloid beta deposition and regional glucose metabolism in Chinese PCA patients, comparing them directly with those of typical Alzheimer’s disease (TAD). Seven PCA patients, 6 TAD patients and 5 controls underwent neuropsychological assessment, MRI scan, 11 C-PIB PET scan and 18 F-FDG PET scan. Cerebral atrophy including ventricular enlargement, posterior atrophy and medial temporal lobe atrophy were evaluated with MRI. The uptake of 11 C-PIB was quantified at the voxel level using the standardized uptake value ratio. Comparisons of regional cerebral glucose metabolism were calculated with statistical parametric mapping. PCA patients showed significant impairment on visuospatial function in neuropsychological assessment. And PCA patients showed more severe posterior atrophy and less severe left medial temporal lobe atrophy compared with TAD patients. The data from 11 C-PIB PET scanning showed that amyloid beta deposition in PCA was comparable to TAD. Moreover, in PCA the results from 18 F-FDG PET scanning revealed significant hypometabolism in the temporoparietooccipital region and identified specific hypometabolism in the right occipital lobe, compared with TAD. Our study thus provides a preliminary view of PCA in Chinese patients. A further study with a larger number of subjects would be recommended to confirm these findings.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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    Reliability and Validity Study of Clinical Ultrasound Imaging on Lateral Curvature of Adolescent Idiopathic Scoliosis (2015)
    Public Library of Science (PLoS)
    In: PLoS ONE
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    Publication Date: 2015-08-13
    Description: by Q. Wang, M. Li, Edmond H. M. Lou, M. S. Wong Background Non-ionizing radiation imaging assessment has been advocated for the patients with adolescent idiopathic scoliosis (AIS). As one of the radiation-free methods, ultrasound imaging has gained growing attention in scoliosis assessment over the past decade. The center of laminae (COL) method has been proposed to measure the spinal curvature in the coronal plane of ultrasound image. However, the reliability and validity of this ultrasound method have not been validated in the clinical setting. Objectives To evaluate the reliability and validity of clinical ultrasound imaging on lateral curvature measurements of AIS with their corresponding magnetic resonance imaging (MRI) measurements. Methods Thirty curves (ranged 10.2°–68.2°) from sixteen patients with AIS were eligible for this study. The ultrasound scan was performed using a 3-D ultrasound unit within the same morning of MRI examination. Two researchers were involved in data collection of these two examinations. The COL method was used to measure the coronal curvature in ultrasound image, compared with the Cobb method in MRI. The intra- and inter-rater reliability of the COL method was evaluated by intra-class correlation coefficient (ICC). The validity of this method was analyzed by paired Student’s t -test, Bland–Altman statistics and Pearson correlation coefficient. The level of significance was set as 0.05. Results The COL method showed high intra- and inter-rater reliabilities (both with ICC (2, K) 〉0.9, p
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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    Robust Gene-Gene Interaction Analysis in Genome Wide Association Studies (2015)
    Public Library of Science (PLoS)
    In: PLoS ONE
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    Publication Date: 2015-08-13
    Description: by Yongkang Kim, Taesung Park Genome-wide association studies (GWAS) have successfully discovered hundreds of associations between genetic variants and complex traits. Most GWAS have focused on the identification of single variants. It has been shown that most of the variants that were discovered by GWAS could only partially explain disease heritability. The explanation for this missing heritability is generally believed to be gene-gene (GG) or gene-environment (GE) interactions and other structural variants. Generalized multifactor dimensionality reduction (GMDR) has been proven to be reasonably powerful in detecting GG and GE interactions; however, its performance has been found to decline when outlying quantitative traits are present. This paper proposes a robust GMDR estimation method (based on the L-estimator and M-estimator estimation methods) in an attempt to reduce the effects caused by outlying traits. A comparison of robust GMDR with the original MDR based on simulation studies showed the former method to outperform the latter. The performance of robust GMDR is illustrated through a real GWA example consisting of 8,577 samples from the Korean population using the Homeostasis Model Assessment of Insulin Resistance (HOMA-IR) level as a phenotype. Robust GMDR identified the KCNH1 gene to have strong interaction effects with other genes on the function of insulin secretion.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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    Item Anomaly Detection Based on Dynamic Partition for Time Series in Recommender Systems (2015)
    Public Library of Science (PLoS)
    In: PLoS ONE
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    Publication Date: 2015-08-13
    Description: by Min Gao, Renli Tian, Junhao Wen, Qingyu Xiong, Bin Ling, Linda Yang In recent years, recommender systems have become an effective method to process information overload. However, recommendation technology still suffers from many problems. One of the problems is shilling attacks-attackers inject spam user profiles to disturb the list of recommendation items. There are two characteristics of all types of shilling attacks: 1) Item abnormality: The rating of target items is always maximum or minimum; and 2) Attack promptness: It takes only a very short period time to inject attack profiles. Some papers have proposed item anomaly detection methods based on these two characteristics, but their detection rate, false alarm rate, and universality need to be further improved. To solve these problems, this paper proposes an item anomaly detection method based on dynamic partitioning for time series. This method first dynamically partitions item-rating time series based on important points. Then, we use chi square distribution (χ 2 ) to detect abnormal intervals. The experimental results on MovieLens 100K and 1M indicate that this approach has a high detection rate and a low false alarm rate and is stable toward different attack models and filler sizes.
    Electronic ISSN: 1932-6203
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    Budgetary Impact of Treating Acute Promyelocytic Leukemia Patients with First-Line Arsenic Trioxide and Retinoic Acid from an Italian Payer Perspective (2015)
    Public Library of Science (PLoS)
    In: PLoS ONE
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    Publication Date: 2015-08-13
    Description: by Morgan Kruse, Rebecca Wildner, Gisoo Barnes, Monique Martin, Udo Mueller, Francesco Lo-Coco, Ashutosh Pathak The objective of this study was to estimate the net cost of arsenic trioxide (ATO) added to all- trans retinoic acid (ATRA) compared to ATRA plus chemotherapy when used in first-line acute promyelocytic leukemia (APL) treatment for low to intermediate risk patients from the perspective of the overall Italian healthcare systemA Markov model was developed with 3 health states: stable disease, disease event and death. Each month, patients could move from stable to disease event or die from either state. After a disease event, patients discontinued initial treatment and switched to the other regimen as second-line therapy. Treatment regimens, efficacy and adverse events were derived from published sources and expert opinion; unit costs were collected from standard Italian sources. Clinical outcomes and costs for pre-ATO and post-ATO scenarios were combined with population and product utilization information to calculate the total budgetary impact using a 3-year time horizon; one-way sensitivity analyses were conducted. Three-year cumulative pharmacy costs for ATO+ATRA were €46,700 per-patient versus €6,500 for ATRA+chemotherapy; however, medical costs for ATO+ATRA were €12,300 per-patient versus €30,200 for ATRA+chemotherapy. The total budgetary impact was estimated to be an additional €127,300, €312,500 and €477,800 in the first, second and third years, respectively. The model was most sensitive to changes in the cost of the ATO+ATRA regimen during the consolidation phase. Budgetary impact models are valuable to payers making formulary decisions regarding the access and affordability of new medicines. The cost of treatment analysis showed that pharmacy costs for ATO+ATRA were higher than for ATRA+chemotherapy, while all other evaluated costs were lower for ATO+ATRA treated patients. The average budgetary impact was €305,900 per year overall, representing a 3.5% increase. Further research is needed to determine the cost-effectiveness of ATO+ATRA compared to the current first-line standard of care in APL.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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    DAPK1 Promoter Methylation and Cervical Cancer Risk: A Systematic Review and a Meta-Analysis (2015)
    Public Library of Science (PLoS)
    In: PLoS ONE
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    Publication Date: 2015-08-13
    Description: by Antonella Agodi, Martina Barchitta, Annalisa Quattrocchi, Andrea Maugeri, Manlio Vinciguerra Objective The Death-Associated Protein Kinase 1 ( DAPK1 ) gene has been frequently investigated in cervical cancer (CC). The aim of the present study was to carry out a systematic review and a meta-analysis in order to evaluate DAPK1 promoter methylation as an epigenetic marker for CC risk. Methods A systematic literature search was carried out. The Cochrane software package Review Manager 5.2 was used. The fixed-effects or random-effects models, according to heterogeneity across studies, were used to calculate odds ratios (ORs) and 95% Confidence Intervals (CIs). Furthermore, subgroup analyses were conducted by histological type, assays used to evaluate DAPK1 promoter methylation, and control sample source. Results A total of 20 papers, published between 2001 and 2014, on 1929 samples, were included in the meta-analysis. DAPK1 promoter methylation was associated with an increased CC risk based on the random effects model (OR: 21.20; 95%CI = 11.14–40.35). Omitting the most heterogeneous study, the between study heterogeneity decreased and the association increased (OR: 24.13; 95% CI = 15.83–36.78). The association was also confirmed in all the subgroups analyses. Conclusions A significant strong association between DAPK1 promoter methylation and CC was shown and confirmed independently by histological tumor type, method used to evaluate methylation and source of control samples. Methylation markers may have value in early detection of CC precursor lesions, provide added reassurances of safety for women who are candidates for less frequent screens, and predict outcomes of women infected with human papilloma virus.
    Electronic ISSN: 1932-6203
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    Effect of the synthetic cannabinoid HU-210 on quorum sensing and on the production of quorum sensing-mediated virulence factors by Vibrio harveyi (2015)
    BioMed Central
    Details
    Publication Date: 2015-08-13
    Description: Background: Bacterial populations communicate through the cell density-dependent mechanism of quorum sensing (QS). Vibrio harveyi, one of the best studied model organisms for QS, was used to explore effects of the synthetic cannabinoid HU-210 on QS and different QS-regulated physiological processes in bacteria. Results: Analysis of QS-regulated bioluminescence in wild-type and mutant strains of V. harveyi revealed that HU-210 affects the autoinducer-2 (AI-2) pathway, one of three known QS cascades of V. harveyi. Furthermore, QS-mediated biofilm formation and swimming motility in the mutant strain BB152 (AI-1 − , AI-2 + ) were significantly reduced in the presence of HU-210. HU-210 inhibited QS-mediated virulence factor production without any inhibitory effect on bacterial growth. It also alters the expression of several genes, which are regulated by QS, specifically downregulating the genes of the AI-2 QS cascade. Conclusion: First evidence is being provided for interference of bacterial signal-transduction systems by a synthetic cannabinoid. The effect of HU-210 was specific to the AI-2 cascade in V. harveyi. AI-2 is known as a "universal autoinducer" and interference with its activity opens a broad spectrum of applications for synthetic cannabinoids in future research as a potential anti-QS agent.
    Electronic ISSN: 1471-2180
    Topics: Biology
    Published by BioMed Central
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    Molecular Basis of Gene-Gene Interaction: Cyclic Cross-Regulation of Gene Expression and Post-GWAS Gene-Gene Interaction Involved in Atrial Fibrillation (2015)
    Public Library of Science (PLoS)
    Details
    Publication Date: 2015-08-13
    Description: by Yufeng Huang, Chuchu Wang, Yufeng Yao, Xiaoyu Zuo, Shanshan Chen, Chengqi Xu, Hongfu Zhang, Qiulun Lu, Le Chang, Fan Wang, Pengxia Wang, Rongfeng Zhang, Zhenkun Hu, Qixue Song, Xiaowei Yang, Cong Li, Sisi Li, Yuanyuan Zhao, Qin Yang, Dan Yin, Xiaojing Wang, Wenxia Si, Xiuchun Li, Xin Xiong, Dan Wang, Yuan Huang, Chunyan Luo, Jia Li, Jingjing Wang, Jing Chen, Longfei Wang, Li Wang, Meng Han, Jian Ye, Feifei Chen, Jingqiu Liu, Ying Liu, Gang Wu, Bo Yang, Xiang Cheng, Yuhua Liao, Yanxia Wu, Tie Ke, Qiuyun Chen, Xin Tu, Robert Elston, Shaoqi Rao, Yanzong Yang, Yunlong Xia, Qing K. Wang Atrial fibrillation (AF) is the most common cardiac arrhythmia at the clinic. Recent GWAS identified several variants associated with AF, but they account for
    Print ISSN: 1553-7390
    Electronic ISSN: 1553-7404
    Topics: Biology
    Published by Public Library of Science (PLoS)
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