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Sample records for analysis identifies driver

  1. Identifying Driver Nodes in the Human Signaling Network Using Structural Controllability Analysis.

    Science.gov (United States)

    Liu, Xueming; Pan, Linqiang

    2015-01-01

    Cell signaling governs the basic cellular activities and coordinates the actions in cell. Abnormal regulations in cell signaling processing are responsible for many human diseases, such as diabetes and cancers. With the accumulation of massive data related to human cell signaling, it is feasible to obtain a human signaling network. Some studies have shown that interesting biological phenomenon and drug-targets could be discovered by applying structural controllability analysis to biological networks. In this work, we apply structural controllability to a human signaling network and detect driver nodes, providing a systematic analysis of the role of different proteins in controlling the human signaling network. We find that the proteins in the upstream of the signaling information flow and the low in-degree proteins play a crucial role in controlling the human signaling network. Interestingly, inputting different control signals on the regulators of the cancer-associated genes could cost less than controlling the cancer-associated genes directly in order to control the whole human signaling network in the sense that less drive nodes are needed. This research provides a fresh perspective for controlling the human cell signaling system.

  2. Evolutionary analysis of vision genes identifies potential drivers of visual differences between giraffe and okapi

    Science.gov (United States)

    Agaba, Morris; Cavener, Douglas R.

    2017-01-01

    Background The capacity of visually oriented species to perceive and respond to visual signal is integral to their evolutionary success. Giraffes are closely related to okapi, but the two species have broad range of phenotypic differences including their visual capacities. Vision studies rank giraffe’s visual acuity higher than all other artiodactyls despite sharing similar vision ecological determinants with many of them. The extent to which the giraffe’s unique visual capacity and its difference with okapi is reflected by changes in their vision genes is not understood. Methods The recent availability of giraffe and okapi genomes provided opportunity to identify giraffe and okapi vision genes. Multiple strategies were employed to identify thirty-six candidate mammalian vision genes in giraffe and okapi genomes. Quantification of selection pressure was performed by a combination of branch-site tests of positive selection and clade models of selection divergence through comparing giraffe and okapi vision genes and orthologous sequences from other mammals. Results Signatures of selection were identified in key genes that could potentially underlie giraffe and okapi visual adaptations. Importantly, some genes that contribute to optical transparency of the eye and those that are critical in light signaling pathway were found to show signatures of adaptive evolution or selection divergence. Comparison between giraffe and other ruminants identifies significant selection divergence in CRYAA and OPN1LW. Significant selection divergence was identified in SAG while positive selection was detected in LUM when okapi is compared with ruminants and other mammals. Sequence analysis of OPN1LW showed that at least one of the sites known to affect spectral sensitivity of the red pigment is uniquely divergent between giraffe and other ruminants. Discussion By taking a systemic approach to gene function in vision, the results provide the first molecular clues associated with

  3. Identifying driver mutations in sequenced cancer genomes

    DEFF Research Database (Denmark)

    Raphael, Benjamin J; Dobson, Jason R; Oesper, Layla

    2014-01-01

    High-throughput DNA sequencing is revolutionizing the study of cancer and enabling the measurement of the somatic mutations that drive cancer development. However, the resulting sequencing datasets are large and complex, obscuring the clinically important mutations in a background of errors, noise......, and random mutations. Here, we review computational approaches to identify somatic mutations in cancer genome sequences and to distinguish the driver mutations that are responsible for cancer from random, passenger mutations. First, we describe approaches to detect somatic mutations from high-throughput DNA...... sequencing data, particularly for tumor samples that comprise heterogeneous populations of cells. Next, we review computational approaches that aim to predict driver mutations according to their frequency of occurrence in a cohort of samples, or according to their predicted functional impact on protein...

  4. Identifying Cancer Driver Genes Using Replication-Incompetent Retroviral Vectors

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    Victor M. Bii

    2016-10-01

    Full Text Available Identifying novel genes that drive tumor metastasis and drug resistance has significant potential to improve patient outcomes. High-throughput sequencing approaches have identified cancer genes, but distinguishing driver genes from passengers remains challenging. Insertional mutagenesis screens using replication-incompetent retroviral vectors have emerged as a powerful tool to identify cancer genes. Unlike replicating retroviruses and transposons, replication-incompetent retroviral vectors lack additional mutagenesis events that can complicate the identification of driver mutations from passenger mutations. They can also be used for almost any human cancer due to the broad tropism of the vectors. Replication-incompetent retroviral vectors have the ability to dysregulate nearby cancer genes via several mechanisms including enhancer-mediated activation of gene promoters. The integrated provirus acts as a unique molecular tag for nearby candidate driver genes which can be rapidly identified using well established methods that utilize next generation sequencing and bioinformatics programs. Recently, retroviral vector screens have been used to efficiently identify candidate driver genes in prostate, breast, liver and pancreatic cancers. Validated driver genes can be potential therapeutic targets and biomarkers. In this review, we describe the emergence of retroviral insertional mutagenesis screens using replication-incompetent retroviral vectors as a novel tool to identify cancer driver genes in different cancer types.

  5. Visual behaviour analysis and driver cognitive model

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    Baujon, J.; Basset, M.; Gissinger, G.L. [Mulhouse Univ., (France). MIPS/MIAM Lab.

    2001-07-01

    Recent studies on driver behaviour have shown that perception - mainly visual but also proprioceptive perception - plays a key role in the ''driver-vehicle-road'' system and so considerably affects the driver's decision making. Within the framework of the behaviour analysis and studies low-cost system (BASIL), this paper presents a correlative, qualitative and quantitative study, comparing the information given by visual perception and by the trajectory followed. This information will help to obtain a cognitive model of the Rasmussen type according to different driver classes. Many experiments in real driving situations have been carried out for different driver classes and for a given trajectory profile, using a test vehicle and innovative, specially designed, real-time tools, such as the vision system or the positioning module. (orig.)

  6. How to identify the key factors that affect driver perception of accident risk. A comparison between Italian and Spanish driver behavior.

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    de Oña, Juan; de Oña, Rocio; Eboli, Laura; Forciniti, Carmen; Mazzulla, Gabriella

    2014-12-01

    Road crashes can be caused by different factors, including infrastructure, vehicles, and human variables. Many research studies have focused solely on identifying the key factors that cause road crashes. From these studies, it emerged that human factors have the most relevant impact on accident severity. More specifically, accident severity depends on several factors related directly to the driver, i.e., driving experience, driver's socio-economic characteristics, and driving behavior and attitudes. In this paper, we investigate driver behaviors and attitudes while driving and specifically focus on different methods for identifying the factors that most affect the driver's perception of accident risk. To this end, we designed and conducted a survey in two different European contexts: the city of Cosenza, which is located in the south of Italy, and the city of Granada, which is located in the south of Spain. Samples of drivers were contacted for their opinions on certain aspects of driving rules and attitudes while driving, and different types of questions were addressed to the drivers to assess their judgments of these aspects. Consequently, different methods of data analysis were applied to determine the aspects that heavily influence driver perception of accident risk. An experiment based on the stated preferences (SP) was carried out with the drivers, and the SP data were analyzed using an ordered probit (OP) model. Interesting findings emerged from different analyses of the data and from the comparisons among the data collected in the two different territorial contexts. We found that both Italian and Spanish drivers consider driving in an altered psychophysical state and violating the overtaking rules to be the most risky behaviors.

  7. Functional analysis of non-hotspot AKT1 mutants found in human breast cancers identifies novel driver mutations: implications for personalized medicine

    OpenAIRE

    Yi, Kyung H.; Axtmayer, Jossette; Gustin, John P.; Rajpurohit, Anandita; Lauring, Josh

    2012-01-01

    The phosphatidylinositol 3-kinase (PI3-kinase)-Akt-mTOR pathway is mutated at high frequency in human breast cancer, and this pathway is the focus of active drug discovery and clinical investigation. Trials of personalized cancer therapy seek to leverage knowledge of cancer gene mutations by using mutations to guide the choice of targeted therapies. At the same time, cancer genome sequencing studies are identifying low frequency variants of unknown significance in known cancer genes, as well ...

  8. An Evolutionary Approach for Identifying Driver Mutations in Colorectal Cancer.

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    Jasmine Foo

    2015-09-01

    Full Text Available The traditional view of cancer as a genetic disease that can successfully be treated with drugs targeting mutant onco-proteins has motivated whole-genome sequencing efforts in many human cancer types. However, only a subset of mutations found within the genomic landscape of cancer is likely to provide a fitness advantage to the cell. Distinguishing such "driver" mutations from innocuous "passenger" events is critical for prioritizing the validation of candidate mutations in disease-relevant models. We design a novel statistical index, called the Hitchhiking Index, which reflects the probability that any observed candidate gene is a passenger alteration, given the frequency of alterations in a cross-sectional cancer sample set, and apply it to a mutational data set in colorectal cancer. Our methodology is based upon a population dynamics model of mutation accumulation and selection in colorectal tissue prior to cancer initiation as well as during tumorigenesis. This methodology can be used to aid in the prioritization of candidate mutations for functional validation and contributes to the process of drug discovery.

  9. Leptospirosis outbreaks in Nicaragua: identifying critical areas and exploring drivers for evidence-based planning.

    Science.gov (United States)

    Schneider, Maria Cristina; Nájera, Patricia; Aldighieri, Sylvain; Bacallao, Jorge; Soto, Aida; Marquiño, Wilmer; Altamirano, Lesbia; Saenz, Carlos; Marin, Jesus; Jimenez, Eduardo; Moynihan, Matthew; Espinal, Marcos

    2012-11-01

    Leptospirosis is an epidemic-prone zoonotic disease that occurs worldwide. In Central America, leptospirosis outbreaks have been reported in almost all countries; Nicaragua in particular has faced several outbreaks. The objective of this study was to stratify the risk and identify "critical areas" for leptospirosis outbreaks in Nicaragua, and to perform an exploratory analysis of potential "drivers". This ecological study includes the entire country (153 municipalities). Cases from 2004 to 2010 were obtained from the country's health information system, demographic and socioeconomic variables from its Census, and environmental data from external sources. Criteria for risk stratification of leptospirosis were defined. Nicaragua reported 1,980 cases of leptospirosis during this period, with the highest percentage of cases (26.36%) in León, followed by Chinandega (15.35%). Among the 153 municipalities, 48 were considered critical areas, 85 were endemic and 20 silent. Using spatial and statistical analysis, the variable presenting the most evident pattern of association with critical areas defined by top quintile of incidence rate is the percentage of municipal surface occupied by the soil combination of cambisol (over pyroclastic and lava bedrock) and andosol (over a volcanic ashes foundation). Precipitation and percentage of rural population are also associated with critical areas. This methodology and findings could be used for Nicaragua's Leptospirosis Intersectoral Plan, and to identify possible risk areas in other countries with similar drivers.

  10. Data Fusion for Driver Behaviour Analysis

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    Juan Carmona

    2015-10-01

    Full Text Available A driver behaviour analysis tool is presented. The proposal offers a novel contribution based on low-cost hardware and advanced software capabilities based on data fusion. The device takes advantage of the information provided by the in-vehicle sensors using Controller Area Network Bus (CAN-BUS, an Inertial Measurement Unit (IMU and a GPS. By fusing this information, the system can infer the behaviour of the driver, providing aggressive behaviour detection. By means of accurate GPS-based localization, the system is able to add context information, such as digital map information, speed limits, etc. Several parameters and signals are taken into account, both in the temporal and frequency domains, to provide real time behaviour detection. The system was tested in urban, interurban and highways scenarios.

  11. Molecular profiling of low grade serous ovarian tumours identifies novel candidate driver genes.

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    Hunter, Sally M; Anglesio, Michael S; Ryland, Georgina L; Sharma, Raghwa; Chiew, Yoke-Eng; Rowley, Simone M; Doyle, Maria A; Li, Jason; Gilks, C Blake; Moss, Phillip; Allan, Prue E; Stephens, Andrew N; Huntsman, David G; deFazio, Anna; Bowtell, David D; Gorringe, Kylie L; Campbell, Ian G

    2015-11-10

    Low grade serous ovarian tumours are a rare and under-characterised histological subtype of epithelial ovarian tumours, with little known of the molecular drivers and facilitators of tumorigenesis beyond classic oncogenic RAS/RAF mutations. With a move towards targeted therapies due to the chemoresistant nature of this subtype, it is pertinent to more fully characterise the genetic events driving this tumour type, some of which may influence response to therapy and/or development of drug resistance. We performed genome-wide high-resolution genomic copy number analysis (Affymetrix SNP6.0) and mutation hotspot screening (KRAS, BRAF, NRAS, HRAS, ERBB2 and TP53) to compare a large cohort of ovarian serous borderline tumours (SBTs, n = 57) with low grade serous carcinomas (LGSCs, n = 19). Whole exome sequencing was performed for 13 SBTs, nine LGSCs and one mixed low/high grade carcinoma. Copy number aberrations were detected in 61% (35/57) of SBTs, compared to 100% (19/19) of LGSCs. Oncogenic RAS/RAF/ERBB2 mutations were detected in 82.5% (47/57) of SBTs compared to 63% (12/19) of LGSCs, with NRAS mutations detected only in LGSC. Some copy number aberrations appeared to be enriched in LGSC, most significantly loss of 9p and homozygous deletions of the CDKN2A/2B locus. Exome sequencing identified BRAF, KRAS, NRAS, USP9X and EIF1AX as the most frequently mutated genes. We have identified markers of progression from borderline to LGSC and novel drivers of LGSC. USP9X and EIF1AX have both been linked to regulation of mTOR, suggesting that mTOR inhibitors may be a key companion treatment for targeted therapy trials of MEK and RAF inhibitors.

  12. Identifying drivers for consumer acceptance and purchase intent of corn tortilla.

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    Herrera-Corredor, J A; Saidu, J E P; Khachatryan, A; Prinyawiwatkul, W; Carballo-Carballo, A; Zepeda-Bautista, R

    2007-11-01

    The traditional production of corn tortilla has been modified by new processing technologies to make possible a commercial-scale production; this practice has resulted in products having sensory properties different from those produced by the traditional method. There is no published information on sensory attributes driving acceptance and purchase intent of corn tortillas. Identifying sensory drivers for acceptance and purchase intent of corn tortillas will help commercially produce products that satisfy consumers' expectations. A consumer study was conducted to evaluate acceptance and purchase intent of corn tortillas and determine drivers of acceptance and purchase intent of the products. Ten samples of corn tortillas were selected to represent a variety of corn tortillas available in the Mexican market. Three hundred Mexican consumers evaluated acceptability of appearance, color, thickness, rollability, resistance to tearing, aroma, chewiness, taste and aftertaste, and overall liking using a 9-point hedonic scale. Overall acceptance and purchase intent were determined with a yes/no scale. Analysis of variance and multivariate analysis of variance revealed that consumers were able to differentiate differences in sensory acceptability among 10 samples. For example, 2 homemade and 1 small commercial-scale samples, with an overall liking score of 6.6 to 6.7, were more acceptable than others. Rollability, resistance to tearing, and chewiness were attributes underlying overall differences among 10 samples. Attributes determining overall acceptance of corn tortillas were chewiness and overall liking. Purchase intent was influenced by overall appearance, rollability, chewiness, taste, and overall liking. This study revealed critical sensory attributes and their weights given by Mexican consumers when making decisions for acceptance and purchase intent of corn tortilla.

  13. Understanding the health of lorry drivers in context: A critical discourse analysis.

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    Caddick, Nick; Varela-Mato, Veronica; Nimmo, Myra A; Clemes, Stacey; Yates, Tom; King, James A

    2017-01-01

    This article moves beyond previous attempts to understand health problems in the lives of professional lorry drivers by placing the study of drivers' health in a wider social and cultural context. A combination of methods including focus groups, interviews and observations were used to collect data from a group of 24 lorry drivers working at a large transport company in the United Kingdom. Employing a critical discourse analysis, we identified the dominant discourses and subject positions shaping the formation of drivers' health and lifestyle choices. This analysis was systematically combined with an exploration of the gendered ways in which an almost exclusively male workforce talked about health. Findings revealed that drivers were constituted within a neoliberal economic discourse, which is reflective of the broader social structure, and which partly restricted drivers' opportunities for healthy living. Concurrently, drivers adopted the subject position of 'average man' as a way of defending their personal and masculine status in regards to health and to justify jettisoning approaches to healthy living that were deemed too extreme or irrational in the face of the constraints of their working lives. Suggestions for driver health promotion include refocusing on the social and cultural - rather than individual - underpinnings of driver health issues and a move away from moralistic approaches to health promotion.

  14. Stability analysis of automobile driver steering control

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    Allen, R. W.

    1981-01-01

    In steering an automobile, the driver must basically control the direction of the car's trajectory (heading angle) and the lateral deviation of the car relative to a delineated pathway. A previously published linear control model of driver steering behavior which is analyzed from a stability point of view is considered. A simple approximate expression for a stability parameter, phase margin, is derived in terms of various driver and vehicle control parameters, and boundaries for stability are discussed. A field test study is reviewed that includes the measurement of driver steering control parameters. Phase margins derived for a range of vehicle characteristics are found to be generally consistent with known adaptive properties of the human operator. The implications of these results are discussed in terms of driver adaptive behavior.

  15. Identifying tectonic and climatic drivers for deep-marine siliciclastic systems: Middle Eocene, Spanish Pyrenees

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    Pickering, K. T.; Scotchman, J. I.; Robinson, S. A.

    2009-12-01

    Analysis of the sedimentary record in deep time requires the deconvolution of tectonic and climatic drivers. The deep-marine siliciclastic systems in the Middle Eocene Ainsa-Jaca basin, Spanish Pyrenees, with their excellent outcrops and good temporal resolution, provide an opportunity to identify the relative importance of tectonic and climatic drivers on deposition over ~10 Myr at a time when the Earth’s climate was shifting from a greenhouse to icehouse conditions. The cumulative ~4 km of stratigraphy contains 8 sandy systems with a total of ~25 discrete channelized sandbodies that accumulated in water depths of ~400-800 m, and that were controlled by the ~400-kyr Milkankovitch frequency with modes, at ~100 kyr and ~41 kyr (possibly stacked ~23-kyr) influencing bottom-water conditions, causing periodic stratification in the water column across a submarine sill within the eastern, more proximal depositional systems in the Ainsa basin. We also identify a range of sub-Milankovitch millennial-scale cycles (Scotchman et al. 2009). In the Ainsa basin, the interplay of basin-bounding growth anticlines defined and controlled the position and stacking patterns of the sandy systems and their constituent channelized sandbodies, in a process of seesaw tectonics by: (i) Westward lateral offset-stacking of channelized sandbodies due to growth of the eastern anticline (Mediano), and (ii) Eastward (orogenwards) back-stepping of the depositional axis of each sandy system, due to phases of relative uplift of the opposing Boltaña growth anticline. The first-order control on accommodation, and the flow paths, for deep-marine sedimentation were tectonic, with the pacing of the supply of coarse siliciclastics being driven by global climatic processes, particularly Milankovitch-type frequencies. The dominance of eccentricity and obliquity is similar to results from the continental lacustrine Eocene Green River Formation, and the observations from ODP Site 1258 that the early to

  16. Urinalysis and hair analysis for illicit drugs of driver applicants and drivers in the trucking industry.

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    Mieczkowski, Tom

    2010-07-01

    The purpose of this article is to compare the differential rate of detection of illicit drugs when using two distinct sample types, hair and urine specimens. The specimens were collected from persons who applied for employment as a truck driver, or were collected from randomly selected currently employed truck drivers. The data is examined for job applicants and employees to determine if any differences in outcomes are associated with employment status or specimen type. The data is also assessed for specific patterns associated with particular drugs and their assay outcomes. Overall, it was determined that drug positive cases are relatively rare. Job applicants are more likely to test positive for an illicit drug than a currently employed driver. Applicants are more frequently positive for a drug by a factor of 3 for both urinalysis and hair analysis when compared to currently employed drivers. Approximately 2% of applicants were urine positive and 9% hair positive for an illegal drug. Considering employed truck drivers 0.6% were drug positive by urinalysis and 3% when using hair analysis. It is concluded that hair assays detect more drug use than urinalysis. It is also concluded that when urine and hair assay outcomes are non-concordant the typical case is a positive hair analysis with a negative urinalysis.

  17. Focal chromosomal copy number aberrations identify CMTM8 and GPR177 as new candidate driver genes in osteosarcoma.

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    Joeri Both

    Full Text Available Osteosarcoma is an aggressive bone tumor that preferentially develops in adolescents. The tumor is characterized by an abundance of genomic aberrations, which hampers the identification of the driver genes involved in osteosarcoma tumorigenesis. Our study aims to identify these genes by the investigation of focal copy number aberrations (CNAs, <3 Mb. For this purpose, we subjected 26 primary tumors of osteosarcoma patients to high-resolution single nucleotide polymorphism array analyses and identified 139 somatic focal CNAs. Of these, 72 had at least one gene located within or overlapping the focal CNA, with a total of 94 genes. For 84 of these genes, the expression status in 31 osteosarcoma samples was determined by expression microarray analysis. This enabled us to identify the genes of which the over- or underexpression was in more than 35% of cases in accordance to their copy number status (gain or loss. These candidate genes were subsequently validated in an independent set and furthermore corroborated as driver genes by verifying their role in other tumor types. We identified CMTM8 as a new candidate tumor suppressor gene and GPR177 as a new candidate oncogene in osteosarcoma. In osteosarcoma, CMTM8 has been shown to suppress EGFR signaling. In other tumor types, CMTM8 is known to suppress the activity of the oncogenic protein c-Met and GPR177 is known as an overexpressed upstream regulator of the Wnt-pathway. Further studies are needed to determine whether these proteins also exert the latter functions in osteosarcoma tumorigenesis.

  18. Exploring Driver Injury Severity at Intersection: An Ordered Probit Analysis

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    Yaping Zhang

    2015-02-01

    Full Text Available It is well known that intersections are the most hazardous locations; however, only little is known about driver injury severity in intersection crashes. Hence, the main goal of this study was to further examine the different factors contributing to driver injury severity involved in fatal crashes at intersections. Data used for the present analysis was from the US DOT-Fatality Analysis Reporting System (FARS crash database from the year 2011. An ordered probit model was employed to fit the fatal crash data and analyze the factors impacting each injury severity level. The analysis results displayed that driver injury severity is significantly affected by many factors. They include driver age and gender, driver ethnicity, vehicle type and age (years of use, crash type, driving drunk, speeding, violating stop sign, cognitively distracted driving, and seat belt usage. These findings from the current study are beneficial to form a solid basis for adopting corresponding measures to effectively drop injury severity suffering from intersection crash. More insights into the effects of risk factors on driver injury severity could be acquired using more advanced statistical models.

  19. Method for identifying drivers, barriers and synergies related to the deployment of a CO2 pipeline network : A case study for the Iberian Peninsula and Morocco

    NARCIS (Netherlands)

    Berghout, Niels; Cabal, Helena; Gouveia, João Pedro; van den Broek, Machteld; Faaij, André

    2015-01-01

    This paper provides a method to identify drivers, barriers and synergies (DBS) related to the deployment of a CO2 pipeline network. The method was demonstrated for the West Mediterranean region (WMR) (i.e. Spain, Portugal and Morocco). The method comprises a literature review, analysis of

  20. Characteristics of Chinese Driver Behavior

    OpenAIRE

    LI J

    2014-01-01

    The high growth rate of vehicle ownership and many novel drivers in China determine the special features of Chinese driver behavior. This thesis introduces a comparative study on driver behavior by the analysis of saturation flow at urban intersections, Driver Behavior Questionnaire surveys, focus group discussion, and in-car tests. The main characteristics of Chinese driver behavior have been identified. A new method is developed for a simulation model calibration based on the study results.

  1. Colorectal cancer driver genes identified by patient specific comparison of cytogenetic microarray

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    Mohammad Azhar Aziz

    2014-12-01

    Full Text Available Colorectal cancer (CRC, which has high prevalence in Saudi Arabia and worldwide, needs better understanding by exploiting the latest available cytogenetic microarrays. We used biopsy tissue from consenting colorectal cancer patients to extract DNA and carry out microarray analysis using a CytoScan HD platform from Affymetrix. Patient specific comparisons of tumor–normal pairs were carried out. To find out the high probability key players, we performed Genomic Identification of Significant Targets in Cancer analysis and found 144 genes to form the list of driver genes. Of these, 24 genes attained high GISTIC scores and suggest being significantly associated with CRC. Loss of heterozygosity and uniparental disomy were found to affect 9 genes and suggest different mechanisms associated with CRC in every patient. Here we present the details of the methods used in carrying out the above analyses. Also, we provide some additional data on biomarker analysis that would complement the findings.

  2. Thermal analysis of LED lamps for optimal driver integration

    NARCIS (Netherlands)

    Perpiñà, X.; Werkhoven, R.J.; Vellvehi, M.; Jakovenko, J.; Jordà, X.; Kunen, J.M.G.; Bancken, P.; Bolt, P.J.

    2015-01-01

    This paper studies the thermal influence of a light-emitting diode (LED) driver on a retrofit LED lamp, also reporting on a procedure for its thermal characterization and multiscale modeling. In this analysis, temperature is measured by infrared thermography and monitoring specific locations with th

  3. What the drivers do and do not tell you: using verbal protocol analysis to investigate driver behaviour in emergency situations.

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    Banks, Victoria A; Stanton, Neville A; Harvey, Catherine

    2014-01-01

    Although task analysis of pedestrian detection can provide us with useful insights into how a driver may behave in emergency situations, the cognitive elements of driver decision-making are less well understood. To assist in the design of future Advanced Driver Assistance Systems, such as Autonomous Emergency Brake systems, it is essential that the cognitive elements of the driving task are better understood. This paper uses verbal protocol analysis in an exploratory fashion to uncover the thought processes underlying behavioural outcomes represented by hard data collected using the Southampton University Driving Simulator.

  4. Integrated exon level expression analysis of driver genes explain their role in colorectal cancer.

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    Mohammad Azhar Aziz

    Full Text Available Integrated analysis of genomic and transcriptomic level changes holds promise for a better understanding of colorectal cancer (CRC biology. There is a pertinent need to explain the functional effect of genome level changes by integrating the information at the transcript level. Using high resolution cytogenetics array, we had earlier identified driver genes by 'Genomic Identification of Significant Targets In Cancer (GISTIC' analysis of paired tumour-normal samples from colorectal cancer patients. In this study, we analyze these driver genes at three levels using exon array data--gene, exon and network. Gene level analysis revealed a small subset to experience differential expression. These results were reinforced by carrying out separate differential expression analyses (SAM and LIMMA. ATP8B1 was found to be the novel gene associated with CRC that shows changes at cytogenetic, gene and exon levels. Splice index of 29 exons corresponding to 13 genes was found to be significantly altered in tumour samples. Driver genes were used to construct regulatory networks for tumour and normal groups. There were rearrangements in transcription factor genes suggesting the presence of regulatory switching. The regulatory pattern of AHR gene was found to have the most significant alteration. Our results integrate data with focus on driver genes resulting in highly enriched novel molecules that need further studies to establish their role in CRC.

  5. Training State and Community Instructors in Use of NHTSA Curriculum Packages: Driver Improvement Analysis, Driver License Examiner-Supervisor and Traffic Record Analysis.

    Science.gov (United States)

    Burgener, V. E.; Tiryakioglu, Dona

    A series of five national instructor training institutes were planned for each of three emerging highway safety technician areas for which curriculum packages have been prepared (Driver Improvement Analysis, Driver License Examiner-Supervisor, and Traffic Record Analysis). Technical Education Research Centers and Dunlap & Associates…

  6. A cognitive Analysis of truck Drivers' right-hand Turns

    DEFF Research Database (Denmark)

    G. Sieker, Tobias; G. Skulason, Thorgeir; Sletting, Kristian

    2016-01-01

    using several brief glances in mirrors, and that the front and near-zone mirrors are never used during right-hand turns. Controlling the vehicle is found to be more or less automatic, whereas their focus is on the orientation about surroundings. Lastly, the drivers’ behavior is discussed in relation......This paper presents an investigation of truck drivers’ performance during right-hand turns performed in intersections with traffic lights in order to elicit the truck drivers’ domain, decision-making processes, and the strategies used while executing the turn. To gain knowledge about this, a truck...... driving instructor is interviewed, and four truck drivers are observed and interviewed. This results in a cognitive work analysis with the phases work domain analysis, control task analysis and strategies analysis. Through this study it is indicated that many different types of information are sought...

  7. Comparative oncogenomic analysis of copy number alterations in human and zebrafish tumors enables cancer driver discovery.

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    GuangJun Zhang

    2013-08-01

    Full Text Available The identification of cancer drivers is a major goal of current cancer research. Finding driver genes within large chromosomal events is especially challenging because such alterations encompass many genes. Previously, we demonstrated that zebrafish malignant peripheral nerve sheath tumors (MPNSTs are highly aneuploid, much like human tumors. In this study, we examined 147 zebrafish MPNSTs by massively parallel sequencing and identified both large and focal copy number alterations (CNAs. Given the low degree of conserved synteny between fish and mammals, we reasoned that comparative analyses of CNAs from fish versus human MPNSTs would enable elimination of a large proportion of passenger mutations, especially on large CNAs. We established a list of orthologous genes between human and zebrafish, which includes approximately two-thirds of human protein-coding genes. For the subset of these genes found in human MPNST CNAs, only one quarter of their orthologues were co-gained or co-lost in zebrafish, dramatically narrowing the list of candidate cancer drivers for both focal and large CNAs. We conclude that zebrafish-human comparative analysis represents a powerful, and broadly applicable, tool to enrich for evolutionarily conserved cancer drivers.

  8. Inferring the drivers of discarding practices from observer data to identify appropriate fishery‐specific solutions

    DEFF Research Database (Denmark)

    Catchpole, Tom; Rochet, Marie‐Joëlle; Madsen, Niels

    2012-01-01

    Discard patterns are affected initially by catch compositions, which are determined by environmental factors, the fishing gear used, and fishing tactics, and finally by fishers, when they decide which parts of the catch to retain. An understanding of the drivers of discard practices is essential...... with associated quota that are above the MLS or minimum length landed. The model is applied to data from the full English observer programme and to French, Danish, Greek, and Spanish case study métiers. The proportionate contribution of the different categories is determined, the differences between métiers...

  9. A possibility to identify the vehicle driver through complex forensic and criminalistic expertise--case report.

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    Păduraru, G; Knieling, A; Scripcaru, C; Iliescu, Diana Bulgaru

    2014-01-01

    Traffic accidents can have more or less dramatic consequences that involve penal and civil responsibility with amplitude extending over long periods of time. In many cases, substitution of the driver with the passenger in order to avoid criminal responsibility is often remarked. The substitution takes place with the passenger's agreement or, in cases with dramatic consequences (coma or death), without his/her consent. These situations are encountered in civil cases regarding insurance fraud. In addition to forensic medical expertise, to aid the experts, mathematical modeling and computer simulation of the dynamics of vehicle passengers is a tool that completes the criminal expertise of traffic accidents. This paper presents the method of identification of the person driving the vehicle based on the computer simulation of vehicle occupants' dynamics.

  10. Born to roam? Surveying cat owners in Tasmania, Australia, to identify the drivers and barriers to cat containment.

    Science.gov (United States)

    McLeod, Lynette J; Hine, Donald W; Bengsen, Andrew J

    2015-12-01

    Free-roaming domestic cats, Felis catus, are a major public nuisance in neighbourhoods across the world, and have been linked to biodiversity loss and a host of community health problems. Owners who let their cats roam, also place their cats at risk of serious injury. One management strategy that is gaining considerable support involves encouraging cat owners to contain their pets within their property. Contemporary behaviour change models highlight the importance of identifying drivers and barriers that encourage and discourage target behaviours such as cat containment. Results from a random dial phone survey of 356 cat owners in northern Tasmania identified four distinct cat containment profiles: owners who contained their cat all the time, owners who only contained their cat at night, owners who sporadically contained their cat with no set routine, and owners who made no attempt to contain their pet. Our results indicated that cat-owners' decisions to contain or not contain their cats were guided by a range of factors including owners' beliefs about their ability to implement an effective containment strategy and their views about the physical and psychological needs of their cats. The results are discussed in terms of improving the behavioural effectiveness of cat containment interventions by selecting appropriate behavioural change tools for the identified drivers and barriers, and developing targeted engagement strategies and messaging.

  11. Significant drivers of the virtual water trade evaluated with a multivariate regression analysis

    Science.gov (United States)

    Tamea, Stefania; Laio, Francesco; Ridolfi, Luca

    2014-05-01

    International trade of food is vital for the food security of many countries, which rely on trade to compensate for an agricultural production insufficient to feed the population. At the same time, food trade has implications on the distribution and use of water resources, because through the international trade of food commodities, countries virtually displace the water used for food production, known as "virtual water". Trade thus implies a network of virtual water fluxes from exporting to importing countries, which has been estimated to displace more than 2 billions of m3 of water per year, or about the 2% of the annual global precipitation above land. It is thus important to adequately identify the dynamics and the controlling factors of the virtual water trade in that it supports and enables the world food security. Using the FAOSTAT database of international trade and the virtual water content available from the Water Footprint Network, we reconstructed 25 years (1986-2010) of virtual water fluxes. We then analyzed the dependence of exchanged fluxes on a set of major relevant factors, that includes: population, gross domestic product, arable land, virtual water embedded in agricultural production and dietary consumption, and geographical distance between countries. Significant drivers have been identified by means of a multivariate regression analysis, applied separately to the export and import fluxes of each country; temporal trends are outlined and the relative importance of drivers is assessed by a commonality analysis. Results indicate that population, gross domestic product and geographical distance are the major drivers of virtual water fluxes, with a minor (but non-negligible) contribution given by the agricultural production of exporting countries. Such drivers have become relevant for an increasing number of countries throughout the years, with an increasing variance explained by the distance between countries and a decreasing role of the gross

  12. Identifying drivers of overall satisfaction in patients receiving HIV primary care: a cross-sectional study.

    Directory of Open Access Journals (Sweden)

    Bich N Dang

    Full Text Available OBJECTIVE: This study seeks to understand the drivers of overall patient satisfaction in a predominantly low-income, ethnic-minority population of HIV primary care patients. The study's primary aims were to determine 1 the component experiences which contribute to patients' evaluations of their overall satisfaction with care received, and 2 the relative contribution of each component experience in explaining patients' evaluation of overall satisfaction. METHODS: We conducted a cross-sectional study of 489 adult patients receiving HIV primary care at two clinics in Houston, Texas, from January 13-April 21, 2011. The participation rate among eligible patients was 94%. The survey included 15 questions about various components of the care experience, 4 questions about the provider experience and 3 questions about overall care. To ensure that the survey was appropriately tailored to our clinic population and the list of component experiences reflected all aspects of the care experience salient to patients, we conducted in-depth interviews with key providers and clinic staff and pre-tested the survey instrument with patients. RESULTS: Patients' evaluation of their provider correlated the strongest with their overall satisfaction (standardized β = 0.445, p<0.001 and accounted for almost half of the explained variance. Access and availability, like clinic hours and ease of calling the clinic, also correlated with overall satisfaction, but less strongly. Wait time and parking, despite receiving low patient ratings, did not correlate with overall satisfaction. CONCLUSIONS: The patient-provider relationship far exceeds other component experiences of care in its association with overall satisfaction. Our study suggests that interventions to improve overall patient satisfaction should focus on improving patients' evaluation of their provider.

  13. Analysis of drivers' characteristics in car-following theory

    Science.gov (United States)

    Zhang, Geng; Sun, Di-Hua; Liu, Hui; Zhao, Min

    2014-09-01

    In recent years, the influence of drivers' behaviors on traffic flow has attracted considerable attention according to Transportation Cyber Physical Systems. In this paper, an extended car-following model is presented by considering drivers' timid or aggressive characteristics. The impact of drivers' timid or aggressive characteristics on the stability of traffic flow has been analyzed through linear stability theory and nonlinear reductive perturbation method. Numerical simulation shows that the propagating behavior of traffic density waves near the critical point can be described by the kink-antikink soliton of the mKdV equation. The good agreement between the numerical simulation and the analytical results shows that drivers' characteristics play an important role in traffic jamming transition.

  14. Stability Analysis of Transportation Networks with Multiscale Driver Decisions

    CERN Document Server

    Como, Giacomo; Acemoglu, Daron; Dahleh, Munther A; Frazzoli, Emilio

    2011-01-01

    Stability of Wardrop equilibria is analyzed for dynamical transportation networks in which the drivers' route choices are influenced by information at multiple temporal and spatial scales. The considered model involves a continuum of indistinguishable drivers commuting between a common origin/destination pair in an acyclic transportation network. The drivers' route choices are affected by their, relatively infrequent, perturbed best responses to global information about the current network congestion levels, as well as their instantaneous local observation of the immediate surroundings as they transit through the network. A novel model is proposed for the drivers' route choice behavior, exhibiting local consistency with their preference toward globally less congested paths as well as myopic decisions in favor of locally less congested paths. The simultaneous evolution of the traffic congestion on the network and of the aggregate path preference is modeled by a system of coupled ordinary differential equations...

  15. Identifying the main drivers of soil carbon response to climate change in arctic and boreal Alaska.

    Science.gov (United States)

    Genet, H.; McGuire, A. D.; He, Y.; Johnson, K.; Wylie, B. K.; Pastick, N. J.; Zhuang, Q.; Zhu, Z.

    2015-12-01

    Boreal and arctic regions represent the largest reservoir of carbon among terrestrial biomes. Most of this carbon is stored deep in the soil in permafrost where frozen organic matter is protected from decomposition. The vulnerability of soil carbon stocks to a changing climate in high latitudes depends on a number of physical and ecological processes. The importance of these processes in controlling the dynamics of soil carbon stocks vary across regions because of variability in vegetation composition, drainage condition, and permafrost characteristics. To better understand the main drivers of the vulnerability of soil carbon stocks to climate change in Alaska, we ran a process-based ecosystem model, the Terrestrial Ecosystem Model. This model explicitly simulates interactions between the carbon cycle and permafrost dynamics and was coupled with a disturbance model and a model of biogenic methane dynamics to assess historical and projected soil carbon dynamics in Alaska, from 1950 to 2100. The uncertainties related to climate, fire regime and atmospheric CO2projections on soil carbon dynamics were quantified by running simulations using climate projections from 2 global circulation models, 3 fossil fuel emission scenarios and 3 alternative fire management scenarios. During the historical period [1950-2009], soil carbon stocks increased by 4.7 TgC/yr in Alaska. Soil carbon stocks decreased in boreal Alaska due to substantial fire activity in the early 2000's. This loss was offset by carbon accumulation in the arctic. Changes in soil carbon stocks from 2010 to 2099 ranged from 8.9 to 25.6 TgC/yr, depending on the climate projections. Soil carbon accumulation was slower in lowlands than in uplands and slower in the boreal than in the arctic regions because of the negative effect of fire activity on soil carbon stocks. Tundra ecosystems were more vulnerable to carbon loss from fire than forest ecosystems because of a lower productivity. As a result, the increase in

  16. Calibrating and Validating a Simulation Model to Identify Drivers of Urban Land Cover Change in the Baltimore, MD Metropolitan Region

    Directory of Open Access Journals (Sweden)

    Claire Jantz

    2014-09-01

    Full Text Available We build upon much of the accumulated knowledge of the widely used SLEUTH urban land change model and offer advances. First, we use SLEUTH’s exclusion/attraction layer to identify and test different urban land cover change drivers; second, we leverage SLEUTH’s self-modification capability to incorporate a demographic model; and third, we develop a validation procedure to quantify the influence of land cover change drivers and assess uncertainty. We found that, contrary to our a priori expectations, new development is not attracted to areas serviced by existing or planned water and sewer infrastructure. However, information about where population and employment growth is likely to occur did improve model performance. These findings point to the dominant role of centrifugal forces in post-industrial cities like Baltimore, MD. We successfully developed a demographic model that allowed us to constrain the SLEUTH model forecasts and address uncertainty related to the dynamic relationship between changes in population and employment and urban land use. Finally, we emphasize the importance of model validation. In this work the validation procedure played a key role in rigorously assessing the impacts of different exclusion/attraction layers and in assessing uncertainty related to population and employment forecasts.

  17. Driver-centred vehicle automation: using network analysis for agent-based modelling of the driver in highly automated driving systems.

    Science.gov (United States)

    Banks, Victoria A; Stanton, Neville A

    2016-11-01

    To the average driver, the concept of automation in driving infers that they can become completely 'hands and feet free'. This is a common misconception, however, one that has been shown through the application of Network Analysis to new Cruise Assist technologies that may feature on our roads by 2020. Through the adoption of a Systems Theoretic approach, this paper introduces the concept of driver-initiated automation which reflects the role of the driver in highly automated driving systems. Using a combination of traditional task analysis and the application of quantitative network metrics, this agent-based modelling paper shows how the role of the driver remains an integral part of the driving system implicating the need for designers to ensure they are provided with the tools necessary to remain actively in-the-loop despite giving increasing opportunities to delegate their control to the automated subsystems. Practitioner Summary: This paper describes and analyses a driver-initiated command and control system of automation using representations afforded by task and social networks to understand how drivers remain actively involved in the task. A network analysis of different driver commands suggests that such a strategy does maintain the driver in the control loop.

  18. Focal chromosomal copy number aberrations identify CMTM8 and GPR177 as new candidate driver genes in osteosarcoma.

    Science.gov (United States)

    Both, Joeri; Krijgsman, Oscar; Bras, Johannes; Schaap, Gerard R; Baas, Frank; Ylstra, Bauke; Hulsebos, Theo J M

    2014-01-01

    Osteosarcoma is an aggressive bone tumor that preferentially develops in adolescents. The tumor is characterized by an abundance of genomic aberrations, which hampers the identification of the driver genes involved in osteosarcoma tumorigenesis. Our study aims to identify these genes by the investigation of focal copy number aberrations (CNAs, GPR177 as a new candidate oncogene in osteosarcoma. In osteosarcoma, CMTM8 has been shown to suppress EGFR signaling. In other tumor types, CMTM8 is known to suppress the activity of the oncogenic protein c-Met and GPR177 is known as an overexpressed upstream regulator of the Wnt-pathway. Further studies are needed to determine whether these proteins also exert the latter functions in osteosarcoma tumorigenesis.

  19. Whole-genome sequencing and comprehensive molecular profiling identify new driver mutations in gastric cancer

    NARCIS (Netherlands)

    Wang, Kai; Yuen, Siu Tsan; Xu, Jiangchun; Lee, Siu Po; Yan, Helen H N; Shi, Stephanie T; Siu, Hoi Cheong; Deng, Shibing; Chu, Kent Man; Law, Simon; Chan, Kok Hoe; Chan, Annie S Y; Tsui, Wai Yin; Ho, Siu Lun; Chan, Anthony K W; Man, Jonathan L K; Foglizzo, Valentina; Ng, Man Kin; Chan, April S; Ching, Yick Pang; Cheng, Grace H W; Xie, Tao; Fernandez, Julio; Li, Vivian S W; Clevers, Hans; Rejto, Paul A; Mao, Mao; Leung, Suet Yi

    2014-01-01

    Gastric cancer is a heterogeneous disease with diverse molecular and histological subtypes. We performed whole-genome sequencing in 100 tumor-normal pairs, along with DNA copy number, gene expression and methylation profiling, for integrative genomic analysis. We found subtype-specific genetic and e

  20. Identifying Immune Drivers of Gulf War Illness Using a Novel Daily Sampling Approach

    Science.gov (United States)

    2015-10-01

    School of Medicine and Department of Psychology compensated us for the sample loss. We selected and ordered a new freezer that will be used to store the...interesting relationships between the immune system and GWI symptoms. First, GWI individuals show abnormally large day-to-day swings in inflammatory...and Younger, J.; Evidence for abnormal cytokine expression in Gulf War Illness: A preliminary analysis of daily immune monitoring data; BMC Immunology

  1. Mapping genetic alterations causing chemoresistance in cancer: identifying the roads by tracking the drivers.

    Science.gov (United States)

    Lønning, P E; Knappskog, S

    2013-11-14

    Although new agents are implemented to cancer therapy, we lack fundamental understandings of the mechanisms of chemoresistance, the main obstacle to cure in cancer. Here we review clinical evidence linking molecular defects to drug resistance across different tumour forms and discuss contemporary experimental evidence exploring these mechanisms. Although evidence, in general, is sparse and fragmentary, merging knowledge links drug resistance, and also sensitivity, to defects in functional pathways having a key role in cell growth arrest or death and DNA repair. As these pathways may act in concert, there is a need to explore multiple mechanisms in parallel. Taking advantage of massive parallel sequencing and other novel high-throughput technologies and base research on biological hypotheses, we now have the possibility to characterize functional defects related to these key pathways and to design a new generation of studies identifying the mechanisms controlling resistance to different treatment regimens in different tumour forms.

  2. Drivers of wetland conversion: a global meta-analysis.

    Directory of Open Access Journals (Sweden)

    Sanneke van Asselen

    Full Text Available Meta-analysis of case studies has become an important tool for synthesizing case study findings in land change. Meta-analyses of deforestation, urbanization, desertification and change in shifting cultivation systems have been published. This present study adds to this literature, with an analysis of the proximate causes and underlying forces of wetland conversion at a global scale using two complementary approaches of systematic review. Firstly, a meta-analysis of 105 case-study papers describing wetland conversion was performed, showing that different combinations of multiple-factor proximate causes, and underlying forces, drive wetland conversion. Agricultural development has been the main proximate cause of wetland conversion, and economic growth and population density are the most frequently identified underlying forces. Secondly, to add a more quantitative component to the study, a logistic meta-regression analysis was performed to estimate the likelihood of wetland conversion worldwide, using globally-consistent biophysical and socioeconomic location factor maps. Significant factors explaining wetland conversion, in order of importance, are market influence, total wetland area (lower conversion probability, mean annual temperature and cropland or built-up area. The regression analyses results support the outcomes of the meta-analysis of the processes of conversion mentioned in the individual case studies. In other meta-analyses of land change, similar factors (e.g., agricultural development, population growth, market/economic factors are also identified as important causes of various types of land change (e.g., deforestation, desertification. Meta-analysis helps to identify commonalities across the various local case studies and identify which variables may lead to individual cases to behave differently. The meta-regression provides maps indicating the likelihood of wetland conversion worldwide based on the location factors that have

  3. Identifying Drivers of Variability and Uncertainty in Lake Metabolism Estimates across the Continent

    Science.gov (United States)

    Roehm, C. L.; Lunch, C. K.; Hanson, P. C.; Solomon, C.

    2013-12-01

    metabolism components. A suite of models and techniques that can more accurately estimate and reflect the characteristics, processes and dynamics imparted by the distinct nature of the ecosystems will be identified and tested. Further, approaches for quantifying errors and uncertainties and error propagation will be discussed. This poster will highlight opportunities to link these data products with other external data sets in order to improve regional estimates of lake metabolism.

  4. Human Leptospirosis Infection in Fiji: An Eco-epidemiological Approach to Identifying Risk Factors and Environmental Drivers for Transmission.

    Directory of Open Access Journals (Sweden)

    Colleen L Lau

    2016-01-01

    Full Text Available Leptospirosis is an important zoonotic disease in the Pacific Islands. In Fiji, two successive cyclones and severe flooding in 2012 resulted in outbreaks with 576 reported cases and 7% case-fatality. We conducted a cross-sectional seroprevalence study and used an eco-epidemiological approach to characterize risk factors and drivers for human leptospirosis infection in Fiji, and aimed to provide an evidence base for improving the effectiveness of public health mitigation and intervention strategies. Antibodies indicative of previous or recent infection were found in 19.4% of 2152 participants (81 communities on the 3 main islands. Questionnaires and geographic information systems data were used to assess variables related to demographics, individual behaviour, contact with animals, socioeconomics, living conditions, land use, and the natural environment. On multivariable logistic regression analysis, variables associated with the presence of Leptospira antibodies included male gender (OR 1.55, iTaukei ethnicity (OR 3.51, living in villages (OR 1.64, lack of treated water at home (OR 1.52, working outdoors (1.64, living in rural areas (OR 1.43, high poverty rate (OR 1.74, living <100m from a major river (OR 1.41, pigs in the community (OR 1.54, high cattle density in the district (OR 1.04 per head/sqkm, and high maximum rainfall in the wettest month (OR 1.003 per mm. Risk factors and drivers for human leptospirosis infection in Fiji are complex and multifactorial, with environmental factors playing crucial roles. With global climate change, severe weather events and flooding are expected to intensify in the South Pacific. Population growth could also lead to more intensive livestock farming; and urbanization in developing countries is often associated with urban and peri-urban slums where diseases of poverty proliferate. Climate change, flooding, population growth, urbanization, poverty and agricultural intensification are important drivers of

  5. Driver style and driver skills – clustering drivers differing in their potential danger in traffic

    DEFF Research Database (Denmark)

    Martinussen, Laila Marianne; Møller, Mette; Prato, Carlo Giacomo

    The Driver Behavior Questionnaire (DBQ) and the Driver Skill Inventory (DSI) are two of the most frequently used measures of driving style and driving skill. The motivation behind the present study was to test drivers’ insight into their own driving ability based on a combined use of the DBQ......, annual mileage and accident involvement. 3908 drivers aged 18–84 participated in the survey. The results suggested that the drivers have good insight into their own driving ability, as the driving skill level mirrored the frequency of aberrant driving behaviors. K-means cluster analysis revealed four...... and the DSI. Moreover, the joint use of the two instruments was applied to identify sub-groups of drivers that differ in their potential danger in traffic, as well as to test for heterogeneity across the population, namely whether the sub-groups of drivers differed in characteristics such as age, gender...

  6. Human Leptospirosis Infection in Fiji: An Eco-epidemiological Approach to Identifying Risk Factors and Environmental Drivers for Transmission.

    Science.gov (United States)

    Lau, Colleen L; Watson, Conall H; Lowry, John H; David, Michael C; Craig, Scott B; Wynwood, Sarah J; Kama, Mike; Nilles, Eric J

    2016-01-01

    Leptospirosis is an important zoonotic disease in the Pacific Islands. In Fiji, two successive cyclones and severe flooding in 2012 resulted in outbreaks with 576 reported cases and 7% case-fatality. We conducted a cross-sectional seroprevalence study and used an eco-epidemiological approach to characterize risk factors and drivers for human leptospirosis infection in Fiji, and aimed to provide an evidence base for improving the effectiveness of public health mitigation and intervention strategies. Antibodies indicative of previous or recent infection were found in 19.4% of 2152 participants (81 communities on the 3 main islands). Questionnaires and geographic information systems data were used to assess variables related to demographics, individual behaviour, contact with animals, socioeconomics, living conditions, land use, and the natural environment. On multivariable logistic regression analysis, variables associated with the presence of Leptospira antibodies included male gender (OR 1.55), iTaukei ethnicity (OR 3.51), living in villages (OR 1.64), lack of treated water at home (OR 1.52), working outdoors (1.64), living in rural areas (OR 1.43), high poverty rate (OR 1.74), living leptospirosis infection in Fiji are complex and multifactorial, with environmental factors playing crucial roles. With global climate change, severe weather events and flooding are expected to intensify in the South Pacific. Population growth could also lead to more intensive livestock farming; and urbanization in developing countries is often associated with urban and peri-urban slums where diseases of poverty proliferate. Climate change, flooding, population growth, urbanization, poverty and agricultural intensification are important drivers of zoonotic disease transmission; these factors may independently, or potentially synergistically, lead to enhanced leptospirosis transmission in Fiji and other similar settings.

  7. An ShRNA Screen Identifies MEIS1 as a Driver of Malignant Peripheral Nerve Sheath Tumors

    Directory of Open Access Journals (Sweden)

    Ami V. Patel

    2016-07-01

    Full Text Available Malignant peripheral nerve sheath tumors (MPNST are rare soft tissue sarcomas that are a major source of mortality in neurofibromatosis type 1 (NF1 patients. To identify MPNST driver genes, we performed a lentiviral short hairpin (sh RNA screen, targeting all 130 genes up-regulated in neurofibroma and MPNSTs versus normal human nerve Schwann cells. NF1 mutant cells show activation of RAS/MAPK signaling, so a counter-screen in RAS mutant carcinoma cells was performed to exclude common RAS-pathway driven genes. We identified 7 genes specific for survival of MPSNT cells, including MEIS1. MEIS1 was frequently amplified or hypomethylated in human MPSNTs, correlating with elevated MEIS1 gene expression. In MPNST cells and in a genetically engineered mouse model, MEIS1 expression in developing nerve glial cells was necessary for MPNST growth. Mechanistically, MEIS1 drives MPNST cell growth via the transcription factor ID1, thereby suppressing expression of the cell cycle inhibitor p27Kip and maintaining cell survival.

  8. Identification of causal genetic drivers of human disease through systems-level analysis of regulatory networks

    Science.gov (United States)

    Chen, James C.; Alvarez, Mariano J.; Talos, Flaminia; Dhruv, Harshil; Rieckhof, Gabrielle E.; Iyer, Archana; Diefes, Kristin L.; Aldape, Kenneth; Berens, Michael; Shen, Michael M.; Califano, Andrea

    2014-01-01

    SUMMARY Identification of driver mutations in human diseases is often limited by cohort size and availability of appropriate statistical models. We propose a novel framework for the systematic discovery of genetic alterations that are causal determinants of disease, by prioritizing genes upstream of functional disease drivers, within regulatory networks inferred de novo from experimental data. We tested this framework by identifying the genetic determinants of the mesenchymal subtype of glioblastoma. Our analysis uncovered KLHL9 deletions as upstream activators of two previously established master regulators of the subtype, C/EBPβ and C/EBPδ. Rescue of KLHL9 expression induced proteasomal degradation of C/EBP proteins, abrogated the mesenchymal signature, and reduced tumor viability in vitro and in vivo. Deletions of KLHL9 were confirmed in >50% of mesenchymal cases in an independent cohort, thus representing the most frequent genetic determinant of the subtype. The method generalized to study other human diseases, including breast cancer and Alzheimer’s disease. PMID:25303533

  9. Analysis of driver's characteristics on a curved road in a lattice model

    Science.gov (United States)

    Kaur, Ramanpreet; Sharma, Sapna

    2017-04-01

    The present paper investigates the effect of driver's behavior on the curved road via lattice hydrodynamic approach. The basic model for straight road is extended for the curved road and the characteristics of driver's behavior is incorporated in the lattice model. The extended model is investigated theoretically by the means of linear stability analysis and the effect of curved road and intensity of influence of driver's behavior on the traffic flow stability is examined. Through nonlinear stability analysis, the modified Korteweg-de Vries (MKdV) equation near the critical point is derived to describe the evolution properties of traffic density waves by applying the reductive perturbation method. Furthermore, the numerical simulation is carried out to validate the theoretical results which indicates that the curved road has a negative influence on the stability of the traffic flow. It is also seen that the traffic jam on a curved road can be suppressed efficiently via taking into account aggressive drivers.

  10. The buzz about bees and poverty alleviation: Identifying drivers and barriers of beekeeping in sub-Saharan Africa

    Science.gov (United States)

    D’Haese, Marijke; Ahikiriza, Elizabeth; Agea, Jacob Godfrey; Jacobs, Frans J.; de Graaf, Dirk C.; Smagghe, Guy; Cross, Paul

    2017-01-01

    The potential of beekeeping to mitigate the exposure of rural sub-Sahara African farmers to economic stochasticity has been widely promoted by an array of development agencies. Robust outcome indicators of the success of beekeeping to improve household well-being are unfortunately lacking. This study aimed to identify the key drivers and barriers of beekeeping adoption at the household level, and quantified the associated income contribution in three agro-ecological zones in Uganda. Beekeepers were generally the most economically disadvantaged people in the study areas and tended to adopt beekeeping following contact with non-government organisations and access to training. Whilst incomes were not statistically lower than their non-beekeeping counterparts; their mean household well-being scores were significantly lower than non-beekeeping households. The inability of beekeeping to significantly improve well-being status can in part be attributed to a lack of both training in bee husbandry and protective equipment provision such as suits, gloves and smokers. These are critical tools for beekeepers as they provide the necessary confidence to manage honey bees. Rather than focussing solely on the socio-economic conditions of farmers to effectively adopt beekeeping, future research should also attempt to evaluate the effectiveness of development agencies’ provision to the beekeeping sector. PMID:28235072

  11. The buzz about bees and poverty alleviation: Identifying drivers and barriers of beekeeping in sub-Saharan Africa.

    Science.gov (United States)

    Amulen, Deborah Ruth; D'Haese, Marijke; Ahikiriza, Elizabeth; Agea, Jacob Godfrey; Jacobs, Frans J; de Graaf, Dirk C; Smagghe, Guy; Cross, Paul

    2017-01-01

    The potential of beekeeping to mitigate the exposure of rural sub-Sahara African farmers to economic stochasticity has been widely promoted by an array of development agencies. Robust outcome indicators of the success of beekeeping to improve household well-being are unfortunately lacking. This study aimed to identify the key drivers and barriers of beekeeping adoption at the household level, and quantified the associated income contribution in three agro-ecological zones in Uganda. Beekeepers were generally the most economically disadvantaged people in the study areas and tended to adopt beekeeping following contact with non-government organisations and access to training. Whilst incomes were not statistically lower than their non-beekeeping counterparts; their mean household well-being scores were significantly lower than non-beekeeping households. The inability of beekeeping to significantly improve well-being status can in part be attributed to a lack of both training in bee husbandry and protective equipment provision such as suits, gloves and smokers. These are critical tools for beekeepers as they provide the necessary confidence to manage honey bees. Rather than focussing solely on the socio-economic conditions of farmers to effectively adopt beekeeping, future research should also attempt to evaluate the effectiveness of development agencies' provision to the beekeeping sector.

  12. Driver behavior in car-to-pedestrian incidents: An application of the Driving Reliability and Error Analysis Method (DREAM).

    Science.gov (United States)

    Habibovic, Azra; Tivesten, Emma; Uchida, Nobuyuki; Bärgman, Jonas; Ljung Aust, Mikael

    2013-01-01

    To develop relevant road safety countermeasures, it is necessary to first obtain an in-depth understanding of how and why safety-critical situations such as incidents, near-crashes, and crashes occur. Video-recordings from naturalistic driving studies provide detailed information on events and circumstances prior to such situations that is difficult to obtain from traditional crash investigations, at least when it comes to the observable driver behavior. This study analyzed causation in 90 video-recordings of car-to-pedestrian incidents captured by onboard cameras in a naturalistic driving study in Japan. The Driving Reliability and Error Analysis Method (DREAM) was modified and used to identify contributing factors and causation patterns in these incidents. Two main causation patterns were found. In intersections, drivers failed to recognize the presence of the conflict pedestrian due to visual obstructions and/or because their attention was allocated towards something other than the conflict pedestrian. In incidents away from intersections, this pattern reoccurred along with another pattern showing that pedestrians often behaved in unexpected ways. These patterns indicate that an interactive advanced driver assistance system (ADAS) able to redirect the driver's attention could have averted many of the intersection incidents, while autonomous systems may be needed away from intersections. Cooperative ADAS may be needed to address issues raised by visual obstructions.

  13. DNA methylation profiling of sorted cells from myelofibrosis patients reveals aberrant epigenetic regulation of immune pathways and identifies early MPN driver genes

    DEFF Research Database (Denmark)

    Nielsen, H. M.; Andersen, C. L.; Kristensen, L. S.;

    2015-01-01

    Methylation 450K BeadChip. Candidate genes were validated by pyrosequencing in a second cohort of 30 MF patients where DNA was extracted from full blood (PB). To identify potential driver genes, the DNA methylation status of candidate genes was likewise analyzed in PB from a larger cohort consisting of 60 ET...

  14. Long-term changes in CO2 emissions in Austria and Czechoslovakia—Identifying the drivers of environmental pressures

    Science.gov (United States)

    Gingrich, Simone; Kušková, Petra; Steinberger, Julia K.

    2011-01-01

    This study presents fossil-fuel related CO2 emissions in Austria and Czechoslovakia (current Czech Republic and Slovakia) for 1830–2000. The drivers of CO2 emissions are discussed by investigating the variables of the standard Kaya identity for 1920–2000 and conducting a comparative Index Decomposition Analysis. Proxy data on industrial production and household consumption are analysed to understand the role of the economic structure. CO2 emissions increased in both countries in the long run. Czechoslovakia was a stronger emitter of CO2 throughout the time period, but per-capita emissions significantly differed only after World War I, when Czechoslovakia and Austria became independent. The difference in CO2 emissions increased until the mid-1980s (the period of communism in Czechoslovakia), explained by the energy intensity and the composition effects, and higher industrial production in Czechoslovakia. Counterbalancing factors were the income effect and household consumption. After the Velvet revolution in 1990, Czechoslovak CO2 emissions decreased, and the energy composition effect (and industrial production) lost importance. Despite their different political and economic development, Austria and Czechoslovakia reached similar levels of per-capita CO2 emissions in the late 20th century. Neither Austrian “eco-efficiency” nor Czechoslovak restructuring have been effective in reducing CO2 emissions to a sustainable level. PMID:21461052

  15. Long-term changes in CO(2) emissions in Austria and Czechoslovakia-Identifying the drivers of environmental pressures.

    Science.gov (United States)

    Gingrich, Simone; Kušková, Petra; Steinberger, Julia K

    2011-02-01

    This study presents fossil-fuel related CO(2) emissions in Austria and Czechoslovakia (current Czech Republic and Slovakia) for 1830-2000. The drivers of CO(2) emissions are discussed by investigating the variables of the standard Kaya identity for 1920-2000 and conducting a comparative Index Decomposition Analysis. Proxy data on industrial production and household consumption are analysed to understand the role of the economic structure. CO(2) emissions increased in both countries in the long run. Czechoslovakia was a stronger emitter of CO(2) throughout the time period, but per-capita emissions significantly differed only after World War I, when Czechoslovakia and Austria became independent. The difference in CO(2) emissions increased until the mid-1980s (the period of communism in Czechoslovakia), explained by the energy intensity and the composition effects, and higher industrial production in Czechoslovakia. Counterbalancing factors were the income effect and household consumption. After the Velvet revolution in 1990, Czechoslovak CO(2) emissions decreased, and the energy composition effect (and industrial production) lost importance. Despite their different political and economic development, Austria and Czechoslovakia reached similar levels of per-capita CO(2) emissions in the late 20th century. Neither Austrian "eco-efficiency" nor Czechoslovak restructuring have been effective in reducing CO(2) emissions to a sustainable level.

  16. Long-term changes in CO{sub 2} emissions in Austria and Czechoslovakia Identifying the drivers of environmental pressures

    Energy Technology Data Exchange (ETDEWEB)

    Simone Gingrich; Petra Kuskova; Julia K. Steinberger [University of Klagenfurt, Wien (Austria). Institute of Social Ecology

    2011-02-15

    This study presents fossil-fuel related CO{sub 2} emissions in Austria and Czechoslovakia (current Czech Republic and Slovakia) for 1830-2000. The drivers of CO{sub 2} emissions are discussed by investigating the variables of the standard Kaya identity for 1920-2000 and conducting a comparative Index Decomposition Analysis. Proxy data on industrial production and household consumption are analysed to understand the role of the economic structure. CO{sub 2} emissions increased in both countries in the long run. Czechoslovakia was a stronger emitter of CO{sub 2} throughout the time period, but per-capita emissions significantly differed only after World War I, when Czechoslovakia and Austria became independent. The difference in CO{sub 2} emissions increased until the mid-1980s (the period of communism in Czechoslovakia), explained by the energy intensity and the composition effects, and higher industrial production in Czechoslovakia. Counterbalancing factors were the income effect and household consumption. After the Velvet revolution in 1990, Czechoslovak CO{sub 2} emissions decreased, and the energy composition effect (and industrial production) lost importance. Despite their different political and economic development, Austria and Czechoslovakia reached similar levels of per-capita CO{sub 2} emissions in the late 20th century. Neither Austrian 'eco-efficiency' nor Czechoslovak restructuring have been effective in reducing CO{sub 2} emissions to a sustainable level. 43 refs., 5 figs., 1 tab.

  17. Long-term changes in CO{sub 2} emissions in Austria and Czechoslovakia. Identifying the drivers of environmental pressures

    Energy Technology Data Exchange (ETDEWEB)

    Gingrich, Simone; Steinberger, Julia K. [Institute of Social Ecology, Faculty for Interdisciplinary Studies Vienna, University of Klagenfurt, Schottenfeldgasse 29/5, 1070 Wien (Austria); Kuskova, Petra [Department of Social Geography and Regional Development, Charles University in Prague (Czech Republic)

    2011-02-15

    This study presents fossil-fuel related CO{sub 2} emissions in Austria and Czechoslovakia (current Czech Republic and Slovakia) for 1830-2000. The drivers of CO{sub 2} emissions are discussed by investigating the variables of the standard Kaya identity for 1920-2000 and conducting a comparative Index Decomposition Analysis. Proxy data on industrial production and household consumption are analysed to understand the role of the economic structure. CO{sub 2} emissions increased in both countries in the long run. Czechoslovakia was a stronger emitter of CO{sub 2} throughout the time period, but per-capita emissions significantly differed only after World War I, when Czechoslovakia and Austria became independent. The difference in CO{sub 2} emissions increased until the mid-1980s (the period of communism in Czechoslovakia), explained by the energy intensity and the composition effects, and higher industrial production in Czechoslovakia. Counterbalancing factors were the income effect and household consumption. After the Velvet revolution in 1990, Czechoslovak CO{sub 2} emissions decreased, and the energy composition effect (and industrial production) lost importance. Despite their different political and economic development, Austria and Czechoslovakia reached similar levels of per-capita CO{sub 2} emissions in the late 20th century. Neither Austrian 'eco-efficiency' nor Czechoslovak restructuring have been effective in reducing CO{sub 2} emissions to a sustainable level. (author)

  18. Driver injury severity outcome analysis in rural interstate highway crashes: a two-level Bayesian logistic regression interpretation.

    Science.gov (United States)

    Chen, Cong; Zhang, Guohui; Liu, Xiaoyue Cathy; Ci, Yusheng; Huang, Helai; Ma, Jianming; Chen, Yanyan; Guan, Hongzhi

    2016-12-01

    There is a high potential of severe injury outcomes in traffic crashes on rural interstate highways due to the significant amount of high speed traffic on these corridors. Hierarchical Bayesian models are capable of incorporating between-crash variance and within-crash correlations into traffic crash data analysis and are increasingly utilized in traffic crash severity analysis. This paper applies a hierarchical Bayesian logistic model to examine the significant factors at crash and vehicle/driver levels and their heterogeneous impacts on driver injury severity in rural interstate highway crashes. Analysis results indicate that the majority of the total variance is induced by the between-crash variance, showing the appropriateness of the utilized hierarchical modeling approach. Three crash-level variables and six vehicle/driver-level variables are found significant in predicting driver injury severities: road curve, maximum vehicle damage in a crash, number of vehicles in a crash, wet road surface, vehicle type, driver age, driver gender, driver seatbelt use and driver alcohol or drug involvement. Among these variables, road curve, functional and disabled vehicle damage in crash, single-vehicle crashes, female drivers, senior drivers, motorcycles and driver alcohol or drug involvement tend to increase the odds of drivers being incapably injured or killed in rural interstate crashes, while wet road surface, male drivers and driver seatbelt use are more likely to decrease the probability of severe driver injuries. The developed methodology and estimation results provide insightful understanding of the internal mechanism of rural interstate crashes and beneficial references for developing effective countermeasures for rural interstate crash prevention.

  19. Determinants and Drivers of Infectious Disease Threat Events in Europe.

    Science.gov (United States)

    Semenza, Jan C; Lindgren, Elisabet; Balkanyi, Laszlo; Espinosa, Laura; Almqvist, My S; Penttinen, Pasi; Rocklöv, Joacim

    2016-04-01

    Infectious disease threat events (IDTEs) are increasing in frequency worldwide. We analyzed underlying drivers of 116 IDTEs detected in Europe during 2008-2013 by epidemic intelligence at the European Centre of Disease Prevention and Control. Seventeen drivers were identified and categorized into 3 groups: globalization and environment, sociodemographic, and public health systems. A combination of >2 drivers was responsible for most IDTEs. The driver category globalization and environment contributed to 61% of individual IDTEs, and the top 5 individual drivers of all IDTEs were travel and tourism, food and water quality, natural environment, global trade, and climate. Hierarchical cluster analysis of all drivers identified travel and tourism as a distinctly separate driver. Monitoring and modeling such disease drivers can help anticipate future IDTEs and strengthen control measures. More important, intervening directly on these underlying drivers can diminish the likelihood of the occurrence of an IDTE and reduce the associated human and economic costs.

  20. Do Restricted Driver's Licenses Lower Crash Risk among Older Drivers? A Survival Analysis of Insurance Data from British Columbia

    Science.gov (United States)

    Nasvadi, Glenyth Caragata; Wister, Andrew

    2009-01-01

    Purpose: Faced with an aging driving population, interest is increasing in the use of restricted licenses or "graduated delicensing" for older drivers to allow them to safely retain a driver's license. The primary purpose of this study was to determine whether restricted licenses are successful at mitigating number of crashes per year…

  1. Using the Hestia bottom-up FFCO2 emissions estimation to identify drivers and hotspots in urban areas

    Science.gov (United States)

    Rao, P.; Patarasuk, R.; Gurney, K. R.; o'Keefe, D.; Song, Y.; Huang, J.; Buchert, M.; Lin, J. C.; Mendoza, D. L.; Ehleringer, J. R.; Eldering, A.; Miller, C. E.; Duren, R. M.

    2015-12-01

    Urban areas occupy 3% of the earth's land surface and generate 75% of the fossil fuel carbon dioxide (FFCO2) emissions. We report on the application of the Hestia Project to the Salt Lake County (SLC) and Los Angeles (LA) domains. Hestia quantifies FFCO2 in fine space-time detail across urban domains using a scientific "bottom-up" approach. We explore the utility of the Hestia to inform both urbanization science and greenhouse gas (GHG) mitigation policy. We focus on the residential sector in SLC and the onroad sector in LA as these sectors are large emissions contributors in each locale, and local governments have some authority and policy levers to mitigate these emissions. Multiple regression using sociodemographic data across SLC census block-groups shows that per capita income exhibits a positive relationship with FFCO2 emissions while household size exhibits a negative relationship, after controlling for total population. Housing units per area (i.e., compact development) has little effect on FFCO2 emissions. Rising income in the high-income group has twice as much impact on the emissions as the low-income group. Household size for the low-income group has four times the impact on the emissions as the high-income group. In LA, onroad FFCO2 emissions account for 49% of total emissions, of which 41% is from arterials (intermediate road class). Arterials also have the largest carbon emissions intensity - FFCO2/vehicle distance travelled (VKT) - possibly from high traffic congestion and fleet composition. Non-interstate hotspot emissions (> 419 tC ln-km-1) are equally dominated by particular arterials and collectors (lowest road class) though collectors have a higher VKT. These hotspots occur largely in LA (67%) and Orange (18%) counties and provide targeted information for onroad emissions reduction. Using Hestia to identify FFCO2 emissions drivers and hotpots can aid state and local policy makers in planning the most effective GHG reductions.

  2. Candidate DNA methylation drivers of acquired cisplatin resistance in ovarian cancer identified by methylome and expression profiling

    NARCIS (Netherlands)

    Zeller, C.; Dai, W.; Steele, N. L.; Siddiq, A.; Walley, A. J.; Wilhelm-Benartzi, C. S. M.; Rizzo, S.; van der Zee, A.; Plumb, J. A.; Brown, R.

    2012-01-01

    Multiple DNA methylation changes in the cancer methylome are associated with the acquisition of drug resistance; however it remains uncertain how many represent critical DNA methylation drivers of chemoresistance. Using isogenic, cisplatin-sensitive/resistant ovarian cancer cell lines and inducing r

  3. The development of a method to measure speed adaptation to traffic complexity: Identifying novice, unsafe, and overconfident drivers.

    NARCIS (Netherlands)

    Craen, S. de Twisk, D.A.M. Hagenzieker, M.P. Elffers, H. & Brookhuis, K.A.

    2008-01-01

    To monitor novice driver performance in the first years of solo driving, a test aimed at assessing speed adaptation to the traffic situation was developed and evaluated. The Adaptation Test consisted of 18 traffic scenes presented in two (almost) identical photographs, which differed in one single d

  4. Computer-aided human factors analysis of the industrial vehicle driver cabin to improve occupational health.

    Science.gov (United States)

    Koushik Balaji, K; Alphin, M S

    2016-09-01

    Industrial vehicle operator's solace and safety have gained significant consideration because of the increment in occupational health issues and accidents. The purpose of this work was to amend the design of the excavator driver cabin through human factor analysis. Thirty operators of excavators who were serving as subjects, were interviewed and identified that their wrist, upper arm and trunk were at a higher risk level while operating. Photograph of the operators was taken and the work environment was simulated. RULA (Rapid Upper Limb Assessment) and REBA (Rapid Entire Body Assessment) scoring was made on different simulated work posture of operators using CATIA V5 and UEAT1.8 softwares. Based on overall RULA and REBA scoring, it was found nearly 46% of the operators were operating at a high hazard level and needed investigation immediately, whereas 35% of operators were at a medium risk level and only 19% of operators were operating safely. The individual RULA and REBA scoring proved prevalence of discomfort in wrist, upper arm and trunk while operating. Identifying the optimized conditions to hold the control levers will help to reduce the operator strain. From the design optimization in excavators, the optimal conditions to hold the control lever is found to be 40cm for popliteal height, 60.51 cm for distance from elbow to ground and 15.07º for reach angle from the seat reference point.

  5. Prediction of magnetic orientation in driver gas associated -Bz events. [in interplanetary medium observed at earth when solar source is identified

    Science.gov (United States)

    Hoeksema, J. T.; Zhao, Xuepu

    1992-01-01

    The source regions of five strong -Bz events detected at 1 AU for which solar sources were identified by Tang et al. (1989) and Tsurutani et al. (1992) are investigated in order to determine whether the magnetic orientation of driver gas in the interplanetary medium observed at the earth can be predicted when its solar source is identified. Three -Bz events were traced to flare-associated coronal mass ejections (CMEs), one to an eruptive prominence associated CME, and one to three possible solar sources. The computed magnetic orientations at the candidate 'release height' (the height where the front of a CME ceases to accelerate) above the flare sites associated with CMEs show the existence of the expected southward field component. It is concluded that the magnetic orientation in flare-associated CME generated driver gas may be predictable.

  6. Factor analysis identifies subgroups of constipation

    Institute of Scientific and Technical Information of China (English)

    Philip G Dinning; Mike Jones; Linda Hunt; Sergio E Fuentealba; Jamshid Kalanter; Denis W King; David Z Lubowski; Nicholas J Talley; Ian J Cook

    2011-01-01

    AIM: To determine whether distinct symptom groupings exist in a constipated population and whether such grouping might correlate with quantifiable pathophysiological measures of colonic dysfunction. METHODS: One hundred and ninety-one patients presenting to a Gastroenterology clinic with constipation and 32 constipated patients responding to a newspaper advertisement completed a 53-item, wide-ranging selfreport questionnaire. One hundred of these patients had colonic transit measured scintigraphically. Factor analysis determined whether constipation-related symptoms grouped into distinct aspects of symptomatology. Cluster analysis was used to determine whether individual patients naturally group into distinct subtypes. RESULTS: Cluster analysis yielded a 4 cluster solution with the presence or absence of pain and laxative unresponsiveness providing the main descriptors. Amongst all clusters there was a considerable proportion of patients with demonstrable delayed colon transit, irritable bowel syndrome positive criteria and regular stool frequency. The majority of patients with these characteristics also reported regular laxative use. CONCLUSION: Factor analysis identified four constipation subgroups, based on severity and laxative unresponsiveness, in a constipated population. However, clear stratification into clinically identifiable groups remains imprecise.

  7. Whole Exome Sequencing Identifies TSC1/TSC2 Biallelic Loss as the Primary and Sufficient Driver Event for Renal Angiomyolipoma Development.

    Science.gov (United States)

    Giannikou, Krinio; Malinowska, Izabela A; Pugh, Trevor J; Yan, Rachel; Tseng, Yuen-Yi; Oh, Coyin; Kim, Jaegil; Tyburczy, Magdalena E; Chekaluk, Yvonne; Liu, Yang; Alesi, Nicola; Finlay, Geraldine A; Wu, Chin-Lee; Signoretti, Sabina; Meyerson, Matthew; Getz, Gad; Boehm, Jesse S; Henske, Elizabeth P; Kwiatkowski, David J

    2016-08-01

    Renal angiomyolipoma is a kidney tumor in the perivascular epithelioid (PEComa) family that is common in patients with Tuberous Sclerosis Complex (TSC) and Lymphangioleiomyomatosis (LAM) but occurs rarely sporadically. Though histologically benign, renal angiomyolipoma can cause life-threatening hemorrhage and kidney failure. Both angiomyolipoma and LAM have mutations in TSC2 or TSC1. However, the frequency and contribution of other somatic events in tumor development is unknown. We performed whole exome sequencing in 32 resected tumor samples (n = 30 angiomyolipoma, n = 2 LAM) from 15 subjects, including three with TSC. Two germline and 22 somatic inactivating mutations in TSC2 were identified, and one germline TSC1 mutation. Twenty of 32 (62%) samples showed copy neutral LOH (CN-LOH) in TSC2 or TSC1 with at least 8 different LOH regions, and 30 of 32 (94%) had biallelic loss of either TSC2 or TSC1. Whole exome sequencing identified a median of 4 somatic non-synonymous coding region mutations (other than in TSC2/TSC1), a mutation rate lower than nearly all other cancer types. Three genes with mutations were known cancer associated genes (BAP1, ARHGAP35 and SPEN), but they were mutated in a single sample each, and were missense variants with uncertain functional effects. Analysis of sixteen angiomyolipomas from a TSC subject showed both second hit point mutations and CN-LOH in TSC2, many of which were distinct, indicating that they were of independent clonal origin. However, three tumors had two shared mutations in addition to private somatic mutations, suggesting a branching evolutionary pattern of tumor development following initiating loss of TSC2. Our results indicate that TSC2 and less commonly TSC1 alterations are the primary essential driver event in angiomyolipoma/LAM, whereas other somatic mutations are rare and likely do not contribute to tumor development.

  8. Whole Exome Sequencing Identifies TSC1/TSC2 Biallelic Loss as the Primary and Sufficient Driver Event for Renal Angiomyolipoma Development.

    Directory of Open Access Journals (Sweden)

    Krinio Giannikou

    2016-08-01

    Full Text Available Renal angiomyolipoma is a kidney tumor in the perivascular epithelioid (PEComa family that is common in patients with Tuberous Sclerosis Complex (TSC and Lymphangioleiomyomatosis (LAM but occurs rarely sporadically. Though histologically benign, renal angiomyolipoma can cause life-threatening hemorrhage and kidney failure. Both angiomyolipoma and LAM have mutations in TSC2 or TSC1. However, the frequency and contribution of other somatic events in tumor development is unknown. We performed whole exome sequencing in 32 resected tumor samples (n = 30 angiomyolipoma, n = 2 LAM from 15 subjects, including three with TSC. Two germline and 22 somatic inactivating mutations in TSC2 were identified, and one germline TSC1 mutation. Twenty of 32 (62% samples showed copy neutral LOH (CN-LOH in TSC2 or TSC1 with at least 8 different LOH regions, and 30 of 32 (94% had biallelic loss of either TSC2 or TSC1. Whole exome sequencing identified a median of 4 somatic non-synonymous coding region mutations (other than in TSC2/TSC1, a mutation rate lower than nearly all other cancer types. Three genes with mutations were known cancer associated genes (BAP1, ARHGAP35 and SPEN, but they were mutated in a single sample each, and were missense variants with uncertain functional effects. Analysis of sixteen angiomyolipomas from a TSC subject showed both second hit point mutations and CN-LOH in TSC2, many of which were distinct, indicating that they were of independent clonal origin. However, three tumors had two shared mutations in addition to private somatic mutations, suggesting a branching evolutionary pattern of tumor development following initiating loss of TSC2. Our results indicate that TSC2 and less commonly TSC1 alterations are the primary essential driver event in angiomyolipoma/LAM, whereas other somatic mutations are rare and likely do not contribute to tumor development.

  9. Systems biology analysis of drivers underlying hallmarks of cancer cell metabolism

    Science.gov (United States)

    Zielinski, Daniel C.; Jamshidi, Neema; Corbett, Austin J.; Bordbar, Aarash; Thomas, Alex; Palsson, Bernhard O.

    2017-01-01

    Malignant transformation is often accompanied by significant metabolic changes. To identify drivers underlying these changes, we calculated metabolic flux states for the NCI60 cell line collection and correlated the variance between metabolic states of these lines with their other properties. The analysis revealed a remarkably consistent structure underlying high flux metabolism. The three primary uptake pathways, glucose, glutamine and serine, are each characterized by three features: (1) metabolite uptake sufficient for the stoichiometric requirement to sustain observed growth, (2) overflow metabolism, which scales with excess nutrient uptake over the basal growth requirement, and (3) redox production, which also scales with nutrient uptake but greatly exceeds the requirement for growth. We discovered that resistance to chemotherapeutic drugs in these lines broadly correlates with the amount of glucose uptake. These results support an interpretation of the Warburg effect and glutamine addiction as features of a growth state that provides resistance to metabolic stress through excess redox and energy production. Furthermore, overflow metabolism observed may indicate that mitochondrial catabolic capacity is a key constraint setting an upper limit on the rate of cofactor production possible. These results provide a greater context within which the metabolic alterations in cancer can be understood.

  10. [Social support and occupational stress relationship analysis of 1 413 train drivers in a railway bureau].

    Science.gov (United States)

    Gu, G Z; Yu, S F; Zhou, W H; Wu, H; Kang, L; Chen, R

    2017-02-06

    Objective: To investigate the social support status of train drivers. Methods: Using cluster sampling, a cross-sectional study was conducted in 1 413 male train drivers (including 301 passenger train drivers, 683 freight train drivers, 85 guest scheduling train drivers, 265 cargo adjustable drivers, and 79 high-speed train drivers) from a railway bureau depot. The survey included individual factors, social support, occupational stressors, strains, personalities, and coping strategy using occupational stress instruments and effort-reward imbalance questionnaire. We compared the difference in social support scores between different drivers, who were divided according to job type and age. Additionally, the correlation between social support score and job strain-related factors was analyzed. The influence of depressive symptoms and job satisfaction were analyzed using a non-conditional logistic multivariate model. Results: The overall average age P(50) (P(25),P(75)) of 1 413 train drivers was 33.92 (27.83,43.58) years. The overall average length of service 12.25 (5.25,22.75) years. A significant difference in social support scores was observed according to job type (H=23.23, Psocial support scores among different age groups were significantly different (H=6.64, P=0.036). The specific scores were ≤30 years (26 (22,31)), 30-40 years (27 (23,33)), and >40 years (27 (22,31)). Correlation analysis revealed that the social support score was negatively associated with job satisfaction (r=-0.43), reward (r=-0.22), working stability (r=-0.23), promotion opportunities (r=-0.12), positive affectivity (r=-0.31), esteem (r=-0.21), and self-esteem (r=-0.20) scores (Psocial support score was positively associated with sleep disorders (r=0.33), external effort (r=0.21), pay within (r=0.12), role conflict (r=0.20), conflict between groups (r=0.17), conflict in groups (r=0.06), responsibility for the others (r=0.06), responsibility for things (r=0.08), physiological needs (r=0

  11. Healthcare Programmes for Truck Drivers in Sub-Saharan Africa: A Systematic Review and Meta-Analysis.

    Directory of Open Access Journals (Sweden)

    Samanta Tresha Lalla-Edward

    Full Text Available Truck drivers have unique health needs, and by virtue of their continuous travel, experience difficulty in accessing healthcare. Currently, planning for effective care is hindered by lack of knowledge about their health needs and about the impact of on-going programmes on this population's health outcomes. We reviewed healthcare programmes implemented for sub-Saharan African truck drivers, assessed the evaluation methods, and examined impact on health outcomes.We searched scientific and institutional databases, and online search engines to include all publications describing a healthcare programme in sub-Saharan Africa where the main clients were truck drivers. We consulted experts and organisations working with mobile populations to identify unpublished reports. Forest plots of impact and outcome indicators with unadjusted risk ratios and 95% confidence intervals were created to map the impact of these programmes. We performed a subgroup analysis by type of indicator using a random-effects model to assess between-study heterogeneity. We conducted a sensitivity analysis to examine both the summary effect estimate chosen (risk difference vs. risk ratio and model to summarise results (fixed vs. random effects.Thirty-seven publications describing 22 healthcare programmes across 30 countries were included from 5,599 unique records. All programmes had an HIV-prevention focus with only three expanding their services to cover conditions other primary healthcare services. Twelve programmes were evaluated and most evaluations assessed changes in input, output, and outcome indicators. Absence of comparison groups, preventing attribution of the effect observed to the programme and lack of biologically confirmed outcomes were the main limitations. Four programmes estimated a quantitative change in HIV prevalence or reported STI incidence, with mixed results, and one provided anecdotal evidence of changes in AIDS-related mortality and social norms. Most

  12. The Global Drivers of Photosynthesis and Light Use Efficiency Seasonality: A Granger Frequency Causality Analysis

    Science.gov (United States)

    Nemani, Ramakrishna R.

    2016-01-01

    Photosynthesis and light use efficiency (LUE) are major factors in the evolution of the continental carbon cycle due to their contribution to gross primary production (GPP). However, while the drivers of photosynthesis and LUE on a plant or canopy scale can often be identified, significant uncertainties exist when modeling these on a global scale. This is due to sparse observations in regions such as the tropics and the lack of a direct global observation dataset. Although others have attempted to address this issue using correlations (Beer, 2010) or calculating GPP from vegetation indices (Running, 2004), in this study we take a new approach. We combine the statistical method of Granger frequency causality and partial Granger frequency causality with remote sensing data products (including sun-induced fluorescence used as a proxy for GPP) to determine the main environmental drivers of GPP across the globe.

  13. Citizen science identifies the effects of nitrogen dioxide and other environmental drivers on tar spot of sycamore.

    Science.gov (United States)

    Gosling, Laura; Ashmore, Mike; Sparks, Tim; Bell, Nigel

    2016-07-01

    Elevated sulphur dioxide (SO2) concentrations were the major cause of the absence of symptoms of tar spot (Rhytisma acerinum) of sycamore (Acer pseudoplatanus), in urban areas in the 1970s. The subsequent large decline in SO2 concentrations has not always been accompanied by increased tar spot symptoms, for reasons that have remained unresolved. We used a large citizen science survey, providing over 1000 records across England, to test two competing hypotheses proposed in earlier studies. We were able to demonstrate the validity of both hypotheses; tar spot symptoms were reduced where there were fewer fallen leaves as a source of inoculum, and elevated nitrogen dioxide concentrations reduced tar spot symptoms above a threshold concentration of about 20 μg m(-3). Symptom severity was also lower at sites with higher temperature and lower rainfall. Our findings demonstrate the power of citizen science to resolve competing hypotheses about the impacts of air pollution and other environmental drivers.

  14. Power Spectral Analysis of Heart Rate Variability of Driver Fatigue

    Institute of Scientific and Technical Information of China (English)

    JIAO Kun; LI Zeng-yong; CHEN Ming; WANG Cheng-tao

    2005-01-01

    This investigation was to evaluate the driving fatigue based on power spectral analysis of heart rate variability (HRV) under vertical vibration. Forty healthy male subjects (29.7±3.5 years) were randomly divided into two groups, Group A (28.8±4.3 years) and Group B (30.6±2.7 years). Group A (experiment group) was required to perform the simulated driving and Group B (control group) kept calm for 90min. The frequency domain indices of HRV such as low frequency (0.040.15 Hz, LF), high frequency (0.15-0.4Hz, HF), LF/HF together with the indices of hemodynamics such as blood pressure (BP) and heart rate (HR) of the subjects between both groups were calculated and analyzed after the simulated driving. There were significances of the former indices between both groups (P<0.05). All the data collected after experiment of Group A was observed the remarkable linear correlation (P<0.05) and parameters and errors of their linear regression equation were stated (α=0.05, P<0.001) in this paper, respectively. The present study investigated that sympathetic activity of the subjects enhanced after the simulated driving while parasympathetic activities decreased. The sympathovagal balance was also improved. As autonomic function indictors of HRV reflected fatigue level, quantitative evaluation of driving mental fatigue from physiological reaction could be possible.

  15. An econometric analysis of the effects of the penalty points system driver's license in Spain.

    Science.gov (United States)

    Castillo-Manzano, José I; Castro-Nuño, Mercedes; Pedregal, Diego J

    2010-07-01

    This article seeks to quantify the effects of the penalty points system driver's license during the 18-month period following its coming into force. This is achieved by means of univariate and multivariate unobserved component models set up in a state space framework estimated using maximum likelihood. A detailed intervention analysis is carried out in order to test for the effects and their duration of the introduction of the penalty points system driver's license in Spain. Other variables, mainly indicators of the level of economic activity in Spain, are also considered. Among the main effects, we can mention an average reduction of almost 12.6% in the number of deaths in highway accidents. It would take at least 2 years for that effect to disappear. For the rest of the safety indicator variables (vehicle occupants injured in highway accidents and vehicle occupants injured in accidents built-up areas) the effects disappeared 1 year after the law coming into force.

  16. Misinterpretation of the strategic significance of cost driver analysis: evidence from management accounting theory and practice

    Directory of Open Access Journals (Sweden)

    Henry T Palowski

    2011-06-01

    Full Text Available This paper traces the development of cost driver theory in the Strategy literature and reflects on misinterpretations of the strategic significance of the theory in related academic disciplines, notably Management Accounting. Management Accounting has largely been responsible for informing costing practice in a wide range of organizational settings. The paper considers one such application- i.e. the case of the Higher Education Funding Council’s (HEFC costing and pricing initiative for UK universities. The project was completed just under five years ago, although details of implementation are still ongoing, to a degree. The systems in place incorporate most of the theoretical flaws outlined in this paper. Rather than providing cost driver analysis to aid the strategic management process in universities, the system appears to represent little more than a compliance and reporting framework between university central administrations and the funding provider, HEFC.

  17. Perturbation and Stability Analysis of the Multi-Anticipative Intelligent Driver Model

    Science.gov (United States)

    Chen, Xi-Qun; Xie, Wei-Jun; Shi, Jing; Shi, Qi-Xin

    This paper discusses three kinds of IDM car-following models that consider both the multi-anticipative behaviors and the reaction delays of drivers. Here, the multi-anticipation comes from two ways: (1) the driver is capable of evaluating the dynamics of several preceding vehicles, and (2) the autonomous vehicles can obtain the velocity and distance information of several preceding vehicles via inter-vehicle communications. In this paper, we study the stability of homogeneous traffic flow. The linear stability analysis indicates that the stable region will generally be enlarged by the multi-anticipative behaviors and reduced by the reaction delays. The temporal amplification and the spatial divergence of velocities for local perturbation are also studied, where the results further prove this conclusion. Simulation results also show that the multi-anticipative behaviors near the bottleneck will lead to a quicker backwards propagation of oscillations.

  18. Analysis of medical and psychological certificates concerning drivers who drove after alcohol use

    Directory of Open Access Journals (Sweden)

    Ewa Latała-Łoś

    2014-08-01

    Full Text Available Background: The aim of the study is to present the health predispositions to drive, assessed during certifying people referred to the Regional Centre for Occupational Medicine in Kielce due to drunk driving or driving after using alcohol. The article mainly presents the results regarding the prevalence of alcohol dependence and other psychiatric disorders in this group. We analyzed health condition at 3 year intervals in the years 2004, 2007 and 2010, adding the population of those who were examined in 2011. Material and Methods: A total of 5701 people were involved, both men and women. Drivers test cards along with the results of biochemical tests and specialist consultations were analyzed. The analysis of the results was performed using the statistical package PQStat 1.4.2.324 Results: Certificates with health contraindications to drive were issued to 6.7% of investigated individuals. Very significant correlation between alcohol dependence syndrome and the level of γ-glutamyl transferase (GGT, alanine aminotransferase (ALT, and aspartate aminotransferase (AST were confirmed. Alcohol dependence was diagnosed in 3.8% of the group. Conclusions: The health state of the drivers met the required certification criteria necessary for obtaining a driving license in more than 93% of the group. The study revealed many diseases in the group of investigated drivers, including 3.8% of alcohol dependence and 5% of mental disorders. The threat of losing driving license has become an important factor motivating drivers to undertake therapy. However, it seems advisable to develop principles for treatment monitoring and exchange of information between the certifying physician and the treating psychiatrist or psychologist. Med Pr 2014;65(4:497–506

  19. Multi- Physics analysis of the RFQ for the Injector Scheme II of CADS Driver Linac

    CERN Document Server

    Jing, Wang; Yuan, He; Xiao-Qi, Zhang

    2013-01-01

    A 162.5 MHz, 2.1 MeV Radio Frequency Quadruples (RFQ) structure is being designed for the Injector Scheme II of China Accelerator Driver System (CADS) driver linac. The RFQ will operate at continuous wave (CW) mode as required. For the CW normal conducting machine, the heat management will be one of the most important issues, since the temperature fluctuation may cause cavity deformation and leading to the resonant frequency shift. Therefor a detailed multi-physics analysis is necessary to ensure that the cavity can be stably worked at the required power level. The multi-physics analysis process includes RF Electromagnetic analysis, Thermal analysis, Mechnical analysis, and this process will be iterated for several cycles until the satisfied solution can be found. As one of the widely accepted measures, the cooling water system is used for frequency fine tunning, so the tunning capability of the cooling water system is also studied at different conditions. The results indicate that with the cooling water syst...

  20. Characteristics of Chinese Driver Behavior

    NARCIS (Netherlands)

    Li, J.

    2014-01-01

    The high growth rate of vehicle ownership and many novel drivers in China determine the special features of Chinese driver behavior. This thesis introduces a comparative study on driver behavior by the analysis of saturation flow at urban intersections, Driver Behavior Questionnaire surveys, focus g

  1. Assessing Modifiable Areal Unit Problem in the Analysis of Deforestation Drivers Using Remote Sensing and Census Data

    Science.gov (United States)

    Mas, J. F.; Pérez Vega, A.; Andablo Reyes, A.; Castillo Santiago, M. A.; Flamenco Sandoval, A.

    2015-08-01

    In order to identify drivers of land use / land cover change (LUCC), the rate of change is often compared with environmental and socio-economic variables such as slope, soil suitability or population density. Socio-economic information is obtained from census data which are collected for individual households but are commonly presented in aggregate on the basis of geographical units as municipalities. However, a common problem, known as the modifiable areal unit problem (MAUP), is that the results of statistical analysis are not independent of the scale and the spatial configuration of the units used to aggregate the information. In this article, we evaluate how strong MAUP effects are for a study on the deforestation drivers in Mexico at municipality level. This was done by taking socio-economic variables from the 2010 Census of Mexico along with environmental variables and the rate of deforestation. As population census is given for each human settlement and environmental variables are obtained from high resolution spatial database, it was possible to aggregate the information using spatial units ("pseudo municipalities") with different sizes in order to observe the effect of scale and aggregation on the values of bivariate correlations (Pearsons r) between pairs of variables. We found that MAUP produces variations in the results, and we observed some variable pairs and some configurations of the spatial units where the effect was substantial.

  2. Stereo sequences analysis for dynamic scene understanding in a driver assistance system

    Science.gov (United States)

    Vishnyakov, Boris V.; Vizilter, Yuri V.; Knyaz, Vladimir A.; Malin, Ivan K.; Vygolov, Oleg V.; Zheltov, Sergey Y.

    2015-05-01

    The improved stereo-based approach for dynamic road scene understanding in a Driver Assistance System (DAS) is presented. System calibration is addressed. Algorithms for road lane detection, road 3D model generation, obstacle predetection and object (vehicle) detection are described. Lane detection is based on the evidence analysis. Obstacle predetection procedure performs the comparison of radial ortophotos, obtained by left and right stereo images. Object detection algorithm is based on recognition of back part of cars by histograms of oriented gradients. Car Stereo Sequences (CSS) Dataset captured by vehicle-based laboratory and published for DAS algorithms testing.

  3. Identifiable Data Files - Medicare Provider Analysis and ...

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Medicare Provider Analysis and Review (MEDPAR) File contains data from claims for services provided to beneficiaries admitted to Medicare certified inpatient...

  4. Identifying Proper Names Based on Association Analysis

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The issue of proper names recognition in Chinese text was discussed. An automatic approach based on association analysis to extract rules from corpus was presented. The method tries to discover rules relevant to external evidence by association analysis, without additional manual effort. These rules can be used to recognize the proper nouns in Chinese texts. The experimental result shows that our method is practical in some applications.Moreover, the method is language independent.

  5. Hair analysis in order to evaluate drug abuse in driver's license regranting procedures.

    Science.gov (United States)

    Tassoni, G; Mirtella, D; Zampi, M; Ferrante, L; Cippitelli, M; Cognigni, E; Froldi, R; Cingolani, M

    2014-11-01

    In Italy, driving under the influence of drugs determines the suspension of the offender's driver's license. To regain the license the person must be drug free during an observation period. People whose license has been revoked or suspended can obtain, or re-obtain their driver's license subject to the judgment of a medical commission. The exclusion of illicit drug use is determined by means of toxicological analysis, mainly on urine or hair matrices. We reported the results of several years of experience of the forensic toxicology laboratory of the University of Macerata in the use of hair analysis for the assessment of past exposure to drugs in people suspected of driving under the influence of drugs. From 2004 to 2013, 8612 hair samples, were analyzed for opiates, cocaine and delta-9-tetrahydrocannabinol (Δ(9)-THC) using gas chromatography/mass spectrometry (GC/MS) method. We used a cutoff (SoHT or national guidelines) to determine the positive data, regardless of the hair sample concentrations. 1213 samples resulted positive, 71.7% were positive for cocaine and metabolites, 19.8% for morphine and metabolites, 8.5% for Δ(9)-THC. We also studied the timeframe of the abuse, as well as gender and age distribution of positive subjects. Moreover, we analyzed the possible deterrent effect of the hair analysis on driving under the influence of psychoactive substances.

  6. Identifying MMORPG Bots: A Traffic Analysis Approach

    Directory of Open Access Journals (Sweden)

    Wen-Chin Chen

    2008-11-01

    Full Text Available Massively multiplayer online role playing games (MMORPGs have become extremely popular among network gamers. Despite their success, one of MMORPG's greatest challenges is the increasing use of game bots, that is, autoplaying game clients. The use of game bots is considered unsportsmanlike and is therefore forbidden. To keep games in order, game police, played by actual human players, often patrol game zones and question suspicious players. This practice, however, is labor-intensive and ineffective. To address this problem, we analyze the traffic generated by human players versus game bots and propose general solutions to identify game bots. Taking Ragnarok Online as our subject, we study the traffic generated by human players and game bots. We find that their traffic is distinguishable by 1 the regularity in the release time of client commands, 2 the trend and magnitude of traffic burstiness in multiple time scales, and 3 the sensitivity to different network conditions. Based on these findings, we propose four strategies and two ensemble schemes to identify bots. Finally, we discuss the robustness of the proposed methods against countermeasures of bot developers, and consider a number of possible ways to manage the increasingly serious bot problem.

  7. Identifying MMORPG Bots: A Traffic Analysis Approach

    Science.gov (United States)

    Chen, Kuan-Ta; Jiang, Jhih-Wei; Huang, Polly; Chu, Hao-Hua; Lei, Chin-Laung; Chen, Wen-Chin

    2008-12-01

    Massively multiplayer online role playing games (MMORPGs) have become extremely popular among network gamers. Despite their success, one of MMORPG's greatest challenges is the increasing use of game bots, that is, autoplaying game clients. The use of game bots is considered unsportsmanlike and is therefore forbidden. To keep games in order, game police, played by actual human players, often patrol game zones and question suspicious players. This practice, however, is labor-intensive and ineffective. To address this problem, we analyze the traffic generated by human players versus game bots and propose general solutions to identify game bots. Taking Ragnarok Online as our subject, we study the traffic generated by human players and game bots. We find that their traffic is distinguishable by 1) the regularity in the release time of client commands, 2) the trend and magnitude of traffic burstiness in multiple time scales, and 3) the sensitivity to different network conditions. Based on these findings, we propose four strategies and two ensemble schemes to identify bots. Finally, we discuss the robustness of the proposed methods against countermeasures of bot developers, and consider a number of possible ways to manage the increasingly serious bot problem.

  8. Identifying nonlinear biomechanical models by multicriteria analysis

    Science.gov (United States)

    Srdjevic, Zorica; Cveticanin, Livija

    2012-02-01

    In this study, the methodology developed by Srdjevic and Cveticanin (International Journal of Industrial Ergonomics 34 (2004) 307-318) for the nonbiased (objective) parameter identification of the linear biomechanical model exposed to vertical vibrations is extended to the identification of n-degree of freedom (DOF) nonlinear biomechanical models. The dynamic performance of the n-DOF nonlinear model is described in terms of response functions in the frequency domain, such as the driving-point mechanical impedance and seat-to-head transmissibility function. For randomly generated parameters of the model, nonlinear equations of motion are solved using the Runge-Kutta method. The appropriate data transformation from the time-to-frequency domain is performed by a discrete Fourier transformation. Squared deviations of the response functions from the target values are used as the model performance evaluation criteria, thus shifting the problem into the multicriteria framework. The objective weights of criteria are obtained by applying the Shannon entropy concept. The suggested methodology is programmed in Pascal and tested on a 4-DOF nonlinear lumped parameter biomechanical model. The identification process over the 2000 generated sets of parameters lasts less than 20 s. The model response obtained with the imbedded identified parameters correlates well with the target values, therefore, justifying the use of the underlying concept and the mathematical instruments and numerical tools applied. It should be noted that the identified nonlinear model has an improved accuracy of the biomechanical response compared to the accuracy of a linear model.

  9. Genome-wide functional genetic screen with the anticancer agent AMPI-109 identifies PRL-3 as an oncogenic driver in triple-negative breast cancers.

    Science.gov (United States)

    Gari, Hamid H; Gearheart, Christy M; Fosmire, Susan; DeGala, Gregory D; Fan, Zeying; Torkko, Kathleen C; Edgerton, Susan M; Lucia, M Scott; Ray, Rahul; Thor, Ann D; Porter, Christopher C; Lambert, James R

    2016-03-29

    Triple-negative breast cancers (TNBC) are among the most aggressive and heterogeneous cancers with a high propensity to invade, metastasize and relapse. Here, we demonstrate that the anticancer compound, AMPI-109, is selectively efficacious in inhibiting proliferation and inducing apoptosis of multiple TNBC subtype cell lines as assessed by activation of pro-apoptotic caspases-3 and 7, PARP cleavage and nucleosomal DNA fragmentation. AMPI-109 had little to no effect on growth in the majority of non-TNBC cell lines examined. We therefore utilized AMPI-109 in a genome-wide shRNA screen in the TNBC cell line, BT-20, to investigate the utility of AMPI-109 as a tool in helping to identify molecular alterations unique to TNBC. Our screen identified the oncogenic phosphatase, PRL-3, as a potentially important driver of TNBC growth, migration and invasion. Through stable lentiviral knock downs and transfection with catalytically impaired PRL-3 in TNBC cells, loss of PRL-3 expression, or functionality, led to substantial growth inhibition. Moreover, AMPI-109 treatment, downregulation of PRL-3 expression or impairment of PRL-3 activity reduced TNBC cell migration and invasion. Histological evaluation of human breast cancers revealed PRL-3 was significantly, though not exclusively, associated with the TNBC subtype and correlated positively with regional and distant metastases, as well as 1 and 3 year relapse free survival. Collectively, our study is proof-of-concept that AMPI-109, a selectively active agent against TNBC cell lines, can be used as a molecular tool to uncover unique drivers of disease progression, such as PRL-3, which we show promotes oncogenic phenotypes in TNBC cells.

  10. Measuring situational avoidance in older drivers: An application of Rasch analysis.

    Science.gov (United States)

    Davis, Jessica; Conlon, Elizabeth; Ownsworth, Tamara; Morrissey, Shirley

    2016-02-01

    Situational avoidance is a form of driving self-regulation at the strategic level of driving behaviour. It has typically been defined as the purposeful avoidance of driving situations perceived as challenging or potentially hazardous. To date, assessment of the psychometric properties of existing scales that measure situational avoidance has been sparse. This study examined the contribution of Rasch analysis to the situational avoidance construct. Three hundred and ninety-nine Australian drivers (M=66.75, SD=10.14, range: 48-91 years) completed the Situational Avoidance Questionnaire (SAQ). Following removal of the item Parallel Parking, the scale conformed to a Rasch model, showing good person separation, sufficient reliability, little disordering of thresholds, and no evidence of differential item functioning by age or gender. The residuals were independent supporting the assumption of unidimensionality and in conforming to a Rasch model, SAQ items were found to be hierarchical or cumulative. Increased avoidance was associated with factors known to be related to driving self-regulation more broadly, including older age, female gender, reduced driving space and frequency, reporting a change in driving in the past five years and poorer indices of health (i.e., self-rated mood, vision and cognitive function). Overall, these results support the use of the SAQ as a psychometrically sound measure of situational avoidance. Application of Rasch analysis to this area of research advances understanding of the driving self-regulation construct and its practice by drivers in baby boomer and older adult generations.

  11. The Global Drivers of Photosynthesis and Light Use Efficiency Seasonality: A Granger Frequency Causality Analysis

    Science.gov (United States)

    Green, J.; Lee, J. E.; Gentine, P.; Berry, J. A.; Konings, A. G.

    2015-12-01

    hotosynthesis and light use efficiency (LUE) are major factors in the evolution of the continental carbon cycle due to their contribution to gross primary production (GPP). However, while the drivers of photosynthesis and LUE on a plant or canopy scale can often be identified, significant uncertainties exist when modeling these on a global scale. This is due to sparse observations in regions such as the tropics and the lack of a direct global observation dataset. Although others have attempted to address this issue using correlations (Beer, 2010) or calculating GPP from vegetation indices (Running, 2004), in this study we take a new approach. We combine the statistical method of Granger frequency causality and partial Granger frequency causality with remote sensing data products (including sun-induced fluorescence used as a proxy for GPP) to determine the main environmental drivers of GPP across the globe. References:Beer, C., M. Reichstein, E. Tomelleri, P. Ciais, M. Jung, N. Carvalhais, C. Ro¨denbeck, M. Altaf Arain, D. Baldocchi, G. B. Bonan, A. Bondeau, A. Cescatti, G. Lasslop, A. Lindroth, M. Lomas, S. Luyssaert, H. Margolis, K. W. Oleson, O. Roupsard, E. Veenendaal, N. Viovy, C. Williams, I. Woodward, and D. Papale, 2010: Terrestrial Gross Carbon Dioxide Uptake: Global Distribution and Covariation with Climate. doi: 10.1126/science.1184984. Running, S.W., Nemani, R. R., Heinsch, F. A., Zhao, M., Reeves, M., Hashimoto, H., 2004. A Continuous Satellite Derived Measure of Global Terrestrial Primary Production. BioScience 54(6), 547-560.

  12. Evolution of the "drivers" of translational cancer epidemiology: analysis of funded grants and the literature.

    Science.gov (United States)

    Lam, Tram Kim; Chang, Christine Q; Rogers, Scott D; Khoury, Muin J; Schully, Sheri D

    2015-04-01

    Concurrently with a workshop sponsored by the National Cancer Institute, we identified key "drivers" for accelerating cancer epidemiology across the translational research continuum in the 21st century: emerging technologies, a multilevel approach, knowledge integration, and team science. To map the evolution of these "drivers" and translational phases (T0-T4) in the past decade, we analyzed cancer epidemiology grants funded by the National Cancer Institute and published literature for 2000, 2005, and 2010. For each year, we evaluated the aims of all new/competing grants and abstracts of randomly selected PubMed articles. Compared with grants based on a single institution, consortium-based grants were more likely to incorporate contemporary technologies (P = 0.012), engage in multilevel analyses (P = 0.010), and incorporate elements of knowledge integration (P = 0.036). Approximately 74% of analyzed grants and publications involved discovery (T0) or characterization (T1) research, suggesting a need for more translational (T2-T4) research. Our evaluation indicated limited research in 1) a multilevel approach that incorporates molecular, individual, social, and environmental determinants and 2) knowledge integration that evaluates the robustness of scientific evidence. Cancer epidemiology is at the cusp of a paradigm shift, and the field will need to accelerate the pace of translating scientific discoveries in order to impart population health benefits. While multi-institutional and technology-driven collaboration is happening, concerted efforts to incorporate other key elements are warranted for the discipline to meet future challenges.

  13. Assessing the relationship between the Driver Behavior Questionnaire and the Driver Skill Inventory: Revealing sub-groups of drivers

    DEFF Research Database (Denmark)

    Martinussen, Laila Marianne; Møller, Mette; Prato, Carlo Giacomo

    2014-01-01

    The Driver Behavior Questionnaire and the Driver Skill Inventory are two of the most frequently used measures of self-reported driving style and driving skill. The motivation behind the present study was to identify sub-groups of drivers that potentially act dangerously in traffic (as measured...... by frequency of aberrant driving behaviors and level of driving skills), as well as to test whether the sub-groups differ in characteristics such as age, gender, annual mileage and accident involvement. Furthermore, the joint analysis of the two instruments was used to test drivers’ assessment of their own...... self-reported driving skills and whether the reported skill level was reflected in the reported aberrant driving behaviors. 3908 drivers aged 18–84 participated in the survey. K-means cluster analysis revealed four distinct sub-groups that differed in driving skills and frequency of aberrant driving...

  14. Novice drivers' individual trajectories of driver behavior over the first three years of driving.

    Science.gov (United States)

    Roman, Gabriela D; Poulter, Damian; Barker, Edward; McKenna, Frank P; Rowe, Richard

    2015-09-01

    Identifying the changes in driving behavior that underlie the decrease in crash risk over the first few months of driving is key to efforts to reduce injury and fatality risk in novice drivers. This study represented a secondary data analysis of 1148 drivers who participated in the UK Cohort II study. The Driver Behavior Questionnaire was completed at 6 months and 1, 2 and 3 years after licensure. Linear latent growth models indicated significant increases across development in all four dimensions of aberrant driving behavior under scrutiny: aggressive violations, ordinary violations, errors and slips. Unconditional and conditional latent growth class analyses showed that the observed heterogeneity in individual trajectories was explained by the presence of multiple homogeneous groups of drivers, each exhibiting specific trajectories of aberrant driver behavior. Initial levels of aberrant driver behavior were important in identifying sub-groups of drivers. All classes showed positive slopes; there was no evidence of a group of drivers whose aberrant behavior decreased over time that might explain the decrease in crash involvement observed over this period. Male gender and younger age predicted membership of trajectories with higher levels of aberrant behavior. These findings highlight the importance of early intervention for improving road safety. We discuss the implications of our findings for understanding the behavioral underpinnings of the decrease in crash involvement observed in the early months of driving.

  15. Long-term changes in CO{sub 2} emissions in Austria and Czechoslovakia-Identifying the drivers of environmental pressures

    Energy Technology Data Exchange (ETDEWEB)

    Gingrich, Simone, E-mail: simone.gingrich@uni-klu.ac.a [Institute of Social Ecology, Faculty for Interdisciplinary Studies Vienna, University of Klagenfurt, Schottenfeldgasse 29/5, 1070 Wien (Austria); Kuskova, Petra [Department of Social Geography and Regional Development, Charles University in Prague (Czech Republic); Steinberger, Julia K. [Institute of Social Ecology, Faculty for Interdisciplinary Studies Vienna, University of Klagenfurt, Schottenfeldgasse 29/5, 1070 Wien (Austria)

    2011-02-15

    This study presents fossil-fuel related CO{sub 2} emissions in Austria and Czechoslovakia (current Czech Republic and Slovakia) for 1830-2000. The drivers of CO{sub 2} emissions are discussed by investigating the variables of the standard Kaya identity for 1920-2000 and conducting a comparative Index Decomposition Analysis. Proxy data on industrial production and household consumption are analysed to understand the role of the economic structure. CO{sub 2} emissions increased in both countries in the long run. Czechoslovakia was a stronger emitter of CO{sub 2} throughout the time period, but per-capita emissions significantly differed only after World War I, when Czechoslovakia and Austria became independent. The difference in CO{sub 2} emissions increased until the mid-1980s (the period of communism in Czechoslovakia), explained by the energy intensity and the composition effects, and higher industrial production in Czechoslovakia. Counterbalancing factors were the income effect and household consumption. After the Velvet revolution in 1990, Czechoslovak CO{sub 2} emissions decreased, and the energy composition effect (and industrial production) lost importance. Despite their different political and economic development, Austria and Czechoslovakia reached similar levels of per-capita CO{sub 2} emissions in the late 20th century. Neither Austrian 'eco-efficiency' nor Czechoslovak restructuring have been effective in reducing CO{sub 2} emissions to a sustainable level. - Research Highlights: {yields}CO{sub 2} emissions in Austria and Czechoslovakia increased during industrialisation. {yields}The differences were strongest during periods of different political regimes. {yields}The main drivers for differences were energy composition and energy intensity.

  16. DRIVER INATTENTION

    Directory of Open Access Journals (Sweden)

    Richard TAY

    2004-01-01

    Full Text Available Driver inattention, especially driver distraction, is an extremely influential but generally neglected contributing factor of road crashes. This paper explores some of the common behaviours associated with several common forms of driver inattention, with respect to their perceived crash risks, rates of self-reported behaviours and whether drivers regulate such behaviours depending on the road and traffic environment, and provides some policy recommendations to address issues raised.

  17. A Statistical Analysis of the Economic Drivers of Battery Energy Storage in Commercial Buildings

    Energy Technology Data Exchange (ETDEWEB)

    Long, Matthew; Simpkins, Travis; Cutler, Dylan; Anderson, Kate

    2016-11-21

    There is significant interest in using battery energy storage systems (BESS) to reduce peak demand charges, and therefore the life cycle cost of electricity, in commercial buildings. This paper explores the drivers of economic viability of BESS in commercial buildings through statistical analysis. A sample population of buildings was generated, a techno-economic optimization model was used to size and dispatch the BESS, and the resulting optimal BESS sizes were analyzed for relevant predictor variables. Explanatory regression analyses were used to demonstrate that peak demand charges are the most significant predictor of an economically viable battery, and that the shape of the load profile is the most significant predictor of the size of the battery.

  18. Error analysis in post linac to driver linac transport beam line of RAON

    Science.gov (United States)

    Kim, Chanmi; Kim, Eun-San

    2016-07-01

    We investigated the effects of magnet errors in the beam transport line connecting the post linac to the driver linac (P2DT) in the Rare Isotope Accelerator in Korea (RAON). The P2DT beam line is bent by 180-degree to send the radioactive Isotope Separation On-line (ISOL) beams accelerated in Linac-3 to Linac-2. This beam line transports beams with multi-charge state 132Sn45,46,47. The P2DT beam line includes 42 quadrupole, 4 dipole and 10 sextupole magnets. We evaluate the effects of errors on the trajectory of the beam by using the TRACK code, which includes the translational and the rotational errors of the quadrupole, dipole and sextupole magnets in the beam line. The purpose of this error analysis is to reduce the rate of beam loss in the P2DT beam line. The distorted beam trajectories can be corrected by using six correctors and seven monitors.

  19. A Statistical Analysis of the Economic Drivers of Battery Energy Storage in Commercial Buildings: Preprint

    Energy Technology Data Exchange (ETDEWEB)

    Long, Matthew; Simpkins, Travis; Cutler, Dylan; Anderson, Katie

    2016-11-01

    There is significant interest in using battery energy storage systems (BESS) to reduce peak demand charges, and therefore the life cycle cost of electricity, in commercial buildings. This paper explores the drivers of economic viability of BESS in commercial buildings through statistical analysis. A sample population of buildings was generated, a techno-economic optimization model was used to size and dispatch the BESS, and the resulting optimal BESS sizes were analyzed for relevant predictor variables. Explanatory regression analyses were used to demonstrate that peak demand charges are the most significant predictor of an economically viable battery, and that the shape of the load profile is the most significant predictor of the size of the battery.

  20. Do drivers have a realistic view of their driving ability?

    DEFF Research Database (Denmark)

    Martinussen, Laila Marianne; Møller, Mette; Prato, Carlo Giacomo

    The Driver Behavior Questionnaire (DBQ) and the Driver Skill Inventory (DSI) are two of the most frequently used measures of driving style and driving skill. The motivation behind the present study was to test drivers’ insight into their own driving ability based on a combined use of the DBQ......, annual mileage and accident involvement. 3908 drivers aged 18–84 participated in the survey. The results suggested that the drivers have good insight into their own driving ability, as the driving skill level mirrored the frequency of aberrant driving behaviors. K-means cluster analysis revealed four...... and the DSI. Moreover, the joint use of the two instruments was applied to identify sub-groups of drivers that differ in their potential danger in traffic, as well as to test for heterogeneity across the population, namely whether the sub-groups of drivers differed in characteristics such as age, gender...

  1. An Analysis of a Contingency Program on Designated Drivers at a College Bar

    Science.gov (United States)

    Kazbour, Richard R.; Bailey, Jon S.

    2010-01-01

    The present study evaluated the effects of prompts and incentives on designated drivers in a bar. We defined the dependent variable as the percentage of customers either functioning as or riding with a designated driver. We used an ABCA design to evaluate the effectiveness of prompts and incentives on the dependent variable. Results indicated that…

  2. Driver pretesting system in Zimbabwe: An analysis of impacts and perceptions

    Directory of Open Access Journals (Sweden)

    Tatenda Mbara

    2009-11-01

    Full Text Available In pursuance of the need to curb corruption in the learner driver testing process as well as enhancing road safety by improving driving skills, the Minister of Transport and Communications in Zimbabwe announced, on 7 July 2007, a new and unique drivertesting procedure which was implemented with effect from 1 September 2007. The new system involved the introduction of a pretesting agent acting between driving schools and the driver competence-testing department. A wholly Government-owned company was given the responsibility to pretest all learner drivers before they proceeded to the final competence test. The objective of this paper is to assess the impacts of driver pretesting on pass rates as well as ascertaining stakeholder and public views and perceptions on corruption, the necessity for driver pretesting and the lessons learnt.

  3. Measuring and Ranking Value Drivers

    NARCIS (Netherlands)

    M.M. Akalu

    2002-01-01

    textabstractAnalysis of the strength of value drivers is crucial to understand their influence in the process of free cash flow generation. The paper addresses the issue of value driver measurement and ranking. The research reveals that, value drivers have similar pattern across industries. Furtherm

  4. A trend analysis of global fire activity. Is it land use or climate the main driver?

    Science.gov (United States)

    Bistinas, Ioannis; Oom, Duarte; Silva, Joao M. N.; Lopez-Saldaña, Gerardo; Pereira, Jose M. C.

    2016-04-01

    We perform a global trend analysis of active fire counts at 0.5o spatial resolution, using 156 months (January 2001 - December 2013) of MODIS Climate Modelling Grid data (TERRA). We use the Contextual Mann-Kendall (CMK) test to assess the statistical significance at cell level and found that 13% of the global land area displays statistically significant active fire count trends, with a slight predominance of negative trends (50.63% of the total significant cells). We perform the same trend analysis with the unexplained variability (residuals) between active fires and the Fire Weather Index (FWI) that is used as a proxy for climate. There is agreement between the main patterns from the trend analysis coming from the residuals and the active fire trends, implying that the main contemporary fire trends are not climate driven. Spatially coherent patches with significant trends were found in all continents (with the obvious exception of Antarctica). The majority of significant trends occur in areas of high fire incidence, and both increasing and decreasing trends appear to be associated with land use change processes. The analysis reveals large negative trends at the Sahel and between Russia and Kazakhstan, whereas a massive and coherent positive trend appears in southeastern Asia. Smaller patches of positive trends appear in southeastern United States and in Mexico, as well as in Brazil and between Argentina and Paraguay, and in Asia in India. There are also negative trends in Brazil, Argentina and in Australia. The study highlights the land use activities as the main driver of these trends, but also the need for data driven analyses and longer time series for future studies in order to gain better knowledge on fire occurrence.

  5. Identifying clinical course patterns in SMS data using cluster analysis

    DEFF Research Database (Denmark)

    Kent, Peter; Kongsted, Alice

    2012-01-01

    ABSTRACT: BACKGROUND: Recently, there has been interest in using the short message service (SMS or text messaging), to gather frequent information on the clinical course of individual patients. One possible role for identifying clinical course patterns is to assist in exploring clinically importa...... of cluster analysis. More research is needed, especially head-to-head studies, to identify which technique is best to use under what circumstances.......ABSTRACT: BACKGROUND: Recently, there has been interest in using the short message service (SMS or text messaging), to gather frequent information on the clinical course of individual patients. One possible role for identifying clinical course patterns is to assist in exploring clinically important...... by spline analysis. However, cluster analysis of SMS data in its original untransformed form may be simpler and offer other advantages. Therefore, the aim of this study was to determine whether cluster analysis could be used for identifying clinical course patterns distinct from the pattern of the whole...

  6. Analysis of a Piezo Electric Driver Circuit for Use in a Fabry-Perot Interferometer

    Directory of Open Access Journals (Sweden)

    Maithya J. Mutuku

    2013-09-01

    Full Text Available The design and fabrication of piezo electric driver circuit is presented and analysed. The output voltage which is a triangular wave voltage and frequency of the driver circuit were measured and set at 80 V peak to peak and an output frequency of 1 KHz. A photo detector circuit which receives the output beam from the confocal Fabry- perot interferometer (CFPI through the photodiode is as well presented

  7. Coal Enterprise Strategic Cost Driver Analysis Based on DEMATEL Method%基于DEMATEL法的煤炭企业战略成本动因分析

    Institute of Scientific and Technical Information of China (English)

    张佳; 张金泉

    2016-01-01

    In strategic cost management, cost driver analysis uses cost drivers to analyze the management and control of strategic cost. Strategic cost drivers are divided into structural cost drivers and execution cost drivers. Starting from the production features analysis of coal enterprise, this paper applies strategic cost driver analysis to production cost research of coal enterprises. The DEMATEL method is introduced to study the internal relevancy of the cost drivers. The synthetic influencing coefficient of the cost drivers are calculated, and the reason-result drawing of cost drivers is drawn. The key strategic cost driver affecting enterprise core competency is found by ordering. Then the key strategic cost driver is optimized to improve enterprises' core competency.%在战略成本管理中,成本动因分析将成本的驱动因素用于分析战略成本的管理与控制,战略成本动因分为结构性成本动因和执行性成本动因两大类.本文从煤炭企业的生产特征分析入手,将战略成本动因分析应用于煤炭企业生产成本研究,引入DE-MATEL法定量研究各项成本动因内部的关联度,计算各成本动因的综合影响系数绘制成本动因的原因—成果图,排序发现影响企业核心竞争力的关键战略成本动因,通过对关键战略成本动因优化进而提升企业核心竞争力.

  8. Enhancing digital driver models: identification of distinct postural strategies used by drivers.

    Science.gov (United States)

    Kyung, Gyouhyung; Nussbaum, Maury A; Babski-Reeves, Kari L

    2010-03-01

    Driver workspace design and evaluation is, in part, based on assumed driving postures of users and determines several ergonomic aspects of a vehicle, such as reach, visibility and postural comfort. Accurately predicting and specifying standard driving postures, hence, are necessary to improve the ergonomic quality of the driver workspace. In this study, a statistical clustering approach was employed to reduce driving posture simulation/prediction errors, assuming that drivers use several distinct postural strategies when interacting with automobiles. 2-D driving postures, described by 16 joint angles, were obtained from 38 participants with diverse demographics (age, gender) and anthropometrics (stature, body mass) and in two vehicle classes (sedans and SUVs). Based on the proximity of joint angle sets, cluster analysis yielded three predominant postural strategies in each vehicle class (i.e. 'lower limb flexed', 'upper limb flexed' and 'extended'). Mean angular differences between clusters ranged from 3.8 to 52.4 degrees for the majority of joints, supporting the practical relevance of the distinct clusters. The existence of such postural strategies should be considered when utilising digital human models (DHMs) to enhance and evaluate driver workspace design ergonomically and proactively. STATEMENT OF RELEVANCE: This study identified drivers' distinct postural strategies, based on actual drivers' behaviours. Such strategies can facilitate accurate positioning of DHMs and hence help design ergonomic driver workspaces.

  9. Test analysis and research on static choice reaction ability of commercial vehicle drivers

    Science.gov (United States)

    Zhang, Lingchao; Wei, Lang; Qiao, Jie; Tian, Shun; Wang, Shengchang

    2017-03-01

    Drivers' choice reaction ability has a certain relation with safe driving. It has important significance to research its influence on traffic safety. Firstly, the paper uses a choice reaction detector developed by research group to detect drivers' choice reaction ability of commercial vehicles, and gets 2641 effective samples. Then by using mathematical statistics method, the paper founds that average reaction time from accident group has no difference with non-accident group, and then introduces a variance rate of reaction time as a new index to replace it. The result shows that the test index choice reaction errors and variance rate of reaction time have positive correlations with accidents. Finally, according to testing results of the detector, the paper formulates a detection threshold with four levels for helping transportation companies to assess commercial vehicles drivers.

  10. Older Drivers

    Science.gov (United States)

    ... in this topic was provided by the National Highway Traffic Safety Administration Topic last reviewed: March 2015 For ... see Traffic Safety Facts 2012: Older Population. (National Highway Traffic Safety Administration). Crashes Down Among Older Drivers Fortunately, ...

  11. An epidemiologic survey of road traffic accidents in Iran:analysis of driver-related factors

    Institute of Scientific and Technical Information of China (English)

    Ghasem Moafian; Mohammad Reza Aghabeigi; Seyed Taghi Heydari; Amin Hoseinzadeh; Kamran Bagheri Lankarani; Yaser Sarikhani

    2013-01-01

    Road traffic accident (RTA)and its related injuries contribute to a significant portion of the burden of diseases in Iran.This paper explores the association between driver-related factors and RTA in the country.Methods:This cross-sectional study was conducted in Iran and all data regarding RTAs from March 20,2010 to June 10,2010 were obtained from the Traffic Police Department.We included 538 588 RTA records,which were classified to control for the main confounders:accident type,final cause of accident,time of accident and driver-related factors.Driver-related factors included sex,educational level,license type,type of injury,duration between accident and getting the driving license and driver's error type.Results:Atotal of 538 588 drivers (91.83% male,sex ratio of almost 13:1) were involved in the RTAs.Among them 423 932 (78.71%) were uninjured; 224 818 (41.74%) had a diploma degree.Grade 2 driving license represented the highest proportion of all driving licenses (290 811,54.00%).The greatest number of accidents took place at 12:00-13:59(75 024,13.93%).The proportion of drivers involved in RTAs decreased from 15.90% in the first year of getting a driving license to 3.13% after 10 years' of driving experience.Neglect of regulations was the commonest cause of traffic crashes (345 589,64.17%).Non-observance of priority and inattention to the front were the most frequent final causes of death (138 175,25.66% and 129 352,24.02%,respectively).We found significant association between type of accident and sex,education,license type,time of accident,final cause of accident,driver's error as well as duration between accident and getting the driving license (all P<0.001).Conclusion:Our results will improve the traffic law enforcement measures,which will change inappropriate behavior of drivers and protect the least experienced road users.

  12. The use of meta-analysis or research synthesis to combine driving simulation or naturalistic study results on driver distraction.

    Science.gov (United States)

    Caird, Jeff K; Johnston, Katherine A; Willness, Chelsea R; Asbridge, Mark

    2014-06-01

    Three important and inter-related topics are addressed in this paper. First, the importance of meta-analysis and research synthesis methods to combine studies on traffic safety, in general, and on driver distraction, in particular, is briefly reviewed. Second, naturalistic, epidemiologic, and driving simulation studies on driver distraction are used to illustrate convergent and divergent results that have accumulated thus far in this domain of research. In particular, mobile phone conversation, passenger presence, and text messaging naturalistic studies use meta-analyses and research syntheses to illustrate important patterns of results that are in need of more in-depth study. Third, a number of driver distraction study limitations such as poorly defined dependent variables, lack of methodological detail, and omission of statistical information prevent the integration of many studies into meta-analyses. In addition, the overall quality of road safety studies suffers from these same limitations and suggestions for improvement are made to guide researchers and reviewers. Practical Applications. The use of research synthesis and meta-analysis provide comprehensive estimates of the impact of distractions on driving performance, which can be used to guide public policy and future research.

  13. A GEOSPATIAL ANALYSIS OF THE RELATIONSHIP BETWEEN ENVIRONMENTAL DRIVERS AND VECTOR-BORNE DISEASES

    Directory of Open Access Journals (Sweden)

    MARIA IOANA VLAD-ȘANDRU

    2015-10-01

    Full Text Available A Geospatial Analysis of the Relationship between Environmental Drivers and Vector-Borne Diseases. Human health is profoundly affected by weather and climate. Environmental health is becoming a major preoccupation on a world-wide scale; there is a close correlation between a population’s state of health and the quality of its environment, considering many infectious diseases are at least partly dependent on environmental factors. When we talk about the environment, we realize that it includes and affects fields of action from our daily life. Earth observation from space, with validation from in situ observations, provide a greater understanding of the environment and enable us to monitor and predict key environmental phenomena and events that can affect our livelihoods and health. Even thought, the use of Earth observation is growing in usefulness for a wide variety of uses, it is extremely unlikely that Earth Observation will be able to detect infectious diseases directly. Instead, Earth observation can be used to detect high NDVI index (and possibly attribute the high surface chlorophyll concentration to a particular disease, and help predict the movement of the agents carrying vector-borne disease. Many diseases need certain temperature and moisture conditions to breed. The primary objective of analyzing environmental health risk and vulnerabilities is to support the Development Regions to strengthen their capacity to assess, visualize and analyze health risks and incorporate the results of this analysis in a health risk map for disaster risk reduction, emergency preparedness and response plans. At the same time, such an analysis applied in health, allows starting the collection and homogenization of baseline data, information and maps to help health authorities and decision makers to take informed decisions in times of crises. Informational Health Platform would be used for the integration of data coming from different sources in order to

  14. BIOELECTRICAL IMPEDANCE VECTOR ANALYSIS IDENTIFIES SARCOPENIA IN NURSING HOME RESIDENTS

    Science.gov (United States)

    Loss of muscle mass and water shifts between body compartments are contributing factors to frailty in the elderly. The body composition changes are especially pronounced in institutionalized elderly. We investigated the ability of single-frequency bioelectrical impedance analysis (BIA) to identify b...

  15. Identifying subgroups of patients using latent class analysis

    DEFF Research Database (Denmark)

    Nielsen, Anne Mølgaard; Kent, Peter; Hestbæk, Lise

    2017-01-01

    BACKGROUND: Heterogeneity in patients with low back pain (LBP) is well recognised and different approaches to subgrouping have been proposed. Latent Class Analysis (LCA) is a statistical technique that is increasingly being used to identify subgroups based on patient characteristics. However, as ...

  16. Drivers of Sales Innovation in Business-To-Business Firms

    DEFF Research Database (Denmark)

    Ritter, Thomas; Geersbro, Jens

    2014-01-01

    This paper defines the term sales innovation, offers an operationalization of the concept, and discusses antecedents of sales innovation in terms of important internal and external drivers. An empirical analysis of 409 B2B firms identifies the internal drivers of sales innovation as increased top...... pressure leads to less innovation in sales. Finally the paper suggests managerial implications as well as avenues of further research in this area....... management focus and increased resource allocation as well as increasing customer and competitor dynamics as external drivers. Despite the suggested positive impact of the degree of competitive pressure on sales innovation, the empirical results suggest a significant negative impact, i.e. competitive...

  17. Analysis Of Traffic Conditions Based On The Percentage Of Drivers Using The Instructions Displayed On VMS Boards

    Directory of Open Access Journals (Sweden)

    Leszek Smolarek

    2015-09-01

    Full Text Available The theme of the publication is to show the influence of human factor on traffic conditions during the traffic incident. The publication also depicts the functionality of the model at which the simulation was performed. The model was constructed in the VISSIM and VISUM software also using Visual Basic for Applications – Excel, [8,9]. By coordinating programs VBA and VISSIM was automated turned on or off the incident as well as turned on or off the VMS with information about the proposed of the alternative route. The additional differentiation of the percentage of drivers using the information displayed enabled to compare the data with identical external conditions influencing at traffic. For statistical analysis of data was used statistical program Statgraphics Centurion which made possible to build a model describing the impact of the behavior of drivers on traffic conditions. It is an innovative approach to modeling the impact on traffic conditions accepted by drivers information transmitted on the boards.

  18. Identifying glioblastoma gene networks based on hypergeometric test analysis.

    Directory of Open Access Journals (Sweden)

    Vasileios Stathias

    Full Text Available Patient specific therapy is emerging as an important possibility for many cancer patients. However, to identify such therapies it is essential to determine the genomic and transcriptional alterations present in one tumor relative to control samples. This presents a challenge since use of a single sample precludes many standard statistical analysis techniques. We reasoned that one means of addressing this issue is by comparing transcriptional changes in one tumor with those observed in a large cohort of patients analyzed by The Cancer Genome Atlas (TCGA. To test this directly, we devised a bioinformatics pipeline to identify differentially expressed genes in tumors resected from patients suffering from the most common malignant adult brain tumor, glioblastoma (GBM. We performed RNA sequencing on tumors from individual GBM patients and filtered the results through the TCGA database in order to identify possible gene networks that are overrepresented in GBM samples relative to controls. Importantly, we demonstrate that hypergeometric-based analysis of gene pairs identifies gene networks that validate experimentally. These studies identify a putative workflow for uncovering differentially expressed patient specific genes and gene networks for GBM and other cancers.

  19. An epidemiologic survey of road traffic accidents in Iran: analysis of driver-related factors

    Directory of Open Access Journals (Sweden)

    Moafian Ghasem

    2013-06-01

    Full Text Available 【Abstract】Objective: Road traffic accident (RTA and its related injuries contribute to a significant portion of the burden of diseases in Iran. This paper explores the as-sociation between driver-related factors and RTA in the country. Methods: This cross-sectional study was conducted in Iran and all data regarding RTAs from March 20, 2010 to June 10, 2010 were obtained from the Traffic Police Department. We included 538 588 RTA records, which were classified to control for the main confounders: accident type, final cause of accident, time of accident and driver-related factors. Driver-related factors included sex, educational level, license type, type of injury, duration between accident and getting the driving license and driver’s error type. Results: A total of 538 588 drivers (91.83% male, sex ratio of almost 13:1 were involved in the RTAs. Among them 423 932 (78.71% were uninjured; 224 818 (41.74% had a diploma degree. Grade 2 driving license represented the highest proportion of all driving licenses (290 811, 54.00%. The greatest number of accidents took place at 12:00-13:59 (75 024, 13.93%. The proportion of drivers involved in RTAs decreased from 15.90% in the first year of getting a driving license to 3.13% after 10 years’ of driving experience. Ne-glect of regulations was the commonest cause of traffic crashes (345 589, 64.17%. Non-observance of priority and inattention to the front were the most frequent final causes of death (138 175, 25.66% and 129 352, 24.02%, respectively. We found significant association between type of acci-dent and sex, education, license type, time of accident, final cause of accident, driver’s error as well as duration between accident and getting the driving license (all P<0.001. Conclusion: Our results will improve the traffic law enforcement measures, which will change inappropriate be-havior of drivers and protect the least experienced road users. Key words: Accidents, traffic; Automobile

  20. Using regulatory and epistatic networks to extend the findings of a genome scan: identifying the gene drivers of pigmentation in merino sheep.

    Directory of Open Access Journals (Sweden)

    Elsa García-Gámez

    Full Text Available Extending genome wide association analysis by the inclusion of gene expression data may assist in the dissection of complex traits. We examined piebald, a pigmentation phenotype in both human and Merino sheep, by analysing multiple data types using a systems approach. First, a case control analysis of 49,034 ovine SNP was performed which confirmed a multigenic basis for the condition. We combined these results with gene expression data from five tissue types analysed with a skin-specific microarray. Promoter sequence analysis of differentially expressed genes allowed us to reverse-engineer a regulatory network. Likewise, by testing two-loci models derived from all pair-wise comparisons across piebald-associated SNP, we generated an epistatic network. At the intersection of both networks, we identified thirteen genes with insulin-like growth factor binding protein 7 (IGFBP7, platelet-derived growth factor alpha (PDGFRA and the tetraspanin platelet activator CD9 at the kernel of the intersection. Further, we report a number of differentially expressed genes in regions containing highly associated SNP including ATRN, DOCK7, FGFR1OP, GLI3, SILV and TBX15. The application of network theory facilitated co-analysis of genetic variation with gene expression, recapitulated aspects of the known molecular biology of skin pigmentation and provided insights into the transcription regulation and epistatic interactions involved in piebald Merino sheep.

  1. Using regulatory and epistatic networks to extend the findings of a genome scan: identifying the gene drivers of pigmentation in merino sheep.

    Science.gov (United States)

    García-Gámez, Elsa; Reverter, Antonio; Whan, Vicki; McWilliam, Sean M; Arranz, Juan José; Kijas, James

    2011-01-01

    Extending genome wide association analysis by the inclusion of gene expression data may assist in the dissection of complex traits. We examined piebald, a pigmentation phenotype in both human and Merino sheep, by analysing multiple data types using a systems approach. First, a case control analysis of 49,034 ovine SNP was performed which confirmed a multigenic basis for the condition. We combined these results with gene expression data from five tissue types analysed with a skin-specific microarray. Promoter sequence analysis of differentially expressed genes allowed us to reverse-engineer a regulatory network. Likewise, by testing two-loci models derived from all pair-wise comparisons across piebald-associated SNP, we generated an epistatic network. At the intersection of both networks, we identified thirteen genes with insulin-like growth factor binding protein 7 (IGFBP7), platelet-derived growth factor alpha (PDGFRA) and the tetraspanin platelet activator CD9 at the kernel of the intersection. Further, we report a number of differentially expressed genes in regions containing highly associated SNP including ATRN, DOCK7, FGFR1OP, GLI3, SILV and TBX15. The application of network theory facilitated co-analysis of genetic variation with gene expression, recapitulated aspects of the known molecular biology of skin pigmentation and provided insights into the transcription regulation and epistatic interactions involved in piebald Merino sheep.

  2. Seven Performance Drivers.

    Science.gov (United States)

    Ross, Linda

    2003-01-01

    Recent work with automotive e-commerce clients led to the development of a performance analysis methodology called the Seven Performance Drivers, including: standards, incentives, capacity, knowledge and skill, measurement, feedback, and analysis. This methodology has been highly effective in introducing and implementing performance improvement.…

  3. Identifying influential factors of business process performance using dependency analysis

    Science.gov (United States)

    Wetzstein, Branimir; Leitner, Philipp; Rosenberg, Florian; Dustdar, Schahram; Leymann, Frank

    2011-02-01

    We present a comprehensive framework for identifying influential factors of business process performance. In particular, our approach combines monitoring of process events and Quality of Service (QoS) measurements with dependency analysis to effectively identify influential factors. The framework uses data mining techniques to construct tree structures to represent dependencies of a key performance indicator (KPI) on process and QoS metrics. These dependency trees allow business analysts to determine how process KPIs depend on lower-level process metrics and QoS characteristics of the IT infrastructure. The structure of the dependencies enables a drill-down analysis of single factors of influence to gain a deeper knowledge why certain KPI targets are not met.

  4. Latent cluster analysis of ALS phenotypes identifies prognostically differing groups.

    Directory of Open Access Journals (Sweden)

    Jeban Ganesalingam

    Full Text Available BACKGROUND: Amyotrophic lateral sclerosis (ALS is a degenerative disease predominantly affecting motor neurons and manifesting as several different phenotypes. Whether these phenotypes correspond to different underlying disease processes is unknown. We used latent cluster analysis to identify groupings of clinical variables in an objective and unbiased way to improve phenotyping for clinical and research purposes. METHODS: Latent class cluster analysis was applied to a large database consisting of 1467 records of people with ALS, using discrete variables which can be readily determined at the first clinic appointment. The model was tested for clinical relevance by survival analysis of the phenotypic groupings using the Kaplan-Meier method. RESULTS: The best model generated five distinct phenotypic classes that strongly predicted survival (p<0.0001. Eight variables were used for the latent class analysis, but a good estimate of the classification could be obtained using just two variables: site of first symptoms (bulbar or limb and time from symptom onset to diagnosis (p<0.00001. CONCLUSION: The five phenotypic classes identified using latent cluster analysis can predict prognosis. They could be used to stratify patients recruited into clinical trials and generating more homogeneous disease groups for genetic, proteomic and risk factor research.

  5. Detection of Driver Drowsiness Using Wavelet Analysis of Heart Rate Variability and a Support Vector Machine Classifier

    Directory of Open Access Journals (Sweden)

    Gang Li

    2013-12-01

    Full Text Available Driving while fatigued is just as dangerous as drunk driving and may result in car accidents. Heart rate variability (HRV analysis has been studied recently for the detection of driver drowsiness. However, the detection reliability has been lower than anticipated, because the HRV signals of drivers were always regarded as stationary signals. The wavelet transform method is a method for analyzing non-stationary signals. The aim of this study is to classify alert and drowsy driving events using the wavelet transform of HRV signals over short time periods and to compare the classification performance of this method with the conventional method that uses fast Fourier transform (FFT-based features. Based on the standard shortest duration for FFT-based short-term HRV evaluation, the wavelet decomposition is performed on 2-min HRV samples, as well as 1-min and 3-min samples for reference purposes. A receiver operation curve (ROC analysis and a support vector machine (SVM classifier are used for feature selection and classification, respectively. The ROC analysis results show that the wavelet-based method performs better than the FFT-based method regardless of the duration of the HRV sample that is used. Finally, based on the real-time requirements for driver drowsiness detection, the SVM classifier is trained using eighty FFT and wavelet-based features that are extracted from 1-min HRV signals from four subjects. The averaged leave-one-out (LOO classification performance using wavelet-based feature is 95% accuracy, 95% sensitivity, and 95% specificity. This is better than the FFT-based results that have 68.8% accuracy, 62.5% sensitivity, and 75% specificity. In addition, the proposed hardware platform is inexpensive and easy-to-use.

  6. Redesign of Transjakarta Bus Driver's Cabin

    Science.gov (United States)

    Mardi Safitri, Dian; Azmi, Nora; Singh, Gurbinder; Astuti, Pudji

    2016-02-01

    Ergonomic risk at work stations with type Seated Work Control was one of the problems faced by Transjakarta bus driver. Currently “Trisakti” type bus, one type of bus that is used by Transjakarta in corridor 9, serving route Pinang Ranti - Pluit, gained many complaints from drivers. From the results of Nordic Body Map questionnaires given to 30 drivers, it was known that drivers feel pain in the neck, arms, hips, and buttocks. Allegedly this was due to the seat position and the button/panel bus has a considerable distance range (1 meter) to be achieved by drivers. In addition, preliminary results of the questionnaire using Workstation Checklist identified their complaints about uncomfortable cushion, driver's seat backrest, and the exact position of the AC is above the driver head. To reduce the risk level of ergonomics, then did research to design the cabin by using a generic approach to designing products. The risk analysis driver posture before the design was done by using Rapid Upper Limb Assessment (RULA), Rapid Entire Body Assessment (REBA), and Quick Exposure Checklist (QEC), while the calculation of the moment the body is done by using software Mannequin Pro V10.2. Furthermore, the design of generic products was done through the stages: need metric-matrix, house of quality, anthropometric data collection, classification tree concept, concept screening, scoring concept, design and manufacture of products in the form of two-dimensional. While the design after design risk analysis driver posture was done by using RULA, REBA, and calculation of moments body as well as the design visualized using software 3DMax. From the results of analysis before the draft design improvements cabin RULA obtained scores of 6, REBA 9, and the result amounted to 57.38% QEC and moment forces on the back is 247.3 LbF.inch and on the right hip is 72.9 LbF.in. While the results of the proposed improvements cabin design RULA obtained scores of 3, REBA 4, and the moment of force on

  7. Identifying Organizational Inefficiencies with Pictorial Process Analysis (PPA

    Directory of Open Access Journals (Sweden)

    David John Patrishkoff

    2013-11-01

    Full Text Available Pictorial Process Analysis (PPA was created by the author in 2004. PPA is a unique methodology which offers ten layers of additional analysis when compared to standard process mapping techniques.  The goal of PPA is to identify and eliminate waste, inefficiencies and risk in manufacturing or transactional business processes at 5 levels in an organization. The highest level being assessed is the process management, followed by the process work environment, detailed work habits, process performance metrics and general attitudes towards the process. This detailed process assessment and analysis is carried out during process improvement brainstorming efforts and Kaizen events. PPA creates a detailed visual efficiency rating for each step of the process under review.  A selection of 54 pictorial Inefficiency Icons (cards are available for use to highlight major inefficiencies and risks that are present in the business process under review. These inefficiency icons were identified during the author's independent research on the topic of why things go wrong in business. This paper will highlight how PPA was developed and show the steps required to conduct Pictorial Process Analysis on a sample manufacturing process. The author has successfully used PPA to dramatically improve business processes in over 55 different industries since 2004.  

  8. Integrative transcriptomics-based identification of cryptic drivers of taxol-resistance genes in ovarian carcinoma cells: Analysis of the androgen receptor.

    Science.gov (United States)

    Sun, Nian-Kang; Huang, Shang-Lang; Lu, Hsing-Pang; Chang, Ting-Chang; Chao, Chuck C-K

    2015-09-29

    A systematic analysis of the genes involved in taxol resistance (txr) has never been performed. In the present study, we created txr ovarian carcinoma cell lines to identify the genes involved in chemoresistance. Transcriptome analysis revealed 1,194 overexpressed genes in txr cells. Among the upregulated genes, more than 12 cryptic transcription factors were identified using MetaCore analysis (including AR, C/EBPβ, ERα, HNF4α, c-Jun/AP-1, c-Myc, and SP-1). Notably, individual silencing of these transcription factors (except HNF4`)sensitized txr cells to taxol. The androgen receptor (AR) and its target genes were selected for further analysis. Silencing AR using RNA interference produced a 3-fold sensitization to taxol in txr cells, a response similar to that produced by silencing abcb1. AR silencing also downregulated the expression of prominent txr gene candidates (including abcb1, abcb6, abcg2, bmp5, fat3, fgfr2, h1f0, srcrb4d, and tmprss15). In contrast, AR activation using the agonist DHT upregulated expression of the target genes. Individually silencing seven out of nine (78%) AR-regulated txr genes sensitized txr cells to taxol. Inhibition of AKT and JNK cellular kinases using chemical inhibitors caused a dramatic suppression of AR expression. These results indicate that the AR represents a critical driver of gene expression involved in txr.

  9. Rice Transcriptome Analysis to Identify Possible Herbicide Quinclorac Detoxification Genes

    Directory of Open Access Journals (Sweden)

    Wenying eXu

    2015-09-01

    Full Text Available Quinclorac is a highly selective auxin-type herbicide, and is widely used in the effective control of barnyard grass in paddy rice fields, improving the world’s rice yield. The herbicide mode of action of quinclorac has been proposed and hormone interactions affect quinclorac signaling. Because of widespread use, quinclorac may be transported outside rice fields with the drainage waters, leading to soil and water pollution and environmental health problems.In this study, we used 57K Affymetrix rice whole-genome array to identify quinclorac signaling response genes to study the molecular mechanisms of action and detoxification of quinclorac in rice plants. Overall, 637 probe sets were identified with differential expression levels under either 6 or 24 h of quinclorac treatment. Auxin-related genes such as GH3 and OsIAAs responded to quinclorac treatment. Gene Ontology analysis showed that genes of detoxification-related family genes were significantly enriched, including cytochrome P450, GST, UGT, and ABC and drug transporter genes. Moreover, real-time RT-PCR analysis showed that top candidate P450 families such as CYP81, CYP709C and CYP72A genes were universally induced by different herbicides. Some Arabidopsis genes for the same P450 family were up-regulated under quinclorac treatment.We conduct rice whole-genome GeneChip analysis and the first global identification of quinclorac response genes. This work may provide potential markers for detoxification of quinclorac and biomonitors of environmental chemical pollution.

  10. Vision based Traffic Sign Detection and Analysis for Intelligent Driver Assistance Systems

    DEFF Research Database (Denmark)

    Møgelmose, Andreas; Trivedi, Mohan M.; Moeslund, Thomas B.

    2012-01-01

    In this paper, we provide a survey of the traffic sign detection literature, detailing detection systems for Traffic Sign Recognition (TSR) for driver assistance. We separately describe the contributions of recent works to the various stages inherent in traffic sign detection: segmentation, feature...... extraction, and final sign detection. While TSR is a well-established research area, we highlight open research issues in the literature, including a dearth of use of publicly-available image databases, and the over-representation of European traffic signs. Further, we discuss future directions for TSR...... research, including integration of context and localization. We also introduce a new public database containing US traffic signs...

  11. Identifying Sources of Difference in Reliability in Content Analysis

    Directory of Open Access Journals (Sweden)

    Elizabeth Murphy

    2005-07-01

    Full Text Available This paper reports on a case study which identifies and illustrates sources of difference in agreement in relation to reliability in a context of quantitative content analysis of a transcript of an online asynchronous discussion (OAD. Transcripts of 10 students in a month-long online asynchronous discussion were coded by two coders using an instrument with two categories, five processes, and 19 indicators of Problem Formulation and Resolution (PFR. Sources of difference were identified in relation to: coders; tasks; and students. Reliability values were calculated at the levels of categories, processes, and indicators. At the most detailed level of coding on the basis of the indicator, findings revealed that the overall level of reliability between coders was .591 when measured with Cohen’s kappa. The difference between tasks at the same level ranged from .349 to .664, and the difference between participants ranged from .390 to .907. Implications for training and research are discussed.

  12. Proteogenomic Analysis Identifies a Novel Human SHANK3 Isoform

    Directory of Open Access Journals (Sweden)

    Fahad Benthani

    2015-05-01

    Full Text Available Mutations of the SHANK3 gene have been associated with autism spectrum disorder. Individuals harboring different SHANK3 mutations display considerable heterogeneity in their cognitive impairment, likely due to the high SHANK3 transcriptional diversity. In this study, we report a novel interaction between the Mutated in colorectal cancer (MCC protein and a newly identified SHANK3 protein isoform in human colon cancer cells and mouse brain tissue. Hence, our proteogenomic analysis identifies a new human long isoform of the key synaptic protein SHANK3 that was not predicted by the human reference genome. Taken together, our findings describe a potential new role for MCC in neurons, a new human SHANK3 long isoform and, importantly, highlight the use of proteomic data towards the re-annotation of GC-rich genomic regions.

  13. Crash protection of stock car racing drivers--application of biomechanical analysis of Indy car crash research.

    Science.gov (United States)

    Melvin, John W; Begeman, Paul C; Faller, Ronald K; Sicking, Dean L; McClellan, Scott B; Maynard, Edwin; Donegan, Michael W; Mallott, Annette M; Gideon, Thomas W

    2006-11-01

    Biomechanical analysis of Indy car crashes using on-board impact recorders (Melvin et al. 1998, Melvin et al. 2001) indicates that Indy car driver protection in high-energy crashes can be achieved in frontal, side, and rear crashes with severities in the range of 100 to 135 G peak deceleration and velocity changes in the range of 50 to 70 mph. These crashes were predominantly single-car impacts with the rigid concrete walls of oval tracks. This impressive level of protection was found to be due to the unique combination of a very supportive and tight-fitting cockpit-seating package, a six-point belt restraint system, and effective head padding with an extremely strong chassis that defines the seat and cockpit of a modern Indy car. In 2000 and 2001, a series of fatal crashes in stock car racing created great concern for improving the crash protection for drivers in those racecars. Unlike the Indy car, the typical racing stock car features a more spacious driver cockpit due to its resemblance to the shape of a passenger car. The typical racing seat used in stock cars did not have the same configuration or support characteristics of the Indy car seat, and five-point belt restraints were used. The tubular steel space frame chassis of a stock car also differs from an Indy car's composite chassis structure in both form and mechanical behavior. This paper describes the application of results of the biomechanical analysis of the Indy car crash studies to the unique requirements of stock car racing driver crash protection. Sled test and full-scale crash test data using both Hybrid III frontal crash anthropomorphic test devices (ATDs) and BioSID side crash ATDs for the purpose of evaluating countermeasures involving restraint systems, seats and head/neck restraints has been instrumental in guiding these developments. In addition, the development of deformable walls for oval tracks (the SAFER Barrier) is described as an adjunct to improved occupant restraint through control

  14. Lidar point density analysis: implications for identifying water bodies

    Science.gov (United States)

    Worstell, Bruce B.; Poppenga, Sandra; Evans, Gayla A.; Prince, Sandra

    2014-01-01

    Most airborne topographic light detection and ranging (lidar) systems operate within the near-infrared spectrum. Laser pulses from these systems frequently are absorbed by water and therefore do not generate reflected returns on water bodies in the resulting void regions within the lidar point cloud. Thus, an analysis of lidar voids has implications for identifying water bodies. Data analysis techniques to detect reduced lidar return densities were evaluated for test sites in Blackhawk County, Iowa, and Beltrami County, Minnesota, to delineate contiguous areas that have few or no lidar returns. Results from this study indicated a 5-meter radius moving window with fewer than 23 returns (28 percent of the moving window) was sufficient for delineating void regions. Techniques to provide elevation values for void regions to flatten water features and to force channel flow in the downstream direction also are presented.

  15. Cluster analysis of clinical data identifies fibromyalgia subgroups.

    Directory of Open Access Journals (Sweden)

    Elisa Docampo

    Full Text Available INTRODUCTION: Fibromyalgia (FM is mainly characterized by widespread pain and multiple accompanying symptoms, which hinder FM assessment and management. In order to reduce FM heterogeneity we classified clinical data into simplified dimensions that were used to define FM subgroups. MATERIAL AND METHODS: 48 variables were evaluated in 1,446 Spanish FM cases fulfilling 1990 ACR FM criteria. A partitioning analysis was performed to find groups of variables similar to each other. Similarities between variables were identified and the variables were grouped into dimensions. This was performed in a subset of 559 patients, and cross-validated in the remaining 887 patients. For each sample and dimension, a composite index was obtained based on the weights of the variables included in the dimension. Finally, a clustering procedure was applied to the indexes, resulting in FM subgroups. RESULTS: VARIABLES CLUSTERED INTO THREE INDEPENDENT DIMENSIONS: "symptomatology", "comorbidities" and "clinical scales". Only the two first dimensions were considered for the construction of FM subgroups. Resulting scores classified FM samples into three subgroups: low symptomatology and comorbidities (Cluster 1, high symptomatology and comorbidities (Cluster 2, and high symptomatology but low comorbidities (Cluster 3, showing differences in measures of disease severity. CONCLUSIONS: We have identified three subgroups of FM samples in a large cohort of FM by clustering clinical data. Our analysis stresses the importance of family and personal history of FM comorbidities. Also, the resulting patient clusters could indicate different forms of the disease, relevant to future research, and might have an impact on clinical assessment.

  16. Estimating likelihood of future crashes for crash-prone drivers

    Directory of Open Access Journals (Sweden)

    Subasish Das

    2015-06-01

    Full Text Available At-fault crash-prone drivers are usually considered as the high risk group for possible future incidents or crashes. In Louisiana, 34% of crashes are repeatedly committed by the at-fault crash-prone drivers who represent only 5% of the total licensed drivers in the state. This research has conducted an exploratory data analysis based on the driver faultiness and proneness. The objective of this study is to develop a crash prediction model to estimate the likelihood of future crashes for the at-fault drivers. The logistic regression method is used by employing eight years' traffic crash data (2004–2011 in Louisiana. Crash predictors such as the driver's crash involvement, crash and road characteristics, human factors, collision type, and environmental factors are considered in the model. The at-fault and not-at-fault status of the crashes are used as the response variable. The developed model has identified a few important variables, and is used to correctly classify at-fault crashes up to 62.40% with a specificity of 77.25%. This model can identify as many as 62.40% of the crash incidence of at-fault drivers in the upcoming year. Traffic agencies can use the model for monitoring the performance of an at-fault crash-prone drivers and making roadway improvements meant to reduce crash proneness. From the findings, it is recommended that crash-prone drivers should be targeted for special safety programs regularly through education and regulations.

  17. Monte Carlo Analysis as a Trajectory Design Driver for the TESS Mission

    Science.gov (United States)

    Nickel, Craig; Lebois, Ryan; Lutz, Stephen; Dichmann, Donald; Parker, Joel

    2016-01-01

    The Transiting Exoplanet Survey Satellite (TESS) will be injected into a highly eccentric Earth orbit and fly 3.5 phasing loops followed by a lunar flyby to enter a mission orbit with lunar 2:1 resonance. Through the phasing loops and mission orbit, the trajectory is significantly affected by lunar and solar gravity. We have developed a trajectory design to achieve the mission orbit and meet mission constraints, including eclipse avoidance and a 30-year geostationary orbit avoidance requirement. A parallelized Monte Carlo simulation was performed to validate the trajectory after injecting common perturbations, including launch dispersions, orbit determination errors, and maneuver execution errors. The Monte Carlo analysis helped identify mission risks and is used in the trajectory selection process.

  18. Monte Carlo Analysis as a Trajectory Design Driver for the Transiting Exoplanet Survey Satellite (TESS) Mission

    Science.gov (United States)

    Nickel, Craig; Parker, Joel; Dichmann, Don; Lebois, Ryan; Lutz, Stephen

    2016-01-01

    The Transiting Exoplanet Survey Satellite (TESS) will be injected into a highly eccentric Earth orbit and fly 3.5 phasing loops followed by a lunar flyby to enter a mission orbit with lunar 2:1 resonance. Through the phasing loops and mission orbit, the trajectory is significantly affected by lunar and solar gravity. We have developed a trajectory design to achieve the mission orbit and meet mission constraints, including eclipse avoidance and a 30-year geostationary orbit avoidance requirement. A parallelized Monte Carlo simulation was performed to validate the trajectory after injecting common perturbations, including launch dispersions, orbit determination errors, and maneuver execution errors. The Monte Carlo analysis helped identify mission risks and is used in the trajectory selection process.

  19. Controllability analysis of the directed human protein interaction network identifies disease genes and drug targets.

    Science.gov (United States)

    Vinayagam, Arunachalam; Gibson, Travis E; Lee, Ho-Joon; Yilmazel, Bahar; Roesel, Charles; Hu, Yanhui; Kwon, Young; Sharma, Amitabh; Liu, Yang-Yu; Perrimon, Norbert; Barabási, Albert-László

    2016-05-03

    The protein-protein interaction (PPI) network is crucial for cellular information processing and decision-making. With suitable inputs, PPI networks drive the cells to diverse functional outcomes such as cell proliferation or cell death. Here, we characterize the structural controllability of a large directed human PPI network comprising 6,339 proteins and 34,813 interactions. This network allows us to classify proteins as "indispensable," "neutral," or "dispensable," which correlates to increasing, no effect, or decreasing the number of driver nodes in the network upon removal of that protein. We find that 21% of the proteins in the PPI network are indispensable. Interestingly, these indispensable proteins are the primary targets of disease-causing mutations, human viruses, and drugs, suggesting that altering a network's control property is critical for the transition between healthy and disease states. Furthermore, analyzing copy number alterations data from 1,547 cancer patients reveals that 56 genes that are frequently amplified or deleted in nine different cancers are indispensable. Among the 56 genes, 46 of them have not been previously associated with cancer. This suggests that controllability analysis is very useful in identifying novel disease genes and potential drug targets.

  20. What Are the Main Drivers of the Bitcoin Price? Evidence from Wavelet Coherence Analysis

    Science.gov (United States)

    Kristoufek, Ladislav

    2015-01-01

    The Bitcoin has emerged as a fascinating phenomenon in the Financial markets. Without any central authority issuing the currency, the Bitcoin has been associated with controversy ever since its popularity, accompanied by increased public interest, reached high levels. Here, we contribute to the discussion by examining the potential drivers of Bitcoin prices, ranging from fundamental sources to speculative and technical ones, and we further study the potential influence of the Chinese market. The evolution of relationships is examined in both time and frequency domains utilizing the continuous wavelets framework, so that we not only comment on the development of the interconnections in time but also distinguish between short-term and long-term connections. We find that the Bitcoin forms a unique asset possessing properties of both a standard financial asset and a speculative one. PMID:25874694

  1. Analysis of factors associated with injury severity in crashes involving young New Zealand drivers

    DEFF Research Database (Denmark)

    Weiss, Harold B.; Kaplan, Sigal; Prato, Carlo Giacomo

    2014-01-01

    fit than a binary and a generalized ordered logit. Results show that the young drivers’ behavior, the presence of passengers and the involvement of vulnerable road users were the most relevant factors associated with higher injury severity in both single-vehicle and two-vehicle crashes. Seatbelt non......-use, inexperience and alcohol use were the deadliest behavioral factors in single-vehicle crashes, while fatigue, reckless driving and seatbelt non-use were the deadliest factors in two-vehicle crashes. The presence of passengers in the young drivers’ vehicle, and in particular a combination of males and females......Young people are a risk to themselves and other road users, as motor vehicle crashes are the leading cause of their death. A thorough understanding of the most important factors associated with injury severity in crashes involving young drivers is important for designing well-targeted restrictive...

  2. What are the main drivers of the Bitcoin price? Evidence from wavelet coherence analysis.

    Science.gov (United States)

    Kristoufek, Ladislav

    2015-01-01

    The Bitcoin has emerged as a fascinating phenomenon in the Financial markets. Without any central authority issuing the currency, the Bitcoin has been associated with controversy ever since its popularity, accompanied by increased public interest, reached high levels. Here, we contribute to the discussion by examining the potential drivers of Bitcoin prices, ranging from fundamental sources to speculative and technical ones, and we further study the potential influence of the Chinese market. The evolution of relationships is examined in both time and frequency domains utilizing the continuous wavelets framework, so that we not only comment on the development of the interconnections in time but also distinguish between short-term and long-term connections. We find that the Bitcoin forms a unique asset possessing properties of both a standard financial asset and a speculative one.

  3. What are the main drivers of the Bitcoin price? Evidence from wavelet coherence analysis.

    Directory of Open Access Journals (Sweden)

    Ladislav Kristoufek

    Full Text Available The Bitcoin has emerged as a fascinating phenomenon in the Financial markets. Without any central authority issuing the currency, the Bitcoin has been associated with controversy ever since its popularity, accompanied by increased public interest, reached high levels. Here, we contribute to the discussion by examining the potential drivers of Bitcoin prices, ranging from fundamental sources to speculative and technical ones, and we further study the potential influence of the Chinese market. The evolution of relationships is examined in both time and frequency domains utilizing the continuous wavelets framework, so that we not only comment on the development of the interconnections in time but also distinguish between short-term and long-term connections. We find that the Bitcoin forms a unique asset possessing properties of both a standard financial asset and a speculative one.

  4. Patient-specific modeling of left ventricular electromechanics as a driver for haemodynamic analysis

    Science.gov (United States)

    Augustin, Christoph M.; Crozier, Andrew; Neic, Aurel; Prassl, Anton J.; Karabelas, Elias; Ferreira da Silva, Tiago; Fernandes, Joao F.; Campos, Fernando; Kuehne, Titus; Plank, Gernot

    2017-01-01

    Aims Models of blood flow in the left ventricle (LV) and aorta are an important tool for analysing the interplay between LV deformation and flow patterns. Typically, image-based kinematic models describing endocardial motion are used as an input to blood flow simulations. While such models are suitable for analysing the hemodynamic status quo, they are limited in predicting the response to interventions that alter afterload conditions. Mechano-fluidic models using biophysically detailed electromechanical (EM) models have the potential to overcome this limitation, but are more costly to build and compute. We report our recent advancements in developing an automated workflow for the creation of such CFD ready kinematic models to serve as drivers of blood flow simulations. Methods and results EM models of the LV and aortic root were created for four pediatric patients treated for either aortic coarctation or aortic valve disease. Using MRI, ECG and invasive pressure recordings, anatomy as well as electrophysiological, mechanical and circulatory model components were personalized. Results The implemented modeling pipeline was highly automated and allowed model construction and execution of simulations of a patient’s heartbeat within 1 day. All models reproduced clinical data with acceptable accuracy. Conclusion Using the developed modeling workflow, the use of EM LV models as driver of fluid flow simulations is becoming feasible. While EM models are costly to construct, they constitute an important and nontrivial step towards fully coupled electro-mechano-fluidic (EMF) models and show promise as a tool for predicting the response to interventions which affect afterload conditions. PMID:28011839

  5. Analysis of an Image Secret Sharing Scheme to Identify Cheaters

    Directory of Open Access Journals (Sweden)

    Jung-San LEe

    2010-09-01

    Full Text Available Secret image sharing mechanisms have been widely applied to the military, e-commerce, and communications fields. Zhao et al. introduced the concept of cheater detection into image sharing schemes recently. This functionality enables the image owner and authorized members to identify the cheater in reconstructing the secret image. Here, we provide an analysis of Zhao et al.¡¦s method: an authorized participant is able to restore the secret image by him/herself. This contradicts the requirement of secret image sharing schemes. The authorized participant utilizes an exhaustive search to achieve the attempt, though, simulation results show that it can be done within a reasonable time period.

  6. Identifying avian sources of faecal contamination using sterol analysis.

    Science.gov (United States)

    Devane, Megan L; Wood, David; Chappell, Andrew; Robson, Beth; Webster-Brown, Jenny; Gilpin, Brent J

    2015-10-01

    Discrimination of the source of faecal pollution in water bodies is an important step in the assessment and mitigation of public health risk. One tool for faecal source tracking is the analysis of faecal sterols which are present in faeces of animals in a range of distinctive ratios. Published ratios are able to discriminate between human and herbivore mammal faecal inputs but are of less value for identifying pollution from wildfowl, which can be a common cause of elevated bacterial indicators in rivers and streams. In this study, the sterol profiles of 50 avian-derived faecal specimens (seagulls, ducks and chickens) were examined alongside those of 57 ruminant faeces and previously published sterol profiles of human wastewater, chicken effluent and animal meatwork effluent. Two novel sterol ratios were identified as specific to avian faecal scats, which, when incorporated into a decision tree with human and herbivore mammal indicative ratios, were able to identify sterols from avian-polluted waterways. For samples where the sterol profile was not consistent with herbivore mammal or human pollution, avian pollution is indicated when the ratio of 24-ethylcholestanol/(24-ethylcholestanol + 24-ethylcoprostanol + 24-ethylepicoprostanol) is ≥0.4 (avian ratio 1) and the ratio of cholestanol/(cholestanol + coprostanol + epicoprostanol) is ≥0.5 (avian ratio 2). When avian pollution is indicated, further confirmation by targeted PCR specific markers can be employed if greater confidence in the pollution source is required. A 66% concordance between sterol ratios and current avian PCR markers was achieved when 56 water samples from polluted waterways were analysed.

  7. Cluster Analysis of Clinical Data Identifies Fibromyalgia Subgroups

    Science.gov (United States)

    Docampo, Elisa; Collado, Antonio; Escaramís, Geòrgia; Carbonell, Jordi; Rivera, Javier; Vidal, Javier; Alegre, José

    2013-01-01

    Introduction Fibromyalgia (FM) is mainly characterized by widespread pain and multiple accompanying symptoms, which hinder FM assessment and management. In order to reduce FM heterogeneity we classified clinical data into simplified dimensions that were used to define FM subgroups. Material and Methods 48 variables were evaluated in 1,446 Spanish FM cases fulfilling 1990 ACR FM criteria. A partitioning analysis was performed to find groups of variables similar to each other. Similarities between variables were identified and the variables were grouped into dimensions. This was performed in a subset of 559 patients, and cross-validated in the remaining 887 patients. For each sample and dimension, a composite index was obtained based on the weights of the variables included in the dimension. Finally, a clustering procedure was applied to the indexes, resulting in FM subgroups. Results Variables clustered into three independent dimensions: “symptomatology”, “comorbidities” and “clinical scales”. Only the two first dimensions were considered for the construction of FM subgroups. Resulting scores classified FM samples into three subgroups: low symptomatology and comorbidities (Cluster 1), high symptomatology and comorbidities (Cluster 2), and high symptomatology but low comorbidities (Cluster 3), showing differences in measures of disease severity. Conclusions We have identified three subgroups of FM samples in a large cohort of FM by clustering clinical data. Our analysis stresses the importance of family and personal history of FM comorbidities. Also, the resulting patient clusters could indicate different forms of the disease, relevant to future research, and might have an impact on clinical assessment. PMID:24098674

  8. Archetypal TRMM Radar Profiles Identified Through Cluster Analysis

    Science.gov (United States)

    Boccippio, Dennis J.

    2003-01-01

    It is widely held that identifiable 'convective regimes' exist in nature, although precise definitions of these are elusive. Examples include land / Ocean distinctions, break / monsoon beahvior, seasonal differences in the Amazon (SON vs DJF), etc. These regimes are often described by differences in the realized local convective spectra, and measured by various metrics of convective intensity, depth, areal coverage and rainfall amount. Objective regime identification may be valuable in several ways: regimes may serve as natural 'branch points' in satellite retrieval algorithms or data assimilation efforts; one example might be objective identification of regions that 'should' share a similar 2-R relationship. Similarly, objectively defined regimes may provide guidance on optimal siting of ground validation efforts. Objectively defined regimes could also serve as natural (rather than arbitrary geographic) domain 'controls' in studies of convective response to environmental forcing. Quantification of convective vertical structure has traditionally involved parametric study of prescribed quantities thought to be important to convective dynamics: maximum radar reflectivity, cloud top height, 30-35 dBZ echo top height, rain rate, etc. Individually, these parameters are somewhat deficient as their interpretation is often nonunique (the same metric value may signify different physics in different storm realizations). Individual metrics also fail to capture the coherence and interrelationships between vertical levels available in full 3-D radar datasets. An alternative approach is discovery of natural partitions of vertical structure in a globally representative dataset, or 'archetypal' reflectivity profiles. In this study, this is accomplished through cluster analysis of a very large sample (0[107) of TRMM-PR reflectivity columns. Once achieved, the rainconditional and unconditional 'mix' of archetypal profile types in a given location and/or season provides a description

  9. Network Analysis Identifies Disease-Specific Pathways for Parkinson's Disease.

    Science.gov (United States)

    Monti, Chiara; Colugnat, Ilaria; Lopiano, Leonardo; Chiò, Adriano; Alberio, Tiziana

    2016-12-21

    Neurodegenerative diseases are characterized by the progressive loss of specific neurons in selected regions of the central nervous system. The main clinical manifestation (movement disorders, cognitive impairment, and/or psychiatric disturbances) depends on the neuron population being primarily affected. Parkinson's disease is a common movement disorder, whose etiology remains mostly unknown. Progressive loss of dopaminergic neurons in the substantia nigra causes an impairment of the motor control. Some of the pathogenetic mechanisms causing the progressive deterioration of these neurons are not specific for Parkinson's disease but are shared by other neurodegenerative diseases, like Alzheimer's disease and amyotrophic lateral sclerosis. Here, we performed a meta-analysis of the literature of all the quantitative proteomic investigations of neuronal alterations in different models of Parkinson's disease, Alzheimer's disease, and amyotrophic lateral sclerosis to distinguish between general and Parkinson's disease-specific pattern of neurodegeneration. Then, we merged proteomics data with genetics information from the DisGeNET database. The comparison of gene and protein information allowed us to identify 25 proteins involved uniquely in Parkinson's disease and we verified the alteration of one of them, i.e., transaldolase 1 (TALDO1), in the substantia nigra of 5 patients. By using open-source bioinformatics tools, we identified the biological processes specifically affected in Parkinson's disease, i.e., proteolysis, mitochondrion organization, and mitophagy. Eventually, we highlighted four cellular component complexes mostly involved in the pathogenesis: the proteasome complex, the protein phosphatase 2A, the chaperonins CCT complex, and the complex III of the respiratory chain.

  10. Social network analysis in identifying influential webloggers: A preliminary study

    Science.gov (United States)

    Hasmuni, Noraini; Sulaiman, Nor Intan Saniah; Zaibidi, Nerda Zura

    2014-12-01

    In recent years, second generation of internet-based services such as weblog has become an effective communication tool to publish information on the Web. Weblogs have unique characteristics that deserve users' attention. Some of webloggers have seen weblogs as appropriate medium to initiate and expand business. These webloggers or also known as direct profit-oriented webloggers (DPOWs) communicate and share knowledge with each other through social interaction. However, survivability is the main issue among DPOW. Frequent communication with influential webloggers is one of the way to keep survive as DPOW. This paper aims to understand the network structure and identify influential webloggers within the network. Proper understanding of the network structure can assist us in knowing how the information is exchanged among members and enhance survivability among DPOW. 30 DPOW were involved in this study. Degree centrality and betweenness centrality measurement in Social Network Analysis (SNA) were used to examine the strength relation and identify influential webloggers within the network. Thus, webloggers with the highest value of these measurements are considered as the most influential webloggers in the network.

  11. Combining hydrology and mosquito population models to identify the drivers of Rift Valley fever emergence in semi-arid regions of West Africa.

    Directory of Open Access Journals (Sweden)

    Valérie Soti

    Full Text Available BACKGROUND: Rift Valley fever (RVF is a vector-borne viral zoonosis of increasing global importance. RVF virus (RVFV is transmitted either through exposure to infected animals or through bites from different species of infected mosquitoes, mainly of Aedes and Culex genera. These mosquitoes are very sensitive to environmental conditions, which may determine their presence, biology, and abundance. In East Africa, RVF outbreaks are known to be closely associated with heavy rainfall events, unlike in the semi-arid regions of West Africa where the drivers of RVF emergence remain poorly understood. The assumed importance of temporary ponds and rainfall temporal distribution therefore needs to be investigated. METHODOLOGY/PRINCIPAL FINDINGS: A hydrological model is combined with a mosquito population model to predict the abundance of the two main mosquito species (Aedes vexans and Culex poicilipes involved in RVFV transmission in Senegal. The study area is an agropastoral zone located in the Ferlo Valley, characterized by a dense network of temporary water ponds which constitute mosquito breeding sites. The hydrological model uses daily rainfall as input to simulate variations of pond surface areas. The mosquito population model is mechanistic, considers both aquatic and adult stages and is driven by pond dynamics. Once validated using hydrological and entomological field data, the model was used to simulate the abundance dynamics of the two mosquito species over a 43-year period (1961-2003. We analysed the predicted dynamics of mosquito populations with regards to the years of main outbreaks. The results showed that the main RVF outbreaks occurred during years with simultaneous high abundances of both species. CONCLUSION/SIGNIFICANCE: Our study provides for the first time a mechanistic insight on RVFV transmission in West Africa. It highlights the complementary roles of Aedes vexans and Culex poicilipes mosquitoes in virus transmission, and recommends

  12. 浅析我国酒后代驾行为--以酒后代驾合同为重心%Analysis on the Behavior of Designated Drivers in China-With the Focus of Designated Drivers Contract

    Institute of Scientific and Technical Information of China (English)

    盛钧俣

    2015-01-01

    With the comparative analysis and case analysis,based on the designated driver contract,the paper presents major viewpoints and cases in China,and mainly analyzes the effectiveness and property of des-ignated divers contract and the infringing problems that are caused by designated driving behaviors. It is point-ed out that although there is no definite legal classification in the behavior of designated driver,its behavior is regulated by the current law,and different behaviors of designated drivers are applicable to different legal rela-tions. In our modern legal system,declaring the legal applicability of both designated drivers and substituted drivers,and the commitment of infringing responsibility caused by designated driving,can be of significance in the regulation development of designated driving service.%采用对比分析法和案例分析法,以酒后代驾合同为突破口,罗列国内主流观点和已判案例,重点分析了酒后代驾合同的效力和性质,以及酒后代驾行为导致的侵权问题。研究指出:虽然酒后代驾行为没有明确的法律分类,但其行为仍然受到已有法律的规范,可根据不同的酒后代驾行为适用不同的法律关系。在我国现行法律体系内,明确酒后代驾双方的法律关系适用和酒后代驾行为导致的侵权责任承担,对于酒后代驾行业的规范发展具有重要意义。

  13. Exome sequence analysis of Kaposiform hemangioendothelioma: identification of putative driver mutations*

    Science.gov (United States)

    Egashira, Sho; Jinnin, Masatoshi; Harada, Miho; Masuguchi, Shinichi; Fukushima, Satoshi; Ihn, Hironobu

    2016-01-01

    BACKGROUND Kaposiform hemangioendothelioma is a rare, intermediate, malignant tumor. The tumor's etiology remains unknown and there are no specific treatments. OBJECTIVE In this study, we performed exome sequencing using DNA from a Kaposiform hemangioendothelioma patient, and found putative candidates for the responsible mutations. METHOD The genomic DNA for exome sequencing was obtained from the tumor tissue and matched normal tissue from the same individual. Exome sequencing was performed on HiSeq2000 sequencer platform. RESULTS Among oncogenes, germline missense single nucleotide variants were observed in the TP53 and APC genes in both the tumor and normal tissue. As tumor-specific somatic mutations, we identified 81 candidate genes, including 4 nonsense changes, 68 missense changes and 9 insertions/deletions. The mutations in ITGB2, IL-32 and DIDO1 were included in them. CONCLUSION This is a pilot study, and future analysis with more patients is needed to clarify: the detailed pathogenesis of this tumor, the novel diagnostic methods by detecting specific mutations, and the new therapeutic strategies targeting the mutation. PMID:28099595

  14. Risk-Adjusted Analysis of Relevant Outcome Drivers for Patients after More Than Two Kidney Transplants

    Directory of Open Access Journals (Sweden)

    Lampros Kousoulas

    2015-01-01

    Full Text Available Renal transplantation is the treatment of choice for patients suffering end-stage renal disease, but as the long-term renal allograft survival is limited, most transplant recipients will face graft loss and will be considered for a retransplantation. The goal of this study was to evaluate the patient and graft survival of the 61 renal transplant recipients after second or subsequent renal transplantation, transplanted in our institution between 1990 and 2010, and to identify risk factors related to inferior outcomes. Actuarial patient survival was 98.3%, 94.8%, and 88.2% after one, three, and five years, respectively. Actuarial graft survival was 86.8%, 80%, and 78.1% after one, three, and five years, respectively. Risk-adjusted analysis revealed that only age at the time of last transplantation had a significant influence on patient survival, whereas graft survival was influenced by multiple immunological and surgical factors, such as the number of HLA mismatches, the type of immunosuppression, the number of surgical complications, need of reoperation, primary graft nonfunction, and acute rejection episodes. In conclusion, third and subsequent renal transplantation constitute a valid therapeutic option, but inferior outcomes should be expected among elderly patients, hyperimmunized recipients, and recipients with multiple operations at the site of last renal transplantation.

  15. Numerical Analysis of the Output-Pulse Shaping Capability of Linear Transformer Drivers

    Science.gov (United States)

    Liu, Peng; Sun, Fengju; Yin, Jiahui; Qiu, Aici

    2011-04-01

    Output-pulse shaping capability of a linear transformer driver (LTD) module under different conditions is studied, by conducting the whole circuit model simulation by using the PSPICE code. Results indicate that a higher impedance profile of the internal transmission line would lead to a wider adjustment range for the output current rise time and a narrower adjustment range for the current peak. The number of cavities in series has a positive effect on the output-pulse shaping capability of LTD. Such an improvement in the output-pulse shaping capability can primarily be ascribed to the increment in the axial electric length of LTD. For a triggering time interval longer than the time taken by a pulse to propagate through the length of one cavity, the output parameters of LTD could be improved significantly. The present insulating capability of gas switches and other elements in the LTD cavities may only tolerate a slightly longer deviation in the triggering time interval. It is feasible for the LTD module to reduce the output current rise time, though it is not useful to improve the peak power effectively.

  16. Performance Analysis: Work Control Events Identified January - August 2010

    Energy Technology Data Exchange (ETDEWEB)

    De Grange, C E; Freeman, J W; Kerr, C E; Holman, G; Marsh, K; Beach, R

    2011-01-14

    This performance analysis evaluated 24 events that occurred at LLNL from January through August 2010. The analysis identified areas of potential work control process and/or implementation weaknesses and several common underlying causes. Human performance improvement and safety culture factors were part of the causal analysis of each event and were analyzed. The collective significance of all events in 2010, as measured by the occurrence reporting significance category and by the proportion of events that have been reported to the DOE ORPS under the ''management concerns'' reporting criteria, does not appear to have increased in 2010. The frequency of reporting in each of the significance categories has not changed in 2010 compared to the previous four years. There is no change indicating a trend in the significance category and there has been no increase in the proportion of occurrences reported in the higher significance category. Also, the frequency of events, 42 events reported through August 2010, is not greater than in previous years and is below the average of 63 occurrences per year at LLNL since 2006. Over the previous four years, an average of 43% of the LLNL's reported occurrences have been reported as either ''management concerns'' or ''near misses.'' In 2010, 29% of the occurrences have been reported as ''management concerns'' or ''near misses.'' This rate indicates that LLNL is now reporting fewer ''management concern'' and ''near miss'' occurrences compared to the previous four years. From 2008 to the present, LLNL senior management has undertaken a series of initiatives to strengthen the work planning and control system with the primary objective to improve worker safety. In 2008, the LLNL Deputy Director established the Work Control Integrated Project Team to develop the core requirements and graded

  17. Global secretome analysis identifies novel mediators of bone metastasis

    Institute of Scientific and Technical Information of China (English)

    Mario Andres Blanco; Gary LeRoy; Zia Khan; Ma(s)a Ale(c)kovi(c); Barry M Zee; Benjamin A Garcia; Yibin Kang

    2012-01-01

    Bone is the one of the most common sites of distant metastasis of solid tumors.Secreted proteins are known to influence pathological interactions between metastatic cancer cells and the bone stroma.To comprehensively profile secreted proteins associated with bone metastasis,we used quantitative and non-quantitative mass spectrometry to globally analyze the secretomes of nine cell lines of varying bone metastatic ability from multiple species and cancer types.By comparing the secretomes of parental cells and their bone metastatic derivatives,we identified the secreted proteins that were uniquely associated with bone metastasis in these cell lines.We then incorporated bioinformatic analyses of large clinical metastasis datasets to obtain a list of candidate novel bone metastasis proteins of several functional classes that were strongly associated with both clinical and experimental bone metastasis.Functional validation of selected proteins indicated that in vivo bone metastasis can be promoted by high expression of (1) the salivary cystatins CST1,CST2,and CST4; (2) the plasminogen activators PLAT and PLAU; or (3) the collagen functionality proteins PLOD2 and COL6A1.Overall,our study has uncovered several new secreted mediators of bone metastasis and therefore demonstrated that secretome analysis is a powerful method for identification of novel biomarkers and candidate therapeutic targets.

  18. Identifying redundancy and exposing provenance in crowdsourced data analysis.

    Science.gov (United States)

    Willett, Wesley; Ginosar, Shiry; Steinitz, Avital; Hartmann, Björn; Agrawala, Maneesh

    2013-12-01

    We present a system that lets analysts use paid crowd workers to explore data sets and helps analysts interactively examine and build upon workers' insights. We take advantage of the fact that, for many types of data, independent crowd workers can readily perform basic analysis tasks like examining views and generating explanations for trends and patterns. However, workers operating in parallel can often generate redundant explanations. Moreover, because workers have different competencies and domain knowledge, some responses are likely to be more plausible than others. To efficiently utilize the crowd's work, analysts must be able to quickly identify and consolidate redundant responses and determine which explanations are the most plausible. In this paper, we demonstrate several crowd-assisted techniques to help analysts make better use of crowdsourced explanations: (1) We explore crowd-assisted strategies that utilize multiple workers to detect redundant explanations. We introduce color clustering with representative selection--a strategy in which multiple workers cluster explanations and we automatically select the most-representative result--and show that it generates clusterings that are as good as those produced by experts. (2) We capture explanation provenance by introducing highlighting tasks and capturing workers' browsing behavior via an embedded web browser, and refine that provenance information via source-review tasks. We expose this information in an explanation-management interface that allows analysts to interactively filter and sort responses, select the most plausible explanations, and decide which to explore further.

  19. A Sensitivity Analysis Approach to Identify Key Environmental Performance Factors

    Directory of Open Access Journals (Sweden)

    Xi Yu

    2014-01-01

    Full Text Available Life cycle assessment (LCA is widely used in design phase to reduce the product’s environmental impacts through the whole product life cycle (PLC during the last two decades. The traditional LCA is restricted to assessing the environmental impacts of a product and the results cannot reflect the effects of changes within the life cycle. In order to improve the quality of ecodesign, it is a growing need to develop an approach which can reflect the changes between the design parameters and product’s environmental impacts. A sensitivity analysis approach based on LCA and ecodesign is proposed in this paper. The key environmental performance factors which have significant influence on the products’ environmental impacts can be identified by analyzing the relationship between environmental impacts and the design parameters. Users without much environmental knowledge can use this approach to determine which design parameter should be first considered when (redesigning a product. A printed circuit board (PCB case study is conducted; eight design parameters are chosen to be analyzed by our approach. The result shows that the carbon dioxide emission during the PCB manufacture is highly sensitive to the area of PCB panel.

  20. Performance Analysis: Work Control Events Identified January - August 2010

    Energy Technology Data Exchange (ETDEWEB)

    De Grange, C E; Freeman, J W; Kerr, C E; Holman, G; Marsh, K; Beach, R

    2011-01-14

    This performance analysis evaluated 24 events that occurred at LLNL from January through August 2010. The analysis identified areas of potential work control process and/or implementation weaknesses and several common underlying causes. Human performance improvement and safety culture factors were part of the causal analysis of each event and were analyzed. The collective significance of all events in 2010, as measured by the occurrence reporting significance category and by the proportion of events that have been reported to the DOE ORPS under the ''management concerns'' reporting criteria, does not appear to have increased in 2010. The frequency of reporting in each of the significance categories has not changed in 2010 compared to the previous four years. There is no change indicating a trend in the significance category and there has been no increase in the proportion of occurrences reported in the higher significance category. Also, the frequency of events, 42 events reported through August 2010, is not greater than in previous years and is below the average of 63 occurrences per year at LLNL since 2006. Over the previous four years, an average of 43% of the LLNL's reported occurrences have been reported as either ''management concerns'' or ''near misses.'' In 2010, 29% of the occurrences have been reported as ''management concerns'' or ''near misses.'' This rate indicates that LLNL is now reporting fewer ''management concern'' and ''near miss'' occurrences compared to the previous four years. From 2008 to the present, LLNL senior management has undertaken a series of initiatives to strengthen the work planning and control system with the primary objective to improve worker safety. In 2008, the LLNL Deputy Director established the Work Control Integrated Project Team to develop the core requirements and graded

  1. Drought and Snow: Analysis of Drivers, Processes and Impacts of Streamflow Droughts in Snow-Dominated Regions

    Science.gov (United States)

    Van Loon, Anne; Laaha, Gregor; Van Lanen, Henny; Parajka, Juraj; Fleig, Anne; Ploum, Stefan

    2016-04-01

    Around the world, drought events with severe socio-economic impacts seem to have a link with winter snowpack. That is the case for the current California drought, but analysing historical archives and drought impact databases for the US and Europe we found many impacts that can be attributed to snowpack anomalies. Agriculture and electricity production (hydropower) were found to be the sectors that are most affected by drought related to snow. In this study, we investigated the processes underlying hydrological drought in snow-dominated regions. We found that drought drivers are different in different regions. In Norway, more than 90% of spring streamflow droughts were preceded by below-average winter precipitation, while both winter air temperature and spring weather were indifferent. In Austria, however, spring streamflow droughts could only be explained by a combination of factors. For most events, winter and spring air temperatures were above average (70% and 65% of events, respectively), and winter and spring precipitation was below average (75% and 80%). Because snow storage results from complex interactions between precipitation and temperature and these variables vary strongly with altitude, snow-related drought drivers have a large spatial variability. The weather input is subsequently modified by land properties. Multiple linear regression between drought severity variables and a large number of catchment characteristics for 44 catchments in Austria showed that storage influences both drought duration and deficit volume. The seasonal storage of water in snow and glaciers was found to be a statistically important variable explaining streamflow drought deficit. Our drought impact analysis in Europe also showed that 40% of the selected drought impacts was caused by a combination of snow-related and other drought types. For example, the combination of a winter drought with a preceding or subsequent summer drought was reported to have a large effect on

  2. The impact of threat appeals on fear arousal and driver behavior: a meta-analysis of experimental research 1990-2011.

    Directory of Open Access Journals (Sweden)

    Rachel N Carey

    Full Text Available The existing empirical research exploring the impact of threat appeals on driver behavior has reported inconsistent findings. In an effort to provide an up-to-date synthesis of the experimental findings, meta-analytic techniques were employed to examine the impact of threat-based messages on fear arousal and on lab-based indices of driving behavior. Experimental studies (k = 13, N = 3044, conducted between 1990 and 2011, were included in the analyses. The aims of the current analysis were (a to examine whether or not the experimental manipulations had a significant impact on evoked fear, (b to examine the impact of threat appeals on three distinct indices of driving, and (c to identify moderators and mediators of the relationship between fear and driving outcomes. Large effects emerged for the level of fear evoked, with experimental groups reporting increased fear arousal in comparison to control groups (r = .64, n = 619, p<.01. The effect of threat appeals on driving outcomes, however, was not significant (r = .03, p = .17. This analysis of the experimental literature indicates that threat appeals can lead to increased fear arousal, but do not appear to have the desired impact on driving behavior. We discuss these findings in the context of threat-based road safety campaigns and future directions for experimental research in this area.

  3. Occupational stress situation analysis of different types of train drivers%不同类别列车司机职业紧张现状分析

    Institute of Scientific and Technical Information of China (English)

    周文慧; 谷桂珍; 吴辉; 余善法

    2014-01-01

    、客运调车司机(R2=0畅38),对列车司机每日紧张感的效应从大到小依次为:动车或高铁司机(R2=0畅54)、普通客车司机(R2=0畅37)、客运调车司机(R2=0畅33)、货车司机(R2=0畅30),对列车司机情感平衡的效应从大到小依次为:动车或高铁司机(R2=0畅47)、普通客车司机(R2=0畅43)、客运调车司机(R2=0畅33)、货车司机(R2=0畅31)。结论 ERI、心理需求、工作中的责任、工作角色、工作冲突以及物理环境等是列车司机的主要职业紧张因素;社会支持是列车司机重要的紧张缓解因素;不同类别的列车司机职业紧张程度不同,动车或高铁司机职业紧张程度最大,货车司机或客运调车司机最小。%Objective To analyze the status of occupational stress in different types of train drivers . Methods By using cluster sampling method , a cross-sectional study was conducted in 1 339 train drivers (including 289 passenger train drivers, 637 freight trains drivers,339 passenger shunting train drivers ,and 74 high speed rail drivers ) from a Railway Bureau depot.The survey included individual factors , occupational stress factors , stress response factors and stress mitigating factors.The occupational stress factors, stress response factors and mitigating factors were measured by the revised effort-reward imbalance (ERI) model questionnaires and occupational stress measurement scale.By using the method of covariance analysized the difference of occupational stress factors of all types train drivers , the method of Stepwise regression was used to analyze the effection ( R2 ) of occupational stress factors and stress mitigating factors on stress response factors .Results Covariance analysis as covariates in age , education level , length of service and marital status showed that the scores of ERI ( 1.58 ±0.05 ) , extrinsic effort ( 19.88 ±0.44 ) , rewards (23.43 ±0.43), intrinsic effort (17.86 ±0

  4. Identifying Ecosystem Services of Rivers and Streams Through Content Analysis

    Science.gov (United States)

    While much ecosystem services research focuses on analysis such as mapping and/or valuation, fewer research efforts are directed toward in-depth understanding of the specific ecological quantities people value. Ecosystem service monitoring and analysis efforts and communications ...

  5. Clinical Genotyping of Non–Small Cell Lung Cancers Using Targeted Next-Generation Sequencing: Utility of Identifying Rare and Co-mutations in Oncogenic Driver Genes

    Directory of Open Access Journals (Sweden)

    Laura J. Tafe

    2016-09-01

    Full Text Available Detection of somatic mutations in non–small cell lung cancers (NSCLCs, especially adenocarcinomas, is important for directing patient care when targeted therapy is available. Here, we present our experience with genotyping NSCLC using the Ion Torrent Personal Genome Machine (PGM and the AmpliSeq Cancer Hotspot Panel v2. We tested 453 NSCLC samples from 407 individual patients using the 50 gene AmpliSeq Cancer Hotspot Panel v2 from May 2013 to July 2015. Using 10 ng of DNA, up to 11 samples were simultaneously sequenced on the Ion Torrent PGM (316 and 318 chips. We identified variants with the Ion Torrent Variant Caller Plugin, and Golden Helix's SVS software was used for annotation and prediction of the significance of the variants. Three hundred ninety-eight samples were successfully sequenced (12.1% failure rate. In all, 633 variants in 41 genes were detected with a median of 2 (range of 0 to 7 variants per sample. Mutations detected in BRAF, EGFR, ERBB2, KRAS, NRAS, and PIK3CA were considered potentially actionable and were identified in 237 samples, most commonly in KRAS (37.9%, EGFR (11.1%, BRAF (4.8%, and PIK3CA (4.3%. In our patient population, all mutations in EGFR, KRAS, and BRAF were mutually exclusive. The Ion Torrent Ampliseq technology can be utilized on small biopsy and cytology specimens, requires very little input DNA, and can be applied in clinical laboratories for genotyping of NSCLC. This targeted next-generation sequencing approach allows for detection of common and also rare mutations that are clinically actionable in multiple patients simultaneously.

  6. The drivers of plant diversity

    DEFF Research Database (Denmark)

    Jensen, Kristine Engemann

    In this thesis we use a “big data” approach to describe and explain large-scale patterns of plant diversity. The botanical data used for the six papers come from three different databases covering the New World, North America, and Europe respectively. The data on plant distributions were combined...... and beta diversity over time for woody forest communities in North America, using a 20 year forest plot dataset from the United States Department of Agriculture Forest Inventory and Analysis program. To assess functional diversity, we combined the plot data with data on four functional traits. Over time...... with environmental data on climate, soil, topography, and disturbance to identify the drivers of macroecological plant diversity patterns. Unless otherwise stated, the botanical data used in the papers come from the Botanical Information and Ecology Network. Paper I describes how we compiled a new plant growth form...

  7. POLITICAL PROCESS DRIVERS OF CORRUPTION IN EASTERN EUROPE

    Directory of Open Access Journals (Sweden)

    Ada-Iuliana POPESCU

    2016-12-01

    Full Text Available Corruption stands as one of the many obstacles to the political and economic security of the Eastern European region. Thus, despite the political and economic instability in the region, Eastern European countries, in and outside of the European Union need to fight corruption collectively and individually. The task is difficult, but hope is justified because the causes of corruption in this part of the region are similar and anti-corruption expertise is available. We believe that a deeper analysis of corruption’s drivers can produce a better articulated and more efficient anti-corruption strategy. This strategy will create an anti-corruption infrastructure that will strengthen the Eastern European Partnership. As a prelude to the deeper analysis that we believe must be a part of this strategy, this paper identifies the main drivers of corruption in the Eastern European Partnership countries and explains why addressing these drivers will strengthen the Eastern European Partnership.

  8. Services Acquisition in the Department of Defense: Analysis of Operational and Performance Data to Identify Drivers of Success

    Science.gov (United States)

    2015-03-24

    including quality, schedule, cost control, business relations, management of key personnel, and utilization of small business . The “Quality” rating assesses...individuals in key positions as outlined in the contract. The “Utilization of Small Business ” rating assesses the contractor’s ability to integrate small ...contract failure included business relations and management of key personnel (Wilhite et al., 2013). • Contracts with a dollar value from $50

  9. Development of a statistical model to identify spatial and meteorological drivers of elevated O3 in Nevada and its application to other rural mountainous regions.

    Science.gov (United States)

    Fine, Rebekka; Miller, Matthieu B; Gustin, Mae Sexauer

    2015-10-15

    Measurements of O3 at relatively remote monitoring sites are useful for quantifying baseline O3, and subsequently the magnitude of O3 not controllable by local regulations. As the National Ambient Air Quality Standard (NAAQS) for O3 becomes more stringent, there is an increased need to quantify baseline O3 particularly in the Western US, where regional and global sources can significantly enhance O3 measured at surface sites, yielding baseline mixing ratios approaching or exceeding the NAAQS threshold. Past work has indicated that meteorological conditions as well as site specific spatial characteristics (e.g. elevation, basin size, gradient) are significantly correlated with O3 intercepted at rural monitoring sites. Here, we use 3 years of measurements from sites throughout rural Nevada to develop a categorical tree model to identify spatial and meteorological characteristics that are associated with elevated baseline O3. Data from other sites in the Intermountain Western US are used to test the applicability of the model for sites throughout the region. Our analyses indicate that increased elevation and basin size were associated with increased frequency of elevated O3. On a daily time scale, relative humidity had the strongest association with observed MDA8 O3. Seventy-four percent of MDA8 O3 observations>60 ppbv occurred when daily minimum relative humidity was 60 ppbv whereas including upper air meteorological measurements improved the accuracy of predicting periods when O3 was >60 ppbv. These findings indicate that transport, rather than local production, influences O3 measurements in Nevada, and that high elevation sites in rural Nevada, are representative of baseline conditions in the Intermountain Western US.

  10. Identifying Drivers of Collective Action for the Co-management of Coastal Marine Fisheries in the Gulf of Nicoya, Costa Rica

    Science.gov (United States)

    García Lozano, Alejandro J.; Heinen, Joel T.

    2016-04-01

    Small-scale fisheries are important for preventing poverty, sustaining local economies, and rural livelihoods, but tend to be negatively impacted by traditional forms of management and overexploitation among other factors. Marine Areas for Responsible Fishing (Áreas Marinas de Pesca Responsable, AMPR) have emerged as a new model for the co-management of small-scale fisheries in Costa Rica, one that involves collaboration between fishers, government agencies, and NGOs. The primary objective of this paper is to elucidate some of the key variables that influence collective action among small-scale fishers in Tárcoles, a community in the Gulf of Nicoya. We examined collective action for the formation of a local marketing cooperative and participation in management through the AMPR. We apply the social-ecological framework as a diagnostic and organizational tool in the analysis of several types of qualitative data, including interviews with key informants, informal interviews, legal documents, and gray literature. Findings illustrate the importance of socio-economic community attributes (e.g., group size, homogeneity, previous cooperation), as well as that of social (e.g., equity) and ecological (e.g., improved stocks) outcomes perceived as favorable by actors. In addition, our work demonstrates the importance of certain kinds of external NGOs for facilitating and sustaining collective action.

  11. Identifying Drivers of Collective Action for the Co-management of Coastal Marine Fisheries in the Gulf of Nicoya, Costa Rica.

    Science.gov (United States)

    García Lozano, Alejandro J; Heinen, Joel T

    2016-04-01

    Small-scale fisheries are important for preventing poverty, sustaining local economies, and rural livelihoods, but tend to be negatively impacted by traditional forms of management and overexploitation among other factors. Marine Areas for Responsible Fishing (Áreas Marinas de Pesca Responsable, AMPR) have emerged as a new model for the co-management of small-scale fisheries in Costa Rica, one that involves collaboration between fishers, government agencies, and NGOs. The primary objective of this paper is to elucidate some of the key variables that influence collective action among small-scale fishers in Tárcoles, a community in the Gulf of Nicoya. We examined collective action for the formation of a local marketing cooperative and participation in management through the AMPR. We apply the social-ecological framework as a diagnostic and organizational tool in the analysis of several types of qualitative data, including interviews with key informants, informal interviews, legal documents, and gray literature. Findings illustrate the importance of socio-economic community attributes (e.g., group size, homogeneity, previous cooperation), as well as that of social (e.g., equity) and ecological (e.g., improved stocks) outcomes perceived as favorable by actors. In addition, our work demonstrates the importance of certain kinds of external NGOs for facilitating and sustaining collective action.

  12. Automobile Driver Fingerprinting

    Directory of Open Access Journals (Sweden)

    Enev Miro

    2016-01-01

    Full Text Available Today’s automobiles leverage powerful sensors and embedded computers to optimize efficiency, safety, and driver engagement. However the complexity of possible inferences using in-car sensor data is not well understood. While we do not know of attempts by automotive manufacturers or makers of after-market components (like insurance dongles to violate privacy, a key question we ask is: could they (or their collection and later accidental leaks of data violate a driver’s privacy? In the present study, we experimentally investigate the potential to identify individuals using sensor data snippets of their natural driving behavior. More specifically we record the in-vehicle sensor data on the controllerarea- network (CAN of a typical modern vehicle (popular 2009 sedan as each of 15 participants (a performed a series of maneuvers in an isolated parking lot, and (b drove the vehicle in traffic along a defined ~ 50 mile loop through the Seattle metropolitan area. We then split the data into training and testing sets, train an ensemble of classifiers, and evaluate identification accuracy of test data queries by looking at the highest voted candidate when considering all possible one-vs-one comparisons. Our results indicate that, at least among small sets, drivers are indeed distinguishable using only incar sensors. In particular, we find that it is possible to differentiate our 15 drivers with 100% accuracy when training with all of the available sensors using 90% of driving data from each person. Furthermore, it is possible to reach high identification rates using less than 8 minutes of training data. When more training data is available it is possible to reach very high identification using only a single sensor (e.g., the brake pedal. As an extension, we also demonstrate the feasibility of performing driver identification across multiple days of data collection

  13. Use of Photogrammetry and Biomechanical Gait analysis to Identify Individuals

    DEFF Research Database (Denmark)

    Larsen, Peter Kastmand; Simonsen, Erik Bruun; Lynnerup, Niels

    Photogrammetry and recognition of gait patterns are valuable tools to help identify perpetrators based on surveillance recordings. We have found that stature but only few other measures have a satisfying reproducibility for use in forensics. Several gait variables with high recognition rates were...

  14. Similarity transformation approach to identifiability analysis of nonlinear compartmental models.

    Science.gov (United States)

    Vajda, S; Godfrey, K R; Rabitz, H

    1989-04-01

    Through use of the local state isomorphism theorem instead of the algebraic equivalence theorem of linear systems theory, the similarity transformation approach is extended to nonlinear models, resulting in finitely verifiable sufficient and necessary conditions for global and local identifiability. The approach requires testing of certain controllability and observability conditions, but in many practical examples these conditions prove very easy to verify. In principle the method also involves nonlinear state variable transformations, but in all of the examples presented in the paper the transformations turn out to be linear. The method is applied to an unidentifiable nonlinear model and a locally identifiable nonlinear model, and these are the first nonlinear models other than bilinear models where the reason for lack of global identifiability is nontrivial. The method is also applied to two models with Michaelis-Menten elimination kinetics, both of considerable importance in pharmacokinetics, and for both of which the complicated nature of the algebraic equations arising from the Taylor series approach has hitherto defeated attempts to establish identifiability results for specific input functions.

  15. Identifying failure mechanisms in LDMOS transistors by analytical stability analysis

    NARCIS (Netherlands)

    Ferrara, A.; Steeneken, P.G.; Boksteen, B.K.; Heringa, A.; Scholten, A.J.; Schmitz, J.; Hueting, R.J.E.

    2014-01-01

    In this work, analytical stability equations are derived and combined with a physics-based model of an LDMOS transistor in order to identify the primary cause of failure in different operating and bias conditions. It is found that there is a gradual boundary between an electrical failure region at h

  16. Detailed profiling of anti-desmoglein autoantibodies identifies anti-Dsg1 reactivity as a key driver of disease activity and clinical expression in pemphigus vulgaris.

    Science.gov (United States)

    Naseer, S Y; Seiffert-Sinha, K; Sinha, A A

    2015-06-01

    With their near-universal presence in patients and ease of clinical measurement, anti-desmoglein (Dsg) antibodies serve as primary candidates for creating prognostic tools in Pemphigus vulgaris (PV). Although the desmoglein compensation hypothesis postulates a clear relationship between anti-Dsg autoantibodies and clinical phenotype in PV, recent studies have questioned the fidelity of this hypothesis as a predictor of lesion morphology. Moreover, few studies address the association of anti-Dsg antibodies to other clinical parameters such as disease phase and age at onset. Using the largest patient repository to date in PV, we present a detailed analysis of anti-desmoglein antibody profiles across a comprehensive range of dynamic (disease phase, therapy, lesion morphology) and temporal (disease duration, age at sampling, age at onset) clinical parameters. Our data highlight the non-traditional but key role of anti-Dsg1 levels in tracking disease activity. We show that declining anti-Dsg1 levels may predict progression from active phase to early remission and long-term maintenance of remission, regardless of lesion morphology. In contrast, many remittent patients have elevated levels of anti-Dsg3 without lesional activity. Furthermore, we describe a unique subset of remittent patients that develop chronic transient lesions (lasting <1 week) in the setting of elevated anti-Dsg3 levels but do not meet the consensus criteria for active phase. Re-classification of patients with transient lesions as "active" may shed new light on pathophysiological processes underlying cycles of blister formation and rapid spontaneous healing in PV. Additionally, we provide evidence for the potential attenuation of the immune response with prolonged disease duration. Our data fit into the broader effort of immunoprofiling to promote data-informed decision-making regarding diagnosis, prognosis and treatment of complex diseases.

  17. Identifying news clusters using Q-analysis and modularity

    OpenAIRE

    2013-01-01

    With online publication and social media taking the main role in dissemination of news, and with the decline of traditional printed media, it has become necessary to devise ways to automatically extract meaningful information from the plethora of sources available and to make that information readily available to interested parties. In this paper we present a method of automated analysis of the underlying structure of online newspapers based on Q-analysis and modularity. We show how the combi...

  18. A multiway analysis for identifying high integrity bovine BACs

    OpenAIRE

    McEwan John C; Brauning Rudiger; McWilliam Sean; Barris Wesley; Ratnakumar Abhirami; Snelling Warren M; Dalrymple Brian P

    2009-01-01

    Abstract Background In large genomics projects involving many different types of analyses of bacterial artificial chromosomes (BACs), such as fingerprinting, end sequencing (BES) and full BAC sequencing there are many opportunities for the identities of BACs to become confused. However, by comparing the results from the different analyses, inconsistencies can be identified and a set of high integrity BACs preferred for future research can be defined. Results The location of each bovine BAC in...

  19. Identifiability analysis of the CSTR river water quality model.

    Science.gov (United States)

    Chen, J; Deng, Y

    2006-01-01

    Conceptual river water quality models are widely known to lack identifiability. The causes for that can be due to model structure errors, observational errors and less frequent samplings. Although significant efforts have been directed towards better identification of river water quality models, it is not clear whether a given model is structurally identifiable. Information is also limited regarding the contribution of different unidentifiability sources. Taking the widely applied CSTR river water quality model as an example, this paper presents a theoretical proof that the CSTR model is indeed structurally identifiable. Its uncertainty is thus dominantly from observational errors and less frequent samplings. Given the current monitoring accuracy and sampling frequency, the unidentifiability from sampling frequency is found to be more significant than that from observational errors. It is also noted that there is a crucial sampling frequency between 0.1 and 1 day, over which the simulated river system could be represented by different illusions and the model application could be far less reliable.

  20. Using Factor Analysis to Identify Topic Preferences Within MBA Courses

    Directory of Open Access Journals (Sweden)

    Earl Chrysler

    2003-02-01

    Full Text Available This study demonstrates the role of a principal components factor analysis in conducting a gap analysis as to the desired characteristics of business alumni. Typically, gap analyses merely compare the emphases that should be given to areas of inquiry with perceptions of actual emphases. As a result, the focus is upon depth of coverage. A neglected area in need of investigation is the breadth of topic dimensions and their differences between the normative (should offer and the descriptive (actually offer. The implications of factor structures, as well as traditional gap analyses, are developed and discussed in the context of outcomes assessment.

  1. Identifying Effective Psychological Treatments of Insomnia: A Meta-Analysis.

    Science.gov (United States)

    Murtagh, Douglas R. R.; Greenwood, Kenneth M.

    1995-01-01

    Clarified efficacy of psychological treatments for insomnia through a meta-analysis of 66 outcome studies representing 139 treatment groups. Psychological treatments produced considerable enhancement of both sleep patterns and the subjective experience of sleep. Participants who were clinically referred and who did not regularly use sedatives…

  2. Using Rasch Analysis to Identify Uncharacteristic Responses to Undergraduate Assessments

    Science.gov (United States)

    Edwards, Antony; Alcock, Lara

    2010-01-01

    Rasch Analysis is a statistical technique that is commonly used to analyse both test data and Likert survey data, to construct and evaluate question item banks, and to evaluate change in longitudinal studies. In this article, we introduce the dichotomous Rasch model, briefly discussing its assumptions. Then, using data collected in an…

  3. Driver style and driver skill – Clustering sub-groups of drivers differing in their potential danger in traffic

    DEFF Research Database (Denmark)

    Martinussen, Laila Marianne; Møller, Mette; Prato, Carlo Giacomo

    The Driver Behavior Questionnaire (DBQ) and the Driver Skill Inventory (DSI) are two of the most frequently used measures of self-reported driving style and driving skill. The motivation behind the present study was to test drivers’ consistency or judgment of their own self-reported driving ability...... based on a combined use of the DBQ and the DSI. Moreover, the joint use of the two instruments was applied to identify sub-groups of drivers that differ in their potential danger in traffic (as measured by frequency of aberrant driving behaviors and level of driving skills), as well as to test whether...... the sub-groups of drivers differed in characteristics such as age, gender, annual mileage and accident involvement. 3908 drivers aged 18–84 participated in the survey. The results suggested that the drivers are consistent in their reporting of driving ability, as the self-reported driving skill level...

  4. Statistical analysis of road-vehicle-driver interaction as an enabler to designing behavioural models

    Science.gov (United States)

    Chakravarty, T.; Chowdhury, A.; Ghose, A.; Bhaumik, C.; Balamuralidhar, P.

    2014-03-01

    Telematics form an important technology enabler for intelligent transportation systems. By deploying on-board diagnostic devices, the signatures of vehicle vibration along with its location and time are recorded. Detailed analyses of the collected signatures offer deep insights into the state of the objects under study. Towards that objective, we carried out experiments by deploying telematics device in one of the office bus that ferries employees to office and back. Data is being collected from 3-axis accelerometer, GPS, speed and the time for all the journeys. In this paper, we present initial results of the above exercise by applying statistical methods to derive information through systematic analysis of the data collected over four months. It is demonstrated that the higher order derivative of the measured Z axis acceleration samples display the properties Weibull distribution when the time axis is replaced by the amplitude of such processed acceleration data. Such an observation offers us a method to predict future behaviour where deviations from prediction are classified as context-based aberrations or progressive degradation of the system. In addition we capture the relationship between speed of the vehicle and median of the jerk energy samples using regression analysis. Such results offer an opportunity to develop a robust method to model road-vehicle interaction thereby enabling us to predict such like driving behaviour and condition based maintenance etc.

  5. Key drivers of airline loyalty.

    Science.gov (United States)

    Dolnicar, Sara; Grabler, Klaus; Grün, Bettina; Kulnig, Anna

    2011-10-01

    This study investigates drivers of airline loyalty. It contributes to the body of knowledge in the area by investigating loyalty for a number of a priori market segments identified by airline management and by using a method which accounts for the multi-step nature of the airline choice process. The study is based on responses from 687 passengers. Results indicate that, at aggregate level, frequent flyer membership, price, the status of being a national carrier and the reputation of the airline as perceived by friends are the variables which best discriminate between travellers loyal to the airline and those who are not. Differences in drivers of airline loyalty for a number of segments were identified. For example, loyalty programs play a key role for business travellers whereas airline loyalty of leisure travellers is difficult to trace back to single factors. For none of the calculated models satisfaction emerged as a key driver of airline loyalty.

  6. Key drivers of airline loyalty

    Science.gov (United States)

    Dolnicar, Sara; Grabler, Klaus; Grün, Bettina; Kulnig, Anna

    2011-01-01

    This study investigates drivers of airline loyalty. It contributes to the body of knowledge in the area by investigating loyalty for a number of a priori market segments identified by airline management and by using a method which accounts for the multi-step nature of the airline choice process. The study is based on responses from 687 passengers. Results indicate that, at aggregate level, frequent flyer membership, price, the status of being a national carrier and the reputation of the airline as perceived by friends are the variables which best discriminate between travellers loyal to the airline and those who are not. Differences in drivers of airline loyalty for a number of segments were identified. For example, loyalty programs play a key role for business travellers whereas airline loyalty of leisure travellers is difficult to trace back to single factors. For none of the calculated models satisfaction emerged as a key driver of airline loyalty. PMID:27064618

  7. Temperature-based Instanton Analysis: Identifying Vulnerability in Transmission Networks

    Energy Technology Data Exchange (ETDEWEB)

    Kersulis, Jonas [Univ. of Michigan, Ann Arbor, MI (United States); Hiskens, Ian [Univ. of Michigan, Ann Arbor, MI (United States); Chertkov, Michael [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Backhaus, Scott N. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Bienstock, Daniel [Columbia Univ., New York, NY (United States)

    2015-04-08

    A time-coupled instanton method for characterizing transmission network vulnerability to wind generation fluctuation is presented. To extend prior instanton work to multiple-time-step analysis, line constraints are specified in terms of temperature rather than current. An optimization formulation is developed to express the minimum wind forecast deviation such that at least one line is driven to its thermal limit. Results are shown for an IEEE RTS-96 system with several wind-farms.

  8. Using Failure Mode and Effects Analysis to design a comfortable automotive driver seat.

    Science.gov (United States)

    Kolich, Mike

    2014-07-01

    Given enough time and use, all designs will fail. There are no fail-free designs. This is especially true when it comes to automotive seating comfort where the characteristics and preferences of individual customers are many and varied. To address this problem, individuals charged with automotive seating comfort development have, traditionally, relied on iterative and, as a result, expensive build-test cycles. Cost pressures being placed on today's vehicle manufacturers have necessitated the search for more efficient alternatives. This contribution aims to fill this need by proposing the application of an analytical technique common to engineering circles (but new to seating comfort development), namely Design Failure Mode and Effects Analysis (DFMEA). An example is offered to describe how development teams can use this systematic and disciplined approach to highlight potential seating comfort failure modes, reduce their risk, and bring capable designs to life.

  9. Drivers of cycling mode-share: analysis of danes travel behavior 1996-2013

    DEFF Research Database (Denmark)

    Nielsen, Thomas Alexander Sick; Mulalic, Ismir; Christiansen, Hjalmar

    2016-01-01

    Denmark, as Europes second cycling nation after the Netherlands, has a cycling mode share of around 15% of all trips. Cycling was decreasing slowly through the 1990s into the 2000s, which inspired substantial investments and promotional efforts to reverse the trend. This paper uses Danish micro-l...... peripheral areas is growing. Other changes include a decreasing `income divide' in cycling as well as a decreasing retirement effect. Results are presented and discussed. (C) 2016 Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license.......-level travel survey data series from 1996 through 2013 to analyze the trend in cycling as main or access mode, as well as the significance of background variables representing key spatial and societal trends. The analysis confirms that the general trend in cycling from 1996 to 2013 was negative irrespective...

  10. Compartmental analysis of dynamic nuclear medicine data: models and identifiability

    Science.gov (United States)

    Delbary, Fabrice; Garbarino, Sara; Vivaldi, Valentina

    2016-12-01

    Compartmental models based on tracer mass balance are extensively used in clinical and pre-clinical nuclear medicine in order to obtain quantitative information on tracer metabolism in the biological tissue. This paper is the first of a series of two that deal with the problem of tracer coefficient estimation via compartmental modelling in an inverse problem framework. Specifically, here we discuss the identifiability problem for a general n-dimension compartmental system and provide uniqueness results in the case of two-compartment and three-compartment compartmental models. The second paper will utilize this framework in order to show how nonlinear regularization schemes can be applied to obtain numerical estimates of the tracer coefficients in the case of nuclear medicine data corresponding to brain, liver and kidney physiology.

  11. Drivers of Vaginal Drug Delivery System Acceptability from Internet-Based Conjoint Analysis.

    Science.gov (United States)

    Primrose, Rachel J; Zaveri, Toral; Bakke, Alyssa J; Ziegler, Gregory R; Moskowitz, Howard R; Hayes, John E

    2016-01-01

    Vaginal microbicides potentially empower women to protect themselves from HIV and other sexually transmitted infections (STIs), especially when culture, religion, or social status may prevent them from negotiating condom use. The open literature contains minimal information on factors that drive user acceptability of women's health products or vaginal drug delivery systems. By understanding what women find to be most important with regard to sensory properties and product functionality, developers can iteratively formulate a more desirable product. Conjoint analysis is a technique widely used in market research to determine what combination of elements influence a consumer's willingness to try or use a product. We applied conjoint analysis here to better understand what sexually-active woman want in a microbicide, toward our goal of formulating a product that is highly acceptable to women. Both sensory and non-sensory attributes were tested, including shape, color, wait time, partner awareness, messiness/leakage, duration of protection, and functionality. Heterosexually active women between 18 and 35 years of age in the United States (n = 302) completed an anonymous online conjoint survey using IdeaMap software. Attributes (product elements) were systematically presented in various combinations; women rated these combinations of a 9-point willingness-to-try scale. By coupling systematic combinations and regression modeling, we can estimate the unique appeal of each element. In this population, a multifunctional product (i.e., broad spectrum STI protection, coupled with conception) is far more desirable than a microbicide targeted solely for HIV protection; we also found partner awareness and leakage are potentially strong barriers to use.

  12. Drivers of Vaginal Drug Delivery System Acceptability from Internet-Based Conjoint Analysis.

    Directory of Open Access Journals (Sweden)

    Rachel J Primrose

    Full Text Available Vaginal microbicides potentially empower women to protect themselves from HIV and other sexually transmitted infections (STIs, especially when culture, religion, or social status may prevent them from negotiating condom use. The open literature contains minimal information on factors that drive user acceptability of women's health products or vaginal drug delivery systems. By understanding what women find to be most important with regard to sensory properties and product functionality, developers can iteratively formulate a more desirable product. Conjoint analysis is a technique widely used in market research to determine what combination of elements influence a consumer's willingness to try or use a product. We applied conjoint analysis here to better understand what sexually-active woman want in a microbicide, toward our goal of formulating a product that is highly acceptable to women. Both sensory and non-sensory attributes were tested, including shape, color, wait time, partner awareness, messiness/leakage, duration of protection, and functionality. Heterosexually active women between 18 and 35 years of age in the United States (n = 302 completed an anonymous online conjoint survey using IdeaMap software. Attributes (product elements were systematically presented in various combinations; women rated these combinations of a 9-point willingness-to-try scale. By coupling systematic combinations and regression modeling, we can estimate the unique appeal of each element. In this population, a multifunctional product (i.e., broad spectrum STI protection, coupled with conception is far more desirable than a microbicide targeted solely for HIV protection; we also found partner awareness and leakage are potentially strong barriers to use.

  13. Drivers of Vaginal Drug Delivery System Acceptability from Internet-Based Conjoint Analysis

    Science.gov (United States)

    Primrose, Rachel J.; Zaveri, Toral; Bakke, Alyssa J.; Ziegler, Gregory R.; Moskowitz, Howard R.; Hayes, John E.

    2016-01-01

    Vaginal microbicides potentially empower women to protect themselves from HIV and other sexually transmitted infections (STIs), especially when culture, religion, or social status may prevent them from negotiating condom use. The open literature contains minimal information on factors that drive user acceptability of women’s health products or vaginal drug delivery systems. By understanding what women find to be most important with regard to sensory properties and product functionality, developers can iteratively formulate a more desirable product. Conjoint analysis is a technique widely used in market research to determine what combination of elements influence a consumer’s willingness to try or use a product. We applied conjoint analysis here to better understand what sexually-active woman want in a microbicide, toward our goal of formulating a product that is highly acceptable to women. Both sensory and non-sensory attributes were tested, including shape, color, wait time, partner awareness, messiness/leakage, duration of protection, and functionality. Heterosexually active women between 18 and 35 years of age in the United States (n = 302) completed an anonymous online conjoint survey using IdeaMap software. Attributes (product elements) were systematically presented in various combinations; women rated these combinations of a 9-point willingness-to-try scale. By coupling systematic combinations and regression modeling, we can estimate the unique appeal of each element. In this population, a multifunctional product (i.e., broad spectrum STI protection, coupled with conception) is far more desirable than a microbicide targeted solely for HIV protection; we also found partner awareness and leakage are potentially strong barriers to use. PMID:26999009

  14. Design of an Integrated Vehicle Chassis Control System with Driver Behavior Identification

    OpenAIRE

    Bing Zhu; Yizhou Chen; Jian Zhao; Yunfu Su

    2015-01-01

    An integrated vehicle chassis control strategy with driver behavior identification is introduced in this paper. In order to identify the different types of driver behavior characteristics, a driver behavior signals acquisition system was established using the dSPACE real-time simulation platform, and the driver inputs of 30 test drivers were collected under the double lane change test condition. Then, driver behavior characteristics were analyzed and identified based on the preview optimal cu...

  15. Factors associated with falling asleep at the wheel among long-distance truck drivers.

    Science.gov (United States)

    McCartt, A T; Rohrbaugh, J W; Hammer, M C; Fuller, S Z

    2000-07-01

    Data on the prevalence and hypothesized predictors of falling asleep while driving were gathered through face-to-face interviews with 593 long-distance truck drivers randomly selected at public and private rest areas and routine roadside truck safety inspections. Hypothesized predictor variables related to drivers' typical work and rest patterns, extent of daytime and night-time drowsiness, symptoms of sleep disorder, measures of driving exposure, and demographic characteristics. A sizeable proportion of long-distance truck drivers reported falling asleep at the wheel of the truck: 47.1% of the survey respondents had ever fallen asleep at the wheel of a truck, and 25.4% had fallen asleep at the wheel in the past year. Factor analysis reduced the large set of predictors to six underlying, independent factors: greater daytime sleepiness; more arduous schedules, with more hours of work and fewer hours off-duty; older, more experienced drivers; shorter, poorer sleep on road; symptoms of sleep disorder; and greater tendency to night-time drowsy driving. Based on multivariate logistic regression, all six factors were predictive of self-reported falling asleep at the wheel. Falling asleep was also associated with not having been alerted by driving over shoulder rumble strips. The results suggest that countermeasures that limit drivers' work hours and enable drivers to get adequate rest and that identify drivers with sleep disorders are appropriate methods to reduce sleepiness-related driving by truck drivers.

  16. Reliability and Availability Studies in the RIA Linac Driver

    CERN Document Server

    Schnirman-Lessner, Eliane

    2005-01-01

    The RIA facility will include various complex systems and must provide radioactive beams to many users simultaneously. The availability of radioactive beams for most experiments at the fully-commissioned facility should be as high as possible within design cost limitations. To make a realistic estimate of the achievable reliability a detailed analysis is required. The RIA driver linac is a complex machine containing a large number of SC resonators and capable of accelerating multiple-charge-state beams. At the pre-CDR stage of the design it is essential to identify critical facility subsystem failures that can prevent the driver linac from operating. The reliability and availability of the driver linac are studied using expert information and data from operating machines such as ATLAS, APS, JLab, and LANL. Availability studies are performed with a Monte-Carlo simulation code previously applied to availability assessments of the NLC facility [http://www.slac.stanford.edu/xorg/accelops/Full/LCoptsfull] and the ...

  17. Driver models for personalised driving assistance

    Science.gov (United States)

    Lefèvre, Stéphanie; Carvalho, Ashwin; Gao, Yiqi; Tseng, H. Eric; Borrelli, Francesco

    2015-12-01

    We propose a learning-based driver modelling approach which can identify manoeuvres performed by drivers on the highway and predict the future driver inputs. We show how this approach can be applied to provide personalised driving assistance. In a first example, the driver model is used to predict unintentional lane departures and a model predictive controller is used to keep the car in the lane. In a second example, the driver model estimates the preferred acceleration of the driver during lane keeping, and a model predictive controller is implemented to provide a personalised adaptive cruise control. For both applications, we use a combination of real data and simulation to evaluate the proposed approaches.

  18. The psychology of intelligence analysis: drivers of prediction accuracy in world politics.

    Science.gov (United States)

    Mellers, Barbara; Stone, Eric; Atanasov, Pavel; Rohrbaugh, Nick; Metz, S Emlen; Ungar, Lyle; Bishop, Michael M; Horowitz, Michael; Merkle, Ed; Tetlock, Philip

    2015-03-01

    This article extends psychological methods and concepts into a domain that is as profoundly consequential as it is poorly understood: intelligence analysis. We report findings from a geopolitical forecasting tournament that assessed the accuracy of more than 150,000 forecasts of 743 participants on 199 events occurring over 2 years. Participants were above average in intelligence and political knowledge relative to the general population. Individual differences in performance emerged, and forecasting skills were surprisingly consistent over time. Key predictors were (a) dispositional variables of cognitive ability, political knowledge, and open-mindedness; (b) situational variables of training in probabilistic reasoning and participation in collaborative teams that shared information and discussed rationales (Mellers, Ungar, et al., 2014); and (c) behavioral variables of deliberation time and frequency of belief updating. We developed a profile of the best forecasters; they were better at inductive reasoning, pattern detection, cognitive flexibility, and open-mindedness. They had greater understanding of geopolitics, training in probabilistic reasoning, and opportunities to succeed in cognitively enriched team environments. Last but not least, they viewed forecasting as a skill that required deliberate practice, sustained effort, and constant monitoring of current affairs.

  19. Intelligent Speed Adaptation for involuntary drivers

    DEFF Research Database (Denmark)

    Agerholm, Niels; Tradisauskas, Nerius; Juhl, Jens

    2012-01-01

    The Danish Intelligent Speed Adaptation (ISA) trial ISA C included 26 commercial cars and 51 drivers a number of whom were involuntary. After a baseline period, ISA was activated for one year. The drivers should identify themselves with a personal key ID before driving. As well as being informative...

  20. Physics at an upgraded Fermilab proton driver

    Energy Technology Data Exchange (ETDEWEB)

    Geer, S.; /Fermilab

    2005-07-01

    In 2004 the Fermilab Long Range Planning Committee identified a new high intensity Proton Driver as an attractive option for the future, primarily motivated by the recent exciting developments in neutrino physics. Over the last few months a physics study has developed the physics case for the Fermilab Proton Driver. The potential physics opportunities are discussed.

  1. Reducing risky driver behaviour through the implementation of a driver risk management system

    Directory of Open Access Journals (Sweden)

    Rose Luke

    2014-03-01

    Full Text Available South Africa has one of the highest incidences of road accidents in the world. Most accidents are avoidable and are caused by driver behaviour and errors. The purpose of this article was to identify the riskiest driver behaviours in commercial fleets in South Africa, to determine the business impact of such behaviour, to establish a framework for the management of risky driver behaviour and to test the framework by applying a leading commercial driver behaviour management system as a case study. The case study comprised three South African commercial fleets. Using data from these fleets, critical incident triangles were used to determine the ratio data of risky driver behaviour to near-collisions and collisions. Based on managing the riskiest driver behaviours as causes of more serious incidents and accidents, the results indicated that through the implementation of an effective driver risk management system, risky incidents were significantly reduced.

  2. Meconium microbiome analysis identifies bacteria correlated with premature birth.

    Directory of Open Access Journals (Sweden)

    Alexandria N Ardissone

    Full Text Available Preterm birth is the second leading cause of death in children under the age of five years worldwide, but the etiology of many cases remains enigmatic. The dogma that the fetus resides in a sterile environment is being challenged by recent findings and the question has arisen whether microbes that colonize the fetus may be related to preterm birth. It has been posited that meconium reflects the in-utero microbial environment. In this study, correlations between fetal intestinal bacteria from meconium and gestational age were examined in order to suggest underlying mechanisms that may contribute to preterm birth.Meconium from 52 infants ranging in gestational age from 23 to 41 weeks was collected, the DNA extracted, and 16S rRNA analysis performed. Resulting taxa of microbes were correlated to clinical variables and also compared to previous studies of amniotic fluid and other human microbiome niches.Increased detection of bacterial 16S rRNA in meconium of infants of <33 weeks gestational age was observed. Approximately 61·1% of reads sequenced were classified to genera that have been reported in amniotic fluid. Gestational age had the largest influence on microbial community structure (R = 0·161; p = 0·029, while mode of delivery (C-section versus vaginal delivery had an effect as well (R = 0·100; p = 0·044. Enterobacter, Enterococcus, Lactobacillus, Photorhabdus, and Tannerella, were negatively correlated with gestational age and have been reported to incite inflammatory responses, suggesting a causative role in premature birth.This provides the first evidence to support the hypothesis that the fetal intestinal microbiome derived from swallowed amniotic fluid may be involved in the inflammatory response that leads to premature birth.

  3. Key drivers for market penetration of biosimilars in Europe

    Science.gov (United States)

    Rémuzat, Cécile; Dorey, Julie; Cristeau, Olivier; Ionescu, Dan; Radière, Guerric; Toumi, Mondher

    2017-01-01

    ABSTRACT Background & Objectives: Potential drivers and barriers of biosimilar uptake were mainly analysed through qualitative approaches. The study objective was to conduct a quantitative analysis and identify drivers of biosimilar uptake of all available biosimilars in the European Union (EU). Methods: A three-step process was established to identify key drivers for the uptake of biosimilars in the top 10 EU member states (MS) pharmaceutical markets (Belgium, France, Germany, Greece, Hungary, Italy, Poland, Spain, Sweden, and the UK): (1) literature review to identify incentive policies in place to enhance biosimilars adoption; (2) assessment of biosimilar market dynamics based on database analysis; (3) regression model analysis on price using the following explicative variables: incentive policies; price difference between the biosimilar and the originator product; distribution channel; generic uptake and generic price cut; pharmaceutical expenditure per capita; and market competition. Results: At the study cut-off date, 20 biosimilars were available on the market. Incentive policies applied to biosimilars were found to be heterogeneous across countries, and uptakes of biosimilars were also very heterogeneous between different therapeutic classes and countries. Results from the model demonstrated that incentive policies and the date of first biosimilar market entry were correlated to biosimilar uptake. Pharmaceutical expenditure per capita and the highest generic uptake were inversely correlated with biosimilar uptake. Average generic price discount over originator and the number of biosimilars showed a trend toward statistical significance for correlation with biosimilar uptake, but did not reach the significance threshold. Biosimilar price discount over original biologic price, the number of analogues, and the distribution channel were not correlated with the biosimilar uptake. Conclusions: Understanding drivers of biosimilar uptake becomes a critical issue to

  4. Key drivers for market penetration of biosimilars in Europe.

    Science.gov (United States)

    Rémuzat, Cécile; Dorey, Julie; Cristeau, Olivier; Ionescu, Dan; Radière, Guerric; Toumi, Mondher

    2017-01-01

    Background & Objectives: Potential drivers and barriers of biosimilar uptake were mainly analysed through qualitative approaches. The study objective was to conduct a quantitative analysis and identify drivers of biosimilar uptake of all available biosimilars in the European Union (EU). Methods: A three-step process was established to identify key drivers for the uptake of biosimilars in the top 10 EU member states (MS) pharmaceutical markets (Belgium, France, Germany, Greece, Hungary, Italy, Poland, Spain, Sweden, and the UK): (1) literature review to identify incentive policies in place to enhance biosimilars adoption; (2) assessment of biosimilar market dynamics based on database analysis; (3) regression model analysis on price using the following explicative variables: incentive policies; price difference between the biosimilar and the originator product; distribution channel; generic uptake and generic price cut; pharmaceutical expenditure per capita; and market competition. Results: At the study cut-off date, 20 biosimilars were available on the market. Incentive policies applied to biosimilars were found to be heterogeneous across countries, and uptakes of biosimilars were also very heterogeneous between different therapeutic classes and countries. Results from the model demonstrated that incentive policies and the date of first biosimilar market entry were correlated to biosimilar uptake. Pharmaceutical expenditure per capita and the highest generic uptake were inversely correlated with biosimilar uptake. Average generic price discount over originator and the number of biosimilars showed a trend toward statistical significance for correlation with biosimilar uptake, but did not reach the significance threshold. Biosimilar price discount over original biologic price, the number of analogues, and the distribution channel were not correlated with the biosimilar uptake. Conclusions: Understanding drivers of biosimilar uptake becomes a critical issue to inform

  5. Fatal and serious road crashes involving young New Zealand drivers: a latent class clustering approach

    DEFF Research Database (Denmark)

    Weiss, Harold B.; Kaplan, Sigal; Prato, Carlo Giacomo

    2016-01-01

    classification that revealed how the identified clusters contain mostly crashes of a particular class and all the crashes of that class. The results raised three major safety concerns for young drivers that should be addressed: (1) reckless driving and traffic law violations; (2) inattention, error, and hazard......The over-representation of young drivers in road crashes remains an important concern worldwide. Cluster analysis has been applied to young driver sub-groups, but its application by analysing crash occurrence is just emerging. We present a classification analysis that advances the field through...... a holistic overview of crash patterns useful for designing youth-targeted road safety programmes. We compiled a database of 8644 New Zealand crashes from 2002 to 2011 involving at least one 15–24-year-old driver and a fatal or serious injury for at least one road user. We considered crash location...

  6. Analysis of land use drivers at the watershed and household level: linking two paradigms at the Philippine forest fringe

    NARCIS (Netherlands)

    Overmars, K.P.; Verburg, P.H.

    2005-01-01

    Land use and land cover change (LUCC) is the result of the complex interactions between behavioural and structural factors (drivers) associated with the demand, technological capacity, social relations and the nature of the environment in question. Although no general theory of land use change exist

  7. DIVIDED ATTENTION IN EXPERIENCED YOUNG AND OLDER DRIVERS - LANE TRACKING AND VISUAL ANALYSIS IN A DYNAMIC DRIVING SIMULATOR

    NARCIS (Netherlands)

    BROUWER, WH; WATERINK, W; VANWOLFFELAAR, PC; ROTHENGATTER, T

    1991-01-01

    A simulated driving task that required the simultaneous execution of two continuous visual tasks was administered to 12 healthy young (mean age 26.1 years) and 12 healthy older (mean age 64.4 years) experienced and currently active drivers. The first task was a compensatory lane-tracking task involv

  8. Driver-Pressure-State-Impact-Response (DPSIR) analysis and risk assessment for soil compaction-A European perspective

    NARCIS (Netherlands)

    Schjønning, Per; Akker, van den J.J.H.; Keller, Thomas; Greve, M.H.; Lamandé, Mathieu; Simojoki, Asko; Stettler, Matthias; Arvidsson, Johan; Breuning-Madsen, Henrik

    2015-01-01

    Compaction of subsoil is a hidden but persistent damage that impairs a range of soil functions and ecosystem services. We analyzed the soil compaction issue in the Driver-Pressure-State-Impact-Response (DPSIR) context. The driving force (DPSIR-D) is the farmers' efforts to sustain economic viabil

  9. Driver Behavior and Motivation.

    Science.gov (United States)

    Thomas, Patricia

    School bus driver behavior and motivation are continuing concerns for leaders/administrators in the field of transportation. Motivation begins with selection of a potential new driver. Drivers must like children and be patient, loyal, and punctual. The applicant's background must be verified, in view of the national concern for child safety.…

  10. Identification of druggable cancer driver genes amplified across TCGA datasets.

    Directory of Open Access Journals (Sweden)

    Ying Chen

    Full Text Available The Cancer Genome Atlas (TCGA projects have advanced our understanding of the driver mutations, genetic backgrounds, and key pathways activated across cancer types. Analysis of TCGA datasets have mostly focused on somatic mutations and translocations, with less emphasis placed on gene amplifications. Here we describe a bioinformatics screening strategy to identify putative cancer driver genes amplified across TCGA datasets. We carried out GISTIC2 analysis of TCGA datasets spanning 16 cancer subtypes and identified 486 genes that were amplified in two or more datasets. The list was narrowed to 75 cancer-associated genes with potential "druggable" properties. The majority of the genes were localized to 14 amplicons spread across the genome. To identify potential cancer driver genes, we analyzed gene copy number and mRNA expression data from individual patient samples and identified 42 putative cancer driver genes linked to diverse oncogenic processes. Oncogenic activity was further validated by siRNA/shRNA knockdown and by referencing the Project Achilles datasets. The amplified genes represented a number of gene families, including epigenetic regulators, cell cycle-associated genes, DNA damage response/repair genes, metabolic regulators, and genes linked to the Wnt, Notch, Hedgehog, JAK/STAT, NF-KB and MAPK signaling pathways. Among the 42 putative driver genes were known driver genes, such as EGFR, ERBB2 and PIK3CA. Wild-type KRAS was amplified in several cancer types, and KRAS-amplified cancer cell lines were most sensitive to KRAS shRNA, suggesting that KRAS amplification was an independent oncogenic event. A number of MAP kinase adapters were co-amplified with their receptor tyrosine kinases, such as the FGFR adapter FRS2 and the EGFR family adapters GRB2 and GRB7. The ubiquitin-like ligase DCUN1D1 and the histone methyltransferase NSD3 were also identified as novel putative cancer driver genes. We discuss the patient tailoring implications

  11. Driver behaviour at roadworks.

    Science.gov (United States)

    Walker, Guy; Calvert, Malcolm

    2015-11-01

    There is an incompatibility between how transport engineers think drivers behave in roadworks and how they actually behave. As a result of this incompatibility we are losing approximately a lane's worth of capacity in addition to those closed by the roadworks themselves. The problem would have little significance were it not for the fact a lane of motorway costs approx. £30 m per mile to construct and £43 k a year to maintain, and that many more roadworks are planned as infrastructure constructed 40 or 50 years previously reaches a critical stage in its lifecycle. Given current traffic volumes, and the sensitivity of road networks to congestion, the effects of roadworks need to be accurately assessed. To do this requires a new ergonomic approach. A large-scale observational study of real traffic conditions was used to identify the issues and impacts, which were then mapped to the ergonomic knowledge-base on driver behaviour, and combined to developed practical guidelines to help in modelling future roadworks scenarios with greater behavioural accuracy. Also stemming from the work are novel directions for the future ergonomic design of roadworks themselves.

  12. The Impact of Driver Inattention on Near-Crash/Crash Risk: An Analysis Using the 100-Car Naturalistic Driving Study Data

    OpenAIRE

    Klauer, Sheila G.; Dingus, Thomas A.; Neale, Vicki L.; Sudweeks, Jeremy D.; Ramsey, D J

    2006-01-01

    The purpose of this report was to conduct in-depth analyses of driver inattention using the driving data collected in the 100-Car Naturalistic Driving Study. An additional database of baseline epochs was reduced from the raw data and used in conjunction with the crash and near-crash data identified as part of the original 100-Car Study to account for exposure and establish near-crash/crash risk. The analyses presented in this report are able to establish direct relationships between driving b...

  13. Analysis of Maize Crop Leaf using Multivariate Image Analysis for Identifying Soil Deficiency

    Directory of Open Access Journals (Sweden)

    S. Sridevy

    2014-11-01

    Full Text Available Image processing analysis for the soil deficiency identification has become an active area of research in this study. The changes in the color of the leaves are used to analyze and identify the deficiency of soil nutrients such as Nitrogen (N, Phosphorus (P and potassium (K by digital color image analysis. This research study focuses on the image analysis of the maize crop leaf using multivariate image analysis. In this proposed novel approach, initially, a color transformation for the input RGB image is formed and this RGB is converted to HSV because RGB is ideal for color generation but HSV is very suitable for color perception. Then green pixels are masked and removed using specific threshold value by applying histogram equalization. This masking approach is done through specific customized filtering approach which exclusively filters the green color of the leaf. After the filtering step, only the deficiency part of the leaf is taken for consideration. Then, a histogram generation is carried out for the deficiency part of the leaf. Then, Multivariate Image Analysis approach using Independent Component Analysis (ICA is carried out to extract a reference eigenspace from a matrix built by unfolding color data from the deficiency part. Test images are also unfolded and projected onto the reference eigenspace and the result is a score matrix which is used to compute nutrient deficiency based on the T2 statistic. In addition, a multi-resolution scheme by scaling down process is carried out to speed up the process. Finally, based on the training samples, the soil deficiency is identified based on the color of the maize crop leaf.

  14. Barriers and drivers towards the incorporation of crop residue in the soil. Analysis of Italian farmers’ opinion with the theory of planned behaviour

    Directory of Open Access Journals (Sweden)

    Luca Bechini

    2015-12-01

    Full Text Available Despite the benefits arising from incorporating crop residue in the soil, some farmers decide to burn or sell it. The objective of the work described in this paper was to quantify the adoption of crop residue incorporation by Italian farmers, and to identify the barriers and drivers that they perceive towards this agricultural management practice. We applied a behavioural approach, based on the theory of planned behaviour. In agriculture, this theory can be used to study individual farmer beliefs to understand the intention to adopt agricultural management practices. Based on preliminary semi-structured interviews with 24 farmers, we have prepared and disseminated a structured questionnaire in dairy farms in the plain of northern Italy, in arable farms in the plain of northern, central, and southern Italy, and in arable farms in the hill of central and southern Italy. The questionnaire contained questions to reveal subjective beliefs of the farmers on the outcomes of incorporating crop residue, and on the referents and control factors that might influence adoption. We have received 315 filled questionnaires from 16 regions and 54 provinces. The survey has identified major drivers and barriers towards the incorporation of crop residue in the soil. The main drivers were the expected improvement of soil quality (higher soil organic matter, improved structure and fertility, the expected increase of grain protein concentration in the following wheat crop, the availability of adequate machinery, the prohibition of burning crop residue, and the knowledge that incorporation is important (which emphasizes the importance of an effective advisory service. The main barriers were the costs of incorporation, the need to increase the use of nitrogen fertiliser when straw is incorporated, and the problems to sow the following crop in the presence of residue. While on the basis of the preliminary interviews we expected that the possibility to sell the straw and

  15. Drivers of Collaborative Advantage

    DEFF Research Database (Denmark)

    Weihe, Gudrid

    Drawing upon extant alliance literature, this article substantiates the argument that we need to look beyond mere structural and formative aspects of cooperation in order to fully understand the performance antecedents of public-private partnerships. Currently, scholarly work on operational...... processes and behavioural dimensions is practically non-existent. This article tries to remedy the current gap in the literature by reviewing research findings on interfirm collaboration (alliances). On that basis a conceptual framework for analyzing partnership processes is developed. Finally......, the antecedents of collaborative advantage are theoretically examined, and the organizational competences contributing to collaborative success are identified. The conclusion is that operational processes and social dynamics are vital drivers of collaborative advantage. Another significant conclusion...

  16. Investigating driver injury severity patterns in rollover crashes using support vector machine models.

    Science.gov (United States)

    Chen, Cong; Zhang, Guohui; Qian, Zhen; Tarefder, Rafiqul A; Tian, Zong

    2016-05-01

    Rollover crash is one of the major types of traffic crashes that induce fatal injuries. It is important to investigate the factors that affect rollover crashes and their influence on driver injury severity outcomes. This study employs support vector machine (SVM) models to investigate driver injury severity patterns in rollover crashes based on two-year crash data gathered in New Mexico. The impacts of various explanatory variables are examined in terms of crash and environmental information, vehicle features, and driver demographics and behavior characteristics. A classification and regression tree (CART) model is utilized to identify significant variables and SVM models with polynomial and Gaussian radius basis function (RBF) kernels are used for model performance evaluation. It is shown that the SVM models produce reasonable prediction performance and the polynomial kernel outperforms the Gaussian RBF kernel. Variable impact analysis reveals that factors including comfortable driving environment conditions, driver alcohol or drug involvement, seatbelt use, number of travel lanes, driver demographic features, maximum vehicle damages in crashes, crash time, and crash location are significantly associated with driver incapacitating injuries and fatalities. These findings provide insights for better understanding rollover crash causes and the impacts of various explanatory factors on driver injury severity patterns.

  17. Event-Based Modeling of Driver Yielding Behavior at Unsignalized Crosswalks.

    Science.gov (United States)

    Schroeder, Bastian J; Rouphail, Nagui M

    2011-07-01

    This research explores factors associated with driver yielding behavior at unsignalized pedestrian crossings and develops predictive models for yielding using logistic regression. It considers the effect of variables describing driver attributes, pedestrian characteristics and concurrent conditions at the crosswalk on the yield response. Special consideration is given to 'vehicle dynamics constraints' that form a threshold for the potential to yield. Similarities are identified to driver reaction in response to the 'amber' indication at a signalized intersection. The logit models were developed from data collected at two unsignalized mid-block crosswalks in North Carolina. The data include 'before' and 'after' observations of two pedestrian safety treatments, an in-street pedestrian crossing sign and pedestrian-actuated in-roadway warning lights.The analysis suggests that drivers are more likely to yield to assertive pedestrians who walk briskly in their approach to the crosswalk. In turn, the yield probability is reduced with higher speeds, deceleration rates and if vehicles are traveling in platoons. The treatment effects proved to be significant and increased the propensity of drivers to yield, but their effectiveness may be dependent on whether the pedestrian activates the treatment.The results of this research provide new insights on the complex interaction of pedestrians and vehicles at unsignalized intersections and have implications for future work towards predictive models for driver yielding behavior. The developed logit models can provide the basis for representing driver yielding behavior in a microsimulation modeling environment.

  18. Exploring older driver crash trend: New Jersey case study

    Directory of Open Access Journals (Sweden)

    Vanvi Trieu

    2014-04-01

    Full Text Available Older drivers age 65 and above are known to experience greater risk on the roadway as well as increasing the risk to other roadway users. Within the next 20 years, their population is expected to increase from 41 million in 2011 to 70 million in 2030. To address this foreseeable change, the nation's recent Moving Ahead for Progress in the 21st Century (MAP-21 act requires state and local governments to examine older drivers and pedestrian risks and implement countermeasures as appropriate. This research was conducted to assist agencies in strategising for future plans, programmes and initiatives to better address the problem presented. This was accomplished by performing a detailed engineering analysis on crash data of older drivers over a 10-year period (2003–2012 from the state of New Jersey to identify crash trends and characteristics. A major finding from this research was the increase in fatal crashes of older drivers as a function of age. Top-ranking collision types with other vehicles and non-vehicles were identified. Crashes as a function of seasonal change, climate and lighting conditions were also examined.

  19. DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer.

    Science.gov (United States)

    Bashashati, Ali; Haffari, Gholamreza; Ding, Jiarui; Ha, Gavin; Lui, Kenneth; Rosner, Jamie; Huntsman, David G; Caldas, Carlos; Aparicio, Samuel A; Shah, Sohrab P

    2012-12-22

    Simultaneous interrogation of tumor genomes and transcriptomes is underway in unprecedented global efforts. Yet, despite the essential need to separate driver mutations modulating gene expression networks from transcriptionally inert passenger mutations, robust computational methods to ascertain the impact of individual mutations on transcriptional networks are underdeveloped. We introduce a novel computational framework, DriverNet, to identify likely driver mutations by virtue of their effect on mRNA expression networks. Application to four cancer datasets reveals the prevalence of rare candidate driver mutations associated with disrupted transcriptional networks and a simultaneous modulation of oncogenic and metabolic networks, induced by copy number co-modification of adjacent oncogenic and metabolic drivers. DriverNet is available on Bioconductor or at http://compbio.bccrc.ca/software/drivernet/.

  20. Toward a Broader Concept of Value: Identifying and Defining Elements for an Expanded Cost-Effectiveness Analysis.

    Science.gov (United States)

    Garrison, Louis P; Kamal-Bahl, Sachin; Towse, Adrian

    2017-02-01

    This commentary identifies and defines potentially useful expansions to traditional cost-effectiveness analysis as often used in health technology assessment. Since the seminal 1977 article by Weinstein and Stason, the recommended approach has been the use of the incremental cost-effectiveness ratio based on the metric of the cost per quality-adjusted life-year gained, allowing comparisons across different technologies. An expanded framework, incorporating a wider range of the elements of value, is proposed. In addition to the core value drivers of health gain and other health system cost savings (if any), we propose adding other less recognized elements related to the value of knowing and informational externalities. We describe each of five factors related to the value of knowing: 1) a reduction in uncertainty, reflecting the benefit of a companion diagnostic increasing the certainty of a patient׳s response to a medicine; 2) insurance value related to greater peace of mind due to protection against catastrophic health and financial loss; 3) the value of hope for a "cure," leading individuals to become risk seekers in some circumstances; 4) real option value due to life extension opening possibilities for individuals to benefit from future innovation; and 5) spillovers or externalities arising from benefits of scientific advances that cannot be entirely appropriated by those making the advances. Further thought and research are needed on how best to measure and integrate these elements into an incremental value framework and on coverage and pricing decisions.

  1. 基于Speed Dreams的驾驶员应激响应分析系统%Drivers' critical response analysis system based on speed dreams engine

    Institute of Scientific and Technical Information of China (English)

    吴初娜; 田学英; 徐云杰; 于鹏程

    2012-01-01

    In order to research drivers' behavior under emergent situations, a drivers' critical response analysis system is presented. The hardware system is a Logitech racing wheel with corresponding mechanical reconstruction. The software system creates typical critical scenes with Speed Dreams and high-speed dynamic collects and records driving behaviors with Joystick monitor method and multi-thread communication technology. Then we obtain drivers' critical response time and summarize relevant laws of data after doing filtering, noise reduction, differential and other data processing and analysis. The results provide reliable support for further research on driving behavior under emergent situations.%为了研究应激状态下的驾驶员行为,提出了一种驾驶员应激响应分析系统.硬件系统以罗技赛车方向盘为基础并进行相应的机械改造,软件系统采用Speed Dreams引擎创建典型应激场景;采用Joystick监控方法以及多线程通讯技术,高速动态采集并记录驾驶行为.对采集数据进行滤波、去噪、微分等处理和分析后,得出驾驶员的应激响应时间及数据间的相关规律.该研究成果可以为应激状态下的驾驶员行为研究提供可靠的数据支持.

  2. Assessing the relationship between the Driver Behavior Questionnaire and the Driver Skill Inventory: Revealing sub-groups of drivers

    DEFF Research Database (Denmark)

    Martinussen, Laila Marianne; Møller, Mette; Prato, Carlo Giacomo

    2014-01-01

    The Driver Behavior Questionnaire and the Driver Skill Inventory are two of the most frequently used measures of self-reported driving style and driving skill. The motivation behind the present study was to identify sub-groups of drivers that potentially act dangerously in traffic (as measured by...... driving behaviors, and vice versa. The present findings highlight the need to look into driver’s attitudes towards safety, and to devise differential interventions targeting specific problematic groups of the population in the attempt to improve road safety nationwide....

  3. Identifying coordinative structure using principal component analysis based on coherence derived from linear systems analysis.

    Science.gov (United States)

    Wang, Xinguang; O'Dwyer, Nicholas; Halaki, Mark; Smith, Richard

    2013-01-01

    Principal component analysis is a powerful and popular technique for capturing redundancy in muscle activity and kinematic patterns. A primary limitation of the correlations or covariances between signals on which this analysis is based is that they do not account for dynamic relations between signals, yet such relations-such as that between neural drive and muscle tension-are widespread in the sensorimotor system. Low correlations may thus be obtained and signals may appear independent despite a dynamic linear relation between them. To address this limitation, linear systems analysis can be used to calculate the matrix of overall coherences between signals, which measures the strength of the relation between signals taking dynamic relations into account. Using ankle, knee, and hip sagittal-plane angles from 6 healthy subjects during ~50% of total variance in the data set, while with overall coherence matrices the first component accounted for > 95% of total variance. The results demonstrate that the dimensionality of the coordinative structure can be overestimated using conventional correlation, whereas a more parsimonious structure is identified with overall coherence.

  4. National Driver Register (NDR) -

    Data.gov (United States)

    Department of Transportation — Information regarding individuals who have had their driver licenses revoked, suspended or otherwise denied for cause, or who have been convicted of certain traffic...

  5. Coincidence analysis for quantifying statistical interrelationships between event time series: on the role of flood events as possible drivers of epidemic outbreaks

    CERN Document Server

    Donges, Jonathan F; Siegmund, Jonatan F; Donner, Reik V

    2015-01-01

    Studying event time series is a powerful concept for analyzing the dynamics of complex dynamical systems in many fields of science. Despite its relevance and wide applicability for interdisciplinary research, the statistical analysis of interrelations between event time series has not received much attention in the literature so far. To this end, in this paper we develop the mathematical foundations of coincidence analysis to provide a framework for quantifying the strength, directionality and time lag of statistical interrelationships between event series. Coincidence analysis allows to formulate and test null hypotheses on the origin of the observed interrelationships including tests based on Poisson processes or, more generally, stochastic point processes with a prescribed inter-event time distribution. Applying the framework to country-level observational data yields evidence that flood events have acted as possible drivers of epidemic outbreaks globally since the 1950s. Facing projected future changes in...

  6. Climatic and management drivers of CO2 exchanges by a production crop: analysis over three successive 4-year cycles.

    Science.gov (United States)

    Buysse, Pauline; Moureaux, Christine; Bodson, Bernard; Aubinet, Marc

    2016-04-01

    Carbon dioxide (CO2) exchanges between crops and the atmosphere are influenced by both climatic and crop management drivers. The investigated crop, situated at the Lonzée Terrestrial Observatory (candidate ICOS site) in the Hesbaye region in Belgium and managed for more than 70 years using conventional farming practices, was monitored over three complete sugar beet/winter wheat/potato/winter wheat rotation cycles from 2004 to 2016. Eddy covariance, automatic and manual soil chambers, leaf diffusion and biomass measurements were performed continuously in order to obtain the daily and seasonal Net Ecosystem Exchange (NEE), Gross Primary Productivity (GPP), total Ecosystem Respiration (TER), Net Primary Productivity (NPP), autotrophic respiration, heterotrophic respiration and Net Biome Production (NBP). Meteorological data and crop management practices were also recorded. Climatic and seasonal evolutions of the carbon balance components were studied and crop carbon budgets were computed both at the yearly and crop rotation cycle scales. On average over the 12 years, NEE was negative but NBP was positive, i.e. as far as carbon exportation by harvest are included in the budget, the site behaved as a carbon source. Impacts of both meteorological drivers and crop management operations on CO2 exchanges were analyzed and compared between crop types, years, and rotation cycles. The uncertainties associated to the carbon fluxes were also evaluated and discussed.

  7. Improved Squeaky Wheel Optimisation for Driver Scheduling

    CERN Document Server

    Aickelin, Uwe; Li, Jingpeng

    2008-01-01

    This paper presents a technique called Improved Squeaky Wheel Optimisation for driver scheduling problems. It improves the original Squeaky Wheel Optimisations effectiveness and execution speed by incorporating two additional steps of Selection and Mutation which implement evolution within a single solution. In the ISWO, a cycle of Analysis-Selection-Mutation-Prioritization-Construction continues until stopping conditions are reached. The Analysis step first computes the fitness of a current solution to identify troublesome components. The Selection step then discards these troublesome components probabilistically by using the fitness measure, and the Mutation step follows to further discard a small number of components at random. After the above steps, an input solution becomes partial and thus the resulting partial solution needs to be repaired. The repair is carried out by using the Prioritization step to first produce priorities that determine an order by which the following Construction step then schedul...

  8. A Simple Wave Driver

    Science.gov (United States)

    Temiz, Burak Kagan; Yavuz, Ahmet

    2015-01-01

    This study was done to develop a simple and inexpensive wave driver that can be used in experiments on string waves. The wave driver was made using a battery-operated toy car, and the apparatus can be used to produce string waves at a fixed frequency. The working principle of the apparatus is as follows: shortly after the car is turned on, the…

  9. Young novice drivers.

    NARCIS (Netherlands)

    2013-01-01

    In The Netherlands, young novice drivers (18-24 years of age) show a crash rate that is five times higher than that of experienced drivers (30-59 years of age). The rate of young males is even seven times as high. The main reasons are lack of driving experience and hazardous behaviour typical of ado

  10. Identifying At-Risk Students in General Chemistry via Cluster Analysis of Affective Characteristics

    Science.gov (United States)

    Chan, Julia Y. K.; Bauer, Christopher F.

    2014-01-01

    The purpose of this study is to identify academically at-risk students in first-semester general chemistry using affective characteristics via cluster analysis. Through the clustering of six preselected affective variables, three distinct affective groups were identified: low (at-risk), medium, and high. Students in the low affective group…

  11. Do Specific Growth Drivers Exist for Firms? A Regional Analysis of Start-ups and Industrial Growth

    Directory of Open Access Journals (Sweden)

    PAUL I. OJEAGA

    2016-06-01

    Full Text Available The study of start-ups, have remained largely a micro economic issue. Firms are the key drivers of industrial sector GDP (or enterprise growth in countries across regions. Few studies have tried to examine the consequence of start-ups in the broad macroeconomics terms on enterprise growth in general with special emphasis on industrial sector output. This study provides a macroeconomic study of the effect of start- ups on industrial sector growth for countries in some specific geographical regions of the world. Panel data is utilized due to it obvious advantages such its ability to utilize a panel of short time frames and its suitability for controlling for omitted variable bias and unobservable heterogeneity across regions. The results show that start-ups remain an intrinsic variable for enterprise growth and industrial sector output discussion in general.

  12. Assessing Reliability of Cellulose Hydrolysis Models to Support Biofuel Process Design – Identifiability and Uncertainty Analysis

    DEFF Research Database (Denmark)

    Sin, Gürkan; Meyer, Anne S.; Gernaey, Krist

    2010-01-01

    The reliability of cellulose hydrolysis models is studied using the NREL model. An identifiability analysis revealed that only 6 out of 26 parameters are identifiable from the available data (typical hydrolysis experiments). Attempting to identify a higher number of parameters (as done in the ori...... to analyze the uncertainty of model predictions. This allows judging the fitness of the model to the purpose under uncertainty. Hence we recommend uncertainty analysis as a proactive solution when faced with model uncertainty, which is the case for biofuel process development research....

  13. The influences of drivers/riders in road traffic crashes in Ghana between 2001 and 2011.

    Science.gov (United States)

    Amo, Thompson

    2014-04-07

    The road traffic accident (RTA) is a global misfortune and the leading cause of death among young drivers. In safeguarding and developing innovative safety strategies to curtail the situation, the factors causing this menace needs proper attention and investigation. The objective of this study is to identify the potential factors responsible for causing a traffic accident in Ghana. In studying these factors extensively, a descriptive study with quantitative technique was employed. Analyses used data between 2001 and 2011 obtained from the Building and Road Research Institute (BRRI) with specific focus on the age, drinking, vehicle defect, driver/rider error, injury, road surface type and weather. A total of 200,528 cases of drivers/riders were analysed and discovered that, people with younger age (21-40) contribute 62.97% of total crashes. Crashes reduce steadily as drivers/riders age increases. Also, the vehicle defect analysis shows that 87.46% of accidents cannot be linked to the fault of the vehicle before incidence, while the majority (75.38%) of drivers/riders had no injury during a traffic accident. Higher number of fatalities are recorded on tar good roads (81.57%) and clear weather (91.75%). The fight against this canker by the authorities must consider periodic refresher courses for younger drivers/riders on traffic law to bring to bear the adherence of good driving/riding principles and attitudes to ensure that safety is guaranteed for all road users in the country.

  14. Alternative to Ritt's Pseudodivision for finding the input-output equations in algebraic structural identifiability analysis

    CERN Document Server

    Meshkat, Nicolette; DiStefano, Joseph J

    2012-01-01

    Differential algebra approaches to structural identifiability analysis of a dynamic system model in many instances heavily depend upon Ritt's pseudodivision at an early step in analysis. The pseudodivision algorithm is used to find the characteristic set, of which a subset, the input-output equations, is used for identifiability analysis. A simpler algorithm is proposed for this step, using Gr\\"obner Bases, along with a proof of the method that includes a reduced upper bound on derivative requirements. Efficacy of the new algorithm is illustrated with two biosystem model examples.

  15. Crash involvement during the different phases of the New Zealand Graduated Driver Licensing System (GDLS)

    NARCIS (Netherlands)

    Lewis Evans, B.

    2010-01-01

    Introduction: The New Zealand Graduated Driver Licensing System (GDLS) is designed to allow novice drivers to gain driving experience under conditions of reduced risk. Method: To examine the effectiveness of the GDLS, an analysis of how the crash involvement of novice drivers changes as drivers move

  16. Physics at a new Fermilab proton driver

    Energy Technology Data Exchange (ETDEWEB)

    Geer, Steve; /Fermilab

    2006-04-01

    In 2004, motivated by the recent exciting developments in neutrino physics, the Fermilab Long Range Planning Committee identified a new high intensity Proton Driver as an attractive option for the future. At the end of 2004 the APS ''Study on the Physics of Neutrinos'' concluded that the future US neutrino program should have, as one of its components, ''A proton driver in the megawatt class or above and neutrino superbeam with an appropriate very large detector capable of observing Cp violation and measuring the neutrino mass-squared differences and mixing parameters with high precision''. The presently proposed Fermilab Proton Driver is designed to accomplish these goals, and is based on, and would help develop, Linear Collider technology. In this paper the Proton Driver parameters are summarized, and the potential physics program is described.

  17. Identification of drivers for modular production

    DEFF Research Database (Denmark)

    Brunoe, Thomas Ditlev; Bossen, Jacob; Nielsen, Kjeld

    2015-01-01

    Todays competitive environment in industry creates a need for companies to enhance their ability to introduce new products faster. To increase rampup speed reconfigurable manufacturing systems is a promising concept, however to implement this production platforms and modular manufacturing...... is required. This paper presents an analysis whether and which module drivers from general product development can be applied to the development process of a modular manufacturing system. The result is a compiled list of modular drivers for manufacturing and examples of their use....

  18. Stereotype threat and hazard perception among provisional license drivers.

    Science.gov (United States)

    Skorich, Daniel P; Webb, Hugh; Stewart, Lisa; Kostyanaya, Maria; Cruwys, Tegan; McNeill, Kathy; Frain, Andrew J; Lim, Li; Jones, Benjamin M; Smyth, Lillian; O'Brien, Kerry J

    2013-05-01

    Stereotype threat refers to the negative impact a stereotype about one's group can have on one's performance in domains relevant to the stereotype. In the current paper, we explore whether the negative stereotype of provisional license drivers (PLDs) might produce stereotype threat in a driving-related hazard perception task. We manipulate threat by asking participants to self-identify as PLDs in a categorization condition, or by reminding PLD participants explicitly of the stereotype of PLDs in an explicit stereotype condition. Results reveal increments in hazard perception in the categorization condition, and decrements in hazard perception in the explicit stereotype condition. Mediation analysis reveals that hazard perception performance is fully mediated by increased effort in the categorization condition and by decreased effort in the explicit stereotype condition. We discuss these findings in terms of their implications for stereotype threat and its mediators, and for public policy that explicitly discriminates between PLDs and other driver groups.

  19. A global analysis of the impacts of urbanization on bird and plant diversity reveals key anthropogenic drivers

    Science.gov (United States)

    Aronson, Myla F. J.; La Sorte, Frank A.; Nilon, Charles H.; Katti, Madhusudan; Goddard, Mark A.; Lepczyk, Christopher A.; Warren, Paige S.; Williams, Nicholas S. G.; Cilliers, Sarel; Clarkson, Bruce; Dobbs, Cynnamon; Dolan, Rebecca; Hedblom, Marcus; Klotz, Stefan; Kooijmans, Jip Louwe; Kühn, Ingolf; MacGregor-Fors, Ian; McDonnell, Mark; Mörtberg, Ulla; Pyšek, Petr; Siebert, Stefan; Sushinsky, Jessica; Werner, Peter; Winter, Marten

    2014-01-01

    Urbanization contributes to the loss of the world's biodiversity and the homogenization of its biota. However, comparative studies of urban biodiversity leading to robust generalities of the status and drivers of biodiversity in cities at the global scale are lacking. Here, we compiled the largest global dataset to date of two diverse taxa in cities: birds (54 cities) and plants (110 cities). We found that the majority of urban bird and plant species are native in the world's cities. Few plants and birds are cosmopolitan, the most common being Columba livia and Poa annua. The density of bird and plant species (the number of species per km2) has declined substantially: only 8% of native bird and 25% of native plant species are currently present compared with estimates of non-urban density of species. The current density of species in cities and the loss in density of species was best explained by anthropogenic features (landcover, city age) rather than by non-anthropogenic factors (geography, climate, topography). As urbanization continues to expand, efforts directed towards the conservation of intact vegetation within urban landscapes could support higher concentrations of both bird and plant species. Despite declines in the density of species, cities still retain endemic native species, thus providing opportunities for regional and global biodiversity conservation, restoration and education. PMID:24523278

  20. The effects of iPod and text-messaging use on driver distraction: a bio-behavioral analysis.

    Science.gov (United States)

    Mouloua, M; Ahern, A; Quevedo, A; Jaramillo, D; Rinalducci, E; Smither, J; Alberti, P; Brill, C

    2012-01-01

    This study was designed to empirically examine the effects of iPod device and text-messaging activities on driver distraction. Sixty participants were asked to perform a driving simulation task while searching for songs using an iPod device or text messaging. Driving errors as measured by lane deviations were recorded and analyzed as a function of the distracters. Physiological measures (EEG) were also recorded during the driving phases in order to measure participant levels of cortical arousal. It was hypothesized that iPod use and text messaging would result in a profound effect on driving ability. The results showed a significant effect of iPod use and text-messaging on driving performance. Increased numbers of driving errors were recorded during the iPod and text-messaging phases than the pre- and post-allocation phases. Higher levels of Theta activity were also observed during the iPod and Text-messaging phase than the pre- and post-allocation phases. Implications for in-vehicle systems design, training, and safety are also discussed.

  1. Proactive driver training program

    Energy Technology Data Exchange (ETDEWEB)

    Vossler, W. [Kinetic Safety Consulting Inc., Grande Prairie, AB (Canada)

    2005-07-01

    Skid avoidance training is a recent approach to driver training and has been employed in various countries with a high degree of success. Among top ranked countries, motor vehicle incidents trends indicate higher incident rates among drivers are often due to lack of knowledge, experience and risk awareness. If lowered age limit experience is attained under direct supervision and in safe training conditions, it was suggested, incident frequency is reduced. A Norway study confirmed an increase in vehicle incident rates after drivers had received skid control training. The drivers were unable to maintain skill levels needed to react to critical driving tasks and had unrealistic expectations of skill after training. However, a skid avoidance training program launched in Sweden in 1999 has resulted in a 50 per cent reduction of vehicle incidents in the last 2 years. Details of the Skidcar System were presented, including details of the driving simulator, where simulation of actual driving situations is achieved by simply adjusting the amount of grip the vehicle has with the driving surface. Instructors modify driving behaviors based upon the driver's ability to maintain grip. There are over 200 units in North America. In addition, a Proactive Light Vehicle Driver Training/ Heavy Vehicle Assessment Program was initiated in 2003, with a motor vehicle incident rate reduction of 50 per cent at the end of 2004. Various examples of situations in which drivers have used their skid avoidance skills to avoid incidents were included. It was noted that the trend among driver training professionals has been towards decision-based rather than skills-based training, as skills-based training will diminish over time, and requires frequent re-training periods. Cognitive and perceptual skills were examined, as well as cognitive, associative and autonomous learning phases. It was concluded that skid avoidance is largely a decision-based skill. tabs, figs.

  2. Research data management and libraries: relationships, activities, drivers and influences.

    Science.gov (United States)

    Pinfield, Stephen; Cox, Andrew M; Smith, Jen

    2014-01-01

    The management of research data is now a major challenge for research organisations. Vast quantities of born-digital data are being produced in a wide variety of forms at a rapid rate in universities. This paper analyses the contribution of academic libraries to research data management (RDM) in the wider institutional context. In particular it: examines the roles and relationships involved in RDM, identifies the main components of an RDM programme, evaluates the major drivers for RDM activities, and analyses the key factors influencing the shape of RDM developments. The study is written from the perspective of library professionals, analysing data from 26 semi-structured interviews of library staff from different UK institutions. This is an early qualitative contribution to the topic complementing existing quantitative and case study approaches. Results show that although libraries are playing a significant role in RDM, there is uncertainty and variation in the relationship with other stakeholders such as IT services and research support offices. Current emphases in RDM programmes are on developments of policies and guidelines, with some early work on technology infrastructures and support services. Drivers for developments include storage, security, quality, compliance, preservation, and sharing with libraries associated most closely with the last three. The paper also highlights a 'jurisdictional' driver in which libraries are claiming a role in this space. A wide range of factors, including governance, resourcing and skills, are identified as influencing ongoing developments. From the analysis, a model is constructed designed to capture the main aspects of an institutional RDM programme. This model helps to clarify the different issues involved in RDM, identifying layers of activity, multiple stakeholders and drivers, and a large number of factors influencing the implementation of any initiative. Institutions may usefully benchmark their activities against the

  3. Using machine vision and data mining techniques to identify cell properties via microfluidic flow analysis

    Science.gov (United States)

    Horowitz, Geoffrey; Bowie, Samuel; Liu, Anna; Stone, Nicholas; Sulchek, Todd; Alexeev, Alexander

    2016-11-01

    In order to quickly identify the wide range of mechanistic properties that are seen in cell populations, a coupled machine vision and data mining analysis is developed to examine high speed videos of cells flowing through a microfluidic device. The microfluidic device contains a microchannel decorated with a periodical array of diagonal ridges. The ridges compress flowing cells that results in complex cell trajectory and induces cell cross-channel drift, both depend on the cell intrinsic mechanical properties that can be used to characterize specific cell lines. Thus, the cell trajectory analysis can yield a parameter set that can serve as a unique identifier of a cell's membership to a specific cell population. By using the correlations between the cell populations and measured cell trajectories in the ridged microchannel, mechanical properties of individual cells and their specific populations can be identified via only information captured using video analysis. Financial support provided by National Science Foundation (NSF) Grant No. CMMI 1538161.

  4. Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci

    OpenAIRE

    Stahl, Eli A; Raychaudhuri, Soumya; Remmers, Elaine F.; Xie, Gang; Eyre, Stephen; Thomson, Brian P.; Li, Yonghong; Kurreeman, Fina A. S.; Zhernakova, Alexandra; Hinks, Anne; Guiducci, Candace; Chen, Robert; Alfredsson, Lars; Amos, Christopher I.; Ardlie, Kristin G.

    2010-01-01

    To identify novel genetic risk factors for rheumatoid arthritis (RA), we conducted a genome-wide association study (GWAS) meta-analysis of 5,539 autoantibody positive RA cases and 20,169 controls of European descent, followed by replication in an independent set of 6,768 RA cases and 8,806 controls. Of 34 SNPs selected for replication, 7 novel RA risk alleles were identified at genome-wide significance (P

  5. Comparative analysis of Salmonella genomes identifies a metabolic network for escalating growth in the inflamed gut.

    Science.gov (United States)

    Nuccio, Sean-Paul; Bäumler, Andreas J

    2014-03-18

    The Salmonella genus comprises a group of pathogens associated with illnesses ranging from gastroenteritis to typhoid fever. We performed an in silico analysis of comparatively reannotated Salmonella genomes to identify genomic signatures indicative of disease potential. By removing numerous annotation inconsistencies and inaccuracies, the process of reannotation identified a network of 469 genes involved in central anaerobic metabolism, which was intact in genomes of gastrointestinal pathogens but degrading in genomes of extraintestinal pathogens. This large network contained pathways that enable gastrointestinal pathogens to utilize inflammation-derived nutrients as well as many of the biochemical reactions used for the enrichment and biochemical discrimination of Salmonella serovars. Thus, comparative genome analysis identifies a metabolic network that provides clues about the strategies for nutrient acquisition and utilization that are characteristic of gastrointestinal pathogens. IMPORTANCE While some Salmonella serovars cause infections that remain localized to the gut, others disseminate throughout the body. Here, we compared Salmonella genomes to identify characteristics that distinguish gastrointestinal from extraintestinal pathogens. We identified a large metabolic network that is functional in gastrointestinal pathogens but decaying in extraintestinal pathogens. While taxonomists have used traits from this network empirically for many decades for the enrichment and biochemical discrimination of Salmonella serovars, our findings suggest that it is part of a "business plan" for growth in the inflamed gastrointestinal tract. By identifying a large metabolic network characteristic of Salmonella serovars associated with gastroenteritis, our in silico analysis provides a blueprint for potential strategies to utilize inflammation-derived nutrients and edge out competing gut microbes.

  6. Drivers and barriers to engage enterprises in environmental management initiatives in Suzhou Industrial Park, China

    Institute of Scientific and Technical Information of China (English)

    Bing ZHANG; Jun BI; Beibei LIU

    2009-01-01

    Small- and medium-sized enterprises (SMEs)play an important role in sustainable development not only for their significant contribution to China's economy, but also for their large share of total discharged pollutants.Therefore, this research takes the enterprises in Suzhou Industrial Park, China as the case study to investigate the environmental management practices of SMEs, and identify drivers and barriers to engaging businesses in environmental management initiatives. It is shown that, as in other countries, SMEs are less active in adopting environmental management initiatives than larger companies. Legislation remains the key driver to engage SMEs in environmental management initiatives. Based on the analysis, policy recommendations are also presented.

  7. An operational modal analysis approach based on parametrically identified multivariable transmissibilities

    Science.gov (United States)

    Devriendt, Christof; De Sitter, Gert; Guillaume, Patrick

    2010-07-01

    In this contribution the approach to identify modal parameters from output-only (scalar) transmissibility measurements [C. Devriendt, P. Guillaume, The use of transmissibility measurements in output-only modal analysis, Mechanical Systems and Signal Processing 21 (7) (2007) 2689-2696] is generalized to multivariable transmissibilities. In general, the poles that are identified from (scalar as well as multivariable) transmissibility measurements do not correspond with the system's poles. However, by combining transmissibility measurements under different loading conditions, it is shown in this paper how model parameters can be identified from multivariable transmissibility measurements.

  8. The effects of texting on driving performance in a driving simulator: the influence of driver age.

    Science.gov (United States)

    Rumschlag, Gordon; Palumbo, Theresa; Martin, Amber; Head, Doreen; George, Rajiv; Commissaris, Randall L

    2015-01-01

    Distracted driving is a significant contributor to motor vehicle accidents and fatalities, and texting is a particularly significant form of driver distraction that continues to be on the rise. The present study examined the influence of driver age (18-59 years old) and other factors on the disruptive effects of texting on simulated driving behavior. While 'driving' the simulator, subjects were engaged in a series of brief text conversations with a member of the research team. The primary dependent variable was the occurrence of Lane Excursions (defined as any time the center of the vehicle moved outside the directed driving lane, e.g., into the lane for oncoming traffic or onto the shoulder of the road), measured as (1) the percent of subjects that exhibited Lane Excursions, (2) the number of Lane Excursions occurring and (3) the percent of the texting time in Lane Excursions. Multiple Regression analyses were used to assess the influence of several factors on driving performance while texting, including text task duration, texting skill level (subject-reported), texting history (#texts/week), driver gender and driver age. Lane Excursions were not observed in the absence of texting, but 66% of subjects overall exhibited Lane Excursions while texting. Multiple Regression analysis for all subjects (N=50) revealed that text task duration was significantly correlated with the number of Lane Excursions, and texting skill level and driver age were significantly correlated with the percent of subjects exhibiting Lane Excursions. Driver gender was not significantly correlated with Lane Excursions during texting. Multiple Regression analysis of only highly skilled texters (N=27) revealed that driver age was significantly correlated with the number of Lane Excursions, the percent of subjects exhibiting Lane Excursions and the percent of texting time in Lane Excursions. In contrast, Multiple Regression analysis of those drivers who self-identified as not highly skilled

  9. Sparse canonical correlation analysis for identifying, connecting and completing gene-expression networks

    Directory of Open Access Journals (Sweden)

    Zwinderman Aeilko H

    2009-09-01

    Full Text Available Abstract Background We generalized penalized canonical correlation analysis for analyzing microarray gene-expression measurements for checking completeness of known metabolic pathways and identifying candidate genes for incorporation in the pathway. We used Wold's method for calculation of the canonical variates, and we applied ridge penalization to the regression of pathway genes on canonical variates of the non-pathway genes, and the elastic net to the regression of non-pathway genes on the canonical variates of the pathway genes. Results We performed a small simulation to illustrate the model's capability to identify new candidate genes to incorporate in the pathway: in our simulations it appeared that a gene was correctly identified if the correlation with the pathway genes was 0.3 or more. We applied the methods to a gene-expression microarray data set of 12, 209 genes measured in 45 patients with glioblastoma, and we considered genes to incorporate in the glioma-pathway: we identified more than 25 genes that correlated > 0.9 with canonical variates of the pathway genes. Conclusion We concluded that penalized canonical correlation analysis is a powerful tool to identify candidate genes in pathway analysis.

  10. Identifying Effective Spelling Interventions Using a Brief Experimental Analysis and Extended Analysis

    Science.gov (United States)

    McCurdy, Merilee; Clure, Lynne F.; Bleck, Amanda A.; Schmitz, Stephanie L.

    2016-01-01

    Spelling is an important skill that is crucial to effective written communication. In this study, brief experimental analysis procedures were used to examine spelling instruction strategies (e.g., whole word correction; word study strategy; positive practice; and cover, copy, and compare) for four students. In addition, an extended analysis was…

  11. Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis

    NARCIS (Netherlands)

    B.F. Voight (Benjamin); L.J. Scott (Laura); V. Steinthorsdottir (Valgerdur); A.D. Morris (Andrew); C. Dina (Christian); R.P. Welch (Ryan); E. Zeggini (Eleftheria); C. Huth (Cornelia); Y.S. Aulchenko (Yurii); G. Thorleifsson (Gudmar); L.J. McCulloch (Laura); T. Ferreira (Teresa); H. Grallert (Harald); N. Amin (Najaf); G. Wu (Guanming); C.J. Willer (Cristen); S. Raychaudhuri (Soumya); S.A. McCarroll (Steven); C. Langenberg (Claudia); O.M. Hofmann (Oliver); J. Dupuis (Josée); L. Qi (Lu); A.V. Segrè (Ayellet); M. van Hoek (Mandy); P. Navarro (Pau); K.G. Ardlie (Kristin); B. Balkau (Beverley); R. Benediktsson (Rafn); A.J. Bennett (Amanda); R. Blagieva (Roza); E.A. Boerwinkle (Eric); L.L. Bonnycastle (Lori); K.B. Boström (Kristina Bengtsson); B. Bravenboer (Bert); S. Bumpstead (Suzannah); N.P. Burtt (Noël); G. Charpentier (Guillaume); P.S. Chines (Peter); M. Cornelis (Marilyn); D.J. Couper (David); G. Crawford (Gabe); A.S.F. Doney (Alex); K.S. Elliott (Katherine); M.R. Erdos (Michael); C.S. Fox (Caroline); C.S. Franklin (Christopher); M. Ganser (Martha); C. Gieger (Christian); N. Grarup (Niels); T. Green (Todd); S. Griffin (Simon); C.J. Groves (Christopher); C. Guiducci (Candace); S. Hadjadj (Samy); N. Hassanali (Neelam); C. Herder (Christian); B. Isomaa (Bo); A.U. Jackson (Anne); P.R.V. Johnson (Paul); T. Jørgensen (Torben); W.H.L. Kao (Wen); N. Klopp (Norman); A. Kong (Augustine); P. Kraft (Peter); J. Kuusisto (Johanna); T. Lauritzen (Torsten); M. Li (Man); A. Lieverse (Aloysius); C.M. Lindgren (Cecilia); V. Lyssenko (Valeriya); M. Marre (Michel); T. Meitinger (Thomas); K. Midthjell (Kristian); M.A. Morken (Mario); N. Narisu (Narisu); P. Nilsson (Peter); K.R. Owen (Katharine); F. Payne (Felicity); J.R.B. Perry (John); A.K. Petersen; C. Platou (Carl); C. Proença (Christine); I. Prokopenko (Inga); W. Rathmann (Wolfgang); N.W. Rayner (Nigel William); N.R. Robertson (Neil); G. Rocheleau (Ghislain); M. Roden (Michael); M.J. Sampson (Michael); R. Saxena (Richa); B.M. Shields (Beverley); P. Shrader (Peter); G. Sigurdsson (Gunnar); T. Sparsø (Thomas); K. Strassburger (Klaus); H.M. Stringham (Heather); Q. Sun (Qi); A.J. Swift (Amy); B. Thorand (Barbara); J. Tichet (Jean); T. Tuomi (Tiinamaija); R.M. van Dam (Rob); T.W. van Haeften (Timon); T.W. van Herpt (Thijs); J.V. van Vliet-Ostaptchouk (Jana); G.B. Walters (Bragi); M.N. Weedon (Michael); C. Wijmenga (Cisca); J.C.M. Witteman (Jacqueline); R.N. Bergman (Richard); S. Cauchi (Stephane); F.S. Collins (Francis); A.L. Gloyn (Anna); U. Gyllensten (Ulf); T. Hansen (Torben); W.A. Hide (Winston); G.A. Hitman (Graham); A. Hofman (Albert); D. Hunter (David); K. Hveem (Kristian); M. Laakso (Markku); K.L. Mohlke (Karen); C.N.A. Palmer (Colin); P.P. Pramstaller (Peter Paul); I. Rudan (Igor); E.J.G. Sijbrands (Eric); L.D. Stein (Lincoln); J. Tuomilehto (Jaakko); A.G. Uitterlinden (André); M. Walker (Mark); N.J. Wareham (Nick); G.R. Abecasis (Gonçalo); B.O. Boehm (Bernhard); H. Campbell (Harry); M.J. Daly (Mark); A.T. Hattersley (Andrew); F.B. Hu (Frank); J.B. Meigs (James); J.S. Pankow (James); O. Pedersen (Oluf); H.E. Wichmann (Erich); I. Barroso (Inês); J.C. Florez (Jose); T.M. Frayling (Timothy); L. Groop (Leif); R. Sladek (Rob); U. Thorsteinsdottir (Unnur); J.F. Wilson (James); T. Illig (Thomas); P. Froguel (Philippe); P. Tikka-Kleemola (Päivi); J-A. Zwart (John-Anker); D. Altshuler (David); M. Boehnke (Michael); M.I. McCarthy (Mark); R.M. Watanabe (Richard)

    2010-01-01

    textabstractBy combining genome-wide association data from 8,130 individuals with type 2 diabetes (T2D) and 38,987 controls of European descent and following up previously unidentified meta-analysis signals in a further 34,412 cases and 59,925 controls, we identified 12 new T2D association signals w

  12. Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis

    NARCIS (Netherlands)

    Voight, Benjamin F.; Scott, Laura J.; Steinthorsdottir, Valgerdur; Morris, Andrew P.; Dina, Christian; Welch, Ryan P.; Zeggini, Eleftheria; Huth, Cornelia; Aulchenko, Yurii S.; Thorleifsson, Gudmar; McCulloch, Laura J.; Ferreira, Teresa; Grallert, Harald; Amin, Najaf; Wu, Guanming; Willer, Cristen J.; Raychaudhuri, Soumya; McCarroll, Steve A.; Langenberg, Claudia; Hofmann, Oliver M.; Dupuis, Josee; Qi, Lu; Segre, Ayellet V.; van Hoek, Mandy; Navarro, Pau; Ardlie, Kristin; Balkau, Beverley; Benediktsson, Rafn; Bennett, Amanda J.; Blagieva, Roza; Boerwinkle, Eric; Bonnycastle, Lori L.; Bostrom, Kristina Bengtsson; Bravenboer, Bert; Bumpstead, Suzannah; Burtt, Noisel P.; Charpentier, Guillaume; Chines, Peter S.; Cornelis, Marilyn; Couper, David J.; Crawford, Gabe; Doney, Alex S. F.; Elliott, Katherine S.; Elliott, Amanda L.; Erdos, Michael R.; Fox, Caroline S.; Franklin, Christopher S.; Ganser, Martha; Gieger, Christian; Grarup, Niels; Green, Todd; Griffin, Simon; Groves, Christopher J.; Guiducci, Candace; Hadjadj, Samy; Hassanali, Neelam; Herder, Christian; Isomaa, Bo; Jackson, Anne U.; Johnson, Paul R. V.; Jorgensen, Torben; Kao, Wen H. L.; Klopp, Norman; Kong, Augustine; Kraft, Peter; Kuusisto, Johanna; Lauritzen, Torsten; Li, Man; Lieverse, Aloysius; Lindgren, Cecilia M.; Lyssenko, Valeriya; Marre, Michel; Meitinger, Thomas; Midthjell, Kristian; Morken, Mario A.; Narisu, Narisu; Nilsson, Peter; Owen, Katharine R.; Payne, Felicity; Perry, John R. B.; Petersen, Ann-Kristin; Platou, Carl; Proenca, Christine; Prokopenko, Inga; Rathmann, Wolfgang; Rayner, N. William; Robertson, Neil R.; Rocheleau, Ghislain; Roden, Michael; Sampson, Michael J.; Saxena, Richa; Shields, Beverley M.; Shrader, Peter; Sigurdsson, Gunnar; Sparso, Thomas; Strassburger, Klaus; Stringham, Heather M.; Sun, Qi; Swift, Amy J.; Thorand, Barbara; Tichet, Jean; Tuomi, Tiinamaija; van Dam, Rob M.; van Haeften, Timon W.; van Herpt, Thijs; van Vliet-Ostaptchouk, Jana V.; Walters, G. Bragi; Weedon, Michael N.; Wijmenga, Cisca; Witteman, Jacqueline; Bergman, Richard N.; Cauchi, Stephane; Collins, Francis S.; Gloyn, Anna L.; Gyllensten, Ulf; Hansen, Torben; Hide, Winston A.; Hitman, Graham A.; Hofman, Albert; Hunter, David J.; Hveem, Kristian; Laakso, Markku; Mohlke, Karen L.; Morris, Andrew D.; Palmer, Colin N. A.; Pramstaller, Peter P.; Rudan, Igor; Sijbrands, Eric; Stein, Lincoln D.; Tuomilehto, Jaakko; Uitterlinden, Andre; Walker, Mark; Wareham, Nicholas J.; Watanabe, Richard M.; Abecasis, Goncalo R.; Boehm, Bernhard O.; Campbell, Harry; Daly, Mark J.; Hattersley, Andrew T.; Hu, Frank B.; Meigs, James B.; Pankow, James S.; Pedersen, Oluf; Wichmann, H-Erich; Barroso, Ines; Florez, Jose C.; Frayling, Timothy M.; Groop, Leif; Sladek, Rob; Thorsteinsdottir, Unnur; Wilson, James F.; Illig, Thomas; Froguel, Philippe; van Duijn, Cornelia M.; Stefansson, Kari; Altshuler, David; Boehnke, Michael; McCarthy, Mark I.

    2010-01-01

    By combining genome-wide association data from 8,130 individuals with type 2 diabetes (T2D) and 38,987 controls of European descent and following up previously unidentified meta-analysis signals in a further 34,412 cases and 59,925 controls, we identified 12 new T2D association signals with combined

  13. Using Work Action Analysis to Identify Web-Portal Requirements for a Professional Development Program

    Science.gov (United States)

    Nickles, George

    2007-01-01

    This article describes using Work Action Analysis (WAA) as a method for identifying requirements for a web-based portal that supports a professional development program. WAA is a cognitive systems engineering method for modeling multi-agent systems to support design and evaluation. A WAA model of the professional development program of the…

  14. Genome-wide association scan meta-analysis identifies three loci influencing adiposity and fat distribution

    NARCIS (Netherlands)

    C.M. Lindgren (Cecilia); I.M. Heid (Iris); J.C. Randall (Joshua); C. Lamina (Claudia); V. Steinthorsdottir (Valgerdur); L. Qi (Lu); E.K. Speliotes (Elizabeth); G. Thorleifsson (Gudmar); C.J. Willer (Cristen); B.M. Herrera (Blanca); A.U. Jackson (Anne); N. Lim (Noha); P. Scheet (Paul); N. Soranzo (Nicole); N. Amin (Najaf); Y.S. Aulchenko (Yurii); J.C. Chambers (John); A. Drong (Alexander); J. Luan; H.N. Lyon (Helen); F. Rivadeneira Ramirez (Fernando); S. Sanna (Serena); N. Timpson (Nicholas); M.C. Zillikens (Carola); H.Z. Jing; P. Almgren (Peter); S. Bandinelli (Stefania); A.J. Bennett (Amanda); R.N. Bergman (Richard); L.L. Bonnycastle (Lori); S. Bumpstead (Suzannah); S.J. Chanock (Stephen); L. Cherkas (Lynn); P.S. Chines (Peter); L. Coin (Lachlan); C. Cooper (Charles); G. Crawford (Gabe); A. Doering (Angela); A. Dominiczak (Anna); A.S.F. Doney (Alex); S. Ebrahim (Shanil); P. Elliott (Paul); M.R. Erdos (Michael); K. Estrada Gil (Karol); L. Ferrucci (Luigi); G. Fischer (Guido); N.G. Forouhi (Nita); C. Gieger (Christian); H. Grallert (Harald); C.J. Groves (Christopher); S.M. Grundy (Scott); C. Guiducci (Candace); D. Hadley (David); A. Hamsten (Anders); A.S. Havulinna (Aki); A. Hofman (Albert); R. Holle (Rolf); J.W. Holloway (John); T. Illig (Thomas); B. Isomaa (Bo); L.C. Jacobs (Leonie); K. Jameson (Karen); P. Jousilahti (Pekka); F. Karpe (Fredrik); J. Kuusisto (Johanna); J. Laitinen (Jaana); G.M. Lathrop (Mark); D.A. Lawlor (Debbie); M. Mangino (Massimo); W.L. McArdle (Wendy); T. Meitinger (Thomas); M.A. Morken (Mario); A.P. Morris (Andrew); P. Munroe (Patricia); N. Narisu (Narisu); A. Nordström (Anna); B.A. Oostra (Ben); C.N.A. Palmer (Colin); F. Payne (Felicity); J. Peden (John); I. Prokopenko (Inga); F. Renström (Frida); A. Ruokonen (Aimo); V. Salomaa (Veikko); M.S. Sandhu (Manjinder); L.J. Scott (Laura); A. Scuteri (Angelo); K. Silander (Kaisa); K. Song (Kijoung); X. Yuan (Xin); H.M. Stringham (Heather); A.J. Swift (Amy); T. Tuomi (Tiinamaija); M. Uda (Manuela); P. Vollenweider (Peter); G. Waeber (Gérard); C. Wallace (Chris); G.B. Walters (Bragi); M.N. Weedon (Michael); J.C.M. Witteman (Jacqueline); C. Zhang (Cuilin); M. Caulfield (Mark); F.S. Collins (Francis); G.D. Smith; I.N.M. Day (Ian); P.W. Franks (Paul); A.T. Hattersley (Andrew); F.B. Hu (Frank); M.-R. Jarvelin (Marjo-Riitta); A. Kong (Augustine); J.S. Kooner (Jaspal); M. Laakso (Markku); E. Lakatta (Edward); V. Mooser (Vincent); L. Peltonen (Leena Johanna); N.J. Samani (Nilesh); T.D. Spector (Timothy); D.P. Strachan (David); T. Tanaka (Toshiko); J. Tuomilehto (Jaakko); A.G. Uitterlinden (André); P. Tikka-Kleemola (Päivi); N.J. Wareham (Nick); H. Watkins (Hugh); D. Waterworth (Dawn); M. Boehnke (Michael); P. Deloukas (Panagiotis); L. Groop (Leif); D.J. Hunter (David); U. Thorsteinsdottir (Unnur); D. Schlessinger (David); H.E. Wichmann (Erich); T.M. Frayling (Timothy); G.R. Abecasis (Gonçalo); J.N. Hirschhorn (Joel); R.J.F. Loos (Ruth); J-A. Zwart (John-Anker); K.L. Mohlke (Karen); I. Barroso (Inês); M.I. McCarthy (Mark)

    2009-01-01

    textabstractTo identify genetic loci influencing central obesity and fat distribution, we performed a meta-analysis of 16 genome-wide association studies (GWAS, N = 38,580) informative for adult waist circumference (WC) and waist-hip ratio (WHR). We selected 26 SNPs for follow-up, for which the evid

  15. Examination of a One-Trial Brief Experimental Analysis to Identify Reading Fluency Interventions

    Science.gov (United States)

    Andersen, Melissa N.; Daly, Edward J., III; Young, Nicholas D.

    2013-01-01

    This study sought to evaluate whether a one-trial brief experimental analysis (OTBEA) would reliably and validly identify effective treatments to improve oral reading fluency for 6 elementary school students referred for reading problems. An OTBEA was conducted with each participant to assess the effects of skill- and performance-based treatment…

  16. Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis

    DEFF Research Database (Denmark)

    Voight, Benjamin F; Scott, Laura J; Steinthorsdottir, Valgerdur;

    2010-01-01

    By combining genome-wide association data from 8,130 individuals with type 2 diabetes (T2D) and 38,987 controls of European descent and following up previously unidentified meta-analysis signals in a further 34,412 cases and 59,925 controls, we identified 12 new T2D association signals...

  17. Identifying Barriers in Implementing Outcomes-Based Assessment Program Review: A Grounded Theory Analysis

    Science.gov (United States)

    Bresciani, Marilee J.

    2011-01-01

    The purpose of this grounded theory study was to identify the typical barriers encountered by faculty and administrators when implementing outcomes-based assessment program review. An analysis of interviews with faculty and administrators at nine institutions revealed a theory that faculty and administrators' promotion, tenure (if applicable),…

  18. Bioinformatics analysis identifies several intrinsically disordered human E3 ubiquitin-protein ligases

    DEFF Research Database (Denmark)

    Boomsma, Wouter Krogh; Nielsen, Sofie Vincents; Lindorff-Larsen, Kresten;

    2016-01-01

    conduct a bioinformatics analysis to examine >600 human and S. cerevisiae E3 ligases to identify enzymes that are similar to San1 in terms of function and/or mechanism of substrate recognition. An initial sequence-based database search was found to detect candidates primarily based on the homology...

  19. Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci

    NARCIS (Netherlands)

    Stahl, Eli A.; Raychaudhuri, Soumya; Remmers, Elaine F.; Xie, Gang; Eyre, Stephen; Thomson, Brian P.; Li, Yonghong; Kurreeman, Fina A. S.; Zhernakova, Alexandra; Hinks, Anne; Guiducci, Candace; Chen, Robert; Alfredsson, Lars; Amos, Christopher I.; Ardlie, Kristin G.; Barton, Anne; Bowes, John; Brouwer, Elisabeth; Burtt, Noel P.; Catanese, Joseph J.; Coblyn, Jonathan; Coenen, Marieke J. H.; Costenbader, Karen H.; Criswell, Lindsey A.; Crusius, J. Bart A.; Cui, Jing; de Bakker, Paul I. W.; De Jager, Philip L.; Ding, Bo; Emery, Paul; Flynn, Edward; Harrison, Pille; Hocking, Lynne J.; Huizinga, Tom W. J.; Kastner, Daniel L.; Ke, Xiayi; Lee, Annette T.; Liu, Xiangdong; Martin, Paul; Morgan, Ann W.; Padyukov, Leonid; Posthumus, Marcel D.; Radstake, Timothy R. D. J.; Reid, David M.; Seielstad, Mark; Seldin, Michael F.; Shadick, Nancy A.; Steer, Sophia; Tak, Paul P.; Thomson, Wendy; van der Helm-van Mil, Annette H. M.; van der Horst-Bruinsma, Irene E.; van der Schoot, C. Ellen; van Riel, Piet L. C. M.; Weinblatt, Michael E.; Wilson, Anthony G.; Wolbink, Gert Jan; Wordsworth, B. Paul; Wijmenga, Cisca; Karlson, Elizabeth W.; Toes, Rene E. M.; de Vries, Niek; Begovich, Ann B.; Worthington, Jane; Siminovitch, Katherine A.; Gregersen, Peter K.; Klareskog, Lars; Plenge, Robert M.

    2010-01-01

    To identify new genetic risk factors for rheumatoid arthritis, we conducted a genome-wide association study meta-analysis of 5,539 autoantibody-positive individuals with rheumatoid arthritis (cases) and 20,169 controls of European descent, followed by replication in an independent set of 6,768 rheum

  20. Identifying Skill Requirements for GIS Positions: A Content Analysis of Job Advertisements

    Science.gov (United States)

    Hong, Jung Eun

    2016-01-01

    This study identifies the skill requirements for geographic information system (GIS) positions, including GIS analysts, programmers/developers/engineers, specialists, and technicians, through a content analysis of 946 GIS job advertisements from 2007-2014. The results indicated that GIS job applicants need to possess high levels of GIS analysis…

  1. Clinical Trial Registries Are of Minimal Use for Identifying Selective Outcome and Analysis Reporting

    Science.gov (United States)

    Norris, Susan L.; Holmer, Haley K.; Fu, Rongwei; Ogden, Lauren A.; Viswanathan, Meera S.; Abou-Setta, Ahmed M.

    2014-01-01

    Objective: This study aimed to examine selective outcome reporting (SOR) and selective analysis reporting (SAR) in randomized controlled trials (RCTs) and to explore the usefulness of trial registries for identifying SOR and SAR. Study Design and Setting: We selected one "index outcome" for each of three comparative effectiveness reviews…

  2. When noisy neighbors are a blessing: analysis of gene expression noise identifies coregulated genes

    NARCIS (Netherlands)

    Junker, J.P.; van Oudenaarden, A.

    2012-01-01

    In this issue of Molecular Cell, Stewart-Ornstein et al. (2012) use systematic pair-wise correlation analysis of expression noise in a large number of yeast genes to identify clusters of functionally related genes and signaling pathways responsible for elevated noise.

  3. Identifying sustainability issues using participatory SWOT analysis - A case study of egg production in the Netherlands

    NARCIS (Netherlands)

    Mollenhorst, H.; Boer, de I.J.M.

    2004-01-01

    The aim of this paper was to demonstrate how participatory strengths, weaknesses, opportunities and threats (SWOT) analysis can be used to identify relevant economic, ecological and societal (EES) issues for the assessment of sustainable development. This is illustrated by the case of egg production

  4. Gene expression meta-analysis identifies chromosomal regions involved in ovarian cancer survival

    DEFF Research Database (Denmark)

    Thomassen, Mads; Jochumsen, Kirsten M; Mogensen, Ole;

    2009-01-01

    the relation of gene expression and chromosomal position to identify chromosomal regions of importance for early recurrence of ovarian cancer. By use of *Gene Set Enrichment Analysis*, we have ranked chromosomal regions according to their association to survival. Over-representation analysis including 1......Ovarian cancer cells exhibit complex karyotypic alterations causing deregulation of numerous genes. Some of these genes are probably causal for cancer formation and local growth, whereas others are causal for metastasis and recurrence. By using publicly available data sets, we have investigated......-4 consecutive cytogenetic bands identified regions with increased expression for chromosome 5q12-14, and a very large region of chromosome 7 with the strongest signal at 7p15-13 among tumors from short-living patients. Reduced gene expression was identified at 4q26-32, 6p12-q15, 9p21-q32, and 11p14-11. We...

  5. Final Report on the Fuel Saving Effectiveness of Various Driver Feedback Approaches

    Energy Technology Data Exchange (ETDEWEB)

    Gonder, J.; Earleywine, M.; Sparks, W.

    2011-03-01

    This final report quantifies the fuel-savings opportunities from specific driving behavior changes, identifies factors that influence drivers' receptiveness to adopting fuel-saving behaviors, and assesses various driver feedback approaches.

  6. Research fronts analysis : A bibliometric to identify emerging fields of research

    Science.gov (United States)

    Miwa, Sayaka; Ando, Satoko

    Research fronts analysis identifies emerging areas of research through observing co-clustering in highly-cited papers. This article introduces the concept of research fronts analysis, explains its methodology and provides case examples. It also demonstrates developing research fronts in Japan by looking at the past winners of Thomson Reuters Research Fronts Awards. Research front analysis is currently being used by the Japanese government to determine new trends in science and technology. Information professionals can also utilize this bibliometric as a research evaluation tool.

  7. Drivers of soil organic matter vulnerability to climate change. Part I: Laboratory incubations of Swiss forest soils and radiocarbon analysis

    Science.gov (United States)

    González Domínguez, Beatriz; Studer, Mirjam S.; Niklaus, Pascal A.; Haghipour, Negar; McIntyre, Cameron; Wacker, Lukas; Zimmermann, Stephan; Walthert, Lorenz; Hagedorn, Frank; Abiven, Samuel

    2016-04-01

    Given the key role of soil organic carbon (SOC) on climate and greenhouse gas regulation, there is an increasing need to incorporate the carbon (C) feedback between SOC and the atmosphere into earth system models. The evaluation of these models points towards uncertainties on the response of CO2-C fluxes, derived from the decomposition of SOC, to the influence of controls/drivers. SOC vulnerability refers to the likelihood of losing previously stabilized soil organic matter, by the effect of environmental factors. The objective of this study is to produce a SOC vulnerability ranking of soils and to provide new insights into the influence of environmental and soil properties controls. Research on SOC vulnerability tends to focus on climatic controls and neglect the effect of other factors, such as soil geochemistry and mineralogy, on C stabilization/de-stabilization processes. In this work, we hypothesized that climate (mean annual temperature and soil moisture status proxy at the research sites in the period 1981-2010), soil (pH and % clay) and terrain (slope gradient and orientation) characteristics are the main controls of the CO2-C fluxes from SOC. Following a statistics-based approach, we selected 54 forest sites across Switzerland, which cover a broad spectrum of values for the hypothesized controls. Then, we selected the study sites so that the controls are orthogonal to each other; thus, their effect was not confounded. At each site, we collected three non-overlapping topsoil (i.e. 20 cm) composites within 40 x 40 m2 plots. In the laboratory, we sieved fresh soils at 2 mm and run a 2-weeks pre-incubation, before beginning a 6-months aerobic soil incubation under controlled conditions of moisture and temperature. Periodically, we collected NaOH (1M) traps containing the CO2-C derived from microbial heterotrophic respiration. We calculated the cumulative CO2-C respired and the one-pool SOC decomposition rates from the 54 forest sites, and linked these data to

  8. A Continuing Analysis of Possible Activity Drivers for the Enigmatic Comet 29P/Schwassmann-Wachmann 1

    Science.gov (United States)

    Schambeau, Charles; Fernández, Yanga; Samarasinha, Nalin H.; Mueller, Beatrice E. A.; Sarid, Gal; Meech, Karen Jean; Woodney, Laura

    2016-01-01

    We present results from our effort to understand activity drivers in Comet 29P/Schwassmann-Wachmann 1 (SW1). In a nearly circular orbit around 6 AU, outside of the water-sublimation zone, SW1 is continuously active and experiences frequent outbursts. Our group's effort is focusing on finding constraints on physical and dynamical properties of SW1's nucleus and their incorporation into a thermophysical model [1,2] to explain this behavior. We are currently analyzing coma morphology of SW1 before, during, and after outburst placing constraints on the spin-pole direction, spin period, and surface areas of activity. In addition, we are using the thermal model to investigate if the continuous activity comes from one or multiple processes, such as the release of trapped supervolatiles during the amorphous to crystalline (A-C) water ice phase transition and/or the direct sublimation of pockets of supervolatile ices. The supervolatile ices may be primordial or from the condensation of gases released during the A-C phase transition. To explain the possibly quasi-periodic but frequent outbursts, we are looking into subsurface cavities where internal pressures can build, reaching and exceeding surrounding material strengths [3,4] and/or thermal waves reaching a pocket of supervolatile ices, causing a rapid increase in the sublimation rate. For all these phenomena, the model is constrained by comparing the output dust mass loss rate and its variability with what has been observed through optical imaging of the comet at various points in its orbit. We will present preliminary thermal modeling of a homogeneous progenitor nucleus that evolves into a body showing internal material layering, the generation of CO and CO2 ice pockets, and the production of outbursts, thus bringing us closer to explaining the behavior of this intriguing comet. [1] Sarid, G., et al.: 2005, PASP, 117, 843. [2] Sarid, G.: 2009, PhD Thesis, Tel Aviv Univ. [3] Gronkowski, P., 2014, Astron. Nachr./AN 2, No

  9. A cross-species genetic analysis identifies candidate genes for mouse anxiety and human bipolar disorder

    Directory of Open Access Journals (Sweden)

    David G Ashbrook

    2015-07-01

    Full Text Available Bipolar disorder (BD is a significant neuropsychiatric disorder with a lifetime prevalence of ~1%. To identify genetic variants underlying BD genome-wide association studies (GWAS have been carried out. While many variants of small effect associated with BD have been identified few have yet been confirmed, partly because of the low power of GWAS due to multiple comparisons being made. Complementary mapping studies using murine models have identified genetic variants for behavioral traits linked to BD, often with high power, but these identified regions often contain too many genes for clear identification of candidate genes. In the current study we have aligned human BD GWAS results and mouse linkage studies to help define and evaluate candidate genes linked to BD, seeking to use the power of the mouse mapping with the precision of GWAS. We use quantitative trait mapping for open field test and elevated zero maze data in the largest mammalian model system, the BXD recombinant inbred mouse population, to identify genomic regions associated with these BD-like phenotypes. We then investigate these regions in whole genome data from the Psychiatric Genomics Consortium’s bipolar disorder GWAS to identify candidate genes associated with BD. Finally we establish the biological relevance and pathways of these genes in a comprehensive systems genetics analysis.We identify four genes associated with both mouse anxiety and human BD. While TNR is a novel candidate for BD, we can confirm previously suggested associations with CMYA5, MCTP1 and RXRG. A cross-species, systems genetics analysis shows that MCTP1, RXRG and TNR coexpress with genes linked to psychiatric disorders and identify the striatum as a potential site of action. CMYA5, MCTP1, RXRG and TNR are associated with mouse anxiety and human BD. We hypothesize that MCTP1, RXRG and TNR influence intercellular signaling in the striatum.

  10. Drivers of desertification and their impact

    Science.gov (United States)

    Mantel, S.; Van Lynden, G. V. L.; Karavitis, C. A.; Kosmas, C.; Van der Werff ten Bosch, M. J.

    2012-04-01

    Drivers of desertification and their impact An inventory was made of drivers of desertification and how they impact on the degradation process. The major drivers of desertification were analysed and compared between 16 sites around the globe. For each of these sites factors were scored with a perceived influence on desertification. Most of these factors, from the socio-cultural, environmental, and economic dimensions, appeared to be related to land management and planning and to (de-)population. They cause a number of temporary or permanent changes in the landscape, which, by themselves or in combination, lead to degradation of vegetation and soils. Most sites have several forms of land degradation occurring in and around their study area of which erosion by water is the dominant one. Other degradation types occurring in sites were: wind erosion, soil salinization, seawater intrusion in the groundwater, vegetation and biodiversity decline, groundwater depletion, decreased productivity/ carrying capacity, soil fertility decline, water logging and water pollution. As a first step, data and information was gathered on policies, desertification status and processes and on socio-economic conditions. The DPSIR framework (Driving force, Pressure, State, Impact, Response) provides a structure for assessment of the impact of past measures on the status of the environment or to formulate effective measures. In analysing the data, the different data items were structured in and formulated to elements fitting the DPSIR chain. Then possible connections between these different aspects were analysed. In our analysis nine major drivers were reported for the various sites, of which one was environmental, three drivers were related to land management, one driver was related to planning and policies, three drivers were related to socio-economic conditions, and one driver related to legal land status. Depending on the specific desertification process, factors may be positively or

  11. Alternate laser fusion drivers

    Energy Technology Data Exchange (ETDEWEB)

    Pleasance, L.D.

    1979-11-01

    Over the past few years, several laser systems have been considered as possible laser fusion drivers. Recently, there has been an increasing effort to evaluate these systems in terms of a reactor driver application. The specifications for such a system have become firmer and generally more restrictive. Several of the promising candidates such as the group VI laser, the metal vapor excimers and some solid state lasers can be eliminated on the basis of inefficiency. New solid state systems may impact the long range development of a fusion driver. Of the short wavelength gas lasers, the KrF laser used in conjunction with Raman compression and pulse stacking techniques is the most promising approach. Efficiencies approaching 10% may be possible with this system. While technically feasible, these approaches are complex and costly and are unsatisfying in an aethetic sense. A search for new lasers with more compelling features is still needed.

  12. Cluster analysis of spontaneous preterm birth phenotypes identifies potential associations among preterm birth mechanisms

    Science.gov (United States)

    Esplin, M Sean; Manuck, Tracy A.; Varner, Michael W.; Christensen, Bryce; Biggio, Joseph; Bukowski, Radek; Parry, Samuel; Zhang, Heping; Huang, Hao; Andrews, William; Saade, George; Sadovsky, Yoel; Reddy, Uma M.; Ilekis, John

    2015-01-01

    Objective We sought to employ an innovative tool based on common biological pathways to identify specific phenotypes among women with spontaneous preterm birth (SPTB), in order to enhance investigators' ability to identify to highlight common mechanisms and underlying genetic factors responsible for SPTB. Study Design A secondary analysis of a prospective case-control multicenter study of SPTB. All cases delivered a preterm singleton at SPTB ≤34.0 weeks gestation. Each woman was assessed for the presence of underlying SPTB etiologies. A hierarchical cluster analysis was used to identify groups of women with homogeneous phenotypic profiles. One of the phenotypic clusters was selected for candidate gene association analysis using VEGAS software. Results 1028 women with SPTB were assigned phenotypes. Hierarchical clustering of the phenotypes revealed five major clusters. Cluster 1 (N=445) was characterized by maternal stress, cluster 2 (N=294) by premature membrane rupture, cluster 3 (N=120) by familial factors, and cluster 4 (N=63) by maternal comorbidities. Cluster 5 (N=106) was multifactorial, characterized by infection (INF), decidual hemorrhage (DH) and placental dysfunction (PD). These three phenotypes were highly correlated by Chi-square analysis [PD and DH (p<2.2e-6); PD and INF (p=6.2e-10); INF and DH (p=0.0036)]. Gene-based testing identified the INS (insulin) gene as significantly associated with cluster 3 of SPTB. Conclusion We identified 5 major clusters of SPTB based on a phenotype tool and hierarchal clustering. There was significant correlation between several of the phenotypes. The INS gene was associated with familial factors underlying SPTB. PMID:26070700

  13. Analysis on the R-R interval time series of automobile long distance drivers; Kosoku doro no chojikan soko ni yoru R-R kankakuji keiretsu kaiseki

    Energy Technology Data Exchange (ETDEWEB)

    Moyoshi, M.; Takata, K. [Daido Institute of Technology, Nagoya (Japan); Yokoyama, K. [Nagoya Municipal Women`s College, Nagoya (Japan); Yoshioka, T.; Watanabe, Y. [Toyota National College of Technology, Aichi (Japan)

    1995-04-20

    Analyses were performed on change in living body information as time elapses while driving a car, the differences between automobile drivers and fellow passengers, and between automobile drivers and motorcycle drivers. A comparison on body temperatures in automobile drivers and motorcycle drivers shows sharper changes in the motorcycle drivers. Motorcycles, being different from automobiles, put the drivers exposed to atmosphere during driving, applying larger living body load. Adrenalin increases its concentration when a human is under mental load, so does noradrenalin when under physical load. Both of adrenalin and noradrenalin showed an increasing trend in the afternoon as compared with in the morning. From the comparison with the normal daily life, fellow passengers have also large mental living body load, who were found to have concentration change of nearly two times or more than that in normal conditions. A subject who rode in a car in the first experiment and drove a motorcycle in the second experiment was discovered to have his right hand grasping power decreased remarkably after the second experiment. Fatigue factors unique to motorcycle driving are thought the engine vibration, the hot air, the need of taking balance of the motorcycle attitudes, and stress from noise. 14 refs., 8 figs.

  14. Really Scary Drivers

    Institute of Scientific and Technical Information of China (English)

    马莲花

    2005-01-01

    A new wave of "road killers", or new drivers, on Beijing's streets has prompted traffic authorities to do something to make driving tests more difficult. This year, the move has targeted new drivers to keep them from posing a threat, the Beijing Traffic Management Bureau says. The new test has been adopted citywide and the average pass rate is down to 50 per cent from a previous 80 per cent, at the city's 22 test centers, said Jiang Jing, a bureau press officer. The test now has six mandatory items chosen r...

  15. Sustainable Development in China’s Coastal Area: Based on the Driver-Pressure-State-Welfare-Response Framework and the Data Envelopment Analysis Model

    Directory of Open Access Journals (Sweden)

    Song Wang

    2016-09-01

    Full Text Available The economic development of China’s coastal areas is being constrained by resources and the environment, with sustainable development being the key to solving these problems. The data envelopment analysis (DEA model is widely used to assess sustainable development. However, indicators used in the DEA model are not selected in a scientific and comprehensive manner, which may lead to unrepresentative results. Here, we use the driver-pressure-state-welfare-response (DPSWR framework to select more scientific and comprehensive indicators for a more accurate analysis of efficiency in China’s coastal area. The results show that the efficiencies of most provinces and cities in China’s coastal area have a stable trend. In the time dimension, efficiency was rising before 2008, after which it decreased. In the spatial dimension, China’s coastal provinces and cities are divided into three categories: high efficiency, low efficiency, and greater changes in efficiency. By combining DPSWR and DEA, we produce reliable values for measuring efficiency, with the benefit of avoiding the incomplete selection of DEA indicators.

  16. Genome-wide interaction-based association analysis identified multiple new susceptibility Loci for common diseases.

    Directory of Open Access Journals (Sweden)

    Yang Liu

    2011-03-01

    Full Text Available Genome-wide interaction-based association (GWIBA analysis has the potential to identify novel susceptibility loci. These interaction effects could be missed with the prevailing approaches in genome-wide association studies (GWAS. However, no convincing loci have been discovered exclusively from GWIBA methods, and the intensive computation involved is a major barrier for application. Here, we developed a fast, multi-thread/parallel program named "pair-wise interaction-based association mapping" (PIAM for exhaustive two-locus searches. With this program, we performed a complete GWIBA analysis on seven diseases with stringent control for false positives, and we validated the results for three of these diseases. We identified one pair-wise interaction between a previously identified locus, C1orf106, and one new locus, TEC, that was specific for Crohn's disease, with a Bonferroni corrected P < 0.05 (P = 0.039. This interaction was replicated with a pair of proxy linked loci (P = 0.013 on an independent dataset. Five other interactions had corrected P < 0.5. We identified the allelic effect of a locus close to SLC7A13 for coronary artery disease. This was replicated with a linked locus on an independent dataset (P = 1.09 × 10⁻⁷. Through a local validation analysis that evaluated association signals, rather than locus-based associations, we found that several other regions showed association/interaction signals with nominal P < 0.05. In conclusion, this study demonstrated that the GWIBA approach was successful for identifying novel loci, and the results provide new insights into the genetic architecture of common diseases. In addition, our PIAM program was capable of handling very large GWAS datasets that are likely to be produced in the future.

  17. Analysis of regulatory protease sequences identified through bioinformatic data mining of the Schistosoma mansoni genome

    Directory of Open Access Journals (Sweden)

    Minchella Dennis J

    2009-10-01

    Full Text Available Abstract Background New chemotherapeutic agents against Schistosoma mansoni, an etiological agent of human schistosomiasis, are a priority due to the emerging drug resistance and the inability of current drug treatments to prevent reinfection. Proteases have been under scrutiny as targets of immunological or chemotherapeutic anti-Schistosoma agents because of their vital role in many stages of the parasitic life cycle. Function has been established for only a handful of identified S. mansoni proteases, and the vast majority of these are the digestive proteases; very few of the conserved classes of regulatory proteases have been identified from Schistosoma species, despite their vital role in numerous cellular processes. To that end, we identified protease protein coding genes from the S. mansoni genome project and EST library. Results We identified 255 protease sequences from five catalytic classes using predicted proteins of the S. mansoni genome. The vast majority of these show significant similarity to proteins in KEGG and the Conserved Domain Database. Proteases include calpains, caspases, cytosolic and mitochondrial signal peptidases, proteases that interact with ubiquitin and ubiquitin-like molecules, and proteases that perform regulated intramembrane proteolysis. Comparative analysis of classes of important regulatory proteases find conserved active site domains, and where appropriate, signal peptides and transmembrane helices. Phylogenetic analysis provides support for inferring functional divergence among regulatory aspartic, cysteine, and serine proteases. Conclusion Numerous proteases are identified for the first time in S. mansoni. We characterized important regulatory proteases and focus analysis on these proteases to complement the growing knowledge base of digestive proteases. This work provides a foundation for expanding knowledge of proteases in Schistosoma species and examining their diverse function and potential as targets

  18. Patent Network Analysis and Quadratic Assignment Procedures to Identify the Convergence of Robot Technologies

    Science.gov (United States)

    Lee, Woo Jin; Lee, Won Kyung

    2016-01-01

    Because of the remarkable developments in robotics in recent years, technological convergence has been active in this area. We focused on finding patterns of convergence within robot technology using network analysis of patents in both the USPTO and KIPO. To identify the variables that affect convergence, we used quadratic assignment procedures (QAP). From our analysis, we observed the patent network ecology related to convergence and found technologies that have great potential to converge with other robotics technologies. The results of our study are expected to contribute to setting up convergence based R&D policies for robotics, which can lead new innovation. PMID:27764196

  19. Identifying barriers to patient acceptance of active surveillance: content analysis of online patient communications.

    Directory of Open Access Journals (Sweden)

    Mark V Mishra

    Full Text Available OBJECTIVES: Qualitative research aimed at identifying patient acceptance of active surveillance (AS has been identified as a public health research priority. The primary objective of this study was to determine if analysis of a large-sample of anonymous internet conversations (ICs could be utilized to identify unmet public needs regarding AS. METHODS: English-language ICs regarding prostate cancer (PC treatment with AS from 2002-12 were identified using a novel internet search methodology. Web spiders were developed to mine, aggregate, and analyze content from the world-wide-web for ICs centered on AS. Collection of ICs was not restricted to any specific geographic region of origin. NLP was used to evaluate content and perform a sentiment analysis. Conversations were scored as positive, negative, or neutral. A sentiment index (SI was subsequently calculated according to the following formula to compare temporal trends in public sentiment towards AS: [(# Positive IC/#Total IC-(#Negative IC/#Total IC x 100]. RESULTS: A total of 464 ICs were identified. Sentiment increased from -13 to +2 over the study period. The increase sentiment has been driven by increased patient emphasis on quality-of-life factors and endorsement of AS by national medical organizations. Unmet needs identified in these ICs include: a gap between quantitative data regarding long-term outcomes with AS vs. conventional treatments, desire for treatment information from an unbiased specialist, and absence of public role models managed with AS. CONCLUSIONS: This study demonstrates the potential utility of online patient communications to provide insight into patient preferences and decision-making. Based on our findings, we recommend that multidisciplinary clinics consider including an unbiased specialist to present treatment options and that future decision tools for AS include quantitative data regarding outcomes after AS.

  20. Factor Analysis of the DePaul Symptom Questionnaire: Identifying Core Domains

    OpenAIRE

    Jason, Leonard A.; Sunnquist, Madison; Brown, Abigail; Furst, Jacob; Cid, Marjoe; Farietta, Jillianna; Kot, Bobby; Bloomer, Craig; Nicholson, Laura; Williams, Yolonda; Jantke, Rachel; Newton, Julia L.; Strand, Elin Bolle

    2015-01-01

    The present study attempted to identify critical symptom domains of individuals with Myalgic Encephalomyelitis (ME) and chronic fatigue syndrome (CFS). Using patient and control samples collected in the United States, Great Britain, and Norway, exploratory factor analysis (EFA) was used to establish the underlying factor structure of ME and CFS symptoms. The EFA suggested a four-factor solution: post-exertional malaise, cognitive dysfunction, sleep difficulties, and a combined factor consisti...

  1. Emergent team roles in organizational meetings: Identifying communication patterns via cluster analysis.

    OpenAIRE

    Lehmann-Willenbrock, N.K.; Beck, S.J.; Kauffeld, S.

    2016-01-01

    Previous team role taxonomies have largely relied on self-report data, focused on functional roles, and described individual predispositions or personality traits. Instead, this study takes a communicative approach and proposes that team roles are produced, shaped, and sustained in communicative behaviors. To identify team roles communicatively, 59 regular organizational meetings were videotaped and analyzed. Cluster analysis revealed five emergent roles: the solution seeker, the problem anal...

  2. Integrated Analysis for Identifying Radix Astragali and Its Adulterants Based on DNA Barcoding

    OpenAIRE

    Sihao Zheng; Dewang Liu; Weiguang Ren; Juan Fu; Linfang Huang; Shilin Chen

    2014-01-01

    Radix Astragali is a popular herb used in traditional Chinese medicine for its proimmune and antidiabetic properties. However, methods are needed to help distinguish Radix Astragali from its varied adulterants. DNA barcoding is a widely applicable molecular method used to identify medicinal plants. Yet, its use has been hampered by genetic distance, base variation, and limitations of the bio-NJ tree. Herein, we report the validation of an integrated analysis method for plant species identific...

  3. Genome-wide meta-analysis identifies new susceptibility loci for migraine

    DEFF Research Database (Denmark)

    Anttila, Verneri; Winsvold, Bendik S; Gormley, Padhraig

    2013-01-01

    Migraine is the most common brain disorder, affecting approximately 14% of the adult population, but its molecular mechanisms are poorly understood. We report the results of a meta-analysis across 29 genome-wide association studies, including a total of 23,285 individuals with migraine (cases......) and 95,425 population-matched controls. We identified 12 loci associated with migraine susceptibility (P

  4. Unscented Kalman filter with parameter identifiability analysis for the estimation of multiple parameters in kinetic models

    OpenAIRE

    Baker Syed; Poskar C; Junker Björn

    2011-01-01

    Abstract In systems biology, experimentally measured parameters are not always available, necessitating the use of computationally based parameter estimation. In order to rely on estimated parameters, it is critical to first determine which parameters can be estimated for a given model and measurement set. This is done with parameter identifiability analysis. A kinetic model of the sucrose accumulation in the sugar cane culm tissue developed by Rohwer et al. was taken as a test case model. Wh...

  5. Parallel analysis of tagged deletion mutants efficiently identifies genes involved in endoplasmic reticulum biogenesis.

    Science.gov (United States)

    Wright, Robin; Parrish, Mark L; Cadera, Emily; Larson, Lynnelle; Matson, Clinton K; Garrett-Engele, Philip; Armour, Chris; Lum, Pek Yee; Shoemaker, Daniel D

    2003-07-30

    Increased levels of HMG-CoA reductase induce cell type- and isozyme-specific proliferation of the endoplasmic reticulum. In yeast, the ER proliferations induced by Hmg1p consist of nuclear-associated stacks of smooth ER membranes known as karmellae. To identify genes required for karmellae assembly, we compared the composition of populations of homozygous diploid S. cerevisiae deletion mutants following 20 generations of growth with and without karmellae. Using an initial population of 1,557 deletion mutants, 120 potential mutants were identified as a result of three independent experiments. Each experiment produced a largely non-overlapping set of potential mutants, suggesting that differences in specific growth conditions could be used to maximize the comprehensiveness of similar parallel analysis screens. Only two genes, UBC7 and YAL011W, were identified in all three experiments. Subsequent analysis of individual mutant strains confirmed that each experiment was identifying valid mutations, based on the mutant's sensitivity to elevated HMG-CoA reductase and inability to assemble normal karmellae. The largest class of HMG-CoA reductase-sensitive mutations was a subset of genes that are involved in chromatin structure and transcriptional regulation, suggesting that karmellae assembly requires changes in transcription or that the presence of karmellae may interfere with normal transcriptional regulation.

  6. Hot spot analysis applied to identify ecosystem services potential in Lithuania

    Science.gov (United States)

    Pereira, Paulo; Depellegrin, Daniel; Misiune, Ieva

    2016-04-01

    Hot spot analysis are very useful to identify areas with similar characteristics. This is important for a sustainable use of the territory, since we can identify areas that need to be protected, or restored. This is a great advantage in terms of land use planning and management, since we can allocate resources, reduce the economical costs and do a better intervention in the landscape. Ecosystem services (ES) are different according land use. Since landscape is very heterogeneous, it is of major importance understand their spatial pattern and where are located the areas that provide better ES and the others that provide less services. The objective of this work is to use hot-spot analysis to identify areas with the most valuable ES in Lithuania. CORINE land-cover (CLC) of 2006 was used as the main spatial information. This classification uses a grid of 100 m resolution and extracted a total of 31 land use types. ES ranking was carried out based on expert knowledge. They were asked to evaluate the ES potential of each different CLC from 0 (no potential) to 5 (very high potential). Hot spot analysis were evaluated using the Getis-ord test, which identifies cluster analysis available in ArcGIS toolbox. This tool identifies areas with significantly high low values and significant high values at a p level of 0.05. In this work we used hot spot analysis to assess the distribution of providing, regulating cultural and total (sum of the previous 3) ES. The Z value calculated from Getis-ord was used to statistical analysis to access the clusters of providing, regulating cultural and total ES. ES with high Z value show that they have a high number of cluster areas with high potential of ES. The results showed that the Z-score was significantly different among services (Kruskal Wallis ANOVA =834. 607, pcultural (0.080±1.979) and regulating (0.076±1.961). These results suggested that providing services are more clustered than the remaining. Ecosystem Services Z score were

  7. Improving Driver Performance. A Curriculum for Licensed Drivers.

    Science.gov (United States)

    Highway Users Federation for Safety and Mobility, Washington, DC.

    Curriculum material presented in this manual is for use in the development of an instructional program for drivers who either want or need to improve their driving performance. Three principal units are included: man and highway transportation, driver performance, and factors influencing driver behavior. Each unit is further divided into episodes…

  8. Identifying Innovative Interventions to Promote Healthy Eating Using Consumption-Oriented Food Supply Chain Analysis.

    Science.gov (United States)

    Hawkes, Corinna

    2009-07-01

    The mapping and analysis of supply chains is a technique increasingly used to address problems in the food system. Yet such supply chain management has not yet been applied as a means of encouraging healthier diets. Moreover, most policies recommended to promote healthy eating focus on the consumer end of the chain. This article proposes a consumption-oriented food supply chain analysis to identify the changes needed in the food supply chain to create a healthier food environment, measured in terms of food availability, prices, and marketing. Along with established forms of supply chain analysis, the method is informed by a historical overview of how food supply chains have changed over time. The method posits that the actors and actions in the chain are affected by organizational, financial, technological, and policy incentives and disincentives, which can in turn be levered for change. It presents a preliminary example of the supply of Coca-Cola beverages into school vending machines and identifies further potential applications. These include fruit and vegetable supply chains, local food chains, supply chains for health-promoting versions of food products, and identifying financial incentives in supply chains for healthier eating.

  9. Combination of meta-analysis and graph clustering to identify prognostic markers of ESCC

    Directory of Open Access Journals (Sweden)

    Hongyun Gao

    2012-01-01

    Full Text Available Esophageal squamous cell carcinoma (ESCC is one of the most malignant gastrointestinal cancers and occurs at a high frequency rate in China and other Asian countries. Recently, several molecular markers were identified for predicting ESCC. Notwithstanding, additional prognostic markers, with a clear understanding of their underlying roles, are still required. Through bioinformatics, a graph-clustering method by DPClus was used to detect co-expressed modules. The aim was to identify a set of discriminating genes that could be used for predicting ESCC through graph-clustering and GO-term analysis. The results showed that CXCL12, CYP2C9, TGM3, MAL, S100A9, EMP-1 and SPRR3 were highly associated with ESCC development. In our study, all their predicted roles were in line with previous reports, whereby the assumption that a combination of meta-analysis, graph-clustering and GO-term analysis is effective for both identifying differentially expressed genes, and reflecting on their functions in ESCC.

  10. Combination of meta-analysis and graph clustering to identify prognostic markers of ESCC.

    Science.gov (United States)

    Gao, Hongyun; Wang, Lishan; Cui, Shitao; Wang, Mingsong

    2012-04-01

    Esophageal squamous cell carcinoma (ESCC) is one of the most malignant gastrointestinal cancers and occurs at a high frequency rate in China and other Asian countries. Recently, several molecular markers were identified for predicting ESCC. Notwithstanding, additional prognostic markers, with a clear understanding of their underlying roles, are still required. Through bioinformatics, a graph-clustering method by DPClus was used to detect co-expressed modules. The aim was to identify a set of discriminating genes that could be used for predicting ESCC through graph-clustering and GO-term analysis. The results showed that CXCL12, CYP2C9, TGM3, MAL, S100A9, EMP-1 and SPRR3 were highly associated with ESCC development. In our study, all their predicted roles were in line with previous reports, whereby the assumption that a combination of meta-analysis, graph-clustering and GO-term analysis is effective for both identifying differentially expressed genes, and reflecting on their functions in ESCC.

  11. Simulators in driver training.

    NARCIS (Netherlands)

    2009-01-01

    In 2010, about 150 driving simulators were being used for the basic driver training in the Netherlands. According to theories about how people learn, simulator training has both advantages and disadvantages. In order to be able to learn something from a simulator, its technical quality must be adequ

  12. Effective Boolean dynamics analysis to identify functionally important genes in large-scale signaling networks.

    Science.gov (United States)

    Trinh, Hung-Cuong; Kwon, Yung-Keun

    2015-11-01

    Efficiently identifying functionally important genes in order to understand the minimal requirements of normal cellular development is challenging. To this end, a variety of structural measures have been proposed and their effectiveness has been investigated in recent literature; however, few studies have shown the effectiveness of dynamics-based measures. This led us to investigate a dynamic measure to identify functionally important genes, and the effectiveness of which was verified through application on two large-scale human signaling networks. We specifically consider Boolean sensitivity-based dynamics against an update-rule perturbation (BSU) as a dynamic measure. Through investigations on two large-scale human signaling networks, we found that genes with relatively high BSU values show slower evolutionary rate and higher proportions of essential genes and drug targets than other genes. Gene-ontology analysis showed clear differences between the former and latter groups of genes. Furthermore, we compare the identification accuracies of essential genes and drug targets via BSU and five well-known structural measures. Although BSU did not always show the best performance, it effectively identified the putative set of genes, which is significantly different from the results obtained via the structural measures. Most interestingly, BSU showed the highest synergy effect in identifying the functionally important genes in conjunction with other measures. Our results imply that Boolean-sensitive dynamics can be used as a measure to effectively identify functionally important genes in signaling networks.

  13. Drivers' Red Light Running Behavior Analysis%机动车闯红灯行为影响因素分析

    Institute of Scientific and Technical Information of China (English)

    王雪松; 李佳; 钟楚君

    2015-01-01

    信号控制交叉口由闯红灯引起的交通事故具有较高的伤亡率.为深入了解闯红灯行为的影响因素,利用人工记录与视频观测结合的方法对上海市4个信号控制交叉口进行调查.基于流行病学影响因素研究方法选择未闯红灯行为作为对照组与闯红灯行为对比,以排除无关因素.对调查数据进行行为编码,考虑到各个交叉口的异质性,基于随机效应逻辑斯特模型在交叉口层面分析驾驶环境、驾驶人特点、车辆特征对闯红灯行为的影响.结果表明,本地驾驶人、男性驾驶人、客车更容易闯红灯,流量大会增加闯红灯的可能性;此外,是否为本地车辆、车内是否有乘客对闯红灯行为也有显著影响.%Injury and fatal crash rates are generally higher at signalized intersections due to the red light running problems. To investigate red light running behavior, a research was conducted by collecting data manually and automatically with video cameras at four signalized intersections in Shanghai. Based on the investigation methods commonly used in epidemiology studies, this research compared driving behavior between vehicles running red light and vehicles not running red light to eliminate other influential factors' effect. The different driving behaviors were coded for analysis. Considering the differences in each inter-section's design and traffic flow, the research analyzes the impact of driving environment, characteristics of the drivers and vehicles on red light running behavior based on Random Effect Logistic Regression Model. The results show that local, male drivers and passenger vehicle are more likely to run red light and the probability of red light running increases when traffic volume is higher. In addition, whether the vehi-cle is local and whether there are passengers in the vehicle also have significant impact on red light run-ning behavior.

  14. Analysis of speed control behavior for driver on mountain highway%山区公路上驾驶人的车速控制行为分析

    Institute of Scientific and Technical Information of China (English)

    邵毅明; 毛嘉川; 刘胜川; 徐进

    2011-01-01

    根据大量的路上行驶试验和断面速度观测数据,分析了道路几何线形与驾驶人速度选择行为之间的关系,建立了能够描述弯道行驶、驶进与驶离弯道、直线行驶时的速度选择模型和加、减速度模型,从而生成沿道路里程变化的期望速度曲线.用机械动力学分析软件ADAMS建立汽车的动力学模型,用VB6.0编制道路模块,用VC++7.0编制驾驶人模型,仿真开始阶段生成期望轨迹和期望速度,然后采用前视预瞄的策略进行跟随,实现了车辆的自主驾驶.模拟结果表明:汽车期望速度和行驶路线与汽车实际行驶速度和行驶路线变化趋势相同,以期望速度作为汽车跟随的目标速度,符合汽车的动力学特性要求,能够引领汽车在复杂山区道路上的安全行驶.%The relationship between road geometric characteristic and driving speed was analyzed based on driving experiments and observation data on highways. The mathematic models of acceleration, deceleration and driver's speed control behavior on curve, entering or leaving curve,driving on tangent were obtained, and desired speed profiles along road were generated by the models. A car dynamics model was created by using mechanical dynamics analysis software ADAMS, roadway module was developed by using VB6.0, driver module was developed by using VC++7.0. At the simulation beginning, desired speed and desired path were generated, the car followed them in preview strategy, and the autonomous driving of car was achieved. Simulation result shows that desire speed and desired path change in a same trend with actual driving speed and path. Desired speed can be as the objective for car to follow, it adapts car dynamics characteristics, and can guide the driving of car on complex mountain highways safely. 4 tabs,9 figs, 14 refs.

  15. Identifying key parameters to differentiate groundwater flow systems using multifactorial analysis

    Science.gov (United States)

    Menció, Anna; Folch, Albert; Mas-Pla, Josep

    2012-11-01

    SummaryMultivariate techniques are useful in hydrogeological studies to reduce the complexity of large-scale data sets, and provide more understandable insight into the system hydrology. In this study, principal component analysis (PCA) has been used as an exploratory method to identify the key parameters that define distinct flow systems in the Selva basin (NE Spain). In this statistical analysis, all the information obtained in hydrogeological studies (that is, hydrochemical and isotopic data, but also potentiometric data) is used. Additionally, cluster analysis, based on PCA results, allows the associations between samples to be identified, and thus, corroborates the occurrence of different groundwater fluxes. PCA and cluster analysis reveal that two main groundwater flow systems exist in the Selva basin, each with distinct hydrochemical, isotopic, and potentiometric features. Regional groundwater fluxes are associated with high F- contents, and confined aquifer layers; while local fluxes are linked to nitrate polluted unconfined aquifers with a different recharge rates. In agreement with previous hydrogeological studies, these statistical methods stand as valid screening tools to highlight the fingerprint variables that can be used as indicators to facilitate further, more arduous, analytical approaches and a feasible interpretation of the whole data set.

  16. Efficient behavior of photosynthetic organelles via Pareto optimality, identifiability, and sensitivity analysis.

    Science.gov (United States)

    Carapezza, Giovanni; Umeton, Renato; Costanza, Jole; Angione, Claudio; Stracquadanio, Giovanni; Papini, Alessio; Lió, Pietro; Nicosia, Giuseppe

    2013-05-17

    In this work, we develop methodologies for analyzing and cross comparing metabolic models. We investigate three important metabolic networks to discuss the complexity of biological organization of organisms, modeling, and system properties. In particular, we analyze these metabolic networks because of their biotechnological and basic science importance: the photosynthetic carbon metabolism in a general leaf, the Rhodobacter spheroides bacterium, and the Chlamydomonas reinhardtii alga. We adopt single- and multi-objective optimization algorithms to maximize the CO 2 uptake rate and the production of metabolites of industrial interest or for ecological purposes. We focus both on the level of genes (e.g., finding genetic manipulations to increase the production of one or more metabolites) and on finding concentration enzymes for improving the CO 2 consumption. We find that R. spheroides is able to absorb an amount of CO 2 until 57.452 mmol h (-1) gDW (-1) , while C. reinhardtii obtains a maximum of 6.7331. We report that the Pareto front analysis proves extremely useful to compare different organisms, as well as providing the possibility to investigate them with the same framework. By using the sensitivity and robustness analysis, our framework identifies the most sensitive and fragile components of the biological systems we take into account, allowing us to compare their models. We adopt the identifiability analysis to detect functional relations among enzymes; we observe that RuBisCO, GAPDH, and FBPase belong to the same functional group, as suggested also by the sensitivity analysis.

  17. Gene expression signature analysis identifies vorinostat as a candidate therapy for gastric cancer.

    Directory of Open Access Journals (Sweden)

    Sofie Claerhout

    Full Text Available BACKGROUND: Gastric cancer continues to be one of the deadliest cancers in the world and therefore identification of new drugs targeting this type of cancer is thus of significant importance. The purpose of this study was to identify and validate a therapeutic agent which might improve the outcomes for gastric cancer patients in the future. METHODOLOGY/PRINCIPAL FINDINGS: Using microarray technology, we generated a gene expression profile of human gastric cancer-specific genes from human gastric cancer tissue samples. We used this profile in the Broad Institute's Connectivity Map analysis to identify candidate therapeutic compounds for gastric cancer. We found the histone deacetylase inhibitor vorinostat as the lead compound and thus a potential therapeutic drug for gastric cancer. Vorinostat induced both apoptosis and autophagy in gastric cancer cell lines. Pharmacological and genetic inhibition of autophagy however, increased the therapeutic efficacy of vorinostat, indicating that a combination of vorinostat with autophagy inhibitors may therapeutically be more beneficial. Moreover, gene expression analysis of gastric cancer identified a collection of genes (ITGB5, TYMS, MYB, APOC1, CBX5, PLA2G2A, and KIF20A whose expression was elevated in gastric tumor tissue and downregulated more than 2-fold by vorinostat treatment in gastric cancer cell lines. In contrast, SCGB2A1, TCN1, CFD, APLP1, and NQO1 manifested a reversed pattern. CONCLUSIONS/SIGNIFICANCE: We showed that analysis of gene expression signature may represent an emerging approach to discover therapeutic agents for gastric cancer, such as vorinostat. The observation of altered gene expression after vorinostat treatment may provide the clue to identify the molecular mechanism of vorinostat and those patients likely to benefit from vorinostat treatment.

  18. Quantitative assessment of in-solution digestion efficiency identifies optimal protocols for unbiased protein analysis

    DEFF Research Database (Denmark)

    Leon, Ileana R; Schwämmle, Veit; Jensen, Ole N;

    2013-01-01

    a combination of qualitative and quantitative LC-MS/MS methods and statistical data analysis. In contrast to previous studies we employed both standard qualitative as well as data-independent quantitative workflows to systematically assess trypsin digestion efficiency and bias using mitochondrial protein...... conditions (buffer, RapiGest, deoxycholate, urea), and two methods for removal of detergents prior to analysis of peptides (acid precipitation or phase separation with ethyl acetate). Our data-independent quantitative LC-MS/MS workflow quantified over 3700 distinct peptides with 96% completeness between all...... protocols and replicates, with an average 40% protein sequence coverage and an average of 11 peptides identified per protein. Systematic quantitative and statistical analysis of physicochemical parameters demonstrated that deoxycholate-assisted in-solution digestion combined with phase transfer allows...

  19. Identifying training deficiencies in military pilots by applying the human factors analysis and classification system.

    Science.gov (United States)

    Li, Wen-Chin; Harris, Don

    2013-01-01

    Without accurate analysis, it is difficult to identify training needs and develop the content of training programs required for preventing aviation accidents. The human factors analysis and classification system (HFACS) is based on Reason's system-wide model of human error. In this study, 523 accidents from the Republic of China Air Force were analyzed in which 1762 human errors were categorized. The results of the analysis showed that errors of judgment and poor decision-making were commonly reported amongst pilots. As a result, it was concluded that there was a need for military pilots to be trained specifically in making decisions in tactical environments. However, application of HFACS also allowed the identification of systemic training deficiencies within the organization further contributing to the accidents observed.

  20. A Comprehensive Gene Expression Meta-analysis Identifies Novel Immune Signatures in Rheumatoid Arthritis Patients

    Science.gov (United States)

    Afroz, Sumbul; Giddaluru, Jeevan; Vishwakarma, Sandeep; Naz, Saima; Khan, Aleem Ahmed; Khan, Nooruddin

    2017-01-01

    Rheumatoid arthritis (RA), a symmetric polyarticular arthritis, has long been feared as one of the most disabling forms of arthritis. Identification of gene signatures associated with RA onset and progression would lead toward development of novel diagnostics and therapeutic interventions. This study was undertaken to identify unique gene signatures of RA patients through large-scale meta-profiling of a diverse collection of gene expression data sets. We carried out a meta-analysis of 8 publicly available RA patients’ (107 RA patients and 76 healthy controls) gene expression data sets and further validated a few meta-signatures in RA patients through quantitative real-time PCR (RT-qPCR). We identified a robust meta-profile comprising 33 differentially expressed genes, which were consistently and significantly expressed across all the data sets. Our meta-analysis unearthed upregulation of a few novel gene signatures including PLCG2, HLA-DOB, HLA-F, EIF4E2, and CYFIP2, which were validated in peripheral blood mononuclear cell samples of RA patients. Further, functional and pathway enrichment analysis reveals perturbation of several meta-genes involved in signaling pathways pertaining to inflammation, antigen presentation, hypoxia, and apoptosis during RA. Additionally, PLCG2 (phospholipase Cγ2) popped out as a novel meta-gene involved in most of the pathways relevant to RA including inflammasome activation, platelet aggregation, and activation, thereby suggesting PLCG2 as a potential therapeutic target for controlling excessive inflammation during RA. In conclusion, these findings highlight the utility of meta-analysis approach in identifying novel gene signatures that might provide mechanistic insights into disease onset, progression and possibly lead toward the development of better diagnostic and therapeutic interventions against RA. PMID:28210261

  1. A Comprehensive Gene Expression Meta-analysis Identifies Novel Immune Signatures in Rheumatoid Arthritis Patients.

    Science.gov (United States)

    Afroz, Sumbul; Giddaluru, Jeevan; Vishwakarma, Sandeep; Naz, Saima; Khan, Aleem Ahmed; Khan, Nooruddin

    2017-01-01

    Rheumatoid arthritis (RA), a symmetric polyarticular arthritis, has long been feared as one of the most disabling forms of arthritis. Identification of gene signatures associated with RA onset and progression would lead toward development of novel diagnostics and therapeutic interventions. This study was undertaken to identify unique gene signatures of RA patients through large-scale meta-profiling of a diverse collection of gene expression data sets. We carried out a meta-analysis of 8 publicly available RA patients' (107 RA patients and 76 healthy controls) gene expression data sets and further validated a few meta-signatures in RA patients through quantitative real-time PCR (RT-qPCR). We identified a robust meta-profile comprising 33 differentially expressed genes, which were consistently and significantly expressed across all the data sets. Our meta-analysis unearthed upregulation of a few novel gene signatures including PLCG2, HLA-DOB, HLA-F, EIF4E2, and CYFIP2, which were validated in peripheral blood mononuclear cell samples of RA patients. Further, functional and pathway enrichment analysis reveals perturbation of several meta-genes involved in signaling pathways pertaining to inflammation, antigen presentation, hypoxia, and apoptosis during RA. Additionally, PLCG2 (phospholipase Cγ2) popped out as a novel meta-gene involved in most of the pathways relevant to RA including inflammasome activation, platelet aggregation, and activation, thereby suggesting PLCG2 as a potential therapeutic target for controlling excessive inflammation during RA. In conclusion, these findings highlight the utility of meta-analysis approach in identifying novel gene signatures that might provide mechanistic insights into disease onset, progression and possibly lead toward the development of better diagnostic and therapeutic interventions against RA.

  2. Shortest-path network analysis is a useful approach toward identifying genetic determinants of longevity.

    Directory of Open Access Journals (Sweden)

    J R Managbanag

    Full Text Available BACKGROUND: Identification of genes that modulate longevity is a major focus of aging-related research and an area of intense public interest. In addition to facilitating an improved understanding of the basic mechanisms of aging, such genes represent potential targets for therapeutic intervention in multiple age-associated diseases, including cancer, heart disease, diabetes, and neurodegenerative disorders. To date, however, targeted efforts at identifying longevity-associated genes have been limited by a lack of predictive power, and useful algorithms for candidate gene-identification have also been lacking. METHODOLOGY/PRINCIPAL FINDINGS: We have utilized a shortest-path network analysis to identify novel genes that modulate longevity in Saccharomyces cerevisiae. Based on a set of previously reported genes associated with increased life span, we applied a shortest-path network algorithm to a pre-existing protein-protein interaction dataset in order to construct a shortest-path longevity network. To validate this network, the replicative aging potential of 88 single-gene deletion strains corresponding to predicted components of the shortest-path longevity network was determined. Here we report that the single-gene deletion strains identified by our shortest-path longevity analysis are significantly enriched for mutations conferring either increased or decreased replicative life span, relative to a randomly selected set of 564 single-gene deletion strains or to the current data set available for the entire haploid deletion collection. Further, we report the identification of previously unknown longevity genes, several of which function in a conserved longevity pathway believed to mediate life span extension in response to dietary restriction. CONCLUSIONS/SIGNIFICANCE: This work demonstrates that shortest-path network analysis is a useful approach toward identifying genetic determinants of longevity and represents the first application of

  3. Integrated Analysis for Identifying Radix Astragali and Its Adulterants Based on DNA Barcoding

    Directory of Open Access Journals (Sweden)

    Sihao Zheng

    2014-01-01

    Full Text Available Radix Astragali is a popular herb used in traditional Chinese medicine for its proimmune and antidiabetic properties. However, methods are needed to help distinguish Radix Astragali from its varied adulterants. DNA barcoding is a widely applicable molecular method used to identify medicinal plants. Yet, its use has been hampered by genetic distance, base variation, and limitations of the bio-NJ tree. Herein, we report the validation of an integrated analysis method for plant species identification using DNA barcoding that focuses on genetic distance, identification efficiency, inter- and intraspecific variation, and barcoding gap. We collected 478 sequences from six candidate DNA barcodes (ITS2, ITS, psbA-trnH, rbcL, matK, and COI from 29 species of Radix Astragali and adulterants. The internal transcribed spacer (ITS sequence was demonstrated as the optimal barcode for identifying Radix Astragali and its adulterants. This new analysis method is helpful in identifying Radix Astragali and expedites the utilization and data mining of DNA barcoding.

  4. Messina: a novel analysis tool to identify biologically relevant molecules in disease.

    Directory of Open Access Journals (Sweden)

    Mark Pinese

    Full Text Available BACKGROUND: Morphologically similar cancers display heterogeneous patterns of molecular aberrations and follow substantially different clinical courses. This diversity has become the basis for the definition of molecular phenotypes, with significant implications for therapy. Microarray or proteomic expression profiling is conventionally employed to identify disease-associated genes, however, traditional approaches for the analysis of profiling experiments may miss molecular aberrations which define biologically relevant subtypes. METHODOLOGY/PRINCIPAL FINDINGS: Here we present Messina, a method that can identify those genes that only sometimes show aberrant expression in cancer. We demonstrate with simulated data that Messina is highly sensitive and specific when used to identify genes which are aberrantly expressed in only a proportion of cancers, and compare Messina to contemporary analysis techniques. We illustrate Messina by using it to detect the aberrant expression of a gene that may play an important role in pancreatic cancer. CONCLUSIONS/SIGNIFICANCE: Messina allows the detection of genes with profiles typical of markers of molecular subtype, and complements existing methods to assist the identification of such markers. Messina is applicable to any global expression profiling data, and to allow its easy application has been packaged into a freely-available stand-alone software package.

  5. Design Analysis Rules to Identify Proper Noun from Bengali Sentence for Universal Networking language

    Directory of Open Access Journals (Sweden)

    Md. Syeful Islam

    2014-08-01

    Full Text Available Now-a-days hundreds of millions of people of almost all levels of education and attitudes from different country communicate with each other for different purposes and perform their jobs on internet or other communication medium using various languages. Not all people know all language; therefore it is very difficult to communicate or works on various languages. In this situation the computer scientist introduce various inter language translation program (Machine translation. UNL is such kind of inter language translation program. One of the major problem of UNL is identified a name from a sentence, which is relatively simple in English language, because such entities start with a capital letter. In Bangla we do not have concept of small or capital letters. Thus we find difficulties in understanding whether a word is a proper noun or not. Here we have proposed analysis rules to identify proper noun from a sentence and established post converter which translate the name entity from Bangla to UNL. The goal is to make possible Bangla sentence conversion to UNL and vice versa. UNL system prove that the theoretical analysis of our proposed system able to identify proper noun from Bangla sentence and produce relative Universal word for UNL.

  6. A meta-analysis of 120 246 individuals identifies 18 new loci for fibrinogen concentration.

    Science.gov (United States)

    de Vries, Paul S; Chasman, Daniel I; Sabater-Lleal, Maria; Chen, Ming-Huei; Huffman, Jennifer E; Steri, Maristella; Tang, Weihong; Teumer, Alexander; Marioni, Riccardo E; Grossmann, Vera; Hottenga, Jouke J; Trompet, Stella; Müller-Nurasyid, Martina; Zhao, Jing Hua; Brody, Jennifer A; Kleber, Marcus E; Guo, Xiuqing; Wang, Jie Jin; Auer, Paul L; Attia, John R; Yanek, Lisa R; Ahluwalia, Tarunveer S; Lahti, Jari; Venturini, Cristina; Tanaka, Toshiko; Bielak, Lawrence F; Joshi, Peter K; Rocanin-Arjo, Ares; Kolcic, Ivana; Navarro, Pau; Rose, Lynda M; Oldmeadow, Christopher; Riess, Helene; Mazur, Johanna; Basu, Saonli; Goel, Anuj; Yang, Qiong; Ghanbari, Mohsen; Willemsen, Gonneke; Rumley, Ann; Fiorillo, Edoardo; de Craen, Anton J M; Grotevendt, Anne; Scott, Robert; Taylor, Kent D; Delgado, Graciela E; Yao, Jie; Kifley, Annette; Kooperberg, Charles; Qayyum, Rehan; Lopez, Lorna M; Berentzen, Tina L; Räikkönen, Katri; Mangino, Massimo; Bandinelli, Stefania; Peyser, Patricia A; Wild, Sarah; Trégouët, David-Alexandre; Wright, Alan F; Marten, Jonathan; Zemunik, Tatijana; Morrison, Alanna C; Sennblad, Bengt; Tofler, Geoffrey; de Maat, Moniek P M; de Geus, Eco J C; Lowe, Gordon D; Zoledziewska, Magdalena; Sattar, Naveed; Binder, Harald; Völker, Uwe; Waldenberger, Melanie; Khaw, Kay-Tee; Mcknight, Barbara; Huang, Jie; Jenny, Nancy S; Holliday, Elizabeth G; Qi, Lihong; Mcevoy, Mark G; Becker, Diane M; Starr, John M; Sarin, Antti-Pekka; Hysi, Pirro G; Hernandez, Dena G; Jhun, Min A; Campbell, Harry; Hamsten, Anders; Rivadeneira, Fernando; Mcardle, Wendy L; Slagboom, P Eline; Zeller, Tanja; Koenig, Wolfgang; Psaty, Bruce M; Haritunians, Talin; Liu, Jingmin; Palotie, Aarno; Uitterlinden, André G; Stott, David J; Hofman, Albert; Franco, Oscar H; Polasek, Ozren; Rudan, Igor; Morange, Pierre-Emmanuel; Wilson, James F; Kardia, Sharon L R; Ferrucci, Luigi; Spector, Tim D; Eriksson, Johan G; Hansen, Torben; Deary, Ian J; Becker, Lewis C; Scott, Rodney J; Mitchell, Paul; März, Winfried; Wareham, Nick J; Peters, Annette; Greinacher, Andreas; Wild, Philipp S; Jukema, J Wouter; Boomsma, Dorret I; Hayward, Caroline; Cucca, Francesco; Tracy, Russell; Watkins, Hugh; Reiner, Alex P; Folsom, Aaron R; Ridker, Paul M; O'Donnell, Christopher J; Smith, Nicholas L; Strachan, David P; Dehghan, Abbas

    2016-01-15

    Genome-wide association studies have previously identified 23 genetic loci associated with circulating fibrinogen concentration. These studies used HapMap imputation and did not examine the X-chromosome. 1000 Genomes imputation provides better coverage of uncommon variants, and includes indels. We conducted a genome-wide association analysis of 34 studies imputed to the 1000 Genomes Project reference panel and including ∼120 000 participants of European ancestry (95 806 participants with data on the X-chromosome). Approximately 10.7 million single-nucleotide polymorphisms and 1.2 million indels were examined. We identified 41 genome-wide significant fibrinogen loci; of which, 18 were newly identified. There were no genome-wide significant signals on the X-chromosome. The lead variants of five significant loci were indels. We further identified six additional independent signals, including three rare variants, at two previously characterized loci: FGB and IRF1. Together the 41 loci explain 3% of the variance in plasma fibrinogen concentration.

  7. The systematic functional analysis of plasmodium protein kinases identifies essential regulators of mosquito transmission

    KAUST Repository

    Tewari, Rita

    2010-10-21

    Although eukaryotic protein kinases (ePKs) contribute to many cellular processes, only three Plasmodium falciparum ePKs have thus far been identified as essential for parasite asexual blood stage development. To identify pathways essential for parasite transmission between their mammalian host and mosquito vector, we undertook a systematic functional analysis of ePKs in the genetically tractable rodent parasite Plasmodium berghei. Modeling domain signatures of conventional ePKs identified 66 putative Plasmodium ePKs. Kinomes are highly conserved between Plasmodium species. Using reverse genetics, we show that 23 ePKs are redundant for asexual erythrocytic parasite development in mice. Phenotyping mutants at four life cycle stages in Anopheles stephensi mosquitoes revealed functional clusters of kinases required for sexual development and sporogony. Roles for a putative SR protein kinase (SRPK) in microgamete formation, a conserved regulator of clathrin uncoating (GAK) in ookinete formation, and a likely regulator of energy metabolism (SNF1/KIN) in sporozoite development were identified. 2010 Elsevier Inc.

  8. A study on using texture analysis methods for identifying lobar fissure regions in isotropic CT images.

    Science.gov (United States)

    Wei, Q; Hu, Y

    2009-01-01

    The major hurdle for segmenting lung lobes in computed tomographic (CT) images is to identify fissure regions, which encase lobar fissures. Accurate identification of these regions is difficult due to the variable shape and appearance of the fissures, along with the low contrast and high noise associated with CT images. This paper studies the effectiveness of two texture analysis methods - the gray level co-occurrence matrix (GLCM) and the gray level run length matrix (GLRLM) - in identifying fissure regions from isotropic CT image stacks. To classify GLCM and GLRLM texture features, we applied a feed-forward back-propagation neural network and achieved the best classification accuracy utilizing 16 quantized levels for computing the GLCM and GLRLM texture features and 64 neurons in the input/hidden layers of the neural network. Tested on isotropic CT image stacks of 24 patients with the pathologic lungs, we obtained accuracies of 86% and 87% for identifying fissure regions using the GLCM and GLRLM methods, respectively. These accuracies compare favorably with surgeons/radiologists' accuracy of 80% for identifying fissure regions in clinical settings. This shows promising potential for segmenting lung lobes using the GLCM and GLRLM methods.

  9. Unscented Kalman filter with parameter identifiability analysis for the estimation of multiple parameters in kinetic models

    Directory of Open Access Journals (Sweden)

    Baker Syed

    2011-01-01

    Full Text Available Abstract In systems biology, experimentally measured parameters are not always available, necessitating the use of computationally based parameter estimation. In order to rely on estimated parameters, it is critical to first determine which parameters can be estimated for a given model and measurement set. This is done with parameter identifiability analysis. A kinetic model of the sucrose accumulation in the sugar cane culm tissue developed by Rohwer et al. was taken as a test case model. What differentiates this approach is the integration of an orthogonal-based local identifiability method into the unscented Kalman filter (UKF, rather than using the more common observability-based method which has inherent limitations. It also introduces a variable step size based on the system uncertainty of the UKF during the sensitivity calculation. This method identified 10 out of 12 parameters as identifiable. These ten parameters were estimated using the UKF, which was run 97 times. Throughout the repetitions the UKF proved to be more consistent than the estimation algorithms used for comparison.

  10. Unscented Kalman filter with parameter identifiability analysis for the estimation of multiple parameters in kinetic models.

    Science.gov (United States)

    Baker, Syed Murtuza; Poskar, C Hart; Junker, Björn H

    2011-10-11

    In systems biology, experimentally measured parameters are not always available, necessitating the use of computationally based parameter estimation. In order to rely on estimated parameters, it is critical to first determine which parameters can be estimated for a given model and measurement set. This is done with parameter identifiability analysis. A kinetic model of the sucrose accumulation in the sugar cane culm tissue developed by Rohwer et al. was taken as a test case model. What differentiates this approach is the integration of an orthogonal-based local identifiability method into the unscented Kalman filter (UKF), rather than using the more common observability-based method which has inherent limitations. It also introduces a variable step size based on the system uncertainty of the UKF during the sensitivity calculation. This method identified 10 out of 12 parameters as identifiable. These ten parameters were estimated using the UKF, which was run 97 times. Throughout the repetitions the UKF proved to be more consistent than the estimation algorithms used for comparison.

  11. Bus crash severity in the United-States: The role of driver behavior, service type, road factors and environmental conditions

    DEFF Research Database (Denmark)

    Kaplan, Sigal; Prato, Carlo Giacomo

    for the analysis are retrieved from the General Estimates System (GES) database for the years 2005-2009. Results show that accident severity increases: (i) for young bus drivers under the age of 25; (ii) for drivers beyond the age of 55, and most prominently for drivers over 65 years old; (iii) for female drivers...

  12. Practical In-Depth Analysis of IDS Alerts for Tracing and Identifying Potential Attackers on Darknet

    Directory of Open Access Journals (Sweden)

    Jungsuk Song

    2017-02-01

    Full Text Available The darknet (i.e., a set of unused IP addresses is a very useful solution for observing the global trends of cyber threats and analyzing attack activities on the Internet. Since the darknet is not connected with real systems, in most cases, the incoming packets on the darknet (‘the darknet traffic’ do not contain a payload. This means that we are unable to get real malware from the darknet traffic. This situation makes it difficult for security experts (e.g., academic researchers, engineers, operators, etc. to identify whether the source hosts of the darknet traffic are infected by real malware or not. In this paper, we present the overall procedure of the in-depth analysis between the darknet traffic and IDS alerts using real data collected at the Science and Technology Cyber Security Center (S&T CSC in Korea and provide the detailed in-depth analysis results. The ultimate goal of this paper is to provide practical experience, insight and know-how to security experts so that they are able to identify and trace the root cause of the darknet traffic. The experimental results show that correlation analysis between the darknet traffic and IDS alerts is very useful to discover potential attack hosts, especially internal hosts, and to find out what kinds of malware infected them.

  13. Comparative proteomic analysis of horseweed (Conyza canadensis) biotypes identifies candidate proteins for glyphosate resistance

    Science.gov (United States)

    González-Torralva, Fidel; Brown, Adrian P.; Chivasa, Stephen

    2017-01-01

    Emergence of glyphosate-resistant horseweed (Conyza canadensis) biotypes is an example of how unrelenting use of a single mode of action herbicide in agricultural weed control drives genetic adaptation in targeted species. While in other weeds glyphosate resistance arose from target site mutation or target gene amplification, the resistance mechanism in horseweed uses neither of these, being instead linked to reduced herbicide uptake and/or translocation. The molecular components underpinning horseweed glyphosate-resistance remain unknown. Here, we used an in vitro leaf disc system for comparative analysis of proteins extracted from control and glyphosate-treated tissues of glyphosate-resistant and glyphosate-susceptible biotypes. Analysis of shikimic acid accumulation, ABC-transporter gene expression, and cell death were used to select a suitable glyphosate concentration and sampling time for enriching proteins pivotal to glyphosate resistance. Protein gel analysis and mass spectrometry identified mainly chloroplast proteins differentially expressed between the biotypes before and after glyphosate treatment. Chloroplasts are the organelles in which the shikimate pathway, which is targeted by glyphosate, is located. Calvin cycle enzymes and proteins of unknown function were among the proteins identified. Our study provides candidate proteins that could be pivotal in engendering resistance and implicates chloroplasts as the primary sites driving glyphosate-resistance in horseweed. PMID:28198407

  14. Meta-CART: A tool to identify interactions between moderators in meta-analysis.

    Science.gov (United States)

    Li, Xinru; Dusseldorp, Elise; Meulman, Jacqueline J

    2017-02-01

    In the framework of meta-analysis, moderator analysis is usually performed only univariately. When several study characteristics are available that may account for treatment effect, standard meta-regression has difficulties in identifying interactions between them. To overcome this problem, meta-CART has been proposed: an approach that applies classification and regression trees (CART) to identify interactions, and then subgroup meta-analysis to test the significance of moderator effects. The previous version of meta-CART has its shortcomings: when applying CART, the sample sizes of studies are not taken into account, and the effect sizes are dichotomized around the median value. Therefore, this article proposes new meta-CART extensions, weighting study effect sizes by their accuracy, and using a regression tree to avoid dichotomization. In addition, new pruning rules are proposed. The performance of all versions of meta-CART was evaluated via a Monte Carlo simulation study. The simulation results revealed that meta-regression trees with random-effects weights and a 0.5-standard-error pruning rule perform best. The required sample size for meta-CART to achieve satisfactory performance depends on the number of study characteristics, the magnitude of the interactions, and the residual heterogeneity.

  15. Identifying patients with therapy-resistant depression by using factor analysis

    DEFF Research Database (Denmark)

    Andreasson, K; Liest, V; Lunde, M;

    2010-01-01

    INTRODUCTION: Attempts to identify the factor structure in patients with treatment-resistant depression have been very limited. METHODS: Principal component analysis was performed using the baseline datasets from 3 add-on studies [2 with repetitive transcranial magnetic stimulation and one...... with transcranial pulsed electromagnetic fields (T-PEMF)], in which the relative effect as percentage of improvement during the treatment period was analysed. RESULTS: We identified 2 major factors, the first of which was a general factor. The second was a dual factor consisting of a depression subscale comprising...... the negatively loaded items (covering the pure depression items) and a treatment resistant subscale comprising the positively loaded items (covering lassitude, concentration difficulties and sleep problems). These 2 dual subscales were used as outcome measures. Improvement on the treatment resistant subscale...

  16. Systematic analysis of public domain compound potency data identifies selective molecular scaffolds across druggable target families.

    Science.gov (United States)

    Hu, Ye; Wassermann, Anne Mai; Lounkine, Eugen; Bajorath, Jürgen

    2010-01-28

    Molecular scaffolds that yield target family-selective compounds are of high interest in pharmaceutical research. There continues to be considerable debate in the field as to whether chemotypes with a priori selectivity for given target families and/or targets exist and how they might be identified. What do currently available data tell us? We present a systematic and comprehensive selectivity-centric analysis of public domain target-ligand interactions. More than 200 molecular scaffolds are identified in currently available active compounds that are selective for established target families. A subset of these scaffolds is found to produce compounds with high selectivity for individual targets among closely related ones. These scaffolds are currently underrepresented in approved drugs.

  17. Identifying E-Business Model:A Value Chain-Based Analysis

    Institute of Scientific and Technical Information of China (English)

    ZENG Qingfeng; HUANG Lihua

    2004-01-01

    E-business will change the ways that all companies do business, and most traditional businesses will evolve from their current business model to a combination of place and space via e-business model To choose the proper e-business model becomes the important strategic concern for company to succeed The main objective of this paper is to investigate the analysis framework for identifying e-business model Based on the e-business process, from the value chain to the value net perspective. This paper provides a theoretical framework for identifying e-business models, and results in 11 e-business models. The strategic intend of every e-business model is discussed in the end of this paper. An enterprise e-business model design and implementation can be specified by the combination of one or more among 11 e-business models.

  18. Proteomic analysis of cell lines to identify the irinotecan resistance proteins

    Indian Academy of Sciences (India)

    Xing-Chen Peng; Feng-Ming Gong; Meng Wei; X I Chen; Y E Chen; K E Cheng; Feng Gao; Feng Xu; FENG Bi; Ji-Yan Liu

    2010-12-01

    Chemotherapeutic drug resistance is a frequent cause of treatment failure in colon cancer patients. Several mechanisms have been implicated in drug resistance. However, they are not sufficient to exhaustively account for this resistance emergence. In this study, two-dimensional gel electrophoresis (2-DE) and the PDQuest software analysis were applied to compare the differential expression of irinotecan-resistance-associated protein in human colon adenocarcinoma LoVo cells and irinotecan-resistant LoVo cells (LoVo/irinotecan). The differential protein dots were excised and analysed by ESI-Q-TOF mass spectrometry (MS). Fifteen proteins were identified, including eight proteins with decreased expression and seven proteins with increased expression. The identified known proteins included those that function in diverse biological processes such as cellular transcription, cell apoptosis, electron transport/redox regulation, cell proliferation/differentiation and retinol metabolism pathways. Identification of such proteins could allow improved understanding of the mechanisms leading to the acquisition of chemoresistance.

  19. Qualitative Comparative Analysis: A Hybrid Method for Identifying Factors Associated with Program Effectiveness.

    Science.gov (United States)

    Cragun, Deborah; Pal, Tuya; Vadaparampil, Susan T; Baldwin, Julie; Hampel, Heather; DeBate, Rita D

    2016-07-01

    Qualitative comparative analysis (QCA) was developed over 25 years ago to bridge the qualitative and quantitative research gap. Upon searching PubMed and the Journal of Mixed Methods Research, this review identified 30 original research studies that utilized QCA. Perceptions that QCA is complex and provides few relative advantages over other methods may be limiting QCA adoption. Thus, to overcome these perceptions, this article demonstrates how to perform QCA using data from fifteen institutions that implemented universal tumor screening (UTS) programs to identify patients at high risk for hereditary colorectal cancer. In this example, QCA revealed a combination of conditions unique to effective UTS programs. Results informed additional research and provided a model for improving patient follow-through after a positive screen.

  20. Gastric Cancer Associated Genes Identified by an Integrative Analysis of Gene Expression Data

    Science.gov (United States)

    Jiang, Bing; Li, Shuwen; Jiang, Zhi

    2017-01-01

    Gastric cancer is one of the most severe complex diseases with high morbidity and mortality in the world. The molecular mechanisms and risk factors for this disease are still not clear since the cancer heterogeneity caused by different genetic and environmental factors. With more and more expression data accumulated nowadays, we can perform integrative analysis for these data to understand the complexity of gastric cancer and to identify consensus players for the heterogeneous cancer. In the present work, we screened the published gene expression data and analyzed them with integrative tool, combined with pathway and gene ontology enrichment investigation. We identified several consensus differentially expressed genes and these genes were further confirmed with literature mining; at last, two genes, that is, immunoglobulin J chain and C-X-C motif chemokine ligand 17, were screened as novel gastric cancer associated genes. Experimental validation is proposed to further confirm this finding. PMID:28232943

  1. Gene-network analysis identifies susceptibility genes related to glycobiology in autism.

    Directory of Open Access Journals (Sweden)

    Bert van der Zwaag

    Full Text Available The recent identification of copy-number variation in the human genome has opened up new avenues for the discovery of positional candidate genes underlying complex genetic disorders, especially in the field of psychiatric disease. One major challenge that remains is pinpointing the susceptibility genes in the multitude of disease-associated loci. This challenge may be tackled by reconstruction of functional gene-networks from the genes residing in these loci. We applied this approach to autism spectrum disorder (ASD, and identified the copy-number changes in the DNA of 105 ASD patients and 267 healthy individuals with Illumina Humanhap300 Beadchips. Subsequently, we used a human reconstructed gene-network, Prioritizer, to rank candidate genes in the segmental gains and losses in our autism cohort. This analysis highlighted several candidate genes already known to be mutated in cognitive and neuropsychiatric disorders, including RAI1, BRD1, and LARGE. In addition, the LARGE gene was part of a sub-network of seven genes functioning in glycobiology, present in seven copy-number changes specifically identified in autism patients with limited co-morbidity. Three of these seven copy-number changes were de novo in the patients. In autism patients with a complex phenotype and healthy controls no such sub-network was identified. An independent systematic analysis of 13 published autism susceptibility loci supports the involvement of genes related to glycobiology as we also identified the same or similar genes from those loci. Our findings suggest that the occurrence of genomic gains and losses of genes associated with glycobiology are important contributors to the development of ASD.

  2. Finite Element Creep-Fatigue Analysis of a Welded Furnace Roll for Identifying Failure Root Cause

    Science.gov (United States)

    Yang, Y. P.; Mohr, W. C.

    2015-11-01

    Creep-fatigue induced failures are often observed in engineering components operating under high temperature and cyclic loading. Understanding the creep-fatigue damage process and identifying failure root cause are very important for preventing such failures and improving the lifetime of engineering components. Finite element analyses including a heat transfer analysis and a creep-fatigue analysis were conducted to model the cyclic thermal and mechanical process of a furnace roll in a continuous hot-dip coating line. Typically, the roll has a short life, heat transfer analysis was conducted to predict the temperature history of the roll by modeling heat convection from hot air inside the furnace. The creep-fatigue analysis was performed by inputting the predicted temperature history and applying mechanical loads. The analysis results showed that the failure was resulted from a creep-fatigue mechanism rather than a creep mechanism. The difference of material properties between the filler metal and the base metal is the root cause for the roll failure, which induces higher creep strain and stress in the interface between the weld and the HAZ.

  3. Systematic enrichment analysis of gene expression profiling studies identifies consensus pathways implicated in colorectal cancer development

    Directory of Open Access Journals (Sweden)

    Jesús Lascorz

    2011-01-01

    Full Text Available Background: A large number of gene expression profiling (GEP studies on colorectal carcinogenesis have been performed but no reliable gene signature has been identified so far due to the lack of reproducibility in the reported genes. There is growing evidence that functionally related genes, rather than individual genes, contribute to the etiology of complex traits. We used, as a novel approach, pathway enrichment tools to define functionally related genes that are consistently up- or down-regulated in colorectal carcinogenesis. Materials and Methods: We started the analysis with 242 unique annotated genes that had been reported by any of three recent meta-analyses covering GEP studies on genes differentially expressed in carcinoma vs normal mucosa. Most of these genes (218, 91.9% had been reported in at least three GEP studies. These 242 genes were submitted to bioinformatic analysis using a total of nine tools to detect enrichment of Gene Ontology (GO categories or Kyoto Encyclopedia of Genes and Genomes (KEGG pathways. As a final consistency criterion the pathway categories had to be enriched by several tools to be taken into consideration. Results: Our pathway-based enrichment analysis identified the categories of ribosomal protein constituents, extracellular matrix receptor interaction, carbonic anhydrase isozymes, and a general category related to inflammation and cellular response as significantly and consistently overrepresented entities. Conclusions: We triaged the genes covered by the published GEP literature on colorectal carcinogenesis and subjected them to multiple enrichment tools in order to identify the consistently enriched gene categories. These turned out to have known functional relationships to cancer development and thus deserve further investigation.

  4. A sequence-based approach to identify reference genes for gene expression analysis

    Directory of Open Access Journals (Sweden)

    Chari Raj

    2010-08-01

    Full Text Available Abstract Background An important consideration when analyzing both microarray and quantitative PCR expression data is the selection of appropriate genes as endogenous controls or reference genes. This step is especially critical when identifying genes differentially expressed between datasets. Moreover, reference genes suitable in one context (e.g. lung cancer may not be suitable in another (e.g. breast cancer. Currently, the main approach to identify reference genes involves the mining of expression microarray data for highly expressed and relatively constant transcripts across a sample set. A caveat here is the requirement for transcript normalization prior to analysis, and measurements obtained are relative, not absolute. Alternatively, as sequencing-based technologies provide digital quantitative output, absolute quantification ensues, and reference gene identification becomes more accurate. Methods Serial analysis of gene expression (SAGE profiles of non-malignant and malignant lung samples were compared using a permutation test to identify the most stably expressed genes across all samples. Subsequently, the specificity of the reference genes was evaluated across multiple tissue types, their constancy of expression was assessed using quantitative RT-PCR (qPCR, and their impact on differential expression analysis of microarray data was evaluated. Results We show that (i conventional references genes such as ACTB and GAPDH are highly variable between cancerous and non-cancerous samples, (ii reference genes identified for lung cancer do not perform well for other cancer types (breast and brain, (iii reference genes identified through SAGE show low variability using qPCR in a different cohort of samples, and (iv normalization of a lung cancer gene expression microarray dataset with or without our reference genes, yields different results for differential gene expression and subsequent analyses. Specifically, key established pathways in lung

  5. Stress prevention in bus drivers: Evaluation of 13 natural experiments

    NARCIS (Netherlands)

    Kompier, M.A.J.; Aust, B.; Berg, A.M. van den; Siegrist, J.

    2000-01-01

    The research aim was to select, compare, and analyze interventions and preventive actions from international bus companies to decrease bus drivers' occupational stress and sickness absenteeism. Through networking, international surveys, and literature study, 13 "natural experiments" were identified

  6. Cluster analysis for identifying sub-groups and selecting potential discriminatory variables in human encephalitis

    Directory of Open Access Journals (Sweden)

    Crowcroft Natasha S

    2010-12-01

    Full Text Available Abstract Background Encephalitis is an acute clinical syndrome of the central nervous system (CNS, often associated with fatal outcome or permanent damage, including cognitive and behavioural impairment, affective disorders and epileptic seizures. Infection of the central nervous system is considered to be a major cause of encephalitis and more than 100 different pathogens have been recognized as causative agents. However, a large proportion of cases have unknown disease etiology. Methods We perform hierarchical cluster analysis on a multicenter England encephalitis data set with the aim of identifying sub-groups in human encephalitis. We use the simple matching similarity measure which is appropriate for binary data sets and performed variable selection using cluster heatmaps. We also use heatmaps to visually assess underlying patterns in the data, identify the main clinical and laboratory features and identify potential risk factors associated with encephalitis. Results Our results identified fever, personality and behavioural change, headache and lethargy as the main characteristics of encephalitis. Diagnostic variables such as brain scan and measurements from cerebrospinal fluids are also identified as main indicators of encephalitis. Our analysis revealed six major clusters in the England encephalitis data set. However, marked within-cluster heterogeneity is observed in some of the big clusters indicating possible sub-groups. Overall, the results show that patients are clustered according to symptom and diagnostic variables rather than causal agents. Exposure variables such as recent infection, sick person contact and animal contact have been identified as potential risk factors. Conclusions It is in general assumed and is a common practice to group encephalitis cases according to disease etiology. However, our results indicate that patients are clustered with respect to mainly symptom and diagnostic variables rather than causal agents

  7. Understanding Collateral Evolution in Linux Device Drivers

    DEFF Research Database (Denmark)

    Padioleau, Yoann; Lawall, Julia Laetitia; Muller, Gilles

    2006-01-01

    no tools to help in this process, collateral evolution is thus time consuming and error prone.In this paper, we present a qualitative and quantitative assessment of collateral evolution in Linux device driver code. We provide a taxonomy of evolutions and collateral evolutions, and use an automated patch......-analysis tool that we have developed to measure the number of evolutions and collateral evolutions that affect device drivers between Linux versions 2.2 and 2.6. In particular, we find that from one version of Linux to the next, collateral evolutions can account for up to 35% of the lines modified in such code....

  8. Factor Analysis of the DePaul Symptom Questionnaire: Identifying Core Domains.

    Science.gov (United States)

    Jason, Leonard A; Sunnquist, Madison; Brown, Abigail; Furst, Jacob; Cid, Marjoe; Farietta, Jillianna; Kot, Bobby; Bloomer, Craig; Nicholson, Laura; Williams, Yolonda; Jantke, Rachel; Newton, Julia L; Strand, Elin Bolle

    2015-09-01

    The present study attempted to identify critical symptom domains of individuals with Myalgic Encephalomyelitis (ME) and chronic fatigue syndrome (CFS). Using patient and control samples collected in the United States, Great Britain, and Norway, exploratory factor analysis (EFA) was used to establish the underlying factor structure of ME and CFS symptoms. The EFA suggested a four-factor solution: post-exertional malaise, cognitive dysfunction, sleep difficulties, and a combined factor consisting of neuroendocrine, autonomic, and immune dysfunction symptoms. The use of empirical methods could help better understand the fundamental symptom domains of this illness.

  9. Analysis of Paired Primary-Metastatic Hormone-Receptor Positive Breast Tumors (HRPBC Uncovers Potential Novel Drivers of Hormonal Resistance.

    Directory of Open Access Journals (Sweden)

    Luis Manso

    Full Text Available We sought to identify genetic variants associated with disease relapse and failure to hormonal treatment in hormone-receptor positive breast cancer (HRPBC. We analyzed a series of HRPBC with distant relapse, by sequencing pairs (n = 11 of tumors (primary and metastases at >800X. Comparative genomic hybridization was performed as well. Top hits, based on the frequency of alteration and severity of the changes, were tested in the TCGA series. Genes determining the most parsimonious prognostic signature were studied for their functional role in vitro, by performing cell growth assays in hormonal-deprivation conditions, a setting that mimics treatment with aromatase inhibitors. Severe alterations were recurrently found in 18 genes in the pairs. However, only MYC, DNAH5, CSFR1, EPHA7, ARID1B, and KMT2C preserved an independent prognosis impact and/or showed a significantly different incidence of alterations between relapsed and non-relapsed cases in the TCGA series. The signature composed of MYC, KMT2C, and EPHA7 best discriminated the clinical course, (overall survival 90,7 vs. 144,5 months; p = 0.0001. Having an alteration in any of the genes of the signature implied a hazard ratio of death of 3.25 (p<0.0001, and early relapse during the adjuvant hormonal treatment. The presence of the D348N mutation in KMT2C and/or the T666I mutation in the kinase domain of EPHA7 conferred hormonal resistance in vitro. Novel inactivating mutations in KMT2C and EPHA7, which confer hormonal resistance, are linked to adverse clinical course in HRPBC.

  10. Analysis of Drivers'Behavior at Signalized Intersection%信号交叉口驾驶员行为博弈分析

    Institute of Scientific and Technical Information of China (English)

    黄选伟; 汪晶; 张邻

    2015-01-01

    为了研究车辆通过信号交叉口时的驾驶员决策行为,从博弈角度出发,根据影响驾驶员决策行为的性格因素,以及不同策略之间的势因素,通过时间细化,建立基于重复博弈下影响驾驶员决策行为的效用函数.通过驾驶员在行进过程中的决策行为,分析驾驶员获得的效用,得到动态博弈中驾驶员的最优决策.同时通过实例验证模型的可行性.例证表明:第一,对于冲动型的驾驶员在决策初始时刻最可能选择减速策略;第二,温和型的驾驶员选择加速或减速策略;第三,谨慎型的驾驶员选择减速策略.%In order to study the decision-making behavior of drivers at the signalized intersection, this study estab-lishes a utility function of drivers' driving behavior by reference to dynamic reduplicate game theory based on the drivers'personality that affects decision-making behavior and time refinement, and the relative potential factors among different strategies . According to the drivers'decision-making behavior in the process of driving and ana-lyzing the utility of the drivers'decision-making behavior, the drivers'optimal decision behaviors in a dynamic game are obtained, and the feasibility of the model is simultaneously verified. Experiments show that during deci-sion-making①impulsive drivers are more willing to choose deceleration strategy;②mild drivers prefer accelera-tion strategy or deceleration strategy;and③cautious drivers choose deceleration strategy.

  11. Whole Genome Analysis of Injectional Anthrax Identifies Two Disease Clusters Spanning More Than 13 Years

    Directory of Open Access Journals (Sweden)

    Paul Keim

    2015-11-01

    Lay Person Interpretation: Injectional anthrax has been plaguing heroin drug users across Europe for more than 10 years. In order to better understand this outbreak, we assessed genomic relationships of all available injectional anthrax strains from four countries spanning a >12 year period. Very few differences were identified using genome-based analysis, but these differentiated the isolates into two distinct clusters. This strongly supports a hypothesis of at least two separate anthrax spore contamination events perhaps during the drug production processes. Identification of two events would not have been possible from standard epidemiological analysis. These comprehensive data will be invaluable for classifying future injectional anthrax isolates and for future geographic attribution.

  12. Identifying Chemistry Prospective Teachers' Difficulties Encountered in Practice of The Subject Area Textbook Analysis Course

    Directory of Open Access Journals (Sweden)

    Zeynep Bak Kibar

    2010-12-01

    Full Text Available Prospective teachers should already be aware of possible mistakes in the textbooks and have knowledge of textbooks selection procedure and criteria. These knowledge is tried to being gained to prospective teachers at the Subject Area Textbook Analysis Course. It is important to identify the difficulties they encountered and the skills they gained from the point of implementing effectively this lesson. To research these problems, a case study was realized with 38 student teachers from Department of Secondary Science and Mathematics Education Chemistry Teaching Program at the Karadeniz Technical University Faculty of Fatih Education. Results suggest that prospective teachers gained the knowledge of research, teaching life, writing report, and analyzing textbook. Also, it was determined that they had difficulties in group working, literature reviewing, report writing, analyzing textbook, and critical analysis.

  13. Identifying energy saving opportunities in buildings by the analysis of time series data

    Energy Technology Data Exchange (ETDEWEB)

    Ferreira, Vasco [ENERGAIA- Energy Management Agency of Gaia, Vila Nova de Gaia (Portugal); Fleming, Paul; Ajiboye, Paul [De Montfort Univ., Leicester (United Kingdom). Inst. of Energy and Sustainable Development

    2003-07-01

    This paper describes how the analysis of time series energy data can be used to identify energy saving opportunities in buildings. Using readily available historic records of energy consumption, particularly quarter-hourly and half-hourly electricity time-series data, and with basic knowledge of the building, potential energy saving opportunities can be highlighted. A review of energy monitoring and targeting (MandT) procedures and techniques of analysing time series data have been carried out. The analysis of electricity time series data has been reviewed in the UK. This has involved analysing demand for power in 8 office buildings. Three different analytical approaches have been applied, simple visualisation and interpretation of energy use patterns, contour mapping and recurrent cumulative sum deviation (CUSUM). This paper concludes that such approaches to analyse electrical power demand could increase the cost-effectiveness and reliability of energy audits and surveys.

  14. Gene expression meta-analysis identifies metastatic pathways and transcription factors in breast cancer

    DEFF Research Database (Denmark)

    Thomassen, Mads; Tan, Qihua; Kruse, Torben

    2008-01-01

    tumors compared to non-metastasizing tumors. Meta-analysis has been used to determine overrepresentation of pathways and transcription factors targets, concordant deregulated in metastasizing breast tumors, in several data sets. RESULTS: The major findings are upregulation of cell cycle pathways...... system, angiogenesis, DNA repair and several signal transduction pathways are associated to metastasis. Finally several transcription factors e.g. E2F, NFY, and YY1 are identified as being involved in metastasis. CONCLUSIONS: By pathway meta-analysis many biological mechanisms beyond major...... studies. Besides classification of outcome, these global expression patterns may reflect biological mechanisms involved in metastasis of breast cancer. Our purpose has been to investigate pathways and transcription factors involved in metastasis by use of gene expression data sets. METHODS: We have...

  15. Towards a typology of business process management professionals: identifying patterns of competences through latent semantic analysis

    Science.gov (United States)

    Müller, Oliver; Schmiedel, Theresa; Gorbacheva, Elena; vom Brocke, Jan

    2016-01-01

    While researchers have analysed the organisational competences that are required for successful Business Process Management (BPM) initiatives, individual BPM competences have not yet been studied in detail. In this study, latent semantic analysis is used to examine a collection of 1507 BPM-related job advertisements in order to develop a typology of BPM professionals. This empirical analysis reveals distinct ideal types and profiles of BPM professionals on several levels of abstraction. A closer look at these ideal types and profiles confirms that BPM is a boundary-spanning field that requires interdisciplinary sets of competence that range from technical competences to business and systems competences. Based on the study's findings, it is posited that individual and organisational alignment with the identified ideal types and profiles is likely to result in high employability and organisational BPM success.

  16. Genomic Analysis of Uterine Lavage Fluid Detects Early Endometrial Cancers and Reveals a Prevalent Landscape of Driver Mutations in Women without Histopathologic Evidence of Cancer: A Prospective Cross-Sectional Study

    Science.gov (United States)

    Camacho, Sandra Catalina; Schumacher, Cassie A.; Irish, Jonathan C.; Harkins, Timothy T.; Belfer, Rachel; Kalir, Tamara; Reva, Boris; Dottino, Peter; Martignetti, John A.

    2016-01-01

    in tumor but at allele fractions significantly less than 1%. Of the remaining 95 patients diagnosed with benign or non-cancer pathology, 44 had no significant cancer mutations detected. Intriguingly, 51 patients without histopathologic evidence of cancer had relatively high allele fraction (1.0%–30.4%), cancer-associated mutations. Participants with detected driver and potential driver mutations were significantly older (mean age mutated = 57.96, 95% confidence interval [CI]: 3.30–∞, mean age no mutations = 50.35; p-value = 0.002; Benjamini-Hochberg [BH] adjusted p-value = 0.015) and more likely to be post-menopausal (p-value = 0.004; BH-adjusted p-value = 0.015) than those without these mutations. No associations were detected between mutation status and race/ethnicity, body mass index, diabetes, parity, and smoking status. Long-term follow-up was not presently available in this prospective study for those women without histopathologic evidence of cancer. Conclusions Using ultra-deep NGS, we identified somatic mutations in DNA extracted both from cell pellets and a never previously reported cfDNA fraction from the uterine lavage. Using our targeted sequencing approach, endometrial driver mutations were identified in all seven women who received a cancer diagnosis based on classic histopathology of tissue curettage obtained at the time of hysteroscopy. In addition, relatively high allele fraction driver mutations were identified in the lavage fluid of approximately half of the women without a cancer diagnosis. Increasing age and post-menopausal status were associated with the presence of these cancer-associated mutations, suggesting the prevalent existence of a premalignant landscape in women without clinical evidence of cancer. Given that a uterine lavage can be easily and quickly performed even outside of the operating room and in a physician’s office-based setting, our findings suggest the future possibility of this approach for screening women for the

  17. Analysis on spatio-temporal trends and drivers in vegetation growth during recent decades in Xinjiang, China

    Science.gov (United States)

    Du, Jiaqiang; Shu, Jianmin; Yin, Junqi; Yuan, Xinjie; Jiaerheng, Ahati; Xiong, Shanshan; He, Ping; Liu, Weiling

    2015-06-01

    Vegetation plays an important role in regulating the terrestrial carbon balance and the climate system, and also overwhelmingly dominates the provisioning of ecosystem services. In this study, a non-stationary 1982-2012 AVHRR NDVI3g time series, the newest dataset, were used to evaluate spatio-temporal patterns of seasonal vegetation changes in Xinjiang province of China at regional, biome and pixel scales over progressively longer periods from 18 to 31 years, starting in 1982, and their linkages to climatic factors and human activities were analyzed. At regional scale, the increases were statistically significant for autumn NDVI during fourteen periods, for growing season and summer NDVI during the most periods, and for spring only during the first four periods. The rates of NDVI increase in growing season and all seasons significantly decreased over fourteen periods. At pixel scale, areas with significant browning rapidly increased over fourteen periods for growing season and all seasons, and these areas were mainly concentrated in northern desert of Xinjiang. Vegetation growth in Xinjiang was regulated by both moisture and thermal conditions: the response of NDVI in spring and autumn was more sensitive to thermal factors, such as temperature and potential evapotranspiration, and correlations between NDVI and precipitation and between NDVI and humidity index were stronger in summer and growing season. Extensive use of fertilizers and expanded farmland irrigated area increased vegetation growth for cropland. However, the rapid increase in the proportion of cotton cultivation and use of drip irrigation may reduce spring NDVI in the part of farmlands. Trend analysis during the multiple nested time series may contribute to a better and deep understanding of NDVI dynamic and foreseeing changes in the future. Accordingly, NDVI in Xinjiang will continuously increase at regional scale and the areas showing significant browning will also furthermore grow.

  18. Multicomponent statistical analysis to identify flow and transport processes in a highly-complex environment

    Science.gov (United States)

    Moeck, Christian; Radny, Dirk; Borer, Paul; Rothardt, Judith; Auckenthaler, Adrian; Berg, Michael; Schirmer, Mario

    2016-11-01

    A combined approach of multivariate statistical analysis, namely factor analysis (FA) and hierarchical cluster analysis (HCA), interpretation of geochemical processes, stable water isotope data and organic micropollutants enabling to assess spatial patterns of water types was performed for a study area in Switzerland, where drinking water production is close to different potential input pathways for contamination. To avoid drinking water contamination, artificial groundwater recharge with surface water into an aquifer is used to create a hydraulic barrier between potential intake pathways for contamination and drinking water extraction wells. Inter-aquifer mixing in the subsurface is identified, where a high amount of artificial infiltrated surface water is mixed with a lesser amount of water originating from the regional flow pathway in the vicinity of drinking water extraction wells. The spatial distribution of different water types can be estimated and a conceptual system understanding is developed. Results of the multivariate statistical analysis are comparable with gained information from isotopic data and organic micropollutants analyses. The integrated approach using different kinds of observations can be easily transferred to a variety of hydrological settings to synthesise and evaluate large hydrochemical datasets. The combination of additional data with different information content is conceivable and enabled effective interpretation of hydrological processes. Using the applied approach leads to more sound conceptual system understanding acting as the very basis to develop improved water resources management practices in a sustainable way.

  19. Identifying changes in the support networks of end-of-life carers using social network analysis.

    Science.gov (United States)

    Leonard, Rosemary; Horsfall, Debbie; Noonan, Kerrie

    2015-06-01

    End-of-life caring is often associated with reduced social networks for both the dying person and for the carer. However, those adopting a community participation and development approach, see the potential for the expansion and strengthening of networks. This paper uses Knox, Savage and Harvey's definitions of three generations social network analysis to analyse the caring networks of people with a terminal illness who are being cared for at home and identifies changes in these caring networks that occurred over the period of caring. Participatory network mapping of initial and current networks was used in nine focus groups. The analysis used key concepts from social network analysis (size, density, transitivity, betweenness and local clustering) together with qualitative analyses of the group's reflections on the maps. The results showed an increase in the size of the networks and that ties between the original members of the network strengthened. The qualitative data revealed the importance between core and peripheral network members and the diverse contributions of the network members. The research supports the value of third generation social network analysis and the potential for end-of-life caring to build social capital.

  20. Mutual exclusivity analysis of genetic and epigenetic drivers in melanoma identifies a link between p14ARF and retinoic acid receptor β signaling

    DEFF Research Database (Denmark)

    Dahl, Christina; Christensen, Claus; Jonsson, Goran

    2013-01-01

    affecting p14ARF (P melanocytes, and that the steady-state levels of p14ARF in these cells...... are regulated via RARβ. Furthermore, we show that the ability of ATRA to induce senescence is reduced in p14ARF-depleted melanocytes, and we provide proof-of-concept that ATRA can induce irreversible growth arrest in melanoma cells with an intact RARβ-p14ARF axis, independent of p16INK4A and p53 status...

  1. Comprehensive genomic analysis of malignant pleural mesothelioma identifies recurrent mutations, gene fusions and splicing alterations.

    Science.gov (United States)

    Bueno, Raphael; Stawiski, Eric W; Goldstein, Leonard D; Durinck, Steffen; De Rienzo, Assunta; Modrusan, Zora; Gnad, Florian; Nguyen, Thong T; Jaiswal, Bijay S; Chirieac, Lucian R; Sciaranghella, Daniele; Dao, Nhien; Gustafson, Corinne E; Munir, Kiara J; Hackney, Jason A; Chaudhuri, Amitabha; Gupta, Ravi; Guillory, Joseph; Toy, Karen; Ha, Connie; Chen, Ying-Jiun; Stinson, Jeremy; Chaudhuri, Subhra; Zhang, Na; Wu, Thomas D; Sugarbaker, David J; de Sauvage, Frederic J; Richards, William G; Seshagiri, Somasekar

    2016-04-01

    We analyzed transcriptomes (n = 211), whole exomes (n = 99) and targeted exomes (n = 103) from 216 malignant pleural mesothelioma (MPM) tumors. Using RNA-seq data, we identified four distinct molecular subtypes: sarcomatoid, epithelioid, biphasic-epithelioid (biphasic-E) and biphasic-sarcomatoid (biphasic-S). Through exome analysis, we found BAP1, NF2, TP53, SETD2, DDX3X, ULK2, RYR2, CFAP45, SETDB1 and DDX51 to be significantly mutated (q-score ≥ 0.8) in MPMs. We identified recurrent mutations in several genes, including SF3B1 (∼2%; 4/216) and TRAF7 (∼2%; 5/216). SF3B1-mutant samples showed a splicing profile distinct from that of wild-type tumors. TRAF7 alterations occurred primarily in the WD40 domain and were, except in one case, mutually exclusive with NF2 alterations. We found recurrent gene fusions and splice alterations to be frequent mechanisms for inactivation of NF2, BAP1 and SETD2. Through integrated analyses, we identified alterations in Hippo, mTOR, histone methylation, RNA helicase and p53 signaling pathways in MPMs.

  2. Gene network analysis in a pediatric cohort identifies novel lung function genes.

    Directory of Open Access Journals (Sweden)

    Bruce A Ong

    Full Text Available Lung function is a heritable trait and serves as an important clinical predictor of morbidity and mortality for pulmonary conditions in adults, however, despite its importance, no studies have focused on uncovering pediatric-specific loci influencing lung function. To identify novel genetic determinants of pediatric lung function, we conducted a genome-wide association study (GWAS of four pulmonary function traits, including FVC, FEV1, FEV1/FVC and FEF25-75% in 1556 children. Further, we carried out gene network analyses for each trait including all SNPs with a P-value of <1.0 × 10(-3 from the individual GWAS. The GWAS identified SNPs with notable trends towards association with the pulmonary function measures, including the previously described INTS12 locus association with FEV1 (pmeta=1.41 × 10(-7. The gene network analyses identified 34 networks of genes associated with pulmonary function variables in Caucasians. Of those, the glycoprotein gene network reached genome-wide significance for all four variables. P-value range pmeta=6.29 × 10(-4 - 2.80 × 10(-8 on meta-analysis. In this study, we report on specific pathways that are significantly associated with pediatric lung function at genome-wide significance. In addition, we report the first loci associated with lung function in both pediatric Caucasian and African American populations.

  3. Genome-wide association scan meta-analysis identifies three Loci influencing adiposity and fat distribution.

    Directory of Open Access Journals (Sweden)

    Cecilia M Lindgren

    2009-06-01

    Full Text Available To identify genetic loci influencing central obesity and fat distribution, we performed a meta-analysis of 16 genome-wide association studies (GWAS, N = 38,580 informative for adult waist circumference (WC and waist-hip ratio (WHR. We selected 26 SNPs for follow-up, for which the evidence of association with measures of central adiposity (WC and/or WHR was strong and disproportionate to that for overall adiposity or height. Follow-up studies in a maximum of 70,689 individuals identified two loci strongly associated with measures of central adiposity; these map near TFAP2B (WC, P = 1.9x10(-11 and MSRA (WC, P = 8.9x10(-9. A third locus, near LYPLAL1, was associated with WHR in women only (P = 2.6x10(-8. The variants near TFAP2B appear to influence central adiposity through an effect on overall obesity/fat-mass, whereas LYPLAL1 displays a strong female-only association with fat distribution. By focusing on anthropometric measures of central obesity and fat distribution, we have identified three loci implicated in the regulation of human adiposity.

  4. Quantitative bioassay to identify antimicrobial drugs through drug interaction fingerprint analysis.

    Science.gov (United States)

    Weinstein, Zohar B; Zaman, Muhammad H

    2017-02-16

    Drug interaction analysis, which reports the extent to which the presence of one drug affects the efficacy of another, is a powerful tool to select potent combinatorial therapies and predict connectivity between cellular components. Combinatorial effects of drug pairs often vary even for drugs with similar mechanism of actions. Therefore, drug interaction fingerprinting may be harnessed to differentiate drug identities. We developed a method to analyze drug interactions for the application of identifying active pharmaceutical ingredients, an essential step to assess drug quality. We developed a novel approach towards the identification of active pharmaceutical ingredients by comparing drug interaction fingerprint similarity metrics such as correlation and Euclidean distance. To expedite this method, we used bioluminescent E. coli in a simplified checkerboard assay to generate unique drug interaction fingerprints of antimicrobial drugs. Of 30 antibiotics studied, 29 could be identified based on their drug interaction fingerprints. We present drug interaction fingerprint analysis as a cheap, sensitive and quantitative method towards substandard and counterfeit drug detection.

  5. Pathway analysis of smoking quantity in multiple GWAS identifies cholinergic and sensory pathways.

    Directory of Open Access Journals (Sweden)

    Oscar Harari

    Full Text Available Cigarette smoking is a common addiction that increases the risk for many diseases, including lung cancer and chronic obstructive pulmonary disease. Genome-wide association studies (GWAS have successfully identified and validated several susceptibility loci for nicotine consumption and dependence. However, the trait variance explained by these genes is only a small fraction of the estimated genetic risk. Pathway analysis complements single marker methods by including biological knowledge into the evaluation of GWAS, under the assumption that causal variants lie in functionally related genes, enabling the evaluation of a broad range of signals. Our approach to the identification of pathways enriched for multiple genes associated with smoking quantity includes the analysis of two studies and the replication of common findings in a third dataset. This study identified pathways for the cholinergic receptors, which included SNPs known to be genome-wide significant; as well as novel pathways, such as genes involved in the sensory perception of smell, that do not contain any single SNP that achieves that stringent threshold.

  6. Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci

    Science.gov (United States)

    Stahl, Eli A.; Raychaudhuri, Soumya; Remmers, Elaine F.; Xie, Gang; Eyre, Stephen; Thomson, Brian P.; Li, Yonghong; Kurreeman, Fina A. S.; Zhernakova, Alexandra; Hinks, Anne; Guiducci, Candace; Chen, Robert; Alfredsson, Lars; Amos, Christopher I.; Ardlie, Kristin G.; Barton, Anne; Bowes, John; Brouwer, Elisabeth; Burtt, Noel P.; Catanese, Joseph J.; Coblyn, Jonathan; Coenen, Marieke JH; Costenbader, Karen H.; Criswell, Lindsey A.; Crusius, J. Bart A.; Cui, Jing; de Bakker, Paul I.W.; De Jager, Phillip L.; Ding, Bo; Emery, Paul; Flynn, Edward; Harrison, Pille; Hocking, Lynne J.; Huizinga, Tom W. J.; Kastner, Daniel L.; Ke, Xiayi; Lee, Annette T.; Liu, Xiangdong; Martin, Paul; Morgan, Ann W.; Padyukov, Leonid; Posthumus, Marcel D.; Radstake, Timothy RDJ; Reid, David M.; Seielstad, Mark; Seldin, Michael F.; Shadick, Nancy A.; Steer, Sophia; Tak, Paul P.; Thomson, Wendy; van der Helm-van Mil, Annette H. M.; van der Horst-Bruinsma, Irene E.; van der Schoot, C. Ellen; van Riel, Piet LCM; Weinblatt, Michael E.; Wilson, Anthony G.; Wolbink, Gert Jan; Wordsworth, Paul; Wijmenga, Cisca; Karlson, Elizabeth W.; Toes, Rene E. M.; de Vries, Niek; Begovich, Ann B.; Worthington, Jane; Siminovitch, Katherine A.; Gregersen, Peter K.; Klareskog, Lars; Plenge, Robert M.

    2014-01-01

    To identify novel genetic risk factors for rheumatoid arthritis (RA), we conducted a genome-wide association study (GWAS) meta-analysis of 5,539 autoantibody positive RA cases and 20,169 controls of European descent, followed by replication in an independent set of 6,768 RA cases and 8,806 controls. Of 34 SNPs selected for replication, 7 novel RA risk alleles were identified at genome-wide significance (P<5×10−8) in analysis of all 41,282 samples. The associated SNPs are near genes of known immune function, including IL6ST, SPRED2, RBPJ, CCR6, IRF5, and PXK. We also refined the risk alleles at two established RA risk loci (IL2RA and CCL21) and confirmed the association at AFF3. These new associations bring the total number of confirmed RA risk loci to 31 among individuals of European ancestry. An additional 11 SNPs replicated at P<0.05, many of which are validated autoimmune risk alleles, suggesting that most represent bona fide RA risk alleles. PMID:20453842

  7. Proteomic analysis identifies interleukin 11 regulated plasma membrane proteins in human endometrial epithelial cells in vitro

    Directory of Open Access Journals (Sweden)

    Stanton Peter G

    2011-05-01

    Full Text Available Abstract Background During the peri-implantation period, the embryo adheres to an adequately prepared or receptive endometrial surface epithelium. Abnormal embryo adhesion to the endometrium results in embryo implantation failure and infertility. Endometrial epithelial cell plasma membrane proteins critical in regulating adhesion may potentially be infertility biomarkers or targets for treating infertility. Interleukin (IL 11 regulates human endometrial epithelial cells (hEEC adhesion. Its production is abnormal in women with infertility. The objective of the study was to identify IL11 regulated plasma membrane proteins in hEEC in vitro using a proteomic approach. Methods Using a 2D-differential in-gel electrophoresis (DIGE electrophoresis combined with LCMS/MS mass spectrometry approach, we identified 20 unique plasma membrane proteins differentially regulated by IL11 in ECC-1 cells, a hEEC derived cell line. Two IL11 regulated proteins with known roles in cell adhesion, annexin A2 (ANXA2 and flotillin-1 (FLOT1, were validated by Western blot and immunocytochemistry in hEEC lines (ECC-1 and an additional cell line, Ishikawa and primary hEEC. Flotilin-1 was further validated by immunohistochemistry in human endometrium throughout the menstrual cycle (n = 6-8/cycle. Results 2D-DIGE analysis identified 4 spots that were significantly different between control and IL11 treated group. Of these 4 spots, there were 20 proteins that were identified with LCMS/MS. Two proteins; ANXA2 and FLOT1 were chosen for further analyses and have found to be significantly up-regulated following IL11 treatment. Western blot analysis showed a 2-fold and a 2.5-fold increase of ANXA2 in hEEC membrane fraction of ECC-1 and Ishikawa cells respectively. Similarly, a 1.8-fold and a 2.3/2.4-fold increase was also observed for FLOT1 in hEEC membrane fraction of ECC-1 and Ishikawa cells respectively. In vitro, IL11 induced stronger ANXA2 expression on cell surface of primary h

  8. Drivers and moderators of business decline

    Directory of Open Access Journals (Sweden)

    Marius Pretorius

    2010-12-01

    Full Text Available Purpose: Reports of business failure elicit various reactions, while research in this domain often appears to be limited by a lack of access to information about failure and by the negativity that surrounds it. Those who have experienced failure do not readily talk about it, or they disappear from the radar screen of researchers. Yet failure is preceded by decline which, when focused on strategically, can reduce eventual failures if early action is taken. The main purpose of this study is to develop a conceptual framework or typology of the drivers and moderators of business decline. Design/methodology/approach: After applying the "grounded theory" approach to the academic literature on decline and failure, a conceptual framework for the variables that drive and moderate business decline is proposed. Findings: The study proposes that decline has three core drivers, three peripheral drivers and four moderators. The core drivers identified are: resource munificence; leadership as origin; and causality (strategic versus operational origin of decline. The three peripheral drivers are: unique preconditions; continuous decisions impact; and extremes dichotomy. The study describes four moderators of the drivers: life cycle stage; stakeholder perspective; quantitative versus qualitative nature of signs and causes; and finally the age and size effects. Research limitations/implications: The proposed conceptual framework is based on literature only, although it has found support during discussions with practitioners. It is proposed to readers of this journal for scrutiny and validation. Practical implications: Strategists need to understand what drives decline in order to act timeously; practitioners who have an insight into the moderators with their impacts could make better decisions in response to decline in organisations and possibly avoid business failure. Originality/Value: Understanding business decline is still a huge theoretical challenge, which

  9. Methylation Linear Discriminant Analysis (MLDA for identifying differentially methylated CpG islands

    Directory of Open Access Journals (Sweden)

    Vass J Keith

    2008-08-01

    Full Text Available Abstract Background Hypermethylation of promoter CpG islands is strongly correlated to transcriptional gene silencing and epigenetic maintenance of the silenced state. As well as its role in tumor development, CpG island methylation contributes to the acquisition of resistance to chemotherapy. Differential Methylation Hybridisation (DMH is one technique used for genome-wide DNA methylation analysis. The study of such microarray data sets should ideally account for the specific biological features of DNA methylation and the non-symmetrical distribution of the ratios of unmethylated and methylated sequences hybridised on the array. We have therefore developed a novel algorithm tailored to this type of data, Methylation Linear Discriminant Analysis (MLDA. Results MLDA was programmed in R (version 2.7.0 and the package is available at CRAN 1. This approach utilizes linear regression models of non-normalised hybridisation data to define methylation status. Log-transformed signal intensities of unmethylated controls on the microarray are used as a reference. The signal intensities of DNA samples digested with methylation sensitive restriction enzymes and mock digested are then transformed to the likelihood of a locus being methylated using this reference. We tested the ability of MLDA to identify loci differentially methylated as analysed by DMH between cisplatin sensitive and resistant ovarian cancer cell lines. MLDA identified 115 differentially methylated loci and 23 out of 26 of these loci have been independently validated by Methylation Specific PCR and/or bisulphite pyrosequencing. Conclusion MLDA has advantages for analyzing methylation data from CpG island microarrays, since there is a clear rational for the definition of methylation status, it uses DMH data without between-group normalisation and is less influenced by cross-hybridisation of loci. The MLDA algorithm successfully identified differentially methylated loci between two classes of

  10. Drivers anticipate lead-vehicle conflicts during automated longitudinal control: Sensory cues capture driver attention and promote appropriate and timely responses.

    Science.gov (United States)

    Morando, Alberto; Victor, Trent; Dozza, Marco

    2016-12-01

    Adaptive Cruise Control (ACC) has been shown to reduce the exposure to critical situations by maintaining a safe speed and headway. It has also been shown that drivers adapt their visual behavior in response to the driving task demand with ACC, anticipating an impending lead vehicle conflict by directing their eyes to the forward path before a situation becomes critical. The purpose of this paper is to identify the causes related to this anticipatory mechanism, by investigating drivers' visual behavior while driving with ACC when a potential critical situation is encountered, identified as a forward collision warning (FCW) onset (including false positive warnings). This paper discusses how sensory cues capture attention to the forward path in anticipation of the FCW onset. The analysis used the naturalistic database EuroFOT to examine visual behavior with respect to two manually-coded metrics, glance location and glance eccentricity, and then related the findings to vehicle data (such as speed, acceleration, and radar information). Three sensory cues (longitudinal deceleration, looming, and brake lights) were found to be relevant for capturing driver attention and increase glances to the forward path in anticipation of the threat; the deceleration cue seems to be dominant. The results also show that the FCW acts as an effective attention-orienting mechanism when no threat anticipation is present. These findings, relevant to the study of automation, provide additional information about drivers' response to potential lead-vehicle conflicts when longitudinal control is automated. Moreover, these results suggest that sensory cues are important for alerting drivers to an impending critical situation, allowing for a prompt reaction.

  11. Real-time analysis application for identifying bursty local areas related to emergency topics.

    Science.gov (United States)

    Sakai, Tatsuhiro; Tamura, Keiichi

    2015-01-01

    Since social media started getting more attention from users on the Internet, social media has been one of the most important information source in the world. Especially, with the increasing popularity of social media, data posted on social media sites are rapidly becoming collective intelligence, which is a term used to refer to new media that is displacing traditional media. In this paper, we focus on geotagged tweets on the Twitter site. These geotagged tweets are referred to as georeferenced documents because they include not only a short text message, but also the documents' posting time and location. Many researchers have been tackling the development of new data mining techniques for georeferenced documents to identify and analyze emergency topics, such as natural disasters, weather, diseases, and other incidents. In particular, the utilization of geotagged tweets to identify and analyze natural disasters has received much attention from administrative agencies recently because some case studies have achieved compelling results. In this paper, we propose a novel real-time analysis application for identifying bursty local areas related to emergency topics. The aim of our new application is to provide new platforms that can identify and analyze the localities of emergency topics. The proposed application is composed of three core computational intelligence techniques: the Naive Bayes classifier technique, the spatiotemporal clustering technique, and the burst detection technique. Moreover, we have implemented two types of application interface: a Web application interface and an android application interface. To evaluate the proposed application, we have implemented a real-time weather observation system embedded the proposed application. we used actual crawling geotagged tweets posted on the Twitter site. The weather observation system successfully detected bursty local areas related to observed emergency weather topics.

  12. Transcriptomic analysis using olive varieties and breeding progenies identify candidate genes involved in plant architecture

    Directory of Open Access Journals (Sweden)

    Juan José eGonzález Plaza

    2016-03-01

    Full Text Available Plant architecture is a critical trait in fruit crops that can significantly influence yield, pruning, planting density and harvesting. Little is known about how plant architecture is genetically determined in olive, were most of the existing varieties are traditional with an architecture poorly suited for modern growing and harvesting systems. In the present study, we have carried out microarray analysis of meristematic tissue to compare expression profiles of olive varieties displaying differences in architecture, as well as seedlings from their cross pooled on the basis of their sharing architecture-related phenotypes. The microarray used, previously developed by our group has already been applied to identify candidates genes involved in regulating juvenile to adult transition in the shoot apex of seedlings. Varieties with distinct architecture phenotypes and individuals from segregating progenies displaying opposite architecture features were used to link phenotype to expression. Here, we identify 2,252 differentially expressed genes associated to differences in plant architecture. Microarray results were validated by quantitative RT-PCR carried out on genes with functional annotation likely related to plant architecture. Twelve of these genes were further analyzed in individual seedlings of the corresponding pool. We also examined Arabidopsis mutants in putative orthologs of these targeted candidate genes, finding altered architecture for most of them. This supports a functional conservation between species and potential biological relevance of the candidate genes identified. This study is the first to identify genes associated to plant architecture in olive, and the results obtained could be of great help in future programs aimed at selecting phenotypes adapted to modern cultivation practices in this species.

  13. Transcriptomic Analysis Using Olive Varieties and Breeding Progenies Identifies Candidate Genes Involved in Plant Architecture.

    Science.gov (United States)

    González-Plaza, Juan J; Ortiz-Martín, Inmaculada; Muñoz-Mérida, Antonio; García-López, Carmen; Sánchez-Sevilla, José F; Luque, Francisco; Trelles, Oswaldo; Bejarano, Eduardo R; De La Rosa, Raúl; Valpuesta, Victoriano; Beuzón, Carmen R

    2016-01-01

    Plant architecture is a critical trait in fruit crops that can significantly influence yield, pruning, planting density and harvesting. Little is known about how plant architecture is genetically determined in olive, were most of the existing varieties are traditional with an architecture poorly suited for modern growing and harvesting systems. In the present study, we have carried out microarray analysis of meristematic tissue to compare expression profiles of olive varieties displaying differences in architecture, as well as seedlings from their cross pooled on the basis of their sharing architecture-related phenotypes. The microarray used, previously developed by our group has already been applied to identify candidates genes involved in regulating juvenile to adult transition in the shoot apex of seedlings. Varieties with distinct architecture phenotypes and individuals from segregating progenies displaying opposite architecture features were used to link phenotype to expression. Here, we identify 2252 differentially expressed genes (DEGs) associated to differences in plant architecture. Microarray results were validated by quantitative RT-PCR carried out on genes with functional annotation likely related to plant architecture. Twelve of these genes were further analyzed in individual seedlings of the corresponding pool. We also examined Arabidopsis mutants in putative orthologs of these targeted candidate genes, finding altered architecture for most of them. This supports a functional conservation between species and potential biological relevance of the candidate genes identified. This study is the first to identify genes associated to plant architecture in olive, and the results obtained could be of great help in future programs aimed at selecting phenotypes adapted to modern cultivation practices in this species.

  14. Platelet-Related Variants Identified by Exomechip Meta-analysis in 157,293 Individuals.

    Science.gov (United States)

    Eicher, John D; Chami, Nathalie; Kacprowski, Tim; Nomura, Akihiro; Chen, Ming-Huei; Yanek, Lisa R; Tajuddin, Salman M; Schick, Ursula M; Slater, Andrew J; Pankratz, Nathan; Polfus, Linda; Schurmann, Claudia; Giri, Ayush; Brody, Jennifer A; Lange, Leslie A; Manichaikul, Ani; Hill, W David; Pazoki, Raha; Elliot, Paul; Evangelou, Evangelos; Tzoulaki, Ioanna; Gao, He; Vergnaud, Anne-Claire; Mathias, Rasika A; Becker, Diane M; Becker, Lewis C; Burt, Amber; Crosslin, David R; Lyytikäinen, Leo-Pekka; Nikus, Kjell; Hernesniemi, Jussi; Kähönen, Mika; Raitoharju, Emma; Mononen, Nina; Raitakari, Olli T; Lehtimäki, Terho; Cushman, Mary; Zakai, Neil A; Nickerson, Deborah A; Raffield, Laura M; Quarells, Rakale; Willer, Cristen J; Peloso, Gina M; Abecasis, Goncalo R; Liu, Dajiang J; Deloukas, Panos; Samani, Nilesh J; Schunkert, Heribert; Erdmann, Jeanette; Fornage, Myriam; Richard, Melissa; Tardif, Jean-Claude; Rioux, John D; Dube, Marie-Pierre; de Denus, Simon; Lu, Yingchang; Bottinger, Erwin P; Loos, Ruth J F; Smith, Albert Vernon; Harris, Tamara B; Launer, Lenore J; Gudnason, Vilmundur; Velez Edwards, Digna R; Torstenson, Eric S; Liu, Yongmei; Tracy, Russell P; Rotter, Jerome I; Rich, Stephen S; Highland, Heather M; Boerwinkle, Eric; Li, Jin; Lange, Ethan; Wilson, James G; Mihailov, Evelin; Mägi, Reedik; Hirschhorn, Joel; Metspalu, Andres; Esko, Tõnu; Vacchi-Suzzi, Caterina; Nalls, Mike A; Zonderman, Alan B; Evans, Michele K; Engström, Gunnar; Orho-Melander, Marju; Melander, Olle; O'Donoghue, Michelle L; Waterworth, Dawn M; Wallentin, Lars; White, Harvey D; Floyd, James S; Bartz, Traci M; Rice, Kenneth M; Psaty, Bruce M; Starr, J M; Liewald, David C M; Hayward, Caroline; Deary, Ian J; Greinacher, Andreas; Völker, Uwe; Thiele, Thomas; Völzke, Henry; van Rooij, Frank J A; Uitterlinden, André G; Franco, Oscar H; Dehghan, Abbas; Edwards, Todd L; Ganesh, Santhi K; Kathiresan, Sekar; Faraday, Nauder; Auer, Paul L; Reiner, Alex P; Lettre, Guillaume; Johnson, Andrew D

    2016-07-01

    Platelet production, maintenance, and clearance are tightly controlled processes indicative of platelets' important roles in hemostasis and thrombosis. Platelets are common targets for primary and secondary prevention of several conditions. They are monitored clinically by complete blood counts, specifically with measurements of platelet count (PLT) and mean platelet volume (MPV). Identifying genetic effects on PLT and MPV can provide mechanistic insights into platelet biology and their role in disease. Therefore, we formed the Blood Cell Consortium (BCX) to perform a large-scale meta-analysis of Exomechip association results for PLT and MPV in 157,293 and 57,617 individuals, respectively. Using the low-frequency/rare coding variant-enriched Exomechip genotyping array, we sought to identify genetic variants associated with PLT and MPV. In addition to confirming 47 known PLT and 20 known MPV associations, we identified 32 PLT and 18 MPV associations not previously observed in the literature across the allele frequency spectrum, including rare large effect (FCER1A), low-frequency (IQGAP2, MAP1A, LY75), and common (ZMIZ2, SMG6, PEAR1, ARFGAP3/PACSIN2) variants. Several variants associated with PLT/MPV (PEAR1, MRVI1, PTGES3) were also associated with platelet reactivity. In concurrent BCX analyses, there was overlap of platelet-associated variants with red (MAP1A, TMPRSS6, ZMIZ2) and white (PEAR1, ZMIZ2, LY75) blood cell traits, suggesting common regulatory pathways with shared genetic architecture among these hematopoietic lineages. Our large-scale Exomechip analyses identified previously undocumented associations with platelet traits and further indicate that several complex quantitative hematological, lipid, and cardiovascular traits share genetic factors.

  15. The definition of and drivers of new product performance

    DEFF Research Database (Denmark)

    Jespersen, Kristina Risom; Juhl, Hans Jørn

    In the last three decades academic research on new product development has tried to identify the drivers of new product development performance. This body of research is characterised by a vast amount of different definitions of both the drivers of new product performance and the performance...... concept. Hence it may be difficult to compare results from different studies and to come up with more general conclusions about the most influential drivers of new product performance. This article is an attempt to summarize, categorize and analyze the results from the most often cited studies...... on the drivers of new product development performance. Firstly this article will provide a discussion and a categorization of drivers and a discussion and categorization of the different measures of new product performance. In that part of the article we will also discuss the pros and cons of the different...

  16. Co-expression Analysis Identifies CRC and AP1 the Regulator of Arabidopsis Fatty Acid Biosynthesis

    Institute of Scientific and Technical Information of China (English)

    Xinxin Han; Linlin Yin; Hongwei Xue

    2012-01-01

    Fatty acids (FAs) play crucial rules in signal transduction and plant development,however,the regulation of FA metabolism is still poorly understood.To study the relevant regulatory network,fifty-eight FA biosynthesis genes including de novo synthases,desaturases and elongases were selected as "guide genes" to construct the co-expression network.Calculation of the correlation between all Arabidopsis thaliana (L.) genes with each guide gene by Arabidopsis co-expression dating mining tools (ACT)identifies 797 candidate FA-correlated genes.Gene ontology (GO) analysis of these co-expressed genes showed they are tightly correlated to photosynthesis and carbohydrate metabolism,and function in many processes.Interestingly,63 transcription factors (TFs) were identified as candidate FA biosynthesis regulators and 8 TF families are enriched.Two TF genes,CRC and AP1,both correlating with 8 FA guide genes,were further characterized.Analyses of the ap1 and crc mutant showed the altered total FA composition of mature seeds.The contents of palmitoleic acid,stearic acid,arachidic acid and eicosadienoic acid are decreased,whereas that of oleic acid is increased in ap1 and crc seeds,which is consistent with the qRT-PCR analysis revealing the suppressed expression of the corresponding guide genes.In addition,yeast one-hybrid analysis and electrophoretic mobility shift assay (EMSA) revealed that CRC can bind to the promoter regions of KCS7 and KCS15,indicating that CRC may directly regulate FA biosynthesis.

  17. Identifying and Tracking Individual Updraft Cores using Cluster Analysis: A TWP-ICE case study

    Science.gov (United States)

    Li, X.; Tao, W.; Collis, S. M.; Varble, A.

    2013-12-01

    Cumulus parameterizations in GCMs depend strongly on the vertical velocity structures of convective updraft cores, or plumes. There hasn't been an accurate way of identifying these cores. The majority of previous studies treat the updraft as a single grid column entity, thus missing many intrinsic characteristics, e.g., the size, strength and spatial orientation of an individual core, its life cycle, and the time variations of the entrainment/detrainment rates associated with its life cycle. In this study, we attempt to apply an innovative algorithm based on the centroid-based k-means cluster analysis to improve our understanding of convection and its associated updraft cores. Both 3-D Doppler radar retrievals and cloud-resolving model simulations of a TWP-ICE campaign case during the monsoon period will be used to test and improve this algorithm. This will provide for more in-depth comparisons between CRM simulations and observations that were not possible previously using the traditional piecewise analysis with each updraft column. The first step is to identify the strongest cores (maximum velocity >10 m/s), since they are well defined and produce definite answers when the cluster analysis algorithm is applied. The preliminary results show that the radar retrieved updraft cores are smaller in size and with the maximum velocity located uniformly at higher levels compared with model simulations. Overall, the model simulations produce much stronger cores compared with the radar retrievals. Within the model simulations, the bulk microphysical scheme simulation produces stronger cores than the spectral bin microphysical scheme. Planned researches include using high temporal-resolution simulations to further track the life cycle of individual updraft cores and study their characteristics.

  18. Utilizing a Photo-Analysis Software for Content Identifying Method (CIM

    Directory of Open Access Journals (Sweden)

    Nejad Nasim Sahraei

    2015-01-01

    Full Text Available Content Identifying Methodology or (CIM was developed to measure public preferences in order to reveal the common characteristics of landscapes and aspects of underlying perceptions including the individual's reactions to content and spatial configuration, therefore, it can assist with the identification of factors that influenced preference. Regarding the analysis of landscape photographs through CIM, there are several studies utilizing image analysis software, such as Adobe Photoshop, in order to identify the physical contents in the scenes. This study attempts to evaluate public’s ‘preferences for aesthetic qualities of pedestrian bridges in urban areas through a photo-questionnaire survey, in which respondents evaluated images of pedestrian bridges in urban areas. Two groups of images were evaluated as the most and least preferred scenes that concern the highest and lowest mean scores respectively. These two groups were analyzed by CIM and also evaluated based on the respondent’s description of each group to reveal the pattern of preferences and the factors that may affect them. Digimizer Software was employed to triangulate the two approaches and to determine the role of these factors on people’s preferences. This study attempts to introduce the useful software for image analysis which can measure the physical contents and also their spatial organization in the scenes. According to the findings, it is revealed that Digimizer could be a useful tool in CIM approaches through preference studies that utilizes photographs in place of the actual landscape in order to determine the most important factors in public preferences for pedestrian bridges in urban areas.

  19. Mini-DIAL system measurements coupled with multivariate data analysis to identify TIC and TIM simulants: preliminary absorption database analysis.

    Science.gov (United States)

    Gaudio, P.; Malizia, A.; Gelfusa, M.; Martinelli, E.; Di Natale, C.; Poggi, L. A.; Bellecci, C.

    2017-01-01

    Nowadays Toxic Industrial Components (TICs) and Toxic Industrial Materials (TIMs) are one of the most dangerous and diffuse vehicle of contamination in urban and industrial areas. The academic world together with the industrial and military one are working on innovative solutions to monitor the diffusion in atmosphere of such pollutants. In this phase the most common commercial sensors are based on “point detection” technology but it is clear that such instruments cannot satisfy the needs of the smart cities. The new challenge is developing stand-off systems to continuously monitor the atmosphere. Quantum Electronics and Plasma Physics (QEP) research group has a long experience in laser system development and has built two demonstrators based on DIAL (Differential Absorption of Light) technology could be able to identify chemical agents in atmosphere. In this work the authors will present one of those DIAL system, the miniaturized one, together with the preliminary results of an experimental campaign conducted on TICs and TIMs simulants in cell with aim of use the absorption database for the further atmospheric an analysis using the same DIAL system. The experimental results are analysed with standard multivariate data analysis technique as Principal Component Analysis (PCA) to develop a classification model aimed at identifying organic chemical compound in atmosphere. The preliminary results of absorption coefficients of some chemical compound are shown together pre PCA analysis.

  20. Resource utilization and outcomes of intoxicated drivers

    Directory of Open Access Journals (Sweden)

    Camera Lindsay J

    2010-08-01

    Full Text Available Abstract Background The high risk behavior of intoxicated drivers, impaired reaction time, lack of seat belt use, and increased incidence of head injury raises questions of whether pre-hospital use of alcohol leads to a higher injury severity score and worse clinical outcomes. We therefore compared intoxicated and non-intoxicated drivers of motor vehicle crashes with respect to outcome measurements and also describe the resources utilized to achieve those outcomes at our Level 1 trauma center. Methods Retrospective descriptive study (Jan 2002-June 2007 of our trauma registry and financial database comparing intoxicated drivers with blood alcohol levels (BAC > 80 mg/dl (ETOH > 80 with drivers who had a BAC of 0 mg/dl (ETOH = 0. Drivers without a BAC drawn or who had levels ranging from 1 mg/dL to 80 mg/dL were excluded. Data was collected on demographic information (age, gender, injury severity score or ISS, outcome variables (mortality, complications, ICU and hospital LOS, ventilator days and resource utilization (ED LOS, insurance, charges, costs, payments. Statistical analysis: p 80; stratified chi square. Results Out of 1732 drivers, the combined study group (n = 987 of 623 ETOH = 0 and 364 ETOH > 80 had a mean age of 38.8 ± 17.9, ISS of 18.0 ± 12.1, and 69.8%% male. There was no difference in ISS (p = 0.67 or complications (p = 0.38. There was a trend towards decreased mortality (p = 0.06. The ETOH = 0 group had more patients with a prolonged ICU LOS (≥ 5 days, ventilator days (≥ 8 days, and hospital LOS (> 14 days when compared to the ETOH > 80 group (p 80 group tended to be self pay (4.9% vs. 0.7%, p Conclusions The data suggests that intoxicated drivers may have better outcomes and a trend towards reduced mortality. They appeared to be less likely to have prolonged hospital LOS, ICU LOS, and ventilator days. We also observed that intoxicated drivers were more likely to be self-pay, less likely to have charges > $50K, and less likely

  1. Genome-wide analysis of over 106 000 individuals identifies 9 neuroticism-associated loci.

    Science.gov (United States)

    Smith, D J; Escott-Price, V; Davies, G; Bailey, M E S; Colodro-Conde, L; Ward, J; Vedernikov, A; Marioni, R; Cullen, B; Lyall, D; Hagenaars, S P; Liewald, D C M; Luciano, M; Gale, C R; Ritchie, S J; Hayward, C; Nicholl, B; Bulik-Sullivan, B; Adams, M; Couvy-Duchesne, B; Graham, N; Mackay, D; Evans, J; Smith, B H; Porteous, D J; Medland, S E; Martin, N G; Holmans, P; McIntosh, A M; Pell, J P; Deary, I J; O'Donovan, M C

    2016-06-01

    Neuroticism is a personality trait of fundamental importance for psychological well-being and public health. It is strongly associated with major depressive disorder (MDD) and several other psychiatric conditions. Although neuroticism is heritable, attempts to identify the alleles involved in previous studies have been limited by relatively small sample sizes. Here we report a combined meta-analysis of genome-wide association study (GWAS) of neuroticism that includes 91 370 participants from the UK Biobank cohort, 6659 participants from the Generation Scotland: Scottish Family Health Study (GS:SFHS) and 8687 participants from a QIMR (Queensland Institute of Medical Research) Berghofer Medical Research Institute (QIMR) cohort. All participants were assessed using the same neuroticism instrument, the Eysenck Personality Questionnaire-Revised (EPQ-R-S) Short Form's Neuroticism scale. We found a single-nucleotide polymorphism-based heritability estimate for neuroticism of ∼15% (s.e.=0.7%). Meta-analysis identified nine novel loci associated with neuroticism. The strongest evidence for association was at a locus on chromosome 8 (P=1.5 × 10(-15)) spanning 4 Mb and containing at least 36 genes. Other associated loci included interesting candidate genes on chromosome 1 (GRIK3 (glutamate receptor ionotropic kainate 3)), chromosome 4 (KLHL2 (Kelch-like protein 2)), chromosome 17 (CRHR1 (corticotropin-releasing hormone receptor 1) and MAPT (microtubule-associated protein Tau)) and on chromosome 18 (CELF4 (CUGBP elav-like family member 4)). We found no evidence for genetic differences in the common allelic architecture of neuroticism by sex. By comparing our findings with those of the Psychiatric Genetics Consortia, we identified a strong genetic correlation between neuroticism and MDD and a less strong but significant genetic correlation with schizophrenia, although not with bipolar disorder. Polygenic risk scores derived from the primary UK Biobank sample captured

  2. Analysis of chlorocarbon compounds identified in the SAM Investigation of the Mars Science Laboratory mission

    Science.gov (United States)

    Freissinet, Caroline; Mahaffy, P.; Glavin, D.; Buch, A.; Brunner, A.; Eigenbrode, J.; Martin, M.; Miller, K.; Steele, A.; Szopa, C.; SAM; MSL science Team

    2013-10-01

    The gas chromatograph mass spectrometer (GCMS) mode of the Sample Analysis at Mars (SAM) experiment was designed for the separation and identification of the chemical components of the gases released from a solid sample or trapped from the atmosphere. Gases from solid samples are either produced by heating a cell from ambient to >800-1100oC (EGA mode) or by wet chemistry extraction and reactions (not yet employed on Mars). Prior to EGA analysis of portions of the first 3 solid samples (Rocknest, John Klein and Cumberland) collected by MSL and delivered to SAM, an internal SAM blank run was carried out with an empty quartz cup. These blank analyses are required to understand the background signal intrinsic to the GCMS and its gas manifolds and traps. Several peaks have been identified as part of SAM background, some of them below the nmol level, which attests of the sensitivity of the instrument and as-designed performance of the GCMS. The origin of each peak has been investigated, and two major contributors are revealed; residual vapor from one of the chemicals used for SAM wet chemistry experiment: N-methyl-N-tert-butyldimethylsilyl-trifluoroacetamide (MTBSTFA), and the Tenax from the hydrocarbon trap. Supporting lab experiments are in progress to understand the reaction pathways of the molecules identified in the SAM background. These experiments help elucidate which molecules may be interpreted as indigenous to Mars. Of the three solid samples analyzed on 11 runs, it was possible to detect and identify several chlorinated compounds including several chlorohydrocarbons. The chlorine is likely derived from the decomposition of martian perchlorates or other indigenous Cl-containing species while the origin of the carbon is presently under investigation for each detected molecule. To date, a subset these molecules have been identified in lab studies and a terrestrial contribution to the observed products are more easily explained. The combined results from SAM and

  3. How can the polar dome be identified in meteorological analysis model data?

    Science.gov (United States)

    Kunkel, Daniel; Bozem, Heiko; Gutmann, Robert; Hoor, Peter

    2016-04-01

    The thermal stratification of the lower atmosphere at high latitudes causes an isolation of polar regions from lower latitudes. A transport barrier establishes in the region where isentropic surfaces slope upward from near surface to higher altitudes. This barrier is also known as the polar dome. For adiabatic flow the transport of air masses from midlatitudes into high latitudes occurs almost along the isentropic surfaces. Only diabatic processes related to clouds, radiation, or turbulence can foster a transport across the barrier. Such processes can be identified by the material rate of change of potential temperature which have to occur in the vicinity of the polar dome. Thus, to identify regions of exchange, it is first crucial to know where the transport barrier is located. The question arises then which meteorological variables may be suited to identify the location of this transport barrier. A second question is how the shape of the polar dome changes during different time periods of the year? For this we use gridded analysis model data from the European Center for Medium-Range Weather Forecast (ECMWF) with high spatial resolution for several time periods during 2014 and 2015. Especially, we focus on time periods during spring and summer when extensive in-situ measurement campaigns took place in the high Arctic. We define four metrics to identify the location, i.e., the latitude, of the transport barrier at various altitudes, e.g., the surface or a surface of constant pressure in the lower troposphere. These metrics are based on (1) a constant value of potential temperature that intersects a given altitude, (2) the strongest gradient of potential temperature on a given altitude level, and (3) the relative difference between equivalent potential temperature and potential temperature at the surface. The last metric is based on a Lagrangian analysis for which ten days forward and backward trajectories are calculated, starting at each grid point between 45

  4. Genome-wide analysis of over 106 000 individuals identifies 9 neuroticism-associated loci

    Science.gov (United States)

    Smith, D J; Escott-Price, V; Davies, G; Bailey, M E S; Colodro-Conde, L; Ward, J; Vedernikov, A; Marioni, R; Cullen, B; Lyall, D; Hagenaars, S P; Liewald, D C M; Luciano, M; Gale, C R; Ritchie, S J; Hayward, C; Nicholl, B; Bulik-Sullivan, B; Adams, M; Couvy-Duchesne, B; Graham, N; Mackay, D; Evans, J; Smith, B H; Porteous, D J; Medland, S E; Martin, N G; Holmans, P; McIntosh, A M; Pell, J P; Deary, I J; O'Donovan, M C

    2016-01-01

    Neuroticism is a personality trait of fundamental importance for psychological well-being and public health. It is strongly associated with major depressive disorder (MDD) and several other psychiatric conditions. Although neuroticism is heritable, attempts to identify the alleles involved in previous studies have been limited by relatively small sample sizes. Here we report a combined meta-analysis of genome-wide association study (GWAS) of neuroticism that includes 91 370 participants from the UK Biobank cohort, 6659 participants from the Generation Scotland: Scottish Family Health Study (GS:SFHS) and 8687 participants from a QIMR (Queensland Institute of Medical Research) Berghofer Medical Research Institute (QIMR) cohort. All participants were assessed using the same neuroticism instrument, the Eysenck Personality Questionnaire-Revised (EPQ-R-S) Short Form's Neuroticism scale. We found a single-nucleotide polymorphism-based heritability estimate for neuroticism of ∼15% (s.e.=0.7%). Meta-analysis identified nine novel loci associated with neuroticism. The strongest evidence for association was at a locus on chromosome 8 (P=1.5 × 10−15) spanning 4 Mb and containing at least 36 genes. Other associated loci included interesting candidate genes on chromosome 1 (GRIK3 (glutamate receptor ionotropic kainate 3)), chromosome 4 (KLHL2 (Kelch-like protein 2)), chromosome 17 (CRHR1 (corticotropin-releasing hormone receptor 1) and MAPT (microtubule-associated protein Tau)) and on chromosome 18 (CELF4 (CUGBP elav-like family member 4)). We found no evidence for genetic differences in the common allelic architecture of neuroticism by sex. By comparing our findings with those of the Psychiatric Genetics Consortia, we identified a strong genetic correlation between neuroticism and MDD and a less strong but significant genetic correlation with schizophrenia, although not with bipolar disorder. Polygenic risk scores derived from the primary UK Biobank sample captured

  5. The driver, the road, the rules … and the rest? A systems-based approach to young driver road safety.

    Science.gov (United States)

    Scott-Parker, B; Goode, N; Salmon, P

    2015-01-01

    The persistent overrepresentation of young drivers in road crashes is universally recognised. A multitude of factors influencing their behaviour and safety have been identified through methods including crash analyses, simulated and naturalistic driving studies, and self-report measures. Across the globe numerous, diverse, countermeasures have been implemented; the design of the vast majority of these has been informed by a driver-centric approach. An alternative approach gaining popularity in transport safety is the systems approach which considers not only the characteristics of the individual, but also the decisions and actions of other actors within the road transport system, along with the interactions amongst them. This paper argues that for substantial improvements to be made in young driver road safety, what has been learnt from driver-centric research needs to be integrated into a systems approach, thus providing a holistic appraisal of the young driver road safety problem. Only then will more effective opportunities and avenues for intervention be realised.

  6. VIBRATION ANALYSIS ON A COMPOSITE BEAM TO IDENTIFY DAMAGE AND DAMAGE SEVERITY USING FINITE ELEMENT METHOD

    Directory of Open Access Journals (Sweden)

    E.V.V.Ramanamurthy

    2011-07-01

    Full Text Available The objective of this paper is to develop a damage detection method in a composite cantilever beam with an edge crack has been studied using finite element method. A number of analytical, numerical andexperimental techniques are available for the study of damage identification in beams. Studies were carried out for three different types of analysis on a composite cantilever beam with an edge crack as damage. The material used in this analysis is glass-epoxy composite material. The finite element formulation was carried out in the analysis section of the package, known as ANSYS. The types of vibration analysis studied on a composite beam are Modal, Harmonic andTransient analysis. The crack is modeled such that the cantilever beam is replaced with two intact beams with the crack as additional boundary condition. Damage algorithms are used to identify and locate the damage. Damage index method is also used to find the severity of the damage. The results obtained from modal analysis were compared with the transient analysis results.The vibration-based damage detection methods are based on the fact that changes of physical properties (stiffness, mass and damping due to damage will manifest themselves as changes in the structural modal parameters (natural frequencies, mode shapes and modal damping. The task is then to monitor the selected indicators derived from modal parameters to distinguish between undamaged and damaged states. However, the quantitative changes of global modal parameters are not sufficiently sensitive to a local damage. The proposed approach, on the other hand, interprets the dynamic changes caused by damage in a different way. Although the basis for vibration-based damage detection appears intuitive, the implementation in real structures may encounter many significant challenges. The most fundamental issue is the fact that damage typically is a local phenomenon and may not dramatically influence the global dynamic response of a

  7. 不同班次出租车司机高血压危险因素分析%Analysis of risk factors for hypertension among taxi drivers on different shifts

    Institute of Scientific and Technical Information of China (English)

    刘振华; 王欲晓; 闫凤凤; 魏晓珉; 于素芳

    2015-01-01

    Objective To investigate the incidence and risk factors for hypertension among taxi drivers working different shifts.Methods Using the cluster sampling method,415 day-shift and 304 night-shift taxi drivers in Jinan,China were selected and investigated.The influencing factors for hypertension were analyzed,Results The incidence of hypertension in all taxi drivers was 33.2%.The incidence of hypertension in nightshift drivers was significantly higher than that in day-shift drivers (37.8% vs 29.9%,P<0.05).According to multivariate analysis,the incidence of hypertension in day-shift drivers was closely related to body mass index (BMI),working years,working hours,sleep duration,rest days,diet quality,water intake,and smoking,while the incidence of hypertension in night-shift drivers was closely related to BMI,working years,working hours,part-time job,sleep duration,rest days,and drinking.Conclusion BMI,working years,and working hours are the common risk factors for hypertension in day-shift and night-shift drivers.Sleep duration and rest days are the common protective factors.The risk factors for hypertension in taxi drivers vary with different shifts.%目的 了解不同班次出租车司机高血压患病情况及探讨高血压的影响因素.方法 采用整群抽样方法,对济南市415名白班出租车司机和304名夜班出租车司机进行问卷调查,并进行影响因素分析.结果 被调查出租车司机高血压患病率为33.2%,其中白班司机高血压患病率为29.9%,夜班司机高血压患病率为37.8%,夜班司机高血压患病率高于白班司机,差异有统计学意义(P<0.05).多因素分析表明,白班司机高血压患病与体重指数(BMI)、工作年限、工作时长、睡眠时长、休息天数、饮食质量、饮水量和吸烟密切相关;夜班司机高血压患病与BMI、工作年限、工作时长、兼职、睡眠时长、休息天数和饮酒密切相关.结论 BMI、工作年限、工作时长等是

  8. Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles

    Directory of Open Access Journals (Sweden)

    Farshad Farshidfar

    2017-03-01

    Full Text Available Cholangiocarcinoma (CCA is an aggressive malignancy of the bile ducts, with poor prognosis and limited treatment options. Here, we describe the integrated analysis of somatic mutations, RNA expression, copy number, and DNA methylation by The Cancer Genome Atlas of a set of predominantly intrahepatic CCA cases and propose a molecular classification scheme. We identified an IDH mutant-enriched subtype with distinct molecular features including low expression of chromatin modifiers, elevated expression of mitochondrial genes, and increased mitochondrial DNA copy number. Leveraging the multi-platform data, we observed that ARID1A exhibited DNA hypermethylation and decreased expression in the IDH mutant subtype. More broadly, we found that IDH mutations are associated with an expanded histological spectrum of liver tumors with molecular features that stratify with CCA. Our studies reveal insights into the molecular pathogenesis and heterogeneity of cholangiocarcinoma and provide classification information of potential therapeutic significance.

  9. Genomic analysis of 38 Legionella species identifies large and diverse effector repertoires.

    Science.gov (United States)

    Burstein, David; Amaro, Francisco; Zusman, Tal; Lifshitz, Ziv; Cohen, Ofir; Gilbert, Jack A; Pupko, Tal; Shuman, Howard A; Segal, Gil

    2016-02-01

    Infection by the human pathogen Legionella pneumophila relies on the translocation of ∼ 300 virulence proteins, termed effectors, which manipulate host cell processes. However, almost no information exists regarding effectors in other Legionella pathogens. Here we sequenced, assembled and characterized the genomes of 38 Legionella species and predicted their effector repertoires using a previously validated machine learning approach. This analysis identified 5,885 predicted effectors. The effector repertoires of different Legionella species were found to be largely non-overlapping, and only seven core effectors were shared by all species studied. Species-specific effectors had atypically low GC content, suggesting exogenous acquisition, possibly from the natural protozoan hosts of these species. Furthermore, we detected numerous new conserved effector domains and discovered new domain combinations, which allowed the inference of as yet undescribed effector functions. The effector collection and network of domain architectures described here can serve as a roadmap for future studies of effector function and evolution.

  10. A Numerical Procedure for Model Identifiability Analysis Applied to Enzyme Kinetics

    DEFF Research Database (Denmark)

    Daele, Timothy, Van; Van Hoey, Stijn; Gernaey, Krist;

    2015-01-01

    exercise, thereby bypassing the challenging task of model structure determination and identification. Parameter identification problems can thus lead to ill-calibrated models with low predictive power and large model uncertainty. Every calibration exercise should therefore be precededby a proper model...... and Pronzato (1997) and which can be easily set up for any type of model. In this paper the proposed approach is applied to the forward reaction rate of the enzyme kinetics proposed by Shin and Kim(1998). Structural identifiability analysis showed that no local structural model problems were occurring......The proper calibration of models describing enzyme kinetics can be quite challenging. In the literature, different procedures are available to calibrate these enzymatic models in an efficient way. However, in most cases the model structure is already decided on prior to the actual calibration...

  11. Identifying time measurement tampering in the traversal time and hop count analysis (TTHCA) wormhole detection algorithm.

    Science.gov (United States)

    Karlsson, Jonny; Dooley, Laurence S; Pulkkis, Göran

    2013-05-17

    Traversal time and hop count analysis (TTHCA) is a recent wormhole detection algorithm for mobile ad hoc networks (MANET) which provides enhanced detection performance against all wormhole attack variants and network types. TTHCA involves each node measuring the processing time of routing packets during the route discovery process and then delivering the measurements to the source node. In a participation mode (PM) wormhole where malicious nodes appear in the routing tables as legitimate nodes, the time measurements can potentially be altered so preventing TTHCA from successfully detecting the wormhole. This paper analyses the prevailing conditions for time tampering attacks to succeed for PM wormholes, before introducing an extension to the TTHCA detection algorithm called ∆T Vector which is designed to identify time tampering, while preserving low false positive rates. Simulation results confirm that the ∆T Vector extension is able to effectively detect time tampering attacks, thereby providing an important security enhancement to the TTHCA algorithm.

  12. Proteomic Analysis of Pichindé virus Infection Identifies Differential Expression of Prothymosin-α

    Directory of Open Access Journals (Sweden)

    Gavin C. Bowick

    2010-01-01

    Full Text Available The arenaviruses include a number of important pathogens including Lassa virus and Junin virus. Presently, the only treatment is supportive care and the antiviral Ribavirin. In the event of an epidemic, patient triage may be required to more effectively manage resources; the development of prognostic biomarker signatures, correlating with disease severity, would allow rational triage. Using a pair of arenaviruses, which cause mild or severe disease, we analyzed extracts from infected cells using SELDI mass spectrometry to characterize potential biomarker profiles. EDGE analysis was used to analyze longitudinal expression differences. Extracts from infected guinea pigs revealed protein peaks which could discriminate between mild or severe infection and between times post-infection. Tandem mass-spectrometry identified several peaks, including the transcriptional regulator prothymosin-α. Further investigation revealed differences in secretion of this peptide. These data show proof of concept that proteomic profiling of host markers could be used as prognostic markers of infectious disease.

  13. Reconstructability analysis as a tool for identifying gene-gene interactions in studies of human diseases.

    Science.gov (United States)

    Shervais, Stephen; Kramer, Patricia L; Westaway, Shawn K; Cox, Nancy J; Zwick, Martin

    2010-01-01

    There are a number of common human diseases for which the genetic component may include an epistatic interaction of multiple genes. Detecting these interactions with standard statistical tools is difficult because there may be an interaction effect, but minimal or no main effect. Reconstructability analysis (RA) uses Shannon's information theory to detect relationships between variables in categorical datasets. We applied RA to simulated data for five different models of gene-gene interaction, and find that even with heritability levels as low as 0.008, and with the inclusion of 50 non-associated genes in the dataset, we can identify the interacting gene pairs with an accuracy of > or =80%. We applied RA to a real dataset of type 2 non-insulin-dependent diabetes (NIDDM) cases and controls, and closely approximated the results of more conventional single SNP disease association studies. In addition, we replicated prior evidence for epistatic interactions between SNPs on chromosomes 2 and 15.

  14. Factor analysis of 27Al MAS NMR spectra for identifying nanocrystalline phases in amorphous geopolymers.

    Science.gov (United States)

    Urbanova, Martina; Kobera, Libor; Brus, Jiri

    2013-11-01

    Nanostructured materials offer enhanced physicochemical properties because of the large interfacial area. Typically, geopolymers with specifically synthesized nanosized zeolites are a promising material for the sorption of pollutants. The structural characterization of these aluminosilicates, however, continues to be a challenge. To circumvent complications resulting from the amorphous character of the aluminosilicate matrix and from the low concentrations of nanosized crystallites, we have proposed a procedure based on factor analysis of (27)Al MAS NMR spectra. The capability of the proposed method was tested on geopolymers that exhibited various tendencies to crystallize (i) completely amorphous systems, (ii) X-ray amorphous systems with nanocrystalline phases, and (iii) highly crystalline systems. Although the recorded (27)Al MAS NMR spectra did not show visible differences between the amorphous systems (i) and the geopolymers with the nanocrystalline phase (ii), the applied factor analysis unambiguously distinguished these materials. The samples were separated into the well-defined clusters, and the systems with the evolving crystalline phase were identified even before any crystalline fraction was detected by X-ray powder diffraction. Reliability of the proposed procedure was verified by comparing it with (29)Si MAS NMR spectra. Factor analysis of (27)Al MAS NMR spectra thus has the ability to reveal spectroscopic features corresponding to the nanocrystalline phases. Because the measurement time of (27)Al MAS NMR spectra is significantly shorter than that of (29)Si MAS NMR data, the proposed procedure is particularly suitable for the analysis of large sets of specifically synthesized geopolymers in which the formation of the limited fractions of nanocrystalline phases is desired.

  15. Automated local bright feature image analysis of nuclear proteindistribution identifies changes in tissue phenotype

    Energy Technology Data Exchange (ETDEWEB)

    Knowles, David; Sudar, Damir; Bator, Carol; Bissell, Mina

    2006-02-01

    The organization of nuclear proteins is linked to cell and tissue phenotypes. When cells arrest proliferation, undergo apoptosis, or differentiate, the distribution of nuclear proteins changes. Conversely, forced alteration of the distribution of nuclear proteins modifies cell phenotype. Immunostaining and fluorescence microscopy have been critical for such findings. However, there is an increasing need for quantitative analysis of nuclear protein distribution to decipher epigenetic relationships between nuclear structure and cell phenotype, and to unravel the mechanisms linking nuclear structure and function. We have developed imaging methods to quantify the distribution of fluorescently-stained nuclear protein NuMA in different mammary phenotypes obtained using three-dimensional cell culture. Automated image segmentation of DAPI-stained nuclei was generated to isolate thousands of nuclei from three-dimensional confocal images. Prominent features of fluorescently-stained NuMA were detected using a novel local bright feature analysis technique, and their normalized spatial density calculated as a function of the distance from the nuclear perimeter to its center. The results revealed marked changes in the distribution of the density of NuMA bright features as non-neoplastic cells underwent phenotypically normal acinar morphogenesis. In contrast, we did not detect any reorganization of NuMA during the formation of tumor nodules by malignant cells. Importantly, the analysis also discriminated proliferating non-neoplastic cells from proliferating malignant cells, suggesting that these imaging methods are capable of identifying alterations linked not only to the proliferation status but also to the malignant character of cells. We believe that this quantitative analysis will have additional applications for classifying normal and pathological tissues.

  16. Driver D220.12 DRIVER-test-bed: Architecture, Integration and Orchestration

    OpenAIRE

    Berg, T.W. van den

    2015-01-01

    This deliverable describes the recommended architecture of the DRIVER Test Bed. The architecture description is developed in two iterations identified by the deliverable numbers D22.11 D220.12, and this deliverable concerns the second iteration, with initial and preliminary information on test bed services.

  17. Driver D220.12 DRIVER-test-bed: Architecture, Integration and Orchestration

    NARCIS (Netherlands)

    Berg, T.W. van den

    2015-01-01

    This deliverable describes the recommended architecture of the DRIVER Test Bed. The architecture description is developed in two iterations identified by the deliverable numbers D22.11 D220.12, and this deliverable concerns the second iteration, with initial and preliminary information on test bed s

  18. Using Principal Component Analysis to Identify Priority Neighbourhoods for Health Services Delivery by Ranking Socioeconomic Status

    Science.gov (United States)

    Friesen, Christine Elizabeth; Seliske, Patrick; Papadopoulos, Andrew

    2016-01-01

    Objectives. Socioeconomic status (SES) is a comprehensive indicator of health status and is useful in area-level health research and informing public health resource allocation. Principal component analysis (PCA) is a useful tool for developing SES indices to identify area-level disparities in SES within communities. While SES research in Canada has relied on census data, the voluntary nature of the 2011 National Household Survey challenges the validity of its data, especially income variables. This study sought to determine the appropriateness of replacing census income information with tax filer data in neighbourhood SES index development. Methods. Census and taxfiler data for Guelph, Ontario were retrieved for the years 2005, 2006, and 2011. Data were extracted for eleven income and non-income SES variables. PCA was employed to identify significant principal components from each dataset and weights of each contributing variable. Variable-specific factor scores were applied to standardized census and taxfiler data values to produce SES scores. Results. The substitution of taxfiler income variables for census income variables yielded SES score distributions and neighbourhood SES classifications that were similar to SES scores calculated using entirely census variables. Combining taxfiler income variables with census non-income variables also produced clearer SES level distinctions. Internal validation procedures indicated that utilizing multiple principal components produced clearer SES level distinctions than using only the first principal component. Conclusion. Identifying socioeconomic disparities between neighbourhoods is an important step in assessing the level of disadvantage of communities. The ability to replace census income information with taxfiler data to develop SES indices expands the versatility of public health research and planning in Canada, as more data sources can be explored. The apparent usefulness of PCA also contributes to the improvement

  19. Contextual Hub Analysis Tool (CHAT): A Cytoscape app for identifying contextually relevant hubs in biological networks

    Science.gov (United States)

    Wiencko, Heather L.; Bernal-Llinares, Manuel; Bryan, Kenneth; Lynn, David J.

    2016-01-01

    Highly connected nodes (hubs) in biological networks are topologically important to the structure of the network and have also been shown to be preferentially associated with a range of phenotypes of interest. The relative importance of a hub node, however, can change depending on the biological context. Here, we report a Cytoscape app, the Contextual Hub Analysis Tool (CHAT), which enables users to easily construct and visualize a network of interactions from a gene or protein list of interest, integrate contextual information, such as gene expression or mass spectrometry data, and identify hub nodes that are more highly connected to contextual nodes (e.g. genes or proteins that are differentially expressed) than expected by chance. In a case study, we use CHAT to construct a network of genes that are differentially expressed in Dengue fever, a viral infection. CHAT was used to identify and compare contextual and degree-based hubs in this network. The top 20 degree-based hubs were enriched in pathways related to the cell cycle and cancer, which is likely due to the fact that proteins involved in these processes tend to be highly connected in general. In comparison, the top 20 contextual hubs were enriched in pathways commonly observed in a viral infection including pathways related to the immune response to viral infection. This analysis shows that such contextual hubs are considerably more biologically relevant than degree-based hubs and that analyses which rely on the identification of hubs solely based on their connectivity may be biased towards nodes that are highly connected in general rather than in the specific context of interest. Availability: CHAT is available for Cytoscape 3.0+ and can be installed via the Cytoscape App Store ( http://apps.cytoscape.org/apps/chat). PMID:27853512

  20. Transcriptome Analysis Identifies Key Candidate Genes Mediating Purple Ovary Coloration in Asiatic Hybrid Lilies

    Science.gov (United States)

    Xu, Leifeng; Yang, Panpan; Yuan, Suxia; Feng, Yayan; Xu, Hua; Cao, Yuwei; Ming, Jun

    2016-01-01

    Lily tepals have a short lifespan. Once the tepals senesce, the ornamental value of the flower is lost. Some cultivars have attractive purple ovaries and fruits which greatly enhance the ornamental value of Asiatic hybrid lilies. However, little is known about the molecular mechanisms of anthocyanin biosynthesis in Asiatic hybrid lily ovaries. To investigate the transcriptional network that governs purple ovary coloration in Asiatic hybrid lilies, we obtained transcriptome data from green ovaries (S1) and purple ovaries (S2) of Asiatic “Tiny Padhye”. Comparative transcriptome analysis revealed 4228 differentially expressed genes. Differential expression analysis revealed that ten unigenes including four CHS genes, one CHI gene, one F3H gene, one F3′H gene, one DFR gene, one UFGT gene, and one 3RT gene were significantly up-regulated in purple ovaries. One MYB gene, LhMYB12-Lat, was identified as a key transcription factor determining the distribution of anthocyanins in Asiatic hybrid lily ovaries. Further qPCR results showed unigenes related to anthocyanin biosynthesis were highly expressed in purple ovaries of three purple-ovaried Asiatic hybrid lilies at stages 2 and 3, while they showed an extremely low level of expression in ovaries of three green-ovaried Asiatic hybrid lilies during all developmental stages. In addition, shading treatment significantly decreased pigment accumulation by suppressing the expression of several unigenes related to anthocyanin biosynthesis in ovaries of Asiatic “Tiny Padhye”. Lastly, a total of 15,048 Simple Sequence Repeats (SSRs) were identified in 13,710 sequences, and primer pairs for SSRs were designed. The results could further our understanding of the molecular mechanisms of anthocyanin biosynthesis in Asiatic hybrid lily ovaries. PMID:27879624

  1. Contextual Hub Analysis Tool (CHAT): A Cytoscape app for identifying contextually relevant hubs in biological networks.

    Science.gov (United States)

    Muetze, Tanja; Goenawan, Ivan H; Wiencko, Heather L; Bernal-Llinares, Manuel; Bryan, Kenneth; Lynn, David J

    2016-01-01

    Highly connected nodes (hubs) in biological networks are topologically important to the structure of the network and have also been shown to be preferentially associated with a range of phenotypes of interest. The relative importance of a hub node, however, can change depending on the biological context. Here, we report a Cytoscape app, the Contextual Hub Analysis Tool (CHAT), which enables users to easily construct and visualize a network of interactions from a gene or protein list of interest, integrate contextual information, such as gene expression or mass spectrometry data, and identify hub nodes that are more highly connected to contextual nodes (e.g. genes or proteins that are differentially expressed) than expected by chance. In a case study, we use CHAT to construct a network of genes that are differentially expressed in Dengue fever, a viral infection. CHAT was used to identify and compare contextual and degree-based hubs in this network. The top 20 degree-based hubs were enriched in pathways related to the cell cycle and cancer, which is likely due to the fact that proteins involved in these processes tend to be highly connected in general. In comparison, the top 20 contextual hubs were enriched in pathways commonly observed in a viral infection including pathways related to the immune response to viral infection. This analysis shows that such contextual hubs are considerably more biologically relevant than degree-based hubs and that analyses which rely on the identification of hubs solely based on their connectivity may be biased towards nodes that are highly connected in general rather than in the specific context of interest.

  2. Integrative omics analysis of rheumatoid arthritis identifies non-obvious therapeutic targets.

    Directory of Open Access Journals (Sweden)

    John W Whitaker

    Full Text Available Identifying novel therapeutic targets for the treatment of disease is challenging. To this end, we developed a genome-wide approach of candidate gene prioritization. We independently collocated sets of genes that were implicated in rheumatoid arthritis (RA pathogenicity through three genome-wide assays: (i genome-wide association studies (GWAS, (ii differentially expression in RA fibroblast-like synoviocytes (FLS, and (iii differentially methylation in RA FLS. Integrated analysis of these complementary data sets identified a significant enrichment of multi-evidence genes (MEGs within pathways relating to RA pathogenicity. One MEG is Engulfment and Cell Motility Protein-1 (ELMO1, a gene not previously considered as a therapeutic target in RA FLS. We demonstrated in RA FLS that ELMO1 is: (i expressed, (ii promotes cell migration and invasion, and (iii regulates Rac1 activity. Thus, we created links between ELMO1 and RA pathogenicity, which in turn validates ELMO1 as a potential RA therapeutic target. This study illustrated the power of MEG-based approaches for therapeutic target identification.

  3. Copy number analysis identifies novel interactions between genomic loci in ovarian cancer.

    Directory of Open Access Journals (Sweden)

    Kylie L Gorringe

    Full Text Available Ovarian cancer is a heterogeneous disease displaying complex genomic alterations, and consequently, it has been difficult to determine the most relevant copy number alterations with the scale of studies to date. We obtained genome-wide copy number alteration (CNA data from four different SNP array platforms, with a final data set of 398 ovarian tumours, mostly of the serous histological subtype. Frequent CNA aberrations targeted many thousands of genes. However, high-level amplicons and homozygous deletions enabled filtering of this list to the most relevant. The large data set enabled refinement of minimal regions and identification of rare amplicons such as at 1p34 and 20q11. We performed a novel co-occurrence analysis to assess cooperation and exclusivity of CNAs and analysed their relationship to patient outcome. Positive associations were identified between gains on 19 and 20q, gain of 20q and loss of X, and between several regions of loss, particularly 17q. We found weak correlations of CNA at genomic loci such as 19q12 with clinical outcome. We also assessed genomic instability measures and found a correlation of the number of higher amplitude gains with poorer overall survival. By assembling the largest collection of ovarian copy number data to date, we have been able to identify the most frequent aberrations and their interactions.

  4. Copy number analysis identifies novel interactions between genomic loci in ovarian cancer.

    Science.gov (United States)

    Gorringe, Kylie L; George, Joshy; Anglesio, Michael S; Ramakrishna, Manasa; Etemadmoghadam, Dariush; Cowin, Prue; Sridhar, Anita; Williams, Louise H; Boyle, Samantha E; Yanaihara, Nozomu; Okamoto, Aikou; Urashima, Mitsuyoshi; Smyth, Gordon K; Campbell, Ian G; Bowtell, David D L

    2010-09-10

    Ovarian cancer is a heterogeneous disease displaying complex genomic alterations, and consequently, it has been difficult to determine the most relevant copy number alterations with the scale of studies to date. We obtained genome-wide copy number alteration (CNA) data from four different SNP array platforms, with a final data set of 398 ovarian tumours, mostly of the serous histological subtype. Frequent CNA aberrations targeted many thousands of genes. However, high-level amplicons and homozygous deletions enabled filtering of this list to the most relevant. The large data set enabled refinement of minimal regions and identification of rare amplicons such as at 1p34 and 20q11. We performed a novel co-occurrence analysis to assess cooperation and exclusivity of CNAs and analysed their relationship to patient outcome. Positive associations were identified between gains on 19 and 20q, gain of 20q and loss of X, and between several regions of loss, particularly 17q. We found weak correlations of CNA at genomic loci such as 19q12 with clinical outcome. We also assessed genomic instability measures and found a correlation of the number of higher amplitude gains with poorer overall survival. By assembling the largest collection of ovarian copy number data to date, we have been able to identify the most frequent aberrations and their interactions.

  5. Deep Proteome Analysis Identifies Age-Related Processes in C. elegans.

    Science.gov (United States)

    Narayan, Vikram; Ly, Tony; Pourkarimi, Ehsan; Murillo, Alejandro Brenes; Gartner, Anton; Lamond, Angus I; Kenyon, Cynthia

    2016-08-01

    Effective network analysis of protein data requires high-quality proteomic datasets. Here, we report a near doubling in coverage of the C. elegans adult proteome, identifying >11,000 proteins in total with ∼9,400 proteins reproducibly detected in three biological replicates. Using quantitative mass spectrometry, we identify proteins whose abundances vary with age, revealing a concerted downregulation of proteins involved in specific metabolic pathways and upregulation of cellular stress responses with advancing age. Among these are ∼30 peroxisomal proteins, including the PRX-5/PEX5 import protein. Functional experiments confirm that protein import into the peroxisome is compromised in vivo in old animals. We also studied the behavior of the set of age-variant proteins in chronologically age-matched, long-lived daf-2 insulin/IGF-1-pathway mutants. Unexpectedly, the levels of many of these age-variant proteins did not scale with extended lifespan. This indicates that, despite their youthful appearance and extended lifespans, not all aspects of aging are reset in these long-lived mutants.

  6. Supervised multivariate analysis of sequence groups to identify specificity determining residues

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    Higgins Desmond G

    2007-04-01

    Full Text Available Abstract Background Proteins that evolve from a common ancestor can change functionality over time, and it is important to be able identify residues that cause this change. In this paper we show how a supervised multivariate statistical method, Between Group Analysis (BGA, can be used to identify these residues from families of proteins with different substrate specifities using multiple sequence alignments. Results We demonstrate the usefulness of this method on three different test cases. Two of these test cases, the Lactate/Malate dehydrogenase family and Nucleotidyl Cyclases, consist of two functional groups. The other family, Serine Proteases consists of three groups. BGA was used to analyse and visualise these three families using two different encoding schemes for the amino acids. Conclusion This overall combination of methods in this paper is powerful and flexible while being computationally very fast and simple. BGA is especially useful because it can be used to analyse any number of functional classes. In the examples we used in this paper, we have only used 2 or 3 classes for demonstration purposes but any number can be used and visualised.

  7. Phylogenetic analysis of rubella viruses identified in Uganda, 2003-2012.

    Science.gov (United States)

    Namuwulya, Prossy; Abernathy, Emily; Bukenya, Henry; Bwogi, Josephine; Tushabe, Phionah; Birungi, Molly; Seguya, Ronald; Kabaliisa, Theopista; Alibu, Vincent P; Kayondo, Jonathan K; Rivailler, Pierre; Icenogle, Joseph; Bakamutumaho, Barnabas

    2014-12-01

    Molecular data on rubella viruses are limited in Uganda despite the importance of congenital rubella syndrome (CRS). Routine rubella vaccination, while not administered currently in Uganda, is expected to begin by 2015. The World Health Organization recommends that countries without rubella vaccination programs assess the burden of rubella and CRS before starting a routine vaccination program. Uganda is already involved in integrated case-based surveillance, including laboratory testing to confirm measles and rubella, but molecular epidemiologic aspects of rubella circulation have so far not been documented in Uganda. Twenty throat swab or oral fluid samples collected from 12 districts during routine rash and fever surveillance between 2003 and 2012 were identified as rubella virus RNA positive and PCR products encompassing the region used for genotyping were sequenced. Phylogenetic analysis of the 20 sequences identified 19 genotype 1G viruses and 1 genotype 1E virus. Genotype-specific trees showed that the Uganda viruses belonged to specific clusters for both genotypes 1G and 1E and grouped with similar sequences from neighboring countries. Genotype 1G was predominant in Uganda. More epidemiological and molecular epidemiological data are required to determine if genotype 1E is also endemic in Uganda. The information obtained in this study will assist the immunization program in monitoring changes in circulating genotypes.

  8. Analysis of Pigeon (Columba) Ovary Transcriptomes to Identify Genes Involved in Blue Light Regulation.

    Science.gov (United States)

    Wang, Ying; Ding, Jia-Tong; Yang, Hai-Ming; Yan, Zheng-Jie; Cao, Wei; Li, Yang-Bai

    2015-01-01

    Monochromatic light is widely applied to promote poultry reproductive performance, yet little is currently known regarding the mechanism by which light wavelengths affect pigeon reproduction. Recently, high-throughput sequencing technologies have been used to provide genomic information for solving this problem. In this study, we employed Illumina Hiseq 2000 to identify differentially expressed genes in ovary tissue from pigeons under blue and white light conditions and de novo transcriptome assembly to construct a comprehensive sequence database containing information on the mechanisms of follicle development. A total of 157,774 unigenes (mean length: 790 bp) were obtained by the Trinity program, and 35.83% of these unigenes were matched to genes in a non-redundant protein database. Gene description, gene ontology, and the clustering of orthologous group terms were performed to annotate the transcriptome assembly. Differentially expressed genes between blue and white light conditions included those related to oocyte maturation, hormone biosynthesis, and circadian rhythm. Furthermore, 17,574 SSRs and 533,887 potential SNPs were identified in this transcriptome assembly. This work is the first transcriptome analysis of the Columba ovary using Illumina technology, and the resulting transcriptome and differentially expressed gene data can facilitate further investigations into the molecular mechanism of the effect of blue light on follicle development and reproduction in pigeons and other bird species.

  9. Analysis of Pigeon (Columba Ovary Transcriptomes to Identify Genes Involved in Blue Light Regulation.

    Directory of Open Access Journals (Sweden)

    Ying Wang

    Full Text Available Monochromatic light is widely applied to promote poultry reproductive performance, yet little is currently known regarding the mechanism by which light wavelengths affect pigeon reproduction. Recently, high-throughput sequencing technologies have been used to provide genomic information for solving this problem. In this study, we employed Illumina Hiseq 2000 to identify differentially expressed genes in ovary tissue from pigeons under blue and white light conditions and de novo transcriptome assembly to construct a comprehensive sequence database containing information on the mechanisms of follicle development. A total of 157,774 unigenes (mean length: 790 bp were obtained by the Trinity program, and 35.83% of these unigenes were matched to genes in a non-redundant protein database. Gene description, gene ontology, and the clustering of orthologous group terms were performed to annotate the transcriptome assembly. Differentially expressed genes between blue and white light conditions included those related to oocyte maturation, hormone biosynthesis, and circadian rhythm. Furthermore, 17,574 SSRs and 533,887 potential SNPs were identified in this transcriptome assembly. This work is the first transcriptome analysis of the Columba ovary using Illumina technology, and the resulting transcriptome and differentially expressed gene data can facilitate further investigations into the molecular mechanism of the effect of blue light on follicle development and reproduction in pigeons and other bird species.

  10. Comparative analysis of methods for identifying recurrent copy number alterations in cancer.

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    Xiguo Yuan

    Full Text Available Recurrent copy number alterations (CNAs play an important role in cancer genesis. While a number of computational methods have been proposed for identifying such CNAs, their relative merits remain largely unknown in practice since very few efforts have been focused on comparative analysis of the methods. To facilitate studies of recurrent CNA identification in cancer genome, it is imperative to conduct a comprehensive comparison of performance and limitations among existing methods. In this paper, six representative methods proposed in the latest six years are compared. These include one-stage and two-stage approaches, working with raw intensity ratio data and discretized data respectively. They are based on various techniques such as kernel regression, correlation matrix diagonal segmentation, semi-parametric permutation and cyclic permutation schemes. We explore multiple criteria including type I error rate, detection power, Receiver Operating Characteristics (ROC curve and the area under curve (AUC, and computational complexity, to evaluate performance of the methods under multiple simulation scenarios. We also characterize their abilities on applications to two real datasets obtained from cancers with lung adenocarcinoma and glioblastoma. This comparison study reveals general characteristics of the existing methods for identifying recurrent CNAs, and further provides new insights into their strengths and weaknesses. It is believed helpful to accelerate the development of novel and improved methods.

  11. 视觉分心时驾驶人注视行为特性分析%Analysis of Drivers' Gazing Behavior during Visual Distraction

    Institute of Scientific and Technical Information of China (English)

    马勇; 付锐; 王畅; 郭应时; 袁伟; 宋殿明

    2013-01-01

    To explore the influences of visual distraction on drivers gazing behavior,and study the gazing behavior patterns during visual distraction,data on driver's eye movement data were recorded with a noncontact eye tracker faceLAB 5.0 when carrying out the naturalistic driving tests.By dividing drivers gazing area into four parts,driver's fixation frequencies and eyes off-road time duration features were analyzed.The results show that during the driver's eyes off-road,in-vehicle gazing is above 60%,and the fixation frequency on left rear-mirror is higher than that on right rear-mirror.About 90% duration of gazing behavior is shorter than 1.0 s,and more than 50% duration times are of 0.4-0.8 s.The average duration time for drivers gazing on left rear-mirror,dashboard and audio instruments are closely,while it is longer than these 3 areas for drivers gazing on right rear-mirror.%为探寻视觉分心对驾驶人注视行为的影响,研究视觉分心时的驾驶人注视行为,用非接触式眼动仪采集多位被试驾驶人在实际驾驶过程中的眼动数据,并将其注视区域分为4部分,分析驾驶人视线离开前方区域情况下的注视频次及注视时长特性.结果表明:驾驶人在视线离开前方区域情况下,超过60%的注视对象是车内区域,且驾驶人观察左后视镜区域的次数高于右后视镜区域.约90%的注视时长小于1.0s,注视时长为0.4~0.8 s的比例超过50%.驾驶人对左后视镜、仪表板和音响设备区域的注视时长均值比较接近,而对右后视镜的注视时长均值大于这3个区域.

  12. 上海市出租车司机饮食行为现状调查%Analysis on dietary behaviors among taxi drivers in Shanghai City

    Institute of Scientific and Technical Information of China (English)

    宋峻; 赖建强; 邹淑蓉; 段一凡; 黄翠花; 朱珍妮; 施爱珍; 姜培珍; 汪正园

    2012-01-01

    Objective To understand the dietary behaviors and practices characteristic among taxi drivers in Shanghai, and provide evidence for health policy making. Methods By using the method of random intercept, 1018 taxi drivers were randomly sampled from taxi parking in Shanghai Hongqiao Airport and a questionnaire survey was conducted. Results 98.4% of taxi drivers ate outside and 44. 6% of them had meals outside 3 times per day. 96. 6% of taxi drivers who took breakfast had inadequate breakfast nutrition. The proportion of adequate nutritional breakfast was only 0. 9%. The proportions of taxi drivers without breakfast, lunch or dinner were 3. 0% , 2. 0% and 2.4% , respectively. Dietary structure of lunch and dinner among taxi drivers were " grain + meat + vegetables" when they worked outside. The reasons for choosing eatery were sanitary and amount, few of them considered about nutrition. Only 4% of them thought over nutrition, and the proportion of urban drivers who considered about nutrition was higher than that of rural drivers. Conclusion Eating disorders, unreasonable distribution of meals and dietary structures still exist in taxi drivers. The health education on nutrition should be enhanced among taxi drivers to reduce the incidences of obesity and overweight and prevent chronic diseases like hypertension.%目的 了解出租车司机饮食行为和膳食结构的特点,为相关部门制定健康教育策略提供依据.方法 以随机拦截的方法,对上海虹桥机场蓄车池中的1018名出租车司机进行问卷调查.结果 出租车司机每日在外就餐以及1日3餐均在外就餐的比例分别为98.4%和44.6%;吃早餐的司机中96.6%的司机的早餐营养不充足,仅0.9%的司机早餐营养充足;司机中不吃早餐、午餐和晚餐的比例分别为3.0%、2.0%和2.4%;司机工作在外时,午餐和晚餐主要是“主食+荤菜+素菜”的膳食构成模式,较少选择水果;司机选择午餐和晚餐的就

  13. Drivers for Malaysian SMEs to Go Green

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    M. Krishna Moorthy

    2012-09-01

    Full Text Available Small and Medium Enterprises (SMEs around the world have little knowledge about environmental management and do not understand the concept of environmental management. The concept of green is still very new to Malaysian SME owners/managers, although many green conferences, seminars and campaigns have been carried out for quite some time. The concept for green process and products in Malaysia is at the infancy stage. The drivers of environmental behavior in SMEs are relatively under-researched (Worthington & Patton, 2005 and more needs to be done to help SME owner-managers adopt environmental initiatives (Hitchens et al., 2003 as poor environmental performance is not simply the outcome of negative attitudes by SME owner-managers to the environment. This study identifies five key drivers of environmental management practice for SMEs go green. The five drivers are: economic benefits, financial incentives, stakeholders demand, legislation, resources, motivation and knowledge. The Theory of Planned Behavior (TPB is considered as the most appropriate theory to study the drivers of green environment behavior and to investigate the owners’/managers’ perception and attitude towards Malaysian SMEs’ green concept.

  14. Comparative Transcriptome Analysis Identifies CCDC80 as a Novel Gene Associated with Pulmonary Arterial Hypertension

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    Yuhei eNishimura

    2016-06-01

    Full Text Available Pulmonary arterial hypertension (PAH is a heterogeneous disorder associated with a progressive increase in pulmonary artery resistance and pressure. Although various therapies have been developed, the 5-year survival rate of PAH patients remains low. There is thus an important need to identify novel genes that are commonly dysregulated in PAH of various etiologies and could be used as biomarkers and/or therapeutic targets. In this study, we performed comparative transcriptome analysis of five mammalian PAH datasets downloaded from a public database. We identified 228 differentially expressed genes (DEGs from a rat PAH model caused by inhibition of vascular endothelial growth factor receptor under hypoxic conditions, 379 DEGs from a mouse PAH model associated with systemic sclerosis, 850 DEGs from a mouse PAH model associated with schistosomiasis, 1598 DEGs from one cohort of human PAH patients, and 4260 DEGs from a second cohort of human PAH patients. Gene-by-gene comparison identified four genes that were differentially upregulated or downregulated in parallel in all five sets of DEGs. Expression of coiled-coil domain containing 80 (CCDC80 and anterior gradient 2 genes was significantly increased in the five datasets, whereas expression of SMAD family member 6 and granzyme A was significantly decreased. Weighted gene co-expression network analysis revealed a connection between CCDC80 and collagen type I alpha 1 (COL1A1 expression. To validate the function of CCDC80 in vivo, we knocked out ccdc80 in zebrafish using the clustered regularly interspaced short palindromic repeats (CRISPR/Cas9 system. In vivo imaging of zebrafish expressing a fluorescent protein in endothelial cells showed that ccdc80 deletion significantly increased the diameter of the ventral artery, a vessel supplying blood to the gills. We also demonstrated that expression of col1a1 and endothelin-1 mRNA was significantly decreased in the ccdc80-knockout zebrafish. Finally, we

  15. Identifying patterns in treatment response profiles in acute bipolar mania: a cluster analysis approach

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    Houston John P

    2008-07-01

    Full Text Available Abstract Background Patients with acute mania respond differentially to treatment and, in many cases, fail to obtain or sustain symptom remission. The objective of this exploratory analysis was to characterize response in bipolar disorder by identifying groups of patients with similar manic symptom response profiles. Methods Patients (n = 222 were selected from a randomized, double-blind study of treatment with olanzapine or divalproex in bipolar I disorder, manic or mixed episode, with or without psychotic features. Hierarchical clustering based on Ward's distance was used to identify groups of patients based on Young-Mania Rating Scale (YMRS total scores at each of 5 assessments over 7 weeks. Logistic regression was used to identify baseline predictors for clusters of interest. Results Four distinct clusters of patients were identified: Cluster 1 (n = 64: patients did not maintain a response (YMRS total scores ≤ 12; Cluster 2 (n = 92: patients responded rapidly (within less than a week and response was maintained; Cluster 3 (n = 36: patients responded rapidly but relapsed soon afterwards (YMRS ≥ 15; Cluster 4 (n = 30: patients responded slowly (≥ 2 weeks and response was maintained. Predictive models using baseline variables found YMRS Item 10 (Appearance, and psychosis to be significant predictors for Clusters 1 and 4 vs. Clusters 2 and 3, but none of the baseline characteristics allowed discriminating between Clusters 1 vs. 4. Experiencing a mixed episode at baseline predicted membership in Clusters 2 and 3 vs. Clusters 1 and 4. Treatment with divalproex, larger number of previous manic episodes, lack of disruptive-aggressive behavior, and more prominent depressive symptoms at baseline were predictors for Cluster 3 vs. 2. Conclusion Distinct treatment response profiles can be predicted by clinical features at baseline. The presence of these features as potential risk factors for relapse in patients who have responded to treatment

  16. Functional analysis of TPM domain containing Rv2345 of Mycobacterium tuberculosis identifies its phosphatase activity.

    Science.gov (United States)

    Sinha, Avni; Eniyan, Kandasamy; Sinha, Swati; Lynn, Andrew Michael; Bajpai, Urmi

    2015-07-01

    Mycobacterium tuberculosis (Mtb) is the causal agent of tuberculosis, the second largest infectious disease. With the rise of multi-drug resistant strains of M. tuberculosis, serious challenge lies ahead of us in treating the disease. The availability of complete genome sequence of Mtb has improved the scope for identifying new proteins that would not only further our understanding of biology of the organism but could also serve to discover new drug targets. In this study, Rv2345, a hypothetical membrane protein of M. tuberculosis H37Rv, which is reported to be a putative ortholog of ZipA cell division protein has been assigned function through functional annotation using bioinformatics tools followed by experimental validation. Sequence analysis showed Rv2345 to have a TPM domain at its N-terminal region and predicted it to have phosphatase activity. The TPM domain containing region of Rv2345 was cloned and expressed using pET28a vector in Escherichia coli and purified by Nickel affinity chromatography. The purified TPM domain was tested in vitro and our results confirmed it to have phosphatase activity. The enzyme activity was first checked and optimized with pNPP as substrate, followed by using ATP, which was also found to be used as substrate by the purified protein. Hence sequence analysis followed by in vitro studies characterizes TPM domain of Rv2345 to contain phosphatase activity.

  17. Application of (13)C flux analysis to identify high-productivity CHO metabolic phenotypes.

    Science.gov (United States)

    Templeton, Neil; Smith, Kevin D; McAtee-Pereira, Allison G; Dorai, Haimanti; Betenbaugh, Michael J; Lang, Steven E; Young, Jamey D

    2017-01-23

    Industrial bioprocesses place high demands on the energy metabolism of host cells to meet biosynthetic requirements for maximal protein expression. Identifying metabolic phenotypes that promote high expression is therefore a major goal of the biotech industry. We conducted a series of (13)C flux analysis studies to examine the metabolic response to IgG expression during early stationary phase of CHO cell cultures grown in 3L fed-batch bioreactors. We examined eight clones expressing four different IgGs and compared with three non-expressing host-cell controls. Some clones were genetically manipulated to be apoptosis-resistant by expressing Bcl-2Δ, which correlated with increased IgG production and elevated glucose metabolism. The metabolic phenotypes of the non-expressing, IgG-expressing, and Bcl-2Δ/IgG-expressing clones were fully segregated by hierarchical clustering analysis. Lactate consumption and citric acid cycle fluxes were most strongly associated with specific IgG productivity. These studies indicate that enhanced oxidative metabolism is a characteristic of high-producing CHO cell lines.

  18. Genomic reprograming analysis of the Mesothelial to Mesenchymal Transition identifies biomarkers in peritoneal dialysis patients

    Science.gov (United States)

    Ruiz-Carpio, Vicente; Sandoval, Pilar; Aguilera, Abelardo; Albar-Vizcaíno, Patricia; Perez-Lozano, María Luisa; González-Mateo, Guadalupe T.; Acuña-Ruiz, Adrián; García-Cantalejo, Jesús; Botías, Pedro; Bajo, María Auxiliadora; Selgas, Rafael; Sánchez-Tomero, José Antonio; Passlick-Deetjen, Jutta; Piecha, Dorothea; Büchel, Janine; Steppan, Sonja; López-Cabrera, Manuel

    2017-01-01

    Peritoneal dialysis (PD) is an effective renal replacement therapy, but a significant proportion of patients suffer PD-related complications, which limit the treatment duration. Mesothelial-to-mesenchymal transition (MMT) contributes to the PD-related peritoneal dysfunction. We analyzed the genetic reprograming of MMT to identify new biomarkers that may be tested in PD-patients. Microarray analysis revealed a partial overlapping between MMT induced in vitro and ex vivo in effluent-derived mesothelial cells, and that MMT is mainly a repression process being higher the number of genes that are down-regulated than those that are induced. Cellular morphology and number of altered genes showed that MMT ex vivo could be subdivided into two stages: early/epithelioid and advanced/non-epithelioid. RT-PCR array analysis demonstrated that a number of genes differentially expressed in effluent-derived non-epithelioid cells also showed significant differential expression when comparing standard versus low-GDP PD fluids. Thrombospondin-1 (TSP1), collagen-13 (COL13), vascular endothelial growth factor A (VEGFA), and gremlin-1 (GREM1) were measured in PD effluents, and except GREM1, showed significant differences between early and advanced stages of MMT, and their expression was associated with a high peritoneal transport status. The results establish a proof of concept about the feasibility of measuring MMT-associated secreted protein levels as potential biomarkers in PD. PMID:28327551

  19. Five endometrial cancer risk loci identified through genome-wide association analysis

    Science.gov (United States)

    O’Mara, Tracy A; Painter, Jodie N; Glubb, Dylan M; Flach, Susanne; Lewis, Annabelle; French, Juliet D; Freeman-Mills, Luke; Church, David; Gorman, Maggie; Martin, Lynn; Hodgson, Shirley; Webb, Penelope M; Attia, John; Holliday, Elizabeth G; McEvoy, Mark; Scott, Rodney J; Henders, Anjali K; Martin, Nicholas G; Montgomery, Grant W; Nyholt, Dale R; Ahmed, Shahana; Healey, Catherine S; Shah, Mitul; Dennis, Joe; Fasching, Peter A; Beckmann, Matthias W; Hein, Alexander; Ekici, Arif B; Hall, Per; Czene, Kamila; Darabi, Hatef; Li, Jingmei; Dörk, Thilo; Dürst, Matthias; Hillemanns, Peter; Runnebaum, Ingo; Amant, Frederic; Schrauwen, Stefanie; Zhao, Hui; Lambrechts, Diether; Depreeuw, Jeroen; Dowdy, Sean C; Goode, Ellen L; Fridley, Brooke L; Winham, Stacey J; Njølstad, Tormund S; Salvesen, Helga B; Trovik, Jone; Werner, Henrica MJ; Ashton, Katie; Otton, Geoffrey; Proietto, Tony; Liu, Tao; Mints, Miriam; Tham, Emma; Consortium, CHIBCHA; Jun Li, Mulin; Yip, Shun H; Wang, Junwen; Bolla, Manjeet K; Michailidou, Kyriaki; Wang, Qin; Tyrer, Jonathan P; Dunlop, Malcolm; Houlston, Richard; Palles, Claire; Hopper, John L; Peto, Julian; Swerdlow, Anthony J; Burwinkel, Barbara; Brenner, Hermann; Meindl, Alfons; Brauch, Hiltrud; Lindblom, Annika; Chang-Claude, Jenny; Couch, Fergus J; Giles, Graham G; Kristensen, Vessela N; Cox, Angela; Cunningham, Julie M; Pharoah, Paul D P; Dunning, Alison M; Edwards, Stacey L; Easton, Douglas F; Tomlinson, Ian; Spurdle, Amanda B

    2016-01-01

    We conducted a meta-analysis of three endometrial cancer GWAS and two replication phases totaling 7,737 endometrial cancer cases and 37,144 controls of European ancestry. Genome-wide imputation and meta-analysis identified five novel risk loci of genome-wide significance at likely regulatory regions on chromosomes 13q22.1 (rs11841589, near KLF5), 6q22.31 (rs13328298, in LOC643623 and near HEY2 and NCOA7), 8q24.21 (rs4733613, telomeric to MYC), 15q15.1 (rs937213, in EIF2AK4, near BMF) and 14q32.33 (rs2498796, in AKT1 near SIVA1). A second independent 8q24.21 signal (rs17232730) was found. Functional studies of the 13q22.1 locus showed that rs9600103 (pairwise r2=0.98 with rs11841589) is located in a region of active chromatin that interacts with the KLF5 promoter region. The rs9600103-T endometrial cancer protective allele suppressed gene expression in vitro suggesting that regulation of KLF5 expression, a gene linked to uterine development, is implicated in tumorigenesis. These findings provide enhanced insight into the genetic and biological basis of endometrial cancer. PMID:27135401

  20. Five endometrial cancer risk loci identified through genome-wide association analysis.

    Science.gov (United States)

    Cheng, Timothy H T; Thompson, Deborah J; O'Mara, Tracy A; Painter, Jodie N; Glubb, Dylan M; Flach, Susanne; Lewis, Annabelle; French, Juliet D; Freeman-Mills, Luke; Church, David; Gorman, Maggie; Martin, Lynn; Hodgson, Shirley; Webb, Penelope M; Attia, John; Holliday, Elizabeth G; McEvoy, Mark; Scott, Rodney J; Henders, Anjali K; Martin, Nicholas G; Montgomery, Grant W; Nyholt, Dale R; Ahmed, Shahana; Healey, Catherine S; Shah, Mitul; Dennis, Joe; Fasching, Peter A; Beckmann, Matthias W; Hein, Alexander; Ekici, Arif B; Hall, Per; Czene, Kamila; Darabi, Hatef; Li, Jingmei; Dörk, Thilo; Dürst, Matthias; Hillemanns, Peter; Runnebaum, Ingo; Amant, Frederic; Schrauwen, Stefanie; Zhao, Hui; Lambrechts, Diether; Depreeuw, Jeroen; Dowdy, Sean C; Goode, Ellen L; Fridley, Brooke L; Winham, Stacey J; Njølstad, Tormund S; Salvesen, Helga B; Trovik, Jone; Werner, Henrica M J; Ashton, Katie; Otton, Geoffrey; Proietto, Tony; Liu, Tao; Mints, Miriam; Tham, Emma; Li, Mulin Jun; Yip, Shun H; Wang, Junwen; Bolla, Manjeet K; Michailidou, Kyriaki; Wang, Qin; Tyrer, Jonathan P; Dunlop, Malcolm; Houlston, Richard; Palles, Claire; Hopper, John L; Peto, Julian; Swerdlow, Anthony J; Burwinkel, Barbara; Brenner, Hermann; Meindl, Alfons; Brauch, Hiltrud; Lindblom, Annika; Chang-Claude, Jenny; Couch, Fergus J; Giles, Graham G; Kristensen, Vessela N; Cox, Angela; Cunningham, Julie M; Pharoah, Paul D P; Dunning, Alison M; Edwards, Stacey L; Easton, Douglas F; Tomlinson, Ian; Spurdle, Amanda B

    2016-06-01

    We conducted a meta-analysis of three endometrial cancer genome-wide association studies (GWAS) and two follow-up phases totaling 7,737 endometrial cancer cases and 37,144 controls of European ancestry. Genome-wide imputation and meta-analysis identified five new risk loci of genome-wide significance at likely regulatory regions on chromosomes 13q22.1 (rs11841589, near KLF5), 6q22.31 (rs13328298, in LOC643623 and near HEY2 and NCOA7), 8q24.21 (rs4733613, telomeric to MYC), 15q15.1 (rs937213, in EIF2AK4, near BMF) and 14q32.33 (rs2498796, in AKT1, near SIVA1). We also found a second independent 8q24.21 signal (rs17232730). Functional studies of the 13q22.1 locus showed that rs9600103 (pairwise r(2) = 0.98 with rs11841589) is located in a region of active chromatin that interacts with the KLF5 promoter region. The rs9600103[T] allele that is protective in endometrial cancer suppressed gene expression in vitro, suggesting that regulation of the expression of KLF5, a gene linked to uterine development, is implicated in tumorigenesis. These findings provide enhanced insight into the genetic and biological basis of endometrial cancer.

  1. Functional gene group analysis identifies synaptic gene groups as risk factor for schizophrenia.

    Science.gov (United States)

    Lips, E S; Cornelisse, L N; Toonen, R F; Min, J L; Hultman, C M; Holmans, P A; O'Donovan, M C; Purcell, S M; Smit, A B; Verhage, M; Sullivan, P F; Visscher, P M; Posthuma, D

    2012-10-01

    Schizophrenia is a highly heritable disorder with a polygenic pattern of inheritance and a population prevalence of ~1%. Previous studies have implicated synaptic dysfunction in schizophrenia. We tested the accumulated association of genetic variants in expert-curated synaptic gene groups with schizophrenia in 4673 cases and 4965 healthy controls, using functional gene group analysis. Identifying groups of genes with similar cellular function rather than genes in isolation may have clinical implications for finding additional drug targets. We found that a group of 1026 synaptic genes was significantly associated with the risk of schizophrenia (P=7.6 × 10(-11)) and more strongly associated than 100 randomly drawn, matched control groups of genetic variants (P<0.01). Subsequent analysis of synaptic subgroups suggested that the strongest association signals are derived from three synaptic gene groups: intracellular signal transduction (P=2.0 × 10(-4)), excitability (P=9.0 × 10(-4)) and cell adhesion and trans-synaptic signaling (P=2.4 × 10(-3)). These results are consistent with a role of synaptic dysfunction in schizophrenia and imply that impaired intracellular signal transduction in synapses, synaptic excitability and cell adhesion and trans-synaptic signaling play a role in the pathology of schizophrenia.

  2. Genetic modifier loci of mouse Mfrp(rd6) identified by quantitative trait locus analysis.

    Science.gov (United States)

    Won, Jungyeon; Charette, Jeremy R; Philip, Vivek M; Stearns, Timothy M; Zhang, Weidong; Naggert, Jürgen K; Krebs, Mark P; Nishina, Patsy M

    2014-01-01

    The identification of genes that modify pathological ocular phenotypes in mouse models may improve our understanding of disease mechanisms and lead to new treatment strategies. Here, we identify modifier loci affecting photoreceptor cell loss in homozygous Mfrp(rd6) mice, which exhibit a slowly progressive photoreceptor degeneration. A cohort of 63 F2 homozygous Mfrp(rd6) mice from a (B6.C3Ga-Mfrp(rd6)/J × CAST/EiJ) F1 intercross exhibited a variable number of cell bodies in the retinal outer nuclear layer at 20 weeks of age. Mice were genotyped with a panel of single nucleotide polymorphism markers, and genotypes were correlated with phenotype by quantitative trait locus (QTL) analysis to map modifier loci. A genome-wide scan revealed a statistically significant, protective candidate locus on CAST/EiJ Chromosome 1 and suggestive modifier loci on Chromosomes 6 and 11. Multiple regression analysis of a three-QTL model indicated that the modifier loci on Chromosomes 1 and 6 together account for 26% of the observed phenotypic variation, while the modifier locus on Chromosome 11 explains only an additional 4%. Our findings indicate that the severity of the Mfrp(rd6) retinal degenerative phenotype in mice depends on the strain genetic background and that a significant modifier locus on CAST/EiJ Chromosome 1 protects against Mfrp(rd6)-associated photoreceptor loss.

  3. Identifying differences in the experience of (in)authenticity: a latent class analysis approach.

    Science.gov (United States)

    Lenton, Alison P; Slabu, Letitia; Bruder, Martin; Sedikides, Constantine

    2014-01-01

    Generally, psychologists consider state authenticity - that is, the subjective sense of being one's true self - to be a unitary and unidimensional construct, such that (a) the phenomenological experience of authenticity is thought to be similar no matter its trigger, and (b) inauthenticity is thought to be simply the opposing pole (on the same underlying construct) of authenticity. Using latent class analysis, we put this conceptualization to a test. In order to avoid over-reliance on a Western conceptualization of authenticity, we used a cross-cultural sample (N = 543), comprising participants from Western, South-Asian, East-Asian, and South-East Asian cultures. Participants provided either a narrative in which the described when they felt most like being themselves or one in which they described when they felt least like being themselves. The analysis identified six distinct classes of experiences: two authenticity classes ("everyday" and "extraordinary"), three inauthenticity classes ("self-conscious," "deflated," and "extraordinary"), and a class representing convergence between authenticity and inauthenticity. The classes were phenomenologically distinct, especially with respect to negative affect, private and public self-consciousness, and self-esteem. Furthermore, relatively more interdependent cultures were less likely to report experiences of extraordinary (in)authenticity than relatively more independent cultures. Understanding the many facets of (in)authenticity may enable researchers to connect different findings and explain why the attainment of authenticity can be difficult.

  4. Transcriptome bioinformatic analysis identifies potential therapeutic mechanism of pentylenetetrazole in down syndrome

    Directory of Open Access Journals (Sweden)

    Sharma Abhay

    2010-10-01

    Full Text Available Abstract Background Pentylenetetrazole (PTZ has recently been found to ameliorate cognitive impairment in rodent models of Down syndrome (DS. The mechanism underlying PTZ's therapeutic effect in DS is however not clear. Microarray profiling has previously reported differential expression, both up- and down-regulation, of genes in DS. Given this, transcriptomic data related to PTZ treatment, if available, could be used to understand the drug's therapeutic mechanism in DS. No such mammalian data however exists. Nevertheless, a Drosophila model inspired by PTZ induced kindling plasticity in rodents has recently been described. Microarray profiling has shown PTZ's downregulatory effect on gene expression in the fly heads. Methods In a comparative transcriptomics approach, I have analyzed the available microarray data in order to identify potential therapeutic mechanism of PTZ in DS. In the analysis, summary data of up- and down-regulated genes reported in human DS studies and of down-regulated genes reported in the Drosophila model has been used. Results I find that transcriptomic correlate of chronic PTZ in Drosophila counteracts that of DS. Genes downregulated by PTZ significantly over-represent genes upregulated in DS and under-represent genes downregulated in DS. Further, the genes which are common in the downregulated and upregulated DS set show enrichment for MAP kinase pathway. Conclusion My analysis suggests that downregulation of MAP kinase pathway may mediate therapeutic effect of PTZ in DS. Existing evidence implicating MAP kinase pathway in DS supports this observation.

  5. Transcriptome analysis of Solanum melongena L. (eggplant) fruit to identify putative allergens and their epitopes.

    Science.gov (United States)

    Ramesh, Kumar Ramagoni; Hemalatha, R; Vijayendra, Chary Anchoju; Arshi, Uz Zaman Syed; Dushyant, Singh Baghel; Dinesh, Kumar Bharadwaj

    2016-01-15

    Eggplant is the third most important Solanaceae crop after tomato and potato, particularly in India and China. A transcriptome analysis of eggplant's fruit was performed to study genes involved in medicinal importance and allergies. Illumina HiSeq 2000 system generated 89,763,638 raw reads (~18 Gb) from eggplant. High quality reads (59,039,694) obtained after trimming process, were assembled into a total of 149,224 non redundant set of transcripts. Out of 80,482 annotated sequences of eggplant fruit (BLASTx results against nr-green plant database), 40,752 transcripts showed significant similarity with predicted proteins of Solanum tuberosum (51%) followed by Solanum lycopersicum (34%) and other sequenced plant genomes. With BLASTx top hit analysis against existing allergens, a total of 1986 homologous allergen sequences were found, which had >37% similarity with 48 different allergens existing in the database. From the 48 putative allergens, 526 B-cell linear epitopes were identified using BepiPred linear epitope prediction tool. Transcript sequences generated from this study can be used to map epitopes of monoclonal antibodies and polyclonal sera from patients. With the support of this whole transcriptome catalogue of eggplant fruit, complete list of genes can be predicted based on which secondary structures of proteins may be modeled.

  6. Genome-wide meta-analysis identifies multiple novel associations and ethnic heterogeneity of psoriasis susceptibility.

    Science.gov (United States)

    Yin, Xianyong; Low, Hui Qi; Wang, Ling; Li, Yonghong; Ellinghaus, Eva; Han, Jiali; Estivill, Xavier; Sun, Liangdan; Zuo, Xianbo; Shen, Changbing; Zhu, Caihong; Zhang, Anping; Sanchez, Fabio; Padyukov, Leonid; Catanese, Joseph J; Krueger, Gerald G; Duffin, Kristina Callis; Mucha, Sören; Weichenthal, Michael; Weidinger, Stephan; Lieb, Wolfgang; Foo, Jia Nee; Li, Yi; Sim, Karseng; Liany, Herty; Irwan, Ishak; Teo, Yikying; Theng, Colin T S; Gupta, Rashmi; Bowcock, Anne; De Jager, Philip L; Qureshi, Abrar A; de Bakker, Paul I W; Seielstad, Mark; Liao, Wilson; Ståhle, Mona; Franke, Andre; Zhang, Xuejun; Liu, Jianjun

    2015-04-23

    Psoriasis is a common inflammatory skin disease with complex genetics and different degrees of prevalence across ethnic populations. Here we present the largest trans-ethnic genome-wide meta-analysis (GWMA) of psoriasis in 15,369 cases and 19,517 controls of Caucasian and Chinese ancestries. We identify four novel associations at LOC144817, COG6, RUNX1 and TP63, as well as three novel secondary associations within IFIH1 and IL12B. Fine-mapping analysis of MHC region demonstrates an important role for all three HLA class I genes and a complex and heterogeneous pattern of HLA associations between Caucasian and Chinese populations. Further, trans-ethnic comparison suggests population-specific effect or allelic heterogeneity for 11 loci. These population-specific effects contribute significantly to the ethnic diversity of psoriasis prevalence. This study not only provides novel biological insights into the involvement of immune and keratinocyte development mechanism, but also demonstrates a complex and heterogeneous genetic architecture of psoriasis susceptibility across ethnic populations.

  7. Multi-tissue microarray analysis identifies a molecular signature of regeneration.

    Directory of Open Access Journals (Sweden)

    Sarah E Mercer

    Full Text Available The inability to functionally repair tissues that are lost as a consequence of disease or injury remains a significant challenge for regenerative medicine. The molecular and cellular processes involved in complete restoration of tissue architecture and function are expected to be complex and remain largely unknown. Unlike humans, certain salamanders can completely regenerate injured tissues and lost appendages without scar formation. A parsimonious hypothesis would predict that all of these regenerative activities are regulated, at least in part, by a common set of genes. To test this hypothesis and identify genes that might control conserved regenerative processes, we performed a comprehensive microarray analysis of the early regenerative response in five regeneration-competent tissues from the newt Notophthalmus viridescens. Consistent with this hypothesis, we established a molecular signature for regeneration that consists of common genes or gene family members that exhibit dynamic differential regulation during regeneration in multiple tissue types. These genes include members of the matrix metalloproteinase family and its regulators, extracellular matrix components, genes involved in controlling cytoskeleton dynamics, and a variety of immune response factors. Gene Ontology term enrichment analysis validated and supported their functional activities in conserved regenerative processes. Surprisingly, dendrogram clustering and RadViz classification also revealed that each regenerative tissue had its own unique temporal expression profile, pointing to an inherent tissue-specific regenerative gene program. These new findings demand a reconsideration of how we conceptualize regenerative processes and how we devise new strategies for regenerative medicine.

  8. Quantitative analysis of bristle number in Drosophila mutants identifies genes involved in neural development

    Science.gov (United States)

    Norga, Koenraad K.; Gurganus, Marjorie C.; Dilda, Christy L.; Yamamoto, Akihiko; Lyman, Richard F.; Patel, Prajal H.; Rubin, Gerald M.; Hoskins, Roger A.; Mackay, Trudy F.; Bellen, Hugo J.

    2003-01-01

    BACKGROUND: The identification of the function of all genes that contribute to specific biological processes and complex traits is one of the major challenges in the postgenomic era. One approach is to employ forward genetic screens in genetically tractable model organisms. In Drosophila melanogaster, P element-mediated insertional mutagenesis is a versatile tool for the dissection of molecular pathways, and there is an ongoing effort to tag every gene with a P element insertion. However, the vast majority of P element insertion lines are viable and fertile as homozygotes and do not exhibit obvious phenotypic defects, perhaps because of the tendency for P elements to insert 5' of transcription units. Quantitative genetic analysis of subtle effects of P element mutations that have been induced in an isogenic background may be a highly efficient method for functional genome annotation. RESULTS: Here, we have tested the efficacy of this strategy by assessing the extent to which screening for quantitative effects of P elements on sensory bristle number can identify genes affecting neural development. We find that such quantitative screens uncover an unusually large number of genes that are known to function in neural development, as well as genes with yet uncharacterized effects on neural development, and novel loci. CONCLUSIONS: Our findings establish the use of quantitative trait analysis for functional genome annotation through forward genetics. Similar analyses of quantitative effects of P element insertions will facilitate our understanding of the genes affecting many other complex traits in Drosophila.

  9. Counter-driver shock tube

    Science.gov (United States)

    Tamba, T.; Nguyen, T. M.; Takeya, K.; Harasaki, T.; Iwakawa, A.; Sasoh, A.

    2015-11-01

    A "counter-driver" shock tube was developed. In this device, two counter drivers are actuated with an appropriate delay time to generate the interaction between a shock wave and a flow in the opposite direction which is induced by another shock wave. The conditions for the counter drivers can be set independently. Each driver is activated by a separate electrically controlled diaphragm rupture device, in which a pneumatic piston drives a rupture needle with a temporal jitter of better than 1.1 ms. Operation demonstrations were conducted to evaluate the practical performance.

  10. A meta-analysis to identify animal and management factors influencing gestating sow efficiency.

    Science.gov (United States)

    Douglas, S L; Szyszka, O; Stoddart, K; Edwards, S A; Kyriazakis, I

    2014-12-01

    A meta-analysis on the effects of management and animal-based factors on the reproductive efficiency of gestating sows can provide information on single-factor and interaction effects that may not have been detected in individual studies. This study analyzed the effects of such factors on the number of piglets born alive per litter (BA), piglet birth weight (BiW) and weaning weight (WW), and number of piglets born alive per kilogram of sow feed intake during gestation (BA/FI). A total of 51 papers and 7 data sources were identified for the meta-analysis, out of which 23 papers and 5 sets of production data were useable (a total of 121 treatments). The information gathered included the dependent variables as well as information regarding animal, management, and feed characteristics. While a number of factors were individually significant, the multivariate models identified significant effects only of 1) floor type (P=0.003), sow BW at the end of gestation (P=0.002), and housing (stalls vs. loose; P=0.004) on BA; as floor type and housing were confounded, they were included in 2 separate models. The BA was higher on solid (12.1) in comparison to partly slatted (11.4) and fully slatted floors (10.2); 2) sow gestation environment (P=0.017) and gestation feed allowance (P=0.046) on BiW, with BiW of pigs higher for sows kept outdoors rather than indoors (1.75 versus 1.49 kg); 3) parity number (P=0.003) and feed intake during gestation (P=0.017) on WW; in addition there was an interaction between parity number×feed ME and parity number×feed CP content of feed during gestation on WW, with the positive effects of feed ME and CP contents seen during early rather than later parities; and 4) floor type (P=0.019) and feed crude fiber (P=0.003) for BA/FI with a greater number for those kept on solid floors (5.11) versus partially and fully slatted floors (4.07 and 4.05). The meta-analysis confirmed the significant effect of several well-known factors on the efficiency of

  11. Driver Fatigue Features Extraction

    Directory of Open Access Journals (Sweden)

    Gengtian Niu

    2014-01-01

    Full Text Available Driver fatigue is the main cause of traffic accidents. How to extract the effective features of fatigue is important for recognition accuracy and traffic safety. To solve the problem, this paper proposes a new method of driver fatigue features extraction based on the facial image sequence. In this method, first, each facial image in the sequence is divided into nonoverlapping blocks of the same size, and Gabor wavelets are employed to extract multiscale and multiorientation features. Then the mean value and standard deviation of each block’s features are calculated, respectively. Considering the facial performance of human fatigue is a dynamic process that developed over time, each block’s features are analyzed in the sequence. Finally, Adaboost algorithm is applied to select the most discriminating fatigue features. The proposed method was tested on a self-built database which includes a wide range of human subjects of different genders, poses, and illuminations in real-life fatigue conditions. Experimental results show the effectiveness of the proposed method.

  12. Fast SCR Thyratron Driver

    Energy Technology Data Exchange (ETDEWEB)

    Nguyen, M.N.; /SLAC

    2007-06-18

    As part of an improvement project on the linear accelerator at SLAC, it was necessary to replace the original thyratron trigger generator, which consisted of two chassis, two vacuum tubes, and a small thyratron. All solid-state, fast rise, and high voltage thyratron drivers, therefore, have been developed and built for the 244 klystron modulators. The rack mounted, single chassis driver employs a unique way to control and generate pulses through the use of an asymmetric SCR, a PFN, a fast pulse transformer, and a saturable reactor. The resulting output pulse is 2 kV peak into 50 {Omega} load with pulse duration of 1.5 {mu}s FWHM at 180 Hz. The pulse risetime is less than 40 ns with less than 1 ns jitter. Various techniques are used to protect the SCR from being damaged by high voltage and current transients due to thyratron breakdowns. The end-of-line clipper (EOLC) detection circuit is also integrated into this chassis to interrupt the modulator triggering in the event a high percentage of line reflections occurred.

  13. Potential biomarkers of fatigue identified by plasma metabolome analysis in rats.

    Science.gov (United States)

    Kume, Satoshi; Yamato, Masanori; Tamura, Yasuhisa; Jin, Guanghua; Nakano, Masayuki; Miyashige, Yukiharu; Eguchi, Asami; Ogata, Yoshiyuki; Goda, Nobuhito; Iwai, Kazuhiro; Yamano, Emi; Watanabe, Yasuyoshi; Soga, Tomoyoshi; Kataoka, Yosky

    2015-01-01

    In the present study, prior to the establishment of a method for the clinical diagnosis of chronic fatigue in humans, we validated the utility of plasma metabolomic analysis in a rat model of fatigue using capillary electrophoresis-mass spectrometry (CE-MS). In order to obtain a fatigued animal group, rats were placed in a cage filled with water to a height of 2.2 cm for 5 days. A food-restricted group, in which rats were limited to 10 g/d of food (around 50% of the control group), was also assessed. The food-restricted group exhibited weight reduction similar to that of the fatigued group. CE-MS measurements were performed to evaluate the profile of food intake-dependent metabolic changes, as well as the profile in fatigue loading, resulting in the identification of 48 metabolites in plasma. Multivariate analyses using hierarchical clustering and principal component analysis revealed that the plasma metabolome in the fatigued group showed clear differences from those in the control and food-restricted groups. In the fatigued group, we found distinctive changes in metabolites related to branched-chain amino acid metabolism, urea cycle, and proline metabolism. Specifically, the fatigued group exhibited significant increases in valine, leucine, isoleucine, and 2-oxoisopentanoate, and significant decreases in citrulline and hydroxyproline compared with the control and food-restricted groups. Plasma levels of total nitric oxide were increased in the fatigued group, indicating systemic oxidative stress. Further, plasma metabolites involved in the citrate cycle, such as cis-aconitate and isocitrate, were reduced in the fatigued group. The levels of ATP were significantly decreased in the liver and skeletal muscle, indicative of a deterioration in energy metabolism in these organs. Thus, this comprehensive metabolic analysis furthered our understanding of the pathophysiology of fatigue, and identified potential diagnostic biomarkers based on fatigue pathophysiology.

  14. Potential biomarkers of fatigue identified by plasma metabolome analysis in rats.

    Directory of Open Access Journals (Sweden)

    Satoshi Kume

    Full Text Available In the present study, prior to the establishment of a method for the clinical diagnosis of chronic fatigue in humans, we validated the utility of plasma metabolomic analysis in a rat model of fatigue using capillary electrophoresis-mass spectrometry (CE-MS. In order to obtain a fatigued animal group, rats were placed in a cage filled with water to a height of 2.2 cm for 5 days. A food-restricted group, in which rats were limited to 10 g/d of food (around 50% of the control group, was also assessed. The food-restricted group exhibited weight reduction similar to that of the fatigued group. CE-MS measurements were performed to evaluate the profile of food intake-dependent metabolic changes, as well as the profile in fatigue loading, resulting in the identification of 48 metabolites in plasma. Multivariate analyses using hierarchical clustering and principal component analysis revealed that the plasma metabolome in the fatigued group showed clear differences from those in the control and food-restricted groups. In the fatigued group, we found distinctive changes in metabolites related to branched-chain amino acid metabolism, urea cycle, and proline metabolism. Specifically, the fatigued group exhibited significant increases in valine, leucine, isoleucine, and 2-oxoisopentanoate, and significant decreases in citrulline and hydroxyproline compared with the control and food-restricted groups. Plasma levels of total nitric oxide were increased in the fatigued group, indicating systemic oxidative stress. Further, plasma metabolites involved in the citrate cycle, such as cis-aconitate and isocitrate, were reduced in the fatigued group. The levels of ATP were significantly decreased in the liver and skeletal muscle, indicative of a deterioration in energy metabolism in these organs. Thus, this comprehensive metabolic analysis furthered our understanding of the pathophysiology of fatigue, and identified potential diagnostic biomarkers based on fatigue

  15. Lane-changing model with dynamic consideration of driver's propensity

    Science.gov (United States)

    Wang, Xiaoyuan; Wang, Jianqiang; Zhang, Jinglei; Ban, Xuegang Jeff

    2015-07-01

    Lane-changing is the driver's selection result of the satisfaction degree in different lane driving conditions. There are many different factors influencing lane-changing behavior, such as diversity, randomicity and difficulty of measurement. So it is hard to accurately reflect the uncertainty of drivers' lane-changing behavior. As a result, the research of lane-changing models is behind that of car-following models. Driver's propensity is her/his emotion state or the corresponding preference of a decision or action toward the real objective traffic situations under the influence of various dynamic factors. It represents the psychological characteristics of the driver in the process of vehicle operation and movement. It is an important factor to influence lane-changing. In this paper, dynamic recognition of driver's propensity is considered during simulation based on its time-varying discipline and the analysis of the driver's psycho-physic characteristics. The Analytic Hierarchy Process (AHP) method is used to quantify the hierarchy of driver's dynamic lane-changing decision-making process, especially the influence of the propensity. The model is validated using real data. Test results show that the developed lane-changing model with the dynamic consideration of a driver's time-varying propensity and the AHP method are feasible and with improved accuracy.

  16. Driver Model of a Powered Wheelchair Operation as a Tool of Theoretical Analyses

    Science.gov (United States)

    Ito, Takuma; Inoue, Takenobu; Shino, Motoki; Kamata, Minoru

    This paper describes the construction of a driver model of a powered wheelchair operation for the understanding of the characteristics of the driver. The main targets of existing researches about driver models are the operation of the automobiles and motorcycles, not a low-speed vehicle such as powered wheelchairs. Therefore, we started by verifying the possibility of modeling the turning operation at a corner of a corridor. At first, we conducted an experiment on a daily powered wheelchair user by using his vehicle. High reproducibility of driving and the driving characteristics for the construction of a driver model were both confirmed from the result of the experiment. Next, experiments with driving simulators were conducted for the collection of quantitative driving data. The parameters of the proposed driver model were identified from experimental results. From the simulations with the proposed driver model and identified parameters, the characteristics of the proposed driver model were analyzed.

  17. Drivers' perception of vulnerable road users: a hazard perception approach.

    Science.gov (United States)

    Borowsky, Avinoam; Oron-Gilad, Tal; Meir, Anat; Parmet, Yisrael

    2012-01-01

    The present study examined how experienced and young-inexperienced drivers (either trained in hazard perception or not) respond to and identify pedestrians when they appear in residential roads within populated neighborhoods and in urban roads located outside neighborhoods and usually less populated. As part of a hazard perception test, participants were connected to an eye tracking system and were asked to observe 58 traffic scene movies and press a response button each time they detected a hazardous situation. Analyzing all pedestrian-related events revealed that, regardless of driving experience or training, drivers detect pedestrians less often when they appear in urban areas and more often when they appear in residential areas. Moreover, experienced drivers processed information more efficiently than young-inexperienced drivers (both trained and untrained) when pedestrians were identified. Visual search patterns in urban and residential traffic environments are discussed.

  18. Modes of interactions between environmental drivers and marine biota

    Directory of Open Access Journals (Sweden)

    Philip eBoyd

    2015-02-01

    Full Text Available The responses of marine biota to global ocean change is characterised by multiple environmental drivers that interact to cause non-linear changes in organismal performance. Characterising interactions is critical for us to predict whether multiple drivers will accelerate or mitigate future biological responses. There is now a large body of evidence that drivers do not act independently, a common null model, but rather have synergistic or antagonistic effects on organisms. We review the literature on interactions among environmental drivers such as ocean acidification and warming, and identify three common modes of interaction: physicochemical interactions in the seawater media outside organisms, interactions that operate on organisms directly, for example by altering physiological rates; and interactions that occur through changes in ecosystems, like predation. Interactions can also occur across these levels increasing the number of permutations for interaction, and point to a diverse range of modes of interplay. Identifying the appropriate mode will help generalise interaction types to unstudied contexts.

  19. Novel snail1 target proteins in human colon cancer identified by proteomic analysis.

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    María Jesús Larriba

    Full Text Available BACKGROUND: The transcription factor Snail1 induces epithelial-to-mesenchymal transition (EMT, a process responsible for the acquisition of invasiveness during tumorigenesis. Several transcriptomic studies have reported Snail1-regulated genes in different cell types, many of them involved in cell adhesion. However, only a few studies have used proteomics as a tool for the characterization of proteins mediating EMT. METHODOLOGY/PRINCIPAL FINDINGS: We identified by proteomic analysis using 2D-DIGE electrophoresis combined with MALDI-TOF-TOF and ESI-linear ion trap mass spectrometry a number of proteins with variable functions whose expression is modulated by Snail1 in SW480-ADH human colon cancer cells. Validation was performed by Western blot and immunofluorescence analyses. Snail1 repressed several members of the 14-3-3 family of phosphoserine/phosphothreonine binding proteins and also the expression of the Proliferation-associated protein 2G4 (PA2G4 that was mainly localized at the nuclear Cajal bodies. In contrast, the expression of two proteins involved in RNA processing, the Cleavage and polyadenylation specificity factor subunit 6 (CPSF6 and the Splicing factor proline/glutamine-rich (SFPQ, was higher in Snail1-expressing cells than in controls. The regulation of 14-3-3epsilon, 14-3-3tau, 14-3-3zeta and PA2G4 by Snail1 was reproduced in HT29 colon cancer cells. In addition, we found an inverse correlation between 14-3-3sigma and Snail1 expression in human colorectal tumors. CONCLUSIONS/SIGNIFICANCE: We have identified a set of novel Snail1 target proteins in colon cancer that expand the cellular processes affected by Snail1 and thus its relevance for cell function and phenotype.

  20. Large scale association analysis identifies three susceptibility loci for coronary artery disease.

    Directory of Open Access Journals (Sweden)

    Stephanie Saade

    Full Text Available Genome wide association studies (GWAS and their replications that have associated DNA variants with myocardial infarction (MI and/or coronary artery disease (CAD are predominantly based on populations of European or Eastern Asian descent. Replication of the most significantly associated polymorphisms in multiple populations with distinctive genetic backgrounds and lifestyles is crucial to the understanding of the pathophysiology of a multifactorial disease like CAD. We have used our Lebanese cohort to perform a replication study of nine previously identified CAD/MI susceptibility loci (LTA, CDKN2A-CDKN2B, CELSR2-PSRC1-SORT1, CXCL12, MTHFD1L, WDR12, PCSK9, SH2B3, and SLC22A3, and 88 genes in related phenotypes. The study was conducted on 2,002 patients with detailed demographic, clinical characteristics, and cardiac catheterization results. One marker, rs6922269, in MTHFD1L was significantly protective against MI (OR=0.68, p=0.0035, while the variant rs4977574 in CDKN2A-CDKN2B was significantly associated with MI (OR=1.33, p=0.0086. Associations were detected after adjustment for family history of CAD, gender, hypertension, hyperlipidemia, diabetes, and smoking. The parallel study of 88 previously published genes in related phenotypes encompassed 20,225 markers, three quarters of which with imputed genotypes The study was based on our genome-wide genotype data set, with imputation across the whole genome to HapMap II release 22 using HapMap CEU population as a reference. Analysis was conducted on both the genotyped and imputed variants in the 88 regions covering selected genes. This approach replicated HNRNPA3P1-CXCL12 association with CAD and identified new significant associations of CDKAL1, ST6GAL1, and PTPRD with CAD. Our study provides evidence for the importance of the multifactorial aspect of CAD/MI and describes genes predisposing to their etiology.

  1. Beyond BLASTing: tertiary and quaternary structure analysis helps identify major vault proteins.

    Science.gov (United States)

    Daly, Toni K; Sutherland-Smith, Andrew J; Penny, David

    2013-01-01

    We examine the advantages of going beyond sequence similarity and use both protein three-dimensional (3D) structure prediction and then quaternary structure (docking) of inferred 3D structures to help evaluate whether comparable sequences can fold into homologous structures with sufficient lateral associations for quaternary structure formation. Our test case is the major vault protein (MVP) that oligomerizes in multiple copies to form barrel-like vault particles and is relatively widespread among eukaryotes. We used the iterative threading assembly refinement server (I-TASSER) to predict whether putative MVP sequences identified by BLASTp and PSI Basic Local Alignment Search Tool are structurally similar to the experimentally determined rodent MVP tertiary structures. Then two identical predicted quaternary structures from I-TASSER are analyzed by RosettaDock to test whether a pair-wise association occurs, and hence whether the oligomeric vault complex is likely to form for a given MVP sequence. Positive controls for the method are the experimentally determined rat (Rattus norvegicus) vault X-ray crystal structure and the purple sea urchin (Strongylocentrotus purpuratus) MVP sequence that forms experimentally observed vaults. These and two kinetoplast MVP structural homologs were predicted with high confidence value, and RosettaDock predicted that these MVP sequences would dock laterally and therefore could form oligomeric vaults. As the negative control, I-TASSER did not predict an MVP-like structure from a randomized rat MVP sequence, even when constrained to the rat MVP crystal structure (PDB:2ZUO), thus further validating the method. The protocol identified six putative homologous MVP sequences in the heterobolosean Naegleria gruberi within the excavate kingdom. Two of these sequences are predicted to be structurally similar to rat MVP, despite being in excess of 300 residues shorter. The method can be used generally to help test predictions of homology via

  2. Population viability analysis to identify management priorities for reintroduced elk in the Cumberland Mountains, Tennessee

    Science.gov (United States)

    Kindall, J.L.; Muller, L.I.; Clark, J.D.; Lupardus, J.L.; Murrow, J.L.

    2011-01-01

    We used an individual-based population model to perform a viability analysis to simulate population growth (λ) of 167 elk (Cervus elaphus manitobensis; 71 male and 96 female) released in the Cumberland Mountains, Tennessee, to estimate sustainability (i.e., λ > 1.0) and identify the most appropriate options for managing elk restoration. We transported elk from Elk Island National Park, Alberta, Canada, and from Land Between the Lakes, Kentucky, and reintroduced them beginning in December 2000 and ending in February 2003. We estimated annual survival rates for 156 radio-collared elk from December 2000 until November 2004. We used data from a nearby elk herd in Great Smoky Mountains National Park to simulate pessimistic and optimistic recruitment and performed population viability analyses to evaluate sustainability over a 25-year period. Annual survival averaged 0.799 (Total SE = 0.023). The primary identifiable sources of mortality were poaching, disease from meningeal worm (Parelaphostrongylus tenuis), and accidents (environmental causes and unintentional harvest). Population growth given pessimistic recruitment rates averaged 0.895 over 25 years (0.955 in year 1 to 0.880 in year 25); population growth was not sustainable in 100% of the runs. With the most optimistic estimates of recruitment, mean λ increased to 0.967 (1.038 in year 1 to 0.956 in year 25) with 99.6% of the runs failing to be sustainable. We suggest that further translocation efforts to increase herd size will be ineffective unless survival rates are increased in the Cumberland Mountains.

  3. In-silico analysis of Pasteurella multocida to identify common epitopes between fowl, goat and buffalo.

    Science.gov (United States)

    Ghaffar, Ammarah; Tariq, Aamira

    2016-04-10

    Pasteurella multocida represents a highly diverse group of bacteria infecting various hosts like the fowl, goat and buffalo leading to huge economic loss to the poultry and cattle industry. Previous reports indicated that the outer membrane proteins contribute significantly to the pathogenesis of Pasteurella multocida. The comparative in-silico genome wide analysis of four pathogenic Pasteurella multocida strains (Anand1-poultry, Anand1-goat, PMTB and VTCCBAA264) with their respective hosts was performed. A pipeline was developed to identify the list of non-homologous proteins of Pasteurella multocida strains and their hosts. The list was further analyzed for the identification of the essential outer membrane proteins responsible for the pathogenicity. Outer membrane proteins were further selected from these antigenic proteins on the basis of their pathogenic potential. A common B-cell epitope (TDYRNRDRS, ARRSVTSKEN, and KINDQWRW) determined via sequential and structural approach from the lipopolysaccharide (LPS) assembly outer membrane complex protein was predicted from fowl, goat and buffalo. Furthermore, we identified T-cell epitopes based on the lipopolysaccharide (LPS) assembly outer membrane complex protein via docking studies which were either similar to the B-cell epitopes or were occurring in the same patch except for MHC class II M fowl. We propose that this difference in epitope sequence is due to different interacting MHC class II protein predicted from the fowl. Hence, in the current study we found that a unique epitope based on the common antigenic lipopolysaccharide (LPS) outer membrane complex protein present in fowl, goat and buffalo can be a suitable target for vaccine development against the two economic devastating diseases; fowl cholera (FC) and hemorrhagic septicemia (HS).

  4. Transcriptome analysis identifies genes involved in ethanol response of Saccharomyces cerevisiae in Agave tequilana juice.

    Science.gov (United States)

    Ramirez-Córdova, Jesús; Drnevich, Jenny; Madrigal-Pulido, Jaime Alberto; Arrizon, Javier; Allen, Kirk; Martínez-Velázquez, Moisés; Alvarez-Maya, Ikuri

    2012-08-01

    During ethanol fermentation, yeast cells are exposed to stress due to the accumulation of ethanol, cell growth is altered and the output of the target product is reduced. For Agave beverages, like tequila, no reports have been published on the global gene expression under ethanol stress. In this work, we used microarray analysis to identify Saccharomyces cerevisiae genes involved in the ethanol response. Gene expression of a tequila yeast strain of S. cerevisiae (AR5) was explored by comparing global gene expression with that of laboratory strain S288C, both after ethanol exposure. Additionally, we used two different culture conditions, cells grown in Agave tequilana juice as a natural fermentation media or grown in yeast-extract peptone dextrose as artificial media. Of the 6368 S. cerevisiae genes in the microarray, 657 genes were identified that had different expression responses to ethanol stress due to strain and/or media. A cluster of 28 genes was found over-expressed specifically in the AR5 tequila strain that could be involved in the adaptation to tequila yeast fermentation, 14 of which are unknown such as yor343c, ylr162w, ygr182c, ymr265c, yer053c-a or ydr415c. These could be the most suitable genes for transforming tequila yeast to increase ethanol tolerance in the tequila fermentation process. Other genes involved in response to stress (RFC4, TSA1, MLH1, PAU3, RAD53) or transport (CYB2, TIP20, QCR9) were expressed in the same cluster. Unknown genes could be good candidates for the development of recombinant yeasts with ethanol tolerance for use in industrial tequila fermentation.

  5. Drivers of Acceptance of a New Beverage in Europe

    Directory of Open Access Journals (Sweden)

    Ana Patricia Silva

    2016-05-01

    Full Text Available One of the challenges of studying food consumption behavior is to identify the drivers of choice for a food product. This is particularly important to design and develop new foods for which no previous information is available. Hibiscus sabdariffa L. (Bissap is an herbaceous plant and an important source of vitamins, minerals, and bioactive compounds, which confer a number of potential health benefits to derived products. The consumption of Bissap in beverage form is widespread in Africa and Asia, but not yet in Europe. Therefore, this study aimed to identify the main drivers of consumer acceptance of a traditional African beverage made from Bissap to which they had not been previously exposed. First, three focus groups (n = 22 were performed in Portugal to characterize the sensory profile of four Bissap beverages, to reveal perceptions and attitudes towards Bissap beverages, and to identify potential choice attributes. Subsequently, a full-profile conjoint analysis (n = 99 was performed, where consumers evaluated 37 Bissap beverage profiles, aiming to estimate choice attribute importance and to identify relevant market segments. Focus group findings showed that consumers would choose Bissap because they perceived as a healthy choice, and due to its novelty. The conjoint study showed an ideal profile for a Bissap beverage costing €0.99/L, <18 kcal/100 mL, packaged in Tetra-pack, light red color, and containing labeling information about antioxidants and Bissap. Four clusters of consumers were identified: price sensitive, body concerned, packaging attracted, and demanding, highlighting the most influential choice attributes: price, calories, and packaging. Findings provide useful guidance for new product development of an African product in the European lifestyle. Results might be useful from a nutraceutical point of view and to the food/beverages industry.

  6. Alternative mRNA fates identified in microRNA-associated transcriptome analysis

    Directory of Open Access Journals (Sweden)

    Carroll Adam P

    2012-10-01

    Full Text Available Abstract Background MicroRNA (miRNA are small non-coding RNA molecules which function as nucleic acid-based specificity factors in the universal RNA binding complex known as the RNA induced silencing complex (RISC. In the canonical gene-silencing pathway, these activated RISC particles are associated with RNA decay and gene suppression, however, there is evidence to suggest that in some circumstances they may also stabilise their target RNA and even enhance translation. To further explore the role of miRNA in this context, we performed a genome-wide expression analysis to investigate the molecular consequences of bidirectional modulation of the disease-associated miRNAs miR-181b and miR-107 in multiple human cell lines. Results This data was subjected to pathways analysis and correlated against miRNA targets predicted through seed region homology. This revealed a large number of both conserved and non-conserved miRNA target genes, a selection of which were functionally validated through reporter gene assays. Contrary to expectation we also identified a significant proportion of predicted target genes with both conserved and non-conserved recognition elements that were positively correlated with the modulated miRNA. Finally, a large proportion of miR-181b associated genes devoid of the corresponding miRNA recognition element, were enriched with binding motifs for the E2F1 transcription factor, which is encoded by a miR-181b target gene. Conclusions These findings suggest that miRNA regulate target genes directly through interactions with both conserved and non-conserved target recognition elements, and can lead to both a decrease and increase in transcript abundance. They also multiply their influence through interaction with transcription factor genes exemplified by the observed miR-181b/E2F1 relationship.

  7. Sensory profile and drivers of liking for grape nectar among smoker and nonsmoker consumers

    Directory of Open Access Journals (Sweden)

    Cristiane Ramos Voorpostel

    2014-03-01

    Full Text Available Decreased gustatory and olfactory capacity is one of the problems caused by tobacco use. The objectives of this study were to determine the sensory profile of six grape nectar samples sweetened with different sweeteners and to verify the drivers of liking in two distinct consumer groups: smokers and nonsmokers. The sensory profile was constructed by twelve trained panelists using quantitative descriptive analysis (QDA. Consumer tests were performed with 112 smokers and 112 nonsmokers. Partial least squares regression analyses was used to identify the drivers of acceptance and rejection of the grape nectars among the two consumer groups. According to the QDA, the samples differed regarding six of the nineteen attributes generated. The absolute averages of the affective test were lower in the group of smokers; possibly because smoking influences acceptance and eating preferences, especially with regard to sweet foods. The results showed that the grape flavor was the major driver of preference for acceptance of the nectar, while astringency, wine aroma, bitterness and sweetness, and bitter aftertaste were drivers of rejection in the two groups of consumers, with some differences between the groups.

  8. Refueling Behavior of Flexible Fuel Vehicle Drivers in the Federal Fleet

    Energy Technology Data Exchange (ETDEWEB)

    Daley, R.; Nangle, J.; Boeckman, G.; Miller, M.

    2014-05-01

    Federal fleets are a frequent subject of legislative and executive efforts to lead a national transition to alternative fuels and advanced vehicle technologies. Section 701 of the Energy Policy Act of 2005 requires that all dual-fueled alternative fuel vehicles in the federal fleet be operated on alternative fuel 100% of the time when they have access to it. However, in Fiscal Year (FY) 2012, drivers of federal flex fuel vehicles (FFV) leased through the General Services Administration refueled with E85 24% of the time when it was available--falling well short of the mandate. The U.S. Department of Energy's National Renewable Energy Laboratory completed a 2-year Laboratory Directed Research and Development project to identify the factors that influence the refueling behavior of federal FFV drivers. The project began with two primary hypotheses. First, information scarcity increases the tendency to miss opportunities to purchase E85. Second, even with perfect information, there are limits to how far drivers will go out of their way to purchase E85. This paper discusses the results of the project, which included a June 2012 survey of federal fleet drivers and an empirical analysis of actual refueling behavior from FY 2009 to 2012. This research will aid in the design and implementation of intervention programs aimed at increasing alternative fuel use and reducing petroleum consumption.

  9. Crash and burn? Vehicle, collision, and driver factors that influence motor vehicle collision fires.

    Science.gov (United States)

    Bunn, T L; Slavova, S; Robertson, M

    2012-07-01

    A retrospective population-based case-control study was performed to determine the association between vehicle fires, and vehicle, collision, and driver factors on highways with a posted speed limit of at least 55mph. Data were obtained from the Kentucky Collision Report Analysis for Safer Highways (CRASH) electronic files for 2000-2009 from the Kentucky State Police Records Sections. The results from the final multiple logistic regression show that large trucks were at a higher risk for a collision involving a fire than passenger vehicles and pickup trucks. When controlling for all other variables in the model, vehicles 6 years old and older, driving straight down the highway, and single vehicle collisions were also identified as factors that increase the risk of motor vehicle collision fires on roadways with a posted speed limit of ≥55mph. Of the 2096 vehicles that caught fire, there were 632 (30%) non-fatally injured drivers and 224 (11%) fatally injured drivers. The results of this study have the potential to inform public health messages directed to the transportation industry, particularly semi truck drivers, in regard to fire risk.

  10. Addressing the Multiple Drivers of Wetland Ecosystems Degradation in Lagos, Nigeria

    Science.gov (United States)

    Agboola, J.; Ndimele, P. E.; Odunuga, S.; Akanni, A.; Kosemani, B.; Ahove, M.

    2015-12-01

    Several body of knowledge have noted the importance of wetland ecosystems in climate moderation, resource supply and flood risk reduction amongst others. Relevant as it may, rapidly increasing population and uncontrolled urban development poses a challenge in some regions and require understanding of the ecosystem components and drivers of change over a long period of time. Thus, the main thrust of this paper is to analyse multiple drivers of wetland ecosystems degradation in the last 30 years in the Lagos megacity using field study, desktop review, satellite data and laboratory analysis. Key drivers identified includes: conversion of wetlands to settlements and waste sink, land use planning that neglects wetland conservation and restoration, ineffective legal status for wetlands, over exploitation leading to degradation and fragmentation of wetland ecosystems governance. In stemming further loss of this vital ecosystem, this study adopted and proposed respectively, the Drivers, Pressure, State, Impact and Response (DPSIR) and Integrated Planning Approach (IPA) frameworks in analysing policy and governance issues in wetland development. These analyses figured out amongst others, strict conservation and sustainable use of wetland resources, habitat restoration, climate adaptation measures, legal protection and wetland management institution as major responses to current multiple pressures facing wetland ecosystems in Lagos. For these frameworks to be made meaningful, weak coordination among government agencies and institutional capacity in implementation and law enforcement, unsustainable resource extraction by private/business organization and issues on alternative sources of income on the part of the local communities amongst others needs to be addressed.

  11. Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies

    Science.gov (United States)

    Delmont, Tom O.

    2016-01-01

    High-throughput sequencing provides a fast and cost-effective mean to recover genomes of organisms from all domains of life. However, adequate curation of the assembly results against potential contamination of non-target organisms requires advanced bioinformatics approaches and practices. Here, we re-analyzed the sequencing data generated for the tardigrade Hypsibius dujardini, and created a holistic display of the eukaryotic genome assembly using DNA data originating from two groups and eleven sequencing libraries. By using bacterial single-copy genes, k-mer frequencies, and coverage values of scaffolds we could identify and characterize multiple near-complete bacterial genomes from the raw assembly, and curate a 182 Mbp draft genome for H. dujardini supported by RNA-Seq data. Our results indicate that most contaminant scaffolds were assembled from Moleculo long-read libraries, and most of these contaminants have differed between library preparations. Our re-analysis shows that visualization and curation of eukaryotic genome assemblies can benefit from tools designed to address the needs of today’s microbiologists, who are constantly challenged by the difficulties associated with the identification of distinct microbial genomes in complex environmental metagenomes. PMID:27069789

  12. De Novo Transcriptome Analysis of Allium cepa L. (Onion) Bulb to Identify Allergens and Epitopes.

    Science.gov (United States)

    Rajkumar, Hemalatha; Ramagoni, Ramesh Kumar; Anchoju, Vijayendra Chary; Vankudavath, Raju Naik; Syed, Arshi Uz Zaman

    2015-01-01

    Allium cepa (onion) is a diploid plant with one of the largest nuclear genomes among all diploids. Onion is an example of an under-researched crop which has a complex heterozygous genome. There are no allergenic proteins and genomic data available for onions. This study was conducted to establish a transcriptome catalogue of onion bulb that will enable us to study onion related genes involved in medicinal use and allergies. Transcriptome dataset generated from onion bulb using the Illumina HiSeq 2000 technology showed a total of 99,074,309 high quality raw reads (~20 Gb). Based on sequence homology onion genes were categorized into 49 different functional groups. Most of the genes however, were classified under 'unknown' in all three gene ontology categories. Of the categorized genes, 61.2% showed metabolic functions followed by cellular components such as binding, cellular processes; catalytic activity and cell part. With BLASTx top hit analysis, a total of 2,511 homologous allergenic sequences were found, which had 37-100% similarity with 46 different types of allergens existing in the database. From the 46 contigs or allergens, 521 B-cell linear epitopes were identified using BepiPred linear epitope prediction tool. This is the first comprehensive insight into the transcriptome of onion bulb tissue using the NGS technology, which can be used to map IgE epitopes and prediction of structures and functions of various proteins.

  13. Identifying Major Factors Affecting Groundwater Change in the North China Plain with Grey Relational Analysis

    Directory of Open Access Journals (Sweden)

    Xue Li

    2014-06-01

    Full Text Available The North China Plain (NCP is facing a water crisis under the dual impact of natural and anthropogenic factors. Groundwater levels have declined continuously since 1960, causing a series of environmental problems that have restricted sustainable development in the region. In the present study, we first utilized a previously developed 3D groundwater model to determine changes in groundwater level in the region over the past 50 years (1961–2010. We then applied grey relational analysis (GRA to identify and ordinate major factors that have contributed to these changes. The results show an overall decreasing trend in groundwater levels in this region over the past 50 years and an increase in the water table depth at a rate of approximately 0.36 m/a. Groundwater exploitation showed the most significant correlation with the groundwater table decline, when compared with other factors including precipitation and river leakage. Therefore, human activities should be considered the primary force driving the groundwater level down. The results of this study have implications for developing criteria that consider changes in both climate and socio-economics. Furthermore, since the NCP is one of the most water-scarce and densely populated regions in the world, the analytical approach used in and the insights gained from this study are of international interest.

  14. RCAUSE – A ROOT CAUSE ANALYSIS MODEL TO IDENTIFY THE ROOT CAUSES OF SOFTWARE REENGINEERING PROBLEMS

    Directory of Open Access Journals (Sweden)

    Er. Anand Rajavat

    2011-01-01

    Full Text Available Organizations that wish to modernize their legacy systems, must adopt a financial viable evolution strategy to gratify the needs of modern business environment. There are various options available to modernize legacy system in to more contemporary system. Over the last few years’ legacy system reengineering has emerged as a popular system modernization technique. The reengineering generally focuses on the increased productivity and quality of the system. However many of these efforts are often less than successful because they only concentrate on symptoms of software reengineering risk without targeting root causes of those risk. A subjective assessment (diagnosis of software reengineering risk from different domain of legacy system is required to identify the root causes of those risks. The goal of this paper is to highlight root causes of software reengineering risk. We proposed a root cause analysis model RCause that classify root causes of software reengineering risk in to three distinctive but connected areas of interest i.e. system domain, managerial domain and technical domain. .

  15. Identifying Interventions for Improving Letter Formation: A Brief Experimental Analysis of Students with Intellectual Disabilities

    Directory of Open Access Journals (Sweden)

    E. Rüya ÖZMEN

    2016-09-01

    Full Text Available As a group, students with intellectual disabilities display difficulties in a wide range of academic skills, including the acquisition of basic academic skills such as literacy. Early writing and reading skills must be supported to prepare students with intellectual disabilities to learn to read and write. The goal of this study was to replicate and extend the current research on Brief Experimental Analysis with letter formation. Three students with intellectual disabilities participated in the study. A brief multi-element design was used to test effectiveness of four interventions on letter formation. These interventions included goal setting plus contingent reinforcement, graphical feedback, error correction and modeling. For one student, modeling was effective; for the two remaining students, goal setting plus contingent reinforcement was effective. The results of this study extend the BEA literature by investigating the effects of interventions for improving letter formation in students with intellectual disabilities. The study findings suggest that using BEA to assess the relative contribution of each intervention can identify the most effective interventions for improving letter formation in students with intellectual disabilities.

  16. Suppression subtractive hybridization and comparative expression analysis to identify developmentally regulated genes in filamentous fungi.

    Science.gov (United States)

    Gesing, Stefan; Schindler, Daniel; Nowrousian, Minou

    2013-09-01

    Ascomycetes differentiate four major morphological types of fruiting bodies (apothecia, perithecia, pseudothecia and cleistothecia) that are derived from an ancestral fruiting body. Thus, fruiting body differentiation is most likely controlled by a set of common core genes. One way to identify such genes is to search for genes with evolutionary conserved expression patterns. Using suppression subtractive hybridization (SSH), we selected differentially expressed transcripts in Pyronema confluens (Pezizales) by comparing two cDNA libraries specific for sexual and for vegetative development, respectively. The expression patterns of selected genes from both libraries were verified by quantitative real time PCR. Expression of several corresponding homologous genes was found to be conserved in two members of the Sordariales (Sordaria macrospora and Neurospora crassa), a derived group of ascomycetes that is only distantly related to the Pezizales. Knockout studies with N. crassa orthologues of differentially regulated genes revealed a functional role during fruiting body development for the gene NCU05079, encoding a putative MFS peptide transporter. These data indicate conserved gene expression patterns and a functional role of the corresponding genes during fruiting body development; such genes are candidates of choice for further functional analysis.

  17. Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies

    Directory of Open Access Journals (Sweden)

    Tom O. Delmont

    2016-03-01

    Full Text Available High-throughput sequencing provides a fast and cost-effective mean to recover genomes of organisms from all domains of life. However, adequate curation of the assembly results against potential contamination of non-target organisms requires advanced bioinformatics approaches and practices. Here, we re-analyzed the sequencing data generated for the tardigrade Hypsibius dujardini, and created a holistic display of the eukaryotic genome assembly using DNA data originating from two groups and eleven sequencing libraries. By using bacterial single-copy genes, k-mer frequencies, and coverage values of scaffolds we could identify and characterize multiple near-complete bacterial genomes from the raw assembly, and curate a 182 Mbp draft genome for H. dujardini supported by RNA-Seq data. Our results indicate that most contaminant scaffolds were assembled from Moleculo long-read libraries, and most of these contaminants have differed between library preparations. Our re-analysis shows that visualization and curation of eukaryotic genome assemblies can benefit from tools designed to address the needs of today’s microbiologists, who are constantly challenged by the difficulties associated with the identification of distinct microbial genomes in complex environmental metagenomes.

  18. Mutation Analysis of hCDC4 in AML Cells Identifies a New Intronic Polymorphism

    Directory of Open Access Journals (Sweden)

    Daniel Nowak, Maximilian Mossner, Claudia D. Baldus, Olaf Hopfer, Eckhard Thiel, Wolf-Karsten Hofmann

    2006-01-01

    Full Text Available hCDC4 (FBW7, FBXW7 is a new potential tumor suppressor gene which provides substrate specificity for SCF (Skp–Cullin–F-box ubiquitin ligases and thereby regulates the degradation of potent oncogenes such as cyclin E, Myc, c-Jun and Notch. Mutations in the hCDC4 gene have been found in several solid tumors such as pancreas, colorectal or endometrial cancer. We carried out a mutation analysis of the hCDC4 gene in 35 samples of patients with Acute Myeloid Leukemia (AML to elucidate a possible role of hCDC4 mutations in this disease. By direct DNA sequencing and digestion with Surveyor nuclease one heterozygous mutation in the 5' untranslated region of exon 1, transcript variant 3 was detected. Additionally, we could identify a new intronic SNP downstream of exon 10. The new variation was present in 20% of AML samples and was furthermore confirmed in a panel of 51 healthy individuals where it displayed a frequency of 14%. In conclusion we provide first data that in contrast to several solid tumors, mutations in the hCDC4 gene may not play a pivotal role in the pathogenesis of AML. Furthermore, we describe a new intronic polymorphism with high frequency in the intron sequence of the hCDC4 gene.

  19. Microarray analysis of human monocytes infected with Francisella tularensis identifies new targets of host response subversion.

    Directory of Open Access Journals (Sweden)

    Jonathan P Butchar

    Full Text Available Francisella tularensis is a gram-negative facultative bacterium that causes the disease tularemia, even upon exposure to low numbers of bacteria. One critical characteristic of Francisella is its ability to dampen or subvert the host immune response. In order to help understand the mechanisms by which this occurs, we performed Affymetrix microarray analysis on transcripts from blood monocytes infected with the virulent Type A Schu S4 strain. Results showed that expression of several host response genes were reduced such as those associated with interferon signaling, Toll-like receptor signaling, autophagy and phagocytosis. When compared to microarrays from monocytes infected with the less virulent F. tularensis subsp. novicida, we found qualitative differences and also a general pattern of quantitatively reduced pro-inflammatory signaling pathway genes in the Schu S4 strain. Notably, the PI3K/Akt1 pathway appeared specifically down-regulated following Schu S4 infection and a concomitantly lower cytokine response was observed. This study identifies several new factors potentially important in host cell subversion by the virulent Type A F. tularensis that may serve as novel targets for drug discovery.

  20. Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies.

    Science.gov (United States)

    Delmont, Tom O; Eren, A Murat

    2016-01-01

    High-throughput sequencing provides a fast and cost-effective mean to recover genomes of organisms from all domains of life. However, adequate curation of the assembly results against potential contamination of non-target organisms requires advanced bioinformatics approaches and practices. Here, we re-analyzed the sequencing data generated for the tardigrade Hypsibius dujardini, and created a holistic display of the eukaryotic genome assembly using DNA data originating from two groups and eleven sequencing libraries. By using bacterial single-copy genes, k-mer frequencies, and coverage values of scaffolds we could identify and characterize multiple near-complete bacterial genomes from the raw assembly, and curate a 182 Mbp draft genome for H. dujardini supported by RNA-Seq data. Our results indicate that most contaminant scaffolds were assembled from Moleculo long-read libraries, and most of these contaminants have differed between library preparations. Our re-analysis shows that visualization and curation of eukaryotic genome assemblies can benefit from tools designed to address the needs of today's microbiologists, who are constantly challenged by the difficulties associated with the identification of distinct microbial genomes in complex environmental metagenomes.

  1. Systematic analysis of the PTEN 5' leader identifies a major AUU initiated proteoform.

    Science.gov (United States)

    Tzani, Ioanna; Ivanov, Ivaylo P; Andreev, Dmitri E; Dmitriev, Ruslan I; Dean, Kellie A; Baranov, Pavel V; Atkins, John F; Loughran, Gary

    2016-05-01

    Abundant evidence for translation within the 5' leaders of many human genes is rapidly emerging, especially, because of the advent of ribosome profiling. In most cases, it is believed that the act of translation rather than the encoded peptide is important. However, the wealth of available sequencing data in recent years allows phylogenetic detection of sequences within 5' leaders that have emerged under coding constraint and therefore allow for the prediction of functional 5' leader translation. Using this approach, we previously predicted a CUG-initiated, 173 amino acid N-terminal extension to the human tumour suppressor PTEN. Here, a systematic experimental analysis of translation events in the PTEN 5' leader identifies at least two additional non-AUG-initiated PTEN proteoforms that are expressed in most human cell lines tested. The most abundant extended PTEN proteoform initiates at a conserved AUU codon and extends the canonical AUG-initiated PTEN by 146 amino acids. All N-terminally extended PTEN proteoforms tested retain the ability to downregulate the PI3K pathway. We also provide evidence for the translation of two conserved AUG-initiated upstream open reading frames within the PTEN 5' leader that control the ratio of PTEN proteoforms.

  2. Electroretinogram analysis of relative spectral sensitivity in genetically identified dichromatic macaques.

    Science.gov (United States)

    Hanazawa, A; Mikami, A; Sulistyo Angelika, P; Takenaka, O; Goto, S; Onishi, A; Koike, S; Yamamori, T; Kato, K; Kondo, A; Suryobroto, B; Farajallah, A; Komatsu, H

    2001-07-03

    The retinas of macaque monkeys usually contain three types of photopigment, providing them with trichromatic color vision homologous to that of humans. However, we recently used molecular genetic analysis to identify several macaques with a dichromatic genotype. The affected X chromosome of these animals contains a hybrid gene of long-wavelength-sensitive (L) and middle-wavelength-sensitive (M) photopigments instead of separate genes encoding L and M photopigments. The product of the hybrid gene exhibits a spectral sensitivity close to that of M photopigment; consequently, male monkeys carrying the hybrid gene are genetic protanopes, effectively lacking L photopigment. In the present study, we assessed retinal expression of L photopigment in monkeys carrying the hybrid gene. The relative sensitivities to middle-wavelength (green) and long-wavelength (red) light were measured by electroretinogram flicker photometry. We found the sensitivity to red light to be extremely low in protanopic male monkeys compared with monkeys with the normal genotype. In female heterozygotes, sensitivity to red light was intermediate between the genetic protanopes and normal monkeys. Decreased sensitivity to long wavelengths was thus consistent with genetic loss of L photopigment.

  3. De Novo Transcriptome Analysis of Allium cepa L. (Onion Bulb to Identify Allergens and Epitopes.

    Directory of Open Access Journals (Sweden)

    Hemalatha Rajkumar

    Full Text Available Allium cepa (onion is a diploid plant with one of the largest nuclear genomes among all diploids. Onion is an example of an under-researched crop which has a complex heterozygous genome. There are no allergenic proteins and genomic data available for onions. This study was conducted to establish a transcriptome catalogue of onion bulb that will enable us to study onion related genes involved in medicinal use and allergies. Transcriptome dataset generated from onion bulb using the Illumina HiSeq 2000 technology showed a total of 99,074,309 high quality raw reads (~20 Gb. Based on sequence homology onion genes were categorized into 49 different functional groups. Most of the genes however, were classified under 'unknown' in all three gene ontology categories. Of the categorized genes, 61.2% showed metabolic functions followed by cellular components such as binding, cellular processes; catalytic activity and cell part. With BLASTx top hit analysis, a total of 2,511 homologous allergenic sequences were found, which had 37-100% similarity with 46 different types of allergens existing in the database. From the 46 contigs or allergens, 521 B-cell linear epitopes were identified using BepiPred linear epitope prediction tool. This is the first comprehensive insight into the transcriptome of onion bulb tissue using the NGS technology, which can be used to map IgE epitopes and prediction of structures and functions of various proteins.

  4. Acute toxicity tests and meta-analysis identify gaps in tropical ecotoxicology for amphibians.

    Science.gov (United States)

    Ghose, Sonia L; Donnelly, Maureen A; Kerby, Jacob; Whitfield, Steven M

    2014-09-01

    Amphibian populations are declining worldwide, particularly in tropical regions where amphibian diversity is highest. Pollutants, including agricultural pesticides, have been identified as a potential contributor to decline, yet toxicological studies of tropical amphibians are very rare. The present study assesses toxic effects on amphibians of 10 commonly used commercial pesticides in tropical agriculture using 2 approaches. First, the authors conducted 8-d toxicity assays with formulations of each pesticide using individually reared red-eyed tree frog (Agalychnis callidryas) tadpoles. Second, they conducted a review of available data for the lethal concentration to kill 50% of test animals from the US Environmental Protection Agency's ECOTOX database to allow comparison with their findings. Lethal concentration estimates from the assays ranged over several orders of magnitude. The nematicides terbufos and ethoprophos and the fungicide chlorothalonil were very highly toxic, with evident effects within an order of magnitude of environmental concentrations. Acute toxicity assays and meta-analysis show that nematicides and fungicides are generally more toxic than herbicides yet receive far less research attention than less toxic herbicides. Given that the tropics have a high diversity of amphibians, the findings emphasize the need for research into the effects of commonly used pesticides in tropical countries and should help guide future ecotoxicological research in tropical regions.

  5. Systems analysis of quantitative shRNA-library screens identifies regulators of cell adhesion

    Directory of Open Access Journals (Sweden)

    Huang XiaoDong

    2008-06-01

    Full Text Available Abstract Background High throughput screens with RNA interference technology enable loss-of-function analyses of gene activities in mammalian cells. While the construction of genome-scale shRNA libraries has been successful, results of large-scale screening of those libraries can be difficult to analyze because of the relatively high noise levels and the fact that not all shRNAs in a library are equally effective in silencing gene expression. Results We have screened a library consisting of 43,828 shRNAs directed against 8,500 human genes for functions that are necessary in cell detachment induced by a constitutively activated c-Abl tyrosine kinase. To deal with the issues of noise and uncertainty of knockdown efficiencies, we employed an analytical strategy that combines quantitative data analysis with biological knowledge, i.e. Gene Ontology and pathway information, to increase the power of the RNAi screening technique. Using this strategy we found 16 candidate genes to be involved in Abl-induced disruption of cell adhesion, and verified that the knockdown of IL6ST is associated with enhanced cell attachment. Conclusion Our results suggest that the power of genome-wide quantitative shRNA screens can be significantly increased when analyzed using a systems biology-based approach to identify functional gene networks.

  6. Genome-Wide Pathway Analysis Identifies Genetic Pathways Associated with Psoriasis.

    Science.gov (United States)

    Aterido, Adrià; Julià, Antonio; Ferrándiz, Carlos; Puig, Lluís; Fonseca, Eduardo; Fernández-López, Emilia; Dauden, Esteban; Sánchez-Carazo, José Luís; López-Estebaranz, José Luís; Moreno-Ramírez, David; Vanaclocha, Francisco; Herrera, Enrique; de la Cueva, Pablo; Dand, Nick; Palau, Núria; Alonso, Arnald; López-Lasanta, María; Tortosa, Raül; García-Montero, Andrés; Codó, Laia; Gelpí, Josep Lluís; Bertranpetit, Jaume; Absher, Devin; Capon, Francesca; Myers, Richard M; Barker, Jonathan N; Marsal, Sara

    2016-03-01

    Psoriasis is a chronic inflammatory disease with a complex genetic architecture. To date, the psoriasis heritability is only partially explained. However, there is increasing evidence that the missing heritability in psoriasis could be explained by multiple genetic variants of low effect size from common genetic pathways. The objective of this study was to identify new genetic variation associated with psoriasis risk at the pathway level. We genotyped 598,258 single nucleotide polymorphisms in a discovery cohort of 2,281 case-control individuals from Spain. We performed a genome-wide pathway analysis using 1,053 reference biological pathways. A total of 14 genetic pathways (PFDR ≤ 2.55 × 10(-2)) were found to be significantly associated with psoriasis risk. Using an independent validation cohort of 7,353 individuals from the UK, a total of 6 genetic pathways were significantly replicated (PFDR ≤ 3.46 × 10(-2)). We found genetic pathways that had not been previously associated with psoriasis risk such as retinol metabolism (Pcombined = 1.84 × 10(-4)), the transport of inorganic ions and amino acids (Pcombined = 1.57 × 10(-7)), and post-translational protein modification (Pcombined = 1.57 × 10(-7)). In the latter pathway, MGAT5 showed a strong network centrality, and its association with psoriasis risk was further validated in an additional case-control cohort of 3,429 individuals (P psoriasis susceptibility.

  7. Does assisted driving behavior lead to safety-critical encounters with unequipped vehicles' drivers?

    Science.gov (United States)

    Preuk, Katharina; Stemmler, Eric; Schießl, Caroline; Jipp, Meike

    2016-10-01

    With Intelligent Transport Systems (e.g., traffic light assistance systems) assisted drivers are able to show driving behavior in anticipation of upcoming traffic situations. In the years to come, the penetration rate of such systems will be low. Therefore, the majority of vehicles will not be equipped with these systems. Unequipped vehicles' drivers may not expect the driving behavior of assisted drivers. However, drivers' predictions and expectations can play a significant role in their reaction times. Thus, safety issues could arise when unequipped vehicles' drivers encounter driving behavior of assisted drivers. This is why we tested how unequipped vehicles' drivers (N=60) interpreted and reacted to the driving behavior of an assisted driver. We used a multi-driver simulator with three drivers. The three drivers were driving in a line. The lead driver in the line was a confederate who was followed by two unequipped vehicles' drivers. We varied the equipment of the confederate with an Intelligent Transport System: The confederate was equipped either with or without a traffic light assistance system. The traffic light assistance system provided a start-up maneuver before a light turned green. Therefore, the assisted confederate seemed to show unusual deceleration behavior by coming to a halt at an unusual distance from the stop line at the red traffic light. The unusual distance was varied as we tested a moderate (4m distance from the stop line) and an extreme (10m distance from the stop line) parameterization of the system. Our results showed that the extreme parametrization resulted in shorter minimal time-to-collision of the unequipped vehicles' drivers. One rear-end crash was observed. These results provided initial evidence that safety issues can arise when unequipped vehicles' drivers encounter assisted driving behavior. We recommend that future research identifies counteractions to prevent these safety issues. Moreover, we recommend that system developers

  8. Alcohol and marijuana use while driving--an unexpected crash risk in Pakistani commercial drivers: a cross-sectional survey

    Directory of Open Access Journals (Sweden)

    Mir Mohammed

    2012-02-01

    Full Text Available Abstract Background A significant proportion of road traffic crashes are attributable to alcohol and marijuana use while driving globally. Sale and use of both substances is illegal in Pakistan and is not considered a threat for road traffic injuries. However literature hints that this may not be the case. We did this study to assess usage of alcohol and marijuana in Pakistani commercial drivers. Methods A sample of 857 commercial bus and truck drivers was interviewed in October 2008 at the largest commercial vehicle station in Rawalpindi and Islamabad, Pakistan. Time location cluster sampling was used to select the subjects and a structured questionnaire was used to assess the basic demographic profile, substance abuse habits of the drivers while on the road, and reasons for usage of illicit substances while driving were recorded. Self reported information was collected after obtaining informed consent. Chi square and fisher exact tests were used to assess differences between groups and logistic regression was used to identify significant associations between driver characteristics and alcohol and marijuana use. Results Almost 10% of truck drivers use alcohol while driving on Pakistani roads. Marijuana use is almost 30% in some groups. Statistically different patterns of usage are seen between population subgroups based on age, ethnicity, education, and marital status. Regression analysis shows association of alcohol and marijuana use with road rage and error behaviours, and also with an increased risk of being involved in road crashes. The reported reasons for using alcohol or marijuana show a general lack of awareness of the hazardous nature of this practice among the commercial driver population. Conclusion Alcohol and marijuana use is highly prevalent in Pakistani commercial drivers. The issue needs to be recognized by concerned authorities and methods such as random breath tests and sobriety check points need to be employed for proper law

  9. Qualitative analysis of land use change pressures, conditions and drivers in rural-urban fringes: A case of Nairobi rural-urban fringe, Kenya

    OpenAIRE

    Aggrey Daniel Maina Thuo

    2013-01-01

    This paper is grounded on the truism that the planet's future is urban. However, urban growth process is bringing rapid economic, social and physical changes. These changes are bringing rapid transformations in areas concerned, especially on land uses in rural-urban fringes. While this is happening, the pressures and drivers are not well documented and understood, particularly so for rural-urban fringes in developing countries such as Kenya.This paper is based on a qualitative research approa...

  10. Climatic and management drivers of CO2 exchanges by a production crop: Analysis over three successive 4-year crop rotation cycles

    OpenAIRE

    Buysse, Pauline; Manise, Tanguy; De Ligne, Anne; Moureaux, Christine; Bodson, Bernard; Heinesch, Bernard; Aubinet, Marc

    2016-01-01

    Carbon dioxide (CO2) exchanges between crops and the atmosphere are influenced by both climatic and crop management drivers. The investigated crop, situated at the Lonzée Terrestrial Observatory (LTO, candidate ICOS site) in Belgium and managed for more than 70 years using conventional farming practices, was monitored over three complete sugar beet/winter wheat/potato/winter wheat rotation cycles from 2004 to 2016. Continuous eddy-covariance measurements and regular biomass samplings were per...

  11. Identifying associations between genomic alterations in tumors.

    Science.gov (United States)

    George, Joshy; Gorringe, Kylie L; Smyth, Gordon K; Bowtell, David D L

    2013-01-01

    Single-nucleotide polymorphism (SNP) mapping arrays are a reliable method for identifying somatic copy number alterations in cancer samples. Though this is immensely useful to identify potential driver genes, it is not sufficient to identify genes acting in a concerted manner. In cancer cells, co-amplified genes have been shown to provide synergistic effects, and genomic alterations targeting a pathway have been shown to occur in a mutually exclusive manner. We therefore developed a bioinformatic method for detecting such gene pairs using an integrated analysis of genomic copy number and gene expression data. This approach allowed us to identify a gene pair that is co-amplified and co-expressed in high-grade serous ovarian cancer. This finding provided information about the interaction of specific genetic events that contribute to the development and progression of this disease.

  12. A meta-analysis of 87,040 individuals identifies 23 new susceptibility loci for prostate cancer.

    Science.gov (United States)

    Al Olama, Ali Amin; Kote-Jarai, Zsofia; Berndt, Sonja I; Conti, David V; Schumacher, Fredrick; Han, Ying; Benlloch, Sara; Hazelett, Dennis J; Wang, Zhaoming; Saunders, Ed; Leongamornlert, Daniel; Lindstrom, Sara; Jugurnauth-Little, Sara; Dadaev, Tokhir; Tymrakiewicz, Malgorzata; Stram, Daniel O; Rand, Kristin; Wan, Peggy; Stram, Alex; Sheng, Xin; Pooler, Loreall C; Park, Karen; Xia, Lucy; Tyrer, Jonathan; Kolonel, Laurence N; Le Marchand, Loic; Hoover, Robert N; Machiela, Mitchell J; Yeager, Merideth; Burdette, Laurie; Chung, Charles C; Hutchinson, Amy; Yu, Kai; Goh, Chee; Ahmed, Mahbubl; Govindasami, Koveela; Guy, Michelle; Tammela, Teuvo L J; Auvinen, Anssi; Wahlfors, Tiina; Schleutker, Johanna; Visakorpi, Tapio; Leinonen, Katri A; Xu, Jianfeng; Aly, Markus; Donovan, Jenny; Travis, Ruth C; Key, Tim J; Siddiq, Afshan; Canzian, Federico; Khaw, Kay-Tee; Takahashi, Atsushi; Kubo, Michiaki; Pharoah, Paul; Pashayan, Nora; Weischer, Maren; Nordestgaard, Borge G; Nielsen, Sune F; Klarskov, Peter; Røder, Martin Andreas; Iversen, Peter; Thibodeau, Stephen N; McDonnell, Shannon K; Schaid, Daniel J; Stanford, Janet L; Kolb, Suzanne; Holt, Sarah; Knudsen, Beatrice; Coll, Antonio Hurtado; Gapstur, Susan M; Diver, W Ryan; Stevens, Victoria L; Maier, Christiane; Luedeke, Manuel; Herkommer, Kathleen; Rinckleb, Antje E; Strom, Sara S; Pettaway, Curtis; Yeboah, Edward D; Tettey, Yao; Biritwum, Richard B; Adjei, Andrew A; Tay, Evelyn; Truelove, Ann; Niwa, Shelley; Chokkalingam, Anand P; Cannon-Albright, Lisa; Cybulski, Cezary; Wokołorczyk, Dominika; Kluźniak, Wojciech; Park, Jong; Sellers, Thomas; Lin, Hui-Yi; Isaacs, William B; Partin, Alan W; Brenner, Hermann; Dieffenbach, Aida Karina; Stegmaier, Christa; Chen, Constance; Giovannucci, Edward L; Ma, Jing; Stampfer, Meir; Penney, Kathryn L; Mucci, Lorelei; John, Esther M; Ingles, Sue A; Kittles, Rick A; Murphy, Adam B; Pandha, Hardev; Michael, Agnieszka; Kierzek, Andrzej M; Blot, William; Signorello, Lisa B; Zheng, Wei; Albanes, Demetrius; Virtamo, Jarmo; Weinstein, Stephanie; Nemesure, Barbara; Carpten, John; Leske, Cristina; Wu, Suh-Yuh; Hennis, Anselm; Kibel, Adam S; Rybicki, Benjamin A; Neslund-Dudas, Christine; Hsing, Ann W; Chu, Lisa; Goodman, Phyllis J; Klein, Eric A; Zheng, S Lilly; Batra, Jyotsna; Clements, Judith; Spurdle, Amanda; Teixeira, Manuel R; Paulo, Paula; Maia, Sofia; Slavov, Chavdar; Kaneva, Radka; Mitev, Vanio; Witte, John S; Casey, Graham; Gillanders, Elizabeth M; Seminara, Daniella; Riboli, Elio; Hamdy, Freddie C; Coetzee, Gerhard A; Li, Qiyuan; Freedman, Matthew L; Hunter, David J; Muir, Kenneth; Gronberg, Henrik; Neal, David E; Southey, Melissa; Giles, Graham G; Severi, Gianluca; Cook, Michael B; Nakagawa, Hidewaki; Wiklund, Fredrik; Kraft, Peter; Chanock, Stephen J; Henderson, Brian E; Easton, Douglas F; Eeles, Rosalind A; Haiman, Christopher A

    2014-10-01

    Genome-wide association studies (GWAS) have identified 76 variants associated with prostate cancer risk predominantly in populations of European ancestry. To identify additional susceptibility loci for this common cancer, we conducted a meta-analysis of > 10 million SNPs in 43,303 prostate cancer cases and 43,737 controls from studies in populations of European, African, Japanese and Latino ancestry. Twenty-three new susceptibility loci were identified at association P discover risk loci for disease.

  13. Identifying gender-preferred communication styles within online cancer communities: a retrospective, longitudinal analysis.

    Directory of Open Access Journals (Sweden)

    Kathleen T Durant

    Full Text Available BACKGROUND: The goal of this research is to determine if different gender-preferred social styles can be observed within the user interactions at an online cancer community. To achieve this goal, we identify and measure variables that pertain to each gender-specific social style. METHODS AND FINDINGS: We perform social network and statistical analysis on the communication flow of 8,388 members at six different cancer forums over eight years. Kruskal-Wallis tests were conducted to measure the difference between the number of intimate (and highly intimate dyads, relationship length, and number of communications. We determine that two patients are more likely to form an intimate bond on a gender-specific cancer forum (ovarian P = <0.0001, breast P = 0.0089, prostate P = 0.0021. Two female patients are more likely to form a highly intimate bond on a female-specific cancer forum (Ovarian P<0.0001, Breast P<0.01. Typically a male patient communicates with more members than a female patient (Ovarian forum P = 0.0406, Breast forum P = 0.0013. A relationship between two patients is longer on the gender-specific cancer forums than a connection between two members not identified as patients (ovarian forum P = 0.00406, breast forum P = 0.00013, prostate forum P = .0.0003. CONCLUSION: The high level of interconnectedness among the prostate patients supports the hypothesis that men prefer to socialize in large, interconnected, less-intimate groups. A female patient is more likely to form a highly intimate connection with another female patient; this finding is consistent with the hypothesis that woman prefer fewer, more intimate connections. The relationships of same-gender cancer patients last longer than other relationships; this finding demonstrates homophily within these online communities. Our findings regarding online communication preferences are in agreement with research findings from person-to-person communication

  14. Identifying Gender-Preferred Communication Styles within Online Cancer Communities: A Retrospective, Longitudinal Analysis

    Science.gov (United States)

    Durant, Kathleen T.; McCray, Alexa T.; Safran, Charles

    2012-01-01

    Background The goal of this research is to determine if different gender-preferred social styles can be observed within the user interactions at an online cancer community. To achieve this goal, we identify and measure variables that pertain to each gender-specific social style. Methods and Findings We perform social network and statistical analysis on the communication flow of 8,388 members at six different cancer forums over eight years. Kruskal-Wallis tests were conducted to measure the difference between the number of intimate (and highly intimate) dyads, relationship length, and number of communications. We determine that two patients are more likely to form an intimate bond on a gender-specific cancer forum (ovarian P = <0.0001, breast P = 0.0089, prostate P = 0.0021). Two female patients are more likely to form a highly intimate bond on a female-specific cancer forum (Ovarian P<0.0001, Breast P<0.01). Typically a male patient communicates with more members than a female patient (Ovarian forum P = 0.0406, Breast forum P = 0.0013). A relationship between two patients is longer on the gender-specific cancer forums than a connection between two members not identified as patients (ovarian forum P = 0.00406, breast forum P = 0.00013, prostate forum P = .0.0003). Conclusion The high level of interconnectedness among the prostate patients supports the hypothesis that men prefer to socialize in large, interconnected, less-intimate groups. A female patient is more likely to form a highly intimate connection with another female patient; this finding is consistent with the hypothesis that woman prefer fewer, more intimate connections. The relationships of same-gender cancer patients last longer than other relationships; this finding demonstrates homophily within these online communities. Our findings regarding online communication preferences are in agreement with research findings from person-to-person communication preference studies

  15. Genome wide transcriptome analysis of dendritic cells identifies genes with altered expression in psoriasis.

    Directory of Open Access Journals (Sweden)

    Kata Filkor

    Full Text Available Activation of dendritic cells by different pathogens induces the secretion of proinflammatory mediators resulting in local inflammation. Importantly, innate immunity must be properly controlled, as its continuous activation leads to the development of chronic inflammatory diseases such as psoriasis. Lipopolysaccharide (LPS or peptidoglycan (PGN induced tolerance, a phenomenon of transient unresponsiveness of cells to repeated or prolonged stimulation, proved valuable model for the study of chronic inflammation. Thus, the aim of this study was the identification of the transcriptional diversity of primary human immature dendritic cells (iDCs upon PGN induced tolerance. Using SAGE-Seq approach, a tag-based transcriptome sequencing method, we investigated gene expression changes of primary human iDCs upon stimulation or restimulation with Staphylococcus aureus derived PGN, a widely used TLR2 ligand. Based on the expression pattern of the altered genes, we identified non-tolerizeable and tolerizeable genes. Gene Ontology (GO and Kyoto Encyclopedia of Genes and Genomes (Kegg analysis showed marked enrichment of immune-, cell cycle- and apoptosis related genes. In parallel to the marked induction of proinflammatory mediators, negative feedback regulators of innate immunity, such as TNFAIP3, TNFAIP8, Tyro3 and Mer are markedly downregulated in tolerant cells. We also demonstrate, that the expression pattern of TNFAIP3 and TNFAIP8 is altered in both lesional, and non-lesional skin of psoriatic patients. Finally, we show that pretreatment of immature dendritic cells with anti-TNF-α inhibits the expression of IL-6 and CCL1 in tolerant iDCs and partially releases the suppression of TNFAIP8. Our findings suggest that after PGN stimulation/restimulation the host cell utilizes different mechanisms in order to maintain critical balance between inflammation and tolerance. Importantly, the transcriptome sequencing of stimulated/restimulated iDCs identified

  16. A meta-analysis of genome-wide association studies identifies novel variants associated with osteoarthritis of the hip

    DEFF Research Database (Denmark)

    Evangelou, Evangelos; Kerkhof, Hanneke J; Styrkarsdottir, Unnur

    2014-01-01

    Osteoarthritis (OA) is the most common form of arthritis with a clear genetic component. To identify novel loci associated with hip OA we performed a meta-analysis of genome-wide association studies (GWAS) on European subjects.......Osteoarthritis (OA) is the most common form of arthritis with a clear genetic component. To identify novel loci associated with hip OA we performed a meta-analysis of genome-wide association studies (GWAS) on European subjects....

  17. What happens when drivers face hazards on the road?

    Science.gov (United States)

    Ventsislavova, Petya; Gugliotta, Andres; Peña-Suarez, Elsa; Garcia-Fernandez, Pedro; Eisman, Eduardo; Crundall, David; Castro, Candida

    2016-06-01

    The current study aims to obtain knowledge about the nature of the processes involved in Hazard Perception, using measurement techniques to separate and independently quantify these suspected sub-processes: Sensation, Situation Awareness (recognition, location and projection) and decision-making. It applies Signal Detection Theory analysis to Hazard Perception and Prediction Tasks. To enable the calculation of Signal Detection Theory parameters, video-recorded hazardous vs. quasi-hazardous situations were presented to the participants. In the hazardous situations it is necessary to perform an evasive action, for instance, braking or swerving abruptly, while the quasi-hazardous situations do not require the driver to make any evasive manoeuvre, merely to carry on driving at the same speed and following the same trajectory. A first Multiple Choice Hazard Perception and Prediction test was created to measure participants' performance in a What Happens Next? Task. The sample comprised 143 participants, 47 females and 94 males. Groups of non-offender drivers (learner, novice and experienced) and offender drivers (novice and experienced) were recruited. The Multiple Choice Hazard Perception and Prediction test succeeded in finding differences between drivers according to their driving experience. In fact, differences exist with regard to the level of hazard discrimination (d' prime) by drivers with different experience (learner, novice and experienced drivers) and profile (offenders and non-offenders) and these differences emerge from Signal Detection Theory analysis. In addition, it was found that experienced drivers show higher Situation Awareness than learner or novice drivers. On the other hand, although offenders do worse than non-offenders on the hazard identification question, they do just as well when their Situation Awareness is probed (in fact, they are as aware as non-offenders of what the obstacles on the road are, where they are and what will happen next

  18. A meta-analysis of 87,040 individuals identifies 23 new susceptibility loci for prostate cancer

    DEFF Research Database (Denmark)

    Al Olama, Ali Amin; Kote-Jarai, Zsofia; Berndt, Sonja I

    2014-01-01

    Genome-wide association studies (GWAS) have identified 76 variants associated with prostate cancer risk predominantly in populations of European ancestry. To identify additional susceptibility loci for this common cancer, we conducted a meta-analysis of > 10 million SNPs in 43,303 prostate cancer...

  19. Genome-wide association analysis of more than 120,000 individuals identifies 15 new susceptibility loci for breast cancer

    NARCIS (Netherlands)

    Michailidou, Kyriaki; Beesley, Jonathan; Lindstrom, Sara; Canisius, Sander; Dennis, Joe; Lush, Michael J.; Maranian, Mel J.; Bolla, Manjeet K.; Wang, Qin; Shah, Mitul; Perkins, Barbara J.; Czene, Kamila; Eriksson, Mikael; Darabi, Hatef; Brand, Judith S.; Bojesen, Stig E.; Nordestgaard, Borge G.; Flyger, Henrik; Nielsen, Sune F.; Rahman, Nazneen; Turnbull, Clare; Fletcher, Olivia; Peto, Julian; Gibson, Lorna; dos-Santos-Silva, Isabel; Chang-Claude, Jenny; Flesch-Janys, Dieter; Rudolph, Anja; Eilber, Ursula; Behrens, Sabine; Nevanlinna, Heli; Muranen, Taru A.; Aittomaki, Kristiina; Blomqvist, Carl; Khan, Sofia; Aaltonen, Kirsimari; Ahsan, Habibul; Kibriya, Muhammad G.; Whittemore, Alice S.; John, Esther M.; Malone, Kathleen E.; Gammon, Marilie D.; Santella, Regina M.; Ursin, Giske; Makalic, Enes; Schmidt, Daniel F.; Casey, Graham; Hunter, David J.; Gapstur, Susan M.; Gaudet, Mia M.; Diver, W. Ryan; Haiman, Christopher A.; Schumacher, Fredrick; Henderson, Brian E.; Le Marchand, Loic; Berg, Christine D.; Chanock, Stephen J.; Figueroa, Jonine; Hoover, Robert N.; Lambrechts, Diether; Neven, Patrick; Wildiers, Hans; van Limbergen, Erik; Schmidt, Marjanka K.; Broeks, Annegien; Verhoef, Senno; Cornelissen, Sten; Couch, Fergus J.; Olson, Janet E.; Hallberg, Emily; Vachon, Celine; Waisfisz, Quinten; Meijers-Heijboer, Hanne; Adank, Muriel A.; van der Luijt, Rob B.; Li, Jingmei; Liu, Jianjun; Humphreys, Keith; Kang, Daehee; Choi, Ji-Yeob; Park, Sue K.; Yoo, Keun-Young; Matsuo, Keitaro; Ito, Hidemi; Iwata, Hiroji; Tajima, Kazuo; Guenel, Pascal; Truong, Therese; Mulot, Claire; Sanchez, Marie; Burwinkel, Barbara; Marme, Frederik; Surowy, Harald; Sohn, Christof; Wu, Anna H.; Tseng, Chiu-chen; Van den Berg, David; Stram, Daniel O.; Gonzalez-Neira, Anna; Benitez, Javier; Zamora, M. Pilar; Arias Perez, Jose Ignacio; Shu, Xiao-Ou; Lu, Wei; Gao, Yu-Tang; Cai, Hui; Cox, Angela; Cross, Simon S.; Reed, Malcolm W. R.; Andrulis, Irene L.; Knight, Julia A.; Glendon, Gord; Mulligan, Anna Marie; Sawyer, Elinor J.; Tomlinson, Ian; Kerin, Michael J.; Miller, Nicola; Lindblom, Annika; Margolin, Sara; Teo, Soo Hwang; Yip, Cheng Har; Taib, Nur Aishah Mohd; Tan, Gie-Hooi; Hooning, Maartje J.; Hollestelle, Antoinette; Martens, John W. M.; Collee, J. Margriet; Blot, William; Signorello, Lisa B.; Cai, Qiuyin; Hopper, John L.; Southey, Melissa C.; Tsimiklis, Helen; Apicella, Carmel; Shen, Chen-Yang; Hsiung, Chia-Ni; Wu, Pei-Ei; Hou, Ming-Feng; Kristensen, Vessela N.; Nord, Silje; Alnaes, Grethe I. Grenaker; Giles, Graham G.; Milne, Roger L.; McLean, Catriona; Canzian, Federico; Trichopoulos, Dimitrios; Peeters, Petra; Lund, Eiliv; Sund, Malin; Khaw, Kay-Tee; Gunter, Marc J.; Palli, Domenico; Mortensen, Lotte Maxild; Dossus, Laure; Huerta, Jose-Maria; Meindl, Alfons; Schmutzler, Rita K.; Sutter, Christian; Yang, Rongxi; Muir, Kenneth; Lophatananon, Artitaya; Stewart-Brown, Sarah; Siriwanarangsan, Pornthep; Hartman, Mikael; Miao, Hui; Chia, Kee Seng; Chan, Ching Wan; Fasching, Peter A.; Hein, Alexander; Beckmann, Matthias W.; Haeberle, Lothar; Brenner, Hermann; Dieffenbach, Aida Karina; Arndt, Volker; Stegmaier, Christa; Ashworth, Alan; Orr, Nick; Schoemaker, Minouk J.; Swerdlow, Anthony J.; Brinton, Louise; Garcia-Closas, Montserrat; Zheng, Wei; Halverson, Sandra L.; Shrubsole, Martha; Long, Jirong; Goldberg, Mark S.; Labreche, France; Dumont, Martine; Winqvist, Robert; Pylkas, Katri; Jukkola-Vuorinen, Arja; Grip, Mervi; Brauch, Hiltrud; Hamann, Ute; Bruening, Thomas; Radice, Paolo; Peterlongo, Paolo; Manoukian, Siranoush; Bernard, Loris; Bogdanova, Natalia V.; Doerk, Thilo; Mannermaa, Arto; Kataja, Vesa; Kosma, Veli-Matti; Hartikainen, Jaana M.; Devilee, Peter; Tollenaar, Robert A. E. M.; Seynaeve, Caroline; Van Asperen, Christi J.; Jakubowska, Anna; Lubinski, Jan; Jaworska, Katarzyna; Huzarski, Tomasz; Sangrajrang, Suleeporn; Gaborieau, Valerie; Brennan, Paul; Mckay, James; Slager, Susan; Toland, Amanda E.; Ambrosone, Christine B.; Yannoukakos, Drakoulis; Kabisch, Maria; Torres, Diana; Neuhausen, Susan L.; Anton-Culver, Hoda; Luccarini, Craig; Baynes, Caroline; Ahmed, Shahana; Healey, Catherine S.; Tessier, Daniel C.; Vincent, Daniel; Bacot, Francois; Pita, Guillermo; Rosario Alonso, M.; Alvarez, Nuria; Herrero, Daniel; Simard, Jacques; Pharoah, Paul P. D. P.; Kraft, Peter; Dunning, Alison M.; Chenevix-Trench, Georgia; Hall, Per; Easton, Douglas F.

    2015-01-01

    Genome-wide association studies (GWAS) and large-scale replication studies have identified common variants in 79 loci associated with breast cancer, explaining similar to 14% of the familial risk of the disease. To identify new susceptibility loci, we performed a meta-analysis of 11 GWAS, comprising

  20. Genome-wide association analysis of more than 120,000 individuals identifies 15 new susceptibility loci for breast cancer

    NARCIS (Netherlands)

    K. Michailidou (Kyriaki); J. Beesley (Jonathan); S. Lindstrom (Stephen); S. Canisius (Sander); J. Dennis (Joe); M. Lush (Michael); M. Maranian (Melanie); M.K. Bolla (Manjeet); Q. Wang (Qing); M. Shah (Mitul); B. Perkins (Barbara); K. Czene (Kamila); M. Eriksson (Mikael); H. Darabi (Hatef); J.S. Brand (Judith S.); S.E. Bojesen (Stig); B.G. Nordestgaard (Børge); H. Flyger (Henrik); S.F. Nielsen (Sune); N. Rahman (Nazneen); C. Turnbull (Clare); O. Fletcher (Olivia); J. Peto (Julian); L.J. Gibson (Lorna); I. dos Santos Silva (Isabel); J. Chang-Claude (Jenny); D. Flesch-Janys (Dieter); A. Rudolph (Anja); U. Eilber (Ursula); T.W. Behrens (Timothy); H. Nevanlinna (Heli); T.A. Muranen (Taru); K. Aittomäki (Kristiina); C. Blomqvist (Carl); S. Khan (Sofia); K. Aaltonen (Kirsimari); H. Ahsan (Habibul); M.G. Kibriya (Muhammad); A.S. Whittemore (Alice S.); E.M. John (Esther M.); K.E. Malone (Kathleen E.); M.D. Gammon (Marilie); R.M. Santella (Regina M.); G. Ursin (Giske); E. Makalic (Enes); D.F. Schmidt (Daniel); G. Casey (Graham); D.J. Hunter (David J.); S.M. Gapstur (Susan M.); M.M. Gaudet (Mia); W.R. Diver (Ryan); C.A. Haiman (Christopher A.); F.R. Schumacher (Fredrick); B.E. Henderson (Brian); L. Le Marchand (Loic); C.D. Berg (Christine); S.J. Chanock (Stephen); J.D. Figueroa (Jonine); R.N. Hoover (Robert N.); D. Lambrechts (Diether); P. Neven (Patrick); H. Wildiers (Hans); E. van Limbergen (Erik); M.K. Schmidt (Marjanka); A. Broeks (Annegien); S. Verhoef; S. Cornelissen (Sten); F.J. Couch (Fergus); J.E. Olson (Janet); B. Hallberg (Boubou); C. Vachon (Celine); Q. Waisfisz (Quinten); E.J. Meijers-Heijboer (Hanne); M.A. Adank (Muriel); R.B. van der Luijt (Rob); J. Li (Jingmei); J. Liu (Jianjun); M.K. Humphreys (Manjeet); D. Kang (Daehee); J.-Y. Choi (Ji-Yeob); S.K. Park (Sue K.); K.Y. Yoo; K. Matsuo (Keitaro); H. Ito (Hidemi); H. Iwata (Hiroji); K. Tajima (Kazuo); P. Guénel (Pascal); T. Truong (Thérèse); C. Mulot (Claire); M. Sanchez (Marie); B. Burwinkel (Barbara); F. Marme (Federick); H. Surowy (Harald); C. Sohn (Christof); A.H. Wu (Anna H); C.-C. Tseng (Chiu-chen); D. Van Den Berg (David); D.O. Stram (Daniel O.); A. González-Neira (Anna); J. Benítez (Javier); M.P. Zamora (Pilar); J.I.A. Perez (Jose Ignacio Arias); X.-O. Shu (Xiao-Ou); W. Lu (Wei); Y. Gao; H. Cai (Hui); A. Cox (Angela); S.S. Cross (Simon); M.W.R. Reed (Malcolm); I.L. Andrulis (Irene); J.A. Knight (Julia); G. Glendon (Gord); A.-M. Mulligan (Anna-Marie); E.J. Sawyer (Elinor); I.P. Tomlinson (Ian); M. Kerin (Michael); N. Miller (Nicola); A. Lindblom (Annika); S. Margolin (Sara); S.H. Teo (Soo Hwang); C.H. Yip (Cheng Har); N.A.M. Taib (Nur Aishah Mohd); G.-H. Tan (Gie-Hooi); M.J. Hooning (Maartje); A. Hollestelle (Antoinette); J.W.M. Martens (John); J. Margriet Collée; W.J. Blot (William); L.B. Signorello (Lisa B.); Q. Cai (Qiuyin); J. Hopper (John); M.C. Southey (Melissa); H. Tsimiklis (Helen); C. Apicella (Carmel); C-Y. Shen (Chen-Yang); C.-N. Hsiung (Chia-Ni); P.-E. Wu (Pei-Ei); M.-F. Hou (Ming-Feng); V. Kristensen (Vessela); S. Nord (Silje); G.G. Alnæs (Grethe Grenaker); G.G. Giles (Graham G.); R.L. Milne (Roger); C.A. McLean (Catriona Ann); F. Canzian (Federico); D. Trichopoulos (Dimitrios); P.H.M. Peeters; E. Lund (Eiliv); R. Sund (Reijo); K.T. Khaw; M.J. Gunter (Marc J.); D. Palli (Domenico); L.M. Mortensen (Lotte Maxild); L. Dossus (Laure); J.-M. Huerta (Jose-Maria); A. Meindl (Alfons); R.K. Schmutzler (Rita); C. Sutter (Christian); R. Yang (Rongxi); K. Muir (Kenneth); A. Lophatananon (Artitaya); S. Stewart-Brown (Sarah); P. Siriwanarangsan (Pornthep); J.M. Hartman (Joost); X. Miao; K.S. Chia (Kee Seng); C.W. Chan (Ching Wan); P.A. Fasching (Peter); R. Hein (Rebecca); M.W. Beckmann (Matthias W.); L. Haeberle (Lothar); H. Brenner (Hermann); A.K. Dieffenbach (Aida Karina); V. Arndt (Volker); C. Stegmaier (Christa); A. Ashworth (Alan); N. Orr (Nick); M. Schoemaker (Minouk); A.J. Swerdlow (Anthony ); L.A. Brinton (Louise); M. García-Closas (Montserrat); W. Zheng (Wei); S.L. Halverson (Sandra L.); M. Shrubsole (Martha); J. Long (Jirong); M.S. Goldberg (Mark); F. Labrèche (France); M. Dumont (Martine); R. Winqvist (Robert); K. Pykäs (Katri); A. Jukkola-Vuorinen (Arja); M. Grip (Mervi); H. Brauch (Hiltrud); U. Hamann (Ute); T. Brüning (Thomas); P. Radice (Paolo); P. Peterlongo (Paolo); S. Manoukian (Siranoush); L. Bernard (Loris); N.V. Bogdanova (Natalia); T. Dörk (Thilo); A. Mannermaa (Arto); V. Kataja (Vesa); V-M. Kosma (Veli-Matti); J.M. Hartikainen (J.); P. Devilee (Peter); R.A.E.M. Tollenaar (Rob); C.M. Seynaeve (Caroline); C.J. van Asperen (Christi); A. Jakubowska (Anna); J. Lubinski (Jan); K. Jaworska (Katarzyna); T. Huzarski (Tomasz); S. Sangrajrang (Suleeporn); V. Gaborieau (Valerie); P. Brennan (Paul); J.D. McKay (James); S. Slager (Susan); A.E. Toland (Amanda); C.B. Ambrosone (Christine B.); D. Yannoukakos (Drakoulis); M. Kabisch (Maria); D. Torres (Diana); S.L. Neuhausen (Susan); H. Anton-Culver (Hoda); C. Luccarini (Craig); C. Baynes (Caroline); S. Ahmed (Shahana); S. Healey (Sue); D.C. Tessier (Daniel C.); D. Vincent (Daniel); F. Bacot (Francois); G. Pita (G.); M.R. Alonso (M Rosario); N. Álvarez (Nuria); D. Herrero (Daniel); J. Simard (Jacques); P.P.D.P. Pharoah (Paul P.D.P.); P. Kraft (Peter); A.M. Dunning (Alison); G. Chenevix-Trench (Georgia); P. Hall (Per); D.F. Easton (Douglas)

    2015-01-01

    textabstractGenome-wide association studies (GWAS) and large-scale replication studies have identified common variants in 79 loci associated with breast cancer, explaining ∼14% of the familial risk of the disease. To identify new susceptibility loci, we performed a meta-analysis of 11 GWAS, comprisi

  1. Genome-wide association analysis of more than 120,000 individuals identifies 15 new susceptibility loci for breast cancer

    DEFF Research Database (Denmark)

    Michailidou, Kyriaki; Beesley, Jonathan; Lindstrom, Sara

    2015-01-01

    Genome-wide association studies (GWAS) and large-scale replication studies have identified common variants in 79 loci associated with breast cancer, explaining ∼14% of the familial risk of the disease. To identify new susceptibility loci, we performed a meta-analysis of 11 GWAS, comprising 15,748...

  2. Identification of Drivers in Traffic Accidents and Determination of Passenger Position in a Vehicle by Finger Marks

    Directory of Open Access Journals (Sweden)

    Matej Trapečar

    2012-01-01

    Full Text Available The following paper aims to illustrate certain investigative activities in the forensic analysis and examination of the scene of traffic accidents. When a traffic accident occurs, the scene must be secured as soon as possible to enable professional and proper forensic investigation. Failure to secure the accident scene might result in losing or contaminating the traces, which makes it more difficult to prove or explain trace evidence in further procedure or even makes such evidence inadmissible. The topic is discussed from the viewpoint of crime scene examination, since analysing and investigating traffic accidents requires a great deal of expertise and attention of the investigators. Complex traffic accidents include feigned accidents, hit-and-run accidents as well as accidents in which the driver and passengers, dead or alive, need to be identified. In identifying the passengers, standard criminal investigation methods as well as police forensic and forensic medicine methods are followed. Such methods include confirming the identities with identity documents, other documents and vehicle ownership, fingerprints, biological traces, fibre traces, contact traces, traces of physical injuries on the driver and passengers, etc. According to the results obtained in fingerprint detection on human skin surfaces, this method can also be applied in confirming physical contact between the driver and the passengers in the accident, e.g. in the event of moving the victims and changing the scene of the accident.   Key words: traffic accidents, accident analysis, driver's identity, passengers' position, finger marks, human skin

  3. Microarray analysis identifies a common set of cellular genes modulated by different HCV replicon clones

    Directory of Open Access Journals (Sweden)

    Gerosolimo Germano

    2008-06-01

    Full Text Available Abstract Background Hepatitis C virus (HCV RNA synthesis and protein expression affect cell homeostasis by modulation of gene expression. The impact of HCV replication on global cell transcription has not been fully evaluated. Thus, we analysed the expression profiles of different clones of human hepatoma-derived Huh-7 cells carrying a self-replicating HCV RNA which express all viral proteins (HCV replicon system. Results First, we compared the expression profile of HCV replicon clone 21-5 with both the Huh-7 parental cells and the 21-5 cured (21-5c cells. In these latter, the HCV RNA has been eliminated by IFN-α treatment. To confirm data, we also analyzed microarray results from both the 21-5 and two other HCV replicon clones, 22-6 and 21-7, compared to the Huh-7 cells. The study was carried out by using the Applied Biosystems (AB Human Genome Survey Microarray v1.0 which provides 31,700 probes that correspond to 27,868 human genes. Microarray analysis revealed a specific transcriptional program induced by HCV in replicon cells respect to both IFN-α-cured and Huh-7 cells. From the original datasets of differentially expressed genes, we selected by Venn diagrams a final list of 38 genes modulated by HCV in all clones. Most of the 38 genes have never been described before and showed high fold-change associated with significant p-value, strongly supporting data reliability. Classification of the 38 genes by Panther System identified functional categories that were significantly enriched in this gene set, such as histones and ribosomal proteins as well as extracellular matrix and intracellular protein traffic. The dataset also included new genes involved in lipid metabolism, extracellular matrix and cytoskeletal network, which may be critical for HCV replication and pathogenesis. Conclusion Our data provide a comprehensive analysis of alterations in gene expression induced by HCV replication and reveal modulation of new genes potentially useful

  4. Transcriptome Analysis of Syringa oblata Lindl. Inflorescence Identifies Genes Associated with Pigment Biosynthesis and Scent Metabolism.

    Directory of Open Access Journals (Sweden)

    Jian Zheng

    Full Text Available Syringa oblata Lindl. is a woody ornamental plant with high economic value and characteristics that include early flowering, multiple flower colors, and strong fragrance. Despite a long history of cultivation, the genetics and molecular biology of S. oblata are poorly understood. Transcriptome and expression profiling data are needed to identify genes and to better understand the biological mechanisms of floral pigments and scents in this species. Nine cDNA libraries were obtained from three replicates of three developmental stages: inflorescence with enlarged flower buds not protruded, inflorescence with corolla lobes not displayed, and inflorescence with flowers fully opened and emitting strong fragrance. Using the Illumina RNA-Seq technique, 319,425,972 clean reads were obtained and were assembled into 104,691 final unigenes (average length of 853 bp, 41.75% of which were annotated in the NCBI non-redundant protein database. Among the annotated unigenes, 36,967 were assigned to gene ontology categories and 19,956 were assigned to eukaryoticorthologous groups. Using the Kyoto Encyclopedia of Genes and Genomes pathway database, 12,388 unigenes were sorted into 286 pathways. Based on these transcriptomic data, we obtained a large number of candidate genes that were differentially expressed at different flower stages and that were related to floral pigment biosynthesis and fragrance metabolism. This comprehensive transcriptomic analysis provides fundamental information on the genes and pathways involved in flower secondary metabolism and development in S. oblata, providing a useful database for further research on S. oblata and other plants of genus Syringa.

  5. Risky driving behaviors for road traffic accident among drivers in Mekele city, Northern Ethiopia

    Directory of Open Access Journals (Sweden)

    Hassen Abrahim

    2011-12-01

    Full Text Available Abstract Background Due to its perception as a disease of development, road traffic accident and related injuries tend to be under recognized as a major health problem in developing countries. However, majority of the world's fatalities on the roads occur in low income and middle income countries. Since the main cause of road traffic accident is attributed to human risky behaviors, it is important to identify significant factors for risky behaviors of drivers. Methods A quantitative cross-sectional study with a sample size of 350 drivers was conducted in April 2011. The study was conducted among Taxi, Bajaj (three tire vehicles and private owned car drivers. After proportion to size allocation for Taxi (75, Baja (103 and private owned car (172 drivers, we used systematic random sampling method to identify illegible study subjects. Data was collected with face to face interview using a pretested questioner. Univariate, bivariate and multivariate analysis was done using SPSS version 16. Results The mean age of the respondents was 28.7 (SD 9.9. Majority were 339 (96.9% males. Significant number of the study subjects 233 (66.6% had risky driving behaviors. More than a quarter 100 (28.6% had less knowledge about basic traffic signs. Majority of drivers 181 (51.7% had negative attitude towards risky driving behaviors. Significant percent of them 148 (42.3% had a habit of using mobile phone while driving vehicle and 28 (9.7% had experience of driving after drinking alcohol. All the Bajaj, 97(62.6% house car and 58(37.4% taxi unfasten their seat belt while driving. Majority 303 (86.6% followed the recommended speed limit of driving. About 66 (18.9% of them had experience of punishment or warning by traffic polices in the previous 1 year and 77 (22% ever had car accident while driving. Conclusions Drivers of secondary education and with high average monthly income were more likely to have risky driving behavior. Having supportive attitude towards risky

  6. Quantifying the drivers of ocean-atmosphere CO2 fluxes

    Science.gov (United States)

    Lauderdale, Jonathan M.; Dutkiewicz, Stephanie; Williams, Richard G.; Follows, Michael J.

    2016-07-01

    A mechanistic framework for quantitatively mapping the regional drivers of air-sea CO2 fluxes at a global scale is developed. The framework evaluates the interplay between (1) surface heat and freshwater fluxes that influence the potential saturated carbon concentration, which depends on changes in sea surface temperature, salinity and alkalinity, (2) a residual, disequilibrium flux influenced by upwelling and entrainment of remineralized carbon- and nutrient-rich waters from the ocean interior, as well as rapid subduction of surface waters, (3) carbon uptake and export by biological activity as both soft tissue and carbonate, and (4) the effect on surface carbon concentrations due to freshwater precipitation or evaporation. In a steady state simulation of a coarse-resolution ocean circulation and biogeochemistry model, the sum of the individually determined components is close to the known total flux of the simulation. The leading order balance, identified in different dynamical regimes, is between the CO2 fluxes driven by surface heat fluxes and a combination of biologically driven carbon uptake and disequilibrium-driven carbon outgassing. The framework is still able to reconstruct simulated fluxes when evaluated using monthly averaged data and takes a form that can be applied consistently in models of different complexity and observations of the ocean. In this way, the framework may reveal differences in the balance of drivers acting across an ensemble of climate model simulations or be applied to an analysis and interpretation of the observed, real-world air-sea flux of CO2.

  7. A landscape ecology approach identifies important drivers of urban biodiversity.

    Science.gov (United States)

    Turrini, Tabea; Knop, Eva

    2015-04-01

    Cities are growing rapidly worldwide, yet a mechanistic understanding of the impact of urbanization on biodiversity is lacking. We assessed the impact of urbanization on arthropod diversity (species richness and evenness) and abundance in a study of six cities and nearby intensively managed agricultural areas. Within the urban ecosystem, we disentangled the relative importance of two key landscape factors affecting biodiversity, namely the amount of vegetated area and patch isolation. To do so, we a priori selected sites that independently varied in the amount of vegetated area in the surrounding landscape at the 500-m scale and patch isolation at the 100-m scale, and we hold local patch characteristics constant. As indicator groups, we used bugs, beetles, leafhoppers, and spiders. Compared to intensively managed agricultural ecosystems, urban ecosystems supported a higher abundance of most indicator groups, a higher number of bug species, and a lower evenness of bug and beetle species. Within cities, a high amount of vegetated area increased species richness and abundance of most arthropod groups, whereas evenness showed no clear pattern. Patch isolation played only a limited role in urban ecosystems, which contrasts findings from agro-ecological studies. Our results show that urban areas can harbor a similar arthropod diversity and abundance compared to intensively managed agricultural ecosystems. Further, negative consequences of urbanization on arthropod diversity can be mitigated by providing sufficient vegetated space in the urban area, while patch connectivity is less important in an urban context. This highlights the need for applying a landscape ecological approach to understand the mechanisms shaping urban biodiversity and underlines the potential of appropriate urban planning for mitigating biodiversity loss.

  8. Evaluation of the Benefits of Reflectorized Sign Posts to Drivers

    Directory of Open Access Journals (Sweden)

    Erdinç Öner

    2013-03-01

    Full Text Available In United States Federal Highway Administration (FHWA provides departments of transportation (DOTs the option of using retroreflective material on sign posts when the DOTs determine that there is a need to draw attention to the sign, especially at night. The State of Ohio Department of Transportation (ODOT required all Stop, Yield, Do Not Enter, and Wrong Way sign posts to be reflectorized with RED reflective sheeting material and all Chevron, Stop Ahead, and One/Two Large Directional Arrow sign posts to be reflectorized with YELLOW (sign background color reflective sheeting material as part of ODOT Comprehensive Highway Safety Plan and FHWA' recommendations.In this study, a photometric analysis and a human factors analysis were conducted to estimate the benefits of reflectorized sign posts to driver visual perception, driver guidance and driver comprehension. The study showed that the reflectorized sign posts improve detection, recognition, and comprehension of traffic signs for drivers, especially in nighttime driving conditions.

  9. The Use of Descriptive Analysis to Identify and Manipulate Schedules of Reinforcement in the Treatment of Food Refusal

    Science.gov (United States)

    Casey, Sean D.; Cooper-Brown, Linda J.; Wacker, David P.; Rankin, Barbara E.

    2006-01-01

    The feeding behaviors of a child diagnosed with failure to thrive were assessed using descriptive analysis methodology to identify the schedules of reinforcement provided by the child's parents. This analysis revealed that the child's appropriate feeding behaviors (i.e., bite acceptance, self-feeding) were on a lean schedule of positive…

  10. A meta-analysis of genome-wide association studies identifies novel variants associated with osteoarthritis of the hip

    NARCIS (Netherlands)

    E. Evangelou (Evangelos); J.M. Kerkhof (Hanneke); U. Styrkarsdottir (Unnur); E.E. Ntzani (Evangelia); S.D. Bos (Steffan); T. Esko (Tõnu); D.S. Evans (Daniel); S. Metrustry (Sarah); K. Panoutsopoulou (Kalliope); Y.F.M. Ramos (Yolande); G. Thorleifsson (Gudmar); K.K. Tsilidis (Konstantinos); N.K. Arden (Nigel); N. Aslam (Nadim); N. Bellamy (Nicholas); F. Birrell (Fraser); F.J. Blanco; A.J. Carr (Andrew Jonathan); K. Chapman (Kay); A.G. Day-Williams (Aaron); P. Deloukas (Panagiotis); M. Doherty (Michael); G. Engström; H.T. Helgadottir (Hafdis); A. Hofman (Albert); T. Ingvarsson (Torvaldur); H. Jonsson (Helgi); A. Keis (Aime); J.C. Keurentjes (J. Christiaan); M. Kloppenburg (Margreet); P.A. Lind (Penelope); A. McCaskie (Andrew); N.G. Martin; A.L. Milani (Alfredo); G.W. Montgomery; R.G.H.H. Nelissen (Rob); M.C. Nevitt (Michael); P. Nilsson (Peter); W.E.R. Ollier (William); N. Parimi (Neeta); A. Rai (Ashok); S.H. Ralston; M.R. Reed (Mike); J.A. Riancho (José); F. Rivadeneira Ramirez (Fernando); C. Rodriguez-Fontenla (Cristina); L. Southam (Lorraine); U. Thorsteinsdottir (Unnur); A. Tsezou (Aspasia); G.A. Wallis (Gillian); J.M. Wilkinson (Mark); A. Gonzalez (Antonio); N.E. Lane; L.S. Lohmander (Stefan); J. Loughlin (John); A. Metspalu (Andres); A.G. Uitterlinden (André); I. Jonsdottir (Ingileif); J-A. Zwart (John-Anker); P.E. Slagboom (Eline); E. Zeggini (Eleftheria); I. Meulenbelt (Ingrid); J.P.A. Ioannidis (John); T.D. Spector (Timothy); J.B.J. van Meurs (Joyce); A.M. Valdes (Ana Maria)

    2013-01-01

    textabstractObjectives: Osteoarthritis (OA) is the most common form of arthritis with a clear genetic component. To identify novel loci associated with hip OA we performed a meta-analysis of genome-wide association studies (GWAS) on European subjects. Methods: We performed a two-stage meta-analysis

  11. Meta-analysis of genome-wide association studies identifies eight new loci for type 2 diabetes in east Asians

    NARCIS (Netherlands)

    Cho, Yoon Shin; Chen, Chien-Hsiun; Hu, Cheng; Long, Jirong; Ong, Rick Twee Hee; Sim, Xueling; Takeuchi, Fumihiko; Wu, Ying; Go, Min Jin; Yamauchi, Toshimasa; Chang, Yi-Cheng; Kwak, Soo Heon; Ma, Ronald C. W.; Yamamoto, Ken; Adair, Linda S.; Aung, Tin; Cai, Qiuyin; Chang, Li-Ching; Chen, Yuan-Tsong; Gao, Yutang; Hu, Frank B.; Kim, Hyung-Lae; Kim, Sangsoo; Kim, Young Jin; Lee, Jeannette Jen-Mai; Lee, Nanette R.; Li, Yun; Liu, Jian Jun; Lu, Wei; Nakamura, Jiro; Nakashima, Eitaro; Ng, Daniel Peng-Keat; Tay, Wan Ting; Tsai, Fuu-Jen; Wong, Tien Yin; Yokota, Mitsuhiro; Zheng, Wei; Zhang, Rong; Wang, Congrong; So, Wing Yee; Ohnaka, Keizo; Ikegami, Hiroshi; Hara, Kazuo; Cho, Young Min; Cho, Nam H.; Chang, Tien-Jyun; Bao, Yuqian; Hedman, Asa K.; Morris, Andrew P.; McCarthy, Mark I.; Takayanagi, Ryoichi; Park, Kyong Soo; Jia, Weiping; Chuang, Lee-Ming; Chan, Juliana C. N.; Maeda, Shiro; Kadowaki, Takashi; Lee, Jong-Young; Wu, Jer-Yuarn; Teo, Yik Ying; Tai, E. Shyong; Shu, Xiao Ou; Mohlke, Karen L.; Kato, Norihiro; Han, Bok-Ghee; Seielstad, Mark

    2012-01-01

    We conducted a three-stage genetic study to identify susceptibility loci for type 2 diabetes (T2D) in east Asian populations. We followed our stage 1 meta-analysis of eight T2D genome-wide association studies (6,952 cases with T2D and 11,865 controls) with a stage 2 in silico replication analysis (5

  12. Meta-analysis of 375,000 individuals identifies 38 susceptibility loci for migraine

    Science.gov (United States)

    Gormley, Padhraig; Anttila, Verneri; Winsvold, Bendik S; Palta, Priit; Esko, Tonu; Pers, Tune H.; Farh, Kai-How; Cuenca-Leon, Ester; Muona, Mikko; Furlotte, Nicholas A; Kurth, Tobias; Ingason, Andres; McMahon, George; Ligthart, Lannie; Terwindt, Gisela M; Kallela, Mikko; Freilinger, Tobias M; Ran, Caroline; Gordon, Scott G; Stam, Anine H; Steinberg, Stacy; Borck, Guntram; Koiranen, Markku; Quaye, Lydia; Adams, Hieab HH; Lehtimäki, Terho; Sarin, Antti-Pekka; Wedenoja, Juho; Hinds, David A; Buring, Julie E; Schürks, Markus; Ridker, Paul M; Hrafnsdottir, Maria Gudlaug; Stefansson, Hreinn; Ring, Susan M; Hottenga, Jouke-Jan; Penninx, Brenda WJH; Färkkilä, Markus; Artto, Ville; Kaunisto, Mari; Vepsäläinen, Salli; Malik, Rainer; Heath, Andrew C; Madden, Pamela A F; Martin, Nicholas G; Montgomery, Grant W; Kurki, Mitja I; Kals, Mart; Mägi, Reedik; Pärn, Kalle; Hämäläinen, Eija; Huang, Hailiang; Byrnes, Andrea E; Franke, Lude; Huang, Jie; Stergiakouli, Evie; Lee, Phil H; Sandor, Cynthia; Webber, Caleb; Cader, Zameel; Muller-Myhsok, Bertram; Schreiber, Stefan; Meitinger, Thomas; Eriksson, Johan G; Salomaa, Veikko; Heikkilä, Kauko; Loehrer, Elizabeth; Uitterlinden, Andre G; Hofman, Albert; van Duijn, Cornelia M; Cherkas, Lynn; Pedersen, Linda M.; Stubhaug, Audun; Nielsen, Christopher S; Männikkä, Minna; Mihailov, Evelin; Milani, Lili; Göbel, Hartmut; Esserlind, Ann-Louise; Christensen, Anne Francke; Hansen, Thomas Folkmann; Werge, Thomas; Kaprio, Jaakko; Aromaa, Arpo J; Raitakari, Olli; Ikram, M Arfan; Spector, Tim; Järvelin, Marjo-Riitta; Metspalu, Andres; Kubisch, Christian; Strachan, David P; Ferrari, Michel D; Belin, Andrea C; Dichgans, Martin; Wessman, Maija; van den Maagdenberg, Arn MJM; Zwart, John-Anker; Boomsma, Dorret I; Smith, George Davey; Stefansson, Kari; Eriksson, Nicholas; Daly, Mark J; Neale, Benjamin M; Olesen, Jes; Chasman, Daniel I; Nyholt, Dale R; Palotie, Aarno

    2017-01-01

    Migraine is a debilitating neurological disorder affecting around 1 in 7 people worldwide, but its molecular mechanisms remain poorly understood. Some debate exists over whether migraine is a disease of vascular dysfunction or a result of neuronal dysfunction with secondary vascular changes. Genome-wide association (GWA) studies have thus far identified 13 independent loci associated with migraine. To identify new susceptibility loci, we performed the largest genetic study of migraine to date, comprising 59,674 cases and 316,078 controls from 22 GWA studies. We identified 44 independent single nucleotide polymorphisms (SNPs) significantly associated with migraine risk (P < 5 × 10−8) that map to 38 distinct genomic loci, including 28 loci not previously reported and the first locus identified on chromosome X. In subsequent computational analyses, the identified loci showed enrichment for genes expressed in vascular and smooth muscle tissues, consistent with a predominant theory of migraine that highlights vascular etiologies. PMID:27322543

  13. Rosalind Driver studentships

    Science.gov (United States)

    1999-11-01

    The School of Education at King's College London can now offer funded studentships to those wishing to undertake research in science education. These studentships, which are funded through the generous benefaction of the late Rosalind Driver, can be for a full-time student (over a maximum of three years) or several part-time students (a maximum of six years). Applications from anyone working in science education are welcome but preference will be given to those originating from practising science teachers. Applicants will be expected to register for the award of a MPhil/PhD or EdD and are normally expected to have a first degree. Preliminary ideas about a topic for investigation would also be helpful. Further details and application forms are obtainable from Chiz Dube, School of Education, King's College London, Franklin - Wilkins Building, Waterloo Road, London SE1 8WA (tel: 020-7848-3089, e-mail: chiz.dube@kcl.ac.uk). The deadline for the first round of applications was the middle of October, but preliminary informal enquiries may be made to Dr Jonathan Osborne at the School of Education (tel: 020-7848-3094, e-mail: jonathan.osborne@kcl.ac.uk).

  14. Transcript