JRC GMO-Amplicons: a collection of nucleic acid sequences related to genetically modified organisms

PubMed Central

Petrillo, Mauro; Angers-Loustau, Alexandre; Henriksson, Peter; Bonfini, Laura; Patak, Alex; Kreysa, Joachim

2015-01-01

The DNA target sequence is the key element in designing detection methods for genetically modified organisms (GMOs). Unfortunately this information is frequently lacking, especially for unauthorized GMOs. In addition, patent sequences are generally poorly annotated, buried in complex and extensive documentation and hard to link to the corresponding GM event. Here, we present the JRC GMO-Amplicons, a database of amplicons collected by screening public nucleotide sequence databanks by in silico determination of PCR amplification with reference methods for GMO analysis. The European Union Reference Laboratory for Genetically Modified Food and Feed (EU-RL GMFF) provides these methods in the GMOMETHODS database to support enforcement of EU legislation and GM food/feed control. The JRC GMO-Amplicons database is composed of more than 240 000 amplicons, which can be easily accessed and screened through a web interface. To our knowledge, this is the first attempt at pooling and collecting publicly available sequences related to GMOs in food and feed. The JRC GMO-Amplicons supports control laboratories in the design and assessment of GMO methods, providing inter-alia in silico prediction of primers specificity and GM targets coverage. The new tool can assist the laboratories in the analysis of complex issues, such as the detection and identification of unauthorized GMOs. Notably, the JRC GMO-Amplicons database allows the retrieval and characterization of GMO-related sequences included in patents documentation. Finally, it can help annotating poorly described GM sequences and identifying new relevant GMO-related sequences in public databases. The JRC GMO-Amplicons is freely accessible through a web-based portal that is hosted on the EU-RL GMFF website. Database URL: http://gmo-crl.jrc.ec.europa.eu/jrcgmoamplicons/ PMID:26424080

JRC GMO-Amplicons: a collection of nucleic acid sequences related to genetically modified organisms.

PubMed

Petrillo, Mauro; Angers-Loustau, Alexandre; Henriksson, Peter; Bonfini, Laura; Patak, Alex; Kreysa, Joachim

2015-01-01

The DNA target sequence is the key element in designing detection methods for genetically modified organisms (GMOs). Unfortunately this information is frequently lacking, especially for unauthorized GMOs. In addition, patent sequences are generally poorly annotated, buried in complex and extensive documentation and hard to link to the corresponding GM event. Here, we present the JRC GMO-Amplicons, a database of amplicons collected by screening public nucleotide sequence databanks by in silico determination of PCR amplification with reference methods for GMO analysis. The European Union Reference Laboratory for Genetically Modified Food and Feed (EU-RL GMFF) provides these methods in the GMOMETHODS database to support enforcement of EU legislation and GM food/feed control. The JRC GMO-Amplicons database is composed of more than 240 000 amplicons, which can be easily accessed and screened through a web interface. To our knowledge, this is the first attempt at pooling and collecting publicly available sequences related to GMOs in food and feed. The JRC GMO-Amplicons supports control laboratories in the design and assessment of GMO methods, providing inter-alia in silico prediction of primers specificity and GM targets coverage. The new tool can assist the laboratories in the analysis of complex issues, such as the detection and identification of unauthorized GMOs. Notably, the JRC GMO-Amplicons database allows the retrieval and characterization of GMO-related sequences included in patents documentation. Finally, it can help annotating poorly described GM sequences and identifying new relevant GMO-related sequences in public databases. The JRC GMO-Amplicons is freely accessible through a web-based portal that is hosted on the EU-RL GMFF website. Database URL: http://gmo-crl.jrc.ec.europa.eu/jrcgmoamplicons/. © The Author(s) 2015. Published by Oxford University Press.

Identifying Key Drivers of Return Reversal with Dynamical Bayesian Factor Graph

PubMed Central

Zhao, Shuai; Tong, Yunhai; Wang, Zitian; Tan, Shaohua

2016-01-01

In the stock market, return reversal occurs when investors sell overbought stocks and buy oversold stocks, reversing the stocks’ price trends. In this paper, we develop a new method to identify key drivers of return reversal by incorporating a comprehensive set of factors derived from different economic theories into one unified dynamical Bayesian factor graph. We then use the model to depict factor relationships and their dynamics, from which we make some interesting discoveries about the mechanism behind return reversals. Through extensive experiments on the US stock market, we conclude that among the various factors, the liquidity factors consistently emerge as key drivers of return reversal, which is in support of the theory of liquidity effect. Specifically, we find that stocks with high turnover rates or high Amihud illiquidity measures have a greater probability of experiencing return reversals. Apart from the consistent drivers, we find other drivers of return reversal that generally change from year to year, and they serve as important characteristics for evaluating the trends of stock returns. Besides, we also identify some seldom discussed yet enlightening inter-factor relationships, one of which shows that stocks in Finance and Insurance industry are more likely to have high Amihud illiquidity measures in comparison with those in other industries. These conclusions are robust for return reversals under different thresholds. PMID:27893780

Identifying Key Drivers of Return Reversal with Dynamical Bayesian Factor Graph.

PubMed

Zhao, Shuai; Tong, Yunhai; Wang, Zitian; Tan, Shaohua

2016-01-01

In the stock market, return reversal occurs when investors sell overbought stocks and buy oversold stocks, reversing the stocks' price trends. In this paper, we develop a new method to identify key drivers of return reversal by incorporating a comprehensive set of factors derived from different economic theories into one unified dynamical Bayesian factor graph. We then use the model to depict factor relationships and their dynamics, from which we make some interesting discoveries about the mechanism behind return reversals. Through extensive experiments on the US stock market, we conclude that among the various factors, the liquidity factors consistently emerge as key drivers of return reversal, which is in support of the theory of liquidity effect. Specifically, we find that stocks with high turnover rates or high Amihud illiquidity measures have a greater probability of experiencing return reversals. Apart from the consistent drivers, we find other drivers of return reversal that generally change from year to year, and they serve as important characteristics for evaluating the trends of stock returns. Besides, we also identify some seldom discussed yet enlightening inter-factor relationships, one of which shows that stocks in Finance and Insurance industry are more likely to have high Amihud illiquidity measures in comparison with those in other industries. These conclusions are robust for return reversals under different thresholds.

Reproducibility and quantitation of amplicon sequencing-based detection

PubMed Central

Zhou, Jizhong; Wu, Liyou; Deng, Ye; Zhi, Xiaoyang; Jiang, Yi-Huei; Tu, Qichao; Xie, Jianping; Van Nostrand, Joy D; He, Zhili; Yang, Yunfeng

2011-01-01

To determine the reproducibility and quantitation of the amplicon sequencing-based detection approach for analyzing microbial community structure, a total of 24 microbial communities from a long-term global change experimental site were examined. Genomic DNA obtained from each community was used to amplify 16S rRNA genes with two or three barcode tags as technical replicates in the presence of a small quantity (0.1% wt/wt) of genomic DNA from Shewanella oneidensis MR-1 as the control. The technical reproducibility of the amplicon sequencing-based detection approach is quite low, with an average operational taxonomic unit (OTU) overlap of 17.2%±2.3% between two technical replicates, and 8.2%±2.3% among three technical replicates, which is most likely due to problems associated with random sampling processes. Such variations in technical replicates could have substantial effects on estimating β-diversity but less on α-diversity. A high variation was also observed in the control across different samples (for example, 66.7-fold for the forward primer), suggesting that the amplicon sequencing-based detection approach could not be quantitative. In addition, various strategies were examined to improve the comparability of amplicon sequencing data, such as increasing biological replicates, and removing singleton sequences and less-representative OTUs across biological replicates. Finally, as expected, various statistical analyses with preprocessed experimental data revealed clear differences in the composition and structure of microbial communities between warming and non-warming, or between clipping and non-clipping. Taken together, these results suggest that amplicon sequencing-based detection is useful in analyzing microbial community structure even though it is not reproducible and quantitative. However, great caution should be taken in experimental design and data interpretation when the amplicon sequencing-based detection approach is used for quantitative

Swarm: robust and fast clustering method for amplicon-based studies.

PubMed

Mahé, Frédéric; Rognes, Torbjørn; Quince, Christopher; de Vargas, Colomban; Dunthorn, Micah

2014-01-01

Popular de novo amplicon clustering methods suffer from two fundamental flaws: arbitrary global clustering thresholds, and input-order dependency induced by centroid selection. Swarm was developed to address these issues by first clustering nearly identical amplicons iteratively using a local threshold, and then by using clusters' internal structure and amplicon abundances to refine its results. This fast, scalable, and input-order independent approach reduces the influence of clustering parameters and produces robust operational taxonomic units.

Efficient error correction for next-generation sequencing of viral amplicons.

PubMed

Skums, Pavel; Dimitrova, Zoya; Campo, David S; Vaughan, Gilberto; Rossi, Livia; Forbi, Joseph C; Yokosawa, Jonny; Zelikovsky, Alex; Khudyakov, Yury

2012-06-25

Next-generation sequencing allows the analysis of an unprecedented number of viral sequence variants from infected patients, presenting a novel opportunity for understanding virus evolution, drug resistance and immune escape. However, sequencing in bulk is error prone. Thus, the generated data require error identification and correction. Most error-correction methods to date are not optimized for amplicon analysis and assume that the error rate is randomly distributed. Recent quality assessment of amplicon sequences obtained using 454-sequencing showed that the error rate is strongly linked to the presence and size of homopolymers, position in the sequence and length of the amplicon. All these parameters are strongly sequence specific and should be incorporated into the calibration of error-correction algorithms designed for amplicon sequencing. In this paper, we present two new efficient error correction algorithms optimized for viral amplicons: (i) k-mer-based error correction (KEC) and (ii) empirical frequency threshold (ET). Both were compared to a previously published clustering algorithm (SHORAH), in order to evaluate their relative performance on 24 experimental datasets obtained by 454-sequencing of amplicons with known sequences. All three algorithms show similar accuracy in finding true haplotypes. However, KEC and ET were significantly more efficient than SHORAH in removing false haplotypes and estimating the frequency of true ones. Both algorithms, KEC and ET, are highly suitable for rapid recovery of error-free haplotypes obtained by 454-sequencing of amplicons from heterogeneous viruses.The implementations of the algorithms and data sets used for their testing are available at: http://alan.cs.gsu.edu/NGS/?q=content/pyrosequencing-error-correction-algorithm.

Swarm: robust and fast clustering method for amplicon-based studies

PubMed Central

Rognes, Torbjørn; Quince, Christopher; de Vargas, Colomban; Dunthorn, Micah

2014-01-01

Popular de novo amplicon clustering methods suffer from two fundamental flaws: arbitrary global clustering thresholds, and input-order dependency induced by centroid selection. Swarm was developed to address these issues by first clustering nearly identical amplicons iteratively using a local threshold, and then by using clusters’ internal structure and amplicon abundances to refine its results. This fast, scalable, and input-order independent approach reduces the influence of clustering parameters and produces robust operational taxonomic units. PMID:25276506

Obstructive sleep apnea among commercial motor vehicle drivers: using evidence-based practice to identify risk factors.

PubMed

Olszewski, Kimberly; Wolf, Debra

2013-11-01

Commercial motor vehicle driving is a hazardous occupation, having the third highest fatality rate among common U.S. jobs. Among the estimated 14 million U.S. commercial motor vehicle drivers, the prevalence of obstructive sleep apnea is reported to be 17% to 28%. Despite the identified increased prevalence of obstructive sleep apnea among commercial motor vehicle drivers, federal law does not require that they be screened for obstructive sleep apnea. This article presents an evidence-based practice change project; the authors developed, implemented, and evaluated a screening program to identify commercial motor vehicle drivers' risk for obstructive sleep apnea during commercial driver medical examinations. The results of this practice change indicated screening for obstructive sleep apnea during the commercial driver medical examination led to improved identification of obstructive sleep apnea risk among commercial motor vehicle drivers and should be a clinical standard in occupational health clinics. Copyright 2013, SLACK Incorporated.

Can vehicle longitudinal jerk be used to identify aggressive drivers? An examination using naturalistic driving data.

PubMed

Feng, Fred; Bao, Shan; Sayer, James R; Flannagan, Carol; Manser, Michael; Wunderlich, Robert

2017-07-01

This paper investigated the characteristics of vehicle longitudinal jerk (change rate of acceleration with respect to time) by using vehicle sensor data from an existing naturalistic driving study. The main objective was to examine whether vehicle jerk contains useful information that could be potentially used to identify aggressive drivers. Initial investigation showed that there are unique characteristics of vehicle jerk in drivers' gas and brake pedal operations. Thus two jerk-based metrics were examined: (1) driver's frequency of using large positive jerk when pressing the gas pedal, and (2) driver's frequency of using large negative jerk when pressing the brake pedal. To validate the performance of the two metrics, drivers were firstly divided into an aggressive group and a normal group using three classification methods (1) traveling at excessive speed (speeding), (2) following too closely to a front vehicle (tailgating), and (3) their association with crashes or near-crashes in the dataset. The results show that those aggressive drivers defined using any of the three methods above were associated with significantly higher values of the two jerk-based metrics. Between the two metrics the frequency of using large negative jerk seems to have better performance in identifying aggressive drivers. A sensitivity analysis shows the findings were largely consistent with varying parameters in the analysis. The potential applications of this work include developing quantitative surrogate safety measures to identify aggressive drivers and aggressive driving, which could be potentially used to, for example, provide real-time or post-ride performance feedback to the drivers, or warn the surrounding drivers or vehicles using the connected vehicle technologies. Copyright © 2017 Elsevier Ltd. All rights reserved.

Efficient error correction for next-generation sequencing of viral amplicons

PubMed Central

2012-01-01

Background Next-generation sequencing allows the analysis of an unprecedented number of viral sequence variants from infected patients, presenting a novel opportunity for understanding virus evolution, drug resistance and immune escape. However, sequencing in bulk is error prone. Thus, the generated data require error identification and correction. Most error-correction methods to date are not optimized for amplicon analysis and assume that the error rate is randomly distributed. Recent quality assessment of amplicon sequences obtained using 454-sequencing showed that the error rate is strongly linked to the presence and size of homopolymers, position in the sequence and length of the amplicon. All these parameters are strongly sequence specific and should be incorporated into the calibration of error-correction algorithms designed for amplicon sequencing. Results In this paper, we present two new efficient error correction algorithms optimized for viral amplicons: (i) k-mer-based error correction (KEC) and (ii) empirical frequency threshold (ET). Both were compared to a previously published clustering algorithm (SHORAH), in order to evaluate their relative performance on 24 experimental datasets obtained by 454-sequencing of amplicons with known sequences. All three algorithms show similar accuracy in finding true haplotypes. However, KEC and ET were significantly more efficient than SHORAH in removing false haplotypes and estimating the frequency of true ones. Conclusions Both algorithms, KEC and ET, are highly suitable for rapid recovery of error-free haplotypes obtained by 454-sequencing of amplicons from heterogeneous viruses. The implementations of the algorithms and data sets used for their testing are available at: http://alan.cs.gsu.edu/NGS/?q=content/pyrosequencing-error-correction-algorithm PMID:22759430

PCR Amplicon Prediction from Multiplex Degenerate Primer and Probe Sets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gardner, S. N.

2013-08-08

Assessing primer specificity and predicting both desired and off-target amplification products is an essential step for robust PCR assay design. Code is described to predict potential polymerase chain reaction (PCR) amplicons in a large sequence database such as NCBI nt from either singleplex or a large multiplexed set of primers, allowing degenerate primer and probe bases, with target mismatch annotates amplicons with gene information automatically downloaded from NCBI, and optionally it can predict whether there are also TaqMan/Luminex probe matches within predicted amplicons.

A framework for identifying carbon hotspots and forest management drivers

Treesearch

Nilesh Timilsina; Francisco J. Escobedo; Wendell P. Cropper; Amr Abd-Elrahman; Thomas Brandeis; Sonia Delphin; Samuel Lambert

2013-01-01

Spatial analyses of ecosystem system services that are directly relevant to both forest management decision making and conservation in the subtropics are rare. Also, frameworks that identify and map carbon stocks and corresponding forest management drivers using available regional, national, and international-level forest inventory datasets could provide insights into...

Unlabeled oligonucleotides as internal temperature controls for genotyping by amplicon melting.

PubMed

Seipp, Michael T; Durtschi, Jacob D; Liew, Michael A; Williams, Jamie; Damjanovich, Kristy; Pont-Kingdon, Genevieve; Lyon, Elaine; Voelkerding, Karl V; Wittwer, Carl T

2007-07-01

Amplicon melting is a closed-tube method for genotyping that does not require probes, real-time analysis, or allele-specific polymerase chain reaction. However, correct differentiation of homozygous mutant and wild-type samples by melting temperature (Tm) requires high-resolution melting and closely controlled reaction conditions. When three different DNA extraction methods were used to isolate DNA from whole blood, amplicon Tm differences of 0.03 to 0.39 degrees C attributable to the extractions were observed. To correct for solution chemistry differences between samples, complementary unlabeled oligonucleotides were included as internal temperature controls to shift and scale the temperature axis of derivative melting plots. This adjustment was applied to a duplex amplicon melting assay for the methylenetetrahydrofolate reductase variants 1298A>C and 677C>T. High- and low-temperature controls bracketing the amplicon melting region decreased the Tm SD within homozygous genotypes by 47 to 82%. The amplicon melting assay was 100% concordant to an adjacent hybridization probe (HybProbe) melting assay when temperature controls were included, whereas a 3% error rate was observed without temperature correction. In conclusion, internal temperature controls increase the accuracy of genotyping by high-resolution amplicon melting and should also improve results on lower resolution instruments.

Unlabeled Oligonucleotides as Internal Temperature Controls for Genotyping by Amplicon Melting

PubMed Central

Seipp, Michael T.; Durtschi, Jacob D.; Liew, Michael A.; Williams, Jamie; Damjanovich, Kristy; Pont-Kingdon, Genevieve; Lyon, Elaine; Voelkerding, Karl V.; Wittwer, Carl T.

2007-01-01

Amplicon melting is a closed-tube method for genotyping that does not require probes, real-time analysis, or allele-specific polymerase chain reaction. However, correct differentiation of homozygous mutant and wild-type samples by melting temperature (Tm) requires high-resolution melting and closely controlled reaction conditions. When three different DNA extraction methods were used to isolate DNA from whole blood, amplicon Tm differences of 0.03 to 0.39°C attributable to the extractions were observed. To correct for solution chemistry differences between samples, complementary unlabeled oligonucleotides were included as internal temperature controls to shift and scale the temperature axis of derivative melting plots. This adjustment was applied to a duplex amplicon melting assay for the methylenetetrahydrofolate reductase variants 1298A>C and 677C>T. High- and low-temperature controls bracketing the amplicon melting region decreased the Tm SD within homozygous genotypes by 47 to 82%. The amplicon melting assay was 100% concordant to an adjacent hybridization probe (HybProbe) melting assay when temperature controls were included, whereas a 3% error rate was observed without temperature correction. In conclusion, internal temperature controls increase the accuracy of genotyping by high-resolution amplicon melting and should also improve results on lower resolution instruments. PMID:17591926

Contributions to the Nutrient Toolbox: Identifying Drivers, Nutrient Sources, and Attribution of Exceedances

EPA Science Inventory

Nutrients are a leading cause of impairments in the United States, and as a result tools are needed to identify drivers of nutrients and response variables (such as chlorophyll a), nutrient sources, and identify causes of exceedances of water quality thresholds. This presentatio...

LNDriver: identifying driver genes by integrating mutation and expression data based on gene-gene interaction network.

PubMed

Wei, Pi-Jing; Zhang, Di; Xia, Junfeng; Zheng, Chun-Hou

2016-12-23

Cancer is a complex disease which is characterized by the accumulation of genetic alterations during the patient's lifetime. With the development of the next-generation sequencing technology, multiple omics data, such as cancer genomic, epigenomic and transcriptomic data etc., can be measured from each individual. Correspondingly, one of the key challenges is to pinpoint functional driver mutations or pathways, which contributes to tumorigenesis, from millions of functional neutral passenger mutations. In this paper, in order to identify driver genes effectively, we applied a generalized additive model to mutation profiles to filter genes with long length and constructed a new gene-gene interaction network. Then we integrated the mutation data and expression data into the gene-gene interaction network. Lastly, greedy algorithm was used to prioritize candidate driver genes from the integrated data. We named the proposed method Length-Net-Driver (LNDriver). Experiments on three TCGA datasets, i.e., head and neck squamous cell carcinoma, kidney renal clear cell carcinoma and thyroid carcinoma, demonstrated that the proposed method was effective. Also, it can identify not only frequently mutated drivers, but also rare candidate driver genes.

Monitoring therapy responses at the leukemic subclone level by ultra-deep amplicon resequencing in acute myeloid leukemia.

PubMed

Ojamies, P N; Kontro, M; Edgren, H; Ellonen, P; Lagström, S; Almusa, H; Miettinen, T; Eldfors, S; Tamborero, D; Wennerberg, K; Heckman, C; Porkka, K; Wolf, M; Kallioniemi, O

2017-05-01

In our individualized systems medicine program, personalized treatment options are identified and administered to chemorefractory acute myeloid leukemia (AML) patients based on exome sequencing and ex vivo drug sensitivity and resistance testing data. Here, we analyzed how clonal heterogeneity affects the responses of 13 AML patients to chemotherapy or targeted treatments using ultra-deep (average 68 000 × coverage) amplicon resequencing. Using amplicon resequencing, we identified 16 variants from 4 patients (frequency 0.54-2%) that were not detected previously by exome sequencing. A correlation-based method was developed to detect mutation-specific responses in serial samples across multiple time points. Significant subclone-specific responses were observed for both chemotherapy and targeted therapy. We detected subclonal responses in patients where clinical European LeukemiaNet (ELN) criteria showed no response. Subclonal responses also helped to identify putative mechanisms underlying drug sensitivities, such as sensitivity to azacitidine in DNMT3A mutated cell clones and resistance to cytarabine in a subclone with loss of NF1 gene. In summary, ultra-deep amplicon resequencing method enables sensitive quantification of subclonal variants and their responses to therapies. This approach provides new opportunities for designing combinatorial therapies blocking multiple subclones as well as for real-time assessment of such treatments.

Identifying Driver Genomic Alterations in Cancers by Searching Minimum-Weight, Mutually Exclusive Sets

PubMed Central

Lu, Songjian; Lu, Kevin N.; Cheng, Shi-Yuan; Hu, Bo; Ma, Xiaojun; Nystrom, Nicholas; Lu, Xinghua

2015-01-01

An important goal of cancer genomic research is to identify the driving pathways underlying disease mechanisms and the heterogeneity of cancers. It is well known that somatic genome alterations (SGAs) affecting the genes that encode the proteins within a common signaling pathway exhibit mutual exclusivity, in which these SGAs usually do not co-occur in a tumor. With some success, this characteristic has been utilized as an objective function to guide the search for driver mutations within a pathway. However, mutual exclusivity alone is not sufficient to indicate that genes affected by such SGAs are in common pathways. Here, we propose a novel, signal-oriented framework for identifying driver SGAs. First, we identify the perturbed cellular signals by mining the gene expression data. Next, we search for a set of SGA events that carries strong information with respect to such perturbed signals while exhibiting mutual exclusivity. Finally, we design and implement an efficient exact algorithm to solve an NP-hard problem encountered in our approach. We apply this framework to the ovarian and glioblastoma tumor data available at the TCGA database, and perform systematic evaluations. Our results indicate that the signal-oriented approach enhances the ability to find informative sets of driver SGAs that likely constitute signaling pathways. PMID:26317392

Motor vehicle accident or driver suicide? Identifying cases of failed driver suicide in the trauma setting.

PubMed

Henderson, Antony F; Joseph, Anthony P

2012-01-01

Many authors have suggested that some road traffic crashes are disguised suicide attempts. A case report and literature review is used to explore this claim and to examine the frequency and risk factors associated with driver suicide. The author concludes the methodological difficulty of establishing the driver's intent of suicide accounts for an under-estimation of the frequency of this event and that many cases of driver suicide go unrecognised. Familiarity with the risk factors associated with driver suicide may assist in the identification of cases of failed driver suicide and referral to psychiatric services. Copyright © 2011 Elsevier Ltd. All rights reserved.

A Pooled Sequencing Approach Identifies a Candidate Meiotic Driver in Drosophila

PubMed Central

Wei, Kevin H.-C.; Reddy, Hemakumar M.; Rathnam, Chandramouli; Lee, Jimin; Lin, Deanna; Ji, Shuqing; Mason, James M.; Clark, Andrew G.; Barbash, Daniel A.

2017-01-01

Meiotic drive occurs when a selfish element increases its transmission frequency above the Mendelian ratio by hijacking the asymmetric divisions of female meiosis. Meiotic drive causes genomic conflict and potentially has a major impact on genome evolution, but only a few drive loci of large effect have been described. New methods to reliably detect meiotic drive are therefore needed, particularly for discovering moderate-strength drivers that are likely to be more prevalent in natural populations than strong drivers. Here, we report an efficient method that uses sequencing of large pools of backcross (BC1) progeny to test for deviations from Mendelian segregation genome-wide with single-nucleotide polymorphisms (SNPs) that distinguish the parental strains. We show that meiotic drive can be detected by a characteristic pattern of decay in distortion of SNP frequencies, caused by recombination unlinking the driver from distal loci. We further show that control crosses allow allele-frequency distortion caused by meiotic drive to be distinguished from distortion resulting from developmental effects. We used this approach to test whether chromosomes with extreme telomere-length differences segregate at Mendelian ratios, as telomeric regions are a potential hotspot for meiotic drive due to their roles in meiotic segregation and multiple observations of high rates of telomere sequence evolution. Using four different pairings of long and short telomere strains, we find no evidence that extreme telomere-length variation causes meiotic drive in Drosophila. However, we identify one candidate meiotic driver in a centromere-linked region that shows an ∼8% increase in transmission frequency, corresponding to a ∼54:46 segregation ratio. Our results show that candidate meiotic drivers of moderate strength can be readily detected and localized in pools of BC1 progeny. PMID:28258181

Identifying mismatches between institutional perceptions of water-related risk drivers and water management strategies in three river basin areas

NASA Astrophysics Data System (ADS)

Räsänen, Aleksi; Juhola, Sirkku; Monge Monge, Adrián; Käkönen, Mira; Kanninen, Markku; Nygren, Anja

2017-07-01

Water-related risks and vulnerabilities are driven by variety of stressors, including climate and land use change, as well as changes in socio-economic positions and political landscapes. Hence, water governance, which addresses risks and vulnerabilities, should target multiple stressors. We analyze the institutional perceptions of the drivers and strategies for managing water-related risks and vulnerabilities in three regionally important river basin areas located in Finland, Mexico, and Laos. Our analysis is based on data gathered through participatory workshops and complemented by qualitative content analysis of relevant policy documents. The identified drivers and proposed risk reduction strategies showed the multidimensionality and context-specificity of water-related risks and vulnerabilities across study areas. Most of the identified drivers were seen to increase risks, but some of the drivers were positive trends, and drivers also included also policy instruments that can both increase or decrease risks. Nevertheless, all perceived drivers were not addressed with suggested risk reduction strategies. In particular, most of the risk reduction strategies were incremental adjustments, although many of the drivers classified as most important were large-scale trends, such as climate change, land use changes and increase in foreign investments. We argue that there is a scale mismatch between the identified drivers and suggested strategies, which questions the opportunity to manage the drivers by single-scale incremental adjustments. Our study suggests that for more sustainable risk and vulnerability reduction, the root causes of water-related risks and vulnerabilities should be addressed through adaptive multi-scale governance that carefully considers the context-specificity and the multidimensionality of the associated drivers and stressors.

DAMe: a toolkit for the initial processing of datasets with PCR replicates of double-tagged amplicons for DNA metabarcoding analyses.

PubMed

Zepeda-Mendoza, Marie Lisandra; Bohmann, Kristine; Carmona Baez, Aldo; Gilbert, M Thomas P

2016-05-03

DNA metabarcoding is an approach for identifying multiple taxa in an environmental sample using specific genetic loci and taxa-specific primers. When combined with high-throughput sequencing it enables the taxonomic characterization of large numbers of samples in a relatively time- and cost-efficient manner. One recent laboratory development is the addition of 5'-nucleotide tags to both primers producing double-tagged amplicons and the use of multiple PCR replicates to filter erroneous sequences. However, there is currently no available toolkit for the straightforward analysis of datasets produced in this way. We present DAMe, a toolkit for the processing of datasets generated by double-tagged amplicons from multiple PCR replicates derived from an unlimited number of samples. Specifically, DAMe can be used to (i) sort amplicons by tag combination, (ii) evaluate PCR replicates dissimilarity, and (iii) filter sequences derived from sequencing/PCR errors, chimeras, and contamination. This is attained by calculating the following parameters: (i) sequence content similarity between the PCR replicates from each sample, (ii) reproducibility of each unique sequence across the PCR replicates, and (iii) copy number of the unique sequences in each PCR replicate. We showcase the insights that can be obtained using DAMe prior to taxonomic assignment, by applying it to two real datasets that vary in their complexity regarding number of samples, sequencing libraries, PCR replicates, and used tag combinations. Finally, we use a third mock dataset to demonstrate the impact and importance of filtering the sequences with DAMe. DAMe allows the user-friendly manipulation of amplicons derived from multiple samples with PCR replicates built in a single or multiple sequencing libraries. It allows the user to: (i) collapse amplicons into unique sequences and sort them by tag combination while retaining the sample identifier and copy number information, (ii) identify sequences carrying

Amplicon Resequencing Identified Parental Mosaicism for Approximately 10% of “de novo” SCN1A Mutations in Children with Dravet Syndrome

PubMed Central

Xu, Xiaojing; Yang, Xiaoxu; Wu, Qixi; Liu, Aijie; Yang, Xiaoling; Ye, Adam Yongxin; Huang, August Yue; Li, Jiarui; Wang, Meng; Yu, Zhe; Wang, Sheng; Zhang, Zhichao; Wu, Xiru

2015-01-01

ABSTRACT The majority of children with Dravet syndrome (DS) are caused by de novo SCN1A mutations. To investigate the origin of the mutations, we developed and applied a new method that combined deep amplicon resequencing with a Bayesian model to detect and quantify allelic fractions with improved sensitivity. Of 174 SCN1A mutations in DS probands which were considered “de novo” by Sanger sequencing, we identified 15 cases (8.6%) of parental mosaicism. We identified another five cases of parental mosaicism that were also detectable by Sanger sequencing. Fraction of mutant alleles in the 20 cases of parental mosaicism ranged from 1.1% to 32.6%. Thirteen (65% of 20) mutations originated paternally and seven (35% of 20) maternally. Twelve (60% of 20) mosaic parents did not have any epileptic symptoms. Their mutant allelic fractions were significantly lower than those in mosaic parents with epileptic symptoms (P = 0.016). We identified mosaicism with varied allelic fractions in blood, saliva, urine, hair follicle, oral epithelium, and semen, demonstrating that postzygotic mutations could affect multiple somatic cells as well as germ cells. Our results suggest that more sensitive tools for detecting low‐level mosaicism in parents of families with seemingly “de novo” mutations will allow for better informed genetic counseling. PMID:26096185

RUBIC identifies driver genes by detecting recurrent DNA copy number breaks

PubMed Central

van Dyk, Ewald; Hoogstraat, Marlous; ten Hoeve, Jelle; Reinders, Marcel J. T.; Wessels, Lodewyk F. A.

2016-01-01

The frequent recurrence of copy number aberrations across tumour samples is a reliable hallmark of certain cancer driver genes. However, state-of-the-art algorithms for detecting recurrent aberrations fail to detect several known drivers. In this study, we propose RUBIC, an approach that detects recurrent copy number breaks, rather than recurrently amplified or deleted regions. This change of perspective allows for a simplified approach as recursive peak splitting procedures and repeated re-estimation of the background model are avoided. Furthermore, we control the false discovery rate on the level of called regions, rather than at the probe level, as in competing algorithms. We benchmark RUBIC against GISTIC2 (a state-of-the-art approach) and RAIG (a recently proposed approach) on simulated copy number data and on three SNP6 and NGS copy number data sets from TCGA. We show that RUBIC calls more focal recurrent regions and identifies a much larger fraction of known cancer genes. PMID:27396759

Dimensions of aberrant driving behaviours in Tunisia: identifying the relation between Driver Behaviour Questionnaire results and accident data.

PubMed

Mohamed, Dhibi; Lotfi, Belkacem

2016-12-01

In this study, the Manchester Driver Behaviour Questionnaire (DBQ) was used to examine the self-reported driving behaviours of a group of Tunisian drivers (N = 900) and to collect socio-demographic data, driver behaviours and DBQ items. A sample of Tunisian drivers above 18 years was selected. The aim of the present study was to investigate the factorial structure of the DBQ in Tunisia. The principal component analysis identified three factor solutions: inattention errors, dangerous errors and dangerous violations. Logistic regression analysis showed that dangerous errors, dangerous violations and speeding preference factors predicted crash involvement in Tunisia. Speeding is the most common form of aberrant behaviour reported by drivers in the current sample. It remains one of the major road safety concerns.

Formation of Linear Amplicons with Inverted Duplications in Leishmania Requires the MRE11 Nuclease

PubMed Central

Laffitte, Marie-Claude N.; Genois, Marie-Michelle; Mukherjee, Angana; Légaré, Danielle; Masson, Jean-Yves; Ouellette, Marc

2014-01-01

Extrachromosomal DNA amplification is frequent in the protozoan parasite Leishmania selected for drug resistance. The extrachromosomal amplified DNA is either circular or linear, and is formed at the level of direct or inverted homologous repeated sequences that abound in the Leishmania genome. The RAD51 recombinase plays an important role in circular amplicons formation, but the mechanism by which linear amplicons are formed is unknown. We hypothesized that the Leishmania infantum DNA repair protein MRE11 is required for linear amplicons following rearrangements at the level of inverted repeats. The purified LiMRE11 protein showed both DNA binding and exonuclease activities. Inactivation of the LiMRE11 gene led to parasites with enhanced sensitivity to DNA damaging agents. The MRE11−/− parasites had a reduced capacity to form linear amplicons after drug selection, and the reintroduction of an MRE11 allele led to parasites regaining their capacity to generate linear amplicons, but only when MRE11 had an active nuclease activity. These results highlight a novel MRE11-dependent pathway used by Leishmania to amplify portions of its genome to respond to a changing environment. PMID:25474106

SEED 2: a user-friendly platform for amplicon high-throughput sequencing data analyses.

PubMed

Vetrovský, Tomáš; Baldrian, Petr; Morais, Daniel; Berger, Bonnie

2018-02-14

Modern molecular methods have increased our ability to describe microbial communities. Along with the advances brought by new sequencing technologies, we now require intensive computational resources to make sense of the large numbers of sequences continuously produced. The software developed by the scientific community to address this demand, although very useful, require experience of the command-line environment, extensive training and have steep learning curves, limiting their use. We created SEED 2, a graphical user interface for handling high-throughput amplicon-sequencing data under Windows operating systems. SEED 2 is the only sequence visualizer that empowers users with tools to handle amplicon-sequencing data of microbial community markers. It is suitable for any marker genes sequences obtained through Illumina, IonTorrent or Sanger sequencing. SEED 2 allows the user to process raw sequencing data, identify specific taxa, produce of OTU-tables, create sequence alignments and construct phylogenetic trees. Standard dual core laptops with 8 GB of RAM can handle ca. 8 million of Illumina PE 300 bp sequences, ca. 4GB of data. SEED 2 was implemented in Object Pascal and uses internal functions and external software for amplicon data processing. SEED 2 is a freeware software, available at http://www.biomed.cas.cz/mbu/lbwrf/seed/ as a self-contained file, including all the dependencies, and does not require installation. Supplementary data contain a comprehensive list of supported functions. daniel.morais@biomed.cas.cz. Supplementary data are available at Bioinformatics online. © The Author(s) 2018. Published by Oxford University Press.

Characterization of Novel Genes Within 8P11-12 Amplicon in Breast Cancer

DTIC Science & Technology

2007-06-01

C-myc amplification in breast cancer: a meta - analysis of its occurrence and prognostic relevance. Br J Cancer, 83: 1688-1695, 2000. 2. Hui, R...Nass SJ, Dickson RB, Trock BJ. C-myc amplification in breast cancer: a meta - analysis of its occurrence and prognostic relevance. Br J Cancer 2000;83...a detailed genomic and expression analysis of the 8p11-p12 amplicon in breast cancer cell lines and identified several novel candidate genes

A quantitative and qualitative comparison of illumina MiSeq and 454 amplicon sequencing for genotyping the highly polymorphic major histocompatibility complex (MHC) in a non-model species.

PubMed

Razali, Haslina; O'Connor, Emily; Drews, Anna; Burke, Terry; Westerdahl, Helena

2017-07-28

High-throughput sequencing enables high-resolution genotyping of extremely duplicated genes. 454 amplicon sequencing (454) has become the standard technique for genotyping the major histocompatibility complex (MHC) genes in non-model organisms. However, illumina MiSeq amplicon sequencing (MiSeq), which offers a much higher read depth, is now superseding 454. The aim of this study was to quantitatively and qualitatively evaluate the performance of MiSeq in relation to 454 for genotyping MHC class I alleles using a house sparrow (Passer domesticus) dataset with pedigree information. House sparrows provide a good study system for this comparison as their MHC class I genes have been studied previously and, consequently, we had prior expectations concerning the number of alleles per individual. We found that 454 and MiSeq performed equally well in genotyping amplicons with low diversity, i.e. amplicons from individuals that had fewer than 6 alleles. Although there was a higher rate of failure in the 454 dataset in resolving amplicons with higher diversity (6-9 alleles), the same genotypes were identified by both 454 and MiSeq in 98% of cases. We conclude that low diversity amplicons are equally well genotyped using either 454 or MiSeq, but the higher coverage afforded by MiSeq can lead to this approach outperforming 454 in amplicons with higher diversity.

MADGiC: a model-based approach for identifying driver genes in cancer

PubMed Central

Korthauer, Keegan D.; Kendziorski, Christina

2015-01-01

Motivation: Identifying and prioritizing somatic mutations is an important and challenging area of cancer research that can provide new insights into gene function as well as new targets for drug development. Most methods for prioritizing mutations rely primarily on frequency-based criteria, where a gene is identified as having a driver mutation if it is altered in significantly more samples than expected according to a background model. Although useful, frequency-based methods are limited in that all mutations are treated equally. It is well known, however, that some mutations have no functional consequence, while others may have a major deleterious impact. The spatial pattern of mutations within a gene provides further insight into their functional consequence. Properly accounting for these factors improves both the power and accuracy of inference. Also important is an accurate background model. Results: Here, we develop a Model-based Approach for identifying Driver Genes in Cancer (termed MADGiC) that incorporates both frequency and functional impact criteria and accommodates a number of factors to improve the background model. Simulation studies demonstrate advantages of the approach, including a substantial increase in power over competing methods. Further advantages are illustrated in an analysis of ovarian and lung cancer data from The Cancer Genome Atlas (TCGA) project. Availability and implementation: R code to implement this method is available at http://www.biostat.wisc.edu/ kendzior/MADGiC/. Contact: kendzior@biostat.wisc.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25573922

A flexible and economical barcoding approach for highly multiplexed amplicon sequencing of diverse target genes

PubMed Central

Herbold, Craig W.; Pelikan, Claus; Kuzyk, Orest; Hausmann, Bela; Angel, Roey; Berry, David; Loy, Alexander

2015-01-01

High throughput sequencing of phylogenetic and functional gene amplicons provides tremendous insight into the structure and functional potential of complex microbial communities. Here, we introduce a highly adaptable and economical PCR approach to barcoding and pooling libraries of numerous target genes. In this approach, we replace gene- and sequencing platform-specific fusion primers with general, interchangeable barcoding primers, enabling nearly limitless customized barcode-primer combinations. Compared to barcoding with long fusion primers, our multiple-target gene approach is more economical because it overall requires lower number of primers and is based on short primers with generally lower synthesis and purification costs. To highlight our approach, we pooled over 900 different small-subunit rRNA and functional gene amplicon libraries obtained from various environmental or host-associated microbial community samples into a single, paired-end Illumina MiSeq run. Although the amplicon regions ranged in size from approximately 290 to 720 bp, we found no significant systematic sequencing bias related to amplicon length or gene target. Our results indicate that this flexible multiplexing approach produces large, diverse, and high quality sets of amplicon sequence data for modern studies in microbial ecology. PMID:26236305

Evaluation of the reproducibility of amplicon sequencing with Illumina MiSeq platform

PubMed Central

Van Nostrand, Joy D.; Ning, Daliang; Sun, Bo; Xue, Kai; Liu, Feifei; Deng, Ye; Liang, Yuting; Zhou, Jizhong

2017-01-01

Illumina’s MiSeq has become the dominant platform for gene amplicon sequencing in microbial ecology studies; however, various technical concerns, such as reproducibility, still exist. To assess reproducibility, 16S rRNA gene amplicons from 18 soil samples of a reciprocal transplantation experiment were sequenced on an Illumina MiSeq. The V4 region of 16S rRNA gene from each sample was sequenced in triplicate with each replicate having a unique barcode. The average OTU overlap, without considering sequence abundance, at a rarefaction level of 10,323 sequences was 33.4±2.1% and 20.2±1.7% between two and among three technical replicates, respectively. When OTU sequence abundance was considered, the average sequence abundance weighted OTU overlap was 85.6±1.6% and 81.2±2.1% for two and three replicates, respectively. Removing singletons significantly increased the overlap for both (~1–3%, p<0.001). Increasing the sequencing depth to 160,000 reads by deep sequencing increased OTU overlap both when sequence abundance was considered (95%) and when not (44%). However, if singletons were not removed the overlap between two technical replicates (not considering sequence abundance) plateaus at 39% with 30,000 sequences. Diversity measures were not affected by the low overlap as α-diversities were similar among technical replicates while β-diversities (Bray-Curtis) were much smaller among technical replicates than among treatment replicates (e.g., 0.269 vs. 0.374). Higher diversity coverage, but lower OTU overlap, was observed when replicates were sequenced in separate runs. Detrended correspondence analysis indicated that while there was considerable variation among technical replicates, the reproducibility was sufficient for detecting treatment effects for the samples examined. These results suggest that although there is variation among technical replicates, amplicon sequencing on MiSeq is useful for analyzing microbial community structure if used appropriately

Evaluation of the reproducibility of amplicon sequencing with Illumina MiSeq platform.

PubMed

Wen, Chongqing; Wu, Liyou; Qin, Yujia; Van Nostrand, Joy D; Ning, Daliang; Sun, Bo; Xue, Kai; Liu, Feifei; Deng, Ye; Liang, Yuting; Zhou, Jizhong

2017-01-01

Illumina's MiSeq has become the dominant platform for gene amplicon sequencing in microbial ecology studies; however, various technical concerns, such as reproducibility, still exist. To assess reproducibility, 16S rRNA gene amplicons from 18 soil samples of a reciprocal transplantation experiment were sequenced on an Illumina MiSeq. The V4 region of 16S rRNA gene from each sample was sequenced in triplicate with each replicate having a unique barcode. The average OTU overlap, without considering sequence abundance, at a rarefaction level of 10,323 sequences was 33.4±2.1% and 20.2±1.7% between two and among three technical replicates, respectively. When OTU sequence abundance was considered, the average sequence abundance weighted OTU overlap was 85.6±1.6% and 81.2±2.1% for two and three replicates, respectively. Removing singletons significantly increased the overlap for both (~1-3%, p<0.001). Increasing the sequencing depth to 160,000 reads by deep sequencing increased OTU overlap both when sequence abundance was considered (95%) and when not (44%). However, if singletons were not removed the overlap between two technical replicates (not considering sequence abundance) plateaus at 39% with 30,000 sequences. Diversity measures were not affected by the low overlap as α-diversities were similar among technical replicates while β-diversities (Bray-Curtis) were much smaller among technical replicates than among treatment replicates (e.g., 0.269 vs. 0.374). Higher diversity coverage, but lower OTU overlap, was observed when replicates were sequenced in separate runs. Detrended correspondence analysis indicated that while there was considerable variation among technical replicates, the reproducibility was sufficient for detecting treatment effects for the samples examined. These results suggest that although there is variation among technical replicates, amplicon sequencing on MiSeq is useful for analyzing microbial community structure if used appropriately and

Microbes in deep marine sediments viewed through amplicon sequencing and metagenomics

NASA Astrophysics Data System (ADS)

Biddle, J.; Leon, Z. R.; Russell, J. A., III; Martino, A. J.

2016-12-01

Nearly twenty percent of microbial biomass on Earth can be found in the marine subsurface. The majority of this is concentrated on continental margins, which have been investigated by scientific drilling. On the Costa Rica Margin, Iberian Margin and Peru Margins, sediment samples have been investigated through DNA extraction followed by amplicon and metagenomic sequencing. Overall samples show a high degree of microbial diversity, including many lineages of newly defined groups. In this talk, metagenome assembled genomes of unusual lineages will be presented, including their relationships to shallower relatives. From Costa Rica, in particular, we have retrieved deep relatives of Lokiarchaeota and Thorarchaeota, as well as other deeply branching archaeal relatives. We discuss their genome similarities to both other archaea and eukaryotes. From the Iberian Margin, relatives of Atribacteria and Aerophobetes will be discussed. Finally, we will detail the knowledge lost or gained depending on whether samples are studied via amplicon sequencing or total metagenomics, as studies in other environments have shown that up to 15% of microbial diversity is ignored when samples are studied via amplicon sequencing alone.

Using Amplicon Sequencing To Characterize and Monitor Bacterial Diversity in Drinking Water Distribution Systems

PubMed Central

Shaw, Jennifer L. A.; Weyrich, Laura S.; Sawade, Emma; Drikas, Mary; Cooper, Alan J.

2015-01-01

Drinking water assessments use a variety of microbial, physical, and chemical indicators to evaluate water treatment efficiency and product water quality. However, these indicators do not allow the complex biological communities, which can adversely impact the performance of drinking water distribution systems (DWDSs), to be characterized. Entire bacterial communities can be studied quickly and inexpensively using targeted metagenomic amplicon sequencing. Here, amplicon sequencing of the 16S rRNA gene region was performed alongside traditional water quality measures to assess the health, quality, and efficiency of two distinct, full-scale DWDSs: (i) a linear DWDS supplied with unfiltered water subjected to basic disinfection before distribution and (ii) a complex, branching DWDS treated by a four-stage water treatment plant (WTP) prior to disinfection and distribution. In both DWDSs bacterial communities differed significantly after disinfection, demonstrating the effectiveness of both treatment regimes. However, bacterial repopulation occurred further along in the DWDSs, and some end-user samples were more similar to the source water than to the postdisinfection water. Three sample locations appeared to be nitrified, displaying elevated nitrate levels and decreased ammonia levels, and nitrifying bacterial species, such as Nitrospira, were detected. Burkholderiales were abundant in samples containing large amounts of monochloramine, indicating resistance to disinfection. Genera known to contain pathogenic and fecal-associated species were also identified in several locations. From this study, we conclude that metagenomic amplicon sequencing is an informative method to support current compliance-based methods and can be used to reveal bacterial community interactions with the chemical and physical properties of DWDSs. PMID:26162884

"It drives us to do it": pregnant adolescents identify drivers for sexual risk-taking.

PubMed

King Jones, Tammy C

2010-01-01

Sexual risk-taking behaviors have a negative effect on the heath and future of American adolescents. To gain insight into these behaviors and preventative efforts, this study explored the experiences and perceptions of 15 pregnant adolescents using a qualitative feminist approach and in-depth interviews. As participants discussed sex education, each identified influences on sexual decision-making that often overpowered the information received. Content analysis and constant comparison of this data led to the overarching theme "Drivers for Sexual Risk-taking." Drivers were categorized as internal and external and each demonstrated a significant influence on adolescent sexual decision-making. Results of this study can inform the development of educational efforts, reform of social policy, and the focus of future research.

Identifying training needs of logging truck drivers using a skill inventory.

PubMed

Carnahan, B J

2004-11-01

The purpose of this research was to determine if the Driver Skill Inventory (DSI) could be used to characterize the self-assessed driving performance of commercial logging truck drivers. The DSI requires respondents to subjectively evaluate their own ability in regard to 15 different driving skills. The DSI responses of 1000 logging truck drivers were collected across three southeastern states. The underlying hypothesis in the current study was that DSI responses of these drivers would have similar reliability and factor structure as those DSI responses collected from non-commercial drivers in previous studies. Factor analysis of the data confirmed this hypothesis. Statistical analysis revealed that low self-ratings on various safety skill items within the DSI inventory were associated with: (1) inconsistency in using seat belts, (2) inconsistency in performing pre-trip inspections on logging trucks, and (3) committing moving violations. Conversely, high self-ratings ratings on various perceptual-motor skill items were associated with these same at-risk behaviors. The perceptual-motor skill items were also positively associated with negative attitudes toward driving regulations and the number of moving violations incurred over a three-year period. Non-parametric statistical analysis revealed that self-assessments were lowest for DSI skills pertaining to controlling one's anger while driving and managing the truck through a skid or slide. Results of the study confirmed that the DSI can be successfully applied to commercial logging truck drivers as part of an overall comprehensive training needs assessment.

Fast, accurate and easy-to-pipeline methods for amplicon sequence processing

NASA Astrophysics Data System (ADS)

Antonielli, Livio; Sessitsch, Angela

2016-04-01

Next generation sequencing (NGS) technologies established since years as an essential resource in microbiology. While on the one hand metagenomic studies can benefit from the continuously increasing throughput of the Illumina (Solexa) technology, on the other hand the spreading of third generation sequencing technologies (PacBio, Oxford Nanopore) are getting whole genome sequencing beyond the assembly of fragmented draft genomes, making it now possible to finish bacterial genomes even without short read correction. Besides (meta)genomic analysis next-gen amplicon sequencing is still fundamental for microbial studies. Amplicon sequencing of the 16S rRNA gene and ITS (Internal Transcribed Spacer) remains a well-established widespread method for a multitude of different purposes concerning the identification and comparison of archaeal/bacterial (16S rRNA gene) and fungal (ITS) communities occurring in diverse environments. Numerous different pipelines have been developed in order to process NGS-derived amplicon sequences, among which Mothur, QIIME and USEARCH are the most well-known and cited ones. The entire process from initial raw sequence data through read error correction, paired-end read assembly, primer stripping, quality filtering, clustering, OTU taxonomic classification and BIOM table rarefaction as well as alternative "normalization" methods will be addressed. An effective and accurate strategy will be presented using the state-of-the-art bioinformatic tools and the example of a straightforward one-script pipeline for 16S rRNA gene or ITS MiSeq amplicon sequencing will be provided. Finally, instructions on how to automatically retrieve nucleotide sequences from NCBI and therefore apply the pipeline to targets other than 16S rRNA gene (Greengenes, SILVA) and ITS (UNITE) will be discussed.

A fungal mock community control for amplicon sequencing experiments

USDA-ARS?s Scientific Manuscript database

The field of microbial ecology has been profoundly advanced by the ability to profile the composition of complex microbial communities by means of high throughput amplicon sequencing of marker genes amplified directly from environmental genomic DNA extracts. However, it has become increasingly clear...

Using Amplicon Sequencing To Characterize and Monitor Bacterial Diversity in Drinking Water Distribution Systems.

PubMed

Shaw, Jennifer L A; Monis, Paul; Weyrich, Laura S; Sawade, Emma; Drikas, Mary; Cooper, Alan J

2015-09-01

Drinking water assessments use a variety of microbial, physical, and chemical indicators to evaluate water treatment efficiency and product water quality. However, these indicators do not allow the complex biological communities, which can adversely impact the performance of drinking water distribution systems (DWDSs), to be characterized. Entire bacterial communities can be studied quickly and inexpensively using targeted metagenomic amplicon sequencing. Here, amplicon sequencing of the 16S rRNA gene region was performed alongside traditional water quality measures to assess the health, quality, and efficiency of two distinct, full-scale DWDSs: (i) a linear DWDS supplied with unfiltered water subjected to basic disinfection before distribution and (ii) a complex, branching DWDS treated by a four-stage water treatment plant (WTP) prior to disinfection and distribution. In both DWDSs bacterial communities differed significantly after disinfection, demonstrating the effectiveness of both treatment regimes. However, bacterial repopulation occurred further along in the DWDSs, and some end-user samples were more similar to the source water than to the postdisinfection water. Three sample locations appeared to be nitrified, displaying elevated nitrate levels and decreased ammonia levels, and nitrifying bacterial species, such as Nitrospira, were detected. Burkholderiales were abundant in samples containing large amounts of monochloramine, indicating resistance to disinfection. Genera known to contain pathogenic and fecal-associated species were also identified in several locations. From this study, we conclude that metagenomic amplicon sequencing is an informative method to support current compliance-based methods and can be used to reveal bacterial community interactions with the chemical and physical properties of DWDSs. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS.

PubMed

Fosso, Bruno; Santamaria, Monica; Marzano, Marinella; Alonso-Alemany, Daniel; Valiente, Gabriel; Donvito, Giacinto; Monaco, Alfonso; Notarangelo, Pasquale; Pesole, Graziano

2015-07-01

Substantial advances in microbiology, molecular evolution and biodiversity have been carried out in recent years thanks to Metagenomics, which allows to unveil the composition and functions of mixed microbial communities in any environmental niche. If the investigation is aimed only at the microbiome taxonomic structure, a target-based metagenomic approach, here also referred as Meta-barcoding, is generally applied. This approach commonly involves the selective amplification of a species-specific genetic marker (DNA meta-barcode) in the whole taxonomic range of interest and the exploration of its taxon-related variants through High-Throughput Sequencing (HTS) technologies. The accessibility to proper computational systems for the large-scale bioinformatic analysis of HTS data represents, currently, one of the major challenges in advanced Meta-barcoding projects. BioMaS (Bioinformatic analysis of Metagenomic AmpliconS) is a new bioinformatic pipeline designed to support biomolecular researchers involved in taxonomic studies of environmental microbial communities by a completely automated workflow, comprehensive of all the fundamental steps, from raw sequence data upload and cleaning to final taxonomic identification, that are absolutely required in an appropriately designed Meta-barcoding HTS-based experiment. In its current version, BioMaS allows the analysis of both bacterial and fungal environments starting directly from the raw sequencing data from either Roche 454 or Illumina HTS platforms, following two alternative paths, respectively. BioMaS is implemented into a public web service available at https://recasgateway.ba.infn.it/ and is also available in Galaxy at http://galaxy.cloud.ba.infn.it:8080 (only for Illumina data). BioMaS is a friendly pipeline for Meta-barcoding HTS data analysis specifically designed for users without particular computing skills. A comparative benchmark, carried out by using a simulated dataset suitably designed to broadly represent

Evaluation of the reproducibility of amplicon sequencing with Illumina MiSeq platform

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wen, Chongqing; Wu, Liyou; Qin, Yujia

Illumina's MiSeq has become the dominant platform for gene amplicon sequencing in microbial ecology studies; however, various technical concerns, such as reproducibility, still exist. To assess reproducibility, 16S rRNA gene amplicons from 18 soil samples of a reciprocal transplantation experiment were sequenced on an Illumina MiSeq. The V4 region of 16S rRNA gene from each sample was sequenced in triplicate with each replicate having a unique barcode. The average OTU overlap, without considering sequence abundance, at a rarefaction level of 10,323 sequences was 33.4±2.1% and 20.2±1.7% between two and among three technical replicates, respectively. When OTU sequence abundance was considered,more » the average sequence abundance weighted OTU overlap was 85.6±1.6% and 81.2±2.1% for two and three replicates, respectively. Removing singletons significantly increased the overlap for both (~1-3%, p<0.001). Increasing the sequencing depth to 160,000 reads by deep sequencing increased OTU overlap both when sequence abundance was considered (95%) and when not (44%). However, if singletons were not removed the overlap between two technical replicates (not considering sequence abundance) plateaus at 39% with 30,000 sequences. Diversity measures were not affected by the low overlap as α-diversities were similar among technical replicates while β-diversities (Bray-Curtis) were much smaller among technical replicates than among treatment replicates (e.g., 0.269 vs. 0.374). Higher diversity coverage, but lower OTU overlap, was observed when replicates were sequenced in separate runs. Detrended correspondence analysis indicated that while there was considerable variation among technical replicates, the reproducibility was sufficient for detecting treatment effects for the samples examined. These results suggest that although there is variation among technical replicates, amplicon sequencing on MiSeq is useful for analyzing microbial community structure if used

Evaluation of the reproducibility of amplicon sequencing with Illumina MiSeq platform

DOE PAGES

Wen, Chongqing; Wu, Liyou; Qin, Yujia; ...

2017-04-28

Illumina's MiSeq has become the dominant platform for gene amplicon sequencing in microbial ecology studies; however, various technical concerns, such as reproducibility, still exist. To assess reproducibility, 16S rRNA gene amplicons from 18 soil samples of a reciprocal transplantation experiment were sequenced on an Illumina MiSeq. The V4 region of 16S rRNA gene from each sample was sequenced in triplicate with each replicate having a unique barcode. The average OTU overlap, without considering sequence abundance, at a rarefaction level of 10,323 sequences was 33.4±2.1% and 20.2±1.7% between two and among three technical replicates, respectively. When OTU sequence abundance was considered,more » the average sequence abundance weighted OTU overlap was 85.6±1.6% and 81.2±2.1% for two and three replicates, respectively. Removing singletons significantly increased the overlap for both (~1-3%, p<0.001). Increasing the sequencing depth to 160,000 reads by deep sequencing increased OTU overlap both when sequence abundance was considered (95%) and when not (44%). However, if singletons were not removed the overlap between two technical replicates (not considering sequence abundance) plateaus at 39% with 30,000 sequences. Diversity measures were not affected by the low overlap as α-diversities were similar among technical replicates while β-diversities (Bray-Curtis) were much smaller among technical replicates than among treatment replicates (e.g., 0.269 vs. 0.374). Higher diversity coverage, but lower OTU overlap, was observed when replicates were sequenced in separate runs. Detrended correspondence analysis indicated that while there was considerable variation among technical replicates, the reproducibility was sufficient for detecting treatment effects for the samples examined. These results suggest that although there is variation among technical replicates, amplicon sequencing on MiSeq is useful for analyzing microbial community structure if used

Characterizing partial AZFc deletions of the Y chromosome with amplicon-specific sequence markers

PubMed Central

Navarro-Costa, Paulo; Pereira, Luísa; Alves, Cíntia; Gusmão, Leonor; Proença, Carmen; Marques-Vidal, Pedro; Rocha, Tiago; Correia, Sónia C; Jorge, Sónia; Neves, António; Soares, Ana P; Nunes, Joaquim; Calhaz-Jorge, Carlos; Amorim, António; Plancha, Carlos E; Gonçalves, João

2007-01-01

Background The AZFc region of the human Y chromosome is a highly recombinogenic locus containing multi-copy male fertility genes located in repeated DNA blocks (amplicons). These AZFc gene families exhibit slight sequence variations between copies which are considered to have functional relevance. Yet, partial AZFc deletions yield phenotypes ranging from normospermia to azoospermia, thwarting definite conclusions on their real impact on fertility. Results The amplicon content of partial AZFc deletion products was characterized with novel amplicon-specific sequence markers. Data indicate that partial AZFc deletions are a male infertility risk [odds ratio: 5.6 (95% CI: 1.6–30.1)] and although high diversity of partial deletion products and sequence conversion profiles were recorded, the AZFc marker profiles detected in fertile men were also observed in infertile men. Additionally, the assessment of rearrangement recurrence by Y-lineage analysis indicated that while partial AZFc deletions occurred in highly diverse samples, haplotype diversity was minimal in fertile men sharing identical marker profiles. Conclusion Although partial AZFc deletion products are highly heterogeneous in terms of amplicon content, this plasticity is not sufficient to account for the observed phenotypical variance. The lack of causative association between the deletion of specific gene copies and infertility suggests that AZFc gene content might be part of a multifactorial network, with Y-lineage evolution emerging as a possible phenotype modulator. PMID:17903263

Kin-Driver: a database of driver mutations in protein kinases.

PubMed

Simonetti, Franco L; Tornador, Cristian; Nabau-Moretó, Nuria; Molina-Vila, Miguel A; Marino-Buslje, Cristina

2014-01-01

Somatic mutations in protein kinases (PKs) are frequent driver events in many human tumors, while germ-line mutations are associated with hereditary diseases. Here we present Kin-driver, the first database that compiles driver mutations in PKs with experimental evidence demonstrating their functional role. Kin-driver is a manual expert-curated database that pays special attention to activating mutations (AMs) and can serve as a validation set to develop new generation tools focused on the prediction of gain-of-function driver mutations. It also offers an easy and intuitive environment to facilitate the visualization and analysis of mutations in PKs. Because all mutations are mapped onto a multiple sequence alignment, analogue positions between kinases can be identified and tentative new mutations can be proposed for studying by transferring annotation. Finally, our database can also be of use to clinical and translational laboratories, helping them to identify uncommon AMs that can correlate with response to new antitumor drugs. The website was developed using PHP and JavaScript, which are supported by all major browsers; the database was built using MySQL server. Kin-driver is available at: http://kin-driver.leloir.org.ar/ © The Author(s) 2014. Published by Oxford University Press.

Identifying candidate driver genes by integrative ovarian cancer genomics data

NASA Astrophysics Data System (ADS)

Lu, Xinguo; Lu, Jibo

2017-08-01

Integrative analysis of molecular mechanics underlying cancer can distinguish interactions that cannot be revealed based on one kind of data for the appropriate diagnosis and treatment of cancer patients. Tumor samples exhibit heterogeneity in omics data, such as somatic mutations, Copy Number Variations CNVs), gene expression profiles and so on. In this paper we combined gene co-expression modules and mutation modulators separately in tumor patients to obtain the candidate driver genes for resistant and sensitive tumor from the heterogeneous data. The final list of modulators identified are well known in biological processes associated with ovarian cancer, such as CCL17, CACTIN, CCL16, CCL22, APOB, KDF1, CCL11, HNF1B, LRG1, MED1 and so on, which can help to facilitate the discovery of biomarkers, molecular diagnostics, and drug discovery.

CloVR-ITS: Automated internal transcribed spacer amplicon sequence analysis pipeline for the characterization of fungal microbiota

PubMed Central

2013-01-01

Background Besides the development of comprehensive tools for high-throughput 16S ribosomal RNA amplicon sequence analysis, there exists a growing need for protocols emphasizing alternative phylogenetic markers such as those representing eukaryotic organisms. Results Here we introduce CloVR-ITS, an automated pipeline for comparative analysis of internal transcribed spacer (ITS) pyrosequences amplified from metagenomic DNA isolates and representing fungal species. This pipeline performs a variety of steps similar to those commonly used for 16S rRNA amplicon sequence analysis, including preprocessing for quality, chimera detection, clustering of sequences into operational taxonomic units (OTUs), taxonomic assignment (at class, order, family, genus, and species levels) and statistical analysis of sample groups of interest based on user-provided information. Using ITS amplicon pyrosequencing data from a previous human gastric fluid study, we demonstrate the utility of CloVR-ITS for fungal microbiota analysis and provide runtime and cost examples, including analysis of extremely large datasets on the cloud. We show that the largest fractions of reads from the stomach fluid samples were assigned to Dothideomycetes, Saccharomycetes, Agaricomycetes and Sordariomycetes but that all samples were dominated by sequences that could not be taxonomically classified. Representatives of the Candida genus were identified in all samples, most notably C. quercitrusa, while sequence reads assigned to the Aspergillus genus were only identified in a subset of samples. CloVR-ITS is made available as a pre-installed, automated, and portable software pipeline for cloud-friendly execution as part of the CloVR virtual machine package (http://clovr.org). Conclusion The CloVR-ITS pipeline provides fungal microbiota analysis that can be complementary to bacterial 16S rRNA and total metagenome sequence analysis allowing for more comprehensive studies of environmental and host-associated microbial

Impact of Mutation Type and Amplicon Characteristics on Genetic Diversity Measures Generated Using a High-Resolution Melting Diversity Assay

PubMed Central

Cousins, Matthew M.; Donnell, Deborah; Eshleman, Susan H.

2013-01-01

We adapted high-resolution melting (HRM) technology to measure genetic diversity without sequencing. Diversity is measured as a single numeric HRM score. Herein, we determined the impact of mutation types and amplicon characteristics on HRM diversity scores. Plasmids were generated with single-base changes, insertions, and deletions. Different primer sets were used to vary the position of mutations within amplicons. Plasmids and plasmid mixtures were analyzed to determine the impact of mutation type, position, and concentration on HRM scores. The impact of amplicon length and G/C content on HRM scores was also evaluated. Different mutation types affected HRM scores to varying degrees (1-bp deletion < 1-bp change < 3-bp insertion < 9-bp insertion). The impact of mutations on HRM scores was influenced by amplicon length and the position of the mutation within the amplicon. Mutations were detected at concentrations of 5% to 95%, with the greatest impact at 50%. The G/C content altered melting temperature values of amplicons but had no impact on HRM scores. These data are relevant to the design of assays that measure genetic diversity using HRM technology. PMID:23178437

Exploring the effects of spatial autocorrelation when identifying key drivers of wildlife crop-raiding.

PubMed

Songhurst, Anna; Coulson, Tim

2014-03-01

Few universal trends in spatial patterns of wildlife crop-raiding have been found. Variations in wildlife ecology and movements, and human spatial use have been identified as causes of this apparent unpredictability. However, varying spatial patterns of spatial autocorrelation (SA) in human-wildlife conflict (HWC) data could also contribute. We explicitly explore the effects of SA on wildlife crop-raiding data in order to facilitate the design of future HWC studies. We conducted a comparative survey of raided and nonraided fields to determine key drivers of crop-raiding. Data were subsampled at different spatial scales to select independent raiding data points. The model derived from all data was fitted to subsample data sets. Model parameters from these models were compared to determine the effect of SA. Most methods used to account for SA in data attempt to correct for the change in P-values; yet, by subsampling data at broader spatial scales, we identified changes in regression estimates. We consequently advocate reporting both model parameters across a range of spatial scales to help biological interpretation. Patterns of SA vary spatially in our crop-raiding data. Spatial distribution of fields should therefore be considered when choosing the spatial scale for analyses of HWC studies. Robust key drivers of elephant crop-raiding included raiding history of a field and distance of field to a main elephant pathway. Understanding spatial patterns and determining reliable socio-ecological drivers of wildlife crop-raiding is paramount for designing mitigation and land-use planning strategies to reduce HWC. Spatial patterns of HWC are complex, determined by multiple factors acting at more than one scale; therefore, studies need to be designed with an understanding of the effects of SA. Our methods are accessible to a variety of practitioners to assess the effects of SA, thereby improving the reliability of conservation management actions.

Systematic analysis of mutation distribution in three dimensional protein structures identifies cancer driver genes.

PubMed

Fujimoto, Akihiro; Okada, Yukinori; Boroevich, Keith A; Tsunoda, Tatsuhiko; Taniguchi, Hiroaki; Nakagawa, Hidewaki

2016-05-26

Protein tertiary structure determines molecular function, interaction, and stability of the protein, therefore distribution of mutation in the tertiary structure can facilitate the identification of new driver genes in cancer. To analyze mutation distribution in protein tertiary structures, we applied a novel three dimensional permutation test to the mutation positions. We analyzed somatic mutation datasets of 21 types of cancers obtained from exome sequencing conducted by the TCGA project. Of the 3,622 genes that had ≥3 mutations in the regions with tertiary structure data, 106 genes showed significant skew in mutation distribution. Known tumor suppressors and oncogenes were significantly enriched in these identified cancer gene sets. Physical distances between mutations in known oncogenes were significantly smaller than those of tumor suppressors. Twenty-three genes were detected in multiple cancers. Candidate genes with significant skew of the 3D mutation distribution included kinases (MAPK1, EPHA5, ERBB3, and ERBB4), an apoptosis related gene (APP), an RNA splicing factor (SF1), a miRNA processing factor (DICER1), an E3 ubiquitin ligase (CUL1) and transcription factors (KLF5 and EEF1B2). Our study suggests that systematic analysis of mutation distribution in the tertiary protein structure can help identify cancer driver genes.

Systematic analysis of mutation distribution in three dimensional protein structures identifies cancer driver genes

PubMed Central

Fujimoto, Akihiro; Okada, Yukinori; Boroevich, Keith A.; Tsunoda, Tatsuhiko; Taniguchi, Hiroaki; Nakagawa, Hidewaki

2016-01-01

Protein tertiary structure determines molecular function, interaction, and stability of the protein, therefore distribution of mutation in the tertiary structure can facilitate the identification of new driver genes in cancer. To analyze mutation distribution in protein tertiary structures, we applied a novel three dimensional permutation test to the mutation positions. We analyzed somatic mutation datasets of 21 types of cancers obtained from exome sequencing conducted by the TCGA project. Of the 3,622 genes that had ≥3 mutations in the regions with tertiary structure data, 106 genes showed significant skew in mutation distribution. Known tumor suppressors and oncogenes were significantly enriched in these identified cancer gene sets. Physical distances between mutations in known oncogenes were significantly smaller than those of tumor suppressors. Twenty-three genes were detected in multiple cancers. Candidate genes with significant skew of the 3D mutation distribution included kinases (MAPK1, EPHA5, ERBB3, and ERBB4), an apoptosis related gene (APP), an RNA splicing factor (SF1), a miRNA processing factor (DICER1), an E3 ubiquitin ligase (CUL1) and transcription factors (KLF5 and EEF1B2). Our study suggests that systematic analysis of mutation distribution in the tertiary protein structure can help identify cancer driver genes. PMID:27225414

Drivers Are More Physically Active Than Non-Drivers in Older Adults.

PubMed

Amagasa, Shiho; Fukushima, Noritoshi; Kikuchi, Hiroyuki; Takamiya, Tomoko; Odagiri, Yuko; Oka, Koichiro; Inoue, Shigeru

2018-05-28

Car use has been identified as sedentary behavior, although it may enhance mobility, particularly in the older population. This cross-sectional study aimed to compare the time spent in objectively determined sedentary behavior (SB) and physical activity (PA) between older drivers and non-drivers. Four hundred and fifty Japanese older adults (74.3 ± 2.9 years) who had valid accelerometer data were included. They were asked to respond to a questionnaire and wear an accelerometer (HJA-350IT, Omron Healthcare) on their waist for 7 consecutive days in 2015. To compare activity time between drivers and non-drivers, we calculated estimated means using analysis of covariance, adjusting for sociodemographic, physical, and psychological factors and accelerometer wear time. Compared to non-drivers, drivers engaged in more light-intensity PA (LPA) (drivers: 325.0 vs. non-drivers: 289.0 min/day) and moderate-to-vigorous PA (drivers: 37.5 vs. non-drivers: 30.0 min/day) and less SB (drivers: 493.4 vs. non-drivers: 535.9 min/day) (all p < 0.05). After stratification by age, sex, and residential area, larger effect of driving on PA time was found in older-older adults, in men, and in rural residents. Older drivers were found to be more physically active than non-drivers, suggesting more access to outdoor activities or expanding social network.

A Visual Analytics Framework for Identifying Topic Drivers in Media Events.

PubMed

Lu, Yafeng; Wang, Hong; Landis, Steven; Maciejewski, Ross

2017-09-14

Media data has been the subject of large scale analysis with applications of text mining being used to provide overviews of media themes and information flows. Such information extracted from media articles has also shown its contextual value of being integrated with other data, such as criminal records and stock market pricing. In this work, we explore linking textual media data with curated secondary textual data sources through user-guided semantic lexical matching for identifying relationships and data links. In this manner, critical information can be identified and used to annotate media timelines in order to provide a more detailed overview of events that may be driving media topics and frames. These linked events are further analyzed through an application of causality modeling to model temporal drivers between the data series. Such causal links are then annotated through automatic entity extraction which enables the analyst to explore persons, locations, and organizations that may be pertinent to the media topic of interest. To demonstrate the proposed framework, two media datasets and an armed conflict event dataset are explored.

Single-Step Conversion of Cells to Retrovirus Vector Producers with Herpes Simplex Virus–Epstein-Barr Virus Hybrid Amplicons

PubMed Central

Sena-Esteves, Miguel; Saeki, Yoshinaga; Camp, Sara M.; Chiocca, E. Antonio; Breakefield, Xandra O.

1999-01-01

We report here on the development and characterization of a novel herpes simplex virus type 1 (HSV-1) amplicon-based vector system which takes advantage of the host range and retention properties of HSV–Epstein-Barr virus (EBV) hybrid amplicons to efficiently convert cells to retrovirus vector producer cells after single-step transduction. The retrovirus genes gag-pol and env (GPE) and retroviral vector sequences were modified to minimize sequence overlap and cloned into an HSV-EBV hybrid amplicon. Retrovirus expression cassettes were used to generate the HSV-EBV-retrovirus hybrid vectors, HERE and HERA, which code for the ecotropic and the amphotropic envelopes, respectively. Retrovirus vector sequences encoding lacZ were cloned downstream from the GPE expression unit. Transfection of 293T/17 cells with amplicon plasmids yielded retrovirus titers between 106 and 107 transducing units/ml, while infection of the same cells with amplicon vectors generated maximum titers 1 order of magnitude lower. Retrovirus titers were dependent on the extent of transduction by amplicon vectors for the same cell line, but different cell lines displayed varying capacities to produce retrovirus vectors even at the same transduction efficiencies. Infection of human and dog primary gliomas with this system resulted in the production of retrovirus vectors for more than 1 week and the long-term retention and increase in transgene activity over time in these cell populations. Although the efficiency of this system still has to be determined in vivo, many applications are foreseeable for this approach to gene delivery. PMID:10559361

Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information

PubMed Central

McDonald, Daniel; Gonzalez, Antonio; Navas-Molina, Jose A.; Jiang, Lingjing; Xu, Zhenjiang Zech; Winker, Kevin; Kado, Deborah M.; Orwoll, Eric; Manary, Mark; Mirarab, Siavash

2018-01-01

ABSTRACT Recent algorithmic advances in amplicon-based microbiome studies enable the inference of exact amplicon sequence fragments. These new methods enable the investigation of sub-operational taxonomic units (sOTU) by removing erroneous sequences. However, short (e.g., 150-nucleotide [nt]) DNA sequence fragments do not contain sufficient phylogenetic signal to reproduce a reasonable tree, introducing a barrier in the utilization of critical phylogenetically aware metrics such as Faith’s PD or UniFrac. Although fragment insertion methods do exist, those methods have not been tested for sOTUs from high-throughput amplicon studies in insertions against a broad reference phylogeny. We benchmarked the SATé-enabled phylogenetic placement (SEPP) technique explicitly against 16S V4 sequence fragments and showed that it outperforms the conceptually problematic but often-used practice of reconstructing de novo phylogenies. In addition, we provide a BSD-licensed QIIME2 plugin (https://github.com/biocore/q2-fragment-insertion) for SEPP and integration into the microbial study management platform QIITA. IMPORTANCE The move from OTU-based to sOTU-based analysis, while providing additional resolution, also introduces computational challenges. We demonstrate that one popular method of dealing with sOTUs (building a de novo tree from the short sequences) can provide incorrect results in human gut metagenomic studies and show that phylogenetic placement of the new sequences with SEPP resolves this problem while also yielding other benefits over existing methods. PMID:29719869

Non-coding cancer driver candidates identified with a sample- and position-specific model of the somatic mutation rate

PubMed Central

Juul, Malene; Bertl, Johanna; Guo, Qianyun; Nielsen, Morten Muhlig; Świtnicki, Michał; Hornshøj, Henrik; Madsen, Tobias; Hobolth, Asger; Pedersen, Jakob Skou

2017-01-01

Non-coding mutations may drive cancer development. Statistical detection of non-coding driver regions is challenged by a varying mutation rate and uncertainty of functional impact. Here, we develop a statistically founded non-coding driver-detection method, ncdDetect, which includes sample-specific mutational signatures, long-range mutation rate variation, and position-specific impact measures. Using ncdDetect, we screened non-coding regulatory regions of protein-coding genes across a pan-cancer set of whole-genomes (n = 505), which top-ranked known drivers and identified new candidates. For individual candidates, presence of non-coding mutations associates with altered expression or decreased patient survival across an independent pan-cancer sample set (n = 5454). This includes an antigen-presenting gene (CD1A), where 5’UTR mutations correlate significantly with decreased survival in melanoma. Additionally, mutations in a base-excision-repair gene (SMUG1) correlate with a C-to-T mutational-signature. Overall, we find that a rich model of mutational heterogeneity facilitates non-coding driver identification and integrative analysis points to candidates of potential clinical relevance. DOI: http://dx.doi.org/10.7554/eLife.21778.001 PMID:28362259

High-resolution mapping of the 11q13 amplicon and identification of a gene, TAOS1, that is amplified and overexpressed in oral cancer cells

PubMed Central

Huang, Xin; Gollin, Susanne M.; Raja, Siva; Godfrey, Tony E.

2002-01-01

Amplification of chromosomal band 11q13 is a common event in human cancer. It has been reported in about 45% of head and neck carcinomas and in other cancers including esophageal, breast, liver, lung, and bladder cancer. To understand the mechanism of 11q13 amplification and to identify the potential oncogene(s) driving it, we have fine-mapped the structure of the amplicon in oral squamous cell carcinoma cell lines and localized the proximal and distal breakpoints. A 5-Mb physical map of the region has been prepared from which sequence is available. We quantified copy number of sequence-tagged site markers at 42–550 kb intervals along the length of the amplicon and defined the amplicon core and breakpoints by using TaqMan-based quantitative microsatellite analysis. The core of the amplicon maps to a 1.5-Mb region. The proximal breakpoint localizes to two intervals between sequence-tagged site markers, 550 kb and 160 kb in size, and the distal breakpoint maps to a 250 kb interval. The cyclin D1 gene maps to the amplicon core, as do two new expressed sequence tag clusters. We have analyzed one of these expressed sequence tag clusters and now report that it contains a previously uncharacterized gene, TAOS1 (tumor amplified and overexpressed sequence 1), which is both amplified and overexpressed in oral cancer cells. The data suggest that TAOS1 may be an amplification-dependent candidate oncogene with a role in the development and/or progression of human tumors, including oral squamous cell carcinomas. The approach described here should be useful for characterizing amplified genomic regions in a wide variety of tumors. PMID:12172009

Somatic chromosomal engineering identifies BCAN-NTRK1 as a potent glioma driver and therapeutic target.

PubMed

Cook, Peter J; Thomas, Rozario; Kannan, Ram; de Leon, Esther Sanchez; Drilon, Alexander; Rosenblum, Marc K; Scaltriti, Maurizio; Benezra, Robert; Ventura, Andrea

2017-07-11

The widespread application of high-throughput sequencing methods is resulting in the identification of a rapidly growing number of novel gene fusions caused by tumour-specific chromosomal rearrangements, whose oncogenic potential remains unknown. Here we describe a strategy that builds upon recent advances in genome editing and combines ex vivo and in vivo chromosomal engineering to rapidly and effectively interrogate the oncogenic potential of genomic rearrangements identified in human brain cancers. We show that one such rearrangement, an microdeletion resulting in a fusion between Brevican (BCAN) and Neurotrophic Receptor Tyrosine Kinase 1 (NTRK1), is a potent oncogenic driver of high-grade gliomas and confers sensitivity to the experimental TRK inhibitor entrectinib. This work demonstrates that BCAN-NTRK1 is a bona fide human glioma driver and describes a general strategy to define the oncogenic potential of novel glioma-associated genomic rearrangements and to generate accurate preclinical models of this lethal human cancer.

Changing drivers' minds: the evaluation of an advanced driver coaching system.

PubMed

Stanton, N A; Walker, G H; Young, M S; Kazi, T; Salmon, P M

2007-08-01

This paper reports on the study of an advanced driver coaching system. The study distinguishes between different types of post-licensure programmes in order to explore a system based on a model of identifying and responding to hazards, called 'information, position, speed, gear and acceleration' (IPSGA). Previous literature has been sceptical about the benefits of advanced driver education; thus, the current study was designed to control for the effects of coaching drivers in the 'IPSGA' system (the treatment group) against the effects of being accompanied (control group 1), as well as the mere effects of time (control group 2). Measures were taken before the driver coaching began (as a baseline measure) and again after 8 weeks (to see if any changes had occurred). These measures included driver knowledge via a post-drive interview, observations of driving skill and driver attitude using a locus of control scale. The results suggest that advanced driver coaching using the IPSGA system had a beneficial effect on all of these measures. Drivers in the coaching condition improved their situation awareness, driving skills and reduced attributions of external locus of control. The study lends support to the case for one-to-one individualized driver coaching using a systematic model of driving.

Unraveling Core Functional Microbiota in Traditional Solid-State Fermentation by High-Throughput Amplicons and Metatranscriptomics Sequencing

PubMed Central

Song, Zhewei; Du, Hai; Zhang, Yan; Xu, Yan

2017-01-01

Fermentation microbiota is specific microorganisms that generate different types of metabolites in many productions. In traditional solid-state fermentation, the structural composition and functional capacity of the core microbiota determine the quality and quantity of products. As a typical example of food fermentation, Chinese Maotai-flavor liquor production involves a complex of various microorganisms and a wide variety of metabolites. However, the microbial succession and functional shift of the core microbiota in this traditional food fermentation remain unclear. Here, high-throughput amplicons (16S rRNA gene amplicon sequencing and internal transcribed space amplicon sequencing) and metatranscriptomics sequencing technologies were combined to reveal the structure and function of the core microbiota in Chinese soy sauce aroma type liquor production. In addition, ultra-performance liquid chromatography and headspace-solid phase microextraction-gas chromatography-mass spectrometry were employed to provide qualitative and quantitative analysis of the major flavor metabolites. A total of 10 fungal and 11 bacterial genera were identified as the core microbiota. In addition, metatranscriptomic analysis revealed pyruvate metabolism in yeasts (genera Pichia, Schizosaccharomyces, Saccharomyces, and Zygosaccharomyces) and lactic acid bacteria (genus Lactobacillus) classified into two stages in the production of flavor components. Stage I involved high-level alcohol (ethanol) production, with the genus Schizosaccharomyces serving as the core functional microorganism. Stage II involved high-level acid (lactic acid and acetic acid) production, with the genus Lactobacillus serving as the core functional microorganism. The functional shift from the genus Schizosaccharomyces to the genus Lactobacillus drives flavor component conversion from alcohol (ethanol) to acid (lactic acid and acetic acid) in Chinese Maotai-flavor liquor production. Our findings provide insight into the

Unraveling Core Functional Microbiota in Traditional Solid-State Fermentation by High-Throughput Amplicons and Metatranscriptomics Sequencing.

PubMed

Song, Zhewei; Du, Hai; Zhang, Yan; Xu, Yan

2017-01-01

Fermentation microbiota is specific microorganisms that generate different types of metabolites in many productions. In traditional solid-state fermentation, the structural composition and functional capacity of the core microbiota determine the quality and quantity of products. As a typical example of food fermentation, Chinese Maotai-flavor liquor production involves a complex of various microorganisms and a wide variety of metabolites. However, the microbial succession and functional shift of the core microbiota in this traditional food fermentation remain unclear. Here, high-throughput amplicons (16S rRNA gene amplicon sequencing and internal transcribed space amplicon sequencing) and metatranscriptomics sequencing technologies were combined to reveal the structure and function of the core microbiota in Chinese soy sauce aroma type liquor production. In addition, ultra-performance liquid chromatography and headspace-solid phase microextraction-gas chromatography-mass spectrometry were employed to provide qualitative and quantitative analysis of the major flavor metabolites. A total of 10 fungal and 11 bacterial genera were identified as the core microbiota. In addition, metatranscriptomic analysis revealed pyruvate metabolism in yeasts (genera Pichia, Schizosaccharomyces, Saccharomyces , and Zygosaccharomyces ) and lactic acid bacteria (genus Lactobacillus ) classified into two stages in the production of flavor components. Stage I involved high-level alcohol (ethanol) production, with the genus Schizosaccharomyces serving as the core functional microorganism. Stage II involved high-level acid (lactic acid and acetic acid) production, with the genus Lactobacillus serving as the core functional microorganism. The functional shift from the genus Schizosaccharomyces to the genus Lactobacillus drives flavor component conversion from alcohol (ethanol) to acid (lactic acid and acetic acid) in Chinese Maotai-flavor liquor production. Our findings provide insight into

Genomic characterization of biliary tract cancers identifies driver genes and predisposing mutations.

PubMed

Wardell, Christopher P; Fujita, Masashi; Yamada, Toru; Simbolo, Michele; Fassan, Matteo; Karlic, Rosa; Polak, Paz; Kim, Jaegil; Hatanaka, Yutaka; Maejima, Kazuhiro; Lawlor, Rita T; Nakanishi, Yoshitsugu; Mitsuhashi, Tomoko; Fujimoto, Akihiro; Furuta, Mayuko; Ruzzenente, Andrea; Conci, Simone; Oosawa, Ayako; Sasaki-Oku, Aya; Nakano, Kaoru; Tanaka, Hiroko; Yamamoto, Yujiro; Michiaki, Kubo; Kawakami, Yoshiiku; Aikata, Hiroshi; Ueno, Masaki; Hayami, Shinya; Gotoh, Kunihito; Ariizumi, Shun-Ichi; Yamamoto, Masakazu; Yamaue, Hiroki; Chayama, Kazuaki; Miyano, Satoru; Getz, Gad; Scarpa, Aldo; Hirano, Satoshi; Nakamura, Toru; Nakagawa, Hidewaki

2018-05-01

Biliary tract cancers (BTCs) are clinically and pathologically heterogeneous and respond poorly to treatment. Genomic profiling can offer a clearer understanding of their carcinogenesis, classification and treatment strategy. We performed large-scale genome sequencing analyses on BTCs to investigate their somatic and germline driver events and characterize their genomic landscape. We analyzed 412 BTC samples from Japanese and Italian populations, 107 by whole-exome sequencing (WES), 39 by whole-genome sequencing (WGS), and a further 266 samples by targeted sequencing. The subtypes were 136 intrahepatic cholangiocarcinomas (ICCs), 101 distal cholangiocarcinomas (DCCs), 109 peri-hilar type cholangiocarcinomas (PHCs), and 66 gallbladder or cystic duct cancers (GBCs/CDCs). We identified somatic alterations and searched for driver genes in BTCs, finding pathogenic germline variants of cancer-predisposing genes. We predicted cell-of-origin for BTCs by combining somatic mutation patterns and epigenetic features. We identified 32 significantly and commonly mutated genes including TP53, KRAS, SMAD4, NF1, ARID1A, PBRM1, and ATR, some of which negatively affected patient prognosis. A novel deletion of MUC17 at 7q22.1 affected patient prognosis. Cell-of-origin predictions using WGS and epigenetic features suggest hepatocyte-origin of hepatitis-related ICCs. Deleterious germline mutations of cancer-predisposing genes such as BRCA1, BRCA2, RAD51D, MLH1, or MSH2 were detected in 11% (16/146) of BTC patients. BTCs have distinct genetic features including somatic events and germline predisposition. These findings could be useful to establish treatment and diagnostic strategies for BTCs based on genetic information. We here analyzed genomic features of 412 BTC samples from Japanese and Italian populations. A total of 32 significantly and commonly mutated genes were identified, some of which negatively affected patient prognosis, including a novel deletion of MUC17 at 7q22.1. Cell

Driving fatigue in professional drivers: a survey of truck and taxi drivers.

PubMed

Meng, Fanxing; Li, Shuling; Cao, Lingzhi; Li, Musen; Peng, Qijia; Wang, Chunhui; Zhang, Wei

2015-01-01

Fatigue among truck drivers has been studied extensively; however, less is known regarding the fatigue experience of taxi drivers in heavily populated metropolitan areas. This study aimed to compare the differences and similarities between truck and taxi driver fatigue to provide implications for the fatigue management and education of professional drivers. A sample of 274 truck drivers and 286 taxi drivers in Beijing was surveyed via a questionnaire, which included items regarding work characteristics, fatigue experience, accident information, attitude toward fatigue, and methods of counteracting fatigue. Driver fatigue was prevalent among professional drivers, and it was even more serious for taxi drivers. Taxi drivers reported more frequent fatigue experiences and were involved in more accidents. Among the contributing factors to fatigue, prolonged driving time was the most important factor identified by both driver groups. Importantly, the reason for the engagement in prolonged driving was neither due to the lack of awareness concerning the serious outcome of fatigue driving nor because of their poor detection of fatigue. The most probable reason was the optimism bias, as a result of which these professional drivers thought that fatigue was more serious for other drivers than for themselves, and they thought that they were effective in counteracting the effect of fatigue on their driving performance. Moreover, truck drivers tended to employ methods that require stopping to counteract fatigue, whereas taxi drivers preferred methods that were simultaneous with driving. Although both driver groups considered taking a nap as one of the most effective means to address fatigue, this method was not commonly used. Interestingly, these drivers were aware that the methods they frequently used were not the most effective means to counteract fatigue. This study provides knowledge on truck and taxi drivers' characteristics in fatigue experience, fatigue attitude, and

Identifying actionable variants using next generation sequencing in patients with a historical diagnosis of undifferentiated pleomorphic sarcoma.

PubMed

Lewin, Jeremy; Garg, Swati; Lau, Beatrice Y; Dickson, Brendan C; Traub, Frank; Gokgoz, Nalan; Griffin, Anthony M; Ferguson, Peter C; Andrulis, Irene L; Sim, Hao-Wen; Kamel-Reid, Suzanne; Stockley, Tracy L; Siu, Lillian L; Wunder, Jay S; Razak, Albiruni R A

2018-01-01

There are limited data regarding the molecular characterization of undifferentiated pleomorphic sarcomas (UPS; formerly malignant fibrous histiocytoma). This study aimed to investigate the utility of next generation sequencing (NGS) in UPS to identify subsets of patients who harbour actionable mutations. Patients diagnosed with UPS underwent pathological re-evaluation by a pathologist specializing in sarcoma. Tumor DNA was isolated from archived fresh frozen tissue samples and genotyped using NGS with the Illumina MiSeq TruSeq Amplicon Cancer Panel (48 genes, 212 amplicons). In total, 95 patients initially classified with UPS were identified. Following pathology re-review the histological subtypes were reclassified to include: Myxofibrosarcoma (MFS, N = 44); UPS(N = 18); and Others (N = 27; including undifferentiated spindle cell sarcoma (N = 15) and dedifferentiated liposarcoma (N = 6)). Seven cases were excluded from further analysis for other reasons. Baseline demographics of the finalized cohort (N = 88) showed a median age of 66 years (32-95), primarily with stage I-III disease (92%) and high-grade (86%) lesions. Somatic mutations were identified in 31 cases (35%)(Total mutations = 36: solitary mutation(n = 27); two mutations( =n = 3); three mutations(n = 1)). The most commonly identified mutations were in TP53 (n = 24), ATM (n = 3) and PIK3CA (n = 2). Three of 43 patients with MFS and one of 18 patients with UPS had clinically relevant mutations, mainly related to biomarkers of prediction of response; however few had targetable driver mutations. Somatic mutation status did not influence disease free or overall survival. Based on the small number of clinically relevant mutations, these data do not support the routine use of targeted NGS panels outside of research protocols in UPS. © 2017 UICC.

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

PubMed

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.

SPIDER: A Framework for Understanding Driver Distraction.

PubMed

Strayer, David L; Fisher, Donald L

2016-02-01

The objective was to identify key cognitive processes that are impaired when drivers divert attention from driving. Driver distraction is increasingly recognized as a significant source of injuries and fatalities on the roadway. A "SPIDER" model is developed that identifies key cognitive processes that are impaired when drivers divert attention from driving. SPIDER is an acronym standing for scanning, predicting, identifying, decision making, and executing a response. When drivers engage in secondary activities unrelated to the task of driving, SPIDER-related processes are impaired, situation awareness is degraded, and the ability to safely operate a motor vehicle may be compromised. The pattern of interference helps to illuminate the sources of driver distraction and may help guide the integration of new technology into the automobile. © 2015, Human Factors and Ergonomics Society.

Mapping and characterization of the amplicon near APOA2 in 1q23 in human sarcomas by FISH and array CGH

PubMed Central

Kresse, Stine H; Berner, Jeanne-Marie; Meza-Zepeda, Leonardo A; Gregory, Simon G; Kuo, Wen-Lin; Gray, Joe W; Forus, Anne; Myklebost, Ola

2005-01-01

Background Amplification of the q21-q23 region on chromosome 1 is frequently found in sarcomas and a variety of other solid tumours. Previous analyses of sarcomas have indicated the presence of at least two separate amplicons within this region, one located in 1q21 and one located near the apolipoprotein A-II (APOA2) gene in 1q23. In this study we have mapped and characterized the amplicon in 1q23 in more detail. Results We have used fluorescence in situ hybridisation (FISH) and microarray-based comparative genomic hybridisation (array CGH) to map and define the borders of the amplicon in 10 sarcomas. A subregion of approximately 800 kb was identified as the core of the amplicon. The amplification patterns of nine possible candidate target genes located to this subregion were determined by Southern blot analysis. The genes activating transcription factor 6 (ATF6) and dual specificity phosphatase 12 (DUSP12) showed the highest level of amplification, and they were also shown to be over-expressed by quantitative real-time reverse transcription PCR (RT-PCR). In general, the level of expression reflected the level of amplification in the different tumours. DUSP12 was expressed significantly higher than ATF6 in a subset of the tumours. In addition, two genes known to be transcriptionally activated by ATF6, glucose-regulated protein 78 kDa and -94 kDa (GRP78 and GRP94), were shown to be over-expressed in the tumours that showed over-expression of ATF6. Conclusion ATF6 and DUSP12 seem to be the most likely candidate target genes for the 1q23 amplification in sarcomas. Both genes have possible roles in promoting cell growth, which makes them interesting candidate targets. PMID:16274472

Mapping and characterization of the amplicon near APOA2 in 1q23 in human sarcomas by FISH and array CGH.

PubMed

Kresse, Stine H; Berner, Jeanne-Marie; Meza-Zepeda, Leonardo A; Gregory, Simon G; Kuo, Wen-Lin; Gray, Joe W; Forus, Anne; Myklebost, Ola

2005-11-07

Amplification of the q21-q23 region on chromosome 1 is frequently found in sarcomas and a variety of other solid tumours. Previous analyses of sarcomas have indicated the presence of at least two separate amplicons within this region, one located in 1q21 and one located near the apolipoprotein A-II (APOA2) gene in 1q23. In this study we have mapped and characterized the amplicon in 1q23 in more detail. We have used fluorescence in situ hybridisation (FISH) and microarray-based comparative genomic hybridisation (array CGH) to map and define the borders of the amplicon in 10 sarcomas. A subregion of approximately 800 kb was identified as the core of the amplicon. The amplification patterns of nine possible candidate target genes located to this subregion were determined by Southern blot analysis. The genes activating transcription factor 6 (ATF6) and dual specificity phosphatase 12 (DUSP12) showed the highest level of amplification, and they were also shown to be over-expressed by quantitative real-time reverse transcription PCR (RT-PCR). In general, the level of expression reflected the level of amplification in the different tumours. DUSP12 was expressed significantly higher than ATF6 in a subset of the tumours. In addition, two genes known to be transcriptionally activated by ATF6, glucose-regulated protein 78 kDa and -94 kDa (GRP78 and GRP94), were shown to be over-expressed in the tumours that showed over-expression of ATF6. ATF6 and DUSP12 seem to be the most likely candidate target genes for the 1q23 amplification in sarcomas. Both genes have possible roles in promoting cell growth, which makes them interesting candidate targets.

Comprehensive Characterization of Cancer Driver Genes and Mutations.

PubMed

Bailey, Matthew H; Tokheim, Collin; Porta-Pardo, Eduard; Sengupta, Sohini; Bertrand, Denis; Weerasinghe, Amila; Colaprico, Antonio; Wendl, Michael C; Kim, Jaegil; Reardon, Brendan; Ng, Patrick Kwok-Shing; Jeong, Kang Jin; Cao, Song; Wang, Zixing; Gao, Jianjiong; Gao, Qingsong; Wang, Fang; Liu, Eric Minwei; Mularoni, Loris; Rubio-Perez, Carlota; Nagarajan, Niranjan; Cortés-Ciriano, Isidro; Zhou, Daniel Cui; Liang, Wen-Wei; Hess, Julian M; Yellapantula, Venkata D; Tamborero, David; Gonzalez-Perez, Abel; Suphavilai, Chayaporn; Ko, Jia Yu; Khurana, Ekta; Park, Peter J; Van Allen, Eliezer M; Liang, Han; Lawrence, Michael S; Godzik, Adam; Lopez-Bigas, Nuria; Stuart, Josh; Wheeler, David; Getz, Gad; Chen, Ken; Lazar, Alexander J; Mills, Gordon B; Karchin, Rachel; Ding, Li

2018-04-05

Identifying molecular cancer drivers is critical for precision oncology. Multiple advanced algorithms to identify drivers now exist, but systematic attempts to combine and optimize them on large datasets are few. We report a PanCancer and PanSoftware analysis spanning 9,423 tumor exomes (comprising all 33 of The Cancer Genome Atlas projects) and using 26 computational tools to catalog driver genes and mutations. We identify 299 driver genes with implications regarding their anatomical sites and cancer/cell types. Sequence- and structure-based analyses identified >3,400 putative missense driver mutations supported by multiple lines of evidence. Experimental validation confirmed 60%-85% of predicted mutations as likely drivers. We found that >300 MSI tumors are associated with high PD-1/PD-L1, and 57% of tumors analyzed harbor putative clinically actionable events. Our study represents the most comprehensive discovery of cancer genes and mutations to date and will serve as a blueprint for future biological and clinical endeavors. Published by Elsevier Inc.

High-throughput amplicon sequencing and stream benthic bacteria: identifying the best taxonomic level for multiple-stressor research

PubMed Central

Salis, R. K.; Bruder, A.; Piggott, J. J.; Summerfield, T. C.; Matthaei, C. D.

2017-01-01

Disentangling the individual and interactive effects of multiple stressors on microbial communities is a key challenge to our understanding and management of ecosystems. Advances in molecular techniques allow studying microbial communities in situ and with high taxonomic resolution. However, the taxonomic level which provides the best trade-off between our ability to detect multiple-stressor effects versus the goal of studying entire communities remains unknown. We used outdoor mesocosms simulating small streams to investigate the effects of four agricultural stressors (nutrient enrichment, the nitrification inhibitor dicyandiamide (DCD), fine sediment and flow velocity reduction) on stream bacteria (phyla, orders, genera, and species represented by Operational Taxonomic Units with 97% sequence similarity). Community composition was assessed using amplicon sequencing (16S rRNA gene, V3-V4 region). DCD was the most pervasive stressor, affecting evenness and most abundant taxa, followed by sediment and flow velocity. Stressor pervasiveness was similar across taxonomic levels and lower levels did not perform better in detecting stressor effects. Community coverage decreased from 96% of all sequences for abundant phyla to 28% for species. Order-level responses were generally representative of responses of corresponding genera and species, suggesting that this level may represent the best compromise between stressor sensitivity and coverage of bacterial communities. PMID:28327636

Induction of humoral responses to BHV-1 glycoprotein D expressed by HSV-1 amplicon vectors

PubMed Central

Blanc, Andrea Maria; Berois, Mabel Beatriz; Tomé, Lorena Magalí; Epstein, Alberto L.

2012-01-01

Herpes simplex virus type-1 (HSV-1) amplicon vectors are versatile and useful tools for transferring genes into cells that are capable of stimulating a specific immune response to their expressed antigens. In this work, two HSV-1-derived amplicon vectors were generated. One of these expressed the full-length glycoprotein D (gD) of bovine herpesvirus 1 while the second expressed the truncated form of gD (gDtr) which lacked the trans-membrane region. After evaluating gD expression in the infected cells, the ability of both vectors to induce a specific gD immune response was tested in BALB/c mice that were intramuscularly immunized. Specific serum antibody responses were detected in mice inoculated with both vectors, and the response against truncated gD was higher than the response against full-length gD. These results reinforce previous findings that HSV-1 amplicon vectors can potentially deliver antigens to animals and highlight the prospective use of these vectors for treating infectious bovine rhinotracheitis disease. PMID:22437537

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

PubMed

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. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Metatranscriptomics and Amplicon Sequencing Reveal Mutualisms in Seagrass Microbiomes

PubMed Central

Crump, Byron C.; Wojahn, John M.; Tomas, Fiona; Mueller, Ryan S.

2018-01-01

Terrestrial plants benefit from many well-understood mutualistic relationships with root- and leaf-associated microbiomes, but relatively little is known about these relationships for seagrass and other aquatic plants. We used 16S rRNA gene amplicon sequencing and metatranscriptomics to assess potential mutualisms between microorganisms and the seagrasses Zostera marina and Zostera japonica collected from mixed beds in Netarts Bay, OR, United States. The phylogenetic composition of leaf-, root-, and water column-associated bacterial communities were strikingly different, but these communities were not significantly different between plant species. Many taxa present on leaves were related to organisms capable of consuming the common plant metabolic waste product methanol, and of producing agarases, which can limit the growth of epiphytic algae. Taxa present on roots were related to organisms capable of oxidizing toxic sulfur compounds and of fixing nitrogen. Metatranscriptomic sequencing identified expression of genes involved in all of these microbial metabolic processes at levels greater than typical water column bacterioplankton, and also identified expression of genes involved in denitrification and in bacterial synthesis of the plant growth hormone indole-3-acetate. These results provide the first evidence using metatranscriptomics that seagrass microbiomes carry out a broad range of functions that may benefit their hosts, and imply that microbe–plant mutualisms support the health and growth of aquatic plants. PMID:29599758

A universal procedure for primer labelling of amplicons.

PubMed Central

Neilan, B A; Wilton, A N; Jacobs, D

1997-01-01

Detection and visualisation of nucleic acids is integral to genome analyses. Exponential amplification procedures have provided the means for the manipulation of nucleic acid sequences, which were otherwise inaccessible. We describe the development and application of a universal method for the labelling of any PCR product using a single end-labelled primer. Amplification was performed in a single reaction with the resulting amplicon labelled to a high specific activity. The method was adapted to a wide range of PCRs and significantly reduced the expense of such analyses. PMID:9207046

A scenario elicitation methodology to identify the drivers of electricity infrastructure cost in South America

NASA Astrophysics Data System (ADS)

Moksnes, Nandi; Taliotis, Constantinos; Broad, Oliver; de Moura, Gustavo; Howells, Mark

2017-04-01

Developing a set of scenarios to assess a proposed policy or future development pathways requires a certain level of information, as well as establishing the socio-economic context. As the future is difficult to predict, great care in defining the selected scenarios is needed. Even so it can be difficult to assess if the selected scenario is covering the possible solution space. Instead, this paper's methodology develops a large set of scenarios (324) in OSeMOSYS using the SAMBA 2.0 (South America Model Base) model to assess long-term electricity supply scenarios and applies a scenario-discovery statistical data mining algorithm, Patient Rule Induction Method (PRIM). By creating a multidimensional space, regions related to high and low cost can be identified as well as their key driver. The six key drivers are defined a priori in three (high, medium, low) or two levers (high, low): 1) Demand projected from GDP, population, urbanization and transport, 2) Fossil fuel price, 3) Climate change impact on hydropower, 4) Renewable technology learning rate, 5) Discount rate, 6) CO2 emission targets.

Identifying candidate drivers of drug response in heterogeneous cancer by mining high throughput genomics data.

PubMed

Nabavi, Sheida

2016-08-15

With advances in technologies, huge amounts of multiple types of high-throughput genomics data are available. These data have tremendous potential to identify new and clinically valuable biomarkers to guide the diagnosis, assessment of prognosis, and treatment of complex diseases, such as cancer. Integrating, analyzing, and interpreting big and noisy genomics data to obtain biologically meaningful results, however, remains highly challenging. Mining genomics datasets by utilizing advanced computational methods can help to address these issues. To facilitate the identification of a short list of biologically meaningful genes as candidate drivers of anti-cancer drug resistance from an enormous amount of heterogeneous data, we employed statistical machine-learning techniques and integrated genomics datasets. We developed a computational method that integrates gene expression, somatic mutation, and copy number aberration data of sensitive and resistant tumors. In this method, an integrative method based on module network analysis is applied to identify potential driver genes. This is followed by cross-validation and a comparison of the results of sensitive and resistance groups to obtain the final list of candidate biomarkers. We applied this method to the ovarian cancer data from the cancer genome atlas. The final result contains biologically relevant genes, such as COL11A1, which has been reported as a cis-platinum resistant biomarker for epithelial ovarian carcinoma in several recent studies. The described method yields a short list of aberrant genes that also control the expression of their co-regulated genes. The results suggest that the unbiased data driven computational method can identify biologically relevant candidate biomarkers. It can be utilized in a wide range of applications that compare two conditions with highly heterogeneous datasets.

Herpes simplex virus type 1-derived recombinant and amplicon vectors.

PubMed

Fraefel, Cornel; Marconi, Peggy; Epstein, Alberto L

2011-01-01

Herpes simplex virus type 1 (HSV-1) is a human pathogen whose lifestyle is based on a long-term dual interaction with the infected host, being able to establish both lytic and latent infections. The virus genome is a 153 kbp double-stranded DNA molecule encoding more than 80 genes. The interest of HSV-1 as gene transfer vector stems from its ability to infect many different cell types, both quiescent and proliferating cells, the very high packaging capacity of the virus capsid, the outstanding neurotropic adaptations that this virus has evolved, and the fact that it never integrates into the cellular chromosomes, thus avoiding the risk of insertional mutagenesis. Two types of vectors can be derived from HSV-1, recombinant vectors and amplicon vectors, and different methodologies have been developed to prepare large stocks of each type of vector. This chapter summarizes (1) the two approaches most commonly used to prepare recombinant vectors through homologous recombination, either in eukaryotic cells or in bacteria, and (2) the two methodologies currently used to generate helper-free amplicon vectors, either using a bacterial artificial chromosome (BAC)-based approach or a Cre/loxP site-specific recombination strategy.

Targeted RNA-Sequencing with Competitive Multiplex-PCR Amplicon Libraries

PubMed Central

Blomquist, Thomas M.; Crawford, Erin L.; Lovett, Jennie L.; Yeo, Jiyoun; Stanoszek, Lauren M.; Levin, Albert; Li, Jia; Lu, Mei; Shi, Leming; Muldrew, Kenneth; Willey, James C.

2013-01-01

Whole transcriptome RNA-sequencing is a powerful tool, but is costly and yields complex data sets that limit its utility in molecular diagnostic testing. A targeted quantitative RNA-sequencing method that is reproducible and reduces the number of sequencing reads required to measure transcripts over the full range of expression would be better suited to diagnostic testing. Toward this goal, we developed a competitive multiplex PCR-based amplicon sequencing library preparation method that a) targets only the sequences of interest and b) controls for inter-target variation in PCR amplification during library preparation by measuring each transcript native template relative to a known number of synthetic competitive template internal standard copies. To determine the utility of this method, we intentionally selected PCR conditions that would cause transcript amplification products (amplicons) to converge toward equimolar concentrations (normalization) during library preparation. We then tested whether this approach would enable accurate and reproducible quantification of each transcript across multiple library preparations, and at the same time reduce (through normalization) total sequencing reads required for quantification of transcript targets across a large range of expression. We demonstrate excellent reproducibility (R2 = 0.997) with 97% accuracy to detect 2-fold change using External RNA Controls Consortium (ERCC) reference materials; high inter-day, inter-site and inter-library concordance (R2 = 0.97–0.99) using FDA Sequencing Quality Control (SEQC) reference materials; and cross-platform concordance with both TaqMan qPCR (R2 = 0.96) and whole transcriptome RNA-sequencing following “traditional” library preparation using Illumina NGS kits (R2 = 0.94). Using this method, sequencing reads required to accurately quantify more than 100 targeted transcripts expressed over a 107-fold range was reduced more than 10,000-fold, from 2.3×109 to 1

m6A-Driver: Identifying Context-Specific mRNA m6A Methylation-Driven Gene Interaction Networks

PubMed Central

Zhang, Song-Yao; Zhang, Shao-Wu; Liu, Lian; Huang, Yufei

2016-01-01

As the most prevalent mammalian mRNA epigenetic modification, N6-methyladenosine (m6A) has been shown to possess important post-transcriptional regulatory functions. However, the regulatory mechanisms and functional circuits of m6A are still largely elusive. To help unveil the regulatory circuitry mediated by mRNA m6A methylation, we develop here m6A-Driver, an algorithm for predicting m6A-driven genes and associated networks, whose functional interactions are likely to be actively modulated by m6A methylation under a specific condition. Specifically, m6A-Driver integrates the PPI network and the predicted differential m6A methylation sites from methylated RNA immunoprecipitation sequencing (MeRIP-Seq) data using a Random Walk with Restart (RWR) algorithm and then builds a consensus m6A-driven network of m6A-driven genes. To evaluate the performance, we applied m6A-Driver to build the context-specific m6A-driven networks for 4 known m6A (de)methylases, i.e., FTO, METTL3, METTL14 and WTAP. Our results suggest that m6A-Driver can robustly and efficiently identify m6A-driven genes that are functionally more enriched and associated with higher degree of differential expression than differential m6A methylated genes. Pathway analysis of the constructed context-specific m6A-driven gene networks further revealed the regulatory circuitry underlying the dynamic interplays between the methyltransferases and demethylase at the epitranscriptomic layer of gene regulation. PMID:28027310

Analysis and Visualization Tool for Targeted Amplicon Bisulfite Sequencing on Ion Torrent Sequencers

PubMed Central

Pabinger, Stephan; Ernst, Karina; Pulverer, Walter; Kallmeyer, Rainer; Valdes, Ana M.; Metrustry, Sarah; Katic, Denis; Nuzzo, Angelo; Kriegner, Albert; Vierlinger, Klemens; Weinhaeusel, Andreas

2016-01-01

Targeted sequencing of PCR amplicons generated from bisulfite deaminated DNA is a flexible, cost-effective way to study methylation of a sample at single CpG resolution and perform subsequent multi-target, multi-sample comparisons. Currently, no platform specific protocol, support, or analysis solution is provided to perform targeted bisulfite sequencing on a Personal Genome Machine (PGM). Here, we present a novel tool, called TABSAT, for analyzing targeted bisulfite sequencing data generated on Ion Torrent sequencers. The workflow starts with raw sequencing data, performs quality assessment, and uses a tailored version of Bismark to map the reads to a reference genome. The pipeline visualizes results as lollipop plots and is able to deduce specific methylation-patterns present in a sample. The obtained profiles are then summarized and compared between samples. In order to assess the performance of the targeted bisulfite sequencing workflow, 48 samples were used to generate 53 different Bisulfite-Sequencing PCR amplicons from each sample, resulting in 2,544 amplicon targets. We obtained a mean coverage of 282X using 1,196,822 aligned reads. Next, we compared the sequencing results of these targets to the methylation level of the corresponding sites on an Illumina 450k methylation chip. The calculated average Pearson correlation coefficient of 0.91 confirms the sequencing results with one of the industry-leading CpG methylation platforms and shows that targeted amplicon bisulfite sequencing provides an accurate and cost-efficient method for DNA methylation studies, e.g., to provide platform-independent confirmation of Illumina Infinium 450k methylation data. TABSAT offers a novel way to analyze data generated by Ion Torrent instruments and can also be used with data from the Illumina MiSeq platform. It can be easily accessed via the Platomics platform, which offers a web-based graphical user interface along with sample and parameter storage. TABSAT is freely

pyAmpli: an amplicon-based variant filter pipeline for targeted resequencing data.

PubMed

Beyens, Matthias; Boeckx, Nele; Van Camp, Guy; Op de Beeck, Ken; Vandeweyer, Geert

2017-12-14

Haloplex targeted resequencing is a popular method to analyze both germline and somatic variants in gene panels. However, involved wet-lab procedures may introduce false positives that need to be considered in subsequent data-analysis. No variant filtering rationale addressing amplicon enrichment related systematic errors, in the form of an all-in-one package, exists to our knowledge. We present pyAmpli, a platform independent parallelized Python package that implements an amplicon-based germline and somatic variant filtering strategy for Haloplex data. pyAmpli can filter variants for systematic errors by user pre-defined criteria. We show that pyAmpli significantly increases specificity, without reducing sensitivity, essential for reporting true positive clinical relevant mutations in gene panel data. pyAmpli is an easy-to-use software tool which increases the true positive variant call rate in targeted resequencing data. It specifically reduces errors related to PCR-based enrichment of targeted regions.

Towards setting credible speed limits: Identifying factors that affect driver compliance on urban roads.

PubMed

Gargoum, Suliman A; El-Basyouny, Karim; Kim, Amy

2016-10-01

Road geometry, vehicle characteristics, and weather conditions are all factors that impact a driver's perception of a safe or credible speed and, consequently, the driver's decision on whether or not to comply with the posted speed limit. In fact, the role a road's environment plays in a driver's perception of a credible speed limit is a topic that has attracted the interest of many researchers in recent years. Despite that, not many studies have considered using empirical data to investigate what features of the road environment influence a driver's compliance choice. This paper aims to address this matter by exploring the relationships between features of the road surroundings (geometric, temporal factors, and weather conditions) and driver compliance with speed limits. The paper uses data from almost 600 different urban roads in the city of Edmonton, at which over 35 million vehicle spot speeds were collected. Compliance was represented using a categorical ordered response variable, and mixed-effects-logistic-regression models were fitted. Two different models were built, one for arterials and another for collector roads. In general, the findings show that the more restricted drivers become, particularly on arterials, the more likely drivers are to comply with speed limits; potential restrictions include on-street parking and the absence of lateral shoulders. Furthermore, higher traffic activity during peak hours, and presumably on shoulder weekdays, both increase the likelihood of compliance on arterials. Similarly, posted speed limits and traffic volume are both positively correlated with compliance on both arterial and collector roads. The findings of this research provide evidence of the existence of an empirical relationship between road features and compliance, highlighting the importance of setting credible speed limits on roads and the possibility of achieving higher compliance rates through modifications to the road environment. Copyright © 2016

Identifying ecological and fishing drivers of bycatch in a U.S. groundfish fishery.

PubMed

Jannot, Jason E; Holland, Daniel S

2013-10-01

Fisheries bycatch is driven by both ecological (e.g., area, season) and social (e.g., fisher behavior) factors that are often difficult to disentangle. We demonstrate a method for comparing fishery-dependent bycatch to fishery-independent catch to delineate the influence of ecological and social factors on bycatch and provide insights for bycatch management. We used data from commercial fishing vessels in the U.S. west coast trawl groundfish fishery (fishery-dependent data collected by fisheries observers) and scientific data from the U.S. west coast bottom trawl groundfish survey (fishery-independent data) to compare the relative effects of season, time of day, target group, depth, and latitude on the expected catch of 12 bycatch species of management interest. This comparison highlights two important relationships that help identify drivers of bycatch. First, when the effect of season, time of day, depth, or latitude on bycatch in both the commercial and scientific data is positive, ecological processes are likely strong drivers of bycatch, suggesting technical approaches (e.g., temporal or spatial closures, gear modifications) might effectively control bycatch. Alternatively, when the effects of season, time of day, depth, latitude, or target group appear only in the commercial data (but not in survey data), fisher behavior is likely the stronger driver of bycatch, suggesting a need to strengthen incentives for fishers to change behavior to avoid bycatch (e.g., regulatory quotas). Two other patterns emerge that suggest that fishery bycatch is not associated with temporal, target, or spatial variables, implying that either current incentives to avoid bycatch are working (i.e., when survey expected catch is positively correlated with variables, but fishery catch is not) or bycatch is a product of unstudied or stochastic processes (i.e., variables are not correlated with expected catch in either data set) and continued monitoring is recommended. Our analysis

Electrochemical DNA sensor for anthrax toxin activator gene atxA-detection of PCR amplicons.

PubMed

Das, Ritu; Goel, Ajay K; Sharma, Mukesh K; Upadhyay, Sanjay

2015-12-15

We report the DNA probe functionalized electrochemical genosensor for the detection of Bacillus anthracis, specific towards the regulatory gene atxA. The DNA sensor is fabricated on electrochemically deposited gold nanoparticle on self assembled layer of (3-Mercaptopropyl) trimethoxysilane (MPTS) on GC electrode. DNA hybridization is monitored by differential pulse voltammogram (DPV). The modified GC electrode is characterized by atomic force microscopy (AFM), cyclic voltammetry (CV), and electrochemical impedance spectroscopy (EIS) method. We also quantified the DNA probe density on electrode surface by the chronocoulometric method. The detection is specific and selective for atxA gene by DNA probe on the electrode surface. No report is available for the detection of B. anthracis by using atxA an anthrax toxin activator gene. In the light of real and complex sample, we have studied the PCR amplicons of 303, 361 and 568 base pairs by using symmetric and asymmetric PCR approaches. The DNA probe of atxA gene efficiently hybridizes with different base pairs of PCR amplicons. The detection limit is found to be 1.0 pM (S/N ratio=3). The results indicate that the DNA sensor is able to detect synthetic target as well as PCR amplicons of different base pairs. Copyright © 2015 Elsevier B.V. All rights reserved.

Factors associated with self-reported driver sleepiness and incidents in city bus drivers

PubMed Central

ANUND, Anna; IHLSTRÖM, Jonas; FORS, Carina; KECKLUND, Göran; FILTNESS, Ashleigh

2016-01-01

Driver fatigue has received increased attention during recent years and is now considered to be a major contributor to approximately 15–30% of all crashes. However, little is known about fatigue in city bus drivers. It is hypothesized that city bus drivers suffer from sleepiness, which is due to a combination of working conditions, lack of health and reduced sleep quantity and quality. The overall aim with the current study is to investigate if severe driver sleepiness, as indicated by subjective reports of having to fight sleep while driving, is a problem for city based bus drivers in Sweden and if so, to identify the determinants related to working conditions, health and sleep which contribute towards this. The results indicate that driver sleepiness is a problem for city bus drivers, with 19% having to fight to stay awake while driving the bus 2–3 times each week or more and nearly half experiencing this at least 2–4 times per month. In conclusion, severe sleepiness, as indicated by having to fight sleep during driving, was common among the city bus drivers. Severe sleepiness correlated with fatigue related safety risks, such as near crashes. PMID:27098307

Factors associated with self-reported driver sleepiness and incidents in city bus drivers.

PubMed

Anund, Anna; Ihlström, Jonas; Fors, Carina; Kecklund, Göran; Filtness, Ashleigh

2016-08-05

Driver fatigue has received increased attention during recent years and is now considered to be a major contributor to approximately 15-30% of all crashes. However, little is known about fatigue in city bus drivers. It is hypothesized that city bus drivers suffer from sleepiness, which is due to a combination of working conditions, lack of health and reduced sleep quantity and quality. The overall aim with the current study is to investigate if severe driver sleepiness, as indicated by subjective reports of having to fight sleep while driving, is a problem for city based bus drivers in Sweden and if so, to identify the determinants related to working conditions, health and sleep which contribute towards this. The results indicate that driver sleepiness is a problem for city bus drivers, with 19% having to fight to stay awake while driving the bus 2-3 times each week or more and nearly half experiencing this at least 2-4 times per month. In conclusion, severe sleepiness, as indicated by having to fight sleep during driving, was common among the city bus drivers. Severe sleepiness correlated with fatigue related safety risks, such as near crashes.

The strength of graduated drivers license programs and fatalities among teen drivers and passengers.

PubMed

Morrisey, Michael A; Grabowski, David C; Dee, Thomas S; Campbell, Christine

2006-01-01

The purpose of this study is to investigate the effects of differentially stringent graduated drivers license programs on teen driver fatalities, day-time and night-time teen driver fatalities, fatalities of teen drivers with passengers present, and fatalities among teen passengers. The study uses 1992-2002 data on motor vehicle fatalities among 15-17-year-old drivers from the Fatality Analysis Reporting System to identify the effects of "good", "fair", and "marginal" GDL programs based upon designations by the Insurance Institute for Highway Safety. Analysis is conducted using conditional negative binomial regressions with fixed effects. "Good" programs reduce total fatalities among young drivers by 19.4% (c.i. -33.0%, -5.9%). "Fair" programs reduce night-time young driver fatalities by 12.6% (c.i. -23.9%, -1.2%), but have no effect on day-time fatalities. "Marginal" programs had no statistically meaningful effect on driver fatalities. All three types of programs reduced teen passenger fatalities, but the effects of limitations on the number of passengers appear to have had only minimal effects in reducing fatalities among young drivers themselves. Stronger GDL programs are more effective than weaker programs in reducing teenage motor vehicle fatalities.

Determination of characteristics of fatally injured drivers

DOT National Transportation Integrated Search

2001-12-01

The objective of this study was to identify driver characteristics that can be used to predict driver risk of fatal crashes. The study had 3 components: (1) Comparisons were made among drivers who were killed in single-vehicle crashes or were at faul...

Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform.

PubMed

Schirmer, Melanie; Ijaz, Umer Z; D'Amore, Rosalinda; Hall, Neil; Sloan, William T; Quince, Christopher

2015-03-31

With read lengths of currently up to 2 × 300 bp, high throughput and low sequencing costs Illumina's MiSeq is becoming one of the most utilized sequencing platforms worldwide. The platform is manageable and affordable even for smaller labs. This enables quick turnaround on a broad range of applications such as targeted gene sequencing, metagenomics, small genome sequencing and clinical molecular diagnostics. However, Illumina error profiles are still poorly understood and programs are therefore not designed for the idiosyncrasies of Illumina data. A better knowledge of the error patterns is essential for sequence analysis and vital if we are to draw valid conclusions. Studying true genetic variation in a population sample is fundamental for understanding diseases, evolution and origin. We conducted a large study on the error patterns for the MiSeq based on 16S rRNA amplicon sequencing data. We tested state-of-the-art library preparation methods for amplicon sequencing and showed that the library preparation method and the choice of primers are the most significant sources of bias and cause distinct error patterns. Furthermore we tested the efficiency of various error correction strategies and identified quality trimming (Sickle) combined with error correction (BayesHammer) followed by read overlapping (PANDAseq) as the most successful approach, reducing substitution error rates on average by 93%. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Massively parallel sequencing of 17 commonly used forensic autosomal STRs and amelogenin with small amplicons.

PubMed

Kim, Eun Hye; Lee, Hwan Young; Yang, In Seok; Jung, Sang-Eun; Yang, Woo Ick; Shin, Kyoung-Jin

2016-05-01

The next-generation sequencing (NGS) method has been utilized to analyze short tandem repeat (STR) markers, which are routinely used for human identification purposes in the forensic field. Some researchers have demonstrated the successful application of the NGS system to STR typing, suggesting that NGS technology may be an alternative or additional method to overcome limitations of capillary electrophoresis (CE)-based STR profiling. However, there has been no available multiplex PCR system that is optimized for NGS analysis of forensic STR markers. Thus, we constructed a multiplex PCR system for the NGS analysis of 18 markers (13CODIS STRs, D2S1338, D19S433, Penta D, Penta E and amelogenin) by designing amplicons in the size range of 77-210 base pairs. Then, PCR products were generated from two single-sources, mixed samples and artificially degraded DNA samples using a multiplex PCR system, and were prepared for sequencing on the MiSeq system through construction of a subsequent barcoded library. By performing NGS and analyzing the data, we confirmed that the resultant STR genotypes were consistent with those of CE-based typing. Moreover, sequence variations were detected in targeted STR regions. Through the use of small-sized amplicons, the developed multiplex PCR system enables researchers to obtain successful STR profiles even from artificially degraded DNA as well as STR loci which are analyzed with large-sized amplicons in the CE-based commercial kits. In addition, successful profiles can be obtained from mixtures up to a 1:19 ratio. Consequently, the developed multiplex PCR system, which produces small size amplicons, can be successfully applied to STR NGS analysis of forensic casework samples such as mixtures and degraded DNA samples. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

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

PubMed

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. Copyright © 2015 Elsevier B.V. All rights reserved.

Identifying multiple coral reef regimes and their drivers across the Hawaiian archipelago

PubMed Central

Jouffray, Jean-Baptiste; Nyström, Magnus; Norström, Albert V.; Williams, Ivor D.; Wedding, Lisa M.; Kittinger, John N.; Williams, Gareth J.

2015-01-01

Loss of coral reef resilience can lead to dramatic changes in benthic structure, often called regime shifts, which significantly alter ecosystem processes and functioning. In the face of global change and increasing direct human impacts, there is an urgent need to anticipate and prevent undesirable regime shifts and, conversely, to reverse shifts in already degraded reef systems. Such challenges require a better understanding of the human and natural drivers that support or undermine different reef regimes. The Hawaiian archipelago extends across a wide gradient of natural and anthropogenic conditions and provides us a unique opportunity to investigate the relationships between multiple reef regimes, their dynamics and potential drivers. We applied a combination of exploratory ordination methods and inferential statistics to one of the most comprehensive coral reef datasets available in order to detect, visualize and define potential multiple ecosystem regimes. This study demonstrates the existence of three distinct reef regimes dominated by hard corals, turf algae or macroalgae. Results from boosted regression trees show nonlinear patterns among predictors that help to explain the occurrence of these regimes, and highlight herbivore biomass as the key driver in addition to effluent, latitude and depth.

Identifying Effective Drivers for Knowledge Exchange in the United Kingdom

ERIC Educational Resources Information Center

Upton, Stevie

2012-01-01

This paper examines the drivers for knowledge exchange in British research-intensive universities, at a time when research impact is coming to be seen as an increasingly important outcome of research in all disciplines. It provides evidence of an over-emphasis of the economic benefits of knowledge exchange in the policy sphere and of a quite…

Advanced driver assistance systems for teen drivers: Teen and parent impressions, perceived need, and intervention preferences.

PubMed

Weiss, Eve; Fisher Thiel, Megan; Sultana, Nahida; Hannan, Chloe; Seacrist, Thomas

2018-02-28

From the advent of airbags to electronic stability control, technological advances introduced into automobile design have significantly reduced injury and death from motor vehicle crashes. These advances are especially pertinent among teen drivers, a population whose leading cause of death is motor vehicle crashes. Recently developed advanced driver assistance systems (ADAS) have the potential to compensate for skill deficits and reduce overall crash risk. Yet, ADAS is only effective if drivers are willing to use it. Limited research has been conducted on the suitability of ADAS for teen drivers. The goal of this study is to identify teen drivers' perceived need for ADAS, receptiveness to in-vehicle technology, and intervention preferences. The long-term goal is to understand public perceptions and barriers to ADAS use and to help determine how these systems must evolve to meet the needs of the riskiest driving populations. Three focus groups (N = 24) were conducted with licensed teen drivers aged 16-19 years and 2 focus groups with parents of teen drivers (N = 12). Discussion topics included views on how ADAS might influence driving skills and behaviors; trust in technology; and data privacy. Discussions were transcribed; the team used conventional content analysis and open coding methods to identify 12 coding domains and code transcripts with NVivo 10. Interrater reliability testing showed moderate to high kappa scores. Overall, participants recognized potential benefits of ADAS, including improved safety and crash reduction. Teens suggested that ADAS is still developing and therefore has potential to malfunction. Many teens reported a greater trust in their own driving ability over vehicle technology. They expressed that novice drivers should learn to drive on non-ADAS-equipped cars and that ADAS should be considered a supplemental aid. Many teens felt that overreliance on ADAS may increase distracted driving or risky behaviors among teens. Parents also

ICO amplicon NGS data analysis: a Web tool for variant detection in common high-risk hereditary cancer genes analyzed by amplicon GS Junior next-generation sequencing.

PubMed

Lopez-Doriga, Adriana; Feliubadaló, Lídia; Menéndez, Mireia; Lopez-Doriga, Sergio; Morón-Duran, Francisco D; del Valle, Jesús; Tornero, Eva; Montes, Eva; Cuesta, Raquel; Campos, Olga; Gómez, Carolina; Pineda, Marta; González, Sara; Moreno, Victor; Capellá, Gabriel; Lázaro, Conxi

2014-03-01

Next-generation sequencing (NGS) has revolutionized genomic research and is set to have a major impact on genetic diagnostics thanks to the advent of benchtop sequencers and flexible kits for targeted libraries. Among the main hurdles in NGS are the difficulty of performing bioinformatic analysis of the huge volume of data generated and the high number of false positive calls that could be obtained, depending on the NGS technology and the analysis pipeline. Here, we present the development of a free and user-friendly Web data analysis tool that detects and filters sequence variants, provides coverage information, and allows the user to customize some basic parameters. The tool has been developed to provide accurate genetic analysis of targeted sequencing of common high-risk hereditary cancer genes using amplicon libraries run in a GS Junior System. The Web resource is linked to our own mutation database, to assist in the clinical classification of identified variants. We believe that this tool will greatly facilitate the use of the NGS approach in routine laboratories.

Identifying at-risk drivers : a survey of state programs : final report.

DOT National Transportation Integrated Search

1990-01-01

Motor vehicle administrators have long realized that certain drivers present more of safety problem than others. Tests of static visual acuity, knowledge of the rules of the road, and on-the-road driving performance are used to ensure that each drive...

Using expected sequence features to improve basecalling accuracy of amplicon pyrosequencing data.

PubMed

Rask, Thomas S; Petersen, Bent; Chen, Donald S; Day, Karen P; Pedersen, Anders Gorm

2016-04-22

Amplicon pyrosequencing targets a known genetic region and thus inherently produces reads highly anticipated to have certain features, such as conserved nucleotide sequence, and in the case of protein coding DNA, an open reading frame. Pyrosequencing errors, consisting mainly of nucleotide insertions and deletions, are on the other hand likely to disrupt open reading frames. Such an inverse relationship between errors and expectation based on prior knowledge can be used advantageously to guide the process known as basecalling, i.e. the inference of nucleotide sequence from raw sequencing data. The new basecalling method described here, named Multipass, implements a probabilistic framework for working with the raw flowgrams obtained by pyrosequencing. For each sequence variant Multipass calculates the likelihood and nucleotide sequence of several most likely sequences given the flowgram data. This probabilistic approach enables integration of basecalling into a larger model where other parameters can be incorporated, such as the likelihood for observing a full-length open reading frame at the targeted region. We apply the method to 454 amplicon pyrosequencing data obtained from a malaria virulence gene family, where Multipass generates 20 % more error-free sequences than current state of the art methods, and provides sequence characteristics that allow generation of a set of high confidence error-free sequences. This novel method can be used to increase accuracy of existing and future amplicon sequencing data, particularly where extensive prior knowledge is available about the obtained sequences, for example in analysis of the immunoglobulin VDJ region where Multipass can be combined with a model for the known recombining germline genes. Multipass is available for Roche 454 data at http://www.cbs.dtu.dk/services/MultiPass-1.0 , and the concept can potentially be implemented for other sequencing technologies as well.

Older drivers' foot movements : traffic tech.

DOT National Transportation Integrated Search

2017-07-01

This study explored how older drivers use their accelerator and : brake pedals, to identify characteristics that could pose an increased : risk of a pedal application error. The study also explored whether : driver-vehicle fit was related to these ch...

Assessing drivers' response during automated driver support system failures with non-driving tasks.

PubMed

Shen, Sijun; Neyens, David M

2017-06-01

With the increase in automated driver support systems, drivers are shifting from operating their vehicles to supervising their automation. As a result, it is important to understand how drivers interact with these automated systems and evaluate their effect on driver responses to safety critical events. This study aimed to identify how drivers responded when experiencing a safety critical event in automated vehicles while also engaged in non-driving tasks. In total 48 participants were included in this driving simulator study with two levels of automated driving: (a) driving with no automation and (b) driving with adaptive cruise control (ACC) and lane keeping (LK) systems engaged; and also two levels of a non-driving task (a) watching a movie or (b) no non-driving task. In addition to driving performance measures, non-driving task performance and the mean glance duration for the non-driving task were compared between the two levels of automated driving. Drivers using the automated systems responded worse than those manually driving in terms of reaction time, lane departure duration, and maximum steering wheel angle to an induced lane departure event. These results also found that non-driving tasks further impaired driver responses to a safety critical event in the automated system condition. In the automated driving condition, driver responses to the safety critical events were slower, especially when engaged in a non-driving task. Traditional driver performance variables may not necessarily effectively and accurately evaluate driver responses to events when supervising autonomous vehicle systems. Thus, it is important to develop and use appropriate variables to quantify drivers' performance under these conditions. Copyright © 2017 Elsevier Ltd and National Safety Council. All rights reserved.

Mandatory Physician Reporting of At-Risk Drivers: The Older Driver Example.

PubMed

Agimi, Yll; Albert, Steven M; Youk, Ada O; Documet, Patricia I; Steiner, Claudia A

2018-05-08

In a number of states, physicians are mandated by state law to report at-risk drivers to licensing authorities. Often these patients are older adult drivers who may exhibit unsafe driving behaviors, have functional/cognitive impairments, or are diagnosed with conditions such as Alzheimer's disease and/or seizure disorders. The hypothesis that mandatory physician reporting laws reduce the rate of crash-related hospitalizations among older adult drivers was tested. Using retrospective data (2004-2009), this study identified 176,066 older driver crash-related hospitalizations, from the State Inpatient Databases. Three age-specific negative binomial generalized estimating equation models were used to estimate the effect of physician reporting laws on state's incidence rate of crash-related hospitalizations among older drivers. No evidence was found for an independent association between mandatory physician reporting laws and a lower crash hospitalization rate among any of the age groups examined. The main predictor of interest, mandatory physician reporting, failed to explain any significant variation in crash hospitalization rates, when adjusting for other state-specific laws and characteristics. Vision testing at in-person license renewal was a significant predictor of lower crash hospitalization rate, ranging from incidence rate ratio of 0.77 (95% confidence interval 0.62-0.94) among 60- to 64-year olds to 0.83 (95% confidence interval 0.67-0.97) among 80- to 84-year olds. Physician reporting laws and age-based licensing requirements are often at odds with older driver's need to maintain independence. This study examines this balance and finds no evidence of the benefits of mandatory physician reporting requirements on driver crash hospitalizations, suggesting that physician mandates do not yet yield significant older driver safety benefits, possibly to the detriment of older driver's well-being and independence.

Psychological reactions of drivers to railway suicide.

PubMed

Tranah, T; Farmer, R D

1994-02-01

Around 90 London Underground train drivers experience a person jumping or falling in front of their train each year. The majority of these incidents are suicides or attempted suicides. 76 drivers were interviewed in order to assess the range of responses to these incidents. The following psychometric instruments were used: Present State Examination (PSE9); Post-Traumatic Stress Disorder (PTSD) Interview; General Health Questionnaire (GHQ-28); Impact of Events Scale (IES); Post-Traumatic Symptom Scale; Recent Difficulties/Events scale; Perceived Stress Scale and Eysenck Personality Questionnaire (EPQ). When interviewed 1 month after the incident 13 (17.11%) drivers presented with PTSD. Diagnoses other than PTSD e.g. neurotic depression and phobic state were present in 24 (31.58%) drivers (including 12 of the 13 PTSD cases who had one additional diagnosis). On the basis of diagnoses three groups were identified: Group 1 drivers had PTSD and in most cases an additional PSE9 diagnosis; Group 2 drivers had a PSE9 diagnosis only; Group 3 drivers were not cases. 56 drivers were again interviewed 6 months after the incident to assess duration of caseness and/or symptoms and to identify any cases of delayed onset. Two drivers were still cases at 6 months (neurotic depression and phobic state), no driver presented with PTSD at 6 months. At 6 months there was a significant drop in symptom scores compared with measures taken at 1 month. These results suggest that although approximately one-third of drivers suffered a severe psychological reaction following a railway suicide, when interviewed again 6 months after the incident most drivers reported a marked reduction in symptoms.

Genome-wide methylation sequencing of paired primary and metastatic cell lines identifies common DNA methylation changes and a role for EBF3 as a candidate epigenetic driver of melanoma metastasis

PubMed Central

Chatterjee, Aniruddha; Stockwell, Peter A; Ahn, Antonio; Rodger, Euan J; Leichter, Anna L; Eccles, Michael R

2017-01-01

Epigenetic alterations are increasingly implicated in metastasis, whereas very few genetic mutations have been identified as authentic drivers of cancer metastasis. Yet, to date, few studies have identified metastasis-related epigenetic drivers, in part because a framework for identifying driver epigenetic changes in metastasis has not been established. Using reduced representation bisulfite sequencing (RRBS), we mapped genome-wide DNA methylation patterns in three cutaneous primary and metastatic melanoma cell line pairs to identify metastasis-related epigenetic drivers. Globally, metastatic melanoma cell lines were hypomethylated compared to the matched primary melanoma cell lines. Using whole genome RRBS we identified 75 shared (10 hyper- and 65 hypomethylated) differentially methylated fragments (DMFs), which were associated with 68 genes showing significant methylation differences. One gene, Early B Cell Factor 3 (EBF3), exhibited promoter hypermethylation in metastatic cell lines, and was validated with bisulfite sequencing and in two publicly available independent melanoma cohorts (n = 40 and 458 melanomas, respectively). We found that hypermethylation of the EBF3 promoter was associated with increased EBF3 mRNA levels in metastatic melanomas and subsequent inhibition of DNA methylation reduced EBF3 expression. RNAi-mediated knockdown of EBF3 mRNA levels decreased proliferation, migration and invasion in primary and metastatic melanoma cell lines. Overall, we have identified numerous epigenetic changes characterising metastatic melanoma cell lines, including EBF3-induced aggressive phenotypic behaviour with elevated EBF3 expression in metastatic melanoma, suggesting that EBF3 promoter hypermethylation may be a candidate epigenetic driver of metastasis. PMID:28030832

Evaluating the evaluation of cancer driver genes

PubMed Central

Tokheim, Collin J.; Papadopoulos, Nickolas; Kinzler, Kenneth W.; Vogelstein, Bert; Karchin, Rachel

2016-01-01

Sequencing has identified millions of somatic mutations in human cancers, but distinguishing cancer driver genes remains a major challenge. Numerous methods have been developed to identify driver genes, but evaluation of the performance of these methods is hindered by the lack of a gold standard, that is, bona fide driver gene mutations. Here, we establish an evaluation framework that can be applied to driver gene prediction methods. We used this framework to compare the performance of eight such methods. One of these methods, described here, incorporated a machine-learning–based ratiometric approach. We show that the driver genes predicted by each of the eight methods vary widely. Moreover, the P values reported by several of the methods were inconsistent with the uniform values expected, thus calling into question the assumptions that were used to generate them. Finally, we evaluated the potential effects of unexplained variability in mutation rates on false-positive driver gene predictions. Our analysis points to the strengths and weaknesses of each of the currently available methods and offers guidance for improving them in the future. PMID:27911828

Maturation of the Infant Respiratory Microbiota, Environmental Drivers, and Health Consequences. A Prospective Cohort Study.

PubMed

Bosch, Astrid A T M; de Steenhuijsen Piters, Wouter A A; van Houten, Marlies A; Chu, Mei Ling J N; Biesbroek, Giske; Kool, Jolanda; Pernet, Paula; de Groot, Pieter-Kees C M; Eijkemans, Marinus J C; Keijser, Bart J F; Sanders, Elisabeth A M; Bogaert, Debby

2017-12-15

Perinatal and postnatal influences are presumed important drivers of the early-life respiratory microbiota composition. We hypothesized that the respiratory microbiota composition and development in infancy is affecting microbiota stability and thereby resistance against respiratory tract infections (RTIs) over time. To investigate common environmental drivers, including birth mode, feeding type, antibiotic exposure, and crowding conditions, in relation to respiratory tract microbiota maturation and stability, and consecutive risk of RTIs over the first year of life. In a prospectively followed cohort of 112 infants, we characterized the nasopharyngeal microbiota longitudinally from birth on (11 consecutive sample moments and the maximum three RTI samples per subject; in total, n = 1,121 samples) by 16S-rRNA gene amplicon sequencing. Using a microbiota-based machine-learning algorithm, we found that children experiencing a higher number of RTIs in the first year of life already demonstrate an aberrant microbial developmental trajectory from the first month of life on as compared with the reference group (0-2 RTIs/yr). The altered microbiota maturation process coincided with decreased microbial community stability, prolonged reduction of Corynebacterium and Dolosigranulum, enrichment of Moraxella very early in life, followed by later enrichment of Neisseria and Prevotella spp. Independent drivers of these aberrant developmental trajectories of respiratory microbiota members were mode of delivery, infant feeding, crowding, and recent antibiotic use. Our results suggest that environmental drivers impact microbiota development and, consequently, resistance against development of RTIs. This supports the idea that microbiota form the mediator between early-life environmental risk factors for and susceptibility to RTIs over the first year of life.

Transportation needs of the older driver : final report.

DOT National Transportation Integrated Search

1993-01-01

A growing percentage of all drivers are aged 55 and older. The findings of a number of safety studies have also fostered national interest in older driver issues. The needs and problems of Virginia drivers age 55 and older were identified in 10 focus...

A Systems Biology Approach Identifies FUT8 as a Driver of Melanoma Metastasis.

PubMed

Agrawal, Praveen; Fontanals-Cirera, Barbara; Sokolova, Elena; Jacob, Samson; Vaiana, Christopher A; Argibay, Diana; Davalos, Veronica; McDermott, Meagan; Nayak, Shruti; Darvishian, Farbod; Castillo, Mireia; Ueberheide, Beatrix; Osman, Iman; Fenyö, David; Mahal, Lara K; Hernando, Eva

2017-06-12

Association of aberrant glycosylation with melanoma progression is based mainly on analyses of cell lines. Here we present a systems-based study of glycomic changes and corresponding enzymes associated with melanoma metastasis in patient samples. Upregulation of core fucosylation (FUT8) and downregulation of α-1,2 fucosylation (FUT1, FUT2) were identified as features of metastatic melanoma. Using both in vitro and in vivo studies, we demonstrate FUT8 is a driver of melanoma metastasis which, when silenced, suppresses invasion and tumor dissemination. Glycoprotein targets of FUT8 were enriched in cell migration proteins including the adhesion molecule L1CAM. Core fucosylation impacted L1CAM cleavage and the ability of L1CAM to support melanoma invasion. FUT8 and its targets represent therapeutic targets in melanoma metastasis. Copyright © 2017 Elsevier Inc. All rights reserved.

Preferential Allele Expression Analysis Identifies Shared Germline and Somatic Driver Genes in Advanced Ovarian Cancer

PubMed Central

Halabi, Najeeb M.; Martinez, Alejandra; Al-Farsi, Halema; Mery, Eliane; Puydenus, Laurence; Pujol, Pascal; Khalak, Hanif G.; McLurcan, Cameron; Ferron, Gwenael; Querleu, Denis; Al-Azwani, Iman; Al-Dous, Eman; Mohamoud, Yasmin A.; Malek, Joel A.; Rafii, Arash

2016-01-01

Identifying genes where a variant allele is preferentially expressed in tumors could lead to a better understanding of cancer biology and optimization of targeted therapy. However, tumor sample heterogeneity complicates standard approaches for detecting preferential allele expression. We therefore developed a novel approach combining genome and transcriptome sequencing data from the same sample that corrects for sample heterogeneity and identifies significant preferentially expressed alleles. We applied this analysis to epithelial ovarian cancer samples consisting of matched primary ovary and peritoneum and lymph node metastasis. We find that preferentially expressed variant alleles include germline and somatic variants, are shared at a relatively high frequency between patients, and are in gene networks known to be involved in cancer processes. Analysis at a patient level identifies patient-specific preferentially expressed alleles in genes that are targets for known drugs. Analysis at a site level identifies patterns of site specific preferential allele expression with similar pathways being impacted in the primary and metastasis sites. We conclude that genes with preferentially expressed variant alleles can act as cancer drivers and that targeting those genes could lead to new therapeutic strategies. PMID:26735499

Integrating metagenomic and amplicon databases to resolve the phylogenetic and ecological diversity of the Chlamydiae

PubMed Central

Lagkouvardos, Ilias; Weinmaier, Thomas; Lauro, Federico M; Cavicchioli, Ricardo; Rattei, Thomas; Horn, Matthias

2014-01-01

In the era of metagenomics and amplicon sequencing, comprehensive analyses of available sequence data remain a challenge. Here we describe an approach exploiting metagenomic and amplicon data sets from public databases to elucidate phylogenetic diversity of defined microbial taxa. We investigated the phylum Chlamydiae whose known members are obligate intracellular bacteria that represent important pathogens of humans and animals, as well as symbionts of protists. Despite their medical relevance, our knowledge about chlamydial diversity is still scarce. Most of the nine known families are represented by only a few isolates, while previous clone library-based surveys suggested the existence of yet uncharacterized members of this phylum. Here we identified more than 22 000 high quality, non-redundant chlamydial 16S rRNA gene sequences in diverse databases, as well as 1900 putative chlamydial protein-encoding genes. Even when applying the most conservative approach, clustering of chlamydial 16S rRNA gene sequences into operational taxonomic units revealed an unexpectedly high species, genus and family-level diversity within the Chlamydiae, including 181 putative families. These in silico findings were verified experimentally in one Antarctic sample, which contained a high diversity of novel Chlamydiae. In our analysis, the Rhabdochlamydiaceae, whose known members infect arthropods, represents the most diverse and species-rich chlamydial family, followed by the protist-associated Parachlamydiaceae, and a putative new family (PCF8) with unknown host specificity. Available information on the origin of metagenomic samples indicated that marine environments contain the majority of the newly discovered chlamydial lineages, highlighting this environment as an important chlamydial reservoir. PMID:23949660

Determinants and Drivers of Infectious Disease Threat Events in Europe.

PubMed

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.

Determinants and Drivers of Infectious Disease Threat Events in Europe

PubMed Central

Lindgren, Elisabet; Balkanyi, Laszlo; Espinosa, Laura; Almqvist, My S.; Penttinen, Pasi; Rocklöv, Joacim

2016-01-01

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. PMID:26982104

Amplicon sequencing of bacterial microbiota in abortion material from cattle.

PubMed

Vidal, Sara; Kegler, Kristel; Posthaus, Horst; Perreten, Vincent; Rodriguez-Campos, Sabrina

2017-10-10

Abortions in cattle have a significant economic impact on animal husbandry and require prompt diagnosis for surveillance of epizootic infectious agents. Since most abortions are not epizootic but sporadic with often undetected etiologies, this study examined the bacterial community present in the placenta (PL, n = 32) and fetal abomasal content (AC, n = 49) in 64 cases of bovine abortion by next generation sequencing (NGS) of the 16S rRNA gene. The PL and AC from three fetuses of dams that died from non-infectious reasons were included as controls. All samples were analyzed by bacterial culture, and 17 were examined by histopathology. We observed 922 OTUs overall and 267 taxa at the genus level. No detectable bacterial DNA was present in the control samples. The microbial profiles of the PL and AC differed significantly, both in their composition (PERMANOVA), species richness and Chao-1 (Mann-Whitney test). In both organs, Pseudomonas was the most abundant genus. The combination of NGS and culture identified opportunistic pathogens of interest in placentas with lesions, such as Vibrio metschnikovii, Streptococcus uberis, Lactococcus lactis and Escherichia coli. In placentas with lesions where culturing was unsuccessful, Pseudomonas and unidentified Aeromonadaceae were identified by NGS displaying high number of reads. Three cases with multiple possible etiologies and placentas presenting lesions were detected by NGS. Amplicon sequencing has the potential to uncover unknown etiological agents. These new insights on cattle abortion extend our focus to previously understudied opportunistic abortive bacteria.

High-Throughput Sequencing of 16S rRNA Gene Amplicons: Effects of Extraction Procedure, Primer Length and Annealing Temperature

PubMed Central

Sergeant, Martin J.; Constantinidou, Chrystala; Cogan, Tristan; Penn, Charles W.; Pallen, Mark J.

2012-01-01

The analysis of 16S-rDNA sequences to assess the bacterial community composition of a sample is a widely used technique that has increased with the advent of high throughput sequencing. Although considerable effort has been devoted to identifying the most informative region of the 16S gene and the optimal informatics procedures to process the data, little attention has been paid to the PCR step, in particular annealing temperature and primer length. To address this, amplicons derived from 16S-rDNA were generated from chicken caecal content DNA using different annealing temperatures, primers and different DNA extraction procedures. The amplicons were pyrosequenced to determine the optimal protocols for capture of maximum bacterial diversity from a chicken caecal sample. Even at very low annealing temperatures there was little effect on the community structure, although the abundance of some OTUs such as Bifidobacterium increased. Using shorter primers did not reveal any novel OTUs but did change the community profile obtained. Mechanical disruption of the sample by bead beating had a significant effect on the results obtained, as did repeated freezing and thawing. In conclusion, existing primers and standard annealing temperatures captured as much diversity as lower annealing temperatures and shorter primers. PMID:22666455

High-throughput sequencing of 16S rRNA gene amplicons: effects of extraction procedure, primer length and annealing temperature.

PubMed

Sergeant, Martin J; Constantinidou, Chrystala; Cogan, Tristan; Penn, Charles W; Pallen, Mark J

2012-01-01

The analysis of 16S-rDNA sequences to assess the bacterial community composition of a sample is a widely used technique that has increased with the advent of high throughput sequencing. Although considerable effort has been devoted to identifying the most informative region of the 16S gene and the optimal informatics procedures to process the data, little attention has been paid to the PCR step, in particular annealing temperature and primer length. To address this, amplicons derived from 16S-rDNA were generated from chicken caecal content DNA using different annealing temperatures, primers and different DNA extraction procedures. The amplicons were pyrosequenced to determine the optimal protocols for capture of maximum bacterial diversity from a chicken caecal sample. Even at very low annealing temperatures there was little effect on the community structure, although the abundance of some OTUs such as Bifidobacterium increased. Using shorter primers did not reveal any novel OTUs but did change the community profile obtained. Mechanical disruption of the sample by bead beating had a significant effect on the results obtained, as did repeated freezing and thawing. In conclusion, existing primers and standard annealing temperatures captured as much diversity as lower annealing temperatures and shorter primers.

Data and methods for studying commercial motor vehicle driver fatigue, highway safety and long-term driver health.

PubMed

Stern, Hal S; Blower, Daniel; Cohen, Michael L; Czeisler, Charles A; Dinges, David F; Greenhouse, Joel B; Guo, Feng; Hanowski, Richard J; Hartenbaum, Natalie P; Krueger, Gerald P; Mallis, Melissa M; Pain, Richard F; Rizzo, Matthew; Sinha, Esha; Small, Dylan S; Stuart, Elizabeth A; Wegman, David H

2018-03-09

This article summarizes the recommendations on data and methodology issues for studying commercial motor vehicle driver fatigue of a National Academies of Sciences, Engineering, and Medicine study. A framework is provided that identifies the various factors affecting driver fatigue and relating driver fatigue to crash risk and long-term driver health. The relevant factors include characteristics of the driver, vehicle, carrier and environment. Limitations of existing data are considered and potential sources of additional data described. Statistical methods that can be used to improve understanding of the relevant relationships from observational data are also described. The recommendations for enhanced data collection and the use of modern statistical methods for causal inference have the potential to enhance our understanding of the relationship of fatigue to highway safety and to long-term driver health. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Potential applications of next generation DNA sequencing of 16S rRNA gene amplicons in microbial water quality monitoring

PubMed Central

Vierheilig, J.; Savio, D.; Ley, R. E.; Mach, R. L.; Farnleitner, A. H.

2016-01-01

The applicability of next generation DNA sequencing (NGS) methods for water quality assessment has so far not been broadly investigated. This study set out to evaluate the potential of an NGS-based approach in a complex catchment with importance for drinking water abstraction. In this multicompartment investigation, total bacterial communities in water, faeces, soil, and sediment samples were investigated by 454 pyrosequencing of bacterial 16S rRNA gene amplicons to assess the capabilities of this NGS method for (i) the development and evaluation of environmental molecular diagnostics, (ii) direct screening of the bulk bacterial communities, and (iii) the detection of faecal pollution in water. Results indicate that NGS methods can highlight potential target populations for diagnostics and will prove useful for the evaluation of existing and the development of novel DNA-based detection methods in the field of water microbiology. The used approach allowed unveiling of dominant bacterial populations but failed to detect populations with low abundances such as faecal indicators in surface waters. In combination with metadata, NGS data will also allow the identification of drivers of bacterial community composition during water treatment and distribution, highlighting the power of this approach for monitoring of bacterial regrowth and contamination in technical systems. PMID:26606090

High-Throughput Amplicon Sequencing Reveals Distinct Communities within a Corroding Concrete Sewer System

PubMed Central

Dennis, Paul G.; Keller, Jurg; Tyson, Gene W.

2012-01-01

Microbially induced concrete corrosion (MICC) is an important problem in sewers. Here, small-subunit (SSU) rRNA gene amplicon pyrosequencing was used to characterize MICC communities. Microbial community composition differed between wall- and ceiling-associated MICC layers. Acidithiobacillus spp. were present at low abundances, and the communities were dominated by other sulfur-oxidizing-associated lineages. PMID:22843532

An application of the driver behavior questionnaire to Chinese carless young drivers.

PubMed

Zhang, Qian; Jiang, Zuhua; Zheng, Dongpeng; Wang, Yifan; Man, Dong

2013-01-01

Carless young drivers refers to those drivers aged between 18 and 25 years who have a driver's license but seldom have opportunities to practice their driving skills because they do not have their own cars. Due to China's lower private car ownership, many young drivers turn into carless young drivers after licensure, and the safety issue associated with them has become a matter of great concern in China. Because few studies have examined the driving behaviors of these drivers, this study aims to utilize the Driver Behavior Questionnaire (DBQ) to investigate the self-reported driving behaviors of Chinese carless young drivers. A total of 523 Chinese carless young drivers (214 females, 309 males) with an average age of 21.91 years completed a questionnaire including the 27-item DBQ and demographics. The data were first randomized into 2 subsamples for factor analysis and then combined together for the following analyses. Both an exploratory factor analysis (EFA, n = 174) and a confirmatory factor analysis (CFA, n = 349) were performed to investigate the factor structure of the DBQ. Correlation analysis was conducted to examine the relationships between the demographics and the DBQ scales' variables. Multivariate linear regression and logistic regression were performed to investigate the prediction of the DBQ scales and crash involvement in the previous year. The EFA produced a 4-factor structure identified as errors, violations, attention lapses, and memory lapses, and the CFA revealed a good model fit after the removal of one item with a low factor loading and the permission of the error covariance between some items. The Chinese carless young drivers reported a comparatively low level of aberrant driving behaviors. The 3 most frequently reported behaviors were all lapses and the 3 least were all violations. Gender was the only significant predictor of the 2 lapses scales and lifetime mileage was the only significant predictor of the violations scale. Only the

Identifying beliefs underlying pre-drivers' intentions to take risks: An application of the Theory of Planned Behaviour.

PubMed

Rowe, Richard; Andrews, Elizabeth; Harris, Peter R; Armitage, Christopher J; McKenna, Frank P; Norman, Paul

2016-04-01

Novice motorists are at high crash risk during the first few months of driving. Risky behaviours such as speeding and driving while distracted are well-documented contributors to crash risk during this period. To reduce this public health burden, effective road safety interventions need to target the pre-driving period. We use the Theory of Planned Behaviour (TPB) to identify the pre-driver beliefs underlying intentions to drive over the speed limit (N=77), and while over the legal alcohol limit (N=72), talking on a hand-held mobile phone (N=77) and feeling very tired (N=68). The TPB explained between 41% and 69% of the variance in intentions to perform these behaviours. Attitudes were strong predictors of intentions for all behaviours. Subjective norms and perceived behavioural control were significant, though weaker, independent predictors of speeding and mobile phone use. Behavioural beliefs underlying these attitudes could be separated into those reflecting perceived disadvantages (e.g., speeding increases my risk of crash) and advantages (e.g., speeding gives me a thrill). Interventions that can make these beliefs safer in pre-drivers may reduce crash risk once independent driving has begun. Copyright © 2015 Elsevier Ltd. All rights reserved.

Key drivers of airline loyalty.

PubMed

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.

Key drivers of airline loyalty

PubMed Central

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

Macroscale patterns of synchrony identify complex relationships among spatial and temporal ecosystem drivers

USGS Publications Warehouse

Lottig, Noah R.; Tan, Pang-Ning; Wagner, Tyler; Cheruvelil, Kendra Spence; Soranno, Patricia A.; Stanley, Emily H.; Scott, Caren E.; Stow, Craig A.; Yuan, Shuai

2017-01-01

Ecology has a rich history of studying ecosystem dynamics across time and space that has been motivated by both practical management needs and the need to develop basic ideas about pattern and process in nature. In situations in which both spatial and temporal observations are available, similarities in temporal behavior among sites (i.e., synchrony) provide a means of understanding underlying processes that create patterns over space and time. We used pattern analysis algorithms and data spanning 22–25 yr from 601 lakes to ask three questions: What are the temporal patterns of lake water clarity at sub‐continental scales? What are the spatial patterns (i.e., geography) of synchrony for lake water clarity? And, what are the drivers of spatial and temporal patterns in lake water clarity? We found that the synchrony of water clarity among lakes is not spatially structured at sub‐continental scales. Our results also provide strong evidence that the drivers related to spatial patterns in water clarity are not related to the temporal patterns of water clarity. This analysis of long‐term patterns of water clarity and possible drivers contributes to understanding of broad‐scale spatial patterns in the geography of synchrony and complex relationships between spatial and temporal patterns across ecosystems.

Exploratory multinomial logit model-based driver injury severity analyses for teenage and adult drivers in intersection-related crashes.

PubMed

Wu, Qiong; Zhang, Guohui; Ci, Yusheng; Wu, Lina; Tarefder, Rafiqul A; Alcántara, Adélamar Dely

2016-05-18

Teenage drivers are more likely to be involved in severely incapacitating and fatal crashes compared to adult drivers. Moreover, because two thirds of urban vehicle miles traveled are on signal-controlled roadways, significant research efforts are needed to investigate intersection-related teenage driver injury severities and their contributing factors in terms of driver behavior, vehicle-infrastructure interactions, environmental characteristics, roadway geometric features, and traffic compositions. Therefore, this study aims to explore the characteristic differences between teenage and adult drivers in intersection-related crashes, identify the significant contributing attributes, and analyze their impacts on driver injury severities. Using crash data collected in New Mexico from 2010 to 2011, 2 multinomial logit regression models were developed to analyze injury severities for teenage and adult drivers, respectively. Elasticity analyses and transferability tests were conducted to better understand the quantitative impacts of these factors and the teenage driver injury severity model's generality. The results showed that although many of the same contributing factors were found to be significant in the both teenage and adult driver models, certain different attributes must be distinguished to specifically develop effective safety solutions for the 2 driver groups. The research findings are helpful to better understand teenage crash uniqueness and develop cost-effective solutions to reduce intersection-related teenage injury severities and facilitate driver injury mitigation research.

Portable Diagnostic Devices for Identifying Obstructive Sleep Apnea among Commercial Motor Vehicle Drivers: Considerations and Unanswered Questions

PubMed Central

Zhang, Chunbai; Berger, Mark; Malhotra, Atul; Kales, Stefanos N.

2012-01-01

Obstructive sleep apnea (OSA), a syndrome defined by breathing abnormalities during sleep, can lead to fatigue and excessive daytime sleepiness (EDS) with an increased risk of motor vehicle crashes. Identifying commercial motor vehicle operators with unrecognized OSA is a major public health priority. Portable monitors (PMs) are being actively marketed to trucking firms as potentially lower-cost and more accessible alternatives to the reference standard of in-laboratory polysomnography (PSG) in the diagnosis of OSA among commercial motor vehicle operators. Several factors regarding PMs remain uncertain in this unique patient population: their sensitivity and specificity; the cost-benefit ratio of the PMs versus PSG; potential barriers from human factors; and evolving technologic advancement. Human factors that alter test accuracy are a major concern among commercial drivers motivated to gain/maintain employment. Current available data using PMs as a diagnostic tool among CMV operators indicate relatively high data loss and high loss to follow-up. Loss to follow-up has also been an issue using PSG in commercial motor vehicle operators. Furthermore, PM testing and PM results interpretation protocols may have no sleep specialist oversight, and sometimes minimal physician oversight and involvement. Additional studies comparing unattended and unmonitored PMs directly against full in-laboratory PSG are needed to provide evidence for their efficacy among commercial motor vehicle operators. Citation: Zhang C; Berger M; Malhotra A; Kales SN. Portable diagnostic devices for identifying obstructive sleep apnea among commercial motor vehicle drivers: considerations and unanswered questions. SLEEP 2012;35(11):1481-1489. PMID:23115397

Driver behaviour profiles for road safety analysis.

PubMed

Ellison, Adrian B; Greaves, Stephen P; Bliemer, Michiel C J

2015-03-01

Driver behaviour is a contributing factor in over 90 percent of road crashes. As a consequence, there is significant benefit in identifying drivers who engage in unsafe driving practices. Driver behaviour profiles (DBPs) are introduced here as an approach for evaluating driver behaviour as a function of the risk of a casualty crash. They employ data collected using global positioning system (GPS) devices, supplemented with spatiotemporal information. These profiles are comprised of common risk scores that can be used to compare drivers between each other and across time and space. The paper details the development of these DBPs and demonstrates their use as an input into modelling the factors that influence driver behaviour. The results show that even having controlled for the influence of the road environment, these factors remain the strongest predictors of driver behaviour suggesting different spatiotemporal environments elicit a variety of psychological responses in drivers. The approach and outcomes will be of interest to insurance companies in enhancing the risk-profiling of drivers with on-road driving and government through assessing the impacts of behaviour-change interventions. Copyright © 2015 Elsevier Ltd. All rights reserved.

Driver behavior analysis for right-turn drivers at signalized intersections using SHRP 2 naturalistic driving study data.

PubMed

Wu, Jianqing; Xu, Hao

2017-12-01

Understanding driver behavior is important for traffic safety and operation, especially at intersections where different traffic movements conflict. While most driver-behavior studies are based on simulation, this paper documents the analysis of driver-behavior at signalized intersections with the SHRP 2 Naturalistic Driving Study (NDS) data. This study analyzes the different influencing factors on the operation (speed control) and observation of right-turn drivers. A total of 300 NDS trips at six signalized intersections were used, including the NDS time-series sensor data, the forward videos and driver face videos. Different factors of drivers, vehicles, roads and environments were studied for their influence on driver behavior. An influencing index function was developed and the index was calculated for each influencing factor to quantitatively describe its influencing level. The influencing index was applied to prioritize the factors, which facilitates development and selection of safety countermeasures to improve intersection safety. Drivers' speed control was analyzed under different conditions with consideration of the prioritized influencing factors. Vehicle type, traffic signal status, conflicting traffic, conflicting pedestrian and driver age group were identified as the five major influencing factors on driver observation. This research revealed that drivers have high acceleration and low observation frequency under Right-Turn-On-Red (RTOR), which constituted potential danger for other roadway users, especially for pedestrians. As speed has a direct influence on crash rates and severities, the revealed speed patterns of the different situations also benefit selection of safety countermeasures at signalized intersections. Published by Elsevier Ltd.

Graduated driver license compliant teens involved in fatal motor vehicle crashes.

PubMed

Pressley, Joyce C; Addison, Diane; Dawson, Patrick; Nelson, Sharifa S

2015-09-01

Significant reductions in motor vehicle injury mortality have been reported for teen drivers after passage of graduated driver licensing (GDL), seat belt, and no tolerance alcohol and drug laws. Despite this, teen drivers remain a vulnerable population with elevated fatal crash involvement. This study examines driver, vehicle, and crash characteristics of GDL-compliant, belted, and unimpaired teen drivers with the goal of identifying areas where further improvements might be realized. The Fatality Analysis Reporting System (FARS) for 2007 to 2009 was used to examine and classify driver violations/errors in compliant teen drivers (n = 1,571) of passenger vehicles involved in a fatal collision. Teens driving unbelted, non-GDL compliant, or impaired by alcohol or drugs were excluded. Statistical analysis used χ, Fisher's exact and multivariable logistic regression. Odds ratios are reported with 95% confidence intervals. Significance was defined as p < 0.05. Nearly one third (n = 1,571) of teen drivers involved in a fatal motor vehicle crash were GDL compliant, unimpaired, and belted. The majority held an intermediate GDL license (90.6%). Crash-related factors were identified for 63.1% of fatal crashes. Age- and sex-adjusted odds identified overcorrecting, speeding, lane errors, school morning crashes, distractions, and driving on slippery surfaces as having increased odds of fatality for the teen driver as well as newer vehicle models and heavier vehicle weight as protective. Among compliant drivers, weekday crashes before and after school and committing a driving violation at the time of crash were associated with increased risk of driver death and higher incidence of incapacitating injury in surviving drivers. Therapeutic study, level V.

Acceptability and validity of older driver screening with the DrivingHealth Inventory.

PubMed

Edwards, Jerri D; Leonard, Kathleen M; Lunsman, Melissa; Dodson, Joan; Bradley, Stacy; Myers, Charlsie A; Hubble, Bridgette

2008-05-01

Research has indicated that technology can be effectively used to identify high-risk older drivers. However, adaptation of such technology has been limited. Researchers debate whether older drivers represent a safety problem as well as whether they should be screened for driving fitness. The present study examined how drivers feel regarding technological screening and mandatory state testing. The validity and acceptability of a new technological screening battery for identifying high-risk drivers, the DrivingHealth Inventory (DHI), was also evaluated. In a sample of 258 Alabama drivers aged 18-87, older drivers performed significantly worse than younger drivers on sensory, cognitive, and physical subtests of the DHI, and older drivers with a crash history performed worse than older drivers without crashes. Regardless of age, 90% of participants supported states requiring screening for older drivers' license renewal. The majority of the participants (72%) supported use of technological screening batteries such as the DHI as a driver screening tool. Considering the acceptability and potential efficacy of the DHI, it may be a useful tool in evaluating driving fitness among older adults.

Association of Graduated Driver Licensing With Driver, Non-Driver, and Total Fatalities Among Adolescents.

PubMed

Zhu, Motao; Zhao, Songzhu; Long, D Leann; Curry, Allison E

2016-07-01

Graduated driver licensing systems typically require an extended learner permit phase, and create night-time driving or passenger restrictions for adolescent drivers. Restricted driving might increase the use of alternative transportation to replace driving and consequently increase crashes and injuries for passengers, bus riders, pedestrians, and bicyclists. This study examined whether graduated driver licensing increases non-driver fatalities among adolescents, and whether it reduces total traffic fatalities combining drivers and non-drivers. Longitudinal analyses were conducted using data from the 1995-2012 U.S. Fatality Analysis Reporting System. Adjusted rate ratios were estimated for being fatally injured in a crash according to: (1) presence/absence of a graduated driver licensing system; and (2) four levels of graduated driver licensing systems (absent, weak, medium, strong). Analyses were conducted in 2015. Among adolescents aged 16 years, graduated driver licensing was not associated with increased passenger fatalities (adjusted rate ratio, 0.96; 95% CI=0.90, 1.03) or pedestrian and bicyclist fatalities (adjusted rate ratio, 1.09; 95% CI=0.85, 1.39), but was associated with an 11% reduction in total traffic fatalities. Among those aged 17 years, graduated driver licensing was not associated with increased fatalities as passengers, pedestrians, or bicyclists, and was not associated with reduced total traffic fatalities. In general, graduated driver licensing systems were not associated with increased fatalities as passengers, pedestrians, bicyclists, and bus riders. Graduated driver licensing systems were associated with reduced total fatalities of adolescents aged 16 years. Copyright © 2016 American Journal of Preventive Medicine. Published by Elsevier Inc. All rights reserved.

Older Driver and Passenger Collaboration for Wayfinding in Unfamiliar Areas

ERIC Educational Resources Information Center

Bryden, Kelly Jane; Charlton, Judith; Oxley, Jennifer; Lowndes, Georgia

2014-01-01

Passenger collaboration offers a potential compensatory strategy to assist older drivers who have difficulty driving in unfamiliar areas (wayfinding). This article describes a survey of 194 healthy, community-dwelling older drivers and their regular passengers to investigate how passengers assist drivers, and to identify the characteristics of…

Analysis of intra-host genetic diversity of Prunus necrotic ringspot virus (PNRSV) using amplicon next generation sequencing

PubMed Central

Constable, Fiona E.; Nancarrow, Narelle; Plummer, Kim M.; Rodoni, Brendan

2017-01-01

PCR amplicon next generation sequencing (NGS) analysis offers a broadly applicable and targeted approach to detect populations of both high- or low-frequency virus variants in one or more plant samples. In this study, amplicon NGS was used to explore the diversity of the tripartite genome virus, Prunus necrotic ringspot virus (PNRSV) from 53 PNRSV-infected trees using amplicons from conserved gene regions of each of PNRSV RNA1, RNA2 and RNA3. Sequencing of the amplicons from 53 PNRSV-infected trees revealed differing levels of polymorphism across the three different components of the PNRSV genome with a total number of 5040, 2083 and 5486 sequence variants observed for RNA1, RNA2 and RNA3 respectively. The RNA2 had the lowest diversity of sequences compared to RNA1 and RNA3, reflecting the lack of flexibility tolerated by the replicase gene that is encoded by this RNA component. Distinct PNRSV phylo-groups, consisting of closely related clusters of sequence variants, were observed in each of PNRSV RNA1, RNA2 and RNA3. Most plant samples had a single phylo-group for each RNA component. Haplotype network analysis showed that smaller clusters of PNRSV sequence variants were genetically connected to the largest sequence variant cluster within a phylo-group of each RNA component. Some plant samples had sequence variants occurring in multiple PNRSV phylo-groups in at least one of each RNA and these phylo-groups formed distinct clades that represent PNRSV genetic strains. Variants within the same phylo-group of each Prunus plant sample had ≥97% similarity and phylo-groups within a Prunus plant sample and between samples had less ≤97% similarity. Based on the analysis of diversity, a definition of a PNRSV genetic strain was proposed. The proposed definition was applied to determine the number of PNRSV genetic strains in each of the plant samples and the complexity in defining genetic strains in multipartite genome viruses was explored. PMID:28632759

Analysis of intra-host genetic diversity of Prunus necrotic ringspot virus (PNRSV) using amplicon next generation sequencing.

PubMed

Kinoti, Wycliff M; Constable, Fiona E; Nancarrow, Narelle; Plummer, Kim M; Rodoni, Brendan

2017-01-01

PCR amplicon next generation sequencing (NGS) analysis offers a broadly applicable and targeted approach to detect populations of both high- or low-frequency virus variants in one or more plant samples. In this study, amplicon NGS was used to explore the diversity of the tripartite genome virus, Prunus necrotic ringspot virus (PNRSV) from 53 PNRSV-infected trees using amplicons from conserved gene regions of each of PNRSV RNA1, RNA2 and RNA3. Sequencing of the amplicons from 53 PNRSV-infected trees revealed differing levels of polymorphism across the three different components of the PNRSV genome with a total number of 5040, 2083 and 5486 sequence variants observed for RNA1, RNA2 and RNA3 respectively. The RNA2 had the lowest diversity of sequences compared to RNA1 and RNA3, reflecting the lack of flexibility tolerated by the replicase gene that is encoded by this RNA component. Distinct PNRSV phylo-groups, consisting of closely related clusters of sequence variants, were observed in each of PNRSV RNA1, RNA2 and RNA3. Most plant samples had a single phylo-group for each RNA component. Haplotype network analysis showed that smaller clusters of PNRSV sequence variants were genetically connected to the largest sequence variant cluster within a phylo-group of each RNA component. Some plant samples had sequence variants occurring in multiple PNRSV phylo-groups in at least one of each RNA and these phylo-groups formed distinct clades that represent PNRSV genetic strains. Variants within the same phylo-group of each Prunus plant sample had ≥97% similarity and phylo-groups within a Prunus plant sample and between samples had less ≤97% similarity. Based on the analysis of diversity, a definition of a PNRSV genetic strain was proposed. The proposed definition was applied to determine the number of PNRSV genetic strains in each of the plant samples and the complexity in defining genetic strains in multipartite genome viruses was explored.

Obstructive sleep apnea in North American commercial drivers.

PubMed

Kales, Stefanos N; Straubel, Madeleine G

2014-01-01

The most common medical cause of excessive daytime sleepiness (EDS) is obstructive sleep apnea (OSA). Specifically, among an estimated 14 million US commercial drivers, 17-28% or 2.4 to 3.9 million are expected to have OSA. Based on existing epidemiologic evidence, most of these drivers are undiagnosed and not adequately treated. Untreated OSA increases the risk of vehicular crashes as documented in multiple independent studies and by meta-analysis. Therefore, identifying commercial drivers with OSA and having them effectively treated should decrease crash-related fatalities and injuries. Several strategies are available for screening and identifying drivers with OSA. The simplest and most effective objective strategies use body mass index (BMI) cutoffs for obesity. Functional screens are promising adjuncts to other objective tests. The most effective approach will likely be a combination of a good questionnaire; BMI measures; and a careful physician-obtained history complemented by a functional screen.

Using fixed-parameter and random-parameter ordered regression models to identify significant factors that affect the severity of drivers' injuries in vehicle-train collisions.

PubMed

Dabbour, Essam; Easa, Said; Haider, Murtaza

2017-10-01

This study attempts to identify significant factors that affect the severity of drivers' injuries when colliding with trains at railroad-grade crossings by analyzing the individual-specific heterogeneity related to those factors over a period of 15 years. Both fixed-parameter and random-parameter ordered regression models were used to analyze records of all vehicle-train collisions that occurred in the United States from January 1, 2001 to December 31, 2015. For fixed-parameter ordered models, both probit and negative log-log link functions were used. The latter function accounts for the fact that lower injury severity levels are more probable than higher ones. Separate models were developed for heavy and light-duty vehicles. Higher train and vehicle speeds, female, and young drivers (below the age of 21 years) were found to be consistently associated with higher severity of drivers' injuries for both heavy and light-duty vehicles. Furthermore, favorable weather, light-duty trucks (including pickup trucks, panel trucks, mini-vans, vans, and sports-utility vehicles), and senior drivers (above the age of 65 years) were found be consistently associated with higher severity of drivers' injuries for light-duty vehicles only. All other factors (e.g. air temperature, the type of warning devices, darkness conditions, and highway pavement type) were found to be temporally unstable, which may explain the conflicting findings of previous studies related to those factors. Copyright © 2017 Elsevier Ltd. All rights reserved.

Driving, navigation, and vehicular technology: experiences of older drivers and their co-pilots.

PubMed

Vrkljan, Brenda H; Polgar, Janice Miller

2007-12-01

The objective of this article is to explore relationship between older drivers and their passengers (co-pilots) and potential implications of in-vehicle navigation technology on their driving safety. Semi-structured interviews were conducted with 44 healthy, community-dwelling older adults (aged 60-83) or 22 married couples. Males identified themselves as drivers and females identified themselves as passengers (i.e., co-pilot). Findings indicate that operating a motor vehicle in older adulthood is a shared activity between drivers and passengers. Older drivers and co-pilots reported their level of interaction depended on their familiarity with their route. Navigating unfamiliar areas, particularly large urban centers, was identified as the most challenging driving situation. Participants identified their level of collaboration would increase with the advent of in-vehicle navigation technology. Safety concerns related to the use of this technology, included distraction of both drivers and passengers. Differences amongst couples in their perceptions of using this technology were linked to their level of experience with using other forms of technology. Older drivers and passengers identified working closely together when operating a motor vehicle. Further investigation into the effects of in-vehicle navigation technology on the driving safety of older drivers and their co-pilots is warranted.

Shedding Light on the Microbial Community of the Macropod Foregut Using 454-Amplicon Pyrosequencing

PubMed Central

Gulino, Lisa-Maree; Ouwerkerk, Diane; Kang, Alicia Y. H.; Maguire, Anita J.; Kienzle, Marco; Klieve, Athol V.

2013-01-01

Twenty macropods from five locations in Queensland, Australia, grazing on a variety of native pastures were surveyed and the bacterial community of the foregut was examined using 454-amplicon pyrosequencing. Specifically, the V3/V4 region of 16S rRNA gene was examined. A total of 5040 OTUs were identified in the data set (post filtering). Thirty-two OTUs were identified as ‘shared’ OTUS (i.e. present in all samples) belonging to either Firmicutes or Bacteroidetes (Clostridiales/Bacteroidales). These phyla predominated the general microbial community in all macropods. Genera represented within the shared OTUs included: unclassified Ruminococcaceae, unclassified Lachnospiraceae, unclassified Clostridiales, Peptococcus sp. Coprococcus spp., Streptococcus spp., Blautia sp., Ruminoccocus sp., Eubacterium sp., Dorea sp., Oscillospira sp. and Butyrivibrio sp. The composition of the bacterial community of the foregut samples of each the host species (Macropus rufus, Macropus giganteus and Macropus robustus) was significantly different allowing differentiation between the host species based on alpha and beta diversity measures. Specifically, eleven dominant OTUs that separated the three host species were identified and classified as: unclassified Ruminococcaceae, unclassified Bacteroidales, Prevotella spp. and a Syntrophococcus sucromutans. Putative reductive acetogens and fibrolytic bacteria were also identified in samples. Future work will investigate the presence and role of fibrolytics and acetogens in these ecosystems. Ideally, the isolation and characterization of these organisms will be used for enhanced feed efficiency in cattle, methane mitigation and potentially for other industries such as the biofuel industry. PMID:23626688

Shedding light on the microbial community of the macropod foregut using 454-amplicon pyrosequencing.

PubMed

Gulino, Lisa-Maree; Ouwerkerk, Diane; Kang, Alicia Y H; Maguire, Anita J; Kienzle, Marco; Klieve, Athol V

2013-01-01

Twenty macropods from five locations in Queensland, Australia, grazing on a variety of native pastures were surveyed and the bacterial community of the foregut was examined using 454-amplicon pyrosequencing. Specifically, the V3/V4 region of 16S rRNA gene was examined. A total of 5040 OTUs were identified in the data set (post filtering). Thirty-two OTUs were identified as 'shared' OTUS (i.e. present in all samples) belonging to either Firmicutes or Bacteroidetes (Clostridiales/Bacteroidales). These phyla predominated the general microbial community in all macropods. Genera represented within the shared OTUs included: unclassified Ruminococcaceae, unclassified Lachnospiraceae, unclassified Clostridiales, Peptococcus sp. Coprococcus spp., Streptococcus spp., Blautia sp., Ruminoccocus sp., Eubacterium sp., Dorea sp., Oscillospira sp. and Butyrivibrio sp. The composition of the bacterial community of the foregut samples of each the host species (Macropus rufus, Macropus giganteus and Macropus robustus) was significantly different allowing differentiation between the host species based on alpha and beta diversity measures. Specifically, eleven dominant OTUs that separated the three host species were identified and classified as: unclassified Ruminococcaceae, unclassified Bacteroidales, Prevotella spp. and a Syntrophococcus sucromutans. Putative reductive acetogens and fibrolytic bacteria were also identified in samples. Future work will investigate the presence and role of fibrolytics and acetogens in these ecosystems. Ideally, the isolation and characterization of these organisms will be used for enhanced feed efficiency in cattle, methane mitigation and potentially for other industries such as the biofuel industry.

Identification and Evaluation of Single-Nucleotide Polymorphisms in Allotetraploid Peanut (Arachis hypogaea L.) Based on Amplicon Sequencing Combined with High Resolution Melting (HRM) Analysis.

PubMed

Hong, Yanbin; Pandey, Manish K; Liu, Ying; Chen, Xiaoping; Liu, Hong; Varshney, Rajeev K; Liang, Xuanqiang; Huang, Shangzhi

2015-01-01

The cultivated peanut (Arachis hypogaea L.) is an allotetraploid (AABB) species derived from the A-genome (Arachis duranensis) and B-genome (Arachis ipaensis) progenitors. Presence of two versions of a DNA sequence based on the two progenitor genomes poses a serious technical and analytical problem during single nucleotide polymorphism (SNP) marker identification and analysis. In this context, we have analyzed 200 amplicons derived from expressed sequence tags (ESTs) and genome survey sequences (GSS) to identify SNPs in a panel of genotypes consisting of 12 cultivated peanut varieties and two diploid progenitors representing the ancestral genomes. A total of 18 EST-SNPs and 44 genomic-SNPs were identified in 12 peanut varieties by aligning the sequence of A. hypogaea with diploid progenitors. The average frequency of sequence polymorphism was higher for genomic-SNPs than the EST-SNPs with one genomic-SNP every 1011 bp as compared to one EST-SNP every 2557 bp. In order to estimate the potential and further applicability of these identified SNPs, 96 peanut varieties were genotyped using high resolution melting (HRM) method. Polymorphism information content (PIC) values for EST-SNPs ranged between 0.021 and 0.413 with a mean of 0.172 in the set of peanut varieties, while genomic-SNPs ranged between 0.080 and 0.478 with a mean of 0.249. Total 33 SNPs were used for polymorphism detection among the parents and 10 selected lines from mapping population Y13Zh (Zhenzhuhei × Yueyou13). Of the total 33 SNPs, nine SNPs showed polymorphism in the mapping population Y13Zh, and seven SNPs were successfully mapped into five linkage groups. Our results showed that SNPs can be identified in allotetraploid peanut with high accuracy through amplicon sequencing and HRM assay. The identified SNPs were very informative and can be used for different genetic and breeding applications in peanut.

Mutation drivers of immunological responses to cancer

PubMed Central

Porta-Pardo, Eduard; Godzik, Adam

2016-01-01

In cancer immunology, somatic missense mutations have been mostly studied regarding their role in the generation of neoantigens. However, growing evidence suggests that mutations in certain genes, such as CASP8 or TP53, influence the immune response against a tumor by other mechanisms. Identifying these genes and mechanisms is important because, just as the identification of cancer driver genes led to the development of personalized cancer therapies, a comprehensive catalog of such cancer immunity drivers will aid in the development of therapies aimed at restoring antitumor immunity. Here we present an algorithm, domainXplorer, that can be used to identify potential cancer immunity drivers. To demonstrate its potential, we used it to analyze a dataset of 5,164 tumor samples from TCGA and to identify protein domains whose mutation status correlates with the presence of immune cells in cancer tissue (immune infiltrate). We identified 122 such protein regions including several that belong to proteins with known roles in immune response, such as C2, CD163L1, or FCγR2A. In several cases we show that mutations within the same protein can be associated with more or less immune cell infiltration, depending on the specific domain mutated. These results expand the catalog of potential cancer immunity drivers and highlight the importance of taking into account the structural context of somatic mutations when analyzing their potential association with immune phenotypes. PMID:27401919

Physics at an upgraded Fermilab proton driver

DOE Office of Scientific and Technical Information (OSTI.GOV)

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.

The effect of the learner license Graduated Driver Licensing components on teen drivers' crashes.

PubMed

Ehsani, Johnathon Pouya; Bingham, C Raymond; Shope, Jean T

2013-10-01

Most studies evaluating the effectiveness of Graduated Driver Licensing (GDL) have focused on the overall system. Studies examining individual components have rarely accounted for the confounding of multiple, simultaneously implemented components. The purpose of this paper is to quantify the effects of a required learner license duration and required hours of supervised driving on teen driver fatal crashes. States that introduced a single GDL component independent of any other during the period 1990-2009 were identified. Monthly and quarterly fatal crash rates per 100,000 population of 16- and 17-year-old drivers were analyzed using single-state time series analysis, adjusting for adult crash rates and gasoline prices. Using the parameter estimates from each state's time series model, the pooled effect of each GDL component on 16- and 17-year-old drivers' fatal crashes was estimated using a random effects meta-analytic model to combine findings across states. In three states, a six-month minimum learner license duration was associated with a significant decline in combined 16- and 17-year-old drivers' fatal crash rates. The pooled effect of the minimum learner license duration across all states in the sample was associated with a significant change in combined 16- and 17-year-old driver fatal crash rates of -.07 (95% Confidence Interval [CI] -.11, -.03). Following the introduction of 30 h of required supervised driving in one state, novice drivers' fatal crash rates increased 35%. The pooled effect across all states in the study sample of having a supervised driving hour requirement was not significantly different from zero (.04, 95% CI -.15, .22). These findings suggest that a learner license duration of at least six-months may be necessary to achieve a significant decline in teen drivers' fatal crash rates. Evidence of the effect of required hours of supervised driving on teen drivers' fatal crash rates was mixed. Copyright © 2013 Elsevier Ltd. All rights

AMPLISAS: a web server for multilocus genotyping using next-generation amplicon sequencing data.

PubMed

Sebastian, Alvaro; Herdegen, Magdalena; Migalska, Magdalena; Radwan, Jacek

2016-03-01

Next-generation sequencing (NGS) technologies are revolutionizing the fields of biology and medicine as powerful tools for amplicon sequencing (AS). Using combinations of primers and barcodes, it is possible to sequence targeted genomic regions with deep coverage for hundreds, even thousands, of individuals in a single experiment. This is extremely valuable for the genotyping of gene families in which locus-specific primers are often difficult to design, such as the major histocompatibility complex (MHC). The utility of AS is, however, limited by the high intrinsic sequencing error rates of NGS technologies and other sources of error such as polymerase amplification or chimera formation. Correcting these errors requires extensive bioinformatic post-processing of NGS data. Amplicon Sequence Assignment (AMPLISAS) is a tool that performs analysis of AS results in a simple and efficient way, while offering customization options for advanced users. AMPLISAS is designed as a three-step pipeline consisting of (i) read demultiplexing, (ii) unique sequence clustering and (iii) erroneous sequence filtering. Allele sequences and frequencies are retrieved in excel spreadsheet format, making them easy to interpret. AMPLISAS performance has been successfully benchmarked against previously published genotyped MHC data sets obtained with various NGS technologies. © 2015 John Wiley & Sons Ltd.

Physicochemical Drivers of Microbial Community Structure in Sediments of Lake Hazen, Nunavut, Canada.

PubMed

Ruuskanen, Matti O; St Pierre, Kyra A; St Louis, Vincent L; Aris-Brosou, Stéphane; Poulain, Alexandre J

2018-01-01

The Arctic is undergoing rapid environmental change, potentially affecting the physicochemical constraints of microbial communities that play a large role in both carbon and nutrient cycling in lacustrine environments. However, the microbial communities in such Arctic environments have seldom been studied, and the drivers of their composition are poorly characterized. To address these gaps, we surveyed the biologically active surface sediments in Lake Hazen, the largest lake by volume north of the Arctic Circle, and a small lake and shoreline pond in its watershed. High-throughput amplicon sequencing of the 16S rRNA gene uncovered a community dominated by Proteobacteria, Bacteroidetes, and Chloroflexi, similar to those found in other cold and oligotrophic lake sediments. We also show that the microbial community structure in this Arctic polar desert is shaped by pH and redox gradients. This study lays the groundwork for predicting how sediment microbial communities in the Arctic could respond as climate change proceeds to alter their physicochemical constraints.

Driver distraction and driver inattention: definition, relationship and taxonomy.

PubMed

Regan, Michael A; Hallett, Charlene; Gordon, Craig P

2011-09-01

There is accumulating evidence that driver distraction and driver inattention are leading causes of vehicle crashes and incidents. However, as applied psychological constructs, they have been inconsistently defined and the relationship between them remains unclear. In this paper, driver distraction and driver inattention are defined and a taxonomy is presented in which driver distraction is distinguished from other forms of driver inattention. The taxonomy and the definitions provided are intended (a) to provide a common framework for coding different forms of driver inattention as contributing factors in crashes and incidents, so that comparable estimates of their role as contributing factors can be made across different studies, and (b) to make it possible to more accurately interpret and compare, across studies, the research findings for a given form of driver inattention. Copyright © 2011 Elsevier Ltd. All rights reserved.

Simultaneous Identification of Multiple Driver Pathways in Cancer

PubMed Central

Leiserson, Mark D. M.; Blokh, Dima

2013-01-01

Distinguishing the somatic mutations responsible for cancer (driver mutations) from random, passenger mutations is a key challenge in cancer genomics. Driver mutations generally target cellular signaling and regulatory pathways consisting of multiple genes. This heterogeneity complicates the identification of driver mutations by their recurrence across samples, as different combinations of mutations in driver pathways are observed in different samples. We introduce the Multi-Dendrix algorithm for the simultaneous identification of multiple driver pathways de novo in somatic mutation data from a cohort of cancer samples. The algorithm relies on two combinatorial properties of mutations in a driver pathway: high coverage and mutual exclusivity. We derive an integer linear program that finds set of mutations exhibiting these properties. We apply Multi-Dendrix to somatic mutations from glioblastoma, breast cancer, and lung cancer samples. Multi-Dendrix identifies sets of mutations in genes that overlap with known pathways – including Rb, p53, PI(3)K, and cell cycle pathways – and also novel sets of mutually exclusive mutations, including mutations in several transcription factors or other genes involved in transcriptional regulation. These sets are discovered directly from mutation data with no prior knowledge of pathways or gene interactions. We show that Multi-Dendrix outperforms other algorithms for identifying combinations of mutations and is also orders of magnitude faster on genome-scale data. Software available at: http://compbio.cs.brown.edu/software. PMID:23717195

Viability-qPCR for detecting Legionella: Comparison of two assays based on different amplicon lengths.

PubMed

Ditommaso, Savina; Giacomuzzi, Monica; Ricciardi, Elisa; Zotti, Carla M

2015-08-01

Two different real-time quantitative PCR (PMA-qPCR) assays were applied for quantification of Legionella spp. by targeting a long amplicon (approx 400 bp) of 16S rRNA gene and a short amplicon (approx. 100 bp) of 5S rRNA gene. Purified DNA extracts from pure cultures of Legionella spp. and from environmental water samples were quantified. Application of the two assays to quantify Legionella in artificially contaminated water achieved that both assays were able to detect Legionella over a linear range of 10 to 10(5) cells ml(-1). A statistical analysis of the standard curves showed that both assays were linear with a good correlation coefficient (R(2) = 0.99) between the Ct and the copy number. Amplification with the reference assay was the most effective for detecting low copy numbers (1 bacterium per PCR mixture). Using selective quantification of viable Legionella by the PMA-qPCR method we obtained a greater inhibition of the amplification of the 400-bp 16S gene fragment (Δlog(10) = 3.74 ± 0.39 log(10) GU ml(-1)). A complete inhibition of the PCR signal was obtained when heat-killed cells in a concentration below 1 × 10(5) cells ml(-1) were pretreated with PMA. Analysing short amplicon sizes led to only 2.08 log reductions in the Legionella dead-cell signal. When we tested environmental water samples, the two qPCR assays were in good agreement according to the kappa index (0.741). Applying qPCR combined with PMA treatment, we also obtained a good agreement (kappa index 0.615). The comparison of quantitative results shows that both assays yielded the same quantification sensitivity (mean log = 4.59 vs mean log = 4.31). Copyright © 2015 Elsevier Ltd. All rights reserved.

Graduated driver licensing for reducing motor vehicle crashes among young drivers.

PubMed

Russell, Kelly F; Vandermeer, Ben; Hartling, Lisa

2011-10-05

Graduated driver licensing (GDL) has been proposed as a means of reducing crash rates among novice drivers by gradually introducing them to higher risk driving situations. To examine the effectiveness of GDL in reducing crash rates among young drivers. Studies were identified through searching MEDLINE, EMBASE, CINAHL, Healthstar, Web of Science, NTIS Bibliographic Database, TRIS Online, SIGLE, the World Wide Web, conference proceedings, consultation with experts and reference lists in relevant published literature. The searches were conducted from the time of inception to May 2009, and the Cochrane Injuries Group conducted an updated search of the TRANSPORT database in September 2009. Studies were included if: 1) they compared outcomes pre- and post-implementation of a GDL program within the same jurisdiction, 2) comparisons were made between jurisdictions with and without GDL, or 3) both. Studies had to report at least one objective, quantified outcome. Results were not pooled due to substantial heterogeneity. Percentage change was calculated for each year after the intervention, using one year prior to the intervention as baseline. Results were adjusted by internal controls. Analyses were stratified by denominators (population, licensed drivers). Results were calculated for the different crash types and presented for 16 year-olds alone as well as all teenage drivers. We included 34 studies evaluating 21 GDL programs and 2 analyses of >40 US states. GDL programs were implemented in the US (n=16), Canada (n=3), New Zealand (n=1), and Australia (n=1) and varied in their restrictions during the intermediate stage. Based on the Insurance Institute for Highway Safety (IIHS) classification, eleven programs were good, four were fair, five were marginal, one was poor and two could not be assessed. Reductions in crash rates were seen in all jurisdictions and for all crash types. Among 16 year-old drivers, the median decrease in per population adjusted overall crash rates

Drivers of atmospheric evaporative demand during African droughts

NASA Astrophysics Data System (ADS)

Blakeley, S. L.; Harrison, L.; Hobbins, M.; Dewes, C.; Funk, C. C.; Shukla, S.; Husak, G. J.

2017-12-01

Seeking to advance the practice of famine early warning across sub-Saharan Africa we illuminate past drivers of high-impact droughts to gain a better understanding of the evaporative processes involved in drought dynamics. Atmospheric evaporative demand (ETo) is often used to estimate plant water balance and drought impacts to vegetation, and previously demonstrated linkages between precipitation, temperature, and ETo need to be better understood. This work is timely as new data streams will enable near-real-time monitoring of ETo and incorporation of ETo forecasts into seasonal outlooks for African growing seasons. For historical droughts during major growing seasons in sub-Saharan Africa, we evaluate ETo and identify main drivers for drought cases-identified based on below-normal precipitation during the wettest three months of the growing season-and contrast these with the ETo drivers that dominate in wetter years (we also consider droughts triggered by above normal ETo). Our focus is on regions of Africa where adequate precipitation is important for productive agriculture and pastoral activities and where evaporative demand might exacerbate moisture limitations. It is expected that important ETo drivers are partly connected with precipitation-related processes but that there are variations between regions and events. The goal here is to provide a generalized understanding of what aspects of evaporative demand historically have posed an additional hazard to plant stress and how precipitation outcomes are responsible for the ETo drivers. In addition, we explore whether there have been discernible changes through time in regard to ETo drivers during below-normal precipitation seasons. Upper and lower terciles of CHIRPS precipitation are used to identify anomalous dry and wet cases. The ETo dataset spans the 1980-near present period and is calculated following ASCE's formulation of Penman-Monteith method driven by daily temperature, humidity, wind speed, and solar

Effects of driver cell-phone use on driver aggression.

PubMed

McGarva, Andrew R; Ramsey, Matthew; Shear, Suzannah A

2006-04-01

Using 2 field procedures, the authors assessed impacts of cell-phone use on mild forms of driver aggression. Participants were 135 drivers traveling within a city of approximately 17,000 people in an otherwise little-populated region of western North Dakota. The authors videotaped the participants while a confederate driver in a low-status vehicle frustrated them. In Experiment 1, the confederate was traveling well under the posted speed limit. In Experiment 2, the confederate remained motionless at a stoplight that had turned green. When the confederate visibly talked on a hand-held cell phone (n = 67), male drivers exhibited their frustration by honking their horn more quickly and frequently than did drivers in no-cell-phone trials, and female drivers were more angry according to blind judgments of videotaped facial expressions that were compared with those of drivers in no-cell-phone trials (n = 68). The present results suggested that driver cell-phone use contributes to the growing crisis of roadway aggression.

Teaching Driver Education Technology to Novice Drivers.

ERIC Educational Resources Information Center

Young, Anthony

A cybernetic unit in driver education was developed to help grade 10 students develop the skills needed to acquire and process driver education information and prepare for the driving phase of driver education in grade 11. Students used a simulator to engage in a series of scenarios designed to promote development of social, behavioral, and mental…

Aging baby boomers--a blessing or challenge for driver licensing authorities.

PubMed

Dobbs, Bonnie M

2008-08-01

In less than 5 years, the first wave of baby boomers will begin turning 65, with the last wave of boomers entering their senior years in January 2029. Currently, boomers make up a significant percentage of the population in Canada, the United States, and other developed countries. The baby boom generation has had a profound impact on our society over the last six decades, and this large cohort will continue to exert its influence for several decades to come. Central to this article is the rapid growth in the number of persons 65 years of age and older, beginning in 2011, with a corresponding increase in the number of older drivers. The demographic shift has important implications for licensing authorities, the regulatory bodies charged with licensing and 'fitness to drive' decisions. The objectives of this paper are to summarize the published scientific literature on licensing policies and procedures currently in use for older drivers, discuss their limitations, and provide recommendations for meeting the upcoming challenges of an aging baby boomer population of drivers. Online searches were conducted using the following databases: PsycINFO, MEDLINE, Scopus, and TRIS. Google and Google Scholar also were searched for scientific articles. References identified from database and online searches were examined for relevant articles. A number of studies have investigated the utility of different licensing policies and procedures for identifying older drivers who may be at risk for impaired driving performance. Overall, results suggest that current policies and procedures are ineffective in identifying high-risk older drivers. The results also emphasize the need for a different approach for the identification of high risk older drivers by licensing agencies. Recommendations to assist with that goal are provided. The aging of the baby boomer population, combined with the projected high crash rates for this cohort of drivers as it moves through the senior years, underscores

Factors associated with hit-and-run pedestrian fatalities and driver identification.

PubMed

MacLeod, Kara E; Griswold, Julia B; Arnold, Lindsay S; Ragland, David R

2012-03-01

As hit-and-run crashes account for a significant proportion of pedestrian fatalities, a better understanding of these crash types will assist efforts to reduce these fatalities. Of the more than 48,000 pedestrian deaths that were recorded in the United States between 1998 and 2007, 18.1% of them were caused by hit-and-run drivers. Using national data on single pedestrian-motor vehicle fatal crashes (1998-2007), logistic regression analyses were conducted to identify factors related to hit-and-run and to identify factors related to the identification of the hit-and-run driver. Results indicate an increased risk of hit-and-run in the early morning, poor light conditions, and on the weekend. There may also be an association between the type of victim and the likelihood of the driver leaving and being identified. Results also indicate that certain driver characteristics, behavior, and driving history are associated with hit-and-run. Alcohol use and invalid license were among the leading driver factor associated with an increased risk of hit-and-run. Prevention efforts that address such issues could substantially reduce pedestrian fatalities as a result of hit-and-run. However, more information about this driver population may be necessary. Copyright © 2011. Published by Elsevier Ltd.

The driver, the road, the rules … and the rest? A systems-based approach to young driver road safety.

PubMed

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. Copyright © 2014 Elsevier Ltd. All rights reserved.

Naturalistic distraction and driving safety in older drivers

PubMed Central

Aksan, Nazan; Dawson, Jeffrey D.; Emerson, Jamie L.; Yu, Lixi; Uc, Ergun Y.; Anderson, Steven W.; Rizzo, Matthew

2013-01-01

Objective This study aimed to quantify and compare performance of middle-aged and older drivers during a naturalistic distraction paradigm (visual search for roadside targets) and predict older driver performance given functioning in visual, motor, and cognitive domains. Background Distracted driving can imperil healthy adults and may disproportionally affect the safety of older drivers with visual, motor, and cognitive decline. Methods Two hundred and three drivers, 120 healthy older (61 men and 59 women, ages 65 years or greater) and 83 middle-aged drivers (38 men and 45 women, ages 40–64 years), participated in an on-road test in an instrumented vehicle. Outcome measures included performance in roadside target identification (traffic signs and restaurants) and concurrent driver safety. Differences in visual, motor, and cognitive functioning served as predictors. Results Older drivers identified fewer landmarks and drove slower but committed more safety errors than middle-aged drivers. Greater familiarity with local roads benefited performance of middle-aged but not older drivers. Visual cognition predicted both traffic sign identification and safety errors while executive function predicted traffic sign identification over and above vision. Conclusion Older adults are susceptible to driving safety errors while distracted by common secondary visual search tasks that are inherent to driving. The findings underscore that age-related cognitive decline affects older driver management of driving tasks at multiple levels, and can help inform the design of on-road tests and interventions for older drivers. PMID:23964422

Naturalistic distraction and driving safety in older drivers.

PubMed

Aksan, Nazan; Dawson, Jeffrey D; Emerson, Jamie L; Yu, Lixi; Uc, Ergun Y; Anderson, Steven W; Rizzo, Matthew

2013-08-01

In this study, we aimed to quantify and compare performance of middle-aged and older drivers during a naturalistic distraction paradigm (visual search for roadside targets) and to predict older drivers performance given functioning in visual, motor, and cognitive domains. Distracted driving can imperil healthy adults and may disproportionally affect the safety of older drivers with visual, motor, and cognitive decline. A total of 203 drivers, 120 healthy older (61 men and 59 women, ages 65 years and older) and 83 middle-aged drivers (38 men and 45 women, ages 40 to 64 years), participated in an on-road test in an instrumented vehicle. Outcome measures included performance in roadside target identification (traffic signs and restaurants) and concurrent driver safety. Differences in visual, motor, and cognitive functioning served as predictors. Older drivers identified fewer landmarks and drove slower but committed more safety errors than did middle-aged drivers. Greater familiarity with local roads benefited performance of middle-aged but not older drivers.Visual cognition predicted both traffic sign identification and safety errors, and executive function predicted traffic sign identification over and above vision. Older adults are susceptible to driving safety errors while distracted by common secondary visual search tasks that are inherent to driving. The findings underscore that age-related cognitive decline affects older drivers' management of driving tasks at multiple levels and can help inform the design of on-road tests and interventions for older drivers.

Driver anger on the information superhighway: A content analysis of online complaints of offensive driver behaviour.

PubMed

Wickens, Christine M; Wiesenthal, David L; Hall, Ashley; Roseborough, James E W

2013-03-01

In recent years, several websites have been developed allowing drivers to post their complaints about other motorists online. These websites allow drivers to describe the nature of the offensive behaviour and to identify the offending motorist by vehicle type, colour, and license plate number. Some websites also ask drivers to list the location where the event took place and the exact date and time of the offence. The current study was a content analysis of complaints posted to RoadRagers.com between 1999 and 2007 (N=5624). The purpose of the study was to: (1) assess the research value of this novel data source; (2) demonstrate the value of content analysis to the study of driver behaviour; (3) further validate an existing coding scheme; (4) determine whether this new data source would replicate previous research findings regarding the most frequent types of driver complaints and temporal distribution of these reports; (5) provide recommendations for improved driver training and public safety initiatives based on these data. A coding scheme that was originally developed for an assessment of complaints submitted to the Ontario Provincial Police (OPP) (Wickens et al., 2005) was revised to accommodate the new dataset. The inter-rater reliability of the revised coding scheme as applied to the website complaints was very good (kappa=.85). The most frequently reported improper driver behaviours were cutting/weaving, speeding, perceived displays of hostility, and tailgating. Reports were most frequent on weekdays and during the morning and afternoon rush hour. The current study replicated several findings from the analysis of reports to the OPP, but possible differences in the sample and data collection method also produced some differences in findings. The value of content analysis to driver behaviour research and of driver complaint websites as a data source was demonstrated. Implications for driver safety initiatives and future research will be discussed. Copyright �

Examination of Supplemental Driver Training and Online Basic Driver Education

DOT National Transportation Integrated Search

2012-06-01

This report describes supplemental driver training programs and online basic driver education. It coves supplemental driver training that : focused on knowledge and skills beyond those normally found in traditional driver education delivered in the U...

Driver behaviour with adaptive cruise control.

PubMed

Stanton, Neville A; Young, Mark S

2005-08-15

This paper reports on the evaluation of adaptive cruise control (ACC) from a psychological perspective. It was anticipated that ACC would have an effect upon the psychology of driving, i.e. make the driver feel like they have less control, reduce the level of trust in the vehicle, make drivers less situationally aware, but workload might be reduced and driving might be less stressful. Drivers were asked to drive in a driving simulator under manual and ACC conditions. Analysis of variance techniques were used to determine the effects of workload (i.e. amount of traffic) and feedback (i.e. degree of information from the ACC system) on the psychological variables measured (i.e. locus of control, trust, workload, stress, mental models and situation awareness). The results showed that: locus of control and trust were unaffected by ACC, whereas situation awareness, workload and stress were reduced by ACC. Ways of improving situation awareness could include cues to help the driver predict vehicle trajectory and identify conflicts.

Characteristics of fatigued commercial motor vehicle drivers : a preliminary investigation.

DOT National Transportation Integrated Search

2012-12-01

The goal of this research was to identify and correlate easily observable characteristics of drivers to different levels of : fatigue, thus enabling state patrol officers to make more judicious decisions related to driver fatigue. A literature review...

Traffic Operations Control For Older Drivers And Pedestrians: Summary Report

DOT National Transportation Integrated Search

1996-07-01

The purpose of this investigation was to determine which intersection operational characteristics could be altered to accommodate age-related changes. Two key drivers issues were examined in order to identify the specific older driver problems and th...

Identification of constrained cancer driver genes based on mutation timing.

PubMed

Sakoparnig, Thomas; Fried, Patrick; Beerenwinkel, Niko

2015-01-01

Cancer drivers are genomic alterations that provide cells containing them with a selective advantage over their local competitors, whereas neutral passengers do not change the somatic fitness of cells. Cancer-driving mutations are usually discriminated from passenger mutations by their higher degree of recurrence in tumor samples. However, there is increasing evidence that many additional driver mutations may exist that occur at very low frequencies among tumors. This observation has prompted alternative methods for driver detection, including finding groups of mutually exclusive mutations and incorporating prior biological knowledge about gene function or network structure. Dependencies among drivers due to epistatic interactions can also result in low mutation frequencies, but this effect has been ignored in driver detection so far. Here, we present a new computational approach for identifying genomic alterations that occur at low frequencies because they depend on other events. Unlike passengers, these constrained mutations display punctuated patterns of occurrence in time. We test this driver-passenger discrimination approach based on mutation timing in extensive simulation studies, and we apply it to cross-sectional copy number alteration (CNA) data from ovarian cancer, CNA and single-nucleotide variant (SNV) data from breast tumors and SNV data from colorectal cancer. Among the top ranked predicted drivers, we find low-frequency genes that have already been shown to be involved in carcinogenesis, as well as many new candidate drivers. The mutation timing approach is orthogonal and complementary to existing driver prediction methods. It will help identifying from cancer genome data the alterations that drive tumor progression.

Nearing saturation of cancer driver gene discovery.

PubMed

Hsiehchen, David; Hsieh, Antony

2018-06-15

Extensive sequencing efforts of cancer genomes such as The Cancer Genome Atlas (TCGA) have been undertaken to uncover bona fide cancer driver genes which has enhanced our understanding of cancer and revealed therapeutic targets. However, the number of driver gene mutations is bounded, indicating that there must be a point when further sequencing efforts will be excessive. We found that there was a significant positive correlation between sample size and identified driver gene mutations across 33 cancers sequenced by the TCGA, which is expected if additional sequencing is still leading to the identification of more driver genes. However, the rate of new cancer driver genes being discovered with larger samples is declining rapidly. Our analysis provides a general guide for determining which cancer types would likely benefit from additional sequencing efforts, particularly those with relatively high rates of cancer driver gene discovery. Our results argue that past strategies of indiscriminately sequencing as many specimens as possible for all cancer types is becoming inefficient. In addition, without significant investments into applying our knowledge of cancer genomes, we risk sequencing more cancer genomes for the sake of sequencing rather than meaningful patient benefit.

Improving Driver Performance. A Curriculum for Licensed Drivers.

ERIC Educational Resources Information Center

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…

Isolation of cultivation-resistant oomycetes, first detected as amplicon sequences, from roots of herbicide-terminated winter rye

USDA-ARS?s Scientific Manuscript database

The dynamics of microbial communities associated with dying cover crops are of interest because of potential impacts on disease in a subsequent crop, and because of the importance of microbial activity on plant residue to soil organic matter dynamics and nutrient cycling. High throughput amplicon se...

Driver Behavior During Overtaking Maneuvers from the 100-Car Naturalistic Driving Study.

PubMed

Chen, Rong; Kusano, Kristofer D; Gabler, Hampton C

2015-01-01

Lane changes with the intention to overtake the vehicle in front are especially challenging scenarios for forward collision warning (FCW) designs. These overtaking maneuvers can occur at high relative vehicle speeds and often involve no brake and/or turn signal application. Therefore, overtaking presents the potential of erroneously triggering the FCW. A better understanding of driver behavior during lane change events can improve designs of this human-machine interface and increase driver acceptance of FCW. The objective of this study was to aid FCW design by characterizing driver behavior during lane change events using naturalistic driving study data. The analysis was based on data from the 100-Car Naturalistic Driving Study, collected by the Virginia Tech Transportation Institute. The 100-Car study contains approximately 1.2 million vehicle miles of driving and 43,000 h of data collected from 108 primary drivers. In order to identify overtaking maneuvers from a large sample of driving data, an algorithm to automatically identify overtaking events was developed. The lead vehicle and minimum time to collision (TTC) at the start of lane change events was identified using radar processing techniques developed in a previous study. The lane change identification algorithm was validated against video analysis, which manually identified 1,425 lane change events from approximately 126 full trips. Forty-five drivers with valid time series data were selected from the 100-Car study. From the sample of drivers, our algorithm identified 326,238 lane change events. A total of 90,639 lane change events were found to involve a closing lead vehicle. Lane change events were evenly distributed between left side and right side lane changes. The characterization of lane change frequency and minimum TTC was divided into 10 mph speed bins for vehicle travel speeds between 10 and 90 mph. For all lane change events with a closing lead vehicle, the results showed that drivers change

Automobile driver on-road performance test. Volume 1, final report

DOT National Transportation Integrated Search

1981-09-30

The Automobile Driver On-Road Performance Test (ADOPT) was developed during a three-phase project. In Phase 1, 51 candidate behaviors were identified and selected with the help of experts in the fields of traffic safety, measurement of driver perform...

[Experimental and calculated spectra of the amplicons UBC-85 and UBC-126 (RAPD-PCR)].

PubMed

Glazko, G V; Rogozin, I B; Glazko, V I; Zelenaia, L B; Sozinov, A A

1997-01-01

The comparative analysis of experimental amplification spectrum in 13 Ungulata species and counting ones in DNA sequences of different taxa in GenBank (mammalian, other vertebrate, invertebrate, viruses, prokaryote) with the uses of RAPD-PCR primers UBC-85 and UBC-126 was carried out. The particularities of the distribution of amplicons' frequencies in experimental and counting spectrums were revealed, for some of them the similar increased frequencies in mammalian and prokaryotic species were observed.

Railway suicide: the psychological effects on drivers.

PubMed

Farmer, R; Tranah, T; O'Donnell, I; Catalan, J

1992-05-01

People have jumped (or fallen) in front of trains on the London Underground system in increasing numbers throughout the twentieth century. During the past decade there have been about 100 such incidents each year, of which around 90 would involve the train driver witnessing his train strike the person on the track. Most are suicides or attempts at suicide. They represent major unexpected and violent events in the lives of the train drivers and it might be expected that some of them would respond by developing a post-traumatic stress reaction of the type identified by Horowitz (1976) or other adverse psychological reactions or both. The research reported in this paper was designed to characterize the range of responses of drivers to the experiences of killing or injuring members of the public during the course of their daily work. It was found that 16.3% of the drivers involved in incidents did develop post-traumatic stress disorder and that other diagnoses, e.g. depression and phobic states, were present in 39.5% of drivers when interviewed one month after the incident.

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

NASA Astrophysics Data System (ADS)

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

Factors associated with obstructive sleep apnea among commercial motor vehicle drivers.

PubMed

Xie, Wen; Chakrabarty, Sangita; Levine, Robert; Johnson, Roy; Talmage, James B

2011-02-01

Identify factors associated with obstructive sleep apnea (OSA) risk during commercial driver medical examinations. A case-control study was conducted at an occupational health clinic by reviewing the commercial driver medical examinations medical records performed from January 2007 to December 2008. The magnitude of association with OSA was estimated with logistic regression. Among 1890 commercial motor vehicle drivers, 51 were confirmed positive for OSA by polysomnography after initial screening by Joint Task Force guidelines, yielding estimated positive predictive values of 78.5% for the screening criteria. Multivariable logistic regression showed that body mass index ≥ 30 (odds ratio: 26.86), hypertension (odds ratio: 2.57), and diabetes (odds ratio: 2.03) were independently associated with OSA. Medical examiners' use of objectively measurable risk factors, such as obesity, history of hypertension, and/or diabetes, rather than symptoms, may be more effective in identifying undiagnosed OSA in commercial drivers during the commercial driver medical examinations.

Causes, consequences and countermeasures to driver fatigue in the rail industry: The train driver perspective.

PubMed

Filtness, A J; Naweed, A

2017-04-01

Fatigue is an important workplace risk management issue. Within the rail industry, the passing of a stop signal (signal passed at danger; SPAD) is considered to be one of the most major safety breaches which can occur. Train drivers are very aware of the negative consequences associated with a SPAD. Therefore, SPADs provide a practical and applied safety relevant context within which to structure a discussion on fatigue. Focus groups discussing contributing factors to SPADs were undertaken at eight passenger rail organisations across Australia and New Zealand (n = 28 drivers). Data relating to fatigue was extracted and inductively analysed identifying three themes: causes, consequences, and countermeasures (to fatigue). Drivers experienced negative consequences of fatigue, despite existing countermeasures to mitigate it. Organisational culture was a barrier to effective fatigue management. A fatigue assessment tool consistently informed rostering, however, shift swapping was commonplace and often unregulated, reducing any potential positive impact. In discussing fatigue countermeasure strategies, drivers talked interchangeably about mitigating task related fatigue (e.g. increasing cognitive load) and sleepiness (e.g. caffeine). Ensuring the concepts of fatigue and sleepiness are properly understood has the potential to maximise safety. Copyright © 2016 Elsevier Ltd. All rights reserved.

Leptospirosis Outbreaks in Nicaragua: Identifying Critical Areas and Exploring Drivers for Evidence-Based Planning

PubMed Central

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

2012-01-01

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. PMID:23202822

Higher Education Cost Drivers, Including Two Hidden Ones with Cost Containment Possibilities.

ERIC Educational Resources Information Center

Micceri, Ted

Identifying higher education cost drivers and working to limit their effects appears to be a necessity if higher education is to retain the support historically allocated by society. Costs occur for three groups: students, institutions, and society. This paper summarizes information about cost drivers in higher education and identifies two that…

Amplicon Sequencing Reveals Microbiological Signatures in Spent Nuclear Fuel Storage Basins

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bagwell, Christopher E.; Noble, Peter A.; Milliken, Charles E.

Water quality is an important determinant for the structural integrity of alloy cladded fuels and assemblies during long-term wet storage. Detailed characterization of a water filled storage basin for spent nuclear reactor fuel was performed following the formation and proliferation of an amorphous white flocculent. White precipitant was sampled throughout the storage basin for chemical and spectroscopic characterization, and eDNA was extracted for pyrosequencing of bacterial rRNA gene diversity. Accordingly, spectroscopic analyses indicated the precipitant to be primarily amorphous to crystalline aluminum (oxy) hydroxides with minor associated elemental components including Fe, Si, Ti, and U. High levels of dissolved carbonmore » were co-localized with the precipitant relative to bulk water. Bacterial densities were highly variable between sampling locations and with depth; cell numbers (log scale) ranged from 5.6 to 4.89 cells / mL. Bacterial diversity that was physically associated with the aluminum (oxy) hydroxide complexes exceeded an estimated 4,000 OTUs / amplicon library (3% cutoff) and the greatest percent majority of sequences were aligned to the families Burkholderiales (23%), Nitrospiraceae (23%), Hyphomicrobiaceae (17%), and Comamonadaceae (6%). We surmise that episodic changes in the physical and chemical properties of the basin contribute to the polymerization of aluminum (oxy) hydroxides, which in turn can chemisorb nutrients, carbon ligands and bacterial cells from the surrounding bulk aqueous phase. As such, these precipitants should establish favorable microhabitats for bacterial colonization and growth. Comparative analyses of 16S rRNA gene amplicon libraries across diverse environmental landscapes were performed and microbiological signatures unique to the spent nuclear fuel storage basin environment were revealed. These insights could spur the development of tractable bioindicators that are specific of and diagnostic for water quality at

Exome sequencing identifies putative drivers of progression of transient myeloproliferative disorder to AMKL in infants with Down syndrome.

PubMed

Nikolaev, Sergey I; Santoni, Federico; Vannier, Anne; Falconnet, Emilie; Giarin, Emanuela; Basso, Giuseppe; Hoischen, Alexander; Veltman, Joris A; Groet, Jurgen; Nizetic, Dean; Antonarakis, Stylianos E

2013-07-25

Some neonates with Down syndrome (DS) are diagnosed with self-regressing transient myeloproliferative disorder (TMD), and 20% to 30% of those progress to acute megakaryoblastic leukemia (AMKL). We performed exome sequencing in 7 TMD/AMKL cases and copy-number analysis in these and 10 additional cases. All TMD/AMKL samples contained GATA1 mutations. No exome-sequenced TMD/AMKL sample had other recurrently mutated genes. However, 2 of 5 TMD cases, and all AMKL cases, showed mutations/deletions other than GATA1, in genes proven as transformation drivers in non-DS leukemia (EZH2, APC, FLT3, JAK1, PARK2-PACRG, EXT1, DLEC1, and SMC3). One patient at the TMD stage revealed 2 clonal expansions with different GATA1 mutations, of which 1 clone had an additional driver mutation. Interestingly, it was the other clone that gave rise to AMKL after accumulating mutations in 7 other genes. Data suggest that GATA1 mutations alone are sufficient for clonal expansions, and additional driver mutations at the TMD stage do not necessarily predict AMKL progression. Later in infancy, leukemic progression requires "third-hit driver" mutations/somatic copy-number alterations found in non-DS leukemias. Putative driver mutations affecting WNT (wingless-related integration site), JAK-STAT (Janus kinase/signal transducer and activator of transcription), or MAPK/PI3K (mitogen-activated kinase/phosphatidylinositol-3 kinase) pathways were found in all cases, aberrant activation of which converges on overexpression of MYC.

The Cancer Genome Atlas Clinical Explorer: a web and mobile interface for identifying clinical-genomic driver associations.

PubMed

Lee, HoJoon; Palm, Jennifer; Grimes, Susan M; Ji, Hanlee P

2015-10-27

The Cancer Genome Atlas (TCGA) project has generated genomic data sets covering over 20 malignancies. These data provide valuable insights into the underlying genetic and genomic basis of cancer. However, exploring the relationship among TCGA genomic results and clinical phenotype remains a challenge, particularly for individuals lacking formal bioinformatics training. Overcoming this hurdle is an important step toward the wider clinical translation of cancer genomic/proteomic data and implementation of precision cancer medicine. Several websites such as the cBio portal or University of California Santa Cruz genome browser make TCGA data accessible but lack interactive features for querying clinically relevant phenotypic associations with cancer drivers. To enable exploration of the clinical-genomic driver associations from TCGA data, we developed the Cancer Genome Atlas Clinical Explorer. The Cancer Genome Atlas Clinical Explorer interface provides a straightforward platform to query TCGA data using one of the following methods: (1) searching for clinically relevant genes, micro RNAs, and proteins by name, cancer types, or clinical parameters; (2) searching for genomic/proteomic profile changes by clinical parameters in a cancer type; or (3) testing two-hit hypotheses. SQL queries run in the background and results are displayed on our portal in an easy-to-navigate interface according to user's input. To derive these associations, we relied on elastic-net estimates of optimal multiple linear regularized regression and clinical parameters in the space of multiple genomic/proteomic features provided by TCGA data. Moreover, we identified and ranked gene/micro RNA/protein predictors of each clinical parameter for each cancer. The robustness of the results was estimated by bootstrapping. Overall, we identify associations of potential clinical relevance among genes/micro RNAs/proteins using our statistical analysis from 25 cancer types and 18 clinical parameters that

Identification of Constrained Cancer Driver Genes Based on Mutation Timing

PubMed Central

Sakoparnig, Thomas; Fried, Patrick; Beerenwinkel, Niko

2015-01-01

Cancer drivers are genomic alterations that provide cells containing them with a selective advantage over their local competitors, whereas neutral passengers do not change the somatic fitness of cells. Cancer-driving mutations are usually discriminated from passenger mutations by their higher degree of recurrence in tumor samples. However, there is increasing evidence that many additional driver mutations may exist that occur at very low frequencies among tumors. This observation has prompted alternative methods for driver detection, including finding groups of mutually exclusive mutations and incorporating prior biological knowledge about gene function or network structure. Dependencies among drivers due to epistatic interactions can also result in low mutation frequencies, but this effect has been ignored in driver detection so far. Here, we present a new computational approach for identifying genomic alterations that occur at low frequencies because they depend on other events. Unlike passengers, these constrained mutations display punctuated patterns of occurrence in time. We test this driver–passenger discrimination approach based on mutation timing in extensive simulation studies, and we apply it to cross-sectional copy number alteration (CNA) data from ovarian cancer, CNA and single-nucleotide variant (SNV) data from breast tumors and SNV data from colorectal cancer. Among the top ranked predicted drivers, we find low-frequency genes that have already been shown to be involved in carcinogenesis, as well as many new candidate drivers. The mutation timing approach is orthogonal and complementary to existing driver prediction methods. It will help identifying from cancer genome data the alterations that drive tumor progression. PMID:25569148

Graduated driver licensing for reducing motor vehicle crashes among young drivers.

PubMed

Hartling, L; Wiebe, N; Russell, K; Petruk, J; Spinola, C; Klassen, T P

2004-01-01

Graduated driver licensing (GDL) has been proposed as a means of reducing crash rates among novice drivers by gradually introducing them to higher risk driving situations. To examine the effectiveness of GDL systems in reducing crash rates of young drivers. Studies were identified through searches of MEDLINE, EMBASE, CINAHL, Healthstar, Web of Science, NTIS Bibliographic Database, TRIS Online, SIGLE, the World Wide Web, relevant conference proceedings, consultation with experts and authors, and reference lists. The search was not restricted by language or publication status. Studies were included if: 1) they compared outcomes pre- and post-implementation of a GDL program within the same jurisdiction, 2) comparisons were made between jurisdictions with and without GDL, or 3) both. Studies had to report at least one objective, quantified outcome. Two reviewers independently screened searches and assessed the full text of potentially relevant studies for inclusion using a standard form. Data were extracted by one reviewer and checked by a second. Additional data were requested from authors. Results were not pooled due to substantial heterogeneity between studies. Percentage change was calculated for each year after the intervention, using one year prior to the intervention as the baseline rate. Results were adjusted by internal controls. Analyses were stratified by different denominators (population, licensed drivers). Results were calculated for the different crash types (overall, injury, fatal, night-time, alcohol, and those resulting in hospitalization). Results were presented for 16 year-olds alone and all teenage drivers combined. We included 13 studies evaluating 12 GDL programs that were implemented between 1979 and 1998 in the US (n=7), Canada (3), New Zealand (1), and Australia (1). Programs varied in their restrictions during the intermediate stage: e.g. night curfews (8); limitations of extra passengers (2); roadway restrictions (1). Based on the Insurance

An examination of the environmental, driver and vehicle factors associated with the serious and fatal crashes of older rural drivers.

PubMed

Thompson, J P; Baldock, M R J; Mathias, J L; Wundersitz, L N

2013-01-01

Motor vehicle crashes involving rural drivers aged 75 years and over are more than twice as likely to result in a serious or fatal injury as those involving their urban counterparts. The current study examined some of the reasons for this using a database of police-reported crashes (2004-2008) to identify the environmental (lighting, road and weather conditions, road layout, road surface, speed limit), driver (driver error, crash type), and vehicle (vehicle age) factors that are associated with the crashes of older rural drivers. It also determined whether these same factors are associated with an increased likelihood of serious or fatal injury in younger drivers for whom frailty does not contribute to the resulting injury severity. A number of environmental (i.e., undivided, unsealed, curved and inclined roads, and areas with a speed limit of 100km/h or greater) and driver (i.e., collision with a fixed object and rolling over) factors were more frequent in the crashes of older rural drivers and additionally associated with increased injury severity in younger drivers. Moreover, when these environmental factors were entered into a logistic regression model to predict whether older drivers who were involved in crashes did or did not sustain a serious or fatal injury, it was found that each factor independently increased the likelihood of a serious or fatal injury. Changes, such as the provision of divided and sealed roads, greater protection from fixed roadside objects, and reduced speed limits, appear to be indicated in order to improve the safety of the rural driving environment for drivers of all ages. Additionally, older rural drivers should be encouraged to reduce their exposure to these risky circumstances. Copyright © 2012 Elsevier Ltd. All rights reserved.

Comparisons of diazotrophic communities in native and agricultural desert ecosystems reveal plants as important drivers in diversity

PubMed Central

Köberl, Martina; Erlacher, Armin; Ramadan, Elshahat M.; El-Arabi, Tarek F.; Müller, Henry; Bragina, Anastasia; Berg, Gabriele

2015-01-01

Diazotrophs provide the only biological source of fixed atmospheric nitrogen in the biosphere. Although they are the key player for plant-available nitrogen, less is known about their diversity and potential importance in arid ecosystems. We investigated the nitrogenase gene diversity in native and agricultural desert soil as well as within root-associated microbiota of medicinal plants grown in Egypt through the combination of nifH-specific qPCR, fingerprints, amplicon pyrosequencing and fluorescence in situ hybridization–confocal laser scanning microscopy. Although the diazotrophic microbiota were characterized by generally high abundances and diversity, statistically significant differences were found between both soils, the different microhabitats, and between the investigated plants (Matricaria chamomilla L., Calendula officinalis L. and Solanum distichum Schumach. and Thonn.). We observed a considerable community shift from desert to agriculturally used soil that demonstrated a higher abundance and diversity in the agro-ecosystem. The endorhiza was characterized by lower abundances and only a subset of species when compared to the rhizosphere. While the microbiomes of the Asteraceae were similar and dominated by potential root-nodulating rhizobia acquired primarily from soil, the perennial S. distichum generally formed associations with free-living nitrogen fixers. These results underline the importance of diazotrophs in desert ecosystems and additionally identify plants as important drivers in functional gene pool diversity. PMID:26705571

Comparisons of diazotrophic communities in native and agricultural desert ecosystems reveal plants as important drivers in diversity.

PubMed

Köberl, Martina; Erlacher, Armin; Ramadan, Elshahat M; El-Arabi, Tarek F; Müller, Henry; Bragina, Anastasia; Berg, Gabriele

2016-02-01

Diazotrophs provide the only biological source of fixed atmospheric nitrogen in the biosphere. Although they are the key player for plant-available nitrogen, less is known about their diversity and potential importance in arid ecosystems. We investigated the nitrogenase gene diversity in native and agricultural desert soil as well as within root-associated microbiota of medicinal plants grown in Egypt through the combination of nifH-specific qPCR, fingerprints, amplicon pyrosequencing and fluorescence in situ hybridization-confocal laser scanning microscopy. Although the diazotrophic microbiota were characterized by generally high abundances and diversity, statistically significant differences were found between both soils, the different microhabitats, and between the investigated plants (Matricaria chamomilla L., Calendula officinalis L. and Solanum distichum Schumach. and Thonn.). We observed a considerable community shift from desert to agriculturally used soil that demonstrated a higher abundance and diversity in the agro-ecosystem. The endorhiza was characterized by lower abundances and only a subset of species when compared to the rhizosphere. While the microbiomes of the Asteraceae were similar and dominated by potential root-nodulating rhizobia acquired primarily from soil, the perennial S. distichum generally formed associations with free-living nitrogen fixers. These results underline the importance of diazotrophs in desert ecosystems and additionally identify plants as important drivers in functional gene pool diversity. © FEMS 2015.

Medical review of fitness to drive in older drivers: the Maryland experience.

PubMed

Soderstrom, Carl A; Joyce, John J

2008-08-01

Over the next several decades, both the number and percentage of older drivers will increase dramatically. Older age is inherently associated with medical conditions, particularly those involving cognition and vision, that can affect medical fitness to drive. Over a 60-year period, the Maryland Motor Vehicle Administration (MVA) in conjunction with its medical advisory board (MAB) has matured a comprehensive system to identify at-risk older drivers and to assess their medical fitness to drive. This paper describes the medical review process in general, and in particular for older drivers, that has evolved in the state of Maryland. The resources, philosophy and research underpinnings of its MAB review process are examined. Studies of functional screening measures in older drivers indicate that older drivers at risk of being at-fault for future crashes can be identified. The feasibility of using such screening measures for drivers referred to the MVA has been confirmed by practical use for a period of seven years. It is possible to create a medical review process with a goal of "safe mobility for life" that supports preservation of the driving privilege among many older drivers.

Microbial community profiling of fresh basil and pitfalls in taxonomic assignment of enterobacterial pathogenic species based upon 16S rRNA amplicon sequencing.

PubMed

Ceuppens, Siele; De Coninck, Dieter; Bottledoorn, Nadine; Van Nieuwerburgh, Filip; Uyttendaele, Mieke

2017-09-18

Application of 16S rRNA (gene) amplicon sequencing on food samples is increasingly applied for assessing microbial diversity but may as unintended advantage also enable simultaneous detection of any human pathogens without a priori definition. In the present study high-throughput next-generation sequencing (NGS) of the V1-V2-V3 regions of the 16S rRNA gene was applied to identify the bacteria present on fresh basil leaves. However, results were strongly impacted by variations in the bioinformatics analysis pipelines (MEGAN, SILVAngs, QIIME and MG-RAST), including the database choice (Greengenes, RDP and M5RNA) and the annotation algorithm (best hit, representative hit and lowest common ancestor). The use of pipelines with default parameters will lead to discrepancies. The estimate of microbial diversity of fresh basil using 16S rRNA (gene) amplicon sequencing is thus indicative but subject to biases. Salmonella enterica was detected at low frequencies, between 0.1% and 0.4% of bacterial sequences, corresponding with 37 to 166 reads. However, this result was dependent upon the pipeline used: Salmonella was detected by MEGAN, SILVAngs and MG-RAST, but not by QIIME. Confirmation of Salmonella sequences by real-time PCR was unsuccessful. It was shown that taxonomic resolution obtained from the short (500bp) sequence reads of the 16S rRNA gene containing the hypervariable regions V1-V3 cannot allow distinction of Salmonella with closely related enterobacterial species. In conclusion 16S amplicon sequencing, getting the status of standard method in microbial ecology studies of foods, needs expertise on both bioinformatics and microbiology for analysis of results. It is a powerful tool to estimate bacterial diversity but amenable to biases. Limitations concerning taxonomic resolution for some bacterial species or its inability to detect sub-dominant (pathogenic) species should be acknowledged in order to avoid overinterpretation of results. Copyright © 2017 Elsevier B

Circuits of cancer drivers revealed by convergent misregulation of transcription factor targets across tumor types.

PubMed

Gonzalez-Perez, Abel

2016-01-20

Large tumor genome sequencing projects have now uncovered a few hundred genes involved in the onset of tumorigenesis, or drivers, in some two dozen malignancies. One of the main challenges emerging from this catalog of drivers is how to make sense of their heterogeneity in most cancer types. This is key not only to understand how carcinogenesis appears and develops in these malignancies to be able to early diagnose them, but also to open up the possibility to employ therapeutic strategies targeting a driver protein to counteract the alteration of another connected driver. Here, I focus on driver transcription factors and their connection to tumorigensis in several tumor types through the alteration of the expression of their targets. First, I explore their involvement in tumorigenesis as mutational drivers in 28 different tumor types. Then, I collect a list of downstream targets of the all driver transcription factors (TFs), and identify which of them exhibit a differential expression upon alterations of driver transcription factors. I identify the subset of targets of each TF most likely mediating the tumorigenic effect of their driver alterations in each tumor type, and explore their overlap. Furthermore, I am able to identify other driver genes that cause tumorigenesis through the alteration of very similar sets of targets. I thus uncover these circuits of connected drivers which cause tumorigenesis through the perturbation of overlapping cellular pathways in a pan-cancer manner across 15 malignancies. The systematic detection of these circuits may be key to propose novel therapeutic strategies indirectly targeting driver alterations in tumors.

HPV Genotyping of Modified General Primer-Amplicons Is More Analytically Sensitive and Specific by Sequencing than by Hybridization.

PubMed

Meisal, Roger; Rounge, Trine Ballestad; Christiansen, Irene Kraus; Eieland, Alexander Kirkeby; Worren, Merete Molton; Molden, Tor Faksvaag; Kommedal, Øyvind; Hovig, Eivind; Leegaard, Truls Michael; Ambur, Ole Herman

2017-01-01

Sensitive and specific genotyping of human papillomaviruses (HPVs) is important for population-based surveillance of carcinogenic HPV types and for monitoring vaccine effectiveness. Here we compare HPV genotyping by Next Generation Sequencing (NGS) to an established DNA hybridization method. In DNA isolated from urine, the overall analytical sensitivity of NGS was found to be 22% higher than that of hybridization. NGS was also found to be the most specific method and expanded the detection repertoire beyond the 37 types of the DNA hybridization assay. Furthermore, NGS provided an increased resolution by identifying genetic variants of individual HPV types. The same Modified General Primers (MGP)-amplicon was used in both methods. The NGS method is described in detail to facilitate implementation in the clinical microbiology laboratory and includes suggestions for new standards for detection and calling of types and variants with improved resolution.

Child passengers and driver culpability in fatal crashes by driver gender.

PubMed

Maasalo, Ida; Lehtonen, Esko; Pekkanen, Jami; Summala, Heikki

2016-07-03

Studies based on accident statistics generally suggest that the presence of a passenger reduces adult drivers' accident risk. However, passengers have been reported to be a source of distraction in a remarkable portion of distraction-related crashes. Although the effect of passengers on driving performance has been studied extensively, few studies have focused on how a child passenger affects the driver.  A child in a car is a potential distractor for parents, especially for mothers of small children, who often suffer from sleep deficit. The aim of this study was to examine how the presence of child passengers of different ages is associated with a higher driver culpability, which was expected due to child-related distraction and fatigue. The analysis was based on the comprehensive data of fatal crashes studied in-depth by multidisciplinary road accident investigation teams in Finland during 1988-2012. Teams determine the primary party who had the most crucial effect on the origin of the event. We define the primary party as culpable and the others involved as nonculpable drivers. The culpability rate was defined as the percentage of culpable drivers and rates were compared for drivers with a child/teen passenger aged 0-17 years (N = 348), with an adult passenger without children (N = 324), and when driving alone (N = 579), grouped by child age and driver gender.  Drivers with specific risk-related behavior (substantial speeding, driving when intoxicated, unbelted, or without a license) were excluded from the analyses, in order to make the drivers with and without children comparable. Only drivers 26-47 years old were included, representing parents with children 0-9 years of age. Male drivers were less often culpable with 0- to 17-year-old passengers in the car than alone or with adults. This was not the case with female drivers. The gender difference in culpability was most marked with small children age 0-4 years. Female drivers' culpability rate with a 0

A Fresh Look at Driver Education in America

DOT National Transportation Integrated Search

2012-04-01

The objectives of this study were to: (1) identify and review current driver education and training programs in use nationally and : internationally; (2) identify best teaching practices for teenagers; (3) examine the optimal sequencing for the prese...

Dynamics of Driver Distraction: The process of engaging and disengaging

PubMed Central

Lee, John D.

2014-01-01

Driver distraction research has a long history, spanning nearly 50 years, but intensifying over the last decade. The dominant paradigm guiding this research defines distraction in terms of excessive workload and limited attentional resources. This approach largely ignores how drivers come to engage in these tasks and under what conditions they engage and disengage from driving—the dynamics of distraction. The dynamics of distraction identifies breakdowns of interruption management as an important contributor to distraction, leading to describe distraction in terms of failures of task timing, switching, and prioritization. The dynamics of distraction also identifies disengagement in driving (e.g., mind wandering) as a substantial challenge that secondary tasks might exacerbate or mitigate. Increasing vehicle automation accentuates the need to consider these dynamics of distraction. Automation offers drivers more opportunity to engage in distractions and disengage from driving, and can surprise drivers by unexpectedly requiring drivers to quickly re-engage in driving—placing greater importance of interruption management expertise. This review describes distraction in terms of breakdowns in interruption management and problems of engagement, and summarizes how contingency, conditioning, and consequence traps lead to problems of engaging and disengaging in driving and distractions. PMID:24776224

Vibrio Ecology in the Neuse River Estuary, North Carolina, Characterized by Next-Generation Amplicon Sequencing of the Gene Encoding Heat Shock Protein 60 (hsp60).

PubMed

Jesser, Kelsey J; Noble, Rachel T

2018-07-01

Of marine eubacteria, the genus Vibrio is intriguing because member species are relevant to both marine ecology and human health. Many studies have touted the relationships of Vibrio to environmental factors, especially temperature and salinity, to predict total Vibrio abundance but lacked the taxonomic resolution to identify the relationships among species and the key drivers of Vibrio dynamics. To improve next-generation sequencing (NGS) surveys of Vibrio , we have conducted both 16S small subunit rRNA and heat shock protein 60 ( hsp60 ) amplicon sequencing of water samples collected at two well-studied locations in the Neuse River Estuary, NC. Samples were collected between May and December 2016 with enhanced sampling efforts in response to two named storms. Using hsp60 sequences, 21 Vibrio species were identified, including the potential human pathogens V. cholerae , V. parahaemolyticus , and V. vulnificus Changes in the Vibrio community mirrored seasonal and storm-related changes in the water column, especially in response to an influx of nutrient-rich freshwater to the estuary after Hurricane Matthew, which initiated dramatic changes in the overall Vibrio community. Individual species dynamics were wide ranging, indicating that individual Vibrio taxa have unique ecologies and that total Vibrio abundance predictors are insufficient for risk assessments of potentially pathogenic species. Positive relationships between Vibrio , dinoflagellates, and Cyanobacteria were identified, as were intraspecies associations, which further illuminated the interactions of cooccurring Vibrio taxa along environmental gradients. IMPORTANCE The objectives of this research were to utilize a novel approach to improve sequence-based surveys of Vibrio communities and to demonstrate the usefulness of this approach by presenting an analysis of Vibrio dynamics in the context of environmental conditions, with a particular focus on species that cause disease in humans and on storm effects

SBCDDB: Sleeping Beauty Cancer Driver Database for gene discovery in mouse models of human cancers

PubMed Central

Mann, Michael B

2018-01-01

Abstract Large-scale oncogenomic studies have identified few frequently mutated cancer drivers and hundreds of infrequently mutated drivers. Defining the biological context for rare driving events is fundamentally important to increasing our understanding of the druggable pathways in cancer. Sleeping Beauty (SB) insertional mutagenesis is a powerful gene discovery tool used to model human cancers in mice. Our lab and others have published a number of studies that identify cancer drivers from these models using various statistical and computational approaches. Here, we have integrated SB data from primary tumor models into an analysis and reporting framework, the Sleeping Beauty Cancer Driver DataBase (SBCDDB, http://sbcddb.moffitt.org), which identifies drivers in individual tumors or tumor populations. Unique to this effort, the SBCDDB utilizes a single, scalable, statistical analysis method that enables data to be grouped by different biological properties. This allows for SB drivers to be evaluated (and re-evaluated) under different contexts. The SBCDDB provides visual representations highlighting the spatial attributes of transposon mutagenesis and couples this functionality with analysis of gene sets, enabling users to interrogate relationships between drivers. The SBCDDB is a powerful resource for comparative oncogenomic analyses with human cancer genomics datasets for driver prioritization. PMID:29059366

Inappropriate Alarm Rates and Driver Annoyance

DOT National Transportation Integrated Search

1996-02-01

Future in-vehicle crash avoidance warning systems will inevitably deliver : inappropriate alarms from time to time, caused for example, by situations where : algorithms have correctly identified an object but pose no threat or danger to : the driver....

Association of driver air bags with driver fatality: a matched cohort study.

PubMed

Cummings, Peter; McKnight, Barbara; Rivara, Frederick P; Grossman, David C

2002-05-11

To estimate the association of driver air bag presence with driver fatality in road traffic crashes. Matched pair cohort study. All passenger vehicle crashes in the United States during 1990-2000 inclusive. 51 031 driver-passenger pairs in the same vehicle. Relative risk of death within 30 days of a crash. Drivers with an air bag were less likely to die than drivers without an air bag (adjusted relative risk 0.92 (95% confidence interval 0.88 to 0.96)). This estimate was nearly the same whether drivers wore a seat belt (adjusted relative risk 0.93) or not (0.91). Air bags were associated with more protection for women (0.88 (0.82 to 0.93)), than for men (0.94 (0.90 to 0.99)). Drivers wearing a seat belt were less likely to die than unbelted drivers (0.35 (0.33 to 0.36)). Belted drivers with an air bag were less likely to die than unbelted drivers without an air bag (0.32 (0.30 to 0.34)). If the associations are causal the average risk of driver death was reduced 8% (95% confidence interval 4% to 12%) by an air bag. Benefit was similar for belted and unbelted drivers and was slightly greater for women. However, seat belts offered much more protection than air bags.

Profound Tissue Specificity in Proliferation Control Underlies Cancer Drivers and Aneuploidy Patterns.

PubMed

Sack, Laura Magill; Davoli, Teresa; Li, Mamie Z; Li, Yuyang; Xu, Qikai; Naxerova, Kamila; Wooten, Eric C; Bernardi, Ronald J; Martin, Timothy D; Chen, Ting; Leng, Yumei; Liang, Anthony C; Scorsone, Kathleen A; Westbrook, Thomas F; Wong, Kwok-Kin; Elledge, Stephen J

2018-04-05

Genomics has provided a detailed structural description of the cancer genome. Identifying oncogenic drivers that work primarily through dosage changes is a current challenge. Unrestrained proliferation is a critical hallmark of cancer. We constructed modular, barcoded libraries of human open reading frames (ORFs) and performed screens for proliferation regulators in multiple cell types. Approximately 10% of genes regulate proliferation, with most performing in an unexpectedly highly tissue-specific manner. Proliferation drivers in a given cell type showed specific enrichment in somatic copy number changes (SCNAs) from cognate tumors and helped predict aneuploidy patterns in those tumors, implying that tissue-type-specific genetic network architectures underlie SCNA and driver selection in different cancers. In vivo screening confirmed these results. We report a substantial contribution to the catalog of SCNA-associated cancer drivers, identifying 147 amplified and 107 deleted genes as potential drivers, and derive insights about the genetic network architecture of aneuploidy in tumors. Copyright © 2018 Elsevier Inc. All rights reserved.

Fatigue factors affecting metropolitan bus drivers: a qualitative investigation.

PubMed

Biggs, Herbert; Dingsdag, Donald; Stenson, Nick

2009-01-01

Metropolitan bus drivers daily face work in a stressful and draining work environment, exposing them to the serious risk of driver fatigue. However, there has been a dearth of information exploring the unique antecedents and effects of such fatigue. To date, much of the research into metropolitan bus drivers has been under the umbrella of large heavy vehicle driving studies, which include a disproportionally large population of long-haul drivers, who are likely to face a significantly different set of fatigue factors [1]. The present study aimed to investigate which work and environmental factors may cause fatigue in metropolitan bus drivers by seeking drivers' own perspectives on the issues. To this end, focus groups were held at five bus depots in Sydney and Newcastle, with an effort made to include a stratified sample of drivers at each. Each of the groups were invited to nominate what factors they felt were most salient, with a number of common factors emerging across the depots. Key themes identified were: support from management; ticketing and related issues; interaction with passengers; cabin ergonomics; tight route schedules; turn-around and shift irregularity; extended shift cycles; interactions with other road users; and extended commute times.

Association of driver air bags with driver fatality: a matched cohort study

PubMed Central

Cummings, Peter; McKnight, Barbara; Rivara, Frederick P; Grossman, David C

2002-01-01

Objective To estimate the association of driver air bag presence with driver fatality in road traffic crashes. Design Matched pair cohort study. Setting All passenger vehicle crashes in the United States during 1990-2000 inclusive. Subjects 51 031 driver-passenger pairs in the same vehicle. Main outcome measures Relative risk of death within 30 days of a crash. Results Drivers with an air bag were less likely to die than drivers without an air bag (adjusted relative risk 0.92 (95% confidence interval 0.88 to 0.96)). This estimate was nearly the same whether drivers wore a seat belt (adjusted relative risk 0.93) or not (0.91). Air bags were associated with more protection for women (0.88 (0.82 to 0.93)), than for men (0.94 (0.90 to 0.99)). Drivers wearing a seat belt were less likely to die than unbelted drivers (0.35 (0.33 to 0.36)). Belted drivers with an air bag were less likely to die than unbelted drivers without an air bag (0.32 (0.30 to 0.34)). Conclusions If the associations are causal the average risk of driver death was reduced 8% (95% confidence interval 4% to 12%) by an air bag. Benefit was similar for belted and unbelted drivers and was slightly greater for women. However, seat belts offered much more protection than air bags. What is already known on this topicStudies have estimated that driver air bags reduce the risk of death in a road vehicle crash by 10-14%These studies disagree as to whether benefit is greater for drivers wearing a seat belt or for unbelted driversWhat this study addsHaving an air bag was associated with an 8% reduction in the risk of death, whether the driver was belted or notThe reduction in risk was greater for women (12%) than for men (6%)Seat belts provided much greater protection, with seat belt use reducing the risk of death by 65% (or by 68% in combination with an air bag) PMID:12003882

Canary: an atomic pipeline for clinical amplicon assays.

PubMed

Doig, Kenneth D; Ellul, Jason; Fellowes, Andrew; Thompson, Ella R; Ryland, Georgina; Blombery, Piers; Papenfuss, Anthony T; Fox, Stephen B

2017-12-15

High throughput sequencing requires bioinformatics pipelines to process large volumes of data into meaningful variants that can be translated into a clinical report. These pipelines often suffer from a number of shortcomings: they lack robustness and have many components written in multiple languages, each with a variety of resource requirements. Pipeline components must be linked together with a workflow system to achieve the processing of FASTQ files through to a VCF file of variants. Crafting these pipelines requires considerable bioinformatics and IT skills beyond the reach of many clinical laboratories. Here we present Canary, a single program that can be run on a laptop, which takes FASTQ files from amplicon assays through to an annotated VCF file ready for clinical analysis. Canary can be installed and run with a single command using Docker containerization or run as a single JAR file on a wide range of platforms. Although it is a single utility, Canary performs all the functions present in more complex and unwieldy pipelines. All variants identified by Canary are 3' shifted and represented in their most parsimonious form to provide a consistent nomenclature, irrespective of sequencing variation. Further, proximate in-phase variants are represented as a single HGVS 'delins' variant. This allows for correct nomenclature and consequences to be ascribed to complex multi-nucleotide polymorphisms (MNPs), which are otherwise difficult to represent and interpret. Variants can also be annotated with hundreds of attributes sourced from MyVariant.info to give up to date details on pathogenicity, population statistics and in-silico predictors. Canary has been used at the Peter MacCallum Cancer Centre in Melbourne for the last 2 years for the processing of clinical sequencing data. By encapsulating clinical features in a single, easily installed executable, Canary makes sequencing more accessible to all pathology laboratories. Canary is available for download as source

The effects of text messaging on young drivers.

PubMed

Hosking, Simon G; Young, Kristie L; Regan, Michael A

2009-08-01

This study investigated the effects of using a cell phone to retrieve and send text messages on the driving performance of young novice drivers. Young drivers are particularly susceptible to driver distraction and have an increased risk of distraction-related crashes. Distractions from in-vehicle devices, particularly, those that require manual input, are known to cause decrements in driving performance. Twenty young novice drivers used a cell phone to retrieve and send text messages while driving a simulator. The amount of time that drivers spent not looking at the road when text messaging was up to approximately 400% greater than that recorded in baseline (notext-messaging) conditions. Furthermore, drivers' variability in lane position increased up to approximately 50%, and missed lane changes increased 140%. There was also an increase of up to approximately 150% in drivers' variability in following distances to lead vehicles. Previous research has shown that the risk of crashing while dialing a handheld device, such as when text messaging and driving, is more than double that of conversing on a cell phone. The present study has identified the detrimental effects of text messaging on driving performance that may underlie such increased crash risk. More effective road safety measures are needed to prevent and mitigate the adverse effects on driving performance of using cell phones to retrieve and send text messages.

The bias associated with amplicon sequencing does not affect the quantitative assessment of bacterial community dynamics.

PubMed

Ibarbalz, Federico M; Pérez, María Victoria; Figuerola, Eva L M; Erijman, Leonardo

2014-01-01

The performance of two sets of primers targeting variable regions of the 16S rRNA gene V1-V3 and V4 was compared in their ability to describe changes of bacterial diversity and temporal turnover in full-scale activated sludge. Duplicate sets of high-throughput amplicon sequencing data of the two 16S rRNA regions shared a collection of core taxa that were observed across a series of twelve monthly samples, although the relative abundance of each taxon was substantially different between regions. A case in point was the changes in the relative abundance of filamentous bacteria Thiothrix, which caused a large effect on diversity indices, but only in the V1-V3 data set. Yet the relative abundance of Thiothrix in the amplicon sequencing data from both regions correlated with the estimation of its abundance determined using fluorescence in situ hybridization. In nonmetric multidimensional analysis samples were distributed along the first ordination axis according to the sequenced region rather than according to sample identities. The dynamics of microbial communities indicated that V1-V3 and the V4 regions of the 16S rRNA gene yielded comparable patterns of: 1) the changes occurring within the communities along fixed time intervals, 2) the slow turnover of activated sludge communities and 3) the rate of species replacement calculated from the taxa-time relationships. The temperature was the only operational variable that showed significant correlation with the composition of bacterial communities over time for the sets of data obtained with both pairs of primers. In conclusion, we show that despite the bias introduced by amplicon sequencing, the variable regions V1-V3 and V4 can be confidently used for the quantitative assessment of bacterial community dynamics, and provide a proper qualitative account of general taxa in the community, especially when the data are obtained over a convenient time window rather than at a single time point.

The Bias Associated with Amplicon Sequencing Does Not Affect the Quantitative Assessment of Bacterial Community Dynamics

PubMed Central

Figuerola, Eva L. M.; Erijman, Leonardo

2014-01-01

The performance of two sets of primers targeting variable regions of the 16S rRNA gene V1–V3 and V4 was compared in their ability to describe changes of bacterial diversity and temporal turnover in full-scale activated sludge. Duplicate sets of high-throughput amplicon sequencing data of the two 16S rRNA regions shared a collection of core taxa that were observed across a series of twelve monthly samples, although the relative abundance of each taxon was substantially different between regions. A case in point was the changes in the relative abundance of filamentous bacteria Thiothrix, which caused a large effect on diversity indices, but only in the V1–V3 data set. Yet the relative abundance of Thiothrix in the amplicon sequencing data from both regions correlated with the estimation of its abundance determined using fluorescence in situ hybridization. In nonmetric multidimensional analysis samples were distributed along the first ordination axis according to the sequenced region rather than according to sample identities. The dynamics of microbial communities indicated that V1–V3 and the V4 regions of the 16S rRNA gene yielded comparable patterns of: 1) the changes occurring within the communities along fixed time intervals, 2) the slow turnover of activated sludge communities and 3) the rate of species replacement calculated from the taxa–time relationships. The temperature was the only operational variable that showed significant correlation with the composition of bacterial communities over time for the sets of data obtained with both pairs of primers. In conclusion, we show that despite the bias introduced by amplicon sequencing, the variable regions V1–V3 and V4 can be confidently used for the quantitative assessment of bacterial community dynamics, and provide a proper qualitative account of general taxa in the community, especially when the data are obtained over a convenient time window rather than at a single time point. PMID:24923665

Drinking driver and traffic safety project. Volume 2, Probabilities for drinking drivers

DOT National Transportation Integrated Search

1973-10-01

This is the second volume of a final report of a four-year study of drinking drivers. It includes a brief description of a prediction model developed from over 4000 cases, including drinking drivers, recidivist drinking drivers and drivers license ap...

HPV Genotyping of Modified General Primer-Amplicons Is More Analytically Sensitive and Specific by Sequencing than by Hybridization

PubMed Central

Meisal, Roger; Rounge, Trine Ballestad; Christiansen, Irene Kraus; Eieland, Alexander Kirkeby; Worren, Merete Molton; Molden, Tor Faksvaag; Kommedal, Øyvind; Hovig, Eivind; Leegaard, Truls Michael

2017-01-01

Sensitive and specific genotyping of human papillomaviruses (HPVs) is important for population-based surveillance of carcinogenic HPV types and for monitoring vaccine effectiveness. Here we compare HPV genotyping by Next Generation Sequencing (NGS) to an established DNA hybridization method. In DNA isolated from urine, the overall analytical sensitivity of NGS was found to be 22% higher than that of hybridization. NGS was also found to be the most specific method and expanded the detection repertoire beyond the 37 types of the DNA hybridization assay. Furthermore, NGS provided an increased resolution by identifying genetic variants of individual HPV types. The same Modified General Primers (MGP)-amplicon was used in both methods. The NGS method is described in detail to facilitate implementation in the clinical microbiology laboratory and includes suggestions for new standards for detection and calling of types and variants with improved resolution. PMID:28045981

Greater cerebellar gray matter volume in car drivers: an exploratory voxel-based morphometry study

PubMed Central

Sakai, Hiroyuki; Ando, Takafumi; Sadato, Norihiro; Uchiyama, Yuji

2017-01-01

Previous functional neuroimaging studies have identified multiple brain areas associated with distinct aspects of car driving in simulated traffic environments. Few studies, however, have examined brain morphology associated with everyday car-driving experience in real traffic. Thus, the aim of the current study was to identify gray matter volume differences between drivers and non-drivers. We collected T1-weighted structural brain images from 73 healthy young adults (36 drivers and 37 non-drivers). We performed a whole-brain voxel-based morphometry analysis to examine between-group differences in regional gray matter volume. Compared with non-drivers, drivers showed significantly greater gray matter volume in the left cerebellar hemisphere, which has been associated with cognitive rather than motor functioning. In contrast, we found no brain areas with significantly greater gray matter volume in non-drivers compared with drivers. Our findings indicate that experience with everyday car driving in real traffic is associated with greater gray matter volume in the left cerebellar hemisphere. This brain area may be involved in abilities that are critical for driving a car, but are not commonly or frequently used during other daily activities. PMID:28417971

Greater cerebellar gray matter volume in car drivers: an exploratory voxel-based morphometry study.

PubMed

Sakai, Hiroyuki; Ando, Takafumi; Sadato, Norihiro; Uchiyama, Yuji

2017-04-18

Previous functional neuroimaging studies have identified multiple brain areas associated with distinct aspects of car driving in simulated traffic environments. Few studies, however, have examined brain morphology associated with everyday car-driving experience in real traffic. Thus, the aim of the current study was to identify gray matter volume differences between drivers and non-drivers. We collected T1-weighted structural brain images from 73 healthy young adults (36 drivers and 37 non-drivers). We performed a whole-brain voxel-based morphometry analysis to examine between-group differences in regional gray matter volume. Compared with non-drivers, drivers showed significantly greater gray matter volume in the left cerebellar hemisphere, which has been associated with cognitive rather than motor functioning. In contrast, we found no brain areas with significantly greater gray matter volume in non-drivers compared with drivers. Our findings indicate that experience with everyday car driving in real traffic is associated with greater gray matter volume in the left cerebellar hemisphere. This brain area may be involved in abilities that are critical for driving a car, but are not commonly or frequently used during other daily activities.

Prediction and perception of hazards in professional drivers: Does hazard perception skill differ between safe and less-safe fire-appliance drivers?

PubMed

Crundall, David; Kroll, Victoria

2018-05-18

Can hazard perception testing be useful for the emergency services? Previous research has found emergency response drivers' (ERDs) to perform better than controls, however these studies used clips of normal driving. In contrast, the current study filmed footage from a fire-appliance on blue-light training runs through Nottinghamshire, and endeavoured to discriminate between different groups of EDRs based on experience and collision risk. Thirty clips were selected to create two variants of the hazard perception test: a traditional push-button test requiring speeded-responses to hazards, and a prediction test that occludes at hazard onset and provides four possible outcomes for participants to choose between. Three groups of fire-appliance drivers (novices, low-risk experienced and high-risk experienced), and age-matched controls undertook both tests. The hazard perception test only discriminated between controls and all FA drivers, whereas the hazard prediction test was more sensitive, discriminating between high and low-risk experienced fire appliance drivers. Eye movement analyses suggest that the low-risk drivers were better at prioritising the hazardous precursors, leading to better predictive accuracy. These results pave the way for future assessment and training tools to supplement emergency response driver training, while supporting the growing literature that identifies hazard prediction as a more robust measure of driver safety than traditional hazard perception tests. Copyright © 2018 Elsevier Ltd. All rights reserved.

Redesign of Transjakarta Bus Driver's Cabin

NASA Astrophysics Data System (ADS)

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

Competitive amplification of differentially melting amplicons (CADMA) enables sensitive and direct detection of all mutation types by high-resolution melting analysis.

PubMed

Kristensen, Lasse S; Andersen, Gitte B; Hager, Henrik; Hansen, Lise Lotte

2012-01-01

Sensitive and specific mutation detection is of particular importance in cancer diagnostics, prognostics, and individualized patient treatment. However, the majority of molecular methodologies that have been developed with the aim of increasing the sensitivity of mutation testing have drawbacks in terms of specificity, convenience, or costs. Here, we have established a new method, Competitive Amplification of Differentially Melting Amplicons (CADMA), which allows very sensitive and specific detection of all mutation types. The principle of the method is to amplify wild-type and mutated sequences simultaneously using a three-primer system. A mutation-specific primer is designed to introduce melting temperature decreasing mutations in the resulting mutated amplicon, while a second overlapping primer is designed to amplify both wild-type and mutated sequences. When combined with a third common primer very sensitive mutation detection becomes possible, when using high-resolution melting (HRM) as detection platform. The introduction of melting temperature decreasing mutations in the mutated amplicon also allows for further mutation enrichment by fast coamplification at lower denaturation temperature PCR (COLD-PCR). For proof-of-concept, we have designed CADMA assays for clinically relevant BRAF, EGFR, KRAS, and PIK3CA mutations, which are sensitive to, between 0.025% and 0.25%, mutated alleles in a wild-type background. In conclusion, CADMA enables highly sensitive and specific mutation detection by HRM analysis. © 2011 Wiley Periodicals, Inc.

Driver attitudes and behaviors at intersections and potential effectiveness of engineering countermeasures

DOT National Transportation Integrated Search

2006-03-01

This document is an executive summary of the report "Driver attitudes and behaviors at intersections and potential effectiveness of engineering countermeasures", FHWA-HRT-05-078. The objective of the focus group study was to identify driver attitudes...

Incidence of lung cancer among subway drivers in Stockholm.

PubMed

Gustavsson, Per; Bigert, Carolina; Pollán, Marina

2008-07-01

Very high levels of airborne particles have been detected in the subway system in Stockholm. Subway particles are more toxic to DNA in cultured human lung cells than particles from ambient air. This cohort comprised all men in Stockholm County who were gainfully employed in 1970. They were followed for cancer incidence until 1989. Lung cancer cases were identified from the national cancer register. Subway drivers were identified from the census in 1970. The reference cohort comprised all transport and communication workers in Stockholm. There were nine cases of lung cancer among the subway drivers, giving a SIR of 0.82 (95% confidence interval 0.38-1.56). The lung cancer incidence was not increased among the subway drivers. The study gives some evidence against the hypothesis that subway particles would be more potent in inducing lung cancer than particles in ambient air. (c) 2008 Wiley-Liss, Inc.

Safe mobility for elderly drivers--considerations based on expert and self-assessment.

PubMed

Broberg, Thomas; Dukic Willstrand, Tania

2014-05-01

To further understand the needs of the growing population of elderly drivers and create solutions for safe mobility it is important to understand the driving scenarios and aspects in day to day traffic that may be of challenge for this group. More so, individual differences in how drivers perceive their own driving ability may have an effect on how individuals limit their mobility and/or increase their exposure to risk situations, with a potential negative effect on safety. In this study two sets of assessments have been used in order to identify scenarios and aspects needing consideration in creating safe mobility for elderly drivers; an expert assessment using on-road driving together with assessments through semi structured in-depth interviews. This combination also enables categorisation of the drivers, comparing their own perception of their driving performance with the expert assessment based on actual on-road driving. Four different categories of drivers were identified: adequate (positive), over, under and adequate (negative) estimators. A number of important aspects were identified in the study. Adapting speed to the situation and driving too fast, especially on straight roads in the city, is one aspect. Seeking the attention of other road users at intersections and roundabouts is another important consideration identified. Awareness of difficulties related to speed adaptation and attention was low amongst all the driver categories. However, a difference in attitude was seen in the categories with a more humble and acceptant attitude amongst the adequate and under estimator groups, as compared to the over estimators suggesting that the aspect of attitudes is another important factor for consideration. Copyright © 2014 Elsevier Ltd. All rights reserved.

Minimum Required Attention: A Human-Centered Approach to Driver Inattention.

PubMed

Kircher, Katja; Ahlstrom, Christer

2017-05-01

To propose a driver attention theory based on the notion of driving as a satisficing and partially self-paced task and, within this framework, present a definition for driver inattention. Many definitions of driver inattention and distraction have been proposed, but they are difficult to operationalize, and they are either unreasonably strict and inflexible or suffer from hindsight bias. Existing definitions of driver distraction are reviewed and their shortcomings identified. We then present the minimum required attention (MiRA) theory to overcome these shortcomings. Suggestions on how to operationalize MiRA are also presented. MiRA describes which role the attention of the driver plays in the shared "situation awareness of the traffic system." A driver is considered attentive when sampling sufficient information to meet the demands of the system, namely, that he or she fulfills the preconditions to be able to form and maintain a good enough mental representation of the situation. A driver should only be considered inattentive when information sampling is not sufficient, regardless of whether the driver is concurrently executing an additional task or not. The MiRA theory builds on well-established driver attention theories. It goes beyond available driver distraction definitions by first defining what a driver needs to be attentive to, being free from hindsight bias, and allowing the driver to adapt to the current demands of the traffic situation through satisficing and self-pacing. MiRA has the potential to provide the stepping stone for unbiased and operationalizable inattention detection and classification.

[The ability of drivers to give first aid--testing by questionnaire].

PubMed

Goniewicz, M

1998-01-01

Road accidents have become a serious social problem. The scale and complexity of this problem shows clearly that there is a necessity to improve citizens' ability to give first aid which is especially essential in the case of drivers. Thus special training how to give first aid at the accident place seems to be of the primary importance. The objective of this paper is to: 1) identify to what extent the drivers of motor vehicles are prepared to provide first aid for casualties of the road accidents, 2) evaluate the training system of teaching motorists how to give first aid before professional help arrives, 3) identify drivers' views on possibilities of decreasing the number of fatal casualties of the road accidents. The questionnaire was given to 560 employees of local government institutions in the city of Lublin either professional or non-professional drivers. The direct method and anonymous questionnaire were used. The results of the questionnaire revealed clearly that very few drivers are well-prepared to give proper first aid at the accident site. No matter what sex, education or driving experience, the drivers have not got enough skills to give first aid and the effect is enhanced by various psychological barriers. The questioned drivers shared the opinion that first aid training is badly run. The drivers stressed bad quality of the training and the fact that it is impossible to acquire practical skills that may be required in the case of emergency. Drivers' views on possibilities of decreasing the number of fatal casualties of the road accidents included, among others, the following propositions: in addition to the driving licence exam first aid exam should be compulsory severe enforcement and execution of the law which regulates the mandatory first aid giving.

Approaches of truck drivers and non-truck drivers toward reckless on-road behavior.

PubMed

Rosenbloom, Tova; Eldror, Ehud; Shahar, Amit

2009-07-01

The purpose of the study was to compare the reported approaches of truck drivers to those of non-truck drivers toward reckless on-road behaviors. One hundred and sixty-seven adult males, including 70 non-truck drivers, completed the questionnaires voluntarily. The truck drivers were employees of a concrete manufacturing company working at various company plants throughout Israel. Seventy were professional mixer truckers and 27 were tip-truckers. The participants completed the Reckless Driving Self-Report Scale based on Taubman Ben-Ari et al. [Taubman Ben-Ari, O., Florian, V., Mikulincer, M., 1999. The impact of mortality salience on reckless driving: a test of terror management mechanisms. Journal of Personality and Social Psychology 76, 35-45], adapted for truck drivers for this study. It was expected that non-professional, as compared to professional (truck) drivers, would be more permissive regarding reckless driving, since driving risks are less prominent in their daily driving experience. An ANOVA performed on mean reckless-driving scores yielded significant results. The post hoc Schéffe test indicated significantly higher reckless-driving scores for automobile drivers as compared to both mixer-truck driver scores and tip-truck driver scores. In addition, the reckless-driving scores for mixer-truck drivers were significantly higher than the tip-truck driver scores. We discuss various explanations for the findings and consider possible implications for training strategies in organizations as well as for media campaigns focused on mutual safe road use of truck drivers and private vehicle drivers.

Estimated Cost of Crashes in Commercial Drivers Supports Screening and Treatment of Obstructive Sleep Apnea

PubMed Central

Gurubhagavatula, Indira; Nkwuo, Jonathan E.; Maislin, Greg; Pack, Allan I.

2009-01-01

Sleep apnea among commercial drivers may increase the risk of fall-asleep crashes, which incur large expenses. Drivers of passenger cars whose apnea is treated experience lower crash risk. Among community-based holders of commercial driver’s licenses, we considered three methods for identifying sleep apnea syndrome: 1) in-lab polysomnography; 2) selective in-lab polysomnography for high-risk drivers, where high risk is first identified by body mass index, age and gender, followed by oximetry in a subset of drivers; and 3) not screening. The costs for each of these three programs equaled the sum of the costs of testing, treatment of identified cases, and crashes. Assuming that treatment prevents apnea-related crashes, polysomnography is not cost-effective, because it was more expensive than the cost of crashes when no screening is done. Screening with BMI, age and gender, however, with confirmatory in-lab polysomnography only on high-risk drivers was cost-effective, as long as a high proportion (73.8%) of screened drivers accepts treatment. These findings indicate that strategies that reduce reliance on in-laboratory polysomnography may be more cost-effective than not screening, and that treatment acceptance may need to be a condition of employment for affected drivers. PMID:18215538

Finding cancer driver mutations in the era of big data research.

PubMed

Poulos, Rebecca C; Wong, Jason W H

2018-04-02

In the last decade, the costs of genome sequencing have decreased considerably. The commencement of large-scale cancer sequencing projects has enabled cancer genomics to join the big data revolution. One of the challenges still facing cancer genomics research is determining which are the driver mutations in an individual cancer, as these contribute only a small subset of the overall mutation profile of a tumour. Focusing primarily on somatic single nucleotide mutations in this review, we consider both coding and non-coding driver mutations, and discuss how such mutations might be identified from cancer sequencing datasets. We describe some of the tools and database that are available for the annotation of somatic variants and the identification of cancer driver genes. We also address the use of genome-wide variation in mutation load to establish background mutation rates from which to identify driver mutations under positive selection. Finally, we describe the ways in which mutational signatures can act as clues for the identification of cancer drivers, as these mutations may cause, or arise from, certain mutational processes. By defining the molecular changes responsible for driving cancer development, new cancer treatment strategies may be developed or novel preventative measures proposed.

Elderly driver retraining

DOT National Transportation Integrated Search

1982-09-01

This report documents a study of the traffic safety problems associated with elderly drivers. For the purposes of this study, "elderly drivers" are defined as drivers aged 55 years or older. The study involved five major activities. First, research w...

Amplicon Sequencing Reveals Microbiological Signatures in Spent Nuclear Fuel Storage Basins

DOE PAGES

Bagwell, Christopher E.; Noble, Peter A.; Milliken, Charles E.; ...

2018-03-09

Water quality is an important determinant for the structural integrity of alloy cladded fuels and assemblies during long-term wet storage. Detailed characterization of a water filled storage basin for spent nuclear reactor fuel was performed following the formation and proliferation of an amorphous white flocculent. White precipitant was sampled throughout the storage basin for chemical and spectroscopic characterization, and environmental DNA was extracted for 454 pyrosequencing of bacterial 16S rRNA gene diversity. Accordingly, spectroscopic analyses indicated the precipitant to be primarily amorphous to crystalline aluminum (oxy) hydroxides with minor associated elemental components including Fe, Si, Ti, and U. High levelsmore » of organic carbon were co-localized with the precipitant relative to bulk dissolved organic concentrations. Bacterial densities were highly variable between sampling locations and with depth within the water filled storage basin; cell numbers ranged from 4 × 10 3to 4 × 104 cells/mL. Bacterial diversity that was physically associated with the aluminum (oxy) hydroxide complexes exceeded an estimated 4,000 OTUs/amplicon library (3% cutoff) and the majority of sequences were aligned to the families Burkholderiaceae (23%), Nitrospiraceae (23%), Hyphomicrobiaceae (17%), and Comamonadaceae (6%). We surmise that episodic changes in the physical and chemical properties of the basin contribute to the polymerization of aluminum (oxy) hydroxides, which in turn can chemisorb nutrients, carbon ligands and bacterial cells from the surrounding bulk aqueous phase. As such, these precipitants should establish favorable microhabitats for bacterial colonization and growth. Comparative analyses of 16S rRNA gene amplicon libraries across a selection of natural and engineered aquatic ecosystems were performed and microbial community and taxonomic signatures unique to the spent nuclear fuel (SNF) storage basin environment were revealed. These insights could

Amplicon Sequencing Reveals Microbiological Signatures in Spent Nuclear Fuel Storage Basins.

PubMed

Bagwell, Christopher E; Noble, Peter A; Milliken, Charles E; Li, Dien; Kaplan, Daniel I

2018-01-01

Water quality is an important determinant for the structural integrity of alloy cladded fuels and assemblies during long-term wet storage. Detailed characterization of a water filled storage basin for spent nuclear reactor fuel was performed following the formation and proliferation of an amorphous white flocculent. White precipitant was sampled throughout the storage basin for chemical and spectroscopic characterization, and environmental DNA was extracted for 454 pyrosequencing of bacterial 16S rRNA gene diversity. Accordingly, spectroscopic analyses indicated the precipitant to be primarily amorphous to crystalline aluminum (oxy) hydroxides with minor associated elemental components including Fe, Si, Ti, and U. High levels of organic carbon were co-localized with the precipitant relative to bulk dissolved organic concentrations. Bacterial densities were highly variable between sampling locations and with depth within the water filled storage basin; cell numbers ranged from 4 × 10 3 to 4 × 10 4 cells/mL. Bacterial diversity that was physically associated with the aluminum (oxy) hydroxide complexes exceeded an estimated 4,000 OTUs/amplicon library (3% cutoff) and the majority of sequences were aligned to the families Burkholderiaceae (23%), Nitrospiraceae (23%), Hyphomicrobiaceae (17%), and Comamonadaceae (6%). We surmise that episodic changes in the physical and chemical properties of the basin contribute to the polymerization of aluminum (oxy) hydroxides, which in turn can chemisorb nutrients, carbon ligands and bacterial cells from the surrounding bulk aqueous phase. As such, these precipitants should establish favorable microhabitats for bacterial colonization and growth. Comparative analyses of 16S rRNA gene amplicon libraries across a selection of natural and engineered aquatic ecosystems were performed and microbial community and taxonomic signatures unique to the spent nuclear fuel (SNF) storage basin environment were revealed. These insights could spur

Amplicon Sequencing Reveals Microbiological Signatures in Spent Nuclear Fuel Storage Basins

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bagwell, Christopher E.; Noble, Peter A.; Milliken, Charles E.

Water quality is an important determinant for the structural integrity of alloy cladded fuels and assemblies during long-term wet storage. Detailed characterization of a water filled storage basin for spent nuclear reactor fuel was performed following the formation and proliferation of an amorphous white flocculent. White precipitant was sampled throughout the storage basin for chemical and spectroscopic characterization, and environmental DNA was extracted for 454 pyrosequencing of bacterial 16S rRNA gene diversity. Accordingly, spectroscopic analyses indicated the precipitant to be primarily amorphous to crystalline aluminum (oxy) hydroxides with minor associated elemental components including Fe, Si, Ti, and U. High levelsmore » of organic carbon were co-localized with the precipitant relative to bulk dissolved organic concentrations. Bacterial densities were highly variable between sampling locations and with depth within the water filled storage basin; cell numbers ranged from 4 × 10 3to 4 × 104 cells/mL. Bacterial diversity that was physically associated with the aluminum (oxy) hydroxide complexes exceeded an estimated 4,000 OTUs/amplicon library (3% cutoff) and the majority of sequences were aligned to the families Burkholderiaceae (23%), Nitrospiraceae (23%), Hyphomicrobiaceae (17%), and Comamonadaceae (6%). We surmise that episodic changes in the physical and chemical properties of the basin contribute to the polymerization of aluminum (oxy) hydroxides, which in turn can chemisorb nutrients, carbon ligands and bacterial cells from the surrounding bulk aqueous phase. As such, these precipitants should establish favorable microhabitats for bacterial colonization and growth. Comparative analyses of 16S rRNA gene amplicon libraries across a selection of natural and engineered aquatic ecosystems were performed and microbial community and taxonomic signatures unique to the spent nuclear fuel (SNF) storage basin environment were revealed. These insights could

Amplicon Sequencing Reveals Microbiological Signatures in Spent Nuclear Fuel Storage Basins

PubMed Central

Bagwell, Christopher E.; Noble, Peter A.; Milliken, Charles E.; Li, Dien; Kaplan, Daniel I.

2018-01-01

Water quality is an important determinant for the structural integrity of alloy cladded fuels and assemblies during long-term wet storage. Detailed characterization of a water filled storage basin for spent nuclear reactor fuel was performed following the formation and proliferation of an amorphous white flocculent. White precipitant was sampled throughout the storage basin for chemical and spectroscopic characterization, and environmental DNA was extracted for 454 pyrosequencing of bacterial 16S rRNA gene diversity. Accordingly, spectroscopic analyses indicated the precipitant to be primarily amorphous to crystalline aluminum (oxy) hydroxides with minor associated elemental components including Fe, Si, Ti, and U. High levels of organic carbon were co-localized with the precipitant relative to bulk dissolved organic concentrations. Bacterial densities were highly variable between sampling locations and with depth within the water filled storage basin; cell numbers ranged from 4 × 103to 4 × 104 cells/mL. Bacterial diversity that was physically associated with the aluminum (oxy) hydroxide complexes exceeded an estimated 4,000 OTUs/amplicon library (3% cutoff) and the majority of sequences were aligned to the families Burkholderiaceae (23%), Nitrospiraceae (23%), Hyphomicrobiaceae (17%), and Comamonadaceae (6%). We surmise that episodic changes in the physical and chemical properties of the basin contribute to the polymerization of aluminum (oxy) hydroxides, which in turn can chemisorb nutrients, carbon ligands and bacterial cells from the surrounding bulk aqueous phase. As such, these precipitants should establish favorable microhabitats for bacterial colonization and growth. Comparative analyses of 16S rRNA gene amplicon libraries across a selection of natural and engineered aquatic ecosystems were performed and microbial community and taxonomic signatures unique to the spent nuclear fuel (SNF) storage basin environment were revealed. These insights could spur the

Drivers anticipate lead-vehicle conflicts during automated longitudinal control: Sensory cues capture driver attention and promote appropriate and timely responses.

PubMed

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. Copyright © 2016 Elsevier Ltd. All rights reserved.

Technology and teen drivers.

PubMed

Lee, John D

2007-01-01

The rapid evolution of computing, communication, and sensor technology is likely to affect young drivers more than others. The distraction potential of infotainment technology stresses the same vulnerabilities that already lead young drivers to crash more frequently than other drivers. Cell phones, text messaging, MP3 players, and other nomadic devices all present a threat because young drivers may lack the spare attentional capacity for vehicle control and the ability to anticipate and manage hazards. Moreover, young drivers are likely to be the first and most aggressive users of new technology. Fortunately, emerging technology can also support safe driving. Electronic stability control, collision avoidance systems, intelligent speed adaptation, and vehicle tracking systems can all help mitigate the threats to young drivers. However, technology alone is unlikely to make young drivers safer. One promising approach to tailoring technology to teen drivers is to extend proven methods for enhancing young driver safety. The success of graduated drivers license programs (GDL) and the impressive safety benefit of supervised driving suggest ways of tailoring technology to the needs of young drivers. To anticipate the effects of technology on teen driving it may be useful to draw an analogy between the effects of passengers and the effects of technology. Technology can act as a teen passenger and undermine safety or it can act as an adult passenger and enhance safety. Rapidly developing technology may have particularly large effects on teen drivers. To maximize the positive effects and minimize the negative effects will require a broad range of industries to work together. Ideally, vehicle manufacturers would work with infotainment providers, insurance companies, and policy makers to craft new technologies so that they accommodate the needs of young drivers. Without such collaboration young drivers will face even greater challenges to their safety as new technologies emerge.

Observed and projected drivers of emerging infectious diseases in Europe.

PubMed

Semenza, Jan C; Rocklöv, Joacim; Penttinen, Pasi; Lindgren, Elisabet

2016-10-01

Emerging infectious diseases are of international concern because of the potential for, and impact of, pandemics; however, they are difficult to predict. To identify the drivers of disease emergence, we analyzed infectious disease threat events (IDTEs) detected through epidemic intelligence collected at the European Centre for Disease Prevention and Control (ECDC) between 2008 and 2013, and compared the observed results with a 2008 ECDC foresight study of projected drivers of future IDTEs in Europe. Among 10 categories of IDTEs, foodborne and waterborne IDTEs were the most common, vaccine-preventable IDTEs caused the highest number of cases, and airborne IDTEs caused the most deaths. Observed drivers for each IDTE were sorted into three main groups: globalization and environmental drivers contributed to 61% of all IDTEs, public health system drivers contributed to 21%, and social and demographic drivers to 18%. A multiple logistic regression analysis showed that four of the top five drivers for observed IDTEs were in the globalization and environment group. In the observational study, the globalization and environment group was related to all IDTE categories, but only to five of eight categories in the foresight study. Directly targeting these drivers with public health interventions may diminish the chances of IDTE occurrence from the outset. © 2016 New York Academy of Sciences.

Driver Performance in the Moments Surrounding a Microsleep

PubMed Central

Boyle, Linda Ng; Tippin, Jon; Paul, Amit; Rizzo, Matthew

2009-01-01

This study examined if individuals who are at increased risk for drowsy-driving because of obstructive sleep apnea syndrome (OSAS), have impairments in driving performance in the moments during microsleep episodes as opposed to during periods of wakefulness. Twenty-four licensed drivers diagnosed with OSAS based on standard clinical and polysomnographic criteria, participated in an hour-long drive in a high-fidelity driving simulator with synchronous electroencephalographic (EEG) recordings for identification of microsleeps. The drivers showed significant deterioration in vehicle control during the microsleep episodes compared to driving performance in the absence of microsleeps on equivalent segments of roadway. The degree of performance decrement correlated with microsleep duration, particularly on curved roads. Results indicate that driving performance deteriorates during microsleep episodes. Detecting microsleeps in real-time and identifying how these episodes of transition between wakefulness and sleep impair driver performance is relevant to the design and implementation of countermeasures such as drowsy driver detection and alerting systems that use EEG technology. PMID:20090864

Development of an errorable car-following driver model

NASA Astrophysics Data System (ADS)

Yang, H.-H.; Peng, H.

2010-06-01

An errorable car-following driver model is presented in this paper. An errorable driver model is one that emulates human driver's functions and can generate both nominal (error-free), as well as devious (with error) behaviours. This model was developed for evaluation and design of active safety systems. The car-following data used for developing and validating the model were obtained from a large-scale naturalistic driving database. The stochastic car-following behaviour was first analysed and modelled as a random process. Three error-inducing behaviours were then introduced. First, human perceptual limitation was studied and implemented. Distraction due to non-driving tasks was then identified based on the statistical analysis of the driving data. Finally, time delay of human drivers was estimated through a recursive least-square identification process. By including these three error-inducing behaviours, rear-end collisions with the lead vehicle could occur. The simulated crash rate was found to be similar but somewhat higher than that reported in traffic statistics.

Microbial community analysis of the hypersaline water of the Dead Sea using high-throughput amplicon sequencing.

PubMed

Jacob, Jacob H; Hussein, Emad I; Shakhatreh, Muhamad Ali K; Cornelison, Christopher T

2017-10-01

Amplicon sequencing using next-generation technology (bTEFAP ® ) has been utilized in describing the diversity of Dead Sea microbiota. The investigated area is a well-known salt lake in the western part of Jordan found in the lowest geographical location in the world (more than 420 m below sea level) and characterized by extreme salinity (approximately, 34%) in addition to other extreme conditions (low pH, unique ionic composition different from sea water). DNA was extracted from Dead Sea water. A total of 314,310 small subunit RNA (SSU rRNA) sequences were parsed, and 288,452 sequences were then clustered. For alpha diversity analysis, sample was rarefied to 3,000 sequences. The Shannon-Wiener index curve plot reached a plateau at approximately 3,000 sequences indicating that sequencing depth was sufficient to capture the full scope of microbial diversity. Archaea was found to be dominating the sequences (52%), whereas Bacteria constitute 45% of the sequences. Altogether, prokaryotic sequences (which constitute 97% of all sequences) were found to predominate. The findings expand on previous studies by using high-throughput amplicon sequencing to describe the microbial community in an environment which in recent years has been shown to hide some interesting diversity. © 2017 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Evaluation of driver fatigue on two channels of EEG data.

PubMed

Li, Wei; He, Qi-chang; Fan, Xiu-min; Fei, Zhi-min

2012-01-11

Electroencephalogram (EEG) data is an effective indicator to evaluate driver fatigue. The 16 channels of EEG data are collected and transformed into three bands (θ, α, and β) in the current paper. First, 12 types of energy parameters are computed based on the EEG data. Then, Grey Relational Analysis (GRA) is introduced to identify the optimal indicator of driver fatigue, after which, the number of significant electrodes is reduced using Kernel Principle Component Analysis (KPCA). Finally, the evaluation model for driver fatigue is established with the regression equation based on the EEG data from two significant electrodes (Fp1 and O1). The experimental results verify that the model is effective in evaluating driver fatigue. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Exploring rear-end roadway crashes from the driver's perspective

DOT National Transportation Integrated Search

1998-10-01

This pilot study examined rear-end crashes from the driver's perspective to identify self-reported reasons and causes of such crashes, to identify commonalities in the self-reported causes and locations and circumstances of these crashes, and to expl...

Modernization of the Driver Behaviour Questionnaire.

PubMed

Cordazzo, Sheila T D; Scialfa, Charles T; Ross, Rachel Jones

2016-02-01

The current study builds on previous versions of the Driver Behaviour Questionnaire (DBQ) by incorporating a larger sample of driving behaviors targeting inattention, distraction, aggressive driving, and health related to aging. The goals of this study were to determine if the resulting factor structure was consistent with a more contemporary view of unsafe driving behaviors, and to determine whether scores on the factors could predict self-reported collisions and police citations. The instrument was given to a sample of 3295 drivers ranging in age from 19 to 80+ years old. It was divided in two sections, the first to provide demographic information and driving history data and the second containing 105 driver behavior questions. An exploratory factor analysis resulted in a 65-item scale organized in four factors. The factors were labeled tentatively as Inattention Errors, Age-Related Problems, Distraction and Hurry, and Aggressive Violations. Regression analyses showed that the factors were predictors of self-reported, at-fault collisions and police citations. The factor scores found in this research are consistent with a useful theoretical framework for understanding unsafe driver actions, and demonstrate some potential to identify several individual difference variables that predict self-reported collisions and citations. Copyright © 2015 Elsevier Ltd. All rights reserved.

Can we improve clinical prediction of at-risk older drivers?

PubMed Central

Bowers, Alex R.; Anastasio, R. Julius; Sheldon, Sarah S.; O’Connor, Margaret G.; Hollis, Ann M.; Howe, Piers D.; Horowitz, Todd S.

2013-01-01

Objectives To conduct a pilot study to evaluate the predictive value of the Montreal Cognitive Assessment test (MoCA) and a brief test of multiple object tracking (MOT) relative to other tests of cognition and attention in identifying at-risk older drivers, and to determine which combination of tests provided the best overall prediction. Methods Forty-seven currently-licensed drivers (58 to 95 years), primarily from a clinical driving evaluation program, participated. Their performance was measured on: (1) a screening test battery, comprising MoCA, MOT, MiniMental State Examination (MMSE), Trail-Making Test, visual acuity, contrast sensitivity, and Useful Field of View (UFOV); and (2) a standardized road test. Results Eighteen participants were rated at-risk on the road test. UFOV subtest 2 was the best single predictor with an area under the curve (AUC) of .84. Neither MoCA nor MOT was a better predictor of the at-risk outcome than either MMSE or UFOV, respectively. The best four-test combination (MMSE, UFOV subtest 2, visual acuity and contrast sensitivity) was able to identify at-risk drivers with 95% specificity and 80% sensitivity (.91 AUC). Conclusions Although the best four-test combination was much better than a single test in identifying at-risk drivers, there is still much work to do in this field to establish test batteries that have both high sensitivity and specificity. PMID:23954688

Biphasic Study to Characterize Agricultural Biogas Plants by High-Throughput 16S rRNA Gene Amplicon Sequencing and Microscopic Analysis.

PubMed

Maus, Irena; Kim, Yong Sung; Wibberg, Daniel; Stolze, Yvonne; Off, Sandra; Antonczyk, Sebastian; Pühler, Alfred; Scherer, Paul; Schlüter, Andreas

2017-02-28

Process surveillance within agricultural biogas plants (BGPs) was concurrently studied by high-throughput 16S rRNA gene amplicon sequencing and an optimized quantitative microscopic fingerprinting (QMF) technique. In contrast to 16S rRNA gene amplicons, digitalized microscopy is a rapid and cost-effective method that facilitates enumeration and morphological differentiation of the most significant groups of methanogens regarding their shape and characteristic autofluorescent factor 420. Moreover, the fluorescence signal mirrors cell vitality. In this study, four different BGPs were investigated. The results indicated stable process performance in the mesophilic BGPs and in the thermophilic reactor. Bacterial subcommunity characterization revealed significant differences between the four BGPs. Most remarkably, the genera Defluviitoga and Halocella dominated the thermophilic bacterial subcommunity, whereas members of another taxon, Syntrophaceticus , were found to be abundant in the mesophilic BGP. The domain Archaea was dominated by the genus Methanoculleus in all four BGPs, followed by Methanosaeta in BGP1 and BGP3. In contrast, Methanothermobacter members were highly abundant in the thermophilic BGP4. Furthermore, a high consistency between the sequencing approach and the QMF method was shown, especially for the thermophilic BGP. The differences elucidated that using this biphasic approach for mesophilic BGPs provided novel insights regarding disaggregated single cells of Methanosarcina and Methanosaeta species. Both dominated the archaeal subcommunity and replaced coccoid Methanoculleus members belonging to the same group of Methanomicrobiales that have been frequently observed in similar BGPs. This work demonstrates that combining QMF and 16S rRNA gene amplicon sequencing is a complementary strategy to describe archaeal community structures within biogas processes.

Case Study of a Healthy Eating Intervention for Swedish Lorry Drivers

ERIC Educational Resources Information Center

Gill, Peter E.; Wijk, Katarina

2004-01-01

Professional drivers, i.e. lorry, truck, bus and taxi drivers, have been identified as a particular health risk group. An intervention to study the efficacy of a series of educational programmes, involving improved nutritional balance in meals served, food preparation routines and carrying out personal health profiles on staff, was implemented at…

Assessing older drivers: a primary care protocol to evaluate driving safety risk.

PubMed

Murden, Robert A; Unroe, Kathleen

2005-08-01

Most articles on elder drivers offer either general advice, or review testing protocols that divide drivers into two distinct groups: safe or unsafe. We believe it is unreasonable to expect any testing to fully separate drivers into just these two mutually exclusive groups, so we offer a protocol for a more practical approach. This protocol can be applied by primary care physicians. We review the justification for the many steps of this protocol, which have branches that lead to identifying drivers as low risk, high risk (for accidents) or needing further evaluation. Options for further evaluation are provided.

Bus driver sues.

PubMed

1996-09-06

A bus driver, known as John Doe, sued his employer, alleging that he was fired when he voluntarily disclosed that he was HIV-positive and needed a rest from the long hours of driving. The driver sued for back wages, benefits, and compensatory and punitive damages under the New Jersey Law Against Discrimination. Academy Bus tours told the driver he could not return to work without a doctor's examination. Doe has an excellent driving record and was certified as physically fit to work as a bus driver 14 months prior to his termination.

Psychoactive substances in seriously injured drivers in Denmark.

PubMed

Wiese Simonsen, K; Steentoft, A; Bernhoft, I M; Hels, T; Rasmussen, B S; Linnet, K

2013-01-10

This study assesses the presence of a number of psychoactive substances, including alcohol, based on blood samples from 840 seriously injured drivers admitted to five selected hospitals located in five different regions of Denmark. The study was a part of the EU 6th framework program DRUID (Driving Under the Influence of Drugs, Alcohol and Medicines). Blood samples were screened for 30 illegal and legal psychoactive substances and metabolites as well as ethanol. Danish legal limits were used to evaluate the frequency of drivers violating the Danish legislation while limit of quantification (LOQ) was used for monitoring positive drivers. Tramadol is not included in the Danish legislation therefore the general cut off, as decided in the DRUID project was used. Overall, ethanol (18%) was the most frequently identified compound (alone or in combination with other drugs) exceeding the legal limit, which is 0.53g/l in Denmark. The percentage of seriously injured drivers testing positive for medicinal drugs at levels above the Danish legal limit was 6.8%. Benzodiazepines and Z-drugs (6.4%) comprised the majority of this group. One or more illegal drugs (primarily amphetamines and cannabis) were found to be above the Danish legal limit in 4.9% of injured drivers. Young men (median age 31 years) were over-represented among injured drivers who violated Danish law for alcohol and drugs. Diazepam (4.4%), tramadol (3.2%), and clonazepam (3.0%) were the medicinal drugs most frequently detected at levels above LOQ, whereas amphetamines (5.4%) (amphetamine [5.2%] and methamphetamine [1.5%]), tetrahydrocannabinol (3.7%), and cocaine (3.3%), including the metabolite benzoylecgonine, were the most frequently detected illegal drugs. A driver could be positive for more than one substance; therefore, percentages are not mutually exclusive. Poly-drug use was observed in 112 (13%) seriously injured drivers. Tramadol was detected above DRUID cutoffs in 2.1% of seriously injured drivers

Swarm v2: highly-scalable and high-resolution amplicon clustering

PubMed Central

Quince, Christopher; de Vargas, Colomban; Dunthorn, Micah

2015-01-01

Previously we presented Swarm v1, a novel and open source amplicon clustering program that produced fine-scale molecular operational taxonomic units (OTUs), free of arbitrary global clustering thresholds and input-order dependency. Swarm v1 worked with an initial phase that used iterative single-linkage with a local clustering threshold (d), followed by a phase that used the internal abundance structures of clusters to break chained OTUs. Here we present Swarm v2, which has two important novel features: (1) a new algorithm for d = 1 that allows the computation time of the program to scale linearly with increasing amounts of data; and (2) the new fastidious option that reduces under-grouping by grafting low abundant OTUs (e.g., singletons and doubletons) onto larger ones. Swarm v2 also directly integrates the clustering and breaking phases, dereplicates sequencing reads with d = 0, outputs OTU representatives in fasta format, and plots individual OTUs as two-dimensional networks. PMID:26713226

Swarm v2: highly-scalable and high-resolution amplicon clustering.

PubMed

Mahé, Frédéric; Rognes, Torbjørn; Quince, Christopher; de Vargas, Colomban; Dunthorn, Micah

2015-01-01

Previously we presented Swarm v1, a novel and open source amplicon clustering program that produced fine-scale molecular operational taxonomic units (OTUs), free of arbitrary global clustering thresholds and input-order dependency. Swarm v1 worked with an initial phase that used iterative single-linkage with a local clustering threshold (d), followed by a phase that used the internal abundance structures of clusters to break chained OTUs. Here we present Swarm v2, which has two important novel features: (1) a new algorithm for d = 1 that allows the computation time of the program to scale linearly with increasing amounts of data; and (2) the new fastidious option that reduces under-grouping by grafting low abundant OTUs (e.g., singletons and doubletons) onto larger ones. Swarm v2 also directly integrates the clustering and breaking phases, dereplicates sequencing reads with d = 0, outputs OTU representatives in fasta format, and plots individual OTUs as two-dimensional networks.

Driver Education Saves Gas.

ERIC Educational Resources Information Center

American Automobile Association, Falls Church, VA. Traffic Engineering and Safety Dept.

The argument that driver education should be dropped because driver education cars use gas is shortsighted. High school driver education is an excellent vehicle for teaching concepts of energy conservation. A small investment in fuel now can result in major savings of gasoline over a student's lifetime. In addition good driver education courses…

Health assessment of taxi drivers in the city of Tshwane.

PubMed

Ramukumba, Tendani S; Mathikhi, Makwena S

2016-11-30

Taxi driving seems to be a strenuous occupation. There was evidence-based paucity of literature on health assessment of taxi drivers. Meanwhile taxi drivers of South Africa were burdened by communicable and non-communicable diseases including high-level exposure to injuries and criminal attacks. Health assessment of this cohort group enables mitigation to engage in appropriation of relevant interventions related to the occupational needs of taxi drivers. The objective of the study was to conduct health assessment of taxi drivers in the city of Tshwane to identify health risk factors. An exploratory, descriptive and quantitative survey was conducted and anthropometric measurements of blood pressure, body mass index and waist circumference were monitored and recorded on a convenience sample of 69 taxi drivers in Tshwane Municipality. Consent was sought from individual taxi drivers who participated in the study, while taxi rank queue marshals assisted with smooth running of the process. Data were gathered using a questionnaire. Data analysis was performed using statistical STATA II with the assistance of a statistician. The study found that taxi drivers were obese, hypertensive, had type II diabetes-related risk factors, including unhealthy life style practices. The results indicate that the general health of taxi drivers impacts their occupation. The findings implicate that the health status of taxi operators in Tshwane was a serious concern and urgent concerted effort is needed to engage in lifestyle modification of taxi drivers. The need for health promotion and formalised occupational health services was recommended.

Graduated Driver Licensing

PubMed Central

Bates, Lyndel J.; Allen, Siobhan; Armstrong, Kerry; Watson, Barry; King, Mark J.; Davey, Jeremy

2014-01-01

Graduated driver licensing (GDL) aims to gradually increase the exposure of new drivers to more complex driving situations and typically consists of learner, provisional and open licence phases. The first phase, the learner licence, is designed to allow novice drivers to obtain practical driving experience in lower risk situations. The learner licence can delay licensure, encourage novice drivers to learn under supervision, mandate the number of hours of practice required to progress to the next phase and encourage parental involvement. The second phase, the provisional licence, establishes various driving restrictions and thereby reduces exposure to situations of higher risk, such as driving at night, with passengers or after drinking alcohol. Parental involvement with a GDL system appears essential in helping novices obtain sufficient practice and in enforcing compliance with restrictions once the new driver obtains a provisional licence. Given the significant number of young drivers involved in crashes within Oman, GDL is one countermeasure that may be beneficial in reducing crash risk and involvement for this group. PMID:25364543

A critical review of the psychophysiology of driver fatigue.

PubMed

Lal, S K; Craig, A

2001-02-01

Driver fatigue is a major cause of road accidents and has implications for road safety. This review discusses the concepts of fatigue and provides a summary on psychophysiological associations with driver fatigue. A variety of psychophysiological parameters have been used in previous research as indicators of fatigue, with electroencephalography perhaps being the most promising. Most research found changes in theta and delta activity to be strongly linked to transition to fatigue. Therefore, monitoring electroencephalography during driver fatigue may be a promising variable for use in fatigue countermeasure devices. The review also identified anxiety and mood states as factors that may possibly affect driver fatigue. Furthermore, personality and temperament may also influence fatigue. Given the above, understanding the psychology of fatigue may lead to better fatigue management. The findings from this review are discussed in the light of directions for future studies and for the development of fatigue countermeasures.

Negativity Bias in Dangerous Drivers.

PubMed

Chai, Jing; Qu, Weina; Sun, Xianghong; Zhang, Kan; Ge, Yan

2016-01-01

The behavioral and cognitive characteristics of dangerous drivers differ significantly from those of safe drivers. However, differences in emotional information processing have seldom been investigated. Previous studies have revealed that drivers with higher anger/anxiety trait scores are more likely to be involved in crashes and that individuals with higher anger traits exhibit stronger negativity biases when processing emotions compared with control groups. However, researchers have not explored the relationship between emotional information processing and driving behavior. In this study, we examined the emotional information processing differences between dangerous drivers and safe drivers. Thirty-eight non-professional drivers were divided into two groups according to the penalty points that they had accrued for traffic violations: 15 drivers with 6 or more points were included in the dangerous driver group, and 23 drivers with 3 or fewer points were included in the safe driver group. The emotional Stroop task was used to measure negativity biases, and both behavioral and electroencephalograph data were recorded. The behavioral results revealed stronger negativity biases in the dangerous drivers than in the safe drivers. The bias score was correlated with self-reported dangerous driving behavior. Drivers with strong negativity biases reported having been involved in mores crashes compared with the less-biased drivers. The event-related potentials (ERPs) revealed that the dangerous drivers exhibited reduced P3 components when responding to negative stimuli, suggesting decreased inhibitory control of information that is task-irrelevant but emotionally salient. The influence of negativity bias provides one possible explanation of the effects of individual differences on dangerous driving behavior and traffic crashes.

16S rRNA Amplicon Sequencing for Epidemiological Surveys of Bacteria in Wildlife

PubMed Central

Razzauti, Maria; Bard, Emilie; Bernard, Maria; Brouat, Carine; Charbonnel, Nathalie; Dehne-Garcia, Alexandre; Loiseau, Anne; Tatard, Caroline; Tamisier, Lucie; Vayssier-Taussat, Muriel; Vignes, Helene

2016-01-01

ABSTRACT The human impact on natural habitats is increasing the complexity of human-wildlife interactions and leading to the emergence of infectious diseases worldwide. Highly successful synanthropic wildlife species, such as rodents, will undoubtedly play an increasingly important role in transmitting zoonotic diseases. We investigated the potential for recent developments in 16S rRNA amplicon sequencing to facilitate the multiplexing of the large numbers of samples needed to improve our understanding of the risk of zoonotic disease transmission posed by urban rodents in West Africa. In addition to listing pathogenic bacteria in wild populations, as in other high-throughput sequencing (HTS) studies, our approach can estimate essential parameters for studies of zoonotic risk, such as prevalence and patterns of coinfection within individual hosts. However, the estimation of these parameters requires cleaning of the raw data to mitigate the biases generated by HTS methods. We present here an extensive review of these biases and of their consequences, and we propose a comprehensive trimming strategy for managing these biases. We demonstrated the application of this strategy using 711 commensal rodents, including 208 Mus musculus domesticus, 189 Rattus rattus, 93 Mastomys natalensis, and 221 Mastomys erythroleucus, collected from 24 villages in Senegal. Seven major genera of pathogenic bacteria were detected in their spleens: Borrelia, Bartonella, Mycoplasma, Ehrlichia, Rickettsia, Streptobacillus, and Orientia. Mycoplasma, Ehrlichia, Rickettsia, Streptobacillus, and Orientia have never before been detected in West African rodents. Bacterial prevalence ranged from 0% to 90% of individuals per site, depending on the bacterial taxon, rodent species, and site considered, and 26% of rodents displayed coinfection. The 16S rRNA amplicon sequencing strategy presented here has the advantage over other molecular surveillance tools of dealing with a large spectrum of bacterial

A New Approach to Identifying the Drivers of Regulation Compliance Using Multivariate Behavioural Models

PubMed Central

Thomas, Alyssa S.; Milfont, Taciano L.; Gavin, Michael C.

2016-01-01

Non-compliance with fishing regulations can undermine management effectiveness. Previous bivariate approaches were unable to untangle the complex mix of factors that may influence fishers’ compliance decisions, including enforcement, moral norms, perceived legitimacy of regulations and the behaviour of others. We compared seven multivariate behavioural models of fisher compliance decisions using structural equation modeling. An online survey of over 300 recreational fishers tested the ability of each model to best predict their compliance with two fishing regulations (daily and size limits). The best fitting model for both regulations was composed solely of psycho-social factors, with social norms having the greatest influence on fishers’ compliance behaviour. Fishers’ attitude also directly affected compliance with size limit, but to a lesser extent. On the basis of these findings, we suggest behavioural interventions to target social norms instead of increasing enforcement for the focal regulations in the recreational blue cod fishery in the Marlborough Sounds, New Zealand. These interventions could include articles in local newspapers and fishing magazines highlighting the extent of regulation compliance as well as using respected local fishers to emphasize the benefits of compliance through public meetings or letters to the editor. Our methodological approach can be broadly applied by natural resource managers as an effective tool to identify drivers of compliance that can then guide the design of interventions to decrease illegal resource use. PMID:27727292

Graduated driver license nighttime compliance in U.S. teen drivers involved in fatal motor vehicle crashes.

PubMed

Carpenter, Dustin; Pressley, Joyce C

2013-07-01

Examination of teen driver compliance with graduated driver licensing (GDL) laws could be instrumental in identifying factors associated with persistently high motor vehicle mortality rates. Fatality analysis reporting system (FARS) data from the years 2006 to 2009 were used in this nation-wide cross-sectional study of drivers covered by a state nighttime GDL law (n=3492). A new definition of weekend, based on the school night in relation to the teenage social landscape, redefined Friday night as a weekend night and Sunday night as a weekday/school night and compared it to previous weekend definitions. Multiple logistic regression was used to examine independent effects of demographic, behavioral, environmental, contextual, and other factors on compliance with nighttime GDL laws. All analyses were performed in Stata version 11. Given coverage under nighttime GDL laws, drivers aged 15-17 years were non-compliant in 14.9% of the fatal MVCs in which they were involved, and nearly one-fifth (18.8%) of all fatalities aged 15-17 years were associated with non-compliance. Mortality risk was 10% higher using a revised social (school night) versus traditional (Sat-Sun) weekend definitions. In multivariable analysis, drivers non-compliant with nighttime GDL laws were more likely to be drinking (OR=4.97, 3.85-6.40), unbelted (OR=1.58, 1.25-1.99), driving on the weekend (OR=1.82, 1.47-2.24), and killed (OR=1.31, 1.04-1.65). GDL non-compliance contributes to teen motor vehicle mortality. Legislative and enforcement efforts targeting non-school night driving, seatbelt nonuse and alcohol have potential to further reduce teen driving mortality. Copyright © 2012 Elsevier Ltd. All rights reserved.

Negativity Bias in Dangerous Drivers

PubMed Central

Chai, Jing; Qu, Weina; Sun, Xianghong; Zhang, Kan; Ge, Yan

2016-01-01

The behavioral and cognitive characteristics of dangerous drivers differ significantly from those of safe drivers. However, differences in emotional information processing have seldom been investigated. Previous studies have revealed that drivers with higher anger/anxiety trait scores are more likely to be involved in crashes and that individuals with higher anger traits exhibit stronger negativity biases when processing emotions compared with control groups. However, researchers have not explored the relationship between emotional information processing and driving behavior. In this study, we examined the emotional information processing differences between dangerous drivers and safe drivers. Thirty-eight non-professional drivers were divided into two groups according to the penalty points that they had accrued for traffic violations: 15 drivers with 6 or more points were included in the dangerous driver group, and 23 drivers with 3 or fewer points were included in the safe driver group. The emotional Stroop task was used to measure negativity biases, and both behavioral and electroencephalograph data were recorded. The behavioral results revealed stronger negativity biases in the dangerous drivers than in the safe drivers. The bias score was correlated with self-reported dangerous driving behavior. Drivers with strong negativity biases reported having been involved in mores crashes compared with the less-biased drivers. The event-related potentials (ERPs) revealed that the dangerous drivers exhibited reduced P3 components when responding to negative stimuli, suggesting decreased inhibitory control of information that is task-irrelevant but emotionally salient. The influence of negativity bias provides one possible explanation of the effects of individual differences on dangerous driving behavior and traffic crashes. PMID:26765225

A novel ultra high-throughput 16S rRNA gene amplicon sequencing library preparation method for the Illumina HiSeq platform.

PubMed

de Muinck, Eric J; Trosvik, Pål; Gilfillan, Gregor D; Hov, Johannes R; Sundaram, Arvind Y M

2017-07-06

Advances in sequencing technologies and bioinformatics have made the analysis of microbial communities almost routine. Nonetheless, the need remains to improve on the techniques used for gathering such data, including increasing throughput while lowering cost and benchmarking the techniques so that potential sources of bias can be better characterized. We present a triple-index amplicon sequencing strategy to sequence large numbers of samples at significantly lower c ost and in a shorter timeframe compared to existing methods. The design employs a two-stage PCR protocol, incorpo rating three barcodes to each sample, with the possibility to add a fourth-index. It also includes heterogeneity spacers to overcome low complexity issues faced when sequencing amplicons on Illumina platforms. The library preparation method was extensively benchmarked through analysis of a mock community in order to assess biases introduced by sample indexing, number of PCR cycles, and template concentration. We further evaluated the method through re-sequencing of a standardized environmental sample. Finally, we evaluated our protocol on a set of fecal samples from a small cohort of healthy adults, demonstrating good performance in a realistic experimental setting. Between-sample variation was mainly related to batch effects, such as DNA extraction, while sample indexing was also a significant source of bias. PCR cycle number strongly influenced chimera formation and affected relative abundance estimates of species with high GC content. Libraries were sequenced using the Illumina HiSeq and MiSeq platforms to demonstrate that this protocol is highly scalable to sequence thousands of samples at a very low cost. Here, we provide the most comprehensive study of performance and bias inherent to a 16S rRNA gene amplicon sequencing method to date. Triple-indexing greatly reduces the number of long custom DNA oligos required for library preparation, while the inclusion of variable length

Accident Prevention through Driving Skills Assessment and Interventions for Older Drivers: A Programmatic Research Project.

ERIC Educational Resources Information Center

Yee, Darlene; Melichar, Joseph F.

A study examined the effectiveness of a new computer-based multiphasic approach to identifying "at-risk" older drivers and remediating deficits in their driving and traffic safety attitudes, knowledge, and skills. Data collected from 250 older drivers in 3 states were used to develop specifications for computer-based driver improvement modules.…

Driver fatigue and highway driving: a simulator study.

PubMed

Ting, Ping-Huang; Hwang, Jiun-Ren; Doong, Ji-Liang; Jeng, Ming-Chang

2008-06-09

Long duration of driving is a significant cause of fatigue-related accidents on motorways or major roadways. The fatigue caused by driving for extended periods acutely impairs driver alertness and performance and can compromise transportation safety. This study quantitatively measured the progression of driver fatigue and identified the conservative safe duration of continuous highway driving. Thirty young male subjects were analyzed during 90 min of laboratory-simulated highway driving. Sleepiness ratings (SSS) and reaction time (RT) tests were used to assess impairment of driver alertness and vigilance. Additionally, various measures of driving performance recorded throughout the experiment were used to measure temporal deterioration of driver performance from alert to fatigued using principal component analysis (PCA). The analytical results revealed that SSS scores, reaction times (RTs) and unstable driving performance significantly increased over time, indicating that excessive driving time is a significant fatigue factor and potential cause of fatigue-related accidents. Moreover, the analytical results indicated that 80 min was the safe limit for monotonous highway driving. Based on the experimental findings of this study, public awareness of the adverse affects of driver fatigue during long-distance driving should be enhanced. This study provides explicit information of fatigue development that can be used to prevent fatigue-related accidents.

Thermally Activated Driver

NASA Technical Reports Server (NTRS)

Kinard, William H.; Murray, Robert C.; Walsh, Robert F.

1987-01-01

Space-qualified, precise, large-force, thermally activated driver (TAD) developed for use in space on astro-physics experiment to measure abundance of rare actinide-group elements in cosmic rays. Actinide cosmic rays detected using thermally activated driver as heart of event-thermometer (ET) system. Thermal expansion and contraction of silicone oil activates driver. Potential applications in fluid-control systems where precise valve controls are needed.

Modeling of Driver Steering Operations in Lateral Wind Disturbances toward Driver Assistance System

NASA Astrophysics Data System (ADS)

Kurata, Yoshinori; Wada, Takahiro; Kamiji, Norimasa; Doi, Shun'ichi

Disturbances decrease vehicle stability and increase driver's mental and physical workload. Especially unexpected disturbances such as lateral winds have severe effect on vehicle stability and driver's workload. This study aims at building a driver model of steering operations in lateral wind toward developing effective driver assistance system. First, the relationship between the driver's lateral motion and its reactive quick steering behavior is investigated using driving simulator with lateral 1dof motion. In the experiments, four different wind patterns are displayed by the simulator. As the results, strong correlation was found between the driver's head lateral jerk by the lateral disturbance and the angular acceleration of the steering wheel. Then, we build a mathematical model of driver's steering model from lateral disturbance input to steering torque of the reactive quick feed-forward steering based on the experimental results. Finally, validity of the proposed model is shown by comparing the steering torque of experimental results and that of simulation results.

Traffic Safety Facts, 2001: Young Drivers.

ERIC Educational Resources Information Center

National Highway Traffic Safety Administration (DOT), Washington, DC.

This document provides statistical information on U.S. traffic accidents involving young drivers. Data tables include: (1) driver fatalities and drivers involved in fatal crashes among drivers 15 to 20 years old, 1991-2001; (2) drivers involved in fatal crashes and driver involvement rates by age group, 2001; (3) drivers 15 to 20 years old…

Young Drivers. Traffic Safety Facts, 2000.

ERIC Educational Resources Information Center

National Highway Traffic Safety Administration (DOT), Washington, DC.

This document provides statistical information on U.S. traffic accidents involving young drivers. Data tables include: (1) driver fatalities and drivers involved in fatal crashes among drivers 15 to 20 years old, 1990-2000; (2) drivers involved in fatal crashes and driver involvement rates by age group, 2000; (3) drivers 15 to 20 years old…

Occupational Fatalities Among Driver/Sales Workers and Truck Drivers in the United States, 2003–2008

PubMed Central

Chen, Guang X.; Amandus, Harlan E.; Wu, Nan

2015-01-01

Background This study provides a national profile of occupational fatalities among truck drivers and driver-sales workers. Methods Data from the 2003–2008 Census of Fatal Occupational Injuries were used. Cases were extracted specifically for occupational subcategories included in the Driver/Sales Workers and Truck Drivers occupational category: Driver/Sales Workers, Heavy and Tractor-Trailer Truck Drivers, and Light Truck or Delivery Services Drivers. Results In 2003–2008, the group Driver/Sales Workers and Truck Drivers had 5,568 occupational fatalities, representing 17% of all occupational fatalities in the United States. The majority of these fatalities were in the subgroup Heavy and Tractor-Trailer Truck Drivers (85%) and due to transportation incidents (80%). Older and male drivers had higher fatality rates than their counterparts. Conclusions Findings suggest a need for targeted interventions to reduce highway fatalities among heavy truck drivers. Better employment data are needed to separate the three occupational subcategories by worker characteristic and employment history for use in research and prevention efforts. PMID:24811905

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

PubMed

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.

Clonal status of actionable driver events and the timing of mutational processes in cancer evolution

PubMed Central

McGranahan, Nicholas; Favero, Francesco; de Bruin, Elza C.; Birkbak, Nicolai Juul; Szallasi, Zoltan; Swanton, Charles

2015-01-01

Deciphering whether actionable driver mutations are found in all or a subset of tumor cells will likely be required to improve drug development and precision medicine strategies. We analyzed nine cancer types to determine the subclonal frequencies of driver events, to time mutational processes during cancer evolution, and to identify drivers of subclonal expansions. Although mutations in known driver genes typically occurred early in cancer evolution, we also identified later subclonal “actionable” mutations, including BRAF(V600E), IDH1(R132H), PIK3CA(E545K), EGFR(L858R), and KRAS(G12D), which may compromise the efficacy of targeted therapy approaches. More than 20% of IDH1 mutations in glioblastomas, and 15% of mutations in genes in the PI3K(phosphatidylinositol 3-kinase)–AKT–mTOR (mammalian target of rapamycin) signaling axis across all tumor types were subclonal. Mutations in the RAS–MEK (mitogen-activated protein kinase kinase) signaling axis were less likely to be subclonal than mutations in genes associated with PI3K-AKT-mTORsignaling. Analysis of late mutations revealed a link between APOBEC-mediated mutagenesis and the acquisition of subclonal driver mutations and uncovered putative cancer genes involved in subclonal expansions, including CTNNA2 and ATXN1. Our results provide a pan-cancer census of driver events within the context of intratumor heterogeneity and reveal patterns of tumor evolution across cancers. The frequent presence of subclonal driver mutations suggests the need to stratify targeted therapy response according to the proportion of tumor cells in which the driver is identified. PMID:25877892

Clonal status of actionable driver events and the timing of mutational processes in cancer evolution.

PubMed

McGranahan, Nicholas; Favero, Francesco; de Bruin, Elza C; Birkbak, Nicolai Juul; Szallasi, Zoltan; Swanton, Charles

2015-04-15

Deciphering whether actionable driver mutations are found in all or a subset of tumor cells will likely be required to improve drug development and precision medicine strategies. We analyzed nine cancer types to determine the subclonal frequencies of driver events, to time mutational processes during cancer evolution, and to identify drivers of subclonal expansions. Although mutations in known driver genes typically occurred early in cancer evolution, we also identified later subclonal "actionable" mutations, including BRAF (V600E), IDH1 (R132H), PIK3CA (E545K), EGFR (L858R), and KRAS (G12D), which may compromise the efficacy of targeted therapy approaches. More than 20% of IDH1 mutations in glioblastomas, and 15% of mutations in genes in the PI3K (phosphatidylinositol 3-kinase)-AKT-mTOR (mammalian target of rapamycin) signaling axis across all tumor types were subclonal. Mutations in the RAS-MEK (mitogen-activated protein kinase kinase) signaling axis were less likely to be subclonal than mutations in genes associated with PI3K-AKT-mTOR signaling. Analysis of late mutations revealed a link between APOBEC-mediated mutagenesis and the acquisition of subclonal driver mutations and uncovered putative cancer genes involved in subclonal expansions, including CTNNA2 and ATXN1. Our results provide a pan-cancer census of driver events within the context of intratumor heterogeneity and reveal patterns of tumor evolution across cancers. The frequent presence of subclonal driver mutations suggests the need to stratify targeted therapy response according to the proportion of tumor cells in which the driver is identified. Copyright © 2015, American Association for the Advancement of Science.

Key drivers for market penetration of biosimilars in Europe

PubMed Central

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

Key drivers for market penetration of biosimilars in Europe.

PubMed

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

The impact of later trading hours for hotels on levels of impaired driver road crashes and driver breath alcohol levels.

PubMed

Chikritzhs, Tanya; Stockwell, Tim

2006-09-01

To examine the impact of later trading hours for licensed hotels in Perth, Western Australia on levels of associated impaired driver road crashes and driver breath alcohol levels (BALs). Police data on the "last place of drinking" for impaired drivers involved in road crashes and their corresponding BALs were examined to identify those associated with Perth hotels between 1 July 1990 and 30 June 1997. During this period, 43 (23%) of the 186 hotels meeting study criteria were granted an Extended Trading Permit for 1 a.m. closing (ETP hotels), while the rest continued to close at midnight (non-ETP hotels). Time-series analyses employing multiple linear regressions were applied to determine whether an association existed between the introduction of extended trading and (i) monthly levels of impaired driver road crashes associated with ETP hotels and (ii) driver BALs associated with ETP hotels. Trends associated with non-ETP hotels were included as controls and possible confounders were considered. After controlling for the trend in crash rates associated with non-ETP hotels and the introduction of mobile police breath testing stations to Perth freeways, a significant increase in monthly crash rates for ETP hotels was found. This relationship was largely accounted for by higher volumes of high-alcohol content beer, wine and spirits purchased by ETP hotels. No relation was found between driver BALs and the introduction of ETPs. Late trading was associated with increased levels of impaired driver road crashes and alcohol consumption, particularly high-risk alcoholic beverages. Greater numbers of patrons and characteristics specific to clientele of hotels which applied for late trading hours (i.e. younger age, greater propensity to drunk-drive, preference for high-risk beverages) were suggested as having contributed to this increase.

Driver detention times in commercial motor vehicle operations.

DOT National Transportation Integrated Search

2014-12-01

The purpose of this project was to quantitatively identify detention times in the commercial motor vehicle (CMV) : industry. Although there is currently no standard definition, the industry commonly defines detention time as any : time drivers hav...

Using surface-enhanced Raman spectroscopy and electrochemically driven melting to discriminate Yersinia pestis from Y. pseudotuberculosis based on single nucleotide polymorphisms within unpurified polymerase chain reaction amplicons.

PubMed

Papadopoulou, Evanthia; Goodchild, Sarah A; Cleary, David W; Weller, Simon A; Gale, Nittaya; Stubberfield, Michael R; Brown, Tom; Bartlett, Philip N

2015-02-03

The development of sensors for the detection of pathogen-specific DNA, including relevant species/strain level discrimination, is critical in molecular diagnostics with major impacts in areas such as bioterrorism and food safety. Herein, we use electrochemically driven denaturation assays monitored by surface-enhanced Raman spectroscopy (SERS) to target single nucleotide polymorphisms (SNPs) that distinguish DNA amplicons generated from Yersinia pestis, the causative agent of plague, from the closely related species Y. pseudotuberculosis. Two assays targeting SNPs within the groEL and metH genes of these two species have been successfully designed. Polymerase chain reaction (PCR) was used to produce Texas Red labeled single-stranded DNA (ssDNA) amplicons of 262 and 251 bases for the groEL and metH targets, respectively. These amplicons were used in an unpurified form to hybridize to immobilized probes then subjected to electrochemically driven melting. In all cases electrochemically driven melting was able to discriminate between fully homologous DNA and that containing SNPs. The metH assay was particularly challenging due to the presence of only a single base mismatch in the middle of the 251 base long PCR amplicon. However, manipulation of assay conditions (conducting the electrochemical experiments at 10 °C) resulted in greater discrimination between the complementary and mismatched DNA. Replicate data were collected and analyzed for each duplex on different days, using different batches of PCR product and different sphere segment void (SSV) substrates. Despite the variability introduced by these differences, the assays are shown to be reliable and robust providing a new platform for strain discrimination using unpurified PCR samples.

Efficacy of side airbags in reducing driver deaths in driver-side car and SUV collisions.

PubMed

McCartt, Anne T; Kyrychenko, Sergey Y

2007-06-01

To estimate the efficacy of side airbags in preventing driver deaths in passenger vehicles struck on the driver side. Risk ratios for driver deaths per driver-side collision were computed for side airbag-equipped cars and SUVs, relative to vehicles without side airbags. Driver fatality ratios also were calculated for the same vehicles in front and rear impacts, and these were used to adjust the side crash risk ratios for differences in fatality risk unrelated to side airbags. Risk ratios were calculated separately for side airbags providing torso-only protection and side airbags with head protection; almost all head protecting airbags also had airbags protecting the torso. Car driver death risk in driver-side crashes was reduced by 37 percent for head protecting airbags and 26 percent for torso-only side airbags. Car driver death risk was reduced for older and younger drivers, males and females, and drivers of small and midsize cars, and when the striking vehicle was an SUV/pickup or a car/minivan. Death risk for drivers of SUVs was reduced by 52 percent with head protecting side airbags and by 30 percent with torso-only airbags. The effectiveness of side airbags could not be assessed for pickups and minivans due to the small number of these vehicles with airbags involved in crashes. Side airbags substantially reduce the risk of car and SUV driver death in driver-side collisions. Making side airbags with head protection available to drivers and right front passengers in all passenger vehicles could reduce the number of fatalities in motor vehicle crashes in the United States by about 2,000 each year.

Attitudes of Greek Drivers with Focus on Mobile Phone Use While Driving.

PubMed

Yannis, George; Theofilatos, Athanasios; Marinou, Paraskevi

2015-01-01

This article investigates the attitudes and behavior of Greek drivers with specific focus on mobile phone use while driving. The research is based on the data of the pan-European SARTRE 4 survey, which was conducted on a representative sample of Greek drivers in 2011. Analysis of the drivers' behavior was carried out by the statistical methods of factor and cluster analysis. According to the results of factor analysis, Greek drivers' responses in the selected questions were summarized into 4 factors, describing road behavior and accident involvement probability as well as their views on issues concerning other drivers' road behaviors, fatigued driving, enforcement of road safety, and mobile phone use while driving. The results of cluster analysis indicated 5 different groups of Greek drivers--the moderate, the optimistic, the conservative, the risky, and the reasonably cautious--and the characteristics of each group where identified. These results may be useful for the appropriate design of targeted road safety campaigns and other countermeasures.

Examination of supplemental driver training and online basic driver education courses : traffic tech.

DOT National Transportation Integrated Search

2012-08-01

The first six months of unsupervised driving are the most : hazardous in a novice drivers driving experience. Most : States adopted graduated driver licensing (GDL) systems : to give novice drivers experience in a protective environment, : gradual...

Divided attention in young drivers under the influence of alcohol.

PubMed

Freydier, C; Berthelon, C; Bastien-Toniazzo, M; Gineyt, G

2014-06-01

The present research evaluates driving impairment linked to divided attention task and alcohol and determines whether it is higher for novice drivers than for experienced drivers. Novice and experienced drivers participated in three experimental sessions in which blood alcohol concentrations (BACs) were 0.0 g/L, 0.2 g/L, and 0.5 g/L. They performed a divided attention task with a main task of car-following task and an additional task of number parity identification. Driving performance, response time and accuracy on the additional task were measured. ANOVA showed a driving impairment and a decrease in additional task performance from a BAC of 0.5 g/L, particularly for novice drivers. Indeed, the latter adopt more risky behavior such as tailgating. In the divided attention task, driving impairment was found for all drivers and impairment on information processing accuracy was highlighted, notably in peripheral vision. The divided attention task used here provides a relevant method for identifying the effects of alcohol on cognitive functions and could be used in psychopharmacological research. Copyright © 2014 Elsevier Ltd. All rights reserved.

Licensing procedures for older drivers.

DOT National Transportation Integrated Search

2013-09-01

This study examined the driver licensing procedures in all 50 States as they apply to the older (65+) driver. A literature review examined reports of possible declines in older driver capabilities and the ability of a driver licensing agency to scree...

Understanding local-scale drivers of biodiversity outcomes in terrestrial protected areas.

PubMed

Barnes, Megan D; Craigie, Ian D; Dudley, Nigel; Hockings, Marc

2017-07-01

Conservation relies heavily on protected areas (PAs) maintaining their key biodiversity features to meet global biodiversity conservation goals. However, PAs have had variable success, with many failing to fully maintain their biodiversity features. The current literature concerning what drives variability in PA performance is rapidly expanding but unclear, sometimes contradictory, and spread across multiple disciplines. A clear understanding of the drivers of successful biodiversity conservation in PAs is necessary to make them fully effective. Here, we conduct a comprehensive assessment of the current state of knowledge concerning the drivers of biological outcomes within PAs, focusing on those that can be addressed at local scales. We evaluate evidence in support of potential drivers to identify those that enable more successful outcomes and those that impede success and provide a synthetic review. Interactions are discussed where they are known, and we highlight gaps in understanding. We find that elements of PA design, management, and local and national governance challenges, species and system ecology, and sociopolitical context can all influence outcomes. Adjusting PA management to focus on actions and policies that influence the key drivers identified here could improve global biodiversity outcomes. © 2016 New York Academy of Sciences.

Lane change warning threshold based on driver perception characteristics.

PubMed

Wang, Chang; Sun, Qinyu; Fu, Rui; Li, Zhen; Zhang, Qiong

2018-08-01

Lane Change Warning system (LCW) is exploited to alleviate driver workload and improve the safety performance of lane changes. Depending on the secure threshold, the lane change warning system could transmit caution to drivers. Although the system possesses substantial benefits, it may perturb the conventional operating of the driver and affect driver judgment if the warning threshold does not conform to the driver perception of safety. Therefore, it is essential to establish an appropriate warning threshold to enhance the accuracy rate and acceptability of the lane change warning system. This research aims to identify the threshold that conforms to the driver perception of the ability to safely change lanes with a rear vehicle fast approaching. We propose a theoretical warning model of lane change based on a safe minimum distance and deceleration of the rear vehicle. For the purpose of acquiring the different safety levels of lane changes, 30 licensed drivers are recruited and we obtain the extreme moments represented by driver perception characteristics from a Front Extremity Test and a Rear Extremity Test implemented on the freeway. The required deceleration of the rear vehicle corresponding to the extreme time is calculated according to the proposed model. In light of discrepancies in the deceleration in these extremity experiments, we determine two levels of a hierarchical warning system. The purpose of the primary warning is to remind drivers of the existence of potentially dangerous vehicles and the second warning is used to warn the driver to stop changing lanes immediately. We use the signal detection theory to analyze the data. Ultimately, we confirm that the first deceleration threshold is 1.5 m/s 2 and the second deceleration threshold is 2.7 m/s 2 . The findings provide the basis for the algorithm design of LCW and enhance the acceptability of the intelligent system. Copyright © 2018 Elsevier Ltd. All rights reserved.

Predicting and Reducing Driving Mishaps Among Drivers With Type 1 Diabetes

PubMed Central

Gonder-Frederick, Linda A.; Singh, Harsimran; Ingersoll, Karen S.; Banton, Tom; Grabman, Jesse H.; Schmidt, Karen; Clarke, William

2017-01-01

OBJECTIVE Two aims of this study were to develop and validate A) a metric to identify drivers with type 1 diabetes at high risk of future driving mishaps and B) an online intervention to reduce mishaps among high-risk drivers. RESEARCH DESIGN AND METHODS To achieve aim A, in study 1, 371 drivers with type 1 diabetes from three U.S. regions completed a series of established questionnaires about diabetes and driving. They recorded their driving mishaps over the next 12 months. Questionnaire items that uniquely discriminated drivers who did and did not have subsequent driving mishaps were assembled into the Risk Assessment of Diabetic Drivers (RADD) scale. In study 2, 1,737 drivers with type 1 diabetes from all 50 states completed the RADD online. Among these, 118 low-risk (LR) and 372 high-risk (HR) drivers qualified for and consented to participate in a 2-month treatment period followed by 12 monthly recordings of driving mishaps. To address aim B, HR participants were randomized to receive either routine care (RC) or the online intervention “DiabetesDriving.com” (DD.com). Half of the DD.com participants received a motivational interview (MI) at the beginning and end of the treatment period to boost participation and efficacy. All of the LR participants were assigned to RC. In both studies, the primary outcome variable was driving mishaps. RESULTS Related to aim A, in study 1, the RADD demonstrated 61% sensitivity and 75% specificity. Participants in the upper third of the RADD distribution (HR), compared with those in the lower third (LR), reported 3.03 vs. 0.87 mishaps/driver/year, respectively (P < 0.001). In study 2, HR and LR participants receiving RC reported 4.3 and 1.6 mishaps/driver/year, respectively (P < 0.001). Related to aim B, in study 2, MIs did not enhance participation or efficacy, so the DD.com and DD.com + MI groups were combined. DD.com participants reported fewer hypoglycemia-related driving mishaps than HR participants receiving RC (P = 0

Impact of Automation on Drivers' Performance in Agricultural Semi-Autonomous Vehicles.

PubMed

Bashiri, B; Mann, D D

2015-04-01

Drivers' inadequate mental workload has been reported as one of the negative effects of driving assistant systems and in-vehicle automation. The increasing trend of automation in agricultural vehicles raises some concerns about drivers' mental workload in such vehicles. Thus, a human factors perspective is needed to identify the consequences of such automated systems. In this simulator study, the effects of vehicle steering task automation (VSTA) and implement control and monitoring task automation (ICMTA) were investigated using a tractor-air seeder system as a case study. Two performance parameters (reaction time and accuracy of actions) were measured to assess drivers' perceived mental workload. Experiments were conducted using the tractor driving simulator (TDS) located in the Agricultural Ergonomics Laboratory at the University of Manitoba. Study participants were university students with tractor driving experience. According to the results, reaction time and number of errors made by drivers both decreased as the automation level increased. Correlations were found among performance parameters and subjective mental workload reported by the drivers.

The effects of age on crash risk associated with driver distraction.

PubMed

Guo, Feng; Klauer, Sheila G; Fang, Youjia; Hankey, Jonathan M; Antin, Jonathan F; Perez, Miguel A; Lee, Suzanne E; Dingus, Thomas A

2017-02-01

Driver distraction is a major contributing factor to crashes, which are the leading cause of death for the US population under 35 years of age. The prevalence of secondary-task engagement and its impacts on distraction and crashes may vary substantially by driver age. Driving performance and behaviour data were collected continuously using multiple cameras and sensors in situ for 3542 participant drivers recruited for up to 3 years for the Second Strategic Highway Research Program Naturalistic Driving Study. Secondary-task engagement at the onset of crashes and during normal driving segments was identified from videos. A case-cohort approach was used to estimate the crash odds ratios associated with, and the prevalence of, secondary tasks for four age groups: 16-20, 21-29, 30-64 and 65-98 years of age. Only severe crashes (property damage and higher severity) were included in the analysis. Secondary-task-induced distraction posed a consistently higher threat for drivers younger than 30 and above 65 when compared with middle-aged drivers, although senior drivers engaged in secondary tasks much less frequently than their younger counterparts. Secondary tasks with high visual-manual demand (e.g. visual-manual tasks performed on cell phones) affected drivers of all ages. Certain secondary tasks, such as operation of in-vehicle devices and talking/singing, increased the risk for only certain age groups. Teenaged, young adult drivers and senior drivers are more adversely impacted by secondary-task engagement than middle-aged drivers. Visual-manual distractions impact drivers of all ages, whereas cognitive distraction may have a larger impact on young drivers. © The Author 2016; all rights reserved. Published by Oxford University Press on behalf of the International Epidemiological Association

Simulator training with a forward collision warning system: effects on driver-system interactions and driver trust.

PubMed

Koustanaï, Arnaud; Cavallo, Viola; Delhomme, Patricia; Mas, Arnaud

2012-10-01

The study addressed the role of familiarization on a driving simulator with a forward collision warning (FCW) and investigated its impact on driver behavior. Drivers need a good understanding of how an FCW system functions to trust it and use it properly. Theoretical and empirical data suggest that exploring the capacities and limitations of the FCW during the learning period improves operating knowledge and leads to increased driver trust in the system and better driver-system interactions.The authors tested this hypothesis by comparing groups of drivers differing in FCW familiarity. During the familiarization phase, familiarized drivers were trained on the simulator using the FCW, unfamiliarized drivers simply read an FCW manual, and control drivers had no contact with the FCW. During the test, drivers drove the simulator and had to interact with traffic; both familiarized and unfamiliarized drivers used the FCW, whereas controls did not. Simulator familiarization improved driver understanding of FCW operation. Driver-system interactions were more effective: Familiarized drivers had no collisions, longer time headways, and better reactions in most situations. Familiarization increased trust in the FCW but did not raise system acceptance. Familiarization on the simulator had a positive effect on driver-system interactions and on trust in the system. The limitations of the familiarization method are discussed in relation to the driving simulator methodology. Practicing on a driving simulator with driving-assistance systems could facilitate their use during real driving.

Influence of driver nationality on the risk of causing vehicle collisions in Spain.

PubMed

Lardelli Claret, P; Luna del Castillo, J D; Jiménez Moleón, J J; Bueno Cavanillas, A; García Martín, M; Gálvez Vargas, R

2002-05-01

To estimate the association between driver nationality and the risk of causing a collision between vehicles in motion. Retrospective, matched by collision, case-control study. Collisions that occurred in Spain during the period from 1990 to 1999 were studied. Responsible (case) and non-responsible (control) drivers identified in the databases of the Dirección General de Tráfico (General Traffic Directorate) who were involved in a collisions between two or more four wheeled vehicles in motion, in which only one of the drivers had committed a traffic violation. Crude odds ratios (ORs) for the effect of driver nationality on the risk of causing a collision were significantly higher for foreign drivers than for Spanish drivers, and ranged from a minimum of 1.19 (95% CI 1.09 to 1.29) for Portuguese drivers to a maximum of 2.06 (1.88 to 2.27) for British drivers. Corresponding adjusted ORs were slightly lower, but were still significantly higher than 1 for all nationalities except Italian, Belgian, and American (USA). Adjusted ORs were usually higher for collisions that occurred in urban areas than on open roads. Authorities responsible for traffic safety, and drivers in general, should consider foreign drivers in Spain at particularly high risk for causing collisions, especially in urban areas.

A cross "ethnical" comparison of the Driver Behaviour Questionnaire (DBQ) in an economically fast developing country.

PubMed

Bener, Abdulbari; Verjee, Mohamud; Dafeeah, Elnour E; Yousafzai, Mohammad T; Mari, Sundus; Hassib, Ahmed; Al-Khatib, Hamza; Choi, Min Kyung; Nema, Noor; Ozkan, Türker; Lajunen, Timo

2013-05-12

The aim of this study was to compare the driving behaviours of four ethnic groups and to investigate the relationship between violations, errors and lapses of DBQ and accident involvement in Qatar. The Driver Behaviour Questionnaire (DBQ) was used to measure the aberrant driving behaviours leading to accidents. Of 2400 drivers approached, 1824 drivers agreed to participate (76%) and completed the driver behaviour questionnaire and background information. The study revealed that the majority of the Qatari (35.9%) and Jordanian drivers (37.5%) were below 30 years of age, whereas Filipino (42.3%) and Indian subcontinent (34.1%) drivers were in the age group of 30-39 years. Qatari drivers (52%) were involved in most accidents, followed by Jordanians (48.3%). The most common type of collision was a head on collision, which was similar in all four ethnic groups. The Qatari drivers scored higher on almost all items of violations, errors and lapses compared to other ethnic groups, while Filipino drivers were lower on all the items. The most common violation was the same in all four ethnic groups "Disregard the speed limits on a motorway". The most common error item observed was "Queing to turn right/left on to a main road". "Forget where you left your car" and "Hit something when reversing" were the two lapses identified in factor analysis. The present study identified that Qatari drivers scored higher on most of the items of violations, errors and lapses of DBQ compared to other countries, whereas Filipino drivers scored lower in DBQ items.

Turning movements, vehicle offsets and ageing drivers driving behaviour at channelized and unchannelized intersections.

PubMed

Choi, Jaisung; Tay, Richard; Kim, Sangyoup; Jeong, Seungwon

2017-11-01

Ageing drivers experience a higher risk of intersection crashes because of their decrease in driving efficiency, including the decline in cognitive ability, head and neck flexibility, and visual acuity. Although several studies have been conducted to examine the factors associated with ageing driver crashes at intersections, little research has been conducted to examine the differences in the factors related to ageing drivers' turning paths and intersection geometric features. This study aims to improve the safety of ageing drivers at intersections by identifying the maneuvers that are risky for them and tracking their turning movements at selected intersections. We find that ageing drivers experience more crashes at intersections than younger drivers, especially crashes involving turning movements. Furthermore, ageing drivers experience more crashes at unchannelized intersections compared to channelized intersections. In addition, this study finds that ageing drivers exhibit greater and more inconsistent offsets during turning movements compared to those of younger drivers at both channelized and unchannelized intersections. Ageing drivers also tend to make relatively sharper or tighter turns than younger drivers. Hence, transportation engineers and road safety professionals should consider appropriate countermeasures to reduce the risks of crashes involving ageing drivers at intersections. Copyright © 2017 Elsevier Ltd. All rights reserved.

Targeted amplicon sequencing (TAS): a scalable next-gen approach to multilocus, multitaxa phylogenetics.

PubMed

Bybee, Seth M; Bracken-Grissom, Heather; Haynes, Benjamin D; Hermansen, Russell A; Byers, Robert L; Clement, Mark J; Udall, Joshua A; Wilcox, Edward R; Crandall, Keith A

2011-01-01

Next-gen sequencing technologies have revolutionized data collection in genetic studies and advanced genome biology to novel frontiers. However, to date, next-gen technologies have been used principally for whole genome sequencing and transcriptome sequencing. Yet many questions in population genetics and systematics rely on sequencing specific genes of known function or diversity levels. Here, we describe a targeted amplicon sequencing (TAS) approach capitalizing on next-gen capacity to sequence large numbers of targeted gene regions from a large number of samples. Our TAS approach is easily scalable, simple in execution, neither time-nor labor-intensive, relatively inexpensive, and can be applied to a broad diversity of organisms and/or genes. Our TAS approach includes a bioinformatic application, BarcodeCrucher, to take raw next-gen sequence reads and perform quality control checks and convert the data into FASTA format organized by gene and sample, ready for phylogenetic analyses. We demonstrate our approach by sequencing targeted genes of known phylogenetic utility to estimate a phylogeny for the Pancrustacea. We generated data from 44 taxa using 68 different 10-bp multiplexing identifiers. The overall quality of data produced was robust and was informative for phylogeny estimation. The potential for this method to produce copious amounts of data from a single 454 plate (e.g., 325 taxa for 24 loci) significantly reduces sequencing expenses incurred from traditional Sanger sequencing. We further discuss the advantages and disadvantages of this method, while offering suggestions to enhance the approach.

Targeted Amplicon Sequencing (TAS): A Scalable Next-Gen Approach to Multilocus, Multitaxa Phylogenetics

PubMed Central

Bybee, Seth M.; Bracken-Grissom, Heather; Haynes, Benjamin D.; Hermansen, Russell A.; Byers, Robert L.; Clement, Mark J.; Udall, Joshua A.; Wilcox, Edward R.; Crandall, Keith A.

2011-01-01

Next-gen sequencing technologies have revolutionized data collection in genetic studies and advanced genome biology to novel frontiers. However, to date, next-gen technologies have been used principally for whole genome sequencing and transcriptome sequencing. Yet many questions in population genetics and systematics rely on sequencing specific genes of known function or diversity levels. Here, we describe a targeted amplicon sequencing (TAS) approach capitalizing on next-gen capacity to sequence large numbers of targeted gene regions from a large number of samples. Our TAS approach is easily scalable, simple in execution, neither time-nor labor-intensive, relatively inexpensive, and can be applied to a broad diversity of organisms and/or genes. Our TAS approach includes a bioinformatic application, BarcodeCrucher, to take raw next-gen sequence reads and perform quality control checks and convert the data into FASTA format organized by gene and sample, ready for phylogenetic analyses. We demonstrate our approach by sequencing targeted genes of known phylogenetic utility to estimate a phylogeny for the Pancrustacea. We generated data from 44 taxa using 68 different 10-bp multiplexing identifiers. The overall quality of data produced was robust and was informative for phylogeny estimation. The potential for this method to produce copious amounts of data from a single 454 plate (e.g., 325 taxa for 24 loci) significantly reduces sequencing expenses incurred from traditional Sanger sequencing. We further discuss the advantages and disadvantages of this method, while offering suggestions to enhance the approach. PMID:22002916

Graduated driver licensing programs and fatal crashes of 16-year-old drivers: a national evaluation.

PubMed

Chen, Li-Hui; Baker, Susan P; Li, Guohua

2006-07-01

Implementation of graduated driver licensing programs is associated with reductions in crash rates of young drivers, but graduated driver licensing programs vary in their components. The impact of programs with different components is unknown. The purpose of this work was to determine which graduated driver licensing programs are associated with the greatest reductions in fatal motor vehicle crashes involving 16-year-old drivers. We conducted a retrospective study of all 16-year-old drivers involved in fatal crashes in the United States from 1994 through 2004 using data from the Fatality Analysis Reporting System and the US Census Bureau. We measured incidence rate ratios of fatal motor vehicle crashes involving 16-year-old drivers according to graduated driver licensing programs, adjusted for state and year. Compared with state quarters with no graduated driver licensing program components, reductions of 16% to 21% in fatal crash involvement rates of 16-year-old drivers occurred with programs that included > or = 3-month mandatory waiting period, nighttime driving restriction, and either > or = 30 hours of supervised driving or passenger restriction. Reductions of 18% to 21% occurred in state quarters with programs that included > or = 5 of the 7 components examined. Drivers aged 20 to 24 or 25 to 29 years did not experience significant reductions. Comprehensive graduated driver licensing programs are associated with reductions of approximately 20% in 16-year-old drivers' fatal crash involvement rates. The greatest benefit seems to be associated with programs that include age requirements and > or = 3 months of waiting before the intermediate stage, nighttime driving restriction, and either > or = 30 hours of supervised driving or passenger restriction.

Driver landmark and traffic sign identification in early Alzheimer's disease.

PubMed

Uc, E Y; Rizzo, M; Anderson, S W; Shi, Q; Dawson, J D

2005-06-01

To assess visual search and recognition of roadside targets and safety errors during a landmark and traffic sign identification task in drivers with Alzheimer's disease. 33 drivers with probable Alzheimer's disease of mild severity and 137 neurologically normal older adults underwent a battery of visual and cognitive tests and were asked to report detection of specific landmarks and traffic signs along a segment of an experimental drive. The drivers with mild Alzheimer's disease identified significantly fewer landmarks and traffic signs and made more at-fault safety errors during the task than control subjects. Roadside target identification performance and safety errors were predicted by scores on standardised tests of visual and cognitive function. Drivers with Alzheimer's disease are impaired in a task of visual search and recognition of roadside targets; the demands of these targets on visual perception, attention, executive functions, and memory probably increase the cognitive load, worsening driving safety.

RET fusion as a novel driver of medullary thyroid carcinoma.

PubMed

Grubbs, Elizabeth G; Ng, Patrick Kwok-Shing; Bui, Jacquelin; Busaidy, Naifa L; Chen, Ken; Lee, Jeffrey E; Lu, Xinyan; Lu, Hengyu; Meric-Bernstam, Funda; Mills, Gordon B; Palmer, Gary; Perrier, Nancy D; Scott, Kenneth L; Shaw, Kenna R; Waguespack, Steven G; Williams, Michelle D; Yelensky, Roman; Cote, Gilbert J

2015-03-01

Oncogenic RET tyrosine kinase gene fusions and activating mutations have recently been identified in lung cancers, prompting initiation of targeted therapy trials in this disease. Although RET point mutation has been identified as a driver of tumorigenesis in medullary thyroid carcinoma (MTC), no fusions have been described to date. We evaluated the role of RET fusion as an oncogenic driver in MTC. We describe a patient who died from aggressive sporadic MTC < 10 months after diagnosis. Her tumor was evaluated by means of next-generation sequencing, including an intronic capture strategy. A reciprocal translocation involving RET intron 12 was identified. The fusion was validated using a targeted break apart fluorescence in situ hybridization probe, and RNA sequencing confirmed the existence of an in-frame fusion transcript joining MYH13 exon 35 with RET exon 12. Ectopic expression of fusion product in a murine Ba/F3 cell reporter model established strong oncogenicity. Three tyrosine kinase inhibitors currently used to treat MTC in clinical practice blocked tumorigenic cell growth. This finding represents the report of a novel RET fusion, the first of its kind described in MTC. The finding of this potential novel oncogenic mechanism has clear implications for sporadic MTC, which in the majority of cases has no driver mutation identified. The presence of a RET fusion also provides a plausible target for RET tyrosine kinase inhibitor therapies.

Dominant role of drivers' attitude in prevention of road traffic crashes: a study on knowledge, attitude, and practice of drivers in Iran.

PubMed

Mirzaei, Ramazan; Hafezi-Nejad, Nima; Sadegh Sabagh, Mohammad; Ansari Moghaddam, Alireza; Eslami, Vahid; Rakhshani, Fatemeh; Rahimi-Movaghar, Vafa

2014-05-01

Evaluating the relation between Iranian drivers' knowledge, attitude, and practice (KAP) regarding traffic regulations, and their deterministic effect on road traffic crashes (RTCs). Two cities of Tehran and Zahedan, Iran. A cross-sectional study was designed. Using a simplified cluster sampling design, 2200 motor vehicle drivers including 1200 in Tehran and 1000 in Zahedan were selected. Sixty locations in Tehran and 50 in Zahedan were chosen. In each pre-identified location, 20 adult drivers were approached consecutively. A questionnaire developed by researchers was filled by each participant. The questionnaire had four sections including items assessing the demographics, knowledge, attitude and practice of drivers toward traffic regulations. Logistic regression analysis was used to evaluate the relationship between the RTCs and KAP variables. The study sample consisted of 619 (28.1%) occupational and 1580 (71.8%) private drivers. Among them, 86.4% were male. The median age was 33.6 ± 10.83. Drivers in Tehran and Zahedan had no significant differences between their mean scores of KAP items of the questionnaire. Higher knowledge, safer attitude, and safer practice were associated with a decreased number of RTC. After adjusting for possible confounders, increase of one standard deviation in attitude and practice scores (but not knowledge) resulted in 26.4% and 18.5% decrease in RTC, respectively. Finally, considering knowledge, attitude and practice of drivers in one model to assess their mutual effect, it was shown that only attitude is significantly associated with a decrease of RTC (OR=0.76, P=0.007). Increase in attitude and practice accompanied with decreased number of RTCs in Iranian drivers. Specifically, drivers' attitude had the crucial effect. It is not knowledge and standard traffic education; rather it is how such education is registered as an attitude that translates what is being learned into actions. Without safer attitude, even safer self

Identification of elderly drivers whose crash involvement risks are alleviated by passenger presence.

PubMed

Nakagawa, Yoshinori; Park, Kaechang

2014-01-01

It is essential to find measures to compensate for the decline in elderly drivers' driving ability in order to meet their mobility needs and ensure their safety when driving. Although it has been well documented that elderly drivers' risks of crash involvement are alleviated by the presence of passengers, few studies have investigated whether the protective effect of passengers is influenced by driver characteristics including the degree of cognitive impairment. This study aimed to identify subgroups of elderly drivers whose crash involvement risks are more effectively alleviated by passenger presence. After dividing elderly drivers into three levels of cognitive impairment, as measured by the Short-Memory Questionnaire, and two gender groups, the present study found that only male drivers in the middle cognitive level benefited from passenger presence. The effectiveness of passenger presence may be more successfully achieved by proper selection of the appropriate range of cognitive decline and gender.

Driving Behavior among Different Groups of Iranian Drivers Based on Driver Coping Styles

PubMed Central

Lotfi, Saeid; Yazdanirad, Saeid; Pourabdiyan, Siyamak; Hassanzadeh, Akbar; Lotfi, Aliakbar

2017-01-01

Background: This study aimed to assess driving behavior of Iranian drivers based on their coping styles (problem-oriented, emotion-oriented, and avoiding). Methods: This study was conducted on 610 drivers divided into four different groups. The drivers’ behaviors and coping styles were evaluated using driver behavior questionnaire (DBQ) and coping inventory for stressful situations. Results: The results showed a significant difference among the three coping styles regarding the mean scores of DBQ dimensions (P < 0.001). In addition, the emotion-oriented drivers obtained higher mean scores compared to those with other coping styles. Conclusions: It can be concluded that emotion-oriented drivers were more susceptible to crashes compared to those with problem-solving and avoidance coping styles. PMID:28757929

Acoustic Levitation With One Driver

NASA Technical Reports Server (NTRS)

Wang, T. G.; Rudnick, I.; Elleman, D. D.; Stoneburner, J. D.

1985-01-01

Report discusses acoustic levitation in rectangular chamber using one driver mounted at corner. Placement of driver at corner enables it to couple effectively to acoustic modes along all three axes. Use of single driver reduces cost, complexity and weight of levitation system below those of three driver system.

A control theoretic model of driver steering behavior

NASA Technical Reports Server (NTRS)

Donges, E.

1977-01-01

A quantitative description of driver steering behavior such as a mathematical model is presented. The steering task is divided into two levels: (1) the guidance level involving the perception of the instantaneous and future course of the forcing function provided by the forward view of the road, and the response to it in an anticipatory open-loop control mode; (2) the stabilization level whereby any occuring deviations from the forcing function are compensated for in a closed-loop control mode. This concept of the duality of the driver's steering activity led to a newly developed two-level model of driver steering behavior. Its parameters are identified on the basis of data measured in driving simulator experiments. The parameter estimates of both levels of the model show significant dependence on the experimental situation which can be characterized by variables such as vehicle speed and desired path curvature.

The application of amplicon length heterogeneity PCR (LH-PCR) for monitoring the dynamics of soil microbial communities associated with cadaver decomposition.

PubMed

Moreno, Lilliana I; Mills, DeEtta; Fetscher, Jill; John-Williams, Krista; Meadows-Jantz, Lee; McCord, Bruce

2011-03-01

The placement of cadavers in shallow, clandestine graves may alter the microbial and geochemical composition of the underlying and adjacent soils. Using amplicon length heterogeneity-PCR (LH-PCR) the microbial community changes in these soils can be assessed. In this investigation, nine different grave sites were examined over a period of 16weeks. The results indicated that measurable changes occurred in the soil bacterial community during the decomposition process. In this study, amplicons corresponding to anaerobic bacteria, not indigenous to the soil, were shown to produce differences between grave sites and control soils. Among the bacteria linked to these amplicons are those that are most often part of the commensal flora of the intestines, mouth and skin. In addition, over the 16week sampling interval, the level of indicator organisms (i.e., nitrogen fixing bacteria) dropped as the body decomposed and after four weeks of environmental exposure they began to increase again; thus differences in the abundance of nitrogen fixing bacteria were also found to contribute to the variation between controls and grave soils. These results were verified using primers that specifically targeted the nifH gene coding for nitrogenase reductase. LH-PCR provides a fast, robust and reproducible method to measure microbial changes in soil and could be used to determine potential cadaveric contact in a given area. The results obtained with this method could ultimately provide leads to investigators in criminal or missing person scenarios and allow for further analysis using human specific DNA assays to establish the identity of the buried body. Copyright © 2010 Elsevier B.V. All rights reserved.

Aggregate driver model to enable predictable behaviour

NASA Astrophysics Data System (ADS)

Chowdhury, A.; Chakravarty, T.; Banerjee, T.; Balamuralidhar, P.

2015-09-01

The categorization of driving styles, particularly in terms of aggressiveness and skill is an emerging area of interest under the broader theme of intelligent transportation. There are two possible discriminatory techniques that can be applied for such categorization; a microscale (event based) model and a macro-scale (aggregate) model. It is believed that an aggregate model will reveal many interesting aspects of human-machine interaction; for example, we may be able to understand the propensities of individuals to carry out a given task over longer periods of time. A useful driver model may include the adaptive capability of the human driver, aggregated as the individual propensity to control speed/acceleration. Towards that objective, we carried out experiments by deploying smartphone based application to be used for data collection by a group of drivers. Data is primarily being collected from GPS measurements including position & speed on a second-by-second basis, for a number of trips over a two months period. Analysing the data set, aggregate models for individual drivers were created and their natural aggressiveness were deduced. In this paper, we present the initial results for 12 drivers. It is shown that the higher order moments of the acceleration profile is an important parameter and identifier of journey quality. It is also observed that the Kurtosis of the acceleration profiles stores major information about the driving styles. Such an observation leads to two different ranking systems based on acceleration data. Such driving behaviour models can be integrated with vehicle and road model and used to generate behavioural model for real traffic scenario.

Medical review practices for driver licensing volume 3: guidelines and processes in the United States.

DOT National Transportation Integrated Search

2017-04-01

This is the third of three reports examining driver medical review practices in the United States and how : they fulfill the basic functions of identifying, assessing, and rendering licensing decisions on medically or : functionally at-risk drivers. ...

The Roles and Performance of Professional Driving Instructors in Novice Driver Education.

PubMed

Jawi, Zulhaidi M; Deros, Baba M; Rashid, Ahmad A A; Isa, Mohd H M; Awang, Azmi

2017-08-01

This review article aimed to analyse existing literature regarding the roles and performance of professional driving instructors (PDIs) in novice driver education (DE). A systematic classification scheme was adopted to analyse identified articles to determine the study context of PDIs in novice DE, the competency level of PDIs in relation to experienced and learner drivers and the contributions of PDIs to the novice driver learning process. A total of 14 original research articles were identified, with no systematic reviews or meta-analyses available. Overall, all of the articles were found to be inadequate in providing an in-depth understanding of the roles and performance of PDIs in novice DE. There is an urgent need to improve current understanding of the roles of PDIs in novice DE and to work towards an internationally recognised PDI management approach.

The Roles and Performance of Professional Driving Instructors in Novice Driver Education

PubMed Central

Jawi, Zulhaidi M.; Deros, Baba M.; Rashid, Ahmad A. A.; Isa, Mohd H. M.; Awang, Azmi

2017-01-01

This review article aimed to analyse existing literature regarding the roles and performance of professional driving instructors (PDIs) in novice driver education (DE). A systematic classification scheme was adopted to analyse identified articles to determine the study context of PDIs in novice DE, the competency level of PDIs in relation to experienced and learner drivers and the contributions of PDIs to the novice driver learning process. A total of 14 original research articles were identified, with no systematic reviews or meta-analyses available. Overall, all of the articles were found to be inadequate in providing an in-depth understanding of the roles and performance of PDIs in novice DE. There is an urgent need to improve current understanding of the roles of PDIs in novice DE and to work towards an internationally recognised PDI management approach. PMID:29062549

Herpes simplex virus amplicon delivery of a hypoxia-inducible soluble vascular endothelial growth factor receptor (sFlk-1) inhibits angiogenesis and tumor growth in pancreatic adenocarcinoma.

PubMed

Reinblatt, Maura; Pin, Richard H; Bowers, William J; Federoff, Howard J; Fong, Yuman

2005-12-01

Tumor hypoxia induces vascular endothelial growth factor (VEGF) expression, which stimulates angiogenesis and tumor proliferation. The VEGF signaling pathway is inhibited by soluble VEGF receptors (soluble fetal liver kinase 1; sFlk-1), which bind VEGF and block its interaction with endothelial cells. Herpes simplex virus (HSV) amplicons are replication-incompetent viruses used for gene delivery. We attempted to attenuate angiogenesis and inhibit pancreatic tumor growth through HSV amplicon-mediated expression of sFlk-1 under hypoxic control. A multimerized hypoxia-responsive enhancer (10 x HRE) was cloned upstream of the sFlk-1 gene (10 x HRE/sFlk-1). A novel HSV amplicon expressing 10 x HRE/sFlk-1 was genetically engineered (HSV10 x HRE/sFlk-1).Human pancreatic adenocarcinoma cells (AsPC1) were transduced with HSV10 x HRE/sFlk-1 and incubated in normoxia (21% oxygen) or hypoxia (1% oxygen). Capillary inhibition was evaluated by human umbilical vein endothelial cell assay. Western blot assessed sFlk-1 expression. AsPC1 flank tumor xenografts (n = 24) were transduced with HSV10 x HRE/sFlk-1. Media from normoxic AsPC1 transduced with HSV10 x HRE/sFlk-1 yielded a 36% reduction in capillary formation versus controls (P < .05), whereas hypoxic AsPC1 yielded a 76% reduction (P < .005). Western blot of AsPC1 transduced with HSV10 x HRE/sFlk-1 demonstrated greater sFlk-1 expression in hypoxia versus normoxia. AsPC1 flank tumors treated with HSV10 x HRE/sFlk-1 exhibited a 59% reduction in volume versus controls (P < .000001). HSV amplicon delivery of a hypoxia-inducible soluble VEGF receptor significantly reduces new vessel formation and tumor growth. Tumor hypoxia can thus be used to direct antiangiogenic therapy to pancreatic adenocarcinoma.

Idaho Driver Education Instructional Guide. Revised.

ERIC Educational Resources Information Center

Idaho State Dept. of Education, Boise.

This driver education instructional safety guide is organized in three sections: Driver Education; Motorcycle Education; and Driver Education for the Handicapped. The driver education section contains 10 units dealing with the following topics: parent orientation; student orientation; basic control skills; driver performance; driving regulations;…

Exploring the relationship between alcohol and the driver characteristics in motor vehicle accidents.

PubMed

Abdel-Aty, M A; Abdelwahab, H T

2000-07-01

This study examines the differences in alcohol-related accident involvement among different driver groups in the state of Florida. The driver characteristics considered in this study are: age, gender, race, and residency of the driver of a motor vehicle involved in an accident while under the influence of alcohol, drugs, or alcohol and drugs. The main objective of this study is to test whether there are associations between the different driver characteristics and alcohol involvement in traffic accidents, and to identify the high-risk group within each driver factor. This would improve our understanding of the relationship between alcohol involvement, accidents, and the four aforementioned driver factors. It would also enable us to better design educational and awareness programs targeting specific groups in the population to reduce drinking and driving in the state. The relationship between alcohol-related accident involvement and the driver factors are investigated using general descriptive statistics, conditional probabilities and log-linear models. The results showed that the 25-34 age group experience the highest rate of alcohol/drug involvement in accidents. The rates decline with the increase in the age of the drivers. The results also indicated that there are significant relationships between the driver characteristics and alcohol/drug involvement in accidents. Male, white, and in-state drivers were also more involved in alcohol/drugs-related traffic accidents.

Influence of driver nationality on the risk of causing vehicle collisions in Spain

PubMed Central

Lardelli, C; Luna, D; Jimenez, M; Bueno, C; Garcia, M; Galvez, V

2002-01-01

Study objective: To estimate the association between driver nationality and the risk of causing a collision between vehicles in motion. Design: Retrospective, matched by collision, case-control study. Setting: Collisions that occurred in Spain during the period from 1990 to 1999 were studied. Participants: Responsible (case) and non-responsible (control) drivers identified in the databases of the Dirección General de Tráfico (General Traffic Directorate) who were involved in a collisions between two or more four wheeled vehicles in motion, in which only one of the drivers had committed a traffic violation. Main results: Crude odds ratios (ORs) for the effect of driver nationality on the risk of causing a collision were significantly higher for foreign drivers than for Spanish drivers, and ranged from a minimum of 1.19 (95% CI 1.09 to 1.29) for Portuguese drivers to a maximum of 2.06 (1.88 to 2.27) for British drivers. Corresponding adjusted ORs were slightly lower, but were still significantly higher than 1 for all nationalities except Italian, Belgian, and American (USA). Adjusted ORs were usually higher for collisions that occurred in urban areas than on open roads. Conclusions: Authorities responsible for traffic safety, and drivers in general, should consider foreign drivers in Spain at particularly high risk for causing collisions, especially in urban areas. PMID:11964439

Commercial Driver Medical Examinations

PubMed Central

Moffitt, Gary; Hanowski, Richard J.; Kales, Stefanos N.; Porter, Richard J.; Hegmann, Kurt T.

2015-01-01

Objective: The objective of this study was to assess relationships between body mass index (BMI) and comorbid conditions within a large sample of truck drivers. Methods: Commercial driver medical examination data from 88,246 commercial drivers between 2005 and 2012 were analyzed for associations between BMI, medical disorders, and driver certification. Results: Most drivers were obese (53.3%, BMI >30.0 kg/m2) and morbidly obese (26.6%, BMI >35.0 kg/m2), higher than prior reports. Obese drivers were less likely to be certified for 2 years and more likely to report heart disease, hypertension, diabetes mellitus, nervous disorders, sleep disorders, and chronic low back pain (all P < 0.0001). There are relationships between multiple potentially disqualifying conditions and increasing obesity (P < 0.0001). Morbid obesity prevalence increased 8.9% and prevalence of three or more multiple conditions increased fourfold between 2005 and 2012. Conclusions: Obesity is related to multiple medical factors as well as increasing numbers of conditions that limit driving certification. PMID:25710607

Drivers of Environmental Institutional Dynamics in Decentralized African Countries.

PubMed

Hassenforder, Emeline; Barreteau, Olivier; Daniell, Katherine Anne; Pittock, Jamie; Ferrand, Nils

2015-12-01

This paper builds on the assumption that an effective approach to support the sustainability of natural resource management initiatives is institutional "bricolage." We argue that participatory planning processes can foster institutional bricolage by encouraging stakeholders to make their own arrangements based on the hybridization of old and new institutions. This papers aims at identifying how participatory process facilitators can encourage institutional bricolage. Specifically the paper investigates the specific contextual and procedural drivers of institutional dynamics in two case studies: the Rwenzori region in Uganda and the Fogera woreda in Ethiopia. In both cases, participatory planning processes were implemented. This research has three innovative aspects. First, it establishes a clear distinction between six terms which are useful for identifying, describing, and analyzing institutional dynamics: formal and informal; institutions and organizations; and emergence and change. Secondly, it compares the contrasting institutional dynamics in the two case studies. Thirdly, process-tracing is used to identify contextual and procedural drivers to institutional dynamics. We assume that procedural drivers can be used as "levers" by facilitators to trigger institutional bricolage. We found that facilitators need to pay particular attention to the institutional context in which the participatory planning process takes place, and especially at existing institutional gaps or failures. We identified three clusters of procedural levers: the selection and engagement of participants; the legitimacy, knowledge, and ideas of facilitators; and the design of the process, including the scale at which it is developed, the participatory tools used and the management of the diversity of frames.

Drivers of Environmental Institutional Dynamics in Decentralized African Countries

NASA Astrophysics Data System (ADS)

Hassenforder, Emeline; Barreteau, Olivier; Daniell, Katherine Anne; Pittock, Jamie; Ferrand, Nils

2015-12-01

This paper builds on the assumption that an effective approach to support the sustainability of natural resource management initiatives is institutional "bricolage." We argue that participatory planning processes can foster institutional bricolage by encouraging stakeholders to make their own arrangements based on the hybridization of old and new institutions. This papers aims at identifying how participatory process facilitators can encourage institutional bricolage. Specifically the paper investigates the specific contextual and procedural drivers of institutional dynamics in two case studies: the Rwenzori region in Uganda and the Fogera woreda in Ethiopia. In both cases, participatory planning processes were implemented. This research has three innovative aspects. First, it establishes a clear distinction between six terms which are useful for identifying, describing, and analyzing institutional dynamics: formal and informal; institutions and organizations; and emergence and change. Secondly, it compares the contrasting institutional dynamics in the two case studies. Thirdly, process-tracing is used to identify contextual and procedural drivers to institutional dynamics. We assume that procedural drivers can be used as "levers" by facilitators to trigger institutional bricolage. We found that facilitators need to pay particular attention to the institutional context in which the participatory planning process takes place, and especially at existing institutional gaps or failures. We identified three clusters of procedural levers: the selection and engagement of participants; the legitimacy, knowledge, and ideas of facilitators; and the design of the process, including the scale at which it is developed, the participatory tools used and the management of the diversity of frames.

Graduated driver licensing decal law: effect on young probationary drivers.

PubMed

Curry, Allison E; Pfeiffer, Melissa R; Localio, Russell; Durbin, Dennis R

2013-01-01

Decal laws have been implemented internationally to facilitate police enforcement of graduated driver licensing (GDL) restrictions (e.g., passenger limit, nighttime curfew) but have not been evaluated. New Jersey implemented the first decal law in the U.S. on May 1, 2010. The aim of this study was to evaluate the effect of New Jersey's law on the rate of citations issued for violation of GDL restrictions and police-reported crashes among probationary drivers aged <21 years and to estimate the number of probationary drivers whose crashes were prevented by the law. New Jersey's licensing and crash databases were linked from January 1, 2008 to May 31, 2011, and each driver's license status, age, and outcome status were ascertained for each month. Monthly rates were calculated as the proportion of probationary drivers who experienced the outcome in that month. The pre-law period was defined as January 2008-January 2010 and the post-law period as May 2010-May 2011. Negative binomial regression models with robust SEs were used to determine the law's effect on crash and citation rates (adjusted for gender, seasonal trends, and overall trends) and estimate prevented crashes. Analyses were conducted in 2012. In the first year post-law, there was a 14% increase in the GDL citation rate (adjusted rate ratio 1.14 [95% CI=1.05, 1.24]); a 9% reduction in the police-reported crash rate (adjusted rate ratio 0.91 [95% CI=0.86, 0.97]), and an estimated 1624 young probationary drivers for whom a crash was prevented. Findings suggest that the law is positively affecting probationary drivers' safety. Results contribute to building the evidence base for the effectiveness of decal laws and provide valuable information to U.S. and international policymakers who are considering adding decal laws to enhance existing GDL laws. Copyright © 2013 American Journal of Preventive Medicine. Published by Elsevier Inc. All rights reserved.

Investigating Driver Fatigue versus Alertness Using the Granger Causality Network.

PubMed

Kong, Wanzeng; Lin, Weicheng; Babiloni, Fabio; Hu, Sanqing; Borghini, Gianluca

2015-08-05

Driving fatigue has been identified as one of the main factors affecting drivers' safety. The aim of this study was to analyze drivers' different mental states, such as alertness and drowsiness, and find out a neurometric indicator able to detect drivers' fatigue level in terms of brain networks. Twelve young, healthy subjects were recruited to take part in a driver fatigue experiment under different simulated driving conditions. The Electroencephalogram (EEG) signals of the subjects were recorded during the whole experiment and analyzed by using Granger-Causality-based brain effective networks. It was that the topology of the brain networks and the brain's ability to integrate information changed when subjects shifted from the alert to the drowsy stage. In particular, there was a significant difference in terms of strength of Granger causality (GC) in the frequency domain and the properties of the brain effective network i.e., causal flow, global efficiency and characteristic path length between such conditions. Also, some changes were more significant over the frontal brain lobes for the alpha frequency band. These findings might be used to detect drivers' fatigue levels, and as reference work for future studies.

Prostate-Specific and Tumor-Specific Targeting of an Oncolytic HSV-1 Amplicon/Helper Virus for Prostate Cancer Treatment

DTIC Science & Technology

2009-11-01

that differentially expressed tumor suppressor miRNAs can be utilized to control the replication of an oncolytic DNA virus in a tumor-specific...demonstrated that the utilization of the tissue-specific promoter and the miRNA-mediated 3’UTRs in a targeted virotherapy is a viable approach with...elements into the whole HSV-1 viral genome should increase the safety margin substantially. The major advantage of the amplicon/helper system is its

Extracting Fitness Relationships and Oncogenic Patterns among Driver Genes in Cancer.

PubMed

Zhang, Xindong; Gao, Lin; Jia, Songwei

2017-12-25

Driver mutation provides fitness advantage to cancer cells, the accumulation of which increases the fitness of cancer cells and accelerates cancer progression. This work seeks to extract patterns accumulated by driver genes ("fitness relationships") in tumorigenesis. We introduce a network-based method for extracting the fitness relationships of driver genes by modeling the network properties of the "fitness" of cancer cells. Colon adenocarcinoma (COAD) and skin cutaneous malignant melanoma (SKCM) are employed as case studies. Consistent results derived from different background networks suggest the reliability of the identified fitness relationships. Additionally co-occurrence analysis and pathway analysis reveal the functional significance of the fitness relationships with signaling transduction. In addition, a subset of driver genes called the "fitness core" is recognized for each case. Further analyses indicate the functional importance of the fitness core in carcinogenesis, and provide potential therapeutic opportunities in medicinal intervention. Fitness relationships characterize the functional continuity among driver genes in carcinogenesis, and suggest new insights in understanding the oncogenic mechanisms of cancers, as well as providing guiding information for medicinal intervention.

Sleep, Dietary, and Exercise Behavioral Clusters among Truck Drivers with Obesity: Implications for Interventions

PubMed Central

Olson, Ryan; Thompson, Sharon V.; Wipfli, Brad; Hanson, Ginger; Elliot, Diane L.; Anger, W. Kent; Bodner, Todd; Hammer, Leslie B.; Hohn, Elliot; Perrin, Nancy A.

2015-01-01

Objective Our objectives were to describe a sample of truck drivers, identify clusters of drivers with similar patterns in behaviors affecting energy balance (sleep, diet, and exercise), and test for cluster differences in health and psychosocial factors. Methods Participants’ (n=452, BMI M=37.2, 86.4% male) self-reported behaviors were dichotomized prior to hierarchical cluster analysis, which identified groups with similar behavior co-variation. Cluster differences were tested with generalized estimating equations. Results Five behavioral clusters were identified that differed significantly in age, smoking status, diabetes prevalence, lost work days, stress, and social support, but not in BMI. Cluster 2, characterized by the best sleep quality, had significantly lower lost workdays and stress than other clusters. Conclusions Weight management interventions for drivers should explicitly address sleep, and may be maximally effective after establishing socially supportive work environments that reduce stress exposures. PMID:26949883

Sleep, Dietary, and Exercise Behavioral Clusters Among Truck Drivers With Obesity: Implications for Interventions.

PubMed

Olson, Ryan; Thompson, Sharon V; Wipfli, Brad; Hanson, Ginger; Elliot, Diane L; Anger, W Kent; Bodner, Todd; Hammer, Leslie B; Hohn, Elliot; Perrin, Nancy A

2016-03-01

The objectives of the study were to describe a sample of truck drivers, identify clusters of drivers with similar patterns in behaviors affecting energy balance (sleep, diet, and exercise), and test for cluster differences in health safety, and psychosocial factors. Participants' (n = 452, body mass index M = 37.2, 86.4% male) self-reported behaviors were dichotomized prior to hierarchical cluster analysis, which identified groups with similar behavior covariation. Cluster differences were tested with generalized estimating equations. Five behavioral clusters were identified that differed significantly in age, smoking status, diabetes prevalence, lost work days, stress, and social support, but not in body mass index. Cluster 2, characterized by the best sleep quality, had significantly lower lost workdays and stress than other clusters. Weight management interventions for drivers should explicitly address sleep, and may be maximally effective after establishing socially supportive work environments that reduce stress exposures.

Performance of amplicon-based next generation DNA sequencing for diagnostic gene mutation profiling in oncopathology.

PubMed

Sie, Daoud; Snijders, Peter J F; Meijer, Gerrit A; Doeleman, Marije W; van Moorsel, Marinda I H; van Essen, Hendrik F; Eijk, Paul P; Grünberg, Katrien; van Grieken, Nicole C T; Thunnissen, Erik; Verheul, Henk M; Smit, Egbert F; Ylstra, Bauke; Heideman, Daniëlle A M

2014-10-01

Next generation DNA sequencing (NGS) holds promise for diagnostic applications, yet implementation in routine molecular pathology practice requires performance evaluation on DNA derived from routine formalin-fixed paraffin-embedded (FFPE) tissue specimens. The current study presents a comprehensive analysis of TruSeq Amplicon Cancer Panel-based NGS using a MiSeq Personal sequencer (TSACP-MiSeq-NGS) for somatic mutation profiling. TSACP-MiSeq-NGS (testing 212 hotspot mutation amplicons of 48 genes) and a data analysis pipeline were evaluated in a retrospective learning/test set approach (n = 58/n = 45 FFPE-tumor DNA samples) against 'gold standard' high-resolution-melting (HRM)-sequencing for the genes KRAS, EGFR, BRAF and PIK3CA. Next, the performance of the validated test algorithm was assessed in an independent, prospective cohort of FFPE-tumor DNA samples (n = 75). In the learning set, a number of minimum parameter settings was defined to decide whether a FFPE-DNA sample is qualified for TSACP-MiSeq-NGS and for calling mutations. The resulting test algorithm revealed 82% (37/45) compliance to the quality criteria and 95% (35/37) concordant assay findings for KRAS, EGFR, BRAF and PIK3CA with HRM-sequencing (kappa = 0.92; 95% CI = 0.81-1.03) in the test set. Subsequent application of the validated test algorithm to the prospective cohort yielded a success rate of 84% (63/75), and a high concordance with HRM-sequencing (95% (60/63); kappa = 0.92; 95% CI = 0.84-1.01). TSACP-MiSeq-NGS detected 77 mutations in 29 additional genes. TSACP-MiSeq-NGS is suitable for diagnostic gene mutation profiling in oncopathology.

Global desertification: Drivers and feedbacks

NASA Astrophysics Data System (ADS)

D'Odorico, Paolo; Bhattachan, Abinash; Davis, Kyle F.; Ravi, Sujith; Runyan, Christiane W.

2013-01-01

Desertification is a change in soil properties, vegetation or climate, which results in a persistent loss of ecosystem services that are fundamental to sustaining life. Desertification affects large dryland areas around the world and is a major cause of stress in human societies. Here we review recent research on the drivers, feedbacks, and impacts of desertification. A multidisciplinary approach to understanding the drivers and feedbacks of global desertification is motivated by our increasing need to improve global food production and to sustainably manage ecosystems in the context of climate change. Classic desertification theories look at this process as a transition between stable states in bistable ecosystem dynamics. Climate change (i.e., aridification) and land use dynamics are the major drivers of an ecosystem shift to a “desertified” (or “degraded”) state. This shift is typically sustained by positive feedbacks, which stabilize the system in the new state. Desertification feedbacks may involve land degradation processes (e.g., nutrient loss or salinization), changes in rainfall regime resulting from land-atmosphere interactions (e.g., precipitation recycling, dust emissions), or changes in plant community composition (e.g., shrub encroachment, decrease in vegetation cover). We analyze each of these feedback mechanisms and discuss their possible enhancement by interactions with socio-economic drivers. Large scale effects of desertification include the emigration of “environmental refugees” displaced from degraded areas, climatic changes, and the alteration of global biogeochemical cycles resulting from the emission and long-range transport of fine mineral dust. Recent research has identified some possible early warning signs of desertification, which can be used as indicators of resilience loss and imminent shift to desert-like conditions. We conclude with a brief discussion on some desertification control strategies implemented in different

Executive report : toll roads, toll rates, and driver behavior.

DOT National Transportation Integrated Search

2012-12-01

State and federal research has examined toll roads and attempted to identify methods to make toll roads a more attractive option for drivers. Researchers examined various views of toll road transactions and concluded: : Truckers and trucking comp...

Ergonomic work analysis: A case study of bus drivers in the private collective transportation sector.

PubMed

Araújo, Adolfo Vicente; Arcanjo, Gemima Santos; Fernandes, Haroldo; Arcanjo, Georgia Santos

2018-05-03

The collective transportation system is essential to reduce the number of automobiles in the roads. Concerns exist related to quality, comfort and safety of bus driver's workstations. The objective of this study was to improve the driver's workstation in the private collective transportation sector by analyzing ergonomic practices using the Ergonomic Work Analysis (EWA). The EWA was chosen because it seeks to evaluate the labor condition as it relates to the psychophysiological conditions of workers, it complies with regulatory standard 17 (NR17). To identify driver concerns, interviews and questionnaires were administered. The workstation and worker routines were observed. The analysis revealed that the largest number of complaints related to noise, display light and location of the passenger identifier device. Drivers reported discomfort in the knees and lower back. Recommendations were made to improve the workstation and change the routine to minimize the discomfort and ergonomic risk factors.

Multi-locus and long amplicon sequencing approach to study microbial diversity at species level using the MinION™ portable nanopore sequencer

PubMed Central

Sanz, Yolanda

2017-01-01

Abstract The miniaturized and portable DNA sequencer MinION™ has demonstrated great potential in different analyses such as genome-wide sequencing, pathogen outbreak detection and surveillance, human genome variability, and microbial diversity. In this study, we tested the ability of the MinION™ platform to perform long amplicon sequencing in order to design new approaches to study microbial diversity using a multi-locus approach. After compiling a robust database by parsing and extracting the rrn bacterial region from more than 67000 complete or draft bacterial genomes, we demonstrated that the data obtained during sequencing of the long amplicon in the MinION™ device using R9 and R9.4 chemistries were sufficient to study 2 mock microbial communities in a multiplex manner and to almost completely reconstruct the microbial diversity contained in the HM782D and D6305 mock communities. Although nanopore-based sequencing produces reads with lower per-base accuracy compared with other platforms, we presented a novel approach consisting of multi-locus and long amplicon sequencing using the MinION™ MkIb DNA sequencer and R9 and R9.4 chemistries that help to overcome the main disadvantage of this portable sequencing platform. Furthermore, the nanopore sequencing library, constructed with the last releases of pore chemistry (R9.4) and sequencing kit (SQK-LSK108), permitted the retrieval of the higher level of 1D read accuracy sufficient to characterize the microbial species present in each mock community analysed. Improvements in nanopore chemistry, such as minimizing base-calling errors and new library protocols able to produce rapid 1D libraries, will provide more reliable information in the near future. Such data will be useful for more comprehensive and faster specific detection of microbial species and strains in complex ecosystems. PMID:28605506

Cognitive characteristics of older Japanese drivers.

PubMed

Susilowati, Indri H; Yasukouchi, Akira

2012-02-29

Some causes of accidents among older drivers are: not paying attention to traffic signals; missing stop lines; and having to deal with and misjudging emergency situations. These causes of accidents reveal problems with attention and cognition. Such incidents are also related to driver perception and stress-coping mechanisms. It is important to examine the relation of stress reactions to attention and cognition as a factor influencing the causes of accidents commonly involving older drivers. Subjects were 10 young drivers (23.3 ± 3.33 years) and 25 older drivers divided into two groups (older1 [60 to 65 years] and older2 [> 65 years]). This study revealed the correlation within driver stress inventory and driver coping questionnaires parameters was observed only in older drivers. They also needed a longer response time for Trail Making Test A and B. The factors affected the attention and cognition of older drivers by age but not driving experience itself, and coping parameters such as emotion focus, reappraisal, and avoidance were not included as stress inventory parameters. Being prone to fatigue was less for younger drivers than older drivers. Because they have shorter distances, shorter drive times, and no need for expressways, older drivers also had a significantly lower risk of thrill-seeking behaviour and more patience. The intervention addressing their attention skills, aggressive feelings, and emotion focus should be considered. The technological improvements in cars will make older drivers feel safer and make driving easier which might lower the attention paid to the road, and regular driving training might be needed to assess and enhance their safety.

Efficacy of side air bags in reducing driver deaths in driver-side collisions.

PubMed

Braver, Elisa R; Kyrychenko, Sergey Y

2004-03-15

Side air bags, a relatively new technology designed to protect the head and/or torso in side-impact collisions, are becoming increasingly common in automobiles. Their efficacy in preventing US driver deaths among cars struck on the near (driver's) side was examined using data from the Fatality Analysis Reporting System and the General Estimates System. Risk ratios for driver death per nearside collision during 1999-2001 were computed for head/torso and torso-only side air bags in cars from model years 1997-2002, relative to cars without side air bags. Confounding was addressed by adjusting nearside risk ratios for front- and rear-impact mortality, which is unaffected by side air bags. Risk ratios were 0.55 (95% confidence interval: 0.43, 0.71) for head/torso air bags and 0.89 (95% confidence interval: 0.79, 1.01) for torso-only air bags. Risk was reduced when cars with head/torso air bags were struck by cars/minivans (significant) or pickup trucks/sport utility vehicles (nonsignificant). Risk was reduced in two-vehicle collisions and among male drivers and drivers aged 16-64 years. Protective effects associated with torso-only air bags were observed in single-vehicle crashes and among male and 16- to 64-year-old drivers. Head/torso side air bags appear to be very effective in reducing nearside driver deaths, whereas torso-only air bags appear less protective.

Work-related injury factors and safety climate perception in truck drivers.

PubMed

Anderson, Naomi J; Smith, Caroline K; Byrd, Jesse L

2017-08-01

The trucking industry has a high burden of work-related injuries. This study examined factors, such as safety climate perceptions, that may impact injury risk. A random sample of 9800 commercial driver's license holders (CDL) were sent surveys, only 4360 were eligible truck drivers. Descriptive statistics and logistic regression models were developed to describe the population and identify variables associated with work-related injury. 2189 drivers completed the pertinent interview questions. Driving less-than-truckload, daytime sleepiness, pressure to work faster, and having a poor composite score for safety perceptions were all associated with increased likelihood of work-related injury. Positive safety perception score was protective for odds of work-related injury, and increased claim filing when injured. Positive psychological safety climate is associated with decreased likelihood of work-related injury and increased likelihood that a driver injured on the job files a workers' compensation claim. © 2017 Wiley Periodicals, Inc.

Genes encoded within 8q24 on the amplicon of a large extrachromosomal element are selectively repressed during the terminal differentiation of HL-60 cells.

PubMed

Hirano, Tetsuo; Ike, Fumio; Murata, Takehide; Obata, Yuichi; Utiyama, Hiroyasu; Yokoyama, Kazunari K

2008-04-02

Human acute myeloblastic leukemia HL-60 cells become resistant to differentiation during long-term cultivation. After 150 passages, double minute chromosomes (dmins) found in early-passaged cells are replaced by large extrachromosomal elements (LEEs). In a DNA library derived from a purified fraction of LEEs, 12.6% (23/183) of clones were assigned to 8q24 and 9.2% (17/183) were assigned to 14q11 in the human genome. Fluorescence in situ hybridization (FISH) revealed a small aberrant chromosome, which had not been found in early-passaged cells, in addition to the purified LEEs. We determined that each LEE consisted of six discontinuous segments in a region that extended for 4.4Mb over the 8q24 locus. Five genes, namely, Myc (a proto-oncogene), NSMCE2 (for a SUMO ligase), CCDC26 (for a retinoic acid-dependent modulator of myeloid differentiation), TRIB1 (for a regulator of MAPK kinase) and LOC389637 (for a protein of unknown function), were encoded by the amplicon. Breaks in the chromosomal DNA within the amplicon were found in the NSMCE2 and CCDC26 genes. The discontinuous structure of the amplicon unit of the LEEs was identical with that of dmins in HL-60 early-passaged cells. The difference between them seemed, predominantly, to be the number (10-15 copies per LEE versus 2 or 3 copies per dmin) of constituent units. Expression of the Myc, NSMCE2, CCDC26 and LOC389637 and TRIB1 genes was constitutive in all lines of HL-60 cells and that of the first four genes was repressed during the terminal differentiation of early-passaged HL-60 cells. We also detected abnormal transcripts of CCDC26. Our results suggest that these genes were selected during the development of amplicons. They might be amplified and, sometimes, truncated to contribute to the maintenance of HL-60 cells in an undifferentiated state.

Can younger drivers be trained to scan for information that will reduce their risk in roadway traffic scenarios that are hard to identify as hazardous?

PubMed Central

Pradhan, A.K.; Pollatsek, A.; Knodler, M.; Fisher, D.L.

2009-01-01

Younger drivers (18–21 years) are over-involved in crashes. Research suggests that one of the reasons for this over-involvement is their failure to scan areas of the roadway for information about potential risks in situations that are hazardous, but not obviously so. The primary objective of the present study is to develop and evaluate a training program that addresses this failure. It was hypothesised that PC-based hazard anticipation training would increase the likelihood that younger drivers would scan for potential hazards on the open road. In order to test this hypothesis, 12 trained and 12 untrained drivers' eye movements were measured as they drove a vehicle on local residential, feeder and arterial roads. Overall, the trained drivers were significantly more likely to gaze at areas of the roadway that contained information relevant to the reduction of risks (64.4%) than were the untrained drivers (37.4%). Significant training effects were observed even in situations on the road that were quite different from those shown in training. These findings have clear implications for the type of training of teen drivers that is necessary in order to increase their anticipation of hazards. PMID:19296315

Therapeutic modulation of epigenetic drivers of drug resistance in ovarian cancer

PubMed Central

Zeller, Constanze; Brown, Robert

2010-01-01

Epigenetic changes in tumours are associated not only with cancer development and progression, but also with resistance to chemotherapy. Aberrant DNA methylation at CpG islands and associated epigenetic silencing are observed during the acquisition of drug resistance. However, it remains unclear whether all of the observed changes are drivers of drug resistance, causally associated with response of tumours to chemotherapy, or are passenger events representing chance DNA methylation changes. Systematic approaches that link DNA methylation and expression with chemosensitivity will be required to identify key drivers. Such drivers will be important prognostic or predicitive biomarkers, both to existing chemotherapies, but also to epigenetic therapies used to modulate drug resistance. PMID:21789144

Google glass: a driver distraction cause or cure?

PubMed

Sawyer, Ben D; Finomore, Victor S; Calvo, Andres A; Hancock, P A

2014-11-01

We assess the driving distraction potential of texting with Google Glass (Glass), a mobile wearable platform capable of receiving and sending short-message-service and other messaging formats. A known roadway danger, texting while driving has been targeted by legislation and widely banned. Supporters of Glass claim the head-mounted wearable computer is designed to deliver information without concurrent distraction. Existing literature supports the supposition that design decisions incorporated in Glass might facilitate messaging for drivers. We asked drivers in a simulator to drive and use either Glass or a smartphone-based messaging interface, then interrupted them with an emergency brake event. Both the response event and subsequent recovery were analyzed. Glass-delivered messages served to moderate but did not eliminate distracting cognitive demands. A potential passive cost to drivers merely wearing Glass was also observed. Messaging using either device impaired driving as compared to driving without multitasking. Glass in not a panacea as some supporters claim, but it does point the way to design interventions that effect reduced load in multitasking. Discussions of these identified benefits are framed within the potential of new in-vehicle systems that bring both novel forms of distraction and tools for mitigation into the driver's seat.

Understanding the underlying drivers of inpatient cost growth: a literature review.

PubMed

Goetghebeur, Mireille M; Forrest, Sharon; Hay, Joel W

2003-06-01

After the declining growth in inpatient hospital spending that occurred from 1994 through 1998, the recent trend in increased spending has been of concern to many. Understanding the underlying reasons for this new growth will aid decision makers in finding best means to manage inpatient costs. To identify potential contributors to recent growth in inpatient spending. Literature review. Healthcare and economic databases, prominent Web sites, and key journals were searched to identify potential drivers for the 1999-2001 rise in inpatient spending. Initial literature review and state-level regression analyses published in a companion paper were used to identify key explanatory factors, which were further explored. Although many of the contributors to the rise in inpatient costs overlap and are interrelated, the major cost drivers were identified as (1) workforce shortage; (2) new technology; (3) less tightly managed care; and (4) shifting hospital business directions. Underlying factors such as legislation, quality of care, limited access to noninpatient care, pressures on the safety net, population aging, and increasing chronic illness prevalence were found to influence the contributors and healthcare spending in general. Future trends in inpatient spending will depend on the response of the healthcare system to these cost drivers and underlying factors. Potential avenues to control inpatient spending include expanding access to primary care, encouraging cost-effective technology and more efficient hospital market structures, and developing incentives for the healthcare workforce.

Characteristics of fatal road crashes involving unlicensed drivers or riders: Implications for countermeasures.

PubMed

Sagberg, Fridulv

2018-08-01

Drivers or riders without a valid license are involved in 10% of fatal road crashes in Norway. This was shown by an analysis of data from all fatal crashes in the period 2005-2014. A literature review shows that unlicensed drivers have a considerably increased crash risk. Such crashes could be prevented by electronic driver authentication, i.e., a technical system for checking that a driver or rider has legal access to a vehicle before driving is permitted. This can be done by requiring the driver/rider to identify themselves with a national identity number and a unique code or biometric information before driving may commence. The vehicle thereafter verifies license availability and vehicle access by communication with a central register. In more than 80% of fatal crashes with unlicensed drivers/riders, speeding and/or drug influence contributed to the crash. This means that a majority of crashes with unlicensed drivers alternatively could be prevented by already available systems, such as alcolock and speed limit dependent speed adapters. These systems will have a wider influence, by preventing crashes also among licensed drivers. Mandatory implementation of alcolock, speed limiter, and electronic driver authentication in all motorized vehicles is estimated to prevent up to 28% of fatal road crashes, depending on effectiveness of the systems. Copyright © 2018 Elsevier Ltd. All rights reserved.

A Cross “Ethnical” Comparison of the Driver Behaviour Questionnaire (DBQ) in an Economically Fast Developing Country

PubMed Central

Bener, Abdulbari; Verjee, Mohamud; Dafeeah, Elnour E.; Yousafzai, Mohammad T.; Mari, Sundus; Hassib, Ahmed; Al-Khatib, Hamza; Choi, Min Kyung; Nema, Noor; Özkan, Türker; Lajunen, Timo

2013-01-01

Aim: The aim of this study was to compare the driving behaviours of four ethnic groups and to investigate the relationship between violations, errors and lapses of DBQ and accident involvement in Qatar. Subjects and Methods: The Driver Behaviour Questionnaire (DBQ) was used to measure the aberrant driving behaviours leading to accidents. Of 2400 drivers approached, 1824 drivers agreed to participate (76%) and completed the driver behaviour questionnaire and background information. Results: The study revealed that the majority of the Qatari (35.9%) and Jordanian drivers (37.5%) were below 30 years of age, whereas Filipino (42.3%) and Indian subcontinent (34.1%) drivers were in the age group of 30-39 years. Qatari drivers (52%) were involved in most accidents, followed by Jordanians (48.3%). The most common type of collision was a head on collision, which was similar in all four ethnic groups. The Qatari drivers scored higher on almost all items of violations, errors and lapses compared to other ethnic groups, while Filipino drivers were lower on all the items. The most common violation was the same in all four ethnic groups “Disregard the speed limits on a motorway”. The most common error item observed was “Queing to turn right/left on to a main road”. “Forget where you left your car” and “Hit something when reversing” were the two lapses identified in factor analysis. Conclusion: The present study identified that Qatari drivers scored higher on most of the items of violations, errors and lapses of DBQ compared to other countries, whereas Filipino drivers scored lower in DBQ items. PMID:23777732

Cognitive characteristics of older Japanese drivers

PubMed Central

2012-01-01

Background Some causes of accidents among older drivers are: not paying attention to traffic signals; missing stop lines; and having to deal with and misjudging emergency situations. These causes of accidents reveal problems with attention and cognition. Such incidents are also related to driver perception and stress-coping mechanisms. It is important to examine the relation of stress reactions to attention and cognition as a factor influencing the causes of accidents commonly involving older drivers. Finding Subjects were 10 young drivers (23.3 ± 3.33 years) and 25 older drivers divided into two groups (older1 [60 to 65 years] and older2 [> 65 years]). This study revealed the correlation within driver stress inventory and driver coping questionnaires parameters was observed only in older drivers. They also needed a longer response time for Trail Making Test A and B. The factors affected the attention and cognition of older drivers by age but not driving experience itself, and coping parameters such as emotion focus, reappraisal, and avoidance were not included as stress inventory parameters. Being prone to fatigue was less for younger drivers than older drivers. Because they have shorter distances, shorter drive times, and no need for expressways, older drivers also had a significantly lower risk of thrill-seeking behaviour and more patience. Conclusion The intervention addressing their attention skills, aggressive feelings, and emotion focus should be considered. The technological improvements in cars will make older drivers feel safer and make driving easier which might lower the attention paid to the road, and regular driving training might be needed to assess and enhance their safety. PMID:22738158

Does assisted driving behavior lead to safety-critical encounters with unequipped vehicles' drivers?

PubMed

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

Characterization of potential driver mutations involved in human breast cancer by computational approaches

PubMed Central

Rajendran, Barani Kumar; Deng, Chu-Xia

2017-01-01

Breast cancer is the second most frequently occurring form of cancer and is also the second most lethal cancer in women worldwide. A genetic mutation is one of the key factors that alter multiple cellular regulatory pathways and drive breast cancer initiation and progression yet nature of these cancer drivers remains elusive. In this article, we have reviewed various computational perspectives and algorithms for exploring breast cancer driver mutation genes. Using both frequency based and mutational exclusivity based approaches, we identified 195 driver genes and shortlisted 63 of them as candidate drivers for breast cancer using various computational approaches. Finally, we conducted network and pathway analysis to explore their functions in breast tumorigenesis including tumor initiation, progression, and metastasis. PMID:28477017

Student drivers: a study of fatal motor vehicle crashes involving 16-year-old drivers.

PubMed

Gonzales, Michael M; Dickinson, L Miriam; DiGuiseppi, Carolyn; Lowenstein, Steven R

2005-02-01

Motor vehicle crashes are the leading cause of death for US teenagers, accounting for 40% of fatalities. The purpose of this study was to compare novice (aged 16 years) and experienced (aged 25 to 49 years) drivers involved in fatal motor vehicle crashes with respect to crash characteristics and driver behaviors. This cross-sectional study of fatal motor vehicle crashes in Colorado used data from the Fatality Analysis Reporting System (1995 to 2001). Driver and crash variables were compared in the 2 age groups using separate logistic regression models, adjusted for sex, geographic locale, and year. Two thousand four hundred twenty fatal motor vehicle crashes were included; 158 fatalities (6.5%) were novice drivers. Novice drivers were more likely to have been speeding (odds ratio [OR] 1.87, 95% confidence interval [CI] 1.34 to 3.08); driving recklessly (OR 4.78, 95% CI 3.31 to 6.92); charged with a traffic violation (OR 3.08, 95% CI 2.20 to 4.31); in a single-vehicle (OR 1.84, 95% CI 1.32 to 2.57), rollover (OR 1.36, 95% CI 0.97 to 1.91) or run-off-the-road (OR 1.54, 95% CI 1.03 to 2.30) crash; and carrying 2 (OR 4.52, 95% CI 2.75 to 7.41) or more (OR 4.07, 95% CI 2.49 to 6.55) passengers. Safety belt nonuse was high for novice (48%) and experienced (42%) drivers (OR 1.19, 95% CI 0.86 to 1.67). Novice drivers had older cars (mean difference 1.5 years, 95% CI 0.37 to 2.57 years). Novice drivers were less likely to be involved in crashes caused by alcohol (OR 0.24, 95% CI 0.14 to 0.41) or adverse weather (OR 0.37, 95% CI 0.19 to 0.75) and to be driving a sport utility vehicle (OR 0.62, 95% CI 0.39 to 0.97). Fatal motor vehicle crashes involving novice drivers are characterized by speeding, recklessness, single-vehicle and rollover crashes, and traffic law violations, suggesting that novice drivers bear considerable responsibility for their fatal crashes. Moreover, almost half of 16-year-old drivers involved in fatal motor vehicle crashes were not wearing their safety

Driver injury in near- and far-side impacts: Update on the effect of front passenger belt use.

PubMed

Parenteau, Chantal S; Viano, David C

2018-04-03

This is a study that updates earlier research on the influence of a front passenger on the risk for severe driver injury in near-side and far-side impacts. It includes the effects of belt use by the driver and passenger, identifies body regions involved in driver injury, and identifies the sources for severe driver head injury. 1997-2015 NASS-CDS data were used to investigate the risk for Maximum Abbreviated Injury Scale (MAIS) 4 + F driver injury in near-side and far-side impacts by front passenger belt use and as a sole occupant in the driver seat. Side impacts were identified with GAD1 = L or R without rollover (rollover ≤ 0). Front-outboard occupants were included without ejection (ejection = 0). Injury severity was defined by MAIS and fatality (F) by TREATMNT = 1 or INJSEV = 4. Weighted data were determined. The risk for MAIS 4 + F was determined using the number of occupants with known injury status MAIS 0 + F. Standard errors were determined. Overall, belted drivers had greater risks for severe injury in near-side than far-side impacts. As a sole driver, the risk was 0.969 ± 0.212% for near-side and 0.313 ± 0.069% for far-side impacts (P < .005). The driver's risk was 0.933 ± 0.430% with an unbelted passenger and 0.596 ± 0.144% with a belted passenger in near-side impacts. The risk was 2.17 times greater with an unbelted passenger (NS). The driver's risk was 0.782 ± 0.431% with an unbelted passenger and 0.361% ± 0.114% with a belted passenger in far-side impacts. The risk was 1.57 times greater with an unbelted passenger (P < .10). Seat belt use was 66 to 95% effective in preventing MAIS 4 + F injury in the driver. For belted drivers, the head and thorax were the leading body regions for Abbreviated Injury Scale (AIS) 4+ injury. For near-side impacts, the leading sources for AIS 4+ head injury were the left B-pillar, roof, and other vehicle. For far-side impacts, the leading sources were the other occupant, right interior, and roof (8.5%). Seat belt

Prevalence of alcohol and drug use in injured British Columbia drivers

PubMed Central

Brubacher, Jeffrey R; Chan, Herbert; Martz, Walter; Schreiber, William; Asbridge, Mark; Eppler, Jeffrey; Lund, Adam; Macdonald, Scott; Drummer, Olaf; Purssell, Roy; Andolfatto, Gary; Mann, Robert; Brant, Rollin

2016-01-01

Objectives Determine the prevalence of drug use in injured drivers and identify associated demographic factors and crash characteristics. Design Prospective cross-sectional study. Setting Seven trauma centres in British Columbia, Canada (2010–2012). Participants Automobile drivers who had blood obtained within 6 h of a crash. Main outcome measures We analysed blood for cannabis, alcohol and other impairing drugs using liquid chromatography/mass spectrometry (LCMS). Results 1097 drivers met inclusion criteria. 60% were aged 20–50 years, 63.2% were male and 29.0% were admitted to hospital. We found alcohol in 17.8% (15.6% to 20.1%) of drivers. Cannabis was the second most common recreational drug: cannabis metabolites were present in 12.6% (10.7% to 14.7%) of drivers and we detected Δ-9-tetrahydrocannabinol (Δ-9-THC) in 7.3% (5.9% to 9.0%), indicating recent use. Males and drivers aged under 30 years were most likely to use cannabis. We detected cocaine in 2.8% (2.0% to 4.0%) of drivers and amphetamines in 1.2% (0.7% to 2.0%). We also found medications including benzodiazepines (4.0% (2.9% to 5.3%)), antidepressants (6.5% (5.2% to 8.1%)) and diphenhydramine (4.7% (3.5% to 6.2%)). Drivers aged over 50 years and those requiring hospital admission were most likely to have used medications. Overall, 40.1% (37.2% to 43.0%) of drivers tested positive for alcohol or at least one impairing drug and 12.7% (10.7% to 14.7%) tested positive for more than one substance. Conclusions Alcohol, cannabis and a broad range of other impairing drugs are commonly detected in injured drivers. Alcohol is well known to cause crashes, but further research is needed to determine the impact of other drug use, including drug–alcohol and drug–drug combinations, on crash risk. In particular, more work is needed to understand the role of medications in causing crashes to guide driver education programmes and improve public safety. PMID:26966054

Repeated Cross-Sectional Assessment of Commercial Truck Driver Health.

PubMed

Thiese, Matthew S; Moffitt, Gary; Hanowski, Richard J; Kales, Stefanos N; Porter, Richard J; Hegmann, Kurt T

2015-09-01

To assess relationships and trends over time in individual conditions and multiple conditions among a large sample of independent, nonoverlapping truck drivers using a repeated cross-sectional study design. Commercial driver medical examinations were conducted on 95,567 commercial drivers between January 1, 2005, and October 31, 2012. Specific medical conditions that have been identified by the Federal Motor Carrier Safety Administration's Medical Review Board as possibly increasing crash risk were examined. Prevalence and trends over time were analyzed. A total of 8 of the 13 conditions significantly increased from 2005 to 2012. Prevalence of multiple concomitant conditions also increased, with prevalence odds ratios as high as 7.39 (95% confidence interval, 3.92 to 13.98) for four or more conditions in 2012 as compared with 2005. Individual and multiple conditions thought to be associated with increased crash risk significantly increased between 2005 and 2012.

The problem of suspended and revoked drivers who avoid detection at checkpoints.

PubMed

Parrish, Kelly E; Masten, Scott V

2015-01-01

drivers. Using license card readers that can quickly identify SR drivers in real time during routine traffic stops and at DUI/license checkpoints warrants further consideration.

Identifying drivers of divergent methane fluxes from restored wetlands

NASA Astrophysics Data System (ADS)

Chamberlain, S.; Silver, W. L.; Anthony, T.; Hemes, K. S.; Oikawa, P.; Sturtevant, C.; Eichelmann, E.; Matthes, J. H.; Verfaillie, J. G.; Baldocchi, D. D.

2017-12-01

Restored wetlands in the Sacramento-San Joaquin Delta region of California are created, and actively managed, to reduce land subsidence and greenhouse gas (GHG) emissions from drained peatland agriculture. While these wetlands tend to be carbon sinks on a year-to-year basis, variation in methane (CH4) emissions determines whether sites are GHG sources or sinks. Two probable sources of CH4 flux variation across restored wetlands are soil carbon and iron content. These soil properties vary across the region and are a legacy of pre-drainage wetland geomorphology, where alluvium wetlands were mineral rich and carbon poor compared to adjacent peat accumulating sites. We explored drivers of CH4 flux variation from three restored wetlands using eddy covariance, data-driven analyses, and biogeochemical modeling to evaluate alternative hypotheses for observed flux differences. We observed significantly reduced annual CH4 fluxes from wetlands restored on alluvium soils compared to peat sites, and these differences were largest immediately following restoration and gradually reduced over the following three years. Model-based hypothesis testing demonstrates that long-term inhibition of methanogenesis by iron presence is the best explanation for these observations. Soil samplings conducted after four years of continuous inundation demonstrates significantly higher iron concentrations in the alluvium soils, of which 25-30% was in oxidized form capable of inhibiting CH4 production. Using information theory and wavelet analyses, we also demonstrate that CH4 fluxes from the alluvium wetland were decoupled from plant photosynthesis and transport at diel to multiday timescales, as expected when iron reduction inhibits rhizosphere methanogenesis. These findings demonstrate that iron presence is capable of attenuating ecosystem-scale wetland CH4 fluxes, and provide a basis for choosing future wetland restoration sites to minimize CH4 emissions.

Predicting Driver Behavior during the Yellow Interval Using Video Surveillance.

PubMed

Li, Juan; Jia, Xudong; Shao, Chunfu

2016-12-06

At a signalized intersection, drivers must make a stop/go decision at the onset of the yellow signal. Incorrect decisions would lead to red light running (RLR) violations or crashes. This study aims to predict drivers' stop/go decisions and RLR violations during yellow intervals. Traffic data such as vehicle approaching speed, acceleration, distance to the intersection, and occurrence of RLR violations are gathered by a Vehicle Data Collection System (VDCS). An enhanced Gaussian Mixture Model (GMM) is used to extract moving vehicles from target lanes, and the Kalman Filter (KF) algorithm is utilized to acquire vehicle trajectories. The data collected from the VDCS are further analyzed by a sequential logit model, and the relationship between drivers' stop/go decisions and RLR violations is identified. The results indicate that the distance of vehicles to the stop line at the onset of the yellow signal is an important predictor for both drivers' stop/go decisions and RLR violations. In addition, vehicle approaching speed is a contributing factor for stop/go decisions. Furthermore, the accelerations of vehicles after the onset of the yellow signal are positively related to RLR violations. The findings of this study can be used to predict the probability of drivers' RLR violations and improve traffic safety at signalized intersections.

Sleepiness and sleep-disordered breathing in truck drivers : risk analysis of road accidents.

PubMed

Catarino, Rosa; Spratley, Jorge; Catarino, Isabel; Lunet, Nuno; Pais-Clemente, Manuel

2014-03-01

Portugal has one of the highest road traffic fatality rates in Europe. A clear association between sleep-disordered breathing (SDB) and traffic accidents has been previously demonstrated. This study aimed to determine prevalence of excessive daytime sleepiness (EDS) and other sleep disorder symptoms among truck drivers and to identify which individual traits and work habits are associated to increased sleepiness and accident risk. We evaluated a sample of 714 truck drivers using a questionnaire (244 face-to-face interviews, 470 self-administered) that included sociodemographic data, personal habits, previous accidents, Epworth Sleepiness Scale (ESS), and the Berlin questionnaire (BQ). Twenty percent of drivers had EDS and 29 % were at high risk for having obstructive sleep apnea syndrome (OSAS). Two hundred sixty-one drivers (36.6 %) reported near-miss accidents (42.5 % sleep related) and 264 (37.0 %), a driving accident (16.3 % sleep related). ESS score ≥ 11 was a risk factor for both near-miss accidents (odds ratio (OR)=3.84, p<0.01) and accidents (OR=2.25, p<0.01). Antidepressant use was related to accidents (OR=3.30, p=0.03). We found an association between high Mallampati score (III-IV) and near misses (OR=1.89, p=0.04). In this sample of Portuguese truck drivers, we observed a high prevalence of EDS and other sleep disorder symptoms. Accident risk was related to sleepiness and antidepressant use. Identifying drivers at risk for OSAS should be a major priority of medical assessment centers, as a public safety policy.

Comparison of older and younger novice driver crash rates: Informing the need for extended Graduated Driver Licensing restrictions.

PubMed

Curry, Allison E; Metzger, Kristina B; Williams, Allan F; Tefft, Brian C

2017-11-01

Few previous studies have directly compared crash rates of older and younger novice drivers. To inform discussion about whether Graduated Driver Licensing (GDL) policies that are applied in the US for younger novice drivers should be applied to older novice drivers, we conducted a longitudinal study to examine overall, nighttime, and multiple passenger crash rates over the initial four years of licensure differ for novice drivers licensed at different ages. Using data from the New Jersey Traffic Safety Outcomes (NJ-TSO) data warehouse, we selected all NJ drivers who obtained their initial intermediate driver's license from 2006 through 2014 and had at least one month of follow-up from the date of licensure to study end or death (n=1,034,835). Novice drivers were grouped based on age at licensure: age 17; 18-20; 21-24; and 25 or older. We estimated monthly rates for overall crashes (per 10,000 licensed drivers) as well as: late night crashes (11:01 p.m.-4:59 a.m.); early night crashes (9:00 p.m.-11:00 p.m.); and multiple passenger crashes (two or more passengers). Average monthly rates were calculated for specific relevant time periods and Poisson regression models were used to compare rates: (1) between novice driver groups with the same time since licensure; (2) over the first 48 months of licensure within each novice driver group; and (3) between same-aged 21-year-old drivers with varying lengths of licensure. Although initial (three months post-licensure) overall crash rates of novice NJ drivers age 21 and older were higher than rates of same-aged experienced drivers, they were substantially lower than initial rates for 17- to 20-year-old novice drivers, who are licensed under GDL policies. Moreover, older novice drivers experience much less steep crash reductions over the first year of licensure than younger novice drivers. Nighttime crash rates among the 21- to 24-year old and aged 25 and older novice driver groups were stable over the first year of licensure

Preliminary evaluation of the North Carolina graduated driver licensing system : effects on young driver crashes

DOT National Transportation Integrated Search

2000-07-01

In December 1997, North Carolina became the second state to enact a comprehensive Graduated Driver Licensing (GDL) system. The purpose of the GSL is to reduce young driver crashes by introducing beginning drivers to the full range of driving experien...

Driver hand-held mobile phone use and safety belt use.

PubMed

Eby, David W; Vivoda, Jonathon M

2003-11-01

The purposes of the study were to identify hand-held mobile phone use trends for Michigan and to compare safety belt use between users and nonusers. Mobile phone and safety belt use was investigated by a direct observation survey of drivers at intersections in Michigan. Data were weighted to calculate mobile phone use and safety belt use rates statewide. The study showed 2.7% of Michigan drivers were using a mobile phone at any given daylight time. Safety belt use of current mobile phone users was significantly lower than those not using mobile phones.

Investigation of Microbial Diversity in Geothermal Hot Springs in Unkeshwar, India, Based on 16S rRNA Amplicon Metagenome Sequencing

PubMed Central

Mehetre, Gajanan T.; Paranjpe, Aditi; Dastager, Syed G.

2016-01-01

Microbial diversity in geothermal waters of the Unkeshwar hot springs in Maharashtra, India, was studied using 16S rRNA amplicon metagenomic sequencing. Taxonomic analysis revealed the presence of Bacteroidetes, Proteobacteria, Cyanobacteria, Actinobacteria, Archeae, and OD1 phyla. Metabolic function prediction analysis indicated a battery of biological information systems indicating rich and novel microbial diversity, with potential biotechnological applications in this niche. PMID:26950332

Motor vehicle driver injury and socioeconomic status: a cohort study with prospective and retrospective driver injuries.

PubMed

Whitlock, G; Norton, R; Clark, T; Pledger, M; Jackson, R; MacMahon, S

2003-07-01

To investigate the association between motor vehicle driver injury and socioeconomic status. Cohort study with prospective and retrospective outcomes. New Zealand. 10 525 adults (volunteer sample of a multi-industry workforce, n=8008; and a random sample of urban electoral rolls, n=2517). Motor vehicle driver injury resulting in admission of the driver to hospital or the driver's death, or both, during the period 1988-98; hospitalisation and mortality data were obtained by record linkage to national health databases. After adjustment for age and sex, driver injury risk was inversely associated with both occupational status (p for linear trend <0.0001) and educational level (p for linear trend =0.007). Participants in the lowest approximate quartile of occupational status were four times as likely (HR 4.17, 95% CI 2.31 to 7.55) to have experienced a driver injury during follow up as participants in the highest approximate quartile. Participants who had been to secondary school for less than two years were twice as likely (HR 2.26, 95% CI 1.34 to 3.81) to have experienced a driver injury as those who had been to university or polytechnic. There was little evidence that driver injury risk was associated with neighbourhood income (p for linear trend =0.12) CONCLUSIONS: Occupational status and educational level seem to be important determinants of driver injury risk. Driver injury countermeasures should be targeted to people in low status occupations, as well as to people with comparatively little formal education.

Genetic Drivers of Kidney Defects in the DiGeorge Syndrome.

PubMed

Lopez-Rivera, Esther; Liu, Yangfan P; Verbitsky, Miguel; Anderson, Blair R; Capone, Valentina P; Otto, Edgar A; Yan, Zhonghai; Mitrotti, Adele; Martino, Jeremiah; Steers, Nicholas J; Fasel, David A; Vukojevic, Katarina; Deng, Rong; Racedo, Silvia E; Liu, Qingxue; Werth, Max; Westland, Rik; Vivante, Asaf; Makar, Gabriel S; Bodria, Monica; Sampson, Matthew G; Gillies, Christopher E; Vega-Warner, Virginia; Maiorana, Mariarosa; Petrey, Donald S; Honig, Barry; Lozanovski, Vladimir J; Salomon, Rémi; Heidet, Laurence; Carpentier, Wassila; Gaillard, Dominique; Carrea, Alba; Gesualdo, Loreto; Cusi, Daniele; Izzi, Claudia; Scolari, Francesco; van Wijk, Joanna A E; Arapovic, Adela; Saraga-Babic, Mirna; Saraga, Marijan; Kunac, Nenad; Samii, Ali; McDonald-McGinn, Donna M; Crowley, Terrence B; Zackai, Elaine H; Drozdz, Dorota; Miklaszewska, Monika; Tkaczyk, Marcin; Sikora, Przemyslaw; Szczepanska, Maria; Mizerska-Wasiak, Malgorzata; Krzemien, Grazyna; Szmigielska, Agnieszka; Zaniew, Marcin; Darlow, John M; Puri, Prem; Barton, David; Casolari, Emilio; Furth, Susan L; Warady, Bradley A; Gucev, Zoran; Hakonarson, Hakon; Flogelova, Hana; Tasic, Velibor; Latos-Bielenska, Anna; Materna-Kiryluk, Anna; Allegri, Landino; Wong, Craig S; Drummond, Iain A; D'Agati, Vivette; Imamoto, Akira; Barasch, Jonathan M; Hildebrandt, Friedhelm; Kiryluk, Krzysztof; Lifton, Richard P; Morrow, Bernice E; Jeanpierre, Cecile; Papaioannou, Virginia E; Ghiggeri, Gian Marco; Gharavi, Ali G; Katsanis, Nicholas; Sanna-Cherchi, Simone

2017-02-23

The DiGeorge syndrome, the most common of the microdeletion syndromes, affects multiple organs, including the heart, the nervous system, and the kidney. It is caused by deletions on chromosome 22q11.2; the genetic driver of the kidney defects is unknown. We conducted a genomewide search for structural variants in two cohorts: 2080 patients with congenital kidney and urinary tract anomalies and 22,094 controls. We performed exome and targeted resequencing in samples obtained from 586 additional patients with congenital kidney anomalies. We also carried out functional studies using zebrafish and mice. We identified heterozygous deletions of 22q11.2 in 1.1% of the patients with congenital kidney anomalies and in 0.01% of population controls (odds ratio, 81.5; P=4.5×10 -14 ). We localized the main drivers of renal disease in the DiGeorge syndrome to a 370-kb region containing nine genes. In zebrafish embryos, an induced loss of function in snap29, aifm3, and crkl resulted in renal defects; the loss of crkl alone was sufficient to induce defects. Five of 586 patients with congenital urinary anomalies had newly identified, heterozygous protein-altering variants, including a premature termination codon, in CRKL. The inactivation of Crkl in the mouse model induced developmental defects similar to those observed in patients with congenital urinary anomalies. We identified a recurrent 370-kb deletion at the 22q11.2 locus as a driver of kidney defects in the DiGeorge syndrome and in sporadic congenital kidney and urinary tract anomalies. Of the nine genes at this locus, SNAP29, AIFM3, and CRKL appear to be critical to the phenotype, with haploinsufficiency of CRKL emerging as the main genetic driver. (Funded by the National Institutes of Health and others.).

Genetic Drivers of Kidney Defects in the DiGeorge Syndrome

PubMed Central

Lopez-Rivera, E.; Liu, Y.P.; Verbitsky, M.; Anderson, B.R.; Capone, V.P.; Otto, E.A.; Yan, Z.; Mitrotti, A.; Martino, J.; Steers, N.J.; Fasel, D.A.; Vukojevic, K.; Deng, R.; Racedo, S.E.; Liu, Q.; Werth, M.; Westland, R.; Vivante, A.; Makar, G.S.; Bodria, M.; Sampson, M.G.; Gillies, C.E.; Vega-Warner, V.; Maiorana, M.; Petrey, D.S.; Honig, B.; Lozanovski, V.J.; Salomon, R.; Heidet, L.; Carpentier, W.; Gaillard, D.; Carrea, A.; Gesualdo, L.; Cusi, D.; Izzi, C.; Scolari, F.; van Wijk, J.A.E.; Arapovic, A.; Saraga-Babic, M.; Saraga, M.; Kunac, N.; Samii, A.; McDonald-McGinn, D.M.; Crowley, T.B.; Zackai, E.H.; Drozdz, D.; Miklaszewska, M.; Tkaczyk, M.; Sikora, P.; Szczepanska, M.; Mizerska-Wasiak, M.; Krzemien, G.; Szmigielska, A.; Zaniew, M.; Darlow, J.M.; Puri, P.; Barton, D.; Casolari, E.; Furth, S.L.; Warady, B.A.; Gucev, Z.; Hakonarson, H.; Flogelova, H.; Tasic, V.; Latos-Bielenska, A.; Materna-Kiryluk, A.; Allegri, L.; Wong, C.S.; Drummond, I.A.; D’Agati, V.; Imamoto, A.; Barasch, J.M.; Hildebrandt, F.; Kiryluk, K.; Lifton, R.P.; Morrow, B.E.; Jeanpierre, C.; Papaioannou, V.E.; Ghiggeri, G.M.; Gharavi, A.G.; Katsanis, N.; Sanna-Cherchi, S.

2017-01-01

BACKGROUND The DiGeorge syndrome, the most common of the microdeletion syndromes, affects multiple organs, including the heart, the nervous system, and the kidney. It is caused by deletions on chromosome 22q11.2; the genetic driver of the kidney defects is unknown. METHODS We conducted a genomewide search for structural variants in two cohorts: 2080 patients with congenital kidney and urinary tract anomalies and 22,094 controls. We performed exome and targeted resequencing in samples obtained from 586 additional patients with congenital kidney anomalies. We also carried out functional studies using zebrafish and mice. RESULTS We identified heterozygous deletions of 22q11.2 in 1.1% of the patients with congenital kidney anomalies and in 0.01% of population controls (odds ratio, 81.5; P=4.5×10−14). We localized the main drivers of renal disease in the DiGeorge syndrome to a 370-kb region containing nine genes. In zebrafish embryos, an induced loss of function in snap29, aifm3, and crkl resulted in renal defects; the loss of crkl alone was sufficient to induce defects. Five of 586 patients with congenital urinary anomalies had newly identified, heterozygous protein-altering variants, including a premature termination codon, in CRKL. The inactivation of Crkl in the mouse model induced developmental defects similar to those observed in patients with congenital urinary anomalies. CONCLUSIONS We identified a recurrent 370-kb deletion at the 22q11.2 locus as a driver of kidney defects in the DiGeorge syndrome and in sporadic congenital kidney and urinary tract anomalies. Of the nine genes at this locus, SNAP29, AIFM3, and CRKL appear to be critical to the phenotype, with haploinsufficiency of CRKL emerging as the main genetic driver. (Funded by the National Institutes of Health and others.) PMID:28121514

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

PubMed

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

Research Data Management and Libraries: Relationships, Activities, Drivers and Influences

PubMed Central

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

'Mitominis': multiplex PCR analysis of reduced size amplicons for compound sequence analysis of the entire mtDNA control region in highly degraded samples.

PubMed

Eichmann, Cordula; Parson, Walther

2008-09-01

The traditional protocol for forensic mitochondrial DNA (mtDNA) analyses involves the amplification and sequencing of the two hypervariable segments HVS-I and HVS-II of the mtDNA control region. The primers usually span fragment sizes of 300-400 bp each region, which may result in weak or failed amplification in highly degraded samples. Here we introduce an improved and more stable approach using shortened amplicons in the fragment range between 144 and 237 bp. Ten such amplicons were required to produce overlapping fragments that cover the entire human mtDNA control region. These were co-amplified in two multiplex polymerase chain reactions and sequenced with the individual amplification primers. The primers were carefully selected to minimize binding on homoplasic and haplogroup-specific sites that would otherwise result in loss of amplification due to mis-priming. The multiplexes have successfully been applied to ancient and forensic samples such as bones and teeth that showed a high degree of degradation.

Estimating the over-involvement of suspended, revoked, and unlicensed drivers as at-fault drivers in California fatal crashes.

PubMed

Brar, Sukhvir S

2014-09-01

Quasi-induced exposure analysis was used to estimate annual fatal crash involvement rates for validly licensed, suspended or revoked (S/R), and unlicensed drivers in California from 1987 through 2009 using fatal crash data obtained from the National Highway Traffic Safety Administration's Fatality Analysis Reporting System and crash culpability determinations from the California Highway Patrol's Statewide Integrated Traffic Records System. Although there was some year-to-year fluctuation in the annual estimates, S/R and unlicensed drivers were over-involved as at-fault drivers in fatal crashes during every year of the 23-year time period relative to validly licensed drivers. The fatal crash involvement ratios combined across all years were 0.86 for validly licensed drivers, 2.23 for S/R drivers, and 2.34 for unlicensed drivers. Hence, compared to validly licensed drivers, the odds of being at-fault for a fatal crash were 160% higher for S/R drivers (involvement ratio=2.60) and 173% higher for unlicensed drivers (involvement ratio=2.73). The excess risks of S/R and unlicensed drivers are somewhat lower than estimates found in a prior study using the same technique, but the results nonetheless provide evidence that S/R and unlicensed drivers are much more hazardous on the road than are validly licensed drivers and emphasize the importance of using strong countermeasures-including vehicle impoundment-to reduce their high crash risk. These findings support interventions to help reduce driving among S/R and unlicensed drivers. Published by Elsevier Ltd.

The restless mind while driving: drivers' thoughts behind the wheel.

PubMed

Berthié, Gaëlle; Lemercier, Céline; Paubel, Pierre-Vincent; Cour, Maurice; Fort, Alexandra; Galéra, Cédric; Lagarde, Emmanuel; Gabaude, Catherine; Maury, Bertrand

2015-03-01

Recent research has clearly shown that inattention when driving has an indisputable impact on road safety. "Mind wandering" (MW), an inattentional state caused by a shift in attention from the ongoing task to inner thoughts, is not only frequent in everyday activities but also known to impact performance. There is a growing body of research investigating the concept of MW, suggesting potential causes that could foster such a phenomenon. Only one epidemiological study has focused on this issue in a critical driving context (Galéra et al., 2012), and it revealed the harmful effects of MW in increasing the risk of a car crash. Experimental studies rather consider that driver would adduce in MW (Lemercier et al., 2014). When the driving context is too hard or the thought too difficult to proceed, driver reduced their MW. The aim of this paper is to examine this issue using the most recent trip of ordinary drivers whose MW state did not lead to a road accident. Using a questionnaire, information was collected about the participants' most recent trip as a driver, including: (1) personal characteristics, (2) context in which MW occurs, (3) awareness of MW episodes and finally (4) characteristics of the thoughts. revealed that MW affected 85.2% of the drivers, who spent on average 34.74% of their trip in a MW state. Moreover, we found that the contexts which favor MW are situations in which less of the driver's attention is needed to drive, such as familiar commutes, monotonous motorways or by-passes, or when drivers were alone in their cars. In these MW situations, the drivers quickly became aware of their MW episodes. Thoughts tend to involve neutral private concerns, related to present- or future-oriented content. Our findings suggest that MW is a functional state aiming to solve current problems. Future investigations should focus on this critical concept of MW when driving, both to identify safety issues and to provide suitable solutions for drivers subject to a

Identifying climate drivers of infectious disease dynamics: recent advances and challenges ahead

PubMed Central

Walter, Katharine S.; Wesolowski, Amy; Buckee, Caroline O.; Shevliakova, Elena; Tatem, Andrew J.; Boos, William R.; Weinberger, Daniel M.; Pitzer, Virginia E.

2017-01-01

Climate change is likely to profoundly modulate the burden of infectious diseases. However, attributing health impacts to a changing climate requires being able to associate changes in infectious disease incidence with the potentially complex influences of climate. This aim is further complicated by nonlinear feedbacks inherent in the dynamics of many infections, driven by the processes of immunity and transmission. Here, we detail the mechanisms by which climate drivers can shape infectious disease incidence, from direct effects on vector life history to indirect effects on human susceptibility, and detail the scope of variation available with which to probe these mechanisms. We review approaches used to evaluate and quantify associations between climate and infectious disease incidence, discuss the array of data available to tackle this question, and detail remaining challenges in understanding the implications of climate change for infectious disease incidence. We point to areas where synthesis between approaches used in climate science and infectious disease biology provide potential for progress. PMID:28814655

Identifying climate drivers of infectious disease dynamics: recent advances and challenges ahead.

PubMed

Metcalf, C Jessica E; Walter, Katharine S; Wesolowski, Amy; Buckee, Caroline O; Shevliakova, Elena; Tatem, Andrew J; Boos, William R; Weinberger, Daniel M; Pitzer, Virginia E

2017-08-16

Climate change is likely to profoundly modulate the burden of infectious diseases. However, attributing health impacts to a changing climate requires being able to associate changes in infectious disease incidence with the potentially complex influences of climate. This aim is further complicated by nonlinear feedbacks inherent in the dynamics of many infections, driven by the processes of immunity and transmission. Here, we detail the mechanisms by which climate drivers can shape infectious disease incidence, from direct effects on vector life history to indirect effects on human susceptibility, and detail the scope of variation available with which to probe these mechanisms. We review approaches used to evaluate and quantify associations between climate and infectious disease incidence, discuss the array of data available to tackle this question, and detail remaining challenges in understanding the implications of climate change for infectious disease incidence. We point to areas where synthesis between approaches used in climate science and infectious disease biology provide potential for progress. © 2017 The Authors.

"The little squealer" or "the virtual guardian angel"? Young drivers' and their parents' perspective on using a driver monitoring technology and its implications for parent-young driver communication.

PubMed

Guttman, Nurit; Gesser-Edelsburg, Anat

2011-02-01

In-vehicle driving monitoring technologies have the potential to enable young drivers to learn from self-assessment. However, their use is largely dependent on parental involvement. A total of 79 interviews were conducted with young drivers and parents regarding this technology and its use. Most had the experience of having an in-vehicle data recorder installed in the vehicle driven by the young drivers. Parents and the young drivers expressed both appreciation as well as reservations about its potential as a means to enhance the driving safety of young drivers. A surprising finding was that some parents did not check the feedback and said they relied on the young driver to do so. Main concerns related to privacy, parent-young driver relationship, self-esteem and confidence, constructive use of the feedback data, and the limitations of the documentation that can be done by the technology. Providing parents and young drivers with a support system and tools to discuss and utilize the feedback are underscored. Challenges include addressing the invasion of young drivers' privacy and gender differences, and using the monitoring-capacity of the technology to enhance safe driving practices. Implications for programs to enhance communication and a dialogical approach between parents and young drivers are discussed. Copyright © 2010 Elsevier Ltd. All rights reserved.

Prevalence of driver physical factors leading to unintentional lane departure crashes.

PubMed

Cicchino, Jessica B; Zuby, David S

2017-07-04

control. Active lane-keeping assist systems may need to be combined with in-vehicle driver monitoring to identify incapacitated drivers and safely remove them from the roadway if the systems are to reach their maximum potential benefit.

A comparison of drug use in driver fatalities and similarly exposed drivers

DOT National Transportation Integrated Search

1977-07-01

Author's abstract: Crash information, urine, blood and bile samples from 900 fatally injured drivers were collected by medical examiners in 22 areas of the country. Randomly selected living drivers were interviewed at times and places of recent fatal...

Association between older driver characteristics, on-road driving test performance, and crash liability.

PubMed

Keall, Michael D; Frith, William J

2004-06-01

From May 1999, a new system for licensing older drivers was introduced in New Zealand. It included a practical on-road driving test with expanded scope, to be completed every two years from the time the driver turns 80. The relationship between crashes and test performance needed to be studied to inform the debate regarding the testing system. The population studied was all drivers who entered this licensing system during its first three years of operation. They were defined as crash involved if they were involved in an injury crash during the two years following their first licensure under the new system. Logistic regression was used to describe the risk of crash involvement in terms of driving test performance and other driver characteristics. Each driving test failure was associated with a 33% increase in the odds of crash involvement (95% CI 14% to 55%), controlling for age, gender, minor traffic violations, and whether the older driver lived with another licensed driver or not. Minor traffic violations in the two years following the driving test were associated with twice the odds of crash involvement. These results suggest that the new on-road driving test does identify older driver behaviors or limitations that are related to crash liability. It is anticipated that the results presented here will provide essential information for discussing older driver licensing systems, whose impact will grow in importance as the population of drivers ages.

Developing de novo human artificial chromosomes in embryonic stem cells using HSV-1 amplicon technology.

PubMed

Moralli, Daniela; Monaco, Zoia L

2015-02-01

De novo artificial chromosomes expressing genes have been generated in human embryonic stem cells (hESc) and are maintained following differentiation into other cell types. Human artificial chromosomes (HAC) are small, functional, extrachromosomal elements, which behave as normal chromosomes in human cells. De novo HAC are generated following delivery of alpha satellite DNA into target cells. HAC are characterized by high levels of mitotic stability and are used as models to study centromere formation and chromosome organisation. They are successful and effective as gene expression vectors since they remain autonomous and can accommodate larger genes and regulatory regions for long-term expression studies in cells unlike other viral gene delivery vectors currently used. Transferring the essential DNA sequences for HAC formation intact across the cell membrane has been challenging for a number of years. A highly efficient delivery system based on HSV-1 amplicons has been used to target DNA directly to the ES cell nucleus and HAC stably generated in human embryonic stem cells (hESc) at high frequency. HAC were detected using an improved protocol for hESc chromosome harvesting, which consistently produced high-quality metaphase spreads that could routinely detect HAC in hESc. In tumour cells, the input DNA often integrated in the host chromosomes, but in the host ES genome, it remained intact. The hESc containing the HAC formed embryoid bodies, generated teratoma in mice, and differentiated into neuronal cells where the HAC were maintained. The HAC structure and chromatin composition was similar to the endogenous hESc chromosomes. This review will discuss the technological advances in HAC vector delivery using HSV-1 amplicons and the improvements in the identification of de novo HAC in hESc.

Motor vehicle driver injury and socioeconomic status: a cohort study with prospective and retrospective driver injuries

PubMed Central

Whitlock, G; Norton, R; Clark, T; Pledger, M; Jackson, R; MacMahon, S

2003-01-01

Study objective: To investigate the association between motor vehicle driver injury and socioeconomic status. Design: Cohort study with prospective and retrospective outcomes. Setting: New Zealand. Participants: 10 525 adults (volunteer sample of a multi-industry workforce, n=8008; and a random sample of urban electoral rolls, n=2517). Outcome measure: Motor vehicle driver injury resulting in admission of the driver to hospital or the driver's death, or both, during the period 1988–98; hospitalisation and mortality data were obtained by record linkage to national health databases. Main results: After adjustment for age and sex, driver injury risk was inversely associated with both occupational status (p for linear trend <0.0001) and educational level (p for linear trend =0.007). Participants in the lowest approximate quartile of occupational status were four times as likely (HR 4.17, 95% CI 2.31 to 7.55) to have experienced a driver injury during follow up as participants in the highest approximate quartile. Participants who had been to secondary school for less than two years were twice as likely (HR 2.26, 95% CI 1.34 to 3.81) to have experienced a driver injury as those who had been to university or polytechnic. There was little evidence that driver injury risk was associated with neighbourhood income (p for linear trend =0.12) Conclusions: Occupational status and educational level seem to be important determinants of driver injury risk. Driver injury countermeasures should be targeted to people in low status occupations, as well as to people with comparatively little formal education. PMID:12821697

Drivers of Rift Valley fever epidemics in Madagascar.

PubMed

Lancelot, Renaud; Béral, Marina; Rakotoharinome, Vincent Michel; Andriamandimby, Soa-Fy; Héraud, Jean-Michel; Coste, Caroline; Apolloni, Andrea; Squarzoni-Diaw, Cécile; de La Rocque, Stéphane; Formenty, Pierre B H; Bouyer, Jérémy; Wint, G R William; Cardinale, Eric

2017-01-31

Rift Valley fever (RVF) is a vector-borne viral disease widespread in Africa. The primary cycle involves mosquitoes and wild and domestic ruminant hosts. Humans are usually contaminated after contact with infected ruminants. As many environmental, agricultural, epidemiological, and anthropogenic factors are implicated in RVF spread, the multidisciplinary One Health approach was needed to identify the drivers of RVF epidemics in Madagascar. We examined the environmental patterns associated with these epidemics, comparing human and ruminant serological data with environmental and cattle-trade data. In contrast to East Africa, environmental drivers did not trigger the epidemics: They only modulated local Rift Valley fever virus (RVFV) transmission in ruminants. Instead, RVFV was introduced through ruminant trade and subsequent movement of cattle between trade hubs caused its long-distance spread within the country. Contact with cattle brought in from infected districts was associated with higher infection risk in slaughterhouse workers. The finding that anthropogenic rather than environmental factors are the main drivers of RVF infection in humans can be used to design better prevention and early detection in the case of RVF resurgence in the region.

Microbial Diversity in Commercial Bee Pollen from Europe, Chile, and Mexico, Based on 16S rRNA Gene Amplicon Metagenome Sequencing

PubMed Central

Moreno Andrade, Vicente D.; Saldaña Gutiérrez, Carlos; Calvillo Medina, Rosa P.; Cruz Hérnandez, Andrés; Vázquez Cruz, Moisés A.; Torres Ruíz, Alfonso; Romero Gómez, Sergio; Ramos López, Miguel A.; Álvarez-Hidalgo, Erika; López-Gaytan, Silvia B.; Ramírez, Natanahel Salvador; Jones, George H.

2018-01-01

ABSTRACT Bee pollen is a highly nutritive natural foodstuff. Because of its use as a comestible, the association of bacteria with bee pollen is commercially and biologically important. We report here the bacterial diversity of seven bee pollen samples (five from Europe, one from Chile, and one from Mexico) based on 16S rRNA gene amplicon metagenome sequencing. PMID:29773615

Factors associated with civilian drivers involved in crashes with emergency vehicles.

PubMed

Drucker, Christopher; Gerberich, Susan G; Manser, Michael P; Alexander, Bruce H; Church, Timothy R; Ryan, Andrew D; Becic, Ensar

2013-06-01

Motor vehicle crashes involving civilian and emergency vehicles (EVs) have been a known problem that contributes to fatal and nonfatal injuries; however, characteristics associated with civilian drivers have not been examined adequately. This study used data from The National Highway Traffic Safety Administration's Fatality Analysis Reporting System and the National Automotive Sampling System General Estimates System to identify driver, roadway, environmental, and crash factors, and consequences for civilian drivers involved in fatal and nonfatal crashes with in-use and in-transport EVs. In general, drivers involved in emergency-civilian crashes (ECCs) were more often driving: straight through intersections (vs. same direction) of four-points or more (vs. not at intersection); where traffic signals were present (vs. no traffic control device); and at night (vs. midday). For nonfatal ECCs, drivers were more often driving: distracted (vs. not distracted); with vision obstructed by external objects (vs. no obstruction); on dark but lighted roads (vs. daylight); and in opposite directions (vs. same directions) of the EVs. Consequences included increased risk of injury (vs. no injury) and receiving traffic violations (vs. no violation). Fatal ECCs were associated with driving on urban roads (vs. rural), although these types of crashes were less likely to occur on dark roads (vs. daylight). The findings of this study suggest drivers may have difficulties in visually detecting EVs in different environments. Copyright © 2013 Elsevier Ltd. All rights reserved.

Myocardial infarction among male bus, taxi, and lorry drivers in middle Sweden.

PubMed Central

Gustavsson, P; Alfredsson, L; Brunnberg, H; Hammar, N; Jakobsson, R; Reuterwall, C; Ostlin, P

1996-01-01

OBJECTIVES: The aim of the present case-referent study was to investigate the incidence of myocardial infarction among male professional drivers, taking the type of vehicles and area of residence into account. METHODS: The study base comprised all men aged 30-74 in five counties in middle Sweden during 1976-81 or 1976-84. Incident cases of the first episode of myocardial infarction were identified from registers of hospital admissions and causes of deaths. Referents were selected randomly from the study base. Information about occupation was obtained from the national censuses in 1970 and 1975. The possible impact from tobacco smoking and overweight were evaluated by simulations in combination with indirect data on these factors. RESULTS: The incidence of myocardial infarction was increased among bus drivers in Stockholm (relative risk (RR) = 1.53, 95% confidence interval (95% CI) 1.15-2.05), and among taxi drivers both in Stockholm (RR 1.65, 95% CI 1.30-2.11) and in the surrounding rural counties (RR 1.82, 95% CI 1.17-2.82). A smaller increase was found among long distance lorry drivers, whereas the relative risk among short distance lorry drivers was close to unity. Indirect comparisons make it unlikely that the excess among bus drivers in Stockholm could be explained by uncontrolled confounding from tobacco smoking or overweight. A very high proportion (more than 80%) of urban bus drivers in Sweden report a combination of high psychological demands and low control at work. CONCLUSIONS: Different types of drivers are at different risk of myocardial infarction. Bus drivers in urban areas seem to be at an increased risk, which is unlikely to be explained by uncontrolled confounding from tobacco smoking or overweight. Psychosocial work conditions may play a part in the increased incidence of myocardial infarction among urban bus drivers and should be investigated further. PMID:8664960

Taxonomy of Older Driver Behaviors and Crash Risk : Appendix C

DOT National Transportation Integrated Search

2012-02-01

This projects objectives were to identify risky behaviors, driving habits, and exposure patterns that have been shown to increase the likelihood of crash involvement among older drivers; and to classify these crash-contributing factors according t...

The demographics of drivers and victims involved in traffic accidents

DOT National Transportation Integrated Search

1982-11-01

This staff paper develops a study approach to identify the : demographics of drivers and victims involved in traffic : accidents. Such an identification assists in directing safety : campaigns at those specific demographic groups which are most : lik...

Taxonomy of Older Driver Behaviors and Crash Risk : Appendix D

DOT National Transportation Integrated Search

2012-02-01

This projects objectives were to identify risky behaviors, driving habits, and exposure patterns that have been shown to increase the likelihood of crash involvement among older drivers; and to classify these crash-contributing factors according t...

Identification of novel mutational drivers reveals oncogene dependencies in multiple myeloma.

PubMed

Walker, Brian A; Mavrommatis, Konstantinos; Wardell, Christopher P; Ashby, T Cody; Bauer, Michael; Davies, Faith E; Rosenthal, Adam; Wang, Hongwei; Qu, Pingping; Hoering, Antje; Samur, Mehmet; Towfic, Fadi; Ortiz, Maria; Flynt, Erin; Yu, Zhinuan; Yang, Zhihong; Rozelle, Dan; Obenauer, John; Trotter, Matthew; Auclair, Daniel; Keats, Jonathan; Bolli, Niccolo; Fulciniti, Mariateresa; Szalat, Raphael; Moreau, Philippe; Durie, Brian; Stewart, A Keith; Goldschmidt, Hartmut; Raab, Marc S; Einsele, Hermann; Sonneveld, Pieter; San Miguel, Jesus; Lonial, Sagar; Jackson, Graham H; Anderson, Kenneth C; Avet-Loiseau, Herve; Munshi, Nikhil; Thakurta, Anjan; Morgan, Gareth J

2018-06-08

Understanding the profile of oncogene and tumor suppressor gene mutations with their interactions and impact on the prognosis of multiple myeloma (MM) can improve the definition of disease subsets and identify pathways important in disease pathobiology. Using integrated genomics of 1,273 newly diagnosed patients with multiple myeloma we identify 63 driver genes, some of which are novel including IDH1 , IDH2 , HUWE1 , KLHL6 , and PTPN11 Oncogene mutations are significantly more clonal than tumor suppressor mutations, indicating they may exert a bigger selective pressure. Patients with more mutations in driver genes are associated with a worse outcome, as are those with identified mechanisms of genomic instability. Oncogenic dependencies were identified between mutations in driver genes, common regions of copy number change, and primary translocation and hyperdiploidy events. These dependencies included associations with t(4;14) and mutations in FGFR3 , DIS3 and PRKD2 ; t(11;14) with mutations in CCND1 and IRF4 ; t(14;16) with mutations in MAF , BRAF , DIS3 and ATM ; and hyperdiploidy with gain 11q, mutations in FAM46C and MYC rearrangements. These associations indicate that the genomic landscape of myeloma is pre-determined by the primary events upon which further dependencies are built, giving rise to a non-random accumulation of genetic hits. Understanding these dependencies may elucidate potential evolutionary patterns and lead to better treatment regimens. Copyright © 2018 American Society of Hematology.

Drinking Drivers and Drug Use on Weekend Nights in the United States*

PubMed Central

Voas, Robert B.; Lacey, John H.; Jones, Kristina; Scherer, Michael; Compton, Richard

2012-01-01

BACKGROUND Studies of drinking drivers in alcohol-related crashes have shown that high breath-alcohol concentrations (BrACs) are associated with illegal drug use. Until the 2007 National Roadside Survey (NRS), the prevalence of drugs among drinking drivers on U.S. roads was unknown. Using NRS data, we explore how many drivers with positive BrACs may also be using drugs and their significance to current drinking-driving enforcement procedures. METHODS Based on a stratified, random sample covering the 48 U.S. contiguous states, we conducted surveys on weekend nights from July-November 2007. Of the 8,384 eligible motorists contacted, 85.4% provided a breath sample; 70.0%, an oral fluid sample; and 39.1%, a blood sample. We conducted regression analyses on 5,912 participants with a breath test and an oral fluid or blood test. The dependent variables of interest were illegal drugs (cocaine, cannabinoids, street drugs, street amphetamines, and opiates) and medicinal drugs (prescription and over-the-counter). RESULTS 10.5% of nondrinking drivers were using illegal drugs, and 26 to 33% of drivers with illegal BrACs (≥.08 g/dL) were using illegal drugs. Medicinal drug use was more common among nondrinking drivers (4.0%) than among drivers with illegal BrACs (2.4%). CONCLUSIONS The significant relationship between an illegal BrAC and the prevalence of an illegal drug suggests as many as 350,000 illegal drug-using drivers are arrested each year for DWI by U.S. alcohol-impaired driving enforcement. These drug-using drivers need to be identified and appropriate sanctions/treatment programs implemented for them in efforts to extend per se laws to unapprehended drug users. PMID:23265090

Experimental Research in Boost Driver with EDLCs

NASA Astrophysics Data System (ADS)

Matsumoto, Hirokazu

The supply used in servo systems tends to have a high voltage in order to reduce loss and improve the response of motor drives. We propose a new boost motor driver that comprises EDLCs. The proposed driver has a simple structure, wherein the EDLCs are connected in series to the supply, and comprises a charge circuit to charge the EDLCs. The proposed driver has three advantages over conventional boost drivers. The first advantage is that the driver can easily attain the stable boost voltage. The second advantage is that the driver can reduce input power peaks. In a servo system, the input power peaks become greater than the rated power in order to accelerate the motor rapidly. This implies that the equipments that supply power to servo systems must have sufficient power capacity to satisfy the power peaks. The proposed driver can suppress the increase of the power capacity of supply facilities. The third advantage is that the driver can store almost all of the regenerative energy. Conventional drivers have a braking resistor to suppress the increase in the DC link voltage. This causes a considerable reduction in the efficiency. The proposed driver is more efficient than conventional drivers. In this study, the experimental results confirmed the effectiveness of the proposed driver and showed that the drive performance of the proposed driver is the same as that of a conventional driver. Furthermore, it was confirmed that the results of the simulation of a model of the EDLC module, whose capacitance is dependent on the frequency, correspond well with the experimental results.

Investigation of Microbial Diversity in Geothermal Hot Springs in Unkeshwar, India, Based on 16S rRNA Amplicon Metagenome Sequencing.

PubMed

Mehetre, Gajanan T; Paranjpe, Aditi; Dastager, Syed G; Dharne, Mahesh S

2016-02-25

Microbial diversity in geothermal waters of the Unkeshwar hot springs in Maharashtra, India, was studied using 16S rRNA amplicon metagenomic sequencing. Taxonomic analysis revealed the presence of Bacteroidetes, Proteobacteria, Cyanobacteria, Actinobacteria, Archeae, and OD1 phyla. Metabolic function prediction analysis indicated a battery of biological information systems indicating rich and novel microbial diversity, with potential biotechnological applications in this niche. Copyright © 2016 Mehetre et al.

Effects of major-road vehicle speed and driver age and gender on left-turn gap acceptance.

PubMed

Yan, Xuedong; Radwan, Essam; Guo, Dahai

2007-07-01

Because the driver's gap-acceptance maneuver is a complex and risky driving behavior, it is a highly concerned topic for traffic safety and operation. Previous studies have mainly focused on the driver's gap acceptance decision itself but did not pay attention to the maneuver process and driving behaviors. Using a driving simulator experiment for left-turn gap acceptance at a stop-controlled intersection, this study evaluated the effects of major traffic speed and driver age and gender on gap acceptance behaviors. The experiment results illustrate relationships among drivers' left-turn gap decision, driver's acceleration rate, steering action, and the influence of the gap-acceptance maneuver on the vehicles in the major traffic stream. The experiment results identified an association between high crash risk and high traffic speed at stop-controlled intersections. The older drivers, especially older female drivers, displayed a conservative driving attitude as a compensation for reduced driving ability, but also showed to be the most vulnerable group for the relatively complex driving maneuvers.

Prevalence and factors associated with road traffic crash among taxi drivers in Hanoi, Vietnam.

PubMed

La, Quang Ngoc; Lee, Andy H; Meuleners, Lynn B; Van Duong, Dat

2013-01-01

Injury due to road traffic crash is a major cause of ill health and premature deaths in developing countries. Taxis provide a main mode of public transport in Vietnam but there has been little research on the risk of crash for taxi drivers. This retrospective study collected information on taxi crashes for the period 2006-2009 by interviewing drivers from five taxi companies in Hanoi, Vietnam, using a structured questionnaire. Of the total 1214 participants recruited, 276 drivers reported at least one crash, giving an overall crash prevalence of 22.7%. Among the crashed group, 50 drivers (18.1%) were involved in two to four crashes. Logistic regression analysis further identified age of driver, type of driving licence, employment status, perceived sufficiency of income, seat-belt usage, and traffic infringement history to be significantly associated with the crash risk. Further prospective and qualitative studies are recommended to provide detailed crash characteristics as well as behaviour and perception of taxi drivers, so that an effective intervention can be developed to improve road safety and to prevent injury of these commercial drivers. Copyright © 2012 Elsevier Ltd. All rights reserved.

Influence of professional drivers' personality traits on road traffic safety: case study.

PubMed

Živković, Snežana; Nikolić, Vesna; Markič, Mirko

2015-01-01

The purpose of this paper is to present basic elements of the research directed at identifying and determining the personality traits of professional drivers that affect safe, secure and enjoyable ride on public roads. A quantitative method has been used here, whereas data were acquired from a questionnaire based on a sample of 59 professional drivers. Determining personality traits of professional drivers that are in correlation with a safe and pleasant ride on the roads has been enabled by applying the five-factor model of personality ('Big Five') and the Personality Inventory NEO-PI. From these results it was concluded that safe operation of the vehicle in traffic involves the successful 'conduct' of oneself, which recognises the importance of certain personality traits of professional drivers for traffic safety and the need for appropriate professional selection in the case of employment of professional drivers. Research results implicate development of educational programmes aimed at achieving harmony of psychological, physical and sensory health, that is, programmes for permanent informing, educating and training professional drivers for defensive driving. The research opens the way for new research tasks that should help in creating a specific structure of curricula that can be used in a variety of transportation companies and enterprises to improve general and public safety.

Prospect theory based estimation of drivers' risk attitudes in route choice behaviors.

PubMed

Zhou, Lizhen; Zhong, Shiquan; Ma, Shoufeng; Jia, Ning

2014-12-01

This paper applied prospect theory (PT) to describe drivers' route choice behavior under Variable Message Sign (VMS), which presented visual traffic information to assist them to make route choice decisions. A quite rich empirical data from questionnaire and field spot was used to estimate parameters of PT. In order to make the parameters more realistic with drivers' attitudes, they were classified into different types by significant factors influencing their behaviors. Based on the travel time distribution of alternative routes and route choice results from questionnaire, the parameterized value function of each category was figured out, which represented drivers' risk attitudes and choice characteristics. The empirical verification showed that the estimates were acceptable and effective. The result showed drivers' risk attitudes and route choice characteristics could be captured by PT under real-time information shown on VMS. For practical application, once drivers' route choice characteristics and parameters were identified, their route choice behavior under different road conditions could be predicted accurately, which was the basis of traffic guidance measures formulation and implementation for targeted traffic management. Moreover, the heterogeneous risk attitudes among drivers should be considered when releasing traffic information and regulating traffic flow. Copyright © 2014 Elsevier Ltd. All rights reserved.

Online driver's license renewal.

DOT National Transportation Integrated Search

2015-09-01

The Kentucky Department of Vehicle Regulation is exploring the possibility of developing and implementing online : drivers license renewal. The objective of this project was to: 1) evaluate online drivers license and REAL ID renewal : programs ...

Machine learning methods for locating re-entrant drivers from electrograms in a model of atrial fibrillation

NASA Astrophysics Data System (ADS)

McGillivray, Max Falkenberg; Cheng, William; Peters, Nicholas S.; Christensen, Kim

2018-04-01

Mapping resolution has recently been identified as a key limitation in successfully locating the drivers of atrial fibrillation (AF). Using a simple cellular automata model of AF, we demonstrate a method by which re-entrant drivers can be located quickly and accurately using a collection of indirect electrogram measurements. The method proposed employs simple, out-of-the-box machine learning algorithms to correlate characteristic electrogram gradients with the displacement of an electrogram recording from a re-entrant driver. Such a method is less sensitive to local fluctuations in electrical activity. As a result, the method successfully locates 95.4% of drivers in tissues containing a single driver, and 95.1% (92.6%) for the first (second) driver in tissues containing two drivers of AF. Additionally, we demonstrate how the technique can be applied to tissues with an arbitrary number of drivers. In its current form, the techniques presented are not refined enough for a clinical setting. However, the methods proposed offer a promising path for future investigations aimed at improving targeted ablation for AF.

Underbelly injury based identification of the driver in a three-rider motorcycle accident.

PubMed

Liu, Shengxiong; Yin, Zhiyong; Su, Sen; Li, Kui

2016-01-01

This paper presents a three-rider motorcycle accident which took place in a suburb of Chongqing China. In the accident, the motorcycle impacted the terminal of a bridge footpath and led to two riders died and one rider injured. After the accident, one rider received injuries around the groin area including the underbelly area and the perineum area. Another rider suffered from injuries only on the perineum areas. In medico-legal judgments, injuries around the groin area also called groin injuries in victims of motorcycle accidents are usually regarded as "fuel tank injuries" which are commonly found in drivers. But, the injuries around the groin area are sometimes confused with the perineum injuries. Therefore, the perineum injuries are often wrongly reckoned as the "fuel tank injuries" and used to identify the drivers too. Actually, passengers can sometimes suffer from perineum injuries in many head-on impacting motorcycle accidents. It is of vital matters to understand the differences between groin injuries and perineum injuries so that the real driver who should be responsible for the accident can be recognized. In this paper, the three-rider motorcycle accident was presented and the injury information of the three riders was studied in order to distinguish the real driver from the riders. We consider that the groin injury has some differences with the perineum injury and the latter should not always be related to the driver especially in high-speed head-on impacting motorcycle accidents. In addition, the injury on underbelly areas is important to identify the driver. Crown Copyright © 2015. Published by Elsevier Ireland Ltd. All rights reserved.

Analysis of injury severity of drivers involved in single- and two-vehicle crashes on highways in Ontario.

PubMed

Lee, Chris; Li, Xuancheng

2014-10-01

This study analyzes driver's injury severity in single- and two-vehicle crashes and compares the effects of explanatory variables among various types of crashes. The study identified factors affecting injury severity and their effects on severity levels using 5-year crash records for provincial highways in Ontario, Canada. Considering heteroscedasticity in the effects of explanatory variables on injury severity, the heteroscedastic ordered logit (HOL) models were developed for single- and two-vehicle crashes separately. The results of the models show that there exists heteroscedasticity for young drivers (≤30), safety equipment and ejection in the single-vehicle crash model, and female drivers, safety equipment and head-on collision in the two-vehicle crash models. The results also show that young car drivers have opposite effects between single-car and car-car crashes, and sideswipe crashes have opposite effects between car-car and truck-truck crashes. The study demonstrates that separate HOL models for single-vehicle and different types of two-vehicle crashes can identify differential effects of factors on driver's injury severity. Copyright © 2014 Elsevier Ltd. All rights reserved.

Evaluating Older Drivers' Skills

DOT National Transportation Integrated Search

2013-05-01

Research has demonstrated that older drivers pose a higher risk of involvement in fatal crashes at intersections than : younger drivers. Age-triggered restrictions are problematic as research shows that the majority of older people : have unimpaired ...

Predicting performance and safety based on driver fatigue.

PubMed

Mollicone, Daniel; Kan, Kevin; Mott, Chris; Bartels, Rachel; Bruneau, Steve; van Wollen, Matthew; Sparrow, Amy R; Van Dongen, Hans P A

2018-04-02

Fatigue causes decrements in vigilant attention and reaction time and is a major safety hazard in the trucking industry. There is a need to quantify the relationship between driver fatigue and safety in terms of operationally relevant measures. Hard-braking events are a suitable measure for this purpose as they are relatively easily observed and are correlated with collisions and near-crashes. We developed an analytic approach that predicts driver fatigue based on a biomathematical model and then estimates hard-braking events as a function of predicted fatigue, controlling for time of day to account for systematic variations in exposure (traffic density). The analysis used de-identified data from a previously published, naturalistic field study of 106 U.S. commercial motor vehicle (CMV) drivers. Data analyzed included drivers' official duty logs, sleep patterns measured around the clock using wrist actigraphy, and continuous recording of vehicle data to capture hard-braking events. The curve relating predicted fatigue to hard-braking events showed that the frequency of hard-braking events increased as predicted fatigue levels worsened. For each increment on the fatigue scale, the frequency of hard-braking events increased by 7.8%. The results provide proof of concept for a novel approach that predicts fatigue based on drivers' sleep patterns and estimates driving performance in terms of an operational metric related to safety. The approach can be translated to practice by CMV operators to achieve a fatigue risk profile specific to their own settings, in order to support data-driven decisions about fatigue countermeasures that cost-effectively deliver quantifiable operational benefits. Copyright © 2018 Elsevier Ltd. All rights reserved.

Identification of mutated driver pathways in cancer using a multi-objective optimization model.

PubMed

Zheng, Chun-Hou; Yang, Wu; Chong, Yan-Wen; Xia, Jun-Feng

2016-05-01

New-generation high-throughput technologies, including next-generation sequencing technology, have been extensively applied to solve biological problems. As a result, large cancer genomics projects such as the Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium are producing large amount of rich and diverse data in multiple cancer types. The identification of mutated driver genes and driver pathways from these data is a significant challenge. Genome aberrations in cancer cells can be divided into two types: random 'passenger mutation' and functional 'driver mutation'. In this paper, we introduced a Multi-objective Optimization model based on a Genetic Algorithm (MOGA) to solve the maximum weight submatrix problem, which can be employed to identify driver genes and driver pathways promoting cancer proliferation. The maximum weight submatrix problem defined to find mutated driver pathways is based on two specific properties, i.e., high coverage and high exclusivity. The multi-objective optimization model can adjust the trade-off between high coverage and high exclusivity. We proposed an integrative model by combining gene expression data and mutation data to improve the performance of the MOGA algorithm in a biological context. Copyright © 2016 Elsevier Ltd. All rights reserved.

Heavy vehicle driver workload assessment. Task 5, workload assessment protocol

DOT National Transportation Integrated Search

This report presents a description of a prescriptive workload assessment protocol for use in evaluating in-cab devices in heavy vehicles. The primary objective of this heavy vehicle driver workload assessment protocol is to identify the components an...

Model driver screening and evaluation program. Volume 2, Maryland pilot older driver study

DOT National Transportation Integrated Search

2003-05-01

This research project studied the feasibility as well as the scientific validity and utility of performing functional capacity screening with older drivers. A Model Program was described encompassing procedures to detect functionally impaired drivers...

Older drivers: On-road and off-road test results.

PubMed

Selander, Helena; Lee, Hoe C; Johansson, Kurt; Falkmer, Torbjörn

2011-07-01

Eighty-five volunteer drivers, 65-85 years old, without cognitive impairments impacting on their driving were examined, in order to investigate driving errors characteristic for older drivers. In addition, any relationships between cognitive off-road and on-road tests results, the latter being the gold standard, were identified. Performance measurements included Trail Making Test (TMT), Nordic Stroke Driver Screening Assessment (NorSDSA), Useful Field of View (UFOV), self-rating driving performance and the two on-road protocols P-Drive and ROA. Some of the older drivers displayed questionable driving behaviour. In total, 21% of the participants failed the on-road assessment. Some of the specific errors were more serious than others. The most common driving errors embraced speed; exceeding the speed limit or not controlling the speed. Correlations with the P-Drive protocol were established for NorSDSA total score (weak), UFOV subtest 2 (weak), and UFOV subtest 3 (moderate). Correlations with the ROA protocol were established for UFOV subtest 2 (weak) and UFOV subtest 3 (weak). P-Drive and self ratings correlated weakly, whereas no correlation between self ratings and the ROA protocol was found. The results suggest that specific problems or errors seen in an older person's driving can actually be "normal driving behaviours". Copyright © 2011 Elsevier Ltd. All rights reserved.

Functional annotation of rare gene aberration drivers of pancreatic cancer | Office of Cancer Genomics

Cancer.gov

As we enter the era of precision medicine, characterization of cancer genomes will directly influence therapeutic decisions in the clinic. Here we describe a platform enabling functionalization of rare gene mutations through their high-throughput construction, molecular barcoding and delivery to cancer models for in vivo tumour driver screens. We apply these technologies to identify oncogenic drivers of pancreatic ductal adenocarcinoma (PDAC).

Drivers and mechanisms of tree mortality in moist tropical forests.

PubMed

McDowell, Nate; Allen, Craig D; Anderson-Teixeira, Kristina; Brando, Paulo; Brienen, Roel; Chambers, Jeff; Christoffersen, Brad; Davies, Stuart; Doughty, Chris; Duque, Alvaro; Espirito-Santo, Fernando; Fisher, Rosie; Fontes, Clarissa G; Galbraith, David; Goodsman, Devin; Grossiord, Charlotte; Hartmann, Henrik; Holm, Jennifer; Johnson, Daniel J; Kassim, Abd Rahman; Keller, Michael; Koven, Charlie; Kueppers, Lara; Kumagai, Tomo'omi; Malhi, Yadvinder; McMahon, Sean M; Mencuccini, Maurizio; Meir, Patrick; Moorcroft, Paul; Muller-Landau, Helene C; Phillips, Oliver L; Powell, Thomas; Sierra, Carlos A; Sperry, John; Warren, Jeff; Xu, Chonggang; Xu, Xiangtao

2018-02-16

Tree mortality rates appear to be increasing in moist tropical forests (MTFs) with significant carbon cycle consequences. Here, we review the state of knowledge regarding MTF tree mortality, create a conceptual framework with testable hypotheses regarding the drivers, mechanisms and interactions that may underlie increasing MTF mortality rates, and identify the next steps for improved understanding and reduced prediction. Increasing mortality rates are associated with rising temperature and vapor pressure deficit, liana abundance, drought, wind events, fire and, possibly, CO 2 fertilization-induced increases in stand thinning or acceleration of trees reaching larger, more vulnerable heights. The majority of these mortality drivers may kill trees in part through carbon starvation and hydraulic failure. The relative importance of each driver is unknown. High species diversity may buffer MTFs against large-scale mortality events, but recent and expected trends in mortality drivers give reason for concern regarding increasing mortality within MTFs. Models of tropical tree mortality are advancing the representation of hydraulics, carbon and demography, but require more empirical knowledge regarding the most common drivers and their subsequent mechanisms. We outline critical datasets and model developments required to test hypotheses regarding the underlying causes of increasing MTF mortality rates, and improve prediction of future mortality under climate change. No claim to original US government works New Phytologist © 2018 New Phytologist Trust.

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

PubMed

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.

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

PubMed Central

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

A call to improve sampling methodology and reporting in young novice driver research.

PubMed

Scott-Parker, B; Senserrick, T

2017-02-01

Young drivers continue to be over-represented in road crash fatalities despite a multitude of research, communication and intervention. Evidence-based improvement depends to a great extent upon research methodology quality and its reporting, with known limitations in the peer-review process. The aim of the current research was to review the scope of research methodologies applied in 'young driver' and 'teen driver' research and their reporting in four peer-review journals in the field between January 2006 and December 2013. In total, 806 articles were identified and assessed. Reporting omissions included participant gender (11% of papers), response rates (49%), retention rates (39%) and information regarding incentives (44%). Greater breadth and specific improvements in study designs and reporting are thereby identified as a means to further advance the field. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Drivers license display system

NASA Astrophysics Data System (ADS)

Prokoski, Francine J.

1997-01-01

Carjackings are only one of a growing class of law enforcement problems associated with increasingly violent crimes and accidents involving automobiles plays weapons, drugs and alcohol. Police traffic stops have become increasingly dangerous, with an officer having no information about a vehicle's potentially armed driver until approaching him. There are 15 million alcoholics in the US and 90 percent of them have drivers licenses. Many of them continue driving even after their licenses have ben revoked or suspended. There are thousands of unlicensed truck drivers in the country, and also thousands who routinely exceed safe operating periods without rest; often using drugs in an attempt to stay alert. MIKOS has developed the Drivers License Display Systems to reduce these and other related risks. Although every state requires the continuous display of vehicle registration information on every vehicle using public roads, no state yet requires the display of driver license information. The technology exists to provide that feature as an add-on to current vehicles for nominal cost. An initial voluntary market is expected to include: municipal, rental, and high value vehicles which are most likely to be mis-appropriated. It is anticipated that state regulations will eventually require such systems in the future, beginning with commercial vehicles, and then extending to high risk drivers and eventually all vehicles. The MIKOS system offers a dual-display approach which can be deployed now, and which will utilize all existing state licenses without requiring standardization.

Untangling the drivers of nonlinear systems with information theory

NASA Astrophysics Data System (ADS)

Wing, S.; Johnson, J.

2017-12-01

Many systems found in nature are nonlinear. The drivers of the system are often nonlinearly correlated with one another, which makes it a challenge to understand the effects of an individual driver. For example, solar wind velocity (Vsw) and density (nsw) are both found to correlate well with radiation belt fluxes and are thought to be drivers of the magnetospheric dynamics; however, the Vsw is anti-correlated with nsw, which can potentially confuse interpretation of these relationships as causal or coincidental. Information theory can untangle the drivers of these systems, describe the underlying dynamics, and offer constraints to modelers and theorists, leading to better understanding of the systems. Two examples are presented. In the first example, the solar wind drivers of geosynchronous electrons with energy range of 1.8-3.5 MeV are investigated using mutual information (MI), conditional mutual information (CMI), and transfer entropy (TE). The information transfer from Vsw to geosynchronous MeV electron flux (Je) peaks with a lag time (t) of 2 days. As previously reported, Je is anticorrelated with nsw with a lag of 1 day. However, this lag time and anticorrelation can be attributed mainly to the Je(t + 2 days) correlation with Vsw(t) and nsw(t + 1 day) anticorrelation with Vsw(t). Analyses of solar wind driving of the magnetosphere need to consider the large lag times, up to 3 days, in the (Vsw, nsw) anticorrelation. Using CMI to remove the effects of Vsw, the response of Je to nsw is 30% smaller and has a lag time < 24 hr, suggesting that the loss mechanism due to nsw or solar wind dynamic pressure has to start operating in < 24 hr. nsw transfers about 36% as much information as Vsw (the primary driver) to Je. Nonstationarity in the system dynamics are investigated using windowed TE. When the data is ordered according to high or low transfer entropy it is possible to understand details of the triangle distribution that has been identified between Je(t + 2

Mass drivers. 3: Engineering

NASA Technical Reports Server (NTRS)

Arnold, W.; Bowen, S.; Cohen, S.; Fine, K.; Kaplan, D.; Kolm, M.; Kolm, H.; Newman, J.; Oneill, G. K.; Snow, W.

1979-01-01

The last of a series of three papers by the Mass-Driver Group of the 1977 Ames Summer Study is presented. It develops the engineering principles required to implement the basic mass-driver. Optimum component mass trade-offs are derived from a set of four input parameters, and the program used to design a lunar launcher. The mass optimization procedures is then incorporated into a more comprehensive mission optimization program called OPT-4, which evaluates an optimized mass-driver reaction engine and its performance in a range of specified missions. Finally, this paper discusses, to the extent that time permitted, certain peripheral problems: heating effects in buckets due to magnetic field ripple; an approximate derivation of guide force profiles; the mechanics of inserting and releasing payloads; the reaction mass orbits; and a proposed research and development plan for implementing mass drivers.

Microbial Diversity in Commercial Bee Pollen from Europe, Chile, and Mexico, Based on 16S rRNA Gene Amplicon Metagenome Sequencing.

PubMed

Moreno Andrade, Vicente D; Saldaña Gutiérrez, Carlos; Calvillo Medina, Rosa P; Cruz Hérnandez, Andrés; Vázquez Cruz, Moisés A; Torres Ruíz, Alfonso; Romero Gómez, Sergio; Ramos López, Miguel A; Álvarez-Hidalgo, Erika; López-Gaytan, Silvia B; Ramírez, Natanahel Salvador; Jones, George H; Hernandez-Flores, Jose Luis; Campos-Guillén, Juan

2018-05-17

Bee pollen is a highly nutritive natural foodstuff. Because of its use as a comestible, the association of bacteria with bee pollen is commercially and biologically important. We report here the bacterial diversity of seven bee pollen samples (five from Europe, one from Chile, and one from Mexico) based on 16S rRNA gene amplicon metagenome sequencing. Copyright © 2018 Moreno Andrade et al.

Final report on the portable computerized assessments of sleepy drivers in operational environments.

DOT National Transportation Integrated Search

2011-06-01

Excessive daytime sleepiness underpins a large number of the reported motor vehicle crashes. Fair and accurate field : measures are needed to identify at-risk drivers who have been identified as potentially driving in a sleep deprived state on : the ...

Transcending as a driver of development.

PubMed

Travis, Frederick

2016-06-01

This paper draws from three different bodies of research to discuss the hypothesis that age-appropriate experiences enhance brain and cognitive development throughout the life span. These age-appropriate experiences could be considered as the drivers of development at each age, including drivers to foster development beyond adult abstract thinking, as described in Piaget's formal operational stage. We explore how a nurturing caregiver is the driver in the first 2 years of life, how language learning is the driver from 3 to 10 years, and how problem solving is the driver in the teenage years. To develop beyond adult rational thinking, we suggest that the driver is transcending thought, which can result when practicing meditations in the automatic self-transcending category, such as Transcendental Meditation. © 2016 New York Academy of Sciences.

Participatory video-assisted evaluation of truck drivers' work outside cab: deliveries in two types of transport.

PubMed

Reiman, Arto; Pekkala, Janne; Väyrynen, Seppo; Putkonen, Ari; Forsman, Mikael

2014-01-01

The aim of this study was to identify risks and ergonomics discomfort during work of local and short haul delivery truck drivers outside a cab. The study used a video- and computer-based method (VIDAR). VIDAR is a participatory method identifying demanding work situations and their potential risks. The drivers' work was videoed and analysed by subjects and ergonomists. Delivery truck drivers should not be perceived as one group with equal risks because there were significant differences between the 2 types of transportation and specific types of risks. VIDAR produces visual material for risk management processes. VIDAR as a participatory approach stimulates active discussion about work-related risks and discomfort, and about possibilities for improvement. VIDAR may be also applied to work which comprises different working environments.

Impact of graduated driver licensing restrictions on crashes involving young drivers in New Zealand

PubMed Central

Begg, D; Stephenson, S; Alsop, J; Langley, J

2001-01-01

Objective—To determine the impact on young driver crashes of the three main driving restrictions in the New Zealand graduated driver licensing (GDL) system: night-time curfew, no carrying of young passengers, and a blood alcohol limit of 30 mg/100 ml. Method—The database for this study was created by linking police crash reports to hospital inpatient records (1980–95). Multivariate logistic regression was used to compare car crashes involving a young driver licensed before GDL (n=2252) with those who held a restricted graduated licence (n=980) and with those who held a full graduated licence (n=1273), for each of the main driving restrictions. Results—Compared with the pre-GDL group, the restricted licence drivers had fewer crashes at night (p=0.003), fewer involving passengers of all ages (p=0.018), and fewer where alcohol was suspected (p=0.034), but not fewer involving young casualties (p=0.980). Compared with the pre-GDL drivers, those with the full graduated licence had fewer night crashes (p=0.042) but did not differ significantly for any of the other factors examined. Conclusion—These results suggest that some of the GDL restrictions, especially the night-time curfew, have contributed to a reduction in serious crashes involving young drivers. PMID:11770654

Impact of graduated driver licensing restrictions on crashes involving young drivers in New Zealand.

PubMed

Begg, D J; Stephenson, S; Alsop, J; Langley, J

2001-12-01

To determine the impact on young driver crashes of the three main driving restrictions in the New Zealand graduated driver licensing (GDL) system: night-time curfew, no carrying of young passengers, and a blood alcohol limit of 30 mg/100 ml. The database for this study was created by linking police crash reports to hospital inpatient records (1980-95). Multivariate logistic regression was used to compare car crashes involving a young driver licensed before GDL (n=2,252) with those who held a restricted graduated licence (n=980) and with those who held a full graduated licence (n=1,273), for each of the main driving restrictions. Compared with the pre-GDL group, the restricted licence drivers had fewer crashes at night (p=0.003), fewer involving passengers of all ages (p=0.018), and fewer where alcohol was suspected (p=0.034), but not fewer involving young casualties (p=0.980). Compared with the pre-GDL drivers, those with the full graduated licence had fewer night crashes (p=0.042) but did not differ significantly for any of the other factors examined. These results suggest that some of the GDL restrictions, especially the night-time curfew, have contributed to a reduction in serious crashes involving young drivers.

New approach to real-time nucleic acids detection: folding polymerase chain reaction amplicons into a secondary structure to improve cleavage of Förster resonance energy transfer probes in 5′-nuclease assays

PubMed Central

Kutyavin, Igor V.

2010-01-01

The article describes a new technology for real-time polymerase chain reaction (PCR) detection of nucleic acids. Similar to Taqman, this new method, named Snake, utilizes the 5′-nuclease activity of Thermus aquaticus (Taq) DNA polymerase that cleaves dual-labeled Förster resonance energy transfer (FRET) probes and generates a fluorescent signal during PCR. However, the mechanism of the probe cleavage in Snake is different. In this assay, PCR amplicons fold into stem–loop secondary structures. Hybridization of FRET probes to one of these structures leads to the formation of optimal substrates for the 5′-nuclease activity of Taq. The stem–loop structures in the Snake amplicons are introduced by the unique design of one of the PCR primers, which carries a special 5′-flap sequence. It was found that at a certain length of these 5′-flap sequences the folded Snake amplicons have very little, if any, effect on PCR yield but benefit many aspects of the detection process, particularly the signal productivity. Unlike Taqman, the Snake system favors the use of short FRET probes with improved fluorescence background. The head-to-head comparison study of Snake and Taqman revealed that these two technologies have more differences than similarities with respect to their responses to changes in PCR protocol, e.g. the variations in primer concentration, annealing time, PCR asymmetry. The optimal PCR protocol for Snake has been identified. The technology’s real-time performance was compared to a number of conventional assays including Taqman, 3′-MGB-Taqman, Molecular Beacon and Scorpion primers. The test trial showed that Snake supersedes the conventional assays in the signal productivity and detection of sequence variations as small as single nucleotide polymorphisms. Due to the assay’s cost-effectiveness and simplicity of design, the technology is anticipated to quickly replace all known conventional methods currently used for real-time nucleic acid detection

Identifying types of drug intoxication : laboratory evaluation of a subject-examination procedure

DOT National Transportation Integrated Search

1985-05-01

The Los Angeles Police Department (LAPD) has developed a rating procedures for use in detecting drug-impaired drivers. The purpose of the rating procedures is to determine whether the driver is impaired and to identify the responsible drug class (e.g...

Drunk Driver Testing

NASA Technical Reports Server (NTRS)

1984-01-01

Systems Technology, Inc. developed a technique to study/measure behavioral changes brought on by long term isolation is now being used in a system for determining whether a driver is too drunk to drive. Device is intended to discourage intoxicated drivers from taking to the road by advising them they are in no condition to operate a vehicle. System is being tested experimentally in California.

Lone workers attitudes towards their health: views of Ontario truck drivers and their managers.

PubMed

McDonough, Beatrice; Howard, Michelle; Angeles, Ricardo; Dolovich, Lisa; Marzanek-Lefebvre, Francine; Riva, John J; Laryea, Stephanie

2014-05-14

Truck driving is the second most common occupation among Canadian men. Transportation of goods via roads is of crucial importance for the Canadian economy. The industry is responsible annually for $17 billion in GDP and is projected to increase by 28% over the next 10 years. Recruitment is an issue with 20% of drivers projected to retire or leave the profession in the next 10 years. Despite the reliance on transport truck drivers for the delivery of goods which affects Canada's economy and daily living of residents, little is known about the health care needs of this large cohort of primarily male lone workers from a drivers' perspective. Transport truck drivers are independent workers whose non traditional workplace is their tractor, the truck stops and the journey on the road.The objective of this study was to obtain a contextually informed description of lifestyle issues, health and disease risk factors experienced by drivers and perceived by their managers in the truck driving occupation. Using a grounded theory approach, 4 focus groups were conducted with drivers (n = 16) and managers (n = 10) from two trucking companies in Southwestern Ontario to identify the lived experience of the drivers as it relates to preventable risks to health and wellness. A semi structured guided interview was used to explore the lifestyle context of transport truck driving and organizational aspects of the occupation (workplace culture, working conditions and health and wellness promotion). The predominant themes described stress, workplace, communication, lifestyle, driving culture, family, and fatigue concerns. In terms of the transportation work environment, drivers and managers were aware of the profession's potential to foster lifestyle related chronic diseases but described challenges in making the profession more amenable to a healthy lifestyle. Workplace environmental determinants are significant in shaping health behaviours. Chronic disease health risks were the

Bacterial Degraders of Coexisting Dichloromethane, Benzene, and Toluene, Identified by Stable-Isotope Probing.

PubMed

Yoshikawa, Miho; Zhang, Ming; Kurisu, Futoshi; Toyota, Koki

2017-01-01

Most bioremediation studies on volatile organic compounds (VOCs) have focused on a single contaminant or its derived compounds and degraders have been identified under single contaminant conditions. Bioremediation of multiple contaminants remains a challenging issue. To identify a bacterial consortium that degrades multiple VOCs (dichloromethane (DCM), benzene, and toluene), we applied DNA-stable isotope probing. For individual tests, we combined a 13 C-labeled VOC with other two unlabeled VOCs, and prepared three unlabeled VOCs as a reference. Over 11 days, DNA was periodically extracted from the consortia, and the bacterial community was evaluated by next-generation sequencing of bacterial 16S rRNA gene amplicons. Density gradient fractions of the DNA extracts were amplified by universal bacterial primers for the 16S rRNA gene sequences, and the amplicons were analyzed by terminal restriction fragment length polymorphism (T-RFLP) using restriction enzymes: Hha I and Msp I. The T-RFLP fragments were identified by 16S rRNA gene cloning and sequencing. Under all test conditions, the consortia were dominated by Rhodanobacter , Bradyrhizobium / Afipia , Rhizobium , and Hyphomicrobium . DNA derived from Hyphomicrobium and Propioniferax shifted toward heavier fractions under the condition added with 13 C-DCM and 13 C-benzene, respectively, compared with the reference, but no shifts were induced by 13 C-toluene addition. This implies that Hyphomicrobium and Propioniferax were the main DCM and benzene degraders, respectively, under the coexisting condition. The known benzene degrader Pseudomonas sp. was present but not actively involved in the degradation.

Exploring the safety implications of young drivers' behavior, attitudes and perceptions.

PubMed

Hassan, Hany M; Abdel-Aty, Mohamed A

2013-01-01

The present study aims at identifying and quantifying significant factors (i.e., demographic, aberrant driving behavior) associated with young drivers' involvement in at-fault crashes or traffic citations at the ages of 16-17 (while having the Operational License) and 18-24 years old (while having the Full License). A second objective was to investigate the main reason(s) for involvement in risky driving behavior by young drivers. The data used for the analyses were obtained from a self-reported questionnaire survey carried out among 680 young drivers in Central Florida. To achieve these goals, the structural equation modeling approach was adopted. The results revealed that aggressive violations, in-vehicle distractions and demographic characteristics were the significant factors affecting young drivers' involvement in at-fault crashes or traffic violations at the age of 16-17. However, in-vehicle distractions, attitudes toward speeding and demographic characteristics were the significant factors affecting young drivers' crash risk at 18-24. Additionally, the majority of participants reported that "running late" is the main reason for taking risk while driving (i.e., speeding, accept short gaps, or drive so close to the car in front) followed by "racing other cars". Additionally, "exceed speed limits" was the main reason for receiving traffic citations at 16-17 and 18-24 age groups. Practical suggestions on how to reduce crash risk and promote safe driving among young drivers are also discussed. Copyright © 2012 Elsevier Ltd. All rights reserved.

National energy efficient driving system (NEEDS). Volume 2, Driver education program

DOT National Transportation Integrated Search

1981-12-15

Studies were conducted to identify young driver deficiencies in knowledge, attitude, and performance with respect to fuel-efficiency. Five different programs of classroom-only and classroom/in-car instruction were administered experimentally to high ...

The Candidate Cancer Gene Database: a database of cancer driver genes from forward genetic screens in mice.

PubMed

Abbott, Kenneth L; Nyre, Erik T; Abrahante, Juan; Ho, Yen-Yi; Isaksson Vogel, Rachel; Starr, Timothy K

2015-01-01

Identification of cancer driver gene mutations is crucial for advancing cancer therapeutics. Due to the overwhelming number of passenger mutations in the human tumor genome, it is difficult to pinpoint causative driver genes. Using transposon mutagenesis in mice many laboratories have conducted forward genetic screens and identified thousands of candidate driver genes that are highly relevant to human cancer. Unfortunately, this information is difficult to access and utilize because it is scattered across multiple publications using different mouse genome builds and strength metrics. To improve access to these findings and facilitate meta-analyses, we developed the Candidate Cancer Gene Database (CCGD, http://ccgd-starrlab.oit.umn.edu/). The CCGD is a manually curated database containing a unified description of all identified candidate driver genes and the genomic location of transposon common insertion sites (CISs) from all currently published transposon-based screens. To demonstrate relevance to human cancer, we performed a modified gene set enrichment analysis using KEGG pathways and show that human cancer pathways are highly enriched in the database. We also used hierarchical clustering to identify pathways enriched in blood cancers compared to solid cancers. The CCGD is a novel resource available to scientists interested in the identification of genetic drivers of cancer. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

The effects of sleep loss on young drivers' performance: A systematic review.

PubMed

Shekari Soleimanloo, Shamsi; White, Melanie J; Garcia-Hansen, Veronica; Smith, Simon S

2017-01-01

Young drivers (18-24 years) are over-represented in sleep-related crashes (comprising one in five fatal crashes in developed countries) primarily due to decreased sleep opportunity, lower tolerance for sleep loss, and ongoing maturation of brain areas associated with driving-related decision making. Impaired driving performance is the proximal reason for most car crashes. There is still a limited body of evidence examining the effects of sleep loss on young drivers' performance, with discrepancies in the methodologies used, and in the definition of outcomes. This study aimed to identify the direction and magnitude of the effects of sleep loss on young drivers' performance, and to appraise the quality of current evidence via a systematic review. Based on the Preferred Reporting Items for Systematic Reviews and Meta- Analyses (PRISMA) approach, 16 eligible studies were selected for review, and their findings summarised. Next, critical elements of these studies were identified, and the Grading of Recommendations Assessment, Development and Evaluation (GRADE) guidelines augmented to rate those elements. Using those criteria, the quality of individual papers was calculated and the overall body of evidence for each driving outcome were assigned a quality ranking (from 'very low' to 'high-quality'). Two metrics, the standard deviation of lateral position and number of line crossings, were commonly reported outcomes (although in an overall 'low-quality' body of evidence), with significant impairments after sleep loss identified in 50% of studies. While speed-related outcomes and crash events (also with very low- quality evidence) both increased under chronic sleep loss, discrepant findings were reported under conditions of acute total sleep deprivation. It is crucial to obtain more reliable data about the effects of sleep loss on young drivers' performance by using higher quality experimental designs, adopting common protocols, and the use of consistent metrics and

Driver fatigue and road safety on Poland's national roads.

PubMed

Jamroz, Kazimierz; Smolarek, Leszek

2013-01-01

This paper presents an overview of factors causing driver fatigue as described in the literature. Next, a traffic crash database for 2003-2007 is used to identify the causes, circumstances and consequences of accidents caused by driver fatigue on Poland's national roads. The results of the study were used to build a model showing the relationship between the concentration of road accidents and casualties, and the time of day. Finally, the level of relative accident risk at night-time versus daytime is defined. A map shows the risk of death and severe injury on the network of Poland's national roads. The paper suggests to road authorities steps to reduce fatigue-related road accidents in Poland.

Driving decisions when leaving electronic music dance events: driver, passenger, and group effects.

PubMed

Johnson, Mark B; Voas, Robert B; Miller, Brenda A

2012-01-01

The goal of this article was to identify characteristics of drivers and passengers that predicted peer groups whose drivers exit dance clubs with alcohol levels indicative of impairment (blood alcohol content [BAC] ≥ 0.05 g/dL). We used the portal survey methodology to randomly sample groups of electronic music dance event (EMDE) patrons as they entered and exited a club. From May through November 2010, data were collected from 38 EMDEs hosted by 8 clubs in the San Francisco Bay area. Data included in these analyses are results from breath samples for measuring BAC and self-report data on demographics, recent drinking history drinking, drinking intentions, travel to and from the clubs, and the familiarity/experience with other group members. These data were collected from a subset of 175 drivers and 272 passengers. Although drivers drank less than passengers, one driver in 5 groups had a BAC indicative of elevated crash risk (BAC ≥ 0.05 g/dL). Groups of drivers and/or passengers with a recent history of binge drinking were more likely to have drivers with BACs ≥ 0.05 g/dL. One unanticipated finding was that drivers who knew more group members relatively well were more likely to exit the club with a BAC ≥ 0.05 g/dL. Additionally, we found that groups with all female passengers were at greater risk for having a driver whose BAC was ≥ 0.05 g/dL. Some group characteristics predicted drivers who exit clubs with BACs ≥ 0.05 g/dL. One intervention strategy to promote safety might be to encourage group members to reconsider who is sober enough to drive away from the club; for some groups, a change of drivers would be a safer choice, because a passenger may have a relatively safe BAC. Groups of females appear to have a particularly elevated risk of having a driver whose BAC exceeds 0.05 g/dL, and new intervention efforts should be particularly directed to these at-risk groups.

Spatially-explicit modeling of multi-scale drivers of aboveground forest biomass and water yield in watersheds of the Southeastern United States.

PubMed

Ajaz Ahmed, Mukhtar Ahmed; Abd-Elrahman, Amr; Escobedo, Francisco J; Cropper, Wendell P; Martin, Timothy A; Timilsina, Nilesh

2017-09-01

Understanding ecosystem processes and the influence of regional scale drivers can provide useful information for managing forest ecosystems. Examining more local scale drivers of forest biomass and water yield can also provide insights for identifying and better understanding the effects of climate change and management on forests. We used diverse multi-scale datasets, functional models and Geographically Weighted Regression (GWR) to model ecosystem processes at the watershed scale and to interpret the influence of ecological drivers across the Southeastern United States (SE US). Aboveground forest biomass (AGB) was determined from available geospatial datasets and water yield was estimated using the Water Supply and Stress Index (WaSSI) model at the watershed level. Our geostatistical model examined the spatial variation in these relationships between ecosystem processes, climate, biophysical, and forest management variables at the watershed level across the SE US. Ecological and management drivers at the watershed level were analyzed locally to identify whether drivers contribute positively or negatively to aboveground forest biomass and water yield ecosystem processes and thus identifying potential synergies and tradeoffs across the SE US region. Although AGB and water yield drivers varied geographically across the study area, they were generally significantly influenced by climate (rainfall and temperature), land-cover factor1 (Water and barren), land-cover factor2 (wetland and forest), organic matter content high, rock depth, available water content, stand age, elevation, and LAI drivers. These drivers were positively or negatively associated with biomass or water yield which significantly contributes to ecosystem interactions or tradeoff/synergies. Our study introduced a spatially-explicit modelling framework to analyze the effect of ecosystem drivers on forest ecosystem structure, function and provision of services. This integrated model approach facilitates

Drivers within natural drinking groups: an exploration of role selection, motivation, and group influence on driver sobriety.

PubMed

Lange, James E; Johnson, Mark B; Reed, Mark B

2006-01-01

Young people consume alcohol almost exclusively in social contexts, but natural drinking group dynamics are poorly understood. Our research focuses on the drivers' role within natural drinking groups. We conducted breath-test surveys of existing groups of young people at the US/Mexico border crossing before they headed to Tijuana bars, and surveyed them again upon their return. Results indicated an individual's perception of other group member's drinking plans predicts drinking intentions to a greater degree for passengers than drivers. Additionally, drivers who anticipated heavy drinking among other group members returned to the United States with BACs nearly identical to drivers who reported that other group members would not drink at all. This suggests drivers were resistant to normative pressures to drink. Evidence that group-dynamic variables may impact drinking behavior underscores the importance of systematic exploration of natural drinking groups. Furthermore, the knowledge gleaned from studying the dynamics and decision making processes of natural drinking groups could be used to design intervention designed to increase designated driver use and to reduce drinking among designated drivers.

77 FR 75491 - Entry-Level Driver Training; Public Listening Session

Federal Register 2010, 2011, 2012, 2013, 2014

2012-12-20

... identified are supported by research and data analyses, including cost/benefit considerations. The session...-27748] Entry-Level Driver Training; Public Listening Session AGENCY: Federal Motor Carrier Safety Administration (FMCSA), DOT. ACTION: Notice of public listening session. SUMMARY: FMCSA announces that it will...

Drivers of Rift Valley fever epidemics in Madagascar

PubMed Central

Lancelot, Renaud; Béral, Marina; Rakotoharinome, Vincent Michel; Andriamandimby, Soa-Fy; Héraud, Jean-Michel; Coste, Caroline; Apolloni, Andrea; Squarzoni-Diaw, Cécile; de La Rocque, Stéphane; Wint, G. R. William; Cardinale, Eric

2017-01-01

Rift Valley fever (RVF) is a vector-borne viral disease widespread in Africa. The primary cycle involves mosquitoes and wild and domestic ruminant hosts. Humans are usually contaminated after contact with infected ruminants. As many environmental, agricultural, epidemiological, and anthropogenic factors are implicated in RVF spread, the multidisciplinary One Health approach was needed to identify the drivers of RVF epidemics in Madagascar. We examined the environmental patterns associated with these epidemics, comparing human and ruminant serological data with environmental and cattle-trade data. In contrast to East Africa, environmental drivers did not trigger the epidemics: They only modulated local Rift Valley fever virus (RVFV) transmission in ruminants. Instead, RVFV was introduced through ruminant trade and subsequent movement of cattle between trade hubs caused its long-distance spread within the country. Contact with cattle brought in from infected districts was associated with higher infection risk in slaughterhouse workers. The finding that anthropogenic rather than environmental factors are the main drivers of RVF infection in humans can be used to design better prevention and early detection in the case of RVF resurgence in the region. PMID:28096420

In the line of duty: a study of ambulance drivers during the 2010 conflict in Kashmir.

PubMed

Dhar, Shabir Ahmed; Dar, Tahir Ahmed; Wani, Sharief Ahmed; Hussain, Shahid; Dar, Reyaz Ahmed; Wani, Zaid Ahmed; Aazad, Shah; Yaqoob, Suhail; Mansoor, Imtiyaz; Ali, Murtaza Fazal; Ahmed, Muzaffar; Mumtaz, Imran; Azhar, Idrees

2012-08-01

The purpose of this study was to identify the problems faced by ambulance drivers working in a conflict zone. This study was conducted on ambulance drivers working for the four major hospitals in Kashmir, India. The drivers were interviewed and asked a series of 30 work-related questions. The individual interviews were conducted over a three-month period in the valley of Kashmir that was affected by continuous violence, strict curfew, and strikes. A total of 35 ambulance drivers were interviewed. Drivers worked an average of 60 h/wk, and they drove an average of 160 km/d. Twenty-nine (83%) of the drivers experienced >1 threat of physical harm; 18 (54%) experienced physical assaults; and 31 (89%) reported evidence of psychological morbidity associated with their jobs. The atmosphere of conflict on the streets of Kashmir impacted the ambulance drivers adversely, both physically as well as mentally. The stress faced by these professionals in conflict zones during their duty hours should be recognized, and corrective measures must be put in place.

49 CFR 383.23 - Commercial driver's license.

Code of Federal Regulations, 2010 CFR

2010-10-01

... STANDARDS; REQUIREMENTS AND PENALTIES Single License Requirement § 383.23 Commercial driver's license. (a... the single license provision of § 383.21, a driver holding a commercial driver's license issued under... be considered valid commercial drivers' licenses for purposes of behind-the-wheel training on public...

Distracted driving and risk of road crashes among novice and experienced drivers.

PubMed

Klauer, Sheila G; Guo, Feng; Simons-Morton, Bruce G; Ouimet, Marie Claude; Lee, Suzanne E; Dingus, Thomas A

2014-01-02

Distracted driving attributable to the performance of secondary tasks is a major cause of motor vehicle crashes both among teenagers who are novice drivers and among adults who are experienced drivers. We conducted two studies on the relationship between the performance of secondary tasks, including cell-phone use, and the risk of crashes and near-crashes. To facilitate objective assessment, accelerometers, cameras, global positioning systems, and other sensors were installed in the vehicles of 42 newly licensed drivers (16.3 to 17.0 years of age) and 109 adults with more driving experience. During the study periods, 167 crashes and near-crashes among novice drivers and 518 crashes and near-crashes among experienced drivers were identified. The risk of a crash or near-crash among novice drivers increased significantly if they were dialing a cell phone (odds ratio, 8.32; 95% confidence interval [CI], 2.83 to 24.42), reaching for a cell phone (odds ratio, 7.05; 95% CI, 2.64 to 18.83), sending or receiving text messages (odds ratio, 3.87; 95% CI, 1.62 to 9.25), reaching for an object other than a cell phone (odds ratio, 8.00; 95% CI, 3.67 to 17.50), looking at a roadside object (odds ratio, 3.90; 95% CI, 1.72 to 8.81), or eating (odds ratio, 2.99; 95% CI, 1.30 to 6.91). Among experienced drivers, dialing a cell phone was associated with a significantly increased risk of a crash or near-crash (odds ratio, 2.49; 95% CI, 1.38 to 4.54); the risk associated with texting or accessing the Internet was not assessed in this population. The prevalence of high-risk attention to secondary tasks increased over time among novice drivers but not among experienced drivers. The risk of a crash or near-crash among novice drivers increased with the performance of many secondary tasks, including texting and dialing cell phones. (Funded by the Eunice Kennedy Shriver National Institute of Child Health and Human Development and the National Highway Traffic Safety Administration.).

The effects of drug and alcohol consumption on driver injury severities in single-vehicle crashes.

PubMed

Behnood, Ali; Mannering, Fred L

2017-07-04

It is well known that alcohol and drugs influence driving behavior by affecting the central nervous system, awareness, vision, and perception/reaction times, but the resulting effect on driver injuries in car crashes is not fully understood. The purpose of this study was to identify factors affecting the injury severities of unimpaired, alcohol-impaired, and drug-impaired drivers. The current article applies a random parameters logit model to study the differences in injury severities among unimpaired, alcohol-impaired, and drug-impaired drivers. Using data from single-vehicle crashes in Cook County, Illinois, over a 9-year period from January 1, 2004, to December 31, 2012, separate models for unimpaired, alcohol-impaired, and drug-impaired drivers were estimated. A wide range of variables potentially affecting driver injury severity was considered, including roadway and environmental conditions, driver attributes, time and location of the crash, and crash-specific factors. The estimation results show significant differences in the determinants of driver injury severities across groups of unimpaired, alcohol-impaired, and drug-impaired drivers. The findings also show that unimpaired drivers are understandably more responsive to variations in lighting, adverse weather, and road conditions, but these drivers also tend to have much more heterogeneity in their behavioral responses to these conditions, relative to impaired drivers. In addition, age and gender were found to be important determinants of injury severity, but the effects varied significantly across all drivers, particularly among alcohol-impaired drivers. The model estimation results show that statistically significant differences exist in driver injury severities among the unimpaired, alcohol-impaired, and drug-impaired driver groups considered. Specifically, we find that unimpaired drivers tend to have more heterogeneity in their injury outcomes in the presence potentially adverse weather and road surface

Passenger vehicle safety in Australasia for different driver groups.

PubMed

Keall, Michael D; Newstead, Stuart

2011-05-01

Vehicle fleets in developed countries have benefitted from improved technology and regulation leading to safer vehicles. Nevertheless, for various reasons the public do not necessarily choose particular makes and models of cars according to their safety performance. This study aimed to identify areas for potential crashworthiness improvement in the Australasian fleets by studying the distribution of these fleets according to vehicle age and estimated crashworthiness. We used an existing database that encompassed the vast majority of the crash fleets studied, with existing estimates of crashworthiness generated by the Australasian Used Car Safety Ratings project. There were clear tendencies for older and younger people to be driving less safe vehicles that were also generally older. Given that older drivers are more fragile, and hence more liable to be injured in crashes, and younger drivers have a greater propensity to crash, it is clearly undesirable that these driver groups have the least crashworthy vehicles. Some suggestions are made to encourage safer vehicle choices. Copyright © 2010 Elsevier Ltd. All rights reserved.

Ecological drivers of shark distributions along a tropical coastline.

PubMed

Yates, Peter M; Heupel, Michelle R; Tobin, Andrew J; Simpfendorfer, Colin A

2015-01-01

As coastal species experience increasing anthropogenic pressures there is a growing need to characterise the ecological drivers of their abundance and habitat use, and understand how they may respond to changes in their environment. Accordingly, fishery-independent surveys were undertaken to investigate shark abundance along approximately 400 km of the tropical east coast of Australia. Generalised linear models were used to identify ecological drivers of the abundance of immature blacktip Carcharhinus tilstoni/Carcharhinus limbatus, pigeye Carcharhinus amboinensis, and scalloped hammerhead Sphyrna lewini sharks. Results indicated general and species-specific patterns in abundance that were characterised by a range of abiotic and biotic variables. Relationships with turbidity and salinity were similar across multiple species, highlighting the importance of these variables in the functioning of communal shark nurseries. In particular, turbid environments were especially important for all species at typical oceanic salinities. Mangrove proximity, depth, and water temperature were also important; however, their influence varied between species. Ecological drivers may promote spatial diversity in habitat use along environmentally heterogeneous coastlines and may therefore have important implications for population resilience.

Ecological Drivers of Shark Distributions along a Tropical Coastline

PubMed Central

Yates, Peter M.; Heupel, Michelle R.; Tobin, Andrew J.; Simpfendorfer, Colin A.

2015-01-01

As coastal species experience increasing anthropogenic pressures there is a growing need to characterise the ecological drivers of their abundance and habitat use, and understand how they may respond to changes in their environment. Accordingly, fishery-independent surveys were undertaken to investigate shark abundance along approximately 400 km of the tropical east coast of Australia. Generalised linear models were used to identify ecological drivers of the abundance of immature blacktip Carcharhinus tilstoni/Carcharhinus limbatus, pigeye Carcharhinus amboinensis, and scalloped hammerhead Sphyrna lewini sharks. Results indicated general and species-specific patterns in abundance that were characterised by a range of abiotic and biotic variables. Relationships with turbidity and salinity were similar across multiple species, highlighting the importance of these variables in the functioning of communal shark nurseries. In particular, turbid environments were especially important for all species at typical oceanic salinities. Mangrove proximity, depth, and water temperature were also important; however, their influence varied between species. Ecological drivers may promote spatial diversity in habitat use along environmentally heterogeneous coastlines and may therefore have important implications for population resilience. PMID:25853657

Do management practices support or constrain safe driving behaviour? A multi-level investigation in a sample of occupational drivers.

PubMed

Newnam, Sharon; Warmerdam, Amanda; Sheppard, Dianne; Griffin, Mark; Stevenson, Mark

2017-05-01

It has been estimated that one-third of all work-related deaths occur while driving for work-related purposes. Despite this, many organisations are unaware of the practices, beyond those that identify and control the impact of unforeseen events (i.e., risk management), that predispose drivers to risk. This study addresses the issue by identifying the management practices operationalised as, High Performance Workplace Systems (HPWS) that influence safe driver behaviour. The study also explores the value given to safety by senior level management as a moderator of the relationship between HPWS practices and driver behaviour. Each factor was tested within a two level hierarchical model consisting of 911 drivers, nested within 161 supervisors and 83 organisations. The findings highight that under conditions of high investment in job and work design, communication and selection practices, drivers reported poorer driving behaviour. An interaction effect also demonstrated that under conditions of high investment in remuneration, drivers reported safer behaviour, but only when they perceived that managers valued and prioritised safety. The findings challenge current thinking in the management of workplace road safety. Copyright © 2017 Elsevier Ltd. All rights reserved.

Vision-based method for detecting driver drowsiness and distraction in driver monitoring system

NASA Astrophysics Data System (ADS)

Jo, Jaeik; Lee, Sung Joo; Jung, Ho Gi; Park, Kang Ryoung; Kim, Jaihie

2011-12-01

Most driver-monitoring systems have attempted to detect either driver drowsiness or distraction, although both factors should be considered for accident prevention. Therefore, we propose a new driver-monitoring method considering both factors. We make the following contributions. First, if the driver is looking ahead, drowsiness detection is performed; otherwise, distraction detection is performed. Thus, the computational cost and eye-detection error can be reduced. Second, we propose a new eye-detection algorithm that combines adaptive boosting, adaptive template matching, and blob detection with eye validation, thereby reducing the eye-detection error and processing time significantly, which is hardly achievable using a single method. Third, to enhance eye-detection accuracy, eye validation is applied after initial eye detection, using a support vector machine based on appearance features obtained by principal component analysis (PCA) and linear discriminant analysis (LDA). Fourth, we propose a novel eye state-detection algorithm that combines appearance features obtained using PCA and LDA, with statistical features such as the sparseness and kurtosis of the histogram from the horizontal edge image of the eye. Experimental results showed that the detection accuracies of the eye region and eye states were 99 and 97%, respectively. Both driver drowsiness and distraction were detected with a success rate of 98%.

Characteristics of Two Groups of Angry Drivers

ERIC Educational Resources Information Center

Deffenbacher, Jerry L.; Filetti, Linda B.; Richards, Tracy L.; Lynch, Rebekah S.; Oetting, Eugene R.

2003-01-01

High anger drivers acknowledging problems with driving anger and interest in counseling (high anger/problem [HP] drivers) were compared with high and low anger drivers not acknowledging problems with driving anger and seeking counseling (high and low/nonproblem [HNP and LNP, respectively] drivers). High anger groups reported more anger while…

Quantify the Biophysical and Socioeconomic Drivers of Changes in Forest and Agricultural Land in South and Southeast Asia

NASA Astrophysics Data System (ADS)

Xu, X.; Jain, A. K.; Calvin, K. V.

2017-12-01

Due to the rapid socioeconomic development and biophysical factors, South and Southeast Asia (SSEA) has become a hotspot region of land use and land cover changes (LULCCs) in past few decades. Uncovering the drivers of LULCC is crucial for improving the understanding of LULCC processes. Due to the differences from spatiotemporal scales, methods and data sources in previous studies, the quantitative relationships between the LULCC activities and biophysical and socioeconomic drivers at the regional scale of SSEA have not been established. Here we present a comprehensive estimation of the biophysical and socioeconomic drivers of the major LULCC activities in SSEA: changes in forest and agricultural land. We used the Climate Change Initiative land cover data developed by European Space Agency to reveal the dynamics of forest and agricultural land from 1992 to 2015. Then we synthesized 200 publications about LULCC drivers at different spatial scales in SSEA to identify the major drivers of these LULCC activities. Corresponding representative variables of the major drivers were collected. The geographically weighted regression was employed to assess the spatiotemporally heterogeneous drivers of LULCC. Moreover, we validated our results with some national level case studies in SSEA. The results showed that both biophysical conditions such as terrain, soil, and climate, and socioeconomic factors such as migration, poverty, and economy played important roles in driving the changes of forest and agricultural land. The major drivers varied in different locations and periods. Our study integrated the bottom-up knowledge from local scale case studies with the top-down estimation of LULCC drivers, therefore generated more accurate and credible results. The identified biophysical and socioeconomic components could be used to improve the LULCC modelling and projection.

Amplicon restriction patterns associated with nitrogenase activity of root nodules for selection of superior Myrica seedlings.

PubMed

Yanthan, Mhathung; Misra, Arvind K

2013-11-01

Trees of Myrica sp. grow abundantly in the forests of Meghalaya, India. These trees are actinorhizal and harbour nitrogen-fixing Frankia in their root nodules and contribute positively towards the enhancement of nitrogen status of forest areas. They can be used in rejuvenation of mine spoils and nitrogen-depleted fallow lands generated due to slash and burn agriculture practiced in the area. We have studied the association of amplicon restriction patterns (ARPs) of Myrica ribosomal RNA gene and internal transcribed spacer (ITS) region and nitrogenase activity of its root nodules. We found that ARPs thus obtained could be used as markers for early screening of seedlings that could support strains of Frankia that fix atmospheric nitrogen more efficiently.

The reaction times of drivers aged 20 to 80 during a divided attention driving.