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Sample records for additional driver mutation

  1. De Novo Discovery of Mutated Driver Pathways in Cancer

    NASA Astrophysics Data System (ADS)

    Vandin, Fabio; Upfal, Eli; Raphael, Benjamin J.

    Next-generation DNA sequencing technologies are enabling genome-wide measurements of somatic mutations in large numbers of cancer patients. A major challenge in interpretation of this data is to distinguish functional driver mutations that are important for cancer development from random, passenger mutations. A common approach to identify driver mutations is to find genes that are mutated at significant frequency in a large cohort of cancer genomes. This approach is confounded by the observation that driver mutations target multiple cellular signaling and regulatory pathways. Thus, each cancer patient may exhibit a different combination of mutations that are sufficient to perturb the necessary pathways. However, the current understanding of the somatic mutational process of cancer [3,5,6] places two additional constraints on the expected patterns of somatic mutations in a cancer pathway. First, an important cancer pathway should be perturbed in a large number of patients. Thus we expect that with genome-wide measurements of somatic mutations a driver pathway will exhibit high coverage, where most patients will have a mutation in some gene in the pathway. Second, since driver mutations are relatively rare and typically a single driver mutation is sufficient to perturb a pathway, a reasonable assumption is that most patients have a single driver mutation in a pathway. Thus, the genes in a driver pathway exhibit a pattern of mutually exclusive driver mutations, where driver mutations are observed in exactly one gene in the pathway in each patient. There are numerous examples of sets of mutually exclusive mutations [5,6].

  2. A Landscape of Driver Mutations in Melanoma

    PubMed Central

    Hodis, Eran; Watson, Ian R.; Kryukov, Gregory V.; Arold, Stefan T.; Imielinski, Marcin; Theurillat, Jean-Philippe; Nickerson, Elizabeth; Auclair, Daniel; Li, Liren; Place, Chelsea; DiCara, Daniel; Ramos, Alex H.; Lawrence, Michael S.; Cibulskis, Kristian; Sivachenko, Andrey; Voet, Douglas; Saksena, Gordon; Stransky, Nicolas; Onofrio, Robert C.; Winckler, Wendy; Ardlie, Kristin; Wagle, Nikhil; Wargo, Jennifer; Chong, Kelly; Morton, Donald L.; Stemke-Hale, Katherine; Chen, Guo; Noble, Michael; Meyerson, Matthew; Ladbury, John E.; Davies, Michael A.; Gershenwald, Jeffrey E.; Wagner, Stephan N.; Hoon, Dave S.B.; Schadendorf, Dirk; Lander, Eric S.; Gabriel, Stacey B.; Getz, Gad; Garraway, Levi A.; Chin, Lynda

    2012-01-01

    SUMMARY Despite recent insights into melanoma genetics, systematic surveys for driver mutations are challenged by an abundance of passenger mutations caused by carcinogenic ultraviolet (UV) light exposure. We developed a permutation-based framework to address this challenge, employing mutation data from intronic sequences to control for passenger mutational load on a per gene basis. Analysis of large-scale melanoma exome data by this approach discovered six novel melanoma genes (PPP6C, RAC1, SNX31, TACC1, STK19 and ARID2), three of which - RAC1, PPP6C and STK19 - harbored recurrent and potentially targetable mutations. Integration with chromosomal copy number data contextualized the landscape of driver mutations, providing oncogenic insights in BRAF- and NRAS-driven melanoma as well as those without known NRAS/BRAF mutations. The landscape also clarified a mutational basis for RB and p53 pathway deregulation in this malignancy. Finally, the spectrum of driver mutations provided unequivocal genomic evidence for a direct mutagenic role of UV light in melanoma pathogenesis. PMID:22817889

  3. Spatial evolution of tumors with successive driver mutations

    NASA Astrophysics Data System (ADS)

    Antal, Tibor; Krapivsky, P. L.; Nowak, M. A.

    2015-08-01

    We study the influence of driver mutations on the spatial evolutionary dynamics of solid tumors. We start with a cancer clone that expands uniformly in three dimensions giving rise to a spherical shape. We assume that cell division occurs on the surface of the growing tumor. Each cell division has a chance to give rise to a mutation that activates an additional driver gene. The resulting clone has an enhanced growth rate, which generates a local ensemble of faster growing cells, thereby distorting the spherical shape of the tumor. We derive formulas for the abundance and diversity of additional driver mutations as function of time. Our model is semi-deterministic: the spatial growth of cancer clones is deterministic, while mutants arise stochastically.

  4. Driver Missense Mutation Identification Using Feature Selection and Model Fusion.

    PubMed

    Soliman, Ahmed T; Meng, Tao; Chen, Shu-Ching; Iyengar, S S; Iyengar, Puneeth; Yordy, John; Shyu, Mei-Ling

    2015-12-01

    Driver mutations propel oncogenesis and occur much less frequently than passenger mutations. The need for automatic and accurate identification of driver mutations has increased dramatically with the exponential growth of mutation data. Current computational solutions to identify driver mutations rely on sequence homology. Here we construct a machine learning-based framework that does not rely on sequence homology or domain knowledge to predict driver missense mutations. A windowing approach to represent the local environment of the sequence around the mutation point as a mutation sample is applied, followed by extraction of three sequence-level features from each sample. After selecting the most significant features, the support vector machine and multimodal fusion strategies are employed to give final predictions. The proposed framework achieves relatively high performance and outperforms current state-of-the-art algorithms. The ease of deploying the proposed framework and the relatively accurate performance make this solution applicable to large-scale mutation data analyses. PMID:26402258

  5. Cancer Driver Log (CanDL): Catalog of Potentially Actionable Cancer Mutations.

    PubMed

    Damodaran, Senthilkumar; Miya, Jharna; Kautto, Esko; Zhu, Eliot; Samorodnitsky, Eric; Datta, Jharna; Reeser, Julie W; Roychowdhury, Sameek

    2015-09-01

    Massively parallel sequencing technologies have enabled characterization of genomic alterations across multiple tumor types. Efforts have focused on identifying driver mutations because they represent potential targets for therapy. However, because of the presence of driver and passenger mutations, it is often challenging to assign the clinical relevance of specific mutations observed in patients. Currently, there are multiple databases and tools that provide in silico assessment for potential drivers; however, there is no comprehensive resource for mutations with functional characterization. Therefore, we created an expert-curated database of potentially actionable driver mutations for molecular pathologists to facilitate annotation of cancer genomic testing. We reviewed scientific literature to identify variants that have been functionally characterized in vitro or in vivo as driver mutations. We obtained the chromosome location and all possible nucleotide positions for each amino acid change and uploaded them to the Cancer Driver Log (CanDL) database with associated literature reference indicating functional driver evidence. In addition to a simple interface, the database allows users to download all or selected genes as a comma-separated values file for incorporation into their own analysis pipeline. Furthermore, the database includes a mechanism for third-party contributions to support updates for novel driver mutations. Overall, this freely available database will facilitate rapid annotation of cancer genomic testing in molecular pathology laboratories for mutations.

  6. Clonal architectures and driver mutations in metastatic melanomas.

    PubMed

    Ding, Li; Kim, Minjung; Kanchi, Krishna L; Dees, Nathan D; Lu, Charles; Griffith, Malachi; Fenstermacher, David; Sung, Hyeran; Miller, Christopher A; Goetz, Brian; Wendl, Michael C; Griffith, Obi; Cornelius, Lynn A; Linette, Gerald P; McMichael, Joshua F; Sondak, Vernon K; Fields, Ryan C; Ley, Timothy J; Mulé, James J; Wilson, Richard K; Weber, Jeffrey S

    2014-01-01

    To reveal the clonal architecture of melanoma and associated driver mutations, whole genome sequencing (WGS) and targeted extension sequencing were used to characterize 124 melanoma cases. Significantly mutated gene analysis using 13 WGS cases and 15 additional paired extension cases identified known melanoma genes such as BRAF, NRAS, and CDKN2A, as well as a novel gene EPHA3, previously implicated in other cancer types. Extension studies using tumors from another 96 patients discovered a large number of truncation mutations in tumor suppressors (TP53 and RB1), protein phosphatases (e.g., PTEN, PTPRB, PTPRD, and PTPRT), as well as chromatin remodeling genes (e.g., ASXL3, MLL2, and ARID2). Deep sequencing of mutations revealed subclones in the majority of metastatic tumors from 13 WGS cases. Validated mutations from 12 out of 13 WGS patients exhibited a predominant UV signature characterized by a high frequency of C->T transitions occurring at the 3' base of dipyrimidine sequences while one patient (MEL9) with a hypermutator phenotype lacked this signature. Strikingly, a subclonal mutation signature analysis revealed that the founding clone in MEL9 exhibited UV signature but the secondary clone did not, suggesting different mutational mechanisms for two clonal populations from the same tumor. Further analysis of four metastases from different geographic locations in 2 melanoma cases revealed phylogenetic relationships and highlighted the genetic alterations responsible for differential drug resistance among metastatic tumors. Our study suggests that clonal evaluation is crucial for understanding tumor etiology and drug resistance in melanoma.

  7. Clonal architectures and driver mutations in metastatic melanomas.

    PubMed

    Ding, Li; Kim, Minjung; Kanchi, Krishna L; Dees, Nathan D; Lu, Charles; Griffith, Malachi; Fenstermacher, David; Sung, Hyeran; Miller, Christopher A; Goetz, Brian; Wendl, Michael C; Griffith, Obi; Cornelius, Lynn A; Linette, Gerald P; McMichael, Joshua F; Sondak, Vernon K; Fields, Ryan C; Ley, Timothy J; Mulé, James J; Wilson, Richard K; Weber, Jeffrey S

    2014-01-01

    To reveal the clonal architecture of melanoma and associated driver mutations, whole genome sequencing (WGS) and targeted extension sequencing were used to characterize 124 melanoma cases. Significantly mutated gene analysis using 13 WGS cases and 15 additional paired extension cases identified known melanoma genes such as BRAF, NRAS, and CDKN2A, as well as a novel gene EPHA3, previously implicated in other cancer types. Extension studies using tumors from another 96 patients discovered a large number of truncation mutations in tumor suppressors (TP53 and RB1), protein phosphatases (e.g., PTEN, PTPRB, PTPRD, and PTPRT), as well as chromatin remodeling genes (e.g., ASXL3, MLL2, and ARID2). Deep sequencing of mutations revealed subclones in the majority of metastatic tumors from 13 WGS cases. Validated mutations from 12 out of 13 WGS patients exhibited a predominant UV signature characterized by a high frequency of C->T transitions occurring at the 3' base of dipyrimidine sequences while one patient (MEL9) with a hypermutator phenotype lacked this signature. Strikingly, a subclonal mutation signature analysis revealed that the founding clone in MEL9 exhibited UV signature but the secondary clone did not, suggesting different mutational mechanisms for two clonal populations from the same tumor. Further analysis of four metastases from different geographic locations in 2 melanoma cases revealed phylogenetic relationships and highlighted the genetic alterations responsible for differential drug resistance among metastatic tumors. Our study suggests that clonal evaluation is crucial for understanding tumor etiology and drug resistance in melanoma. PMID:25393105

  8. Mutation analysis of 13 driver genes of colorectal cancer-related pathways in Taiwanese patients

    PubMed Central

    Chang, Yuli Christine; Chang, Jan-Gowth; Liu, Ta-Chih; Lin, Chien-Yu; Yang, Shu-Fen; Ho, Cheng-Mao; Chen, William Tzu-Liang; Chang, Ya-Sian

    2016-01-01

    AIM: To investigate the driver gene mutations associated with colorectal cancer (CRC) in the Taiwanese population. METHODS: In this study, 103 patients with CRC were evaluated. The samples consisted of 66 men and 37 women with a median age of 59 years and an age range of 26-86 years. We used high-resolution melting analysis (HRM) and direct DNA sequencing to characterize the mutations in 13 driver genes of CRC-related pathways. The HRM assays were conducted using the LightCycler® 480 Instrument provided with the software LightCycler® 480 Gene Scanning Software Version 1.5. We also compared the clinicopathological data of CRC patients with the driver gene mutation status. RESULTS: Of the 103 patients evaluated, 73.79% had mutations in one of the 13 driver genes. We discovered 18 novel mutations in APC, MLH1, MSH2, PMS2, SMAD4 and TP53 that have not been previously reported. Additionally, we found 16 de novo mutations in APC, BMPR1A, MLH1, MSH2, MSH6, MUTYH and PMS2 in cancerous tissues previously reported in the dbSNP database; however, these mutations could not be detected in peripheral blood cells. The APC mutation correlates with lymph node metastasis (34.69% vs 12.96%, P = 0.009) and cancer stage (34.78% vs 14.04%, P = 0.013). No association was observed between other driver gene mutations and clinicopathological features. Furthermore, having two or more driver gene mutations correlates with the degree of lymph node metastasis (42.86% vs 24.07%, P = 0.043). CONCLUSION: Our findings confirm the importance of 13 CRC-related pathway driver genes in the development of CRC in Taiwanese patients. PMID:26900293

  9. The Importance of Mutational Drivers in GBM.

    PubMed

    Kalkan, Rasime

    2016-01-01

    Glioblastoma (GBM) is the most aggressive primary brain tumor, providing few effective therapeutic options, given the tumor heterogeneity and the accumulation of different genetic abnormalities that cause treatment failure. The many different genetic and epigenetic alterations present in GBM lead to modification of several major signaling pathways resulting in brain tumor growth, progression, and therapeutic resistance. Many functionally important mutations have been discovered, known as neutral passengers. IDH1/2, EZH2, and DNMT3A are the best known epigenetic modifiers in cancer. These mutations are important in determining disease prognosis such that the status of the MGMT gene is a direct target of chemotherapy. For these reasons, newly developed technologies are necessary to determine new candidate targets for targeted-therapy development in GBM. The determination of mutations will aid in this and in the discovery of combinations of targeted and conventional therapies to improve GBM treatment. PMID:27278882

  10. Integrative analysis of mutational and transcriptional profiles reveals driver mutations of metastatic breast cancers.

    PubMed

    Lee, Ji-Hyun; Zhao, Xing-Ming; Yoon, Ina; Lee, Jin Young; Kwon, Nam Hoon; Wang, Yin-Ying; Lee, Kyung-Min; Lee, Min-Joo; Kim, Jisun; Moon, Hyeong-Gon; In, Yongho; Hao, Jin-Kao; Park, Kyung-Mii; Noh, Dong-Young; Han, Wonshik; Kim, Sunghoon

    2016-01-01

    Despite the explosion in the numbers of cancer genomic studies, metastasis is still the major cause of cancer mortality. In breast cancer, approximately one-fifth of metastatic patients survive 5 years. Therefore, detecting the patients at a high risk of developing distant metastasis at first diagnosis is critical for effective treatment strategy. We hereby present a novel systems biology approach to identify driver mutations escalating the risk of metastasis based on both exome and RNA sequencing of our collected 78 normal-paired breast cancers. Unlike driver mutations occurring commonly in cancers as reported in the literature, the mutations detected here are relatively rare mutations occurring in less than half metastatic samples. By supposing that the driver mutations should affect the metastasis gene signatures, we develop a novel computational pipeline to identify the driver mutations that affect transcription factors regulating metastasis gene signatures. We identify driver mutations in ADPGK, NUP93, PCGF6, PKP2 and SLC22A5, which are verified to enhance cancer cell migration and prompt metastasis with in vitro experiments. The discovered somatic mutations may be helpful for identifying patients who are likely to develop distant metastasis. PMID:27625789

  11. Integrative analysis of mutational and transcriptional profiles reveals driver mutations of metastatic breast cancers

    PubMed Central

    Lee, Ji-Hyun; Zhao, Xing-Ming; Yoon, Ina; Lee, Jin Young; Kwon, Nam Hoon; Wang, Yin-Ying; Lee, Kyung-Min; Lee, Min-Joo; Kim, Jisun; Moon, Hyeong-Gon; In, Yongho; Hao, Jin-Kao; Park, Kyung-Mii; Noh, Dong-Young; Han, Wonshik; Kim, Sunghoon

    2016-01-01

    Despite the explosion in the numbers of cancer genomic studies, metastasis is still the major cause of cancer mortality. In breast cancer, approximately one-fifth of metastatic patients survive 5 years. Therefore, detecting the patients at a high risk of developing distant metastasis at first diagnosis is critical for effective treatment strategy. We hereby present a novel systems biology approach to identify driver mutations escalating the risk of metastasis based on both exome and RNA sequencing of our collected 78 normal-paired breast cancers. Unlike driver mutations occurring commonly in cancers as reported in the literature, the mutations detected here are relatively rare mutations occurring in less than half metastatic samples. By supposing that the driver mutations should affect the metastasis gene signatures, we develop a novel computational pipeline to identify the driver mutations that affect transcription factors regulating metastasis gene signatures. We identify driver mutations in ADPGK, NUP93, PCGF6, PKP2 and SLC22A5, which are verified to enhance cancer cell migration and prompt metastasis with in vitro experiments. The discovered somatic mutations may be helpful for identifying patients who are likely to develop distant metastasis.

  12. Integrative analysis of mutational and transcriptional profiles reveals driver mutations of metastatic breast cancers

    PubMed Central

    Lee, Ji-Hyun; Zhao, Xing-Ming; Yoon, Ina; Lee, Jin Young; Kwon, Nam Hoon; Wang, Yin-Ying; Lee, Kyung-Min; Lee, Min-Joo; Kim, Jisun; Moon, Hyeong-Gon; In, Yongho; Hao, Jin-Kao; Park, Kyung-Mii; Noh, Dong-Young; Han, Wonshik; Kim, Sunghoon

    2016-01-01

    Despite the explosion in the numbers of cancer genomic studies, metastasis is still the major cause of cancer mortality. In breast cancer, approximately one-fifth of metastatic patients survive 5 years. Therefore, detecting the patients at a high risk of developing distant metastasis at first diagnosis is critical for effective treatment strategy. We hereby present a novel systems biology approach to identify driver mutations escalating the risk of metastasis based on both exome and RNA sequencing of our collected 78 normal-paired breast cancers. Unlike driver mutations occurring commonly in cancers as reported in the literature, the mutations detected here are relatively rare mutations occurring in less than half metastatic samples. By supposing that the driver mutations should affect the metastasis gene signatures, we develop a novel computational pipeline to identify the driver mutations that affect transcription factors regulating metastasis gene signatures. We identify driver mutations in ADPGK, NUP93, PCGF6, PKP2 and SLC22A5, which are verified to enhance cancer cell migration and prompt metastasis with in vitro experiments. The discovered somatic mutations may be helpful for identifying patients who are likely to develop distant metastasis. PMID:27625789

  13. Altered oncomodules underlie chromatin regulatory factors driver mutations.

    PubMed

    Frigola, Joan; Iturbide, Ane; Lopez-Bigas, Nuria; Peiro, Sandra; Gonzalez-Perez, Abel

    2016-05-24

    Chromatin regulatory factors (CRFs), are known to be involved in tumorigenesis in several cancer types. Nevertheless, the molecular mechanisms through which driver alterations of CRFs cause tumorigenesis remain unknown. Here, we developed a CRFs Oncomodules Discovery approach, which mines several sources of cancer genomics and perturbaomics data. The approach prioritizes sets of genes significantly miss-regulated in primary tumors (oncomodules) bearing mutations of driver CRFs. We applied the approach to eleven TCGA tumor cohorts and uncovered oncomodules potentially associated to mutations of five driver CRFs in three cancer types. Our results revealed, for example, the potential involvement of the mTOR pathway in the development of tumors with loss-of-function mutations of MLL2 in head and neck squamous cell carcinomas. The experimental validation that MLL2 loss-of-function increases the sensitivity of cancer cell lines to mTOR inhibition lends further support to the validity of our approach. The potential oncogenic modules detected by our approach may guide experiments proposing ways to indirectly target driver mutations of CRFs. PMID:27095575

  14. Profiling of potential driver mutations in sarcomas by targeted next generation sequencing.

    PubMed

    Andersson, Carola; Fagman, Henrik; Hansson, Magnus; Enlund, Fredrik

    2016-04-01

    Comprehensive genetic profiling by massively parallel sequencing, commonly known as next generation sequencing (NGS), is becoming the foundation of personalized oncology. For sarcomas very few targeted treatments are currently in routine use. In clinical practice the preoperative diagnostic workup of soft tissue tumours largely relies on core needle biopsies. Although mostly sufficient for histopathological diagnosis, only very limited amounts of formalin fixated paraffin embedded tissue are often available for predictive mutation analysis. Targeted NGS may thus open up new possibilities for comprehensive characterization of scarce biopsies. We therefore set out to search for driver mutations by NGS in a cohort of 55 clinically and morphologically well characterized sarcomas using low input of DNA from formalin fixated paraffin embedded tissues. The aim was to investigate if there are any recurrent or targetable aberrations in cancer driver genes in addition to known chromosome translocations in different types of sarcomas. We employed a panel covering 207 mutation hotspots in 50 cancer-associated genes to analyse DNA from nine gastrointestinal stromal tumours, 14 synovial sarcomas, seven myxoid liposarcomas, 22 Ewing sarcomas and three Ewing-like small round cell tumours at a large sequencing depth to detect also mutations that are subclonal or occur at low allele frequencies. We found nine mutations in eight different potential driver genes, some of which are potentially actionable by currently existing targeted therapies. Even though no recurrent mutations in driver genes were found in the different sarcoma groups, we show that targeted NGS-based sequencing is clearly feasible in a diagnostic setting with very limited amounts of paraffin embedded tissue and may provide novel insights into mesenchymal cell signalling and potentially druggable targets. Interestingly, we also identify five non-synonymous sequence variants in 4 established cancer driver genes in DNA

  15. Evolutionary triage governs fitness in driver and passenger mutations and suggests targeting never mutations

    PubMed Central

    Gatenby, R A.; Cunningham, J. J.; Brown, J. S.

    2014-01-01

    Genetic and epigenetic changes in cancer cells are typically divided into “drivers” and “passengers”. Drug development strategies target driver mutations, but inter- and intra-tumoral heterogeneity usually results in emergence of resistance. Here we model intratumoral evolution in the context of a fecundity/survivorship trade-off. Simulations demonstrate the fitness value, of any genetic change is not fixed but dependent on evolutionary triage governed by initial cell properties, current selection forces, and prior genotypic/phenotypic trajectories. We demonstrate spatial variations in molecular properties of tumor cells are the result of changes in environmental selection forces such as blood flow. Simulated therapies targeting fitness-increasing (driver) mutations usually decrease the tumor burden but almost inevitably fail due to population heterogeneity. An alternative strategy targets gene mutations that are never observed. Because up or down regulation of these genes unconditionally reduces cellular fitness, they are eliminated by evolutionary triage but can be exploited for targeted therapy. PMID:25407411

  16. Putative Breast Cancer Driver Mutations in TBX3 Cause Impaired Transcriptional Repression

    PubMed Central

    Fischer, Kathrin; Pflugfelder, Gert O.

    2015-01-01

    The closely related T-box transcription factors TBX2 and TBX3 are frequently overexpressed in melanoma and various types of human cancers, in particular, breast cancer. The overexpression of TBX2 and TBX3 can have several cellular effects, among them suppression of senescence, promotion of epithelial–mesenchymal transition, and invasive cell motility. In contrast, loss of function of TBX3 and most other human T-box genes causes developmental haploinsufficiency syndromes. Stephens and colleagues (1), by exome sequencing of breast tumor samples, identified five different mutations in TBX3, all affecting the DNA-binding T-domain. One in-frame deletion of a single amino acid, p.N212delN, was observed twice. Due to the clustering of these mutations to the T-domain and for statistical reasons, TBX3 was inferred to be a driver gene in breast cancer. Since mutations in the T-domain generally cause loss of function and because the tumorigenic action of TBX3 has generally been attributed to overexpression, we determined whether the putative driver mutations had loss- or gain-of-function properties. We tested two in-frame deletions, one missense, and one frameshift mutant protein for DNA-binding in vitro, and for target gene repression in cell culture. In addition, we performed an in silico analysis of somatic TBX mutations in breast cancer, collected in The Cancer Genome Atlas (TCGA). Both the experimental and the in silico analysis indicate that the observed mutations predominantly cause loss of TBX3 function. PMID:26579496

  17. Driver Gene Mutations in Stools of Colorectal Carcinoma Patients Detected by Targeted Next-Generation Sequencing.

    PubMed

    Armengol, Gemma; Sarhadi, Virinder K; Ghanbari, Reza; Doghaei-Moghaddam, Masoud; Ansari, Reza; Sotoudeh, Masoud; Puolakkainen, Pauli; Kokkola, Arto; Malekzadeh, Reza; Knuutila, Sakari

    2016-07-01

    Detection of driver gene mutations in stool DNA represents a promising noninvasive approach for screening colorectal cancer (CRC). Amplicon-based next-generation sequencing (NGS) is a good option to study mutations in many cancer genes simultaneously and from a low amount of DNA. Our aim was to assess the feasibility of identifying mutations in 22 cancer driver genes with Ion Torrent technology in stool DNA from a series of 65 CRC patients. The assay was successful in 80% of stool DNA samples. NGS results showed 83 mutations in cancer driver genes, 29 hotspot and 54 novel mutations. One to five genes were mutated in 75% of cases. TP53, KRAS, FBXW7, and SMAD4 were the top mutated genes, consistent with previous studies. Of samples with mutations, 54% presented concomitant mutations in different genes. Phosphatidylinositol 3-kinase/mitogen-activated protein kinase pathway genes were mutated in 70% of samples, with 58% having alterations in KRAS, NRAS, or BRAF. Because mutations in these genes can compromise the efficacy of epidermal growth factor receptor blockade in CRC patients, identifying mutations that confer resistance to some targeted treatments may be useful to guide therapeutic decisions. In conclusion, the data presented herein show that NGS procedures on stool DNA represent a promising tool to detect genetic mutations that could be used in the future for diagnosis, monitoring, or treating CRC. PMID:27155048

  18. Colon tumors with the simultaneous induction of driver mutations in APC, KRAS, and PIK3CA still progress through the adenoma-to-carcinoma sequence

    PubMed Central

    Hadac, Jamie N.; Leystra, Alyssa A.; Olson, Terrah J. Paul; Maher, Molly E.; Payne, Susan N; Yueh, Alexander E.; Schwartz, Alexander R.; Albrecht, Dawn M.; Clipson, Linda; Pasch, Cheri A.; Matkowskyj, Kristina A.; Halberg, Richard B.; Deming, Dustin A.

    2015-01-01

    Human colorectal cancers often possess multiple mutations, including 3–6 driver mutations per tumor. The timing of when these mutations occur during tumor development and progression continues to be debated. More advanced lesions carry a greater number of driver mutations, indicating that colon tumors might progress from adenomas to carcinomas through the stepwise accumulation of mutations following tumor initiation. However, mutations that have been implicated in tumor progression have been identified in normal-appearing epithelial cells of the colon, leaving the possibility that these mutations might be present prior to the initiation of tumorigenesis. We utilized mouse models of colon cancer to investigate whether tumorigenesis still occurs through the adenoma-to-carcinoma sequence when multiple mutations are present at the time of tumor initiation. To create a model in which tumors could concomitantly possess mutations in Apc, Kras, and Pik3ca, we developed a novel minimally invasive technique to administer an adenovirus expressing Cre recombinase to a focal region of the colon. Here we demonstrate that the presence of these additional driver mutations at the time of tumor initiation results in increased tumor multiplicity and an increased rate of progression to invasive adenocarcinomas. These cancers can even metastasize to retroperitoneal lymph nodes or the liver. However, despite having as many as three concomitant driver mutations at the time of initiation, these tumors still proceed through the adenoma-to-carcinoma sequence. PMID:26276752

  19. 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. PMID:26995027

  20. Network-Based Analysis of eQTL Data to Prioritize Driver Mutations

    PubMed Central

    De Maeyer, Dries; Weytjens, Bram; De Raedt, Luc; Marchal, Kathleen

    2016-01-01

    In clonal systems, interpreting driver genes in terms of molecular networks helps understanding how these drivers elicit an adaptive phenotype. Obtaining such a network-based understanding depends on the correct identification of driver genes. In clonal systems, independent evolved lines can acquire a similar adaptive phenotype by affecting the same molecular pathways, a phenomenon referred to as parallelism at the molecular pathway level. This implies that successful driver identification depends on interpreting mutated genes in terms of molecular networks. Driver identification and obtaining a network-based understanding of the adaptive phenotype are thus confounded problems that ideally should be solved simultaneously. In this study, a network-based eQTL method is presented that solves both the driver identification and the network-based interpretation problem. As input the method uses coupled genotype-expression phenotype data (eQTL data) of independently evolved lines with similar adaptive phenotypes and an organism-specific genome-wide interaction network. The search for mutational consistency at pathway level is defined as a subnetwork inference problem, which consists of inferring a subnetwork from the genome-wide interaction network that best connects the genes containing mutations to differentially expressed genes. Based on their connectivity with the differentially expressed genes, mutated genes are prioritized as driver genes. Based on semisynthetic data and two publicly available data sets, we illustrate the potential of the network-based eQTL method to prioritize driver genes and to gain insights in the molecular mechanisms underlying an adaptive phenotype. The method is available at http://bioinformatics.intec.ugent.be/phenetic_eqtl/index.html PMID:26802430

  1. 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

  2. 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

    2016-01-01

    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

  3. Inhibiting Drivers of Non-mutational Drug Tolerance Is a Salvage Strategy for Targeted Melanoma Therapy

    PubMed Central

    Smith, Michael P.; Brunton, Holly; Rowling, Emily J.; Ferguson, Jennifer; Arozarena, Imanol; Miskolczi, Zsofia; Lee, Jessica L.; Girotti, Maria R.; Marais, Richard; Levesque, Mitchell P.; Dummer, Reinhard; Frederick, Dennie T.; Flaherty, Keith T.; Cooper, Zachary A.; Wargo, Jennifer A.; Wellbrock, Claudia

    2016-01-01

    Summary Once melanomas have progressed with acquired resistance to mitogen-activated protein kinase (MAPK)-targeted therapy, mutational heterogeneity presents a major challenge. We therefore examined the therapy phase before acquired resistance had developed and discovered the melanoma survival oncogene MITF as a driver of an early non-mutational and reversible drug-tolerance state, which is induced by PAX3-mediated upregulation of MITF. A drug-repositioning screen identified the HIV1-protease inhibitor nelfinavir as potent suppressor of PAX3 and MITF expression. Nelfinavir profoundly sensitizes BRAF and NRAS mutant melanoma cells to MAPK-pathway inhibitors. Moreover, nelfinavir is effective in BRAF and NRAS mutant melanoma cells isolated from patients progressed on MAPK inhibitor (MAPKi) therapy and in BRAF/NRAS/PTEN mutant tumors. We demonstrate that inhibiting a driver of MAPKi-induced drug tolerance could improve current approaches of targeted melanoma therapy. PMID:26977879

  4. Inhibiting Drivers of Non-mutational Drug Tolerance Is a Salvage Strategy for Targeted Melanoma Therapy.

    PubMed

    Smith, Michael P; Brunton, Holly; Rowling, Emily J; Ferguson, Jennifer; Arozarena, Imanol; Miskolczi, Zsofia; Lee, Jessica L; Girotti, Maria R; Marais, Richard; Levesque, Mitchell P; Dummer, Reinhard; Frederick, Dennie T; Flaherty, Keith T; Cooper, Zachary A; Wargo, Jennifer A; Wellbrock, Claudia

    2016-03-14

    Once melanomas have progressed with acquired resistance to mitogen-activated protein kinase (MAPK)-targeted therapy, mutational heterogeneity presents a major challenge. We therefore examined the therapy phase before acquired resistance had developed and discovered the melanoma survival oncogene MITF as a driver of an early non-mutational and reversible drug-tolerance state, which is induced by PAX3-mediated upregulation of MITF. A drug-repositioning screen identified the HIV1-protease inhibitor nelfinavir as potent suppressor of PAX3 and MITF expression. Nelfinavir profoundly sensitizes BRAF and NRAS mutant melanoma cells to MAPK-pathway inhibitors. Moreover, nelfinavir is effective in BRAF and NRAS mutant melanoma cells isolated from patients progressed on MAPK inhibitor (MAPKi) therapy and in BRAF/NRAS/PTEN mutant tumors. We demonstrate that inhibiting a driver of MAPKi-induced drug tolerance could improve current approaches of targeted melanoma therapy. PMID:26977879

  5. Mutation of cancer driver MLL2 results in transcription stress and genome instability

    PubMed Central

    Kantidakis, Theodoros; Saponaro, Marco; Mitter, Richard; Horswell, Stuart; Kranz, Andrea; Boeing, Stefan; Aygün, Ozan; Kelly, Gavin P.; Matthews, Nik; Stewart, Aengus; Stewart, A. Francis; Svejstrup, Jesper Q.

    2016-01-01

    Genome instability is a recurring feature of tumorigenesis. Mutation in MLL2, encoding a histone methyltransferase, is a driver in numerous different cancer types, but the mechanism is unclear. Here, we present evidence that MLL2 mutation results in genome instability. Mouse cells in which MLL2 gene deletion can be induced display elevated levels of sister chromatid exchange, gross chromosomal aberrations, 53BP1 foci, and micronuclei. Human MLL2 knockout cells are characterized by genome instability as well. Interestingly, MLL2 interacts with RNA polymerase II (RNAPII) and RECQL5, and, although MLL2 mutated cells have normal overall H3K4me levels in genes, nucleosomes in the immediate vicinity of RNAPII are hypomethylated. Importantly, MLL2 mutated cells display signs of substantial transcription stress, and the most affected genes overlap with early replicating fragile sites, show elevated levels of γH2AX, and suffer frequent mutation. The requirement for MLL2 in the maintenance of genome stability in genes helps explain its widespread role in cancer and points to transcription stress as a strong driver in tumorigenesis. PMID:26883360

  6. Mutation of cancer driver MLL2 results in transcription stress and genome instability.

    PubMed

    Kantidakis, Theodoros; Saponaro, Marco; Mitter, Richard; Horswell, Stuart; Kranz, Andrea; Boeing, Stefan; Aygün, Ozan; Kelly, Gavin P; Matthews, Nik; Stewart, Aengus; Stewart, A Francis; Svejstrup, Jesper Q

    2016-02-15

    Genome instability is a recurring feature of tumorigenesis. Mutation in MLL2, encoding a histone methyltransferase, is a driver in numerous different cancer types, but the mechanism is unclear. Here, we present evidence that MLL2 mutation results in genome instability. Mouse cells in which MLL2 gene deletion can be induced display elevated levels of sister chromatid exchange, gross chromosomal aberrations, 53BP1 foci, and micronuclei. Human MLL2 knockout cells are characterized by genome instability as well. Interestingly, MLL2 interacts with RNA polymerase II (RNAPII) and RECQL5, and, although MLL2 mutated cells have normal overall H3K4me levels in genes, nucleosomes in the immediate vicinity of RNAPII are hypomethylated. Importantly, MLL2 mutated cells display signs of substantial transcription stress, and the most affected genes overlap with early replicating fragile sites, show elevated levels of γH2AX, and suffer frequent mutation. The requirement for MLL2 in the maintenance of genome stability in genes helps explain its widespread role in cancer and points to transcription stress as a strong driver in tumorigenesis. PMID:26883360

  7. Recurrent chromosomal gains and heterogeneous driver mutations characterise papillary renal cancer evolution

    PubMed Central

    Kovac, Michal; Navas, Carolina; Horswell, Stuart; Salm, Max; Bardella, Chiara; Rowan, Andrew; Stares, Mark; Castro-Giner, Francesc; Fisher, Rosalie; de Bruin, Elza C.; Kovacova, Monika; Gorman, Maggie; Makino, Seiko; Williams, Jennet; Jaeger, Emma; Jones, Angela; Howarth, Kimberley; Larkin, James; Pickering, Lisa; Gore, Martin; Nicol, David L.; Hazell, Steven; Stamp, Gordon; O’Brien, Tim; Challacombe, Ben; Matthews, Nik; Phillimore, Benjamin; Begum, Sharmin; Rabinowitz, Adam; Varela, Ignacio; Chandra, Ashish; Horsfield, Catherine; Polson, Alexander; Tran, Maxine; Bhatt, Rupesh; Terracciano, Luigi; Eppenberger-Castori, Serenella; Protheroe, Andrew; Maher, Eamonn; El Bahrawy, Mona; Fleming, Stewart; Ratcliffe, Peter; Heinimann, Karl; Swanton, Charles; Tomlinson, Ian

    2015-01-01

    Papillary renal cell carcinoma (pRCC) is an important subtype of kidney cancer with a problematic pathological classification and highly variable clinical behaviour. Here we sequence the genomes or exomes of 31 pRCCs, and in four tumours, multi-region sequencing is undertaken. We identify BAP1, SETD2, ARID2 and Nrf2 pathway genes (KEAP1, NHE2L2 and CUL3) as probable drivers, together with at least eight other possible drivers. However, only ~10% of tumours harbour detectable pathogenic changes in any one driver gene, and where present, the mutations are often predicted to be present within cancer sub-clones. We specifically detect parallel evolution of multiple SETD2 mutations within different sub-regions of the same tumour. By contrast, large copy number gains of chromosomes 7, 12, 16 and 17 are usually early, monoclonal changes in pRCC evolution. The predominance of large copy number variants as the major drivers for pRCC highlights an unusual mode of tumorigenesis that may challenge precision medicine approaches. PMID:25790038

  8. Do mutator mutations fuel tumorigenesis?

    PubMed

    Fox, Edward J; Prindle, Marc J; Loeb, Lawrence A

    2013-12-01

    The mutator phenotype hypothesis proposes that the mutation rate of normal cells is insufficient to account for the large number of mutations found in human cancers. Consequently, human tumors exhibit an elevated mutation rate that increases the likelihood of a tumor acquiring advantageous mutations. The hypothesis predicts that tumors are composed of cells harboring hundreds of thousands of mutations, as opposed to a small number of specific driver mutations, and that malignant cells within a tumor therefore constitute a highly heterogeneous population. As a result, drugs targeting specific mutated driver genes or even pathways of mutated driver genes will have only limited anticancer potential. In addition, because the tumor is composed of such a diverse cell population, tumor cells harboring drug-resistant mutations will exist prior to the administration of any chemotherapeutic agent. We present recent evidence in support of the mutator phenotype hypothesis, major arguments against this concept, and discuss the clinical consequences of tumor evolution fueled by an elevated mutation rate. We also consider the therapeutic possibility of altering the rate of mutation accumulation. Most significantly, we contend that there is a need to fundamentally reconsider current approaches to personalized cancer therapy. We propose that targeting cellular pathways that alter the rate of mutation accumulation in tumors will ultimately prove more effective than attempting to identify and target mutant driver genes or driver pathways.

  9. Somatic PIK3CA mutations as a driver of sporadic venous malformations

    PubMed Central

    Castel, Pau; Carmona, F. Javier; Grego-Bessa, Joaquim; Berger, Michael F.; Viale, Agnès; Anderson, Kathryn V.; Bague, Silvia; Scaltriti, Maurizio; Antonescu, Cristina R.; Baselga, Eulàlia; Baselga, José

    2016-01-01

    Venous malformations (VM) are vascular malformations characterized by enlarged and distorted blood vessel channels. VM grow over time and cause substantial morbidity because of disfigurement, bleeding, and pain, representing a clinical challenge in the absence of effective treatments (Nguyen et al., 2014; Uebelhoer et al., 2012). Somatic mutations may act as drivers of these lesions, as suggested by the identification of TEK mutations in a proportion of VM (Limaye et al., 2009). We report that activating PIK3CA mutations gives rise to sporadic VM in mice, which closely resemble the histology of the human disease. Furthermore, we identified mutations in PIK3CA and related genes of the PI3K (phosphatidylinositol 3-kinase)/AKT pathway in about 30% of human VM that lack TEK alterations. PIK3CA mutations promote downstream signaling and proliferation in endothelial cells and impair normal vasculogenesis in embryonic development. We successfully treated VM in mouse models using pharmacological inhibitors of PI3Kα administered either systemically or topically. This study elucidates the etiology of a proportion of VM and proposes a therapeutic approach for this disease. PMID:27030594

  10. Spatial and temporal homogeneity of driver mutations in diffuse intrinsic pontine glioma.

    PubMed

    Nikbakht, Hamid; Panditharatna, Eshini; Mikael, Leonie G; Li, Rui; Gayden, Tenzin; Osmond, Matthew; Ho, Cheng-Ying; Kambhampati, Madhuri; Hwang, Eugene I; Faury, Damien; Siu, Alan; Papillon-Cavanagh, Simon; Bechet, Denise; Ligon, Keith L; Ellezam, Benjamin; Ingram, Wendy J; Stinson, Caedyn; Moore, Andrew S; Warren, Katherine E; Karamchandani, Jason; Packer, Roger J; Jabado, Nada; Majewski, Jacek; Nazarian, Javad

    2016-04-06

    Diffuse Intrinsic Pontine Gliomas (DIPGs) are deadly paediatric brain tumours where needle biopsies help guide diagnosis and targeted therapies. To address spatial heterogeneity, here we analyse 134 specimens from various neuroanatomical structures of whole autopsy brains from nine DIPG patients. Evolutionary reconstruction indicates histone 3 (H3) K27M--including H3.2K27M--mutations potentially arise first and are invariably associated with specific, high-fidelity obligate partners throughout the tumour and its spread, from diagnosis to end-stage disease, suggesting mutual need for tumorigenesis. These H3K27M ubiquitously-associated mutations involve alterations in TP53 cell-cycle (TP53/PPM1D) or specific growth factor pathways (ACVR1/PIK3R1). Later oncogenic alterations arise in sub-clones and often affect the PI3K pathway. Our findings are consistent with early tumour spread outside the brainstem including the cerebrum. The spatial and temporal homogeneity of main driver mutations in DIPG implies they will be captured by limited biopsies and emphasizes the need to develop therapies specifically targeting obligate oncohistone partnerships.

  11. Spatial and temporal homogeneity of driver mutations in diffuse intrinsic pontine glioma.

    PubMed

    Nikbakht, Hamid; Panditharatna, Eshini; Mikael, Leonie G; Li, Rui; Gayden, Tenzin; Osmond, Matthew; Ho, Cheng-Ying; Kambhampati, Madhuri; Hwang, Eugene I; Faury, Damien; Siu, Alan; Papillon-Cavanagh, Simon; Bechet, Denise; Ligon, Keith L; Ellezam, Benjamin; Ingram, Wendy J; Stinson, Caedyn; Moore, Andrew S; Warren, Katherine E; Karamchandani, Jason; Packer, Roger J; Jabado, Nada; Majewski, Jacek; Nazarian, Javad

    2016-01-01

    Diffuse Intrinsic Pontine Gliomas (DIPGs) are deadly paediatric brain tumours where needle biopsies help guide diagnosis and targeted therapies. To address spatial heterogeneity, here we analyse 134 specimens from various neuroanatomical structures of whole autopsy brains from nine DIPG patients. Evolutionary reconstruction indicates histone 3 (H3) K27M--including H3.2K27M--mutations potentially arise first and are invariably associated with specific, high-fidelity obligate partners throughout the tumour and its spread, from diagnosis to end-stage disease, suggesting mutual need for tumorigenesis. These H3K27M ubiquitously-associated mutations involve alterations in TP53 cell-cycle (TP53/PPM1D) or specific growth factor pathways (ACVR1/PIK3R1). Later oncogenic alterations arise in sub-clones and often affect the PI3K pathway. Our findings are consistent with early tumour spread outside the brainstem including the cerebrum. The spatial and temporal homogeneity of main driver mutations in DIPG implies they will be captured by limited biopsies and emphasizes the need to develop therapies specifically targeting obligate oncohistone partnerships. PMID:27048880

  12. Spatial and temporal homogeneity of driver mutations in diffuse intrinsic pontine glioma

    PubMed Central

    Nikbakht, Hamid; Panditharatna, Eshini; Mikael, Leonie G.; Li, Rui; Gayden, Tenzin; Osmond, Matthew; Ho, Cheng-Ying; Kambhampati, Madhuri; Hwang, Eugene I.; Faury, Damien; Siu, Alan; Papillon-Cavanagh, Simon; Bechet, Denise; Ligon, Keith L.; Ellezam, Benjamin; Ingram, Wendy J.; Stinson, Caedyn; Moore, Andrew S.; Warren, Katherine E.; Karamchandani, Jason; Packer, Roger J.; Jabado, Nada; Majewski, Jacek; Nazarian, Javad

    2016-01-01

    Diffuse Intrinsic Pontine Gliomas (DIPGs) are deadly paediatric brain tumours where needle biopsies help guide diagnosis and targeted therapies. To address spatial heterogeneity, here we analyse 134 specimens from various neuroanatomical structures of whole autopsy brains from nine DIPG patients. Evolutionary reconstruction indicates histone 3 (H3) K27M—including H3.2K27M—mutations potentially arise first and are invariably associated with specific, high-fidelity obligate partners throughout the tumour and its spread, from diagnosis to end-stage disease, suggesting mutual need for tumorigenesis. These H3K27M ubiquitously-associated mutations involve alterations in TP53 cell-cycle (TP53/PPM1D) or specific growth factor pathways (ACVR1/PIK3R1). Later oncogenic alterations arise in sub-clones and often affect the PI3K pathway. Our findings are consistent with early tumour spread outside the brainstem including the cerebrum. The spatial and temporal homogeneity of main driver mutations in DIPG implies they will be captured by limited biopsies and emphasizes the need to develop therapies specifically targeting obligate oncohistone partnerships. PMID:27048880

  13. PRDM14 promotes RAG-dependent Notch1 driver mutations in mouse T-ALL

    PubMed Central

    Carofino, Brandi L.; Ayanga, Bernard; Tracey, Lauren J.; Brooke-Bisschop, Travis

    2016-01-01

    ABSTRACT PRDM14 is an epigenetic regulator known for maintaining embryonic stem cell identity and resetting potency in primordial germ cells. However, hematopoietic expression of Prdm14 at supraphysiological levels results in fully penetrant and rapid-onset T-cell acute lymphoblastic leukemia (T-ALL) in the mouse. Here, we show that PRDM14-induced T-ALLs are driven by NOTCH1, a frequently mutated driver of human T-ALL. Notch1 is activated in this murine model via RAG-dependent promoter deletions and subsequent production of truncated, ligand-independent protein from downstream regions of the Notch1 locus. These T-ALLs also have focal changes in H3K4me3 deposition at the Notch1 locus and global increases in both H3K4me1 and H3K4me3. Using a PRDM14-FLAG mouse model, we show that PRDM14 binds within an intron of Notch1 prior to leukemia development. Our data support the idea that PRDM14 binding promotes a chromatin state that allows access of the RAG recombinase complex to cryptic RAG signal sequences embedded at the Notch1 locus. Indeed, breeding into a RAG recombination-deficient background abrogates T-ALL development and prevents Notch1 deletions, while allowing for transient hematopoietic stem cell (HSC)-like pre-leukemia cell expansion. Together, our data suggest that PRDM14 expands a progenitor cell population while promoting a permissive epigenetic state for the creation of driver mutations (here, in Notch1), enabling cancer development through the misappropriation of endogenous cellular DNA recombination machinery. PMID:27106930

  14. Addition of molecular methods to mutation studies with Drosophila melanogaster

    SciTech Connect

    Lee, W.R. )

    1989-01-01

    For 80 years, Drosophila melanogaster has been used as a major tool in analyzing Mendelian genetics. By using chromosome inversions that suppress crossing over, geneticists have developed a large number of stocks for mutation analysis. These stocks permit numerous tests for specific locus mutations, lethals at multiple loci on any chromosome, chromosome exchanges, insertions, and deletions. The entire genome can be manipulated for a degree of genetic control not found in other germ-line systems. Recombinant DNA techniques now permit analysis of mutations to the nucleotide level. By combining classical genetic analysis with recombinant DNA techniques, it is possible to analyze mutations that range from chromosome aberrations and multilocus deficiencies to single nucleotide transitions.

  15. Balancing Protein Stability and Activity in Cancer: A New Approach for Identifying Driver Mutations Affecting CBL Ubiquitin Ligase Activation.

    PubMed

    Li, Minghui; Kales, Stephen C; Ma, Ke; Shoemaker, Benjamin A; Crespo-Barreto, Juan; Cangelosi, Andrew L; Lipkowitz, Stanley; Panchenko, Anna R

    2016-02-01

    Oncogenic mutations in the monomeric Casitas B-lineage lymphoma (Cbl) gene have been found in many tumors, but their significance remains largely unknown. Several human c-Cbl (CBL) structures have recently been solved, depicting the protein at different stages of its activation cycle and thus providing mechanistic insight underlying how stability-activity tradeoffs in cancer-related proteins-may influence disease onset and progression. In this study, we computationally modeled the effects of missense cancer mutations on structures representing four stages of the CBL activation cycle to identify driver mutations that affect CBL stability, binding, and activity. We found that recurrent, homozygous, and leukemia-specific mutations had greater destabilizing effects on CBL states than random noncancer mutations. We further tested the ability of these computational models, assessing the changes in CBL stability and its binding to ubiquitin-conjugating enzyme E2, by performing blind CBL-mediated EGFR ubiquitination assays in cells. Experimental CBL ubiquitin ligase activity was in agreement with the predicted changes in CBL stability and, to a lesser extent, with CBL-E2 binding affinity. Two thirds of all experimentally tested mutations affected the ubiquitin ligase activity by either destabilizing CBL or disrupting CBL-E2 binding, whereas about one-third of tested mutations were found to be neutral. Collectively, our findings demonstrate that computational methods incorporating multiple protein conformations and stability and binding affinity evaluations can successfully predict the functional consequences of cancer mutations on protein activity, and provide a proof of concept for mutations in CBL. PMID:26676746

  16. Aberrant RNA splicing in cancer; expression changes and driver mutations of splicing factor genes.

    PubMed

    Sveen, A; Kilpinen, S; Ruusulehto, A; Lothe, R A; Skotheim, R I

    2016-05-12

    Alternative splicing is a widespread process contributing to structural transcript variation and proteome diversity. In cancer, the splicing process is commonly disrupted, resulting in both functional and non-functional end-products. Cancer-specific splicing events are known to contribute to disease progression; however, the dysregulated splicing patterns found on a genome-wide scale have until recently been less well-studied. In this review, we provide an overview of aberrant RNA splicing and its regulation in cancer. We then focus on the executors of the splicing process. Based on a comprehensive catalog of splicing factor encoding genes and analyses of available gene expression and somatic mutation data, we identify cancer-associated patterns of dysregulation. Splicing factor genes are shown to be significantly differentially expressed between cancer and corresponding normal samples, and to have reduced inter-individual expression variation in cancer. Furthermore, we identify enrichment of predicted cancer-critical genes among the splicing factors. In addition to previously described oncogenic splicing factor genes, we propose 24 novel cancer-critical splicing factors predicted from somatic mutations. PMID:26300000

  17. Aberrant RNA splicing in cancer; expression changes and driver mutations of splicing factor genes.

    PubMed

    Sveen, A; Kilpinen, S; Ruusulehto, A; Lothe, R A; Skotheim, R I

    2016-05-12

    Alternative splicing is a widespread process contributing to structural transcript variation and proteome diversity. In cancer, the splicing process is commonly disrupted, resulting in both functional and non-functional end-products. Cancer-specific splicing events are known to contribute to disease progression; however, the dysregulated splicing patterns found on a genome-wide scale have until recently been less well-studied. In this review, we provide an overview of aberrant RNA splicing and its regulation in cancer. We then focus on the executors of the splicing process. Based on a comprehensive catalog of splicing factor encoding genes and analyses of available gene expression and somatic mutation data, we identify cancer-associated patterns of dysregulation. Splicing factor genes are shown to be significantly differentially expressed between cancer and corresponding normal samples, and to have reduced inter-individual expression variation in cancer. Furthermore, we identify enrichment of predicted cancer-critical genes among the splicing factors. In addition to previously described oncogenic splicing factor genes, we propose 24 novel cancer-critical splicing factors predicted from somatic mutations.

  18. An atomic view of additive mutational effects in a protein structure

    SciTech Connect

    Skinner, M.M.; Terwilliger, T.C.

    1996-04-01

    Substitution of a single amino acid in a protein will often lead to substantial changes in properties. If these properties could be altered in a rational way then proteins could be readily generated with functions tailored to specific uses. When amino acid substitutions are made at well-separated locations in a single protein, their effects are generally additive. Additivity of effects of amino acid substitutions is very useful because the properties of proteins with any combination of substitutions can be inferred directly from those of the proteins with single changes. It would therefore be of considerable interest to have a means of knowing whether substitutions at a particular pair of sites in a protein are likely to lead to additive effects. The structural basis for additivity of effects of mutations on protein function was examined by determining crystal structures of single and double mutants in the hydrophobic core of gene V protein. Structural effects of mutations were found to be cumulative when two mutations were made in a single protein. Additivity occurs in this case because the regions structurally affected by mutations at the two sites do not overlap even though the sites are separated by only 9 {angstrom}. Structural distortions induced by mutations in gene V protein decrease rapidly, but not isotropically, with distance from the site of mutation. It is anticipated that cases where structural and functional effects of mutations will be additive could be identified simply by examining whether the regions structurally affected by each component mutation overlap.

  19. Somatic mutation profiles in primary colorectal cancers and matching ovarian metastases: Identification of driver and passenger mutations

    PubMed Central

    Crobach, Stijn; Ruano, Dina; van Eijk, Ronald; Schrumpf, Melanie; Fleuren, Gertjan; van Wezel, Tom

    2016-01-01

    Abstract The mutational profiles of primary colorectal cancers (CRCs) and corresponding ovarian metastases were compared. Using a custom‐made next generation sequencing panel, 115 cancer‐driving genes were analyzed in a cohort of 26 primary CRCs and 30 matching ovarian metastases (four with bilateral metastases). To obtain a complete overview of the mutational profile, low thresholds were used in bioinformatics analysis to prevent low frequency passenger mutations from being filtered out. A subset of variants was validated using Sanger and/or hydrolysis probe assays. The mutational landscape of CRC that metastasized to the ovary was not strikingly different from CRC in consecutive series. When comparing primary CRCs and their matching ovarian metastases, there was considerable overlap in the mutations of early affected genes. A subset of mutations demonstrated less overlap, presumably being passenger mutations. In particular, primary CRCs showed a substantially high number of passenger mutations. We also compared the primary CRCs and matching metastases for stratifying variants of six genes (KRAS, NRAS, BRAF, FBXW7, PTEN and PIK3CA) that select for established (EGFR directed) or future targeted therapies. In a total of 31 variants 12 were not found in either of the two locations. Tumours thus differed in the number of discordant variants between the primary tumours and matching metastases. Half of these discordant variants were definitive class 4/5 pathogenic variants. However, in terms of temporal heterogeneity, no clear relationship was observed between the number of discordant variants and the time interval between primary CRCs and the detection of ovarian metastases. This suggests that dormant metastases may be present from the early days of the primary tumours. PMID:27499925

  20. Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma.

    PubMed

    Schwartzentruber, Jeremy; Korshunov, Andrey; Liu, Xiao-Yang; Jones, David T W; Pfaff, Elke; Jacob, Karine; Sturm, Dominik; Fontebasso, Adam M; Quang, Dong-Anh Khuong; Tönjes, Martje; Hovestadt, Volker; Albrecht, Steffen; Kool, Marcel; Nantel, Andre; Konermann, Carolin; Lindroth, Anders; Jäger, Natalie; Rausch, Tobias; Ryzhova, Marina; Korbel, Jan O; Hielscher, Thomas; Hauser, Peter; Garami, Miklos; Klekner, Almos; Bognar, Laszlo; Ebinger, Martin; Schuhmann, Martin U; Scheurlen, Wolfram; Pekrun, Arnulf; Frühwald, Michael C; Roggendorf, Wolfgang; Kramm, Christoph; Dürken, Matthias; Atkinson, Jeffrey; Lepage, Pierre; Montpetit, Alexandre; Zakrzewska, Magdalena; Zakrzewski, Krzystof; Liberski, Pawel P; Dong, Zhifeng; Siegel, Peter; Kulozik, Andreas E; Zapatka, Marc; Guha, Abhijit; Malkin, David; Felsberg, Jörg; Reifenberger, Guido; von Deimling, Andreas; Ichimura, Koichi; Collins, V Peter; Witt, Hendrik; Milde, Till; Witt, Olaf; Zhang, Cindy; Castelo-Branco, Pedro; Lichter, Peter; Faury, Damien; Tabori, Uri; Plass, Christoph; Majewski, Jacek; Pfister, Stefan M; Jabado, Nada

    2012-02-01

    Glioblastoma multiforme (GBM) is a lethal brain tumour in adults and children. However, DNA copy number and gene expression signatures indicate differences between adult and paediatric cases. To explore the genetic events underlying this distinction, we sequenced the exomes of 48 paediatric GBM samples. Somatic mutations in the H3.3-ATRX-DAXX chromatin remodelling pathway were identified in 44% of tumours (21/48). Recurrent mutations in H3F3A, which encodes the replication-independent histone 3 variant H3.3, were observed in 31% of tumours, and led to amino acid substitutions at two critical positions within the histone tail (K27M, G34R/G34V) involved in key regulatory post-translational modifications. Mutations in ATRX (α-thalassaemia/mental retardation syndrome X-linked) and DAXX (death-domain associated protein), encoding two subunits of a chromatin remodelling complex required for H3.3 incorporation at pericentric heterochromatin and telomeres, were identified in 31% of samples overall, and in 100% of tumours harbouring a G34R or G34V H3.3 mutation. Somatic TP53 mutations were identified in 54% of all cases, and in 86% of samples with H3F3A and/or ATRX mutations. Screening of a large cohort of gliomas of various grades and histologies (n = 784) showed H3F3A mutations to be specific to GBM and highly prevalent in children and young adults. Furthermore, the presence of H3F3A/ATRX-DAXX/TP53 mutations was strongly associated with alternative lengthening of telomeres and specific gene expression profiles. This is, to our knowledge, the first report to highlight recurrent mutations in a regulatory histone in humans, and our data suggest that defects of the chromatin architecture underlie paediatric and young adult GBM pathogenesis. PMID:22286061

  1. Integrative genome analyses identify key somatic driver mutations of small cell lung cancer

    PubMed Central

    Peifer, Martin; Fernández-Cuesta, Lynnette; Sos, Martin L; George, Julie; Seidel, Danila; Kasper, Lawryn H; Plenker, Dennis; Leenders, Frauke; Sun, Ruping; Zander, Thomas; Menon, Roopika; Koker, Mirjam; Dahmen, Ilona; Müller, Christian; Di Cerbo, Vincenzo; Schildhaus, Hans-Ulrich; Altmüller, Janine; Baessmann, Ingelore; Becker, Christian; de Wilde, Bram; Vandesompele, Jo; Böhm, Diana; Ansén, Sascha; Gabler, Franziska; Wilkening, Ines; Heynck, Stefanie; Heuckmann, Johannes M; Lu, Xin; Carter, Scott L; Cibulskis, Kristian; Banerji, Shantanu; Getz, Gad; Park, Kwon-Sik; Rauh, Daniel; Grütter, Christian; Fischer, Matthias; Pasqualucci, Laura; Wright, Gavin; Wainer, Zoe; Russell, Prudence; Petersen, Iver; Chen, Yuan; Stoelben, Erich; Ludwig, Corinna; Schnabel, Philipp; Hoffmann, Hans; Muley, Thomas; Brockmann, Michael; Engel-Riedel, Walburga; Muscarella, Lucia A; Fazio, Vito M; Groen, Harry; Timens, Wim; Sietsma, Hannie; Thunnissen, Erik; Smit, Egbert; Heideman, Daniëlle AM; Snijders, Peter JF; Cappuzzo, Federico; Ligorio, Claudia; Damiani, Stefania; Field, John; Solberg, Steinar; Brustugun, Odd Terje; Lund-Iversen, Marius; Sänger, Jörg; Clement, Joachim H; Soltermann, Alex; Moch, Holger; Weder, Walter; Solomon, Benjamin; Soria, Jean-Charles; Validire, Pierre; Besse, Benjamin; Brambilla, Elisabeth; Brambilla, Christian; Lantuejoul, Sylvie; Lorimier, Philippe; Schneider, Peter M; Hallek, Michael; Pao, William; Meyerson, Matthew; Sage, Julien; Shendure, Jay; Schneider, Robert; Büttner, Reinhard; Wolf, Jürgen; Nürnberg, Peter; Perner, Sven; Heukamp, Lukas C; Brindle, Paul K; Haas, Stefan; Thomas, Roman K

    2016-01-01

    Small-cell lung cancer (SCLC) is an aggressive lung tumor subtype with poor survival1–3. We sequenced 29 SCLC exomes, two genomes and 15 transcriptomes and found an extremely high mutation rate of 7.4±1 protein-changing mutations per million basepairs. Therefore, we conducted integrated analyses of the various data sets to identify pathogenetically relevant mutated genes. In all cases we found evidence for inactivation of TP53 and RB1 and identified recurrent mutations in histone-modifying genes, CREBBP, EP300, and MLL. Furthermore, we observed mutations in PTEN, in SLIT2, and EPHA7, as well as focal amplifications of the FGFR1 tyrosine kinase gene. Finally, we detected many of the alterations found in humans in SCLC tumors from p53/Rb1-deficient mice4. Our study implicates histone modification as a major feature of SCLC, reveals potentially therapeutically tractable genome alterations, and provides a generalizable framework for identification of biologically relevant genes in the context of high mutational background. PMID:22941188

  2. Exome and whole genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity

    PubMed Central

    Dulak, Austin M.; Stojanov, Petar; Peng, Shouyong; Lawrence, Michael S.; Fox, Cameron; Stewart, Chip; Bandla, Santhoshi; Imamura, Yu; Schumacher, Steven E.; Shefler, Erica; McKenna, Aaron; Cibulskis, Kristian; Sivachenko, Andrey; Carter, Scott L.; Saksena, Gordon; Voet, Douglas; Ramos, Alex H.; Auclair, Daniel; Thompson, Kristin; Sougnez, Carrie; Onofrio, Robert C.; Guiducci, Candace; Beroukhim, Rameen; Zhou, David; Lin, Lin; Lin, Jules; Reddy, Rishindra; Chang, Andrew; Luketich, James D.; Pennathur, Arjun; Ogino, Shuji; Golub, Todd R.; Gabriel, Stacey B.; Lander, Eric S.; Beer, David G.; Godfrey, Tony E.; Getz, Gad; Bass, Adam J.

    2013-01-01

    The incidence of esophageal adenocarcinoma (EAC) has risen 600% over the last 30 years. With a five-year survival rate of 15%, identification of new therapeutic targets for EAC is greatly important. We analyze the mutation spectra from whole exome sequencing of 149 EAC tumors/normal pairs, 15 of which have also been subjected to whole genome sequencing. We identify a mutational signature defined by a high prevalence of A to C transversions at AA dinucleotides. Statistical analysis of exome data identified significantly mutated 26 genes. Of these genes, four (TP53, CDKN2A, SMAD4, and PIK3CA) have been previously implicated in EAC. The novel significantly mutated genes include chromatin modifying factors and candidate contributors: SPG20, TLR4, ELMO1, and DOCK2. Functional analyses of EAC-derived mutations in ELMO1 reveal increased cellular invasion. Therefore, we suggest a new hypothesis about the potential activation of the RAC1 pathway to be a contributor to EAC tumorigenesis. PMID:23525077

  3. Whole Exome Sequencing of Rapid Autopsy Tumors and Xenograft Models Reveals Possible Driver Mutations Underlying Tumor Progression.

    PubMed

    Xie, Tao; Musteanu, Monica; Lopez-Casas, Pedro P; Shields, David J; Olson, Peter; Rejto, Paul A; Hidalgo, Manuel

    2015-01-01

    Pancreatic Ductal Adenocarcinoma (PDAC) is a highly lethal malignancy due to its propensity to invade and rapidly metastasize and remains very difficult to manage clinically. One major hindrance towards a better understanding of PDAC is the lack of molecular data sets and models representative of end stage disease. Moreover, it remains unclear how molecularly similar patient-derived xenograft (PDX) models are to the primary tumor from which they were derived. To identify potential molecular drivers in metastatic pancreatic cancer progression, we obtained matched primary tumor, metastases and normal (peripheral blood) samples under a rapid autopsy program and performed whole exome sequencing (WES) on tumor as well as normal samples. PDX models were also generated, sequenced and compared to tumors. Across the matched data sets generated for three patients, there were on average approximately 160 single-nucleotide mutations in each sample. The majority of mutations in each patient were shared among the primary and metastatic samples and, importantly, were largely retained in the xenograft models. Based on the mutation prevalence in the primary and metastatic sites, we proposed possible clonal evolution patterns marked by functional mutations affecting cancer genes such as KRAS, TP53 and SMAD4 that may play an important role in tumor initiation, progression and metastasis. These results add to our understanding of pancreatic tumor biology, and demonstrate that PDX models derived from advanced or end-stage likely closely approximate the genetics of the disease in the clinic and thus represent a biologically and clinically relevant pre-clinical platform that may enable the development of effective targeted therapies for PDAC.

  4. High frequency of additional gene mutations in acute myeloid leukemia with MLL partial tandem duplication: DNMT3A mutation is associated with poor prognosis.

    PubMed

    Kao, Hsiao-Wen; Liang, D Cherng; Kuo, Ming-Chung; Wu, Jin-Hou; Dunn, Po; Wang, Po-Nan; Lin, Tung-Liang; Shih, Yu-Shu; Liang, Sung-Tzu; Lin, Tung-Huei; Lai, Chen-Yu; Lin, Chun-Hui; Shih, Lee-Yung

    2015-10-20

    The mutational profiles of acute myeloid leukemia (AML) with partial tandem duplication of mixed-lineage leukemia gene (MLL-PTD) have not been comprehensively studied. We studied 19 gene mutations for 98 patients with MLL-PTD AML to determine the mutation frequency and clinical correlations. MLL-PTD was screened by reverse-transcriptase PCR and confirmed by real-time quantitative PCR. The mutational analyses were performed with PCR-based assays followed by direct sequencing. Gene mutations of signaling pathways occurred in 63.3% of patients, with FLT3-ITD (44.9%) and FLT3-TKD (13.3%) being the most frequent. 66% of patients had gene mutations involving epigenetic regulation, and DNMT3A (32.7%), IDH2 (18.4%), TET2 (18.4%), and IDH1 (10.2%) mutations were most common. Genes of transcription pathways and tumor suppressors accounted for 23.5% and 10.2% of patients. RUNX1 mutation occurred in 23.5% of patients, while none had NPM1 or double CEBPA mutation. 90.8% of MLL-PTD AML patients had at least one additional gene mutation. Of 55 MLL-PTD AML patients who received standard chemotherapy, age older than 50 years and DNMT3A mutation were associated with inferior outcome. In conclusion, gene mutations involving DNA methylation and activated signaling pathway were common co-existed gene mutations. DNMT3A mutation was a poor prognostic factor in MLL-PTD AML.

  5. Aging-Induced Stem Cell Mutations as Drivers for Disease and Cancer.

    PubMed

    Adams, Peter D; Jasper, Heinrich; Rudolph, K Lenhard

    2015-06-01

    Aging is characterized by a decrease in genome integrity, impaired organ maintenance, and an increased risk of cancer, which coincide with clonal dominance of expanded mutant stem and progenitor cell populations in aging tissues, such as the intestinal epithelium, the hematopoietic system, and the male germline. Here we discuss possible explanations for age-associated increases in the initiation and/or progression of mutant stem/progenitor clones and highlight the roles of stem cell quiescence, replication-associated DNA damage, telomere shortening, epigenetic alterations, and metabolic challenges as determinants of stem cell mutations and clonal dominance in aging. PMID:26046760

  6. Distinct H3F3A and H3F3B driver mutations define chondroblastoma and giant cell tumor of bone.

    PubMed

    Behjati, Sam; Tarpey, Patrick S; Presneau, Nadège; Scheipl, Susanne; Pillay, Nischalan; Van Loo, Peter; Wedge, David C; Cooke, Susanna L; Gundem, Gunes; Davies, Helen; Nik-Zainal, Serena; Martin, Sancha; McLaren, Stuart; Goody, Victoria; Goodie, Victoria; Robinson, Ben; Butler, Adam; Teague, Jon W; Halai, Dina; Khatri, Bhavisha; Myklebost, Ola; Baumhoer, Daniel; Jundt, Gernot; Hamoudi, Rifat; Tirabosco, Roberto; Amary, M Fernanda; Futreal, P Andrew; Stratton, Michael R; Campbell, Peter J; Flanagan, Adrienne M

    2013-12-01

    It is recognized that some mutated cancer genes contribute to the development of many cancer types, whereas others are cancer type specific. For genes that are mutated in multiple cancer classes, mutations are usually similar in the different affected cancer types. Here, however, we report exquisite tumor type specificity for different histone H3.3 driver alterations. In 73 of 77 cases of chondroblastoma (95%), we found p.Lys36Met alterations predominantly encoded in H3F3B, which is one of two genes for histone H3.3. In contrast, in 92% (49/53) of giant cell tumors of bone, we found histone H3.3 alterations exclusively in H3F3A, leading to p.Gly34Trp or, in one case, p.Gly34Leu alterations. The mutations were restricted to the stromal cell population and were not detected in osteoclasts or their precursors. In the context of previously reported H3F3A mutations encoding p.Lys27Met and p.Gly34Arg or p.Gly34Val alterations in childhood brain tumors, a remarkable picture of tumor type specificity for histone H3.3 driver alterations emerges, indicating that histone H3.3 residues, mutations and genes have distinct functions.

  7. Molecular Genetic Analysis of Ovarian Brenner Tumors and Associated Mucinous Epithelial Neoplasms: High Variant Concordance and Identification of Mutually Exclusive RAS Driver Mutations and MYC Amplification.

    PubMed

    Tafe, Laura J; Muller, Kristen E; Ananda, Guruprasad; Mitchell, Talia; Spotlow, Vanessa; Patterson, Sara E; Tsongalis, Gregory J; Mockus, Susan M

    2016-03-01

    Benign ovarian Brenner tumors often are associated with mucinous cystic neoplasms, which are hypothesized to share a histogenic origin and progression, however, supporting molecular characterization is limited. Our goal was to identify molecular mechanisms linking these tumors. DNA from six Brenner tumors with paired mucinous tumors, two Brenner tumors not associated with a mucinous neoplasm, and two atypical proliferative (borderline) Brenner tumors was extracted from formalin-fixed, paraffin-embedded tumor samples and sequenced using a 358-gene next-generation sequencing assay. Variant calls were compared within tumor groups to assess somatic mutation profiles. There was high concordance of the variants between paired samples (40% to 75%; P < 0.0001). Four of the six tumor pairs showed KRAS hotspot driver mutations specifically in the mucinous tumor. In the two paired samples that lacked KRAS mutations, MYC amplification was detected in both of the mucinous and the Brenner components; MYC amplification also was detected in a third Brenner tumor. Five of the Brenner tumors had no reportable potential driver alterations. The two atypical proliferative (borderline) Brenner tumors both had RAS mutations. The high degree of coordinate variants between paired Brenner and mucinous tumors supports a shared origin or progression. Differences observed in affected genes and pathways, particularly involving RAS and MYC, may point to molecular drivers of a divergent phenotype and progression of these tumors.

  8. Second-Line Treatment of Non-Small Cell Lung Cancer: New Developments for Tumours Not Harbouring Targetable Oncogenic Driver Mutations.

    PubMed

    Barnfield, Paul C; Ellis, Peter M

    2016-09-01

    Platinum-based doublet chemotherapy with or without bevacizumab is the standard of care for the initial management of advanced and metastatic non-small cell lung cancer (NSCLC) without a targetable molecular abnormality. However, the majority of patients with NSCLC will ultimately develop resistance to initial platinum-based chemotherapy, and many remain candidates for subsequent lines of therapy. Randomised trials over the past 10-15 years have established pemetrexed (non-squamous histology), docetaxel, erlotinib and gefitinib as approved second-line agents in NSCLC without targetable driver mutations or rearrangements. Trials comparing these agents with other chemotherapy, evaluating the addition of an epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI) to chemotherapy or the addition of another targeted agent to erlotinib or gefitinib have all failed to demonstrate an improvement in overall survival for patients with NSCLC. In contrast, recent data comparing therapy with novel monoclonal antibodies against programmed cell death 1 (PD-1) or PD ligand (PD-L1) pathway versus standard chemotherapy following platinum failure have demonstrated significant improvements in overall survival. Therapy with nivolumab or pembrolizumab would now be considered standard second-line therapy in patients without contraindication to immune checkpoint inhibitors. Atezolizumab also appears promising in this setting. PMID:27557830

  9. Beyond Mutations: Additional Mechanisms and Implications of SWI/SNF Complex Inactivation

    PubMed Central

    Marquez, Stefanie B.; Thompson, Kenneth W.; Lu, Li; Reisman, David

    2015-01-01

    SWI/SNF is a major regulator of gene expression. Its role is to facilitate the shifting and exposure of DNA segments within the promoter and other key domains to transcription factors and other essential cellular proteins. This complex interacts with a wide range of proteins and does not function within a single, specific pathway; thus, it is involved in a multitude of cellular processes, including DNA repair, differentiation, development, cell adhesion, and growth control. Given SWI/SNF’s prominent role in these processes, many of which are important for blocking cancer development, it is not surprising that the SWI/SNF complex is targeted during cancer initiation and progression both by mutations and by non-mutational mechanisms. Currently, the understanding of the types of alterations, their frequency, and their impact on the SWI/SNF subunits is an area of intense research that has been bolstered by a recent cadre of NextGen sequencing studies. These studies have revealed mutations in SWI/SNF subunits, indicating that this complex is thus important for cancer development. The purpose of this review is to put into perspective the role of mutations versus other mechanisms in the silencing of SWI/SNF subunits, in particular, BRG1 and BRM. In addition, this review explores the recent development of synthetic lethality and how it applies to this complex, as well as how BRM polymorphisms are becoming recognized as potential clinical biomarkers for cancer risk. Significance: Recent reviews have detailed the occurrence of mutations in nearly all SWI/SNF subunits, which indicates that this complex is an important target for cancer. However, when the frequency of mutations in a given tumor type is compared to the frequency of subunit loss, it becomes clear that other non-mutational mechanisms must play a role in the inactivation of SWI/SNF subunits. Such data indicate that epigenetic mechanisms that are known to regulate BRM may also be involved in the loss of

  10. Massively parallel sequencing of phyllodes tumours of the breast reveals actionable mutations, and TERT promoter hotspot mutations and TERT gene amplification as likely drivers of progression.

    PubMed

    Piscuoglio, Salvatore; Ng, Charlotte Ky; Murray, Melissa; Burke, Kathleen A; Edelweiss, Marcia; Geyer, Felipe C; Macedo, Gabriel S; Inagaki, Akiko; Papanastasiou, Anastasios D; Martelotto, Luciano G; Marchio, Caterina; Lim, Raymond S; Ioris, Rafael A; Nahar, Pooja K; Bruijn, Ino De; Smyth, Lillian; Akram, Muzaffar; Ross, Dara; Petrini, John H; Norton, Larry; Solit, David B; Baselga, Jose; Brogi, Edi; Ladanyi, Marc; Weigelt, Britta; Reis-Filho, Jorge S

    2016-03-01

    Phyllodes tumours (PTs) are breast fibroepithelial lesions that are graded based on histological criteria as benign, borderline or malignant. PTs may recur locally. Borderline PTs and malignant PTs may metastasize to distant sites. Breast fibroepithelial lesions, including PTs and fibroadenomas, are characterized by recurrent MED12 exon 2 somatic mutations. We sought to define the repertoire of somatic genetic alterations in PTs and whether these may assist in the differential diagnosis of these lesions. We collected 100 fibroadenomas, 40 benign PTs, 14 borderline PTs and 22 malignant PTs; six, six and 13 benign, borderline and malignant PTs, respectively, and their matched normal tissue, were subjected to targeted massively parallel sequencing (MPS) using the MSK-IMPACT sequencing assay. Recurrent MED12 mutations were found in 56% of PTs; in addition, mutations affecting cancer genes (eg TP53, RB1, SETD2 and EGFR) were exclusively detected in borderline and malignant PTs. We found a novel recurrent clonal hotspot mutation in the TERT promoter (-124 C>T) in 52% and TERT gene amplification in 4% of PTs. Laser capture microdissection revealed that these mutations were restricted to the mesenchymal component of PTs. Sequencing analysis of the entire cohort revealed that the frequency of TERT alterations increased from benign (18%) to borderline (57%) and to malignant PTs (68%; p < 0.01), and TERT alterations were associated with increased levels of TERT mRNA (p < 0.001). No TERT alterations were observed in fibroadenomas. An analysis of TERT promoter sequencing and gene amplification distinguished PTs from fibroadenomas with a sensitivity and a positive predictive value of 100% (CI 95.38-100%) and 100% (CI 85.86-100%), respectively, and a sensitivity and a negative predictive value of 39% (CI 28.65-51.36%) and 68% (CI 60.21-75.78%), respectively. Our results suggest that TERT alterations may drive the progression of PTs, and may assist in the differential diagnosis

  11. Massively parallel sequencing of phyllodes tumours of the breast reveals actionable mutations, and TERT promoter hotspot mutations and TERT gene amplification as likely drivers of progression.

    PubMed

    Piscuoglio, Salvatore; Ng, Charlotte Ky; Murray, Melissa; Burke, Kathleen A; Edelweiss, Marcia; Geyer, Felipe C; Macedo, Gabriel S; Inagaki, Akiko; Papanastasiou, Anastasios D; Martelotto, Luciano G; Marchio, Caterina; Lim, Raymond S; Ioris, Rafael A; Nahar, Pooja K; Bruijn, Ino De; Smyth, Lillian; Akram, Muzaffar; Ross, Dara; Petrini, John H; Norton, Larry; Solit, David B; Baselga, Jose; Brogi, Edi; Ladanyi, Marc; Weigelt, Britta; Reis-Filho, Jorge S

    2016-03-01

    Phyllodes tumours (PTs) are breast fibroepithelial lesions that are graded based on histological criteria as benign, borderline or malignant. PTs may recur locally. Borderline PTs and malignant PTs may metastasize to distant sites. Breast fibroepithelial lesions, including PTs and fibroadenomas, are characterized by recurrent MED12 exon 2 somatic mutations. We sought to define the repertoire of somatic genetic alterations in PTs and whether these may assist in the differential diagnosis of these lesions. We collected 100 fibroadenomas, 40 benign PTs, 14 borderline PTs and 22 malignant PTs; six, six and 13 benign, borderline and malignant PTs, respectively, and their matched normal tissue, were subjected to targeted massively parallel sequencing (MPS) using the MSK-IMPACT sequencing assay. Recurrent MED12 mutations were found in 56% of PTs; in addition, mutations affecting cancer genes (eg TP53, RB1, SETD2 and EGFR) were exclusively detected in borderline and malignant PTs. We found a novel recurrent clonal hotspot mutation in the TERT promoter (-124 C>T) in 52% and TERT gene amplification in 4% of PTs. Laser capture microdissection revealed that these mutations were restricted to the mesenchymal component of PTs. Sequencing analysis of the entire cohort revealed that the frequency of TERT alterations increased from benign (18%) to borderline (57%) and to malignant PTs (68%; p < 0.01), and TERT alterations were associated with increased levels of TERT mRNA (p < 0.001). No TERT alterations were observed in fibroadenomas. An analysis of TERT promoter sequencing and gene amplification distinguished PTs from fibroadenomas with a sensitivity and a positive predictive value of 100% (CI 95.38-100%) and 100% (CI 85.86-100%), respectively, and a sensitivity and a negative predictive value of 39% (CI 28.65-51.36%) and 68% (CI 60.21-75.78%), respectively. Our results suggest that TERT alterations may drive the progression of PTs, and may assist in the differential diagnosis

  12. Leveraging a Multi-Omics Strategy for Prioritizing Personalized Candidate Mutation-Driver Genes: A Proof-of-Concept Study

    PubMed Central

    Ding, Keyue; Wu, Songfeng; Ying, Wantao; Pan, Qi; Li, Xiaoyuan; Zhao, Dachun; Li, Xianyu; Zhao, Qing; Zhu, Yunping; Ren, Hong; Qian, Xiaohong

    2015-01-01

    The expression of mutant forms of proteins (e.g., oncogenes and tumor suppressors) has implications in cancer biology and clinical practice. Initial efforts have been made to characterize the transcription of tumor-mutated alleles; however, few studies have been reported to link tumor-mutated alleles to proteomics. We aimed to characterize the transcriptional and translational patterns of tumor-mutated alleles. We performed whole-exome sequencing, RNA-seq, and proteome profiling in a hyper-mutated patient of hepatocellular carcinoma. Using the patient as a model, we show that only a small proportion of tumor-mutated alleles were expressed. In this case, 42% and 3.5% of the tumor-mutated alleles were identified to be transcribed and translated, respectively. Compared with genes with germline variations or without mutations, somatic mutations significantly reduced protein expression abundance. Using the transcriptional and translational patterns of tumor-mutated alleles, we classified the mutations into four types, and only one type may be associated with the liver cancer and lead to hepatocarcinogenesis in the patient. Our results demonstrate how tumor-mutated alleles are transcribed and translated, and how the expression enables the classification of somatic mutations that cause cancer. Leveraging multiple ‘omics’ datasets provides a new avenue for understanding patient-specific mutations that underlie carcinogenesis. PMID:26631547

  13. Understanding drivers of the export of dissolved organic carbon from headwater catchments in Germany using Generalised Additive Models

    NASA Astrophysics Data System (ADS)

    Selle, Benny; Tittel, Jörg; Musolff, Andreas

    2015-04-01

    In the literature, several causes of recently increasing concentrations of dissolved organic carbon (DOC) in headwaters across eastern North America and northern and central Europe have been debated. One likely driver of the widespread increase of DOC concentrations since the early to mid 1990s are decreasing depositions of acid rain resulting in an increased solubility of organic carbon compounds including humic acids. Here, we tested the hypothesis if the reduced availability of both nitrate and sulfate stimulated the reduction of ferric iron soil minerals and the mobilisation of DOC. Decreasing depositions often resulted in a reduced availability of both nitrate and sulphate, which are preferred electron acceptors in microbial decomposition processes. As iron minerals act as efficient sorbents of organic compounds in soils its reduction may have caused a release of humic substances and hence an increasing export of DOC from headwater catchments. To test this hypothesis, time series of DOC, dissolved iron, sulfate and nitrate from several German headwater catchments were examined using Generalised Additive Models. Using this modelling technique, discharge corrected time series of concentrations were represented as a sum of a seasonal and a non-linear trend component. Both, the computed trends and seasonalities supported the redox hypothesis.

  14. Understanding drivers of the export of dissolved organic carbon from a German headwater catchment using Generalised Additive Models

    NASA Astrophysics Data System (ADS)

    Selle, Benny; Musolff, Andreas; Tittel, Jörg

    2016-04-01

    In the literature, several causes of recently increasing concentrations of dissolved organic carbon (DOC) in headwaters across eastern North America and northern and central Europe have been debated. One likely driver of the widespread increase of DOC concentrations since the early 1990s are decreasing depositions of acid rain resulting in an increased solubility of organic carbon compounds including humic acids. Here, we tested the hypothesis if the reduced availability of nitrate stimulated the microbial reduction of ferric iron soil minerals and the mobilisation of DOC. Forested catchments are relatively unaffected by agricultural and urban nitrate inputs. In these catchments, decreasing depositions often resulted in a reduced availability of nitrate, which are preferred electron acceptors in microbial decomposition processes. As ferric iron minerals act as efficient sorbents of organic compounds in soils its reduction may cause a release of humic substances and hence an export of DOC. To test this hypothesis, time series of DOC, dissolved iron and nitrate from a forested headwater catchment in Germany were examined using Generalised Additive Models. We found that rising DOC concentrations most likely resulted from a reductive dissolution of iron(III) minerals in soils and the associated mobilisation of adsorbed organic carbon. Phosphate, which can trigger undesired algal growth and is also known to be adsorbed by particulate iron(III), was released as well.

  15. Combinatorial reshaping of a lipase structure for thermostability: additive role of surface stabilizing single point mutations.

    PubMed

    Kumar, Rakesh; Singh, Ranvir; Kaur, Jagdeep

    2014-05-16

    Thermostable lipases are of high priority for industrial applications. In the present study, targeted improvement of the thermostability of a lipase from metagenomic origin was examined by using a combinatorial protein engineering approach exploring additive effects of single amino acid substitutions. A variant (LipR5) was generated after combination of two thermostabilizing mutations (R214C & N355K). Thermostability of the variant enzyme was analyzed by half-life measurement and circular dichroism (CD). To assess whether catalytic properties were affected by mutation, the optimal reaction conditions were determined. The protein LipR5, displayed optimum activity at 50°C and pH 8.0. It showed two fold enhancement in thermostability (at 60°C) as compared to LipR3 (R214C) and nearly 168 fold enhancement as compared to parent enzyme (LipR1). Circular dichroism and fluorescence study suggest that the protein structure had become more rigid and stable to denaturation. Study of 3D model suggested that Lys355 was involved in formation of a Hydrogen bond with OE1 of Glu284. Lys355 was also making salt bridge with OE2 of Glu284. PMID:24751523

  16. Examining the nonparametric effect of drivers' age in rear-end accidents through an additive logistic regression model.

    PubMed

    Ma, Lu; Yan, Xuedong

    2014-06-01

    This study seeks to inspect the nonparametric characteristics connecting the age of the driver to the relative risk of being an at-fault vehicle, in order to discover a more precise and smooth pattern of age impact, which has commonly been neglected in past studies. Records of drivers in two-vehicle rear-end collisions are selected from the general estimates system (GES) 2011 dataset. These extracted observations in fact constitute inherently matched driver pairs under certain matching variables including weather conditions, pavement conditions and road geometry design characteristics that are shared by pairs of drivers in rear-end accidents. The introduced data structure is able to guarantee that the variance of the response variable will not depend on the matching variables and hence provides a high power of statistical modeling. The estimation results exhibit a smooth cubic spline function for examining the nonlinear relationship between the age of the driver and the log odds of being at fault in a rear-end accident. The results are presented with respect to the main effect of age, the interaction effect between age and sex, and the effects of age under different scenarios of pre-crash actions by the leading vehicle. Compared to the conventional specification in which age is categorized into several predefined groups, the proposed method is more flexible and able to produce quantitatively explicit results. First, it confirms the U-shaped pattern of the age effect, and further shows that the risks of young and old drivers change rapidly with age. Second, the interaction effects between age and sex show that female and male drivers behave differently in rear-end accidents. Third, it is found that the pattern of age impact varies according to the type of pre-crash actions exhibited by the leading vehicle. PMID:24642249

  17. 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…

  18. Additive effect of mutations in LDLR and PCSK9 genes on the phenotype of familial hypercholesterolemia.

    PubMed

    Pisciotta, Livia; Priore Oliva, Claudio; Cefalù, Angelo Baldassare; Noto, Davide; Bellocchio, Antonella; Fresa, Raffaele; Cantafora, Alfredo; Patel, Dilip; Averna, Maurizio; Tarugi, Patrizia; Calandra, Sebastiano; Bertolini, Stefano

    2006-06-01

    Patients homozygous or compound heterozygous for LDLR mutations or double heterozygous for LDLR and apo B R3500Q mutation have higher LDL-C levels, more extensive xanthomatosis and more severe premature coronary disease (pCAD) than simple heterozygotes for mutations in either these genes or for missense mutations in PCSK9 gene. It is not known whether combined mutations in LDLR and PKCS9 are associated with such a severe phenotype. We sequenced Apo B and PCSK9 genes in two patients with the clinical diagnosis of homozygous FH who were heterozygous for LDLR gene mutations. Proband Z.P. (LDL-C 13.39 mmol/L and pCAD) was heterozygous for an LDLR mutation (p.E228K) inherited from her father (LDL-C 8.07 mmol/L) and a PCSK9 mutation (p.R496W) from her mother (LDL-C 5.58 mmol/L). Proband L.R. and her sister (LDL-C 11.51 and 10.47 mmol/L, xanthomatosis and carotid atherosclerosis) were heterozygous for an LDLR mutation (p.Y419X) inherited from their mother (LDL-C 6.54 mmol/L) and a PCSK9 mutation (p.N425S) probably from their deceased father. The LDL-C levels in double heterozygotes of these two families were 56 and 44% higher than those found in simple heterozygotes for the two LDLR mutations, respectively. The two PCSK9 mutations are novel and were not found in 110 controls and 80 patients with co-dominant hypercholesterolemia. These observations indicate that rare missense mutations of PCSK9 may worsen the clinical phenotype of patients carrying LDLR mutations. PMID:16183066

  19. A Systems Biology Comparison of Ovarian Cancers Implicates Putative Somatic Driver Mutations through Protein-Protein Interaction Models

    PubMed Central

    Yang, Mary Qu; Elnitski, Laura

    2016-01-01

    Ovarian carcinomas can be aggressive with a high mortality rate (e.g., high-grade serous ovarian carcinomas, or HGSOCs), or indolent with much better long-term outcomes (e.g., low-malignant-potential, or LMP, serous ovarian carcinomas). By comparing LMP and HGSOC tumors, we can gain insight into the mechanisms underlying malignant progression in ovarian cancer. However, previous studies of the two subtypes have been focused on gene expression analysis. Here, we applied a systems biology approach, integrating gene expression profiles derived from two independent data sets containing both LMP and HGSOC tumors with protein-protein interaction data. Genes and related networks implicated by both data sets involved both known and novel disease mechanisms and highlighted the different roles of BRCA1 and CREBBP in the two tumor types. In addition, the incorporation of somatic mutation data revealed that amplification of PAK4 is associated with poor survival in patients with HGSOC. Thus, perturbations in protein interaction networks demonstrate differential trafficking of network information between malignant and benign ovarian cancers. The novel network-based molecular signatures identified here may be used to identify new targets for intervention and to improve the treatment of invasive ovarian cancer as well as early diagnosis. PMID:27788148

  20. Imaging Characteristics of Driver Mutations in EGFR, KRAS, and ALK among Treatment-Naïve Patients with Advanced Lung Adenocarcinoma

    PubMed Central

    Park, Jangchul; Kobayashi, Yoshihisa; Urayama, Kevin Y.; Yamaura, Hidekazu; Yatabe, Yasushi; Hida, Toyoaki

    2016-01-01

    This study aimed to identify the computed tomography characteristics of treatment-naïve patients with lung adenocarcinoma and known driver mutations in EGFR, KRAS, or ALK. Patients with advanced lung adenocarcinoma (stage IIIB–IV) and known mutations in EGFR, KRAS, or ALK were assessed. The radiological findings for the main tumor and intra-thoracic status were retrospectively analyzed in each group, and the groups’ characteristics were compared. We identified 265 treatment-naïve patients with non-small-cell carcinoma, who had EGFR mutations (n = 159), KRAS mutations (n = 55), or ALK rearrangements (n = 51). Among the three groups, we evaluated only patients with stage IIIB–IV lung adenocarcinoma who had EGFR mutations (n = 126), KRAS mutations (n = 35), or ALK rearrangements (n = 47). We found that ground-glass opacity at the main tumor was significantly more common among EGFR-positive patients, compared to ALK-positive patients (p = 0.009). Lymphadenopathy was significantly more common among ALK-positive patients, compared to EGFR-positive patients (p = 0.003). Extranodal invasion was significantly more common among ALK-positive patients, compared to EGFR-positive patients and KRAS-positive patients (p = 0.001 and p = 0.049, respectively). Lymphangitis was significantly more common among ALK-positive patients, compared to EGFR-positive patients (p = 0.049). Pleural effusion was significantly less common among KRAS-positive patients, compared to EGFR-positive patients and ALK-positive patients (p = 0.046 and p = 0.026, respectively). Lung metastases were significantly more common among EGFR-positive patients, compared to KRAS-positive patients and ALK-positive patients (p = 0.007 and p = 0.04, respectively). In conclusion, EGFR mutations were associated with ground-glass opacity, KRAS-positive tumors were generally solid and less likely to metastasize to the lung and pleura, and ALK-positive tumors tended to present with lymphadenopathy, extranodal

  1. The 5q deletion size in myeloid malignancies is correlated to additional chromosomal aberrations and to TP53 mutations.

    PubMed

    Stengel, Anna; Kern, Wolfgang; Haferlach, Torsten; Meggendorfer, Manja; Haferlach, Claudia

    2016-10-01

    Deletions in the long arm of chromosome 5 (del(5q)) are recurrent abnormalities in myeloid malignancies. We analyzed del(5q) and accompanying molecular mutations in MDS, MPN and MDS/MPN cases. A high del(5q) frequency was revealed in MDS (1869/11398 cases; 16%), followed by MDS/MPN (37/1107; 3%) and MPN (97/6373; 2%). To investigate potential associations of the del(5q) size with the respective phenotypes, we applied array CGH analyses in selected cohorts of 61 MDS, 22 MDS/MPN and 23 MPN cases. The size varied between 16 and 119 Mb with no differences between the entities. However, MPN and MDS/MPN cases with del(5q) sole showed a significantly smaller del(5q) than cases with additional aberrations. Sequence analysis of 27 genes revealed ≥1 mutation in 91% of patients. The highest mutation frequencies in the total cohort were observed for TP53 (31%), JAK2 (23%) and DNMT3A (18%). The molecular mutation patterns in the del(5q) cohorts were different between the entities but resembled known patterns of cohorts not selected for del(5q). Further, TP53 mutations were significantly more frequent in cases with a larger deletion size (P = 0.003). The results suggest a correlation of large del(5q) with TP53 mutations and with additional chromosomal aberrations possibly contributing to more severe courses of these cases. © 2016 Wiley Periodicals, Inc. PMID:27218649

  2. Compound mutations in BCR-ABL1 are not major drivers of primary or secondary resistance to ponatinib in CP-CML patients

    PubMed Central

    Hodgson, J. Graeme; Shah, Neil P.; Cortes, Jorge E.; Kim, Dong-Wook; Nicolini, Franck E.; Talpaz, Moshe; Baccarani, Michele; Müller, Martin C.; Li, Jin; Parker, Wendy T.; Lustgarten, Stephanie; Clackson, Tim; Haluska, Frank G.; Guilhot, Francois; Kantarjian, Hagop M.; Soverini, Simona; Hochhaus, Andreas; Hughes, Timothy P.; Rivera, Victor M.; Branford, Susan

    2016-01-01

    BCR-ABL1 kinase domain mutations can confer resistance to first- and second-generation tyrosine kinase inhibitors (TKIs) in chronic myeloid leukemia (CML). In preclinical studies, clinically achievable concentrations of the third-generation BCR-ABL1 TKI ponatinib inhibit T315I and all other single BCR-ABL1 mutants except T315M, which generates a single amino acid exchange, but requires 2 sequential nucleotide exchanges. In addition, certain compound mutants (containing ≥2 mutations in cis) confer resistance. Initial analyses based largely on conventional Sanger sequencing (SS) have suggested that the preclinical relationship between BCR-ABL1 mutation status and ponatinib efficacy is generally recapitulated in patients receiving therapy. Thus far, however, such analyses have been limited by the inability of SS to definitively identify compound mutations or mutations representing less than ∼20% of total alleles (referred to as “low-level mutations”), as well as limited patient follow-up. Here we used next-generation sequencing (NGS) to define the baseline BCR-ABL1 mutation status of 267 heavily pretreated chronic phase (CP)-CML patients from the PACE trial, and used SS to identify clonally dominant mutants that may have developed on ponatinib therapy (30.1 months median follow-up). Durable cytogenetic and molecular responses were observed irrespective of baseline mutation status and included patients with compound mutations. No single or compound mutation was identified that consistently conferred primary and/or secondary resistance to ponatinib in CP-CML patients. Ponatinib is effective in CP-CML irrespective of baseline mutation status. PMID:26603839

  3. Additive loss-of-function proteasome subunit mutations in CANDLE/PRAAS patients promote type I IFN production.

    PubMed

    Brehm, Anja; Liu, Yin; Sheikh, Afzal; Marrero, Bernadette; Omoyinmi, Ebun; Zhou, Qing; Montealegre, Gina; Biancotto, Angelique; Reinhardt, Adam; Almeida de Jesus, Adriana; Pelletier, Martin; Tsai, Wanxia L; Remmers, Elaine F; Kardava, Lela; Hill, Suvimol; Kim, Hanna; Lachmann, Helen J; Megarbane, Andre; Chae, Jae Jin; Brady, Jilian; Castillo, Rhina D; Brown, Diane; Casano, Angel Vera; Gao, Ling; Chapelle, Dawn; Huang, Yan; Stone, Deborah; Chen, Yongqing; Sotzny, Franziska; Lee, Chyi-Chia Richard; Kastner, Daniel L; Torrelo, Antonio; Zlotogorski, Abraham; Moir, Susan; Gadina, Massimo; McCoy, Phil; Wesley, Robert; Rother, Kristina I; Rother, Kristina; Hildebrand, Peter W; Brogan, Paul; Krüger, Elke; Aksentijevich, Ivona; Goldbach-Mansky, Raphaela

    2015-11-01

    Autosomal recessive mutations in proteasome subunit β 8 (PSMB8), which encodes the inducible proteasome subunit β5i, cause the immune-dysregulatory disease chronic atypical neutrophilic dermatosis with lipodystrophy and elevated temperature (CANDLE), which is classified as a proteasome-associated autoinflammatory syndrome (PRAAS). Here, we identified 8 mutations in 4 proteasome genes, PSMA3 (encodes α7), PSMB4 (encodes β7), PSMB9 (encodes β1i), and proteasome maturation protein (POMP), that have not been previously associated with disease and 1 mutation in PSMB8 that has not been previously reported. One patient was compound heterozygous for PSMB4 mutations, 6 patients from 4 families were heterozygous for a missense mutation in 1 inducible proteasome subunit and a mutation in a constitutive proteasome subunit, and 1 patient was heterozygous for a POMP mutation, thus establishing a digenic and autosomal dominant inheritance pattern of PRAAS. Function evaluation revealed that these mutations variably affect transcription, protein expression, protein folding, proteasome assembly, and, ultimately, proteasome activity. Moreover, defects in proteasome formation and function were recapitulated by siRNA-mediated knockdown of the respective subunits in primary fibroblasts from healthy individuals. Patient-isolated hematopoietic and nonhematopoietic cells exhibited a strong IFN gene-expression signature, irrespective of genotype. Additionally, chemical proteasome inhibition or progressive depletion of proteasome subunit gene transcription with siRNA induced transcription of type I IFN genes in healthy control cells. Our results provide further insight into CANDLE genetics and link global proteasome dysfunction to increased type I IFN production. PMID:26524591

  4. Additive loss-of-function proteasome subunit mutations in CANDLE/PRAAS patients promote type I IFN production

    PubMed Central

    Brehm, Anja; Liu, Yin; Sheikh, Afzal; Marrero, Bernadette; Omoyinmi, Ebun; Zhou, Qing; Montealegre, Gina; Biancotto, Angelique; Reinhardt, Adam; Almeida de Jesus, Adriana; Pelletier, Martin; Tsai, Wanxia L.; Remmers, Elaine F.; Kardava, Lela; Hill, Suvimol; Kim, Hanna; Lachmann, Helen J.; Megarbane, Andre; Chae, Jae Jin; Brady, Jilian; Castillo, Rhina D.; Brown, Diane; Casano, Angel Vera; Gao, Ling; Chapelle, Dawn; Huang, Yan; Stone, Deborah; Chen, Yongqing; Sotzny, Franziska; Lee, Chyi-Chia Richard; Kastner, Daniel L.; Torrelo, Antonio; Zlotogorski, Abraham; Moir, Susan; Gadina, Massimo; McCoy, Phil; Wesley, Robert; Rother, Kristina; Hildebrand, Peter W.; Brogan, Paul; Krüger, Elke; Aksentijevich, Ivona; Goldbach-Mansky, Raphaela

    2015-01-01

    Autosomal recessive mutations in proteasome subunit β 8 (PSMB8), which encodes the inducible proteasome subunit β5i, cause the immune-dysregulatory disease chronic atypical neutrophilic dermatosis with lipodystrophy and elevated temperature (CANDLE), which is classified as a proteasome-associated autoinflammatory syndrome (PRAAS). Here, we identified 8 mutations in 4 proteasome genes, PSMA3 (encodes α7), PSMB4 (encodes β7), PSMB9 (encodes β1i), and proteasome maturation protein (POMP), that have not been previously associated with disease and 1 mutation in PSMB8 that has not been previously reported. One patient was compound heterozygous for PSMB4 mutations, 6 patients from 4 families were heterozygous for a missense mutation in 1 inducible proteasome subunit and a mutation in a constitutive proteasome subunit, and 1 patient was heterozygous for a POMP mutation, thus establishing a digenic and autosomal dominant inheritance pattern of PRAAS. Function evaluation revealed that these mutations variably affect transcription, protein expression, protein folding, proteasome assembly, and, ultimately, proteasome activity. Moreover, defects in proteasome formation and function were recapitulated by siRNA-mediated knockdown of the respective subunits in primary fibroblasts from healthy individuals. Patient-isolated hematopoietic and nonhematopoietic cells exhibited a strong IFN gene-expression signature, irrespective of genotype. Additionally, chemical proteasome inhibition or progressive depletion of proteasome subunit gene transcription with siRNA induced transcription of type I IFN genes in healthy control cells. Our results provide further insight into CANDLE genetics and link global proteasome dysfunction to increased type I IFN production. PMID:26524591

  5. A cross-sectional observation study regarding patients and their physician willingness to wait for driver mutation report in nonsmall-cell lung cancer

    PubMed Central

    Joshi, Amit; Patil, Vijay M.; Noronha, Vanita; Ghosh, Joydeep; Bhattacharjee, Atanu; Prabhash, Kumar

    2016-01-01

    Background: Palliative chemotherapy +/− targeted therapy in accordance with mutation profile is the norm in nonsmall-cell lung cancer (NSCLC). The objective of this audit was to determine the proportion of patients and physicians, who are unwilling to wait for the mutation report and the reasons thereof. Materials and Methods: All newly diagnosed NSCLC patients, post biopsy, seen at our center between November 2014 and January 2015 were included. The relationship between patient and physician decision and objective factors was explored by Fisher's exact test. The factors considered were Eastern Cooperative Oncology Group performance status (ECOG PS), the presence of a cough, hemoptysis, fatigue, and breathlessness. The agreement between patients and physician decision was tested by contingency table. Results: Out of 168 patients, 57 were unwilling to wait for driver mutation report (33.9% 95% confidence interval [CI] 27.2-41.4%). The most common reason provided by patients was symptomatic status (23, 40.1%). No other objective factor except PS (P = 0.00) was associated with patient's decision. In 56 patients (33.4% 95% CI 26.6-40.7%), physicians were unwilling to wait. Among the tested factors ECOG PS (P = 0.000), breathlessness (P = 0.00) and fatigue (P = 0.00) were associated with the decision of not waiting for the report. The percentage corrected value of contingency between patients and physician decision was 78.74%. Conclusion: At present, in our setup, nearly one-third of our NSCLC patients opt for immediate chemotherapy treatment and are unwilling to wait for mutation analysis report. The major reasons for such attitude is poor symptom control and deteriorating general condition. PMID:27168703

  6. Stickler syndrome: further mutations in COL11A1 and evidence for additional locus heterogeneity.

    PubMed

    Martin, S; Richards, A J; Yates, J R; Scott, J D; Pope, M; Snead, M P

    1999-01-01

    Stickler syndrome (hereditary arthro-ophthalmopathy) is a dominantly inherited connective tissue disorder with ocular, oro-facial, auditory and skeletal manifestations. It is genetically and phenotypically heterogeneous with the majority of families having mutations in the gene encoding type II collagen (COL2A1) and exhibiting a characteristic 'membranous' or type 1 vitreous phenotype. More recently a novel mutation in the gene encoding the alpha1 chain of type XI collagen (COL11A1) was reported in a Stickler syndrome pedigree with a different 'beaded' or type 2 vitreous phenotype. In the present study five more families with the type 2 vitreous phenotype were examined for linkage to four candidate genes: COL2A1, COL5A2, COL11A1 and COL11A2. Two families were linked to COL11A1 and sequencing identified mutations resulting in shortened alphal(XI) collagen chains, one via exon skipping and the other via a multiexon deletion. One of the families showed weak linkage to COL5A2 but sequencing the open reading frame failed to identify a mutation. In the remaining two families all four loci were excluded by linkage analysis. These data confirm that mutations in COL11A1 cause Stickler syndrome with the type2 vitreous phenotype and also reveal further locus heterogeneity.

  7. Characterization of New Punch Mutations: Identification of Two Additional Mutant Classes

    PubMed Central

    Reynolds, E. R.; O'Donnell, J. M.

    1988-01-01

    The Punch locus of Drosophila melanogaster which encodes the pteridine biosynthetic enzyme, GTP cyclohydrolase, is genetically complex. Lethal alleles of the locus resolve into an array of interallelic complementation groups, and at least one class of mutations is developmentally specific, affecting GTP cyclohydrolase activity only in the heads of adults. All previously isolated Punch alleles were identified on the basis of a mutant eye color phenotype. By screening mutagenized chromosomes over Punch region deficiencies, we have now isolated new alleles on the basis of lethal and visible phenotypes. Most of these alleles fall into previously identified genetic classes, but two new classes of mutations were also found. One class contains two alleles that behave as dominant lethal mutations in some genetic backgrounds. The other class represents a second developmentally specific set of alleles that affect the function of the Punch locus only during embryogenesis. PMID:3136053

  8. Whole-exome and targeted sequencing identify ROBO1 and ROBO2 mutations as progression-related drivers in myelodysplastic syndromes

    PubMed Central

    Xu, Feng; Wu, Ling-Yun; Chang, Chun-Kang; He, Qi; Zhang, Zheng; Liu, Li; Shi, Wen-Hui; Guo, Juan; Zhu, Yang; Zhao, You-Shan; Gu, Shu-Cheng; Fei, Cheng-Ming; Wu, Dong; Zhou, Li-Yu; Su, Ji-Ying; Song, Lu-Xi; Xiao, Chao; Li, Xiao

    2015-01-01

    The progressive mechanism underlying myelodysplastic syndrome remains unknown. Here we identify ROBO1 and ROBO2 as novel progression-related somatic mutations using whole-exome and targeted sequencing in 6 of 16 (37.5%) paired MDS patients with disease progression. Further deep sequencing detects 20 (10.4%) patients with ROBO mutations in a cohort of 193 MDS patients. In addition, copy number loss and loss of heterogeneity (LOH) of ROBO1 and ROBO2 are frequently observed in patients with progression or carrying ROBO mutations. In in vitro experiments, overexpression of ROBO1 or ROBO2 produces anti-proliferative and pro-apoptotic effects in leukaemia cells. However, this effect was lost in ROBO mutants and ROBO-SLIT2 signalling is impaired. Multivariate analysis shows that ROBO mutations are independent factors for predicting poor survival. These findings demonstrate a novel contribution of ROBO mutations to the pathogenesis of MDS and highlight a key role for ROBO-SLIT2 signalling in MDS disease progression. PMID:26608094

  9. Additives

    NASA Technical Reports Server (NTRS)

    Smalheer, C. V.

    1973-01-01

    The chemistry of lubricant additives is discussed to show what the additives are chemically and what functions they perform in the lubrication of various kinds of equipment. Current theories regarding the mode of action of lubricant additives are presented. The additive groups discussed include the following: (1) detergents and dispersants, (2) corrosion inhibitors, (3) antioxidants, (4) viscosity index improvers, (5) pour point depressants, and (6) antifouling agents.

  10. Teen Driver Safety: Additional Research Could Help States Strengthen Graduated Driver Licensing Systems. Report to the Committee on Transportation and Infrastructure and Its Subcommittee on Highways and Transit, House of Representatives. GAO-10-544

    ERIC Educational Resources Information Center

    Fleming, Susan A.

    2010-01-01

    Teen drivers ages 16 to 20 have the highest fatality rate of any age group in the United States. As a result, states have increasingly adopted laws to limit teen driving exposure, such as Graduated Driver Licensing (GDL) systems, which consist of three stages: a learner's permit allowing driving only under supervision; intermediate licensure…

  11. The Evolving Context of Driver Mutations: ROS1 Rearrangement in Metastatic Non-Small Cell Lung Cancer.

    PubMed

    DeCaire, Ximena; Streu, Erin

    2016-09-01

    A previously healthy, 30-year-old Filipino woman presented to an emergency department with complaints of shortness of breath and mild cough. She denied constitutional symptoms, such as night sweats, fevers, loss of appetite, or weight loss. Additional investigation revealed bilateral pleural and pericardial effusions with no obvious lung lesions or masses. The pericardial fluid was drained and preliminary cytology revealed atypical carcinoma cells. Her past medical history included an embryonic pregnancy and a benign breast cyst that was biopsied in the Philippines. She had immigrated to Canada two years earlier, was working full-time, and was living with her sister. She was planning on returning to the Philippines to wed and had a strong support system in Canada. She had never smoked cigarettes or consumed alcohol and had no family history of cancer. The patient was exposed to secondhand smoke as a child.
. PMID:27541546

  12. Treatment-influenced associations of PML-RARα mutations, FLT3 mutations, and additional chromosome abnormalities in relapsed acute promyelocytic leukemia

    PubMed Central

    Moser, Barry K.; Racevskis, Janis; Poiré, Xavier; Bloomfield, Clara D.; Carroll, Andrew J.; Ketterling, Rhett P.; Roulston, Diane; Schachter-Tokarz, Esther; Zhou, Da-cheng; Chen, I-Ming L.; Harvey, Richard; Koval, Greg; Sher, Dorie A.; Feusner, James H.; Tallman, Martin S.; Larson, Richard A.; Powell, Bayard L.; Appelbaum, Frederick R.; Paietta, Elisabeth; Willman, Cheryl L.; Stock, Wendy

    2012-01-01

    Mutations in the all-trans retinoic acid (ATRA)–targeted ligand binding domain of PML-RARα (PRα/LBD+) have been implicated in the passive selection of ATRA-resistant acute promyelocytic leukemia clones leading to disease relapse. Among 45 relapse patients from the ATRA/chemotherapy arm of intergroup protocol C9710, 18 patients harbored PRα/LBD+ (40%), 7 of whom (39%) relapsed Off-ATRA selection pressure, suggesting a possible active role of PRα/LBD+. Of 41 relapse patients coanalyzed, 15 (37%) had FMS-related tyrosine kinase 3 internal tandem duplication mutations (FLT3-ITD+), which were differentially associated with PRα/LBD+ depending on ATRA treatment status at relapse: positively, On-ATRA; negatively, Off-ATRA. Thirteen of 21 patients (62%) had additional chromosome abnormalities (ACAs); all coanalyzed PRα/LBD mutant patients who relapsed off-ATRA (n = 5) had associated ACA. After relapse Off-ATRA, ACA and FLT3-ITD+ were negatively associated and were oppositely associated with presenting white blood count and PML-RARα type: ACA, low, L-isoform; FLT3-ITD+, high, S-isoform. These exploratory results suggest that differing PRα/LBD+ activities may interact with FLT3-ITD+ or ACA, that FLT3-ITD+ and ACA are associated with different intrinsic disease progression pathways manifest at relapse Off-ATRA, and that these different pathways may be short-circuited by ATRA-selectable defects at relapse On-ATRA. ACA and certain PRα/LBD+ were also associated with reduced postrelapse survival. PMID:22734072

  13. An Individual with Blepharophimosis-Ptosis-Epicanthus Inversus Syndrome (BPES) and Additional Features Expands the Phenotype Associated with Mutations in KAT6B

    PubMed Central

    Yu, Hung-Chun; Geiger, Elizabeth A.; Medne, Livija; Zackai, Elaine H.; Shaikh, Tamim H.

    2015-01-01

    Blepharophimosis-Ptosis-Epicanthus Inversus Syndrome (BPES) is an autosomal dominant disorder caused by mutations in FOXL2. We identified an individual with BPES and additional phenotypic features who did not have a FOXL2 mutation. We used whole exome sequencing to identify a de novo mutation in KAT6B (lysine acetyltransferase 6B) in this individual. The mutation was a 2 bp insertion leading to a frameshift which resulted in a premature stop codon. The resulting truncated protein does not have the C-terminal serine/methionine transcription activation domain necessary for interaction with other transcriptional and epigenetic regulators. This mutation likely has a dominant-negative or gain-of-function effect, similar to those observed in other genetic disorders resulting from KAT6B mutations, including Say-Barber-Biesecker-Young-Simpson (SBBYSS) and Genitopatellar syndrome (GTPTS). Thus, our subject’s phenotype broadens the spectrum of clinical findings associated with mutations in KAT6B. Furthermore, our results suggest that individuals with BPES without a FOXL2 mutation should be tested for KAT6B mutations. The transcriptional and epigenetic regulation mediated by KAT6B appears crucial to early developmental processes, which when perturbed can lead to a wide spectrum of phenotypic outcomes. PMID:24458743

  14. Older Drivers

    MedlinePlus

    ... Affects Driving Tips for Safe Driving Making Your Vehicle Safe Regulations Affecting Older Drivers When Driving Skills ... Like drivers of any age, they use their vehicles to go shopping, do errands, and visit the ...

  15. Growth behavior of additional offspring with a beneficial reversal allele in the asymmetric sharply-peaked landscape in the coupled discrete-time mutation-selection model

    NASA Astrophysics Data System (ADS)

    Gill, Wonpyong

    2013-01-01

    The probability of additional offspring with a beneficial reversal allele for growing to a size NC for a range of population sizes N, sequence lengths L, selective advantages s, and measuring parameters C was calculated for a haploid, asexual population in the coupled discrete-time mutation-selection model in an asymmetric sharply-peaked landscape with a positive selective advantage of the reversal allele over the optimal allele. The growing probability in the stochastic region was inversely proportional to the measuring parameter when C < 1 /Ns, bent when C ≈ 1/ Ns and saturated when C > 1/ Ns. The crossing time and the time dependence of the increase in relative density of the reversal allele in the coupled discrete-time mutation-selection model was approximated using the Wright-Fisher two-allele model with the same selective advantage and corresponding effective mutation rate. The growth behavior of additional offspring with the reversal allele in the asymmetric sharply-peaked landscape in the coupled discrete-time mutation-selection model was controlled by the selective advantage of the reversal allele compared to the optimal allele and could be described by using the Wright-Fisher two-allele model, in spite of there being many other alleles with lower fitness, and in spite of there being two alleles, the optimal and reversal allele, separated by a low-fitness valley with a tunable depth and width.

  16. Driver circuit

    NASA Technical Reports Server (NTRS)

    Matsumoto, Raymond T. (Inventor); Higashi, Stanley T. (Inventor)

    1976-01-01

    A driver circuit which has low power requirements, a relatively small number of components and provides flexibility in output voltage setting. The driver circuit comprises, essentially, two portions which are selectively activated by the application of input signals. The output signal is determined by which of the two circuit portions is activated. While each of the two circuit portions operates in a manner similar to silicon controlled rectifiers (SCR), the circuit portions are on only when an input signal is supplied thereto.

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

    PubMed

    Tafe, Laura J; Pierce, Kirsten J; Peterson, Jason D; de Abreu, Francine; Memoli, Vincent A; Black, Candice C; Pettus, Jason R; Marotti, Jonathan D; Gutmann, Edward J; Liu, Xiaoying; Shirai, Keisuke; Dragnev, Konstantin H; Amos, Christopher I; Tsongalis, Gregory J

    2016-09-01

    Detection of somatic mutations in non-small cell lung cancers (NSCLCs), especially adenocarcinomas, is important for directing patient care when targeted therapy is available. Here, we present our experience with genotyping NSCLC using the Ion Torrent Personal Genome Machine (PGM) and the AmpliSeq Cancer Hotspot Panel v2. We tested 453 NSCLC samples from 407 individual patients using the 50 gene AmpliSeq Cancer Hotspot Panel v2 from May 2013 to July 2015. Using 10 ng of DNA, up to 11 samples were simultaneously sequenced on the Ion Torrent PGM (316 and 318 chips). We identified variants with the Ion Torrent Variant Caller Plugin, and Golden Helix's SVS software was used for annotation and prediction of the significance of the variants. Three hundred ninety-eight samples were successfully sequenced (12.1% failure rate). In all, 633 variants in 41 genes were detected with a median of 2 (range of 0 to 7) variants per sample. Mutations detected in BRAF, EGFR, ERBB2, KRAS, NRAS, and PIK3CA were considered potentially actionable and were identified in 237 samples, most commonly in KRAS (37.9%), EGFR (11.1%), BRAF (4.8%), and PIK3CA (4.3%). In our patient population, all mutations in EGFR, KRAS, and BRAF were mutually exclusive. The Ion Torrent Ampliseq technology can be utilized on small biopsy and cytology specimens, requires very little input DNA, and can be applied in clinical laboratories for genotyping of NSCLC. This targeted next-generation sequencing approach allows for detection of common and also rare mutations that are clinically actionable in multiple patients simultaneously. PMID:27659017

  18. A novel P106L mutation in EPSPS and an unknown mechanism(s) act additively to confer resistance to glyphosate in a South African Lolium rigidum population.

    PubMed

    Kaundun, Shiv S; Dale, Richard P; Zelaya, Ian A; Dinelli, Giovanni; Marotti, Ilaria; McIndoe, Eddie; Cairns, Andrew

    2011-04-13

    Glyphosate resistance evolution in weeds is a growing problem in world agriculture. Here, we have investigated the mechanism(s) of glyphosate resistance in a Lolium rigidum population (DAG1) from South Africa. Nucleotide sequencing revealed the existence of at least three EPSPS homologues in the L. rigidum genome and identified a novel proline 106 to leucine substitution (P106L) in 52% DAG1 individuals. This mutation conferred a 1.7-fold resistance increase to glyphosate at the whole plant level. Additionally, a 3.1-fold resistance increase, not linked to metabolism or translocation, was estimated between wild-type P106-DAG1 and P106-STDS sensitive plants. Point accepted mutation analysis suggested that other amino acid substitutions at EPSPS position 106 are likely to be found in nature besides the P106/S/A/T/L point mutations reported to date. This study highlights the importance of minor mechanisms acting additively to confer significant levels of resistance to commercial field rates of glyphosate in weed populations subjected to high selection pressure.

  19. Computer simulation for the growing probability of additional offspring with an advantageous reversal allele in the decoupled continuous-time mutation-selection model

    NASA Astrophysics Data System (ADS)

    Gill, Wonpyong

    2016-01-01

    This study calculated the growing probability of additional offspring with the advantageous reversal allele in an asymmetric sharply-peaked landscape using the decoupled continuous-time mutation-selection model. The growing probability was calculated for various population sizes, N, sequence lengths, L, selective advantages, s, fitness parameters, k and measuring parameters, C. The saturated growing probability in the stochastic region was approximately the effective selective advantage, s*, when C≫1/Ns* and s*≪1. The present study suggests that the growing probability in the stochastic region in the decoupled continuous-time mutation-selection model can be described using the theoretical formula for the growing probability in the Moran two-allele model. The selective advantage ratio, which represents the ratio of the effective selective advantage to the selective advantage, does not depend on the population size, selective advantage, measuring parameter and fitness parameter; instead the selective advantage ratio decreases with the increasing sequence length.

  20. Gene mutations in chronic lymphocytic leukemia.

    PubMed

    Amin, Nisar A; Malek, Sami N

    2016-04-01

    The recent discovery of genes mutated in chronic lymphocytic leukemia (CLL) has stimulated new research into the role of these genes in CLL pathogenesis. CLL cases carry approximately 5-20 mutated genes per exome, a lower number than detected in many human tumors. Of the recurrently mutated genes in CLL, all are mutated in 10% or less of patients when assayed in unselected CLL cohorts at diagnosis. Mutations in TP53 are of major clinical relevance, are often associated with del17p and gain in frequency over time. TP53 mutated and associated del17p states substantially lower response rates, remission duration, and survival in CLL. Mutations in NOTCH1 and SF3B1 are recurrent, often associated with progressive CLL that is also IgVH unmutated and ZAP70-positive and are under investigation as targets for novel therapies and as factors influencing CLL outcome. There are an estimated 20-50 additional mutated genes with frequencies of 1%-5% in CLL; more work is needed to identify these and to study their significance. Finally, of the major biological aberration categories influencing CLL as a disease, gene mutations will need to be placed into context with regard to their ultimate role and importance. Such calibrated appreciation necessitates studies incorporating multiple CLL driver aberrations into biological and clinical analyses. PMID:27040699

  1. Mutational dichotomy in desmoplastic malignant melanoma corroborated by multigene panel analysis.

    PubMed

    Jahn, Stephan W; Kashofer, Karl; Halbwedl, Iris; Winter, Gerlinde; El-Shabrawi-Caelen, Laila; Mentzel, Thomas; Hoefler, Gerald; Liegl-Atzwanger, Bernadette

    2015-07-01

    Desmoplastic malignant melanoma is a distinct melanoma entity histologically subtyped into mixed and pure forms due to significantly reduced lymph node metastases in the pure form. Recent reports investigating common actionable driver mutations have demonstrated a lack of BRAF, NRAS, and KIT mutation in pure desmoplastic melanoma. In search for alternative driver mutations next generation amplicon sequencing for hotspot mutations in 50 genes cardinal to tumorigenesis was performed and in addition the RET G691S polymorphism was investigated. Data from 21 desmoplastic melanomas (12 pure and 9 mixed) were retrieved. Pure desmoplastic melanomas were either devoid of mutations (50%) or displayed mutations in tumor suppressor genes (TP53, CDKN2A, and SMAD4) singularly or in combination with the exception of a PIK3CA double-mutation lacking established biological relevance. Mixed desmoplastic melanomas on the contrary were frequently mutated (89%), and 67% exhibited activating mutations similar to common-type cutaneous malignant melanomas (BRAF, NRAS, FGFR2, and ERBB2). Separate analysis of morphologically heterogeneous tumor areas in four mixed desmoplastic malignant melanomas displayed no difference in mutation status and RET G691 status. GNAQ and GNA11, two oncogenes in BRAF and NRAS wild-type uveal melanomas, were not mutated in our cohort. The RET G691S polymorphism was found in 25% of pure and 38% of mixed desmoplastic melanomas. Apart from RET G691S our findings demonstrate absence of activating driver mutations in pure desmoplastic melanoma beyond previously investigated oncogenes (BRAF, NRAS, and KIT). The findings underline the therapeutic dichotomy of mixed versus pure desmoplastic melanoma with regard to activating mutations primarily of the mitogen-activated protein kinase pathway.

  2. MRP1 and P-glycoprotein expression assays would be useful in the additional detection of treatment non-responders in CML patients without ABL1 mutation.

    PubMed

    Park, Sang Hyuk; Park, Chan-Jeoung; Kim, Dae-Young; Lee, Bo-Ra; Kim, Young Jin; Cho, Young-Uk; Jang, Seongsoo

    2015-10-01

    We evaluated the ability of the rhodamine-123 efflux assay, multidrug resistance-associated protein-1 (MRP1) expression assay and P-glycoprotein (Pgp) expression assay to discriminate chronic myelogenous leukemia (CML) patients who had failed treatment or were at risk of failure. Each assay was performed in blood samples from CML patients (n=224) treated with tyrosine kinase inhibitors, taken at diagnosis (n=14) and follow-up (n=210). Patient samples were categorized as optimal response (n=120), suboptimal response (n=54), and treatment failure (n=36). Treatment-failed patients had a significantly higher MRP1 expression (5.24% vs. 3.54%, P=0.006) and Pgp expression (5.25% vs. 3.48%, P=0.005) than responders. Both MRP1 (%) and Pgp (%) were highly specific (95.2% and 94.5%) and relatively accurate (83.0% and 82.5%) in the detection of treatment non-responders. Of treatment-failed patients, 41.2% had a positive result in at least one assay and of these patients without ABL1 kinase domain mutation, 51.9% were positive in at least one assay. However, the rhodamine-123 efflux assay failed to discriminate two patient groups. Thus, both MRP1 and Pgp expression assays could be useful for additional identification of treatment non-responders in CML patients without ABL1 mutation.

  3. Cancer Missense Mutations Alter Binding Properties of Proteins and Their Interaction Networks

    PubMed Central

    Nishi, Hafumi; Tyagi, Manoj; Teng, Shaolei; Shoemaker, Benjamin A.; Hashimoto, Kosuke; Alexov, Emil; Wuchty, Stefan; Panchenko, Anna R.

    2013-01-01

    Many studies have shown that missense mutations might play an important role in carcinogenesis. However, the extent to which cancer mutations might affect biomolecular interactions remains unclear. Here, we map glioblastoma missense mutations on the human protein interactome, model the structures of affected protein complexes and decipher the effect of mutations on protein-protein, protein-nucleic acid and protein-ion binding interfaces. Although some missense mutations over-stabilize protein complexes, we found that the overall effect of mutations is destabilizing, mostly affecting the electrostatic component of binding energy. We also showed that mutations on interfaces resulted in more drastic changes of amino acid physico-chemical properties than mutations occurring outside the interfaces. Analysis of glioblastoma mutations on interfaces allowed us to stratify cancer-related interactions, identify potential driver genes, and propose two dozen additional cancer biomarkers, including those specific to functions of the nervous system. Such an analysis also offered insight into the molecular mechanism of the phenotypic outcomes of mutations, including effects on complex stability, activity, binding and turnover rate. As a result of mutated protein and gene network analysis, we observed that interactions of proteins with mutations mapped on interfaces had higher bottleneck properties compared to interactions with mutations elsewhere on the protein or unaffected interactions. Such observations suggest that genes with mutations directly affecting protein binding properties are preferably located in central network positions and may influence critical nodes and edges in signal transduction networks. PMID:23799087

  4. Functional annotation of rare gene aberration drivers of pancreatic cancer.

    PubMed

    Tsang, Yiu Huen; Dogruluk, Turgut; Tedeschi, Philip M; Wardwell-Ozgo, Joanna; Lu, Hengyu; Espitia, Maribel; Nair, Nikitha; Minelli, Rosalba; Chong, Zechen; Chen, Fengju; Chang, Qing Edward; Dennison, Jennifer B; Dogruluk, Armel; Li, Min; Ying, Haoqiang; Bertino, Joseph R; Gingras, Marie-Claude; Ittmann, Michael; Kerrigan, John; Chen, Ken; Creighton, Chad J; Eterovic, Karina; Mills, Gordon B; Scott, Kenneth L

    2016-01-01

    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). This approach reveals oncogenic activity for rare gene aberrations in genes including NAD Kinase (NADK), which regulates NADP(H) homeostasis and cellular redox state. We further validate mutant NADK, whose expression provides gain-of-function enzymatic activity leading to a reduction in cellular reactive oxygen species and tumorigenesis, and show that depletion of wild-type NADK in PDAC cell lines attenuates cancer cell growth in vitro and in vivo. These data indicate that annotating rare aberrations can reveal important cancer signalling pathways representing additional therapeutic targets. PMID:26806015

  5. Functional annotation of rare gene aberration drivers of pancreatic cancer

    PubMed Central

    Tsang, Yiu Huen; Dogruluk, Turgut; Tedeschi, Philip M.; Wardwell-Ozgo, Joanna; Lu, Hengyu; Espitia, Maribel; Nair, Nikitha; Minelli, Rosalba; Chong, Zechen; Chen, Fengju; Chang, Qing Edward; Dennison, Jennifer B.; Dogruluk, Armel; Li, Min; Ying, Haoqiang; Bertino, Joseph R.; Gingras, Marie-Claude; Ittmann, Michael; Kerrigan, John; Chen, Ken; Creighton, Chad J.; Eterovic, Karina; Mills, Gordon B.; Scott, Kenneth L.

    2016-01-01

    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). This approach reveals oncogenic activity for rare gene aberrations in genes including NAD Kinase (NADK), which regulates NADP(H) homeostasis and cellular redox state. We further validate mutant NADK, whose expression provides gain-of-function enzymatic activity leading to a reduction in cellular reactive oxygen species and tumorigenesis, and show that depletion of wild-type NADK in PDAC cell lines attenuates cancer cell growth in vitro and in vivo. These data indicate that annotating rare aberrations can reveal important cancer signalling pathways representing additional therapeutic targets. PMID:26806015

  6. Hyperbranching induced by cold-shock or snow-flake mutation in Neurospora crassa is prevented by addition of exogenous calcium.

    PubMed

    Kawano, Cristina Y; Said, Suraia

    2005-01-01

    Hyphal tip growth is a highly polarized process of cell extension, which may be affected by chemical and physical stress. Neurospora crassa exposed to cold-shock lost its polarized growth and dichotomous branches were detected. These effects were not observed in the presence of 500 mM Ca2+. We compared here the morphological pattern of a snow-flake mutant (sn) and the wild-type (wt) exposed to 4 degrees C. Hyphal morphology, nuclei, actin and microtubule distribution were analyzed. No effects on sn hyphal morphology were detected at 4 degrees C. Exogenous Ca2+ converted sn to an essentially wt appearance. The results presented here suggest that sn mutation and cold-shock treatment have affected Ca2+ influx since addition of this cation to sn (30 degrees C) and to wt (4 degrees C) maintained polarized growth and normal nuclear and microtubules distribution.

  7. CALR mutation profile in Irish patients with myeloproliferative neoplasms.

    PubMed

    Haslam, Karl; Conneally, Eibhlin; Flynn, Catherine M; Cahill, Mary R; Gilligan, Oonagh; O'Shea, Derville; Langabeer, Stephen E

    2016-09-01

    Insertion and/or deletion mutations of the CALR gene have recently been demonstrated to be the second most common driver mutations in the myeloproliferative neoplasms (MPNs) of essential thrombocythemia (ET) and primary myelofibrosis (PMF). Given the diagnostic and emerging prognostic significance of these mutations, in addition to the geographical heterogeneity reported, the incidence of CALR mutations was determined in an Irish cohort of patients with MPNs with a view to incorporate this analysis into a prospective screening program. A series of 202 patients with known or suspected ET and PMF were screened for the presence of CALR mutations. CALR mutations were detected in 58 patients. Type 1 and Type 1-like deletion mutations were the most common (n=40) followed by Type 2 and Type 2-like insertion mutations (n=17). The CALR mutation profile in Irish ET and PMF patients appears similar to that in other European populations. Establishment of this mutational profile allows the introduction of a rational, molecular diagnostic algorithm in cases of suspected ET and PMF that will improve clinical management. PMID:27352261

  8. BRAF V600E mutations: a series of case reports in patients with non-small cell lung cancer.

    PubMed

    Goldman, Jamie M; Gray, Jhanelle E

    2015-06-01

    We present a series of five patients with BRAF-mutated non-small cell lung cancer (NSCLC) from the Moffitt Cancer Center and a brief literature review. Information utilized included outside medical records, imaging studies, pathology reports in which simultaneous mutation testing was performed, and clinic visit notes. In addition, we conducted a literature search of background information using the following search terms: "BRAF mutations", "non-small cell lung cancer", and "driver mutations". Several retrospective studies on BRAF mutations in patients with NSCLC found that the majority of these mutations occur in adenocarcinomas and are V600E mutations. From our patients and literature search, we found that BRAF-V600E mutations occur predominantly in female smokers with adenocarcinomas.

  9. 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…

  10. Targetable signaling pathway mutations are associated with malignant phenotype in IDH-mutant gliomas

    PubMed Central

    Wakimoto, Hiroaki; Tanaka, Shota; Curry, William T.; Loebel, Franziska; Zhao, Dan; Tateishi, Kensuke; Chen, Juxiang; Klofas, Lindsay K.; Lelic, Nina; Kim, James C.; Dias-Santagata, Dora; Ellisen, Leif W.; Borger, Darrell R.; Fendt, Sarah-Maria; Heiden, Matthew G. Vander; Batchelor, Tracy T.; Iafrate, A. John; Cahill, Daniel P.; Chi, Andrew S.

    2014-01-01

    PURPOSE Isocitrate dehydrogenase (IDH) gene mutations occur in low-grade and high-grade gliomas. We sought to identify the genetic basis of malignant phenotype heterogeneity in IDH-mutant gliomas. METHODS We prospectively implanted tumor specimens from 20 consecutive IDH1-mutant glioma resections into mouse brains and genotyped all resection specimens using a CLIA-certified molecular panel. Gliomas with cancer driver mutations were tested for sensitivity to targeted inhibitors in vitro. Associations between genomic alterations and outcomes were analyzed in patients. RESULTS By 10 months, 8 of 20 IDH1-mutant gliomas developed intracerebral xenografts. All xenografts maintained mutant IDH1 and high levels of 2-hydroxyglutarate on serial transplantation. All xenograft-producing gliomas harbored “lineage-defining” mutations in CIC (oligodendroglioma) or TP53 (astrocytoma), and 6 of 8 additionally had activating mutations in PIK3CA or amplification of PDGFRA, MET or N-MYC. Only IDH1 and CIC/TP53 mutations were detected in non-xenograft-forming gliomas (P=.0007). Targeted inhibition of the additional alterations decreased proliferation in vitro. Moreover, we detected alterations in known cancer driver genes in 13.4% of IDH-mutant glioma patients, including PIK3CA, KRAS, AKT or PTEN mutation or PDGFRA, MET or N-MYC amplification. IDH/CIC mutant tumors were associated with PIK3CA/KRAS mutations while IDH/TP53 tumors correlated with PDGFRA/MET amplification. Presence of driver alterations at progression was associated with shorter subsequent progression-free survival (median 9.0 vs. 36.1 months, P=.0011). CONCLUSION A subset of IDH-mutant gliomas with mutations in driver oncogenes has a more malignant phenotype in patients. Identification of these alterations may provide an opportunity for use of targeted therapies in these patients. PMID:24714777

  11. Exome-wide mutation profile in benzo[a]pyrene-derived post-stasis and immortal human mammary epithelial cells

    SciTech Connect

    Severson, Paul L.; Vrba, Lukas; Stampfer, Martha R.; Futscher, Bernard W.

    2014-11-04

    Genetic mutations are known to drive cancer progression and certain tumors have mutation signatures that reflect exposures to environmental carcinogens. Benzo[a]pyrene (BaP) has a known mutation signature and has proven capable of inducing changes to DNA sequence that drives normal pre-stasis human mammary epithelial cells (HMEC) past a first tumor suppressor barrier (stasis) and toward immortality. We analyzed normal, pre-stasis HMEC, three independent BaP-derived post-stasis HMEC strains (184Aa, 184Be, 184Ce) and two of their immortal derivatives(184A1 and 184BE1) by whole exome sequencing. The independent post-stasis strains exhibited between 93 and 233 BaP-induced mutations in exons. Seventy percent of the mutations were C:G>A:T transversions, consistent with the known mutation spectrum of BaP. Mutations predicted to impact protein function occurred in several known and putative cancer drivers including p16, PLCG1, MED12, TAF1 in 184Aa; PIK3CG, HSP90AB1, WHSC1L1, LCP1 in 184Be and FANCA, LPP in 184Ce. Biological processes that typically harbor cancer driver mutations such as cell cycle, regulation of cell death and proliferation, RNA processing, chromatin modification and DNA repair were found to have mutations predicted to impact function in each of the post-stasis strains. Spontaneously immortalized HMEC lines derived from two of the BaP-derived post-stasis strains shared greater than 95% of their BaP-induced mutations with their precursor cells. These immortal HMEC had 10 or fewer additional point mutations relative to their post-stasis precursors, but acquired chromosomal anomalies during immortalization that arose independent of BaP. In conclusion, the results of this study indicate that acute exposures of HMEC to high dose BaP recapitulate mutation patterns of human tumors and can induce mutations in a number of cancer driver genes.

  12. Exome-wide Mutation Profile in Benzo[a]pyrene-derived Post-stasis and Immortal Human Mammary Epithelial Cells

    PubMed Central

    Severson, Paul L.; Vrba, Lukas; Stampfer, Martha R.; Futscher, Bernard W.

    2014-01-01

    Genetic mutations are known to drive cancer progression and certain tumors have mutation signatures that reflect exposures to environmental carcinogens. Benzo[a]pyrene (BaP) has a known mutation signature and has proven capable of inducing changes to DNA sequence that drives normal pre-stasis human mammary epithelial cells (HMEC) past a first tumor suppressor barrier (stasis) and towards immortality. We analyzed normal, pre-stasis HMEC, three independent BaP-derived post-stasis HMEC strains (184Aa, 184Be, 184Ce) and two of their immortal derivatives(184A1 and 184BE1) by whole exome sequencing. The independent post-stasis strains exhibited between 93 and 233 BaP-induced mutations in exons. Seventy percent of the mutations were C:G>A:T transversions, consistent with the known mutation spectrum of BaP. Mutations predicted to impact protein function occurred in several known and putative cancer drivers including p16, PLCG1, MED12, TAF1 in 184Aa; PIK3CG, HSP90AB1, WHSC1L1, LCP1 in 184Be and FANCA, LPP in 184Ce. Biological processes that typically harbor cancer driver mutations such as cell cycle, regulation of cell death and proliferation, RNA processing, chromatin modification and DNA repair were found to have mutations predicted to impact function in each of the post-stasis strains. Spontaneously immortalized HMEC lines derived from two of the BaP-derived post-stasis strains shared greater than 95% of their BaP-induced mutations with their precursor cells. These immortal HMEC had 10 or fewer additional point mutations relative to their post-stasis precursors, but acquired chromosomal anomalies during immortalization that arose independent of BaP. The results of this study indicate that acute exposures of HMEC to high dose BaP recapitulate mutation patterns of human tumors and can induce mutations in a number of cancer driver genes. PMID:25435355

  13. Genomic analysis identifies new drivers and progression pathways in skin basal cell carcinoma.

    PubMed

    Bonilla, Ximena; Parmentier, Laurent; King, Bryan; Bezrukov, Fedor; Kaya, Gürkan; Zoete, Vincent; Seplyarskiy, Vladimir B; Sharpe, Hayley J; McKee, Thomas; Letourneau, Audrey; Ribaux, Pascale G; Popadin, Konstantin; Basset-Seguin, Nicole; Ben Chaabene, Rouaa; Santoni, Federico A; Andrianova, Maria A; Guipponi, Michel; Garieri, Marco; Verdan, Carole; Grosdemange, Kerstin; Sumara, Olga; Eilers, Martin; Aifantis, Iannis; Michielin, Olivier; de Sauvage, Frederic J; Antonarakis, Stylianos E; Nikolaev, Sergey I

    2016-04-01

    Basal cell carcinoma (BCC) of the skin is the most common malignant neoplasm in humans. BCC is primarily driven by the Sonic Hedgehog (Hh) pathway. However, its phenotypic variation remains unexplained. Our genetic profiling of 293 BCCs found the highest mutation rate in cancer (65 mutations/Mb). Eighty-five percent of the BCCs harbored mutations in Hh pathway genes (PTCH1, 73% or SMO, 20% (P = 6.6 × 10(-8)) and SUFU, 8%) and in TP53 (61%). However, 85% of the BCCs also harbored additional driver mutations in other cancer-related genes. We observed recurrent mutations in MYCN (30%), PPP6C (15%), STK19 (10%), LATS1 (8%), ERBB2 (4%), PIK3CA (2%), and NRAS, KRAS or HRAS (2%), and loss-of-function and deleterious missense mutations were present in PTPN14 (23%), RB1 (8%) and FBXW7 (5%). Consistent with the mutational profiles, N-Myc and Hippo-YAP pathway target genes were upregulated. Functional analysis of the mutations in MYCN, PTPN14 and LATS1 suggested their potential relevance in BCC tumorigenesis. PMID:26950094

  14. Mutational landscape of EGFR-, MYC-, and Kras-driven genetically engineered mouse models of lung adenocarcinoma

    PubMed Central

    McFadden, David G.; Politi, Katerina; Bhutkar, Arjun; Chen, Frances K.; Song, Xiaoling; Pirun, Mono; Santiago, Philip M.; Kim-Kiselak, Caroline; Platt, James T.; Lee, Emily; Hodges, Emily; Rosebrock, Adam P.; Bronson, Roderick T.; Socci, Nicholas D.; Hannon, Gregory J.; Jacks, Tyler; Varmus, Harold

    2016-01-01

    Genetically engineered mouse models (GEMMs) of cancer are increasingly being used to assess putative driver mutations identified by large-scale sequencing of human cancer genomes. To accurately interpret experiments that introduce additional mutations, an understanding of the somatic genetic profile and evolution of GEMM tumors is necessary. Here, we performed whole-exome sequencing of tumors from three GEMMs of lung adenocarcinoma driven by mutant epidermal growth factor receptor (EGFR), mutant Kirsten rat sarcoma viral oncogene homolog (Kras), or overexpression of MYC proto-oncogene. Tumors from EGFR- and Kras-driven models exhibited, respectively, 0.02 and 0.07 nonsynonymous mutations per megabase, a dramatically lower average mutational frequency than observed in human lung adenocarcinomas. Tumors from models driven by strong cancer drivers (mutant EGFR and Kras) harbored few mutations in known cancer genes, whereas tumors driven by MYC, a weaker initiating oncogene in the murine lung, acquired recurrent clonal oncogenic Kras mutations. In addition, although EGFR- and Kras-driven models both exhibited recurrent whole-chromosome DNA copy number alterations, the specific chromosomes altered by gain or loss were different in each model. These data demonstrate that GEMM tumors exhibit relatively simple somatic genotypes compared with human cancers of a similar type, making these autochthonous model systems useful for additive engineering approaches to assess the potential of novel mutations on tumorigenesis, cancer progression, and drug sensitivity. PMID:27702896

  15. Whole-genome sequencing reveals oncogenic mutations in mycosis fungoides.

    PubMed

    McGirt, Laura Y; Jia, Peilin; Baerenwald, Devin A; Duszynski, Robert J; Dahlman, Kimberly B; Zic, John A; Zwerner, Jeffrey P; Hucks, Donald; Dave, Utpal; Zhao, Zhongming; Eischen, Christine M

    2015-07-23

    The pathogenesis of mycosis fungoides (MF), the most common cutaneous T-cell lymphoma (CTCL), is unknown. Although genetic alterations have been identified, none are considered consistently causative in MF. To identify potential drivers of MF, we performed whole-genome sequencing of MF tumors and matched normal skin. Targeted ultra-deep sequencing of MF samples and exome sequencing of CTCL cell lines were also performed. Multiple mutations were identified that affected the same pathways, including epigenetic, cell-fate regulation, and cytokine signaling, in MF tumors and CTCL cell lines. Specifically, interleukin-2 signaling pathway mutations, including activating Janus kinase 3 (JAK3) mutations, were detected. Treatment with a JAK3 inhibitor significantly reduced CTCL cell survival. Additionally, the mutation data identified 2 other potential contributing factors to MF, ultraviolet light, and a polymorphism in the tumor suppressor p53 (TP53). Therefore, genetic alterations in specific pathways in MF were identified that may be viable, effective new targets for treatment.

  16. Diagnostic value of H3F3A mutations in giant cell tumour of bone compared to osteoclast‐rich mimics

    PubMed Central

    Presneau, Nadège; Baumhoer, Daniel; Behjati, Sam; Pillay, Nischalan; Tarpey, Patrick; Campbell, Peter J; Jundt, Gernot; Hamoudi, Rifat; Wedge, David C; Loo, Peter Van; Hassan, A Bassim; Khatri, Bhavisha; Ye, Hongtao; Tirabosco, Roberto; Amary, M Fernanda

    2015-01-01

    Abstract Driver mutations in the two histone 3.3 (H3.3) genes, H3F3A and H3F3B, were recently identified by whole genome sequencing in 95% of chondroblastoma (CB) and by targeted gene sequencing in 92% of giant cell tumour of bone (GCT). Given the high prevalence of these driver mutations, it may be possible to utilise these alterations as diagnostic adjuncts in clinical practice. Here, we explored the spectrum of H3.3 mutations in a wide range and large number of bone tumours (n = 412) to determine if these alterations could be used to distinguish GCT from other osteoclast‐rich tumours such as aneurysmal bone cyst, nonossifying fibroma, giant cell granuloma, and osteoclast‐rich malignant bone tumours and others. In addition, we explored the driver landscape of GCT through whole genome, exome and targeted sequencing (14 gene panel). We found that H3.3 mutations, namely mutations of glycine 34 in H3F3A, occur in 96% of GCT. We did not find additional driver mutations in GCT, including mutations in IDH1, IDH2, USP6, TP53. The genomes of GCT exhibited few somatic mutations, akin to the picture seen in CB. Overall our observations suggest that the presence of H3F3A p.Gly34 mutations does not entirely exclude malignancy in osteoclast‐rich tumours. However, H3F3A p.Gly34 mutations appear to be an almost essential feature of GCT that will aid pathological evaluation of bone tumours, especially when confronted with small needle core biopsies. In the absence of H3F3A p.Gly34 mutations, a diagnosis of GCT should be made with caution. PMID:27499898

  17. Diagnostic value of H3F3A mutations in giant cell tumour of bone compared to osteoclast-rich mimics.

    PubMed

    Presneau, Nadège; Baumhoer, Daniel; Behjati, Sam; Pillay, Nischalan; Tarpey, Patrick; Campbell, Peter J; Jundt, Gernot; Hamoudi, Rifat; Wedge, David C; Loo, Peter Van; Hassan, A Bassim; Khatri, Bhavisha; Ye, Hongtao; Tirabosco, Roberto; Amary, M Fernanda; Flanagan, Adrienne M

    2015-04-01

    Driver mutations in the two histone 3.3 (H3.3) genes, H3F3A and H3F3B, were recently identified by whole genome sequencing in 95% of chondroblastoma (CB) and by targeted gene sequencing in 92% of giant cell tumour of bone (GCT). Given the high prevalence of these driver mutations, it may be possible to utilise these alterations as diagnostic adjuncts in clinical practice. Here, we explored the spectrum of H3.3 mutations in a wide range and large number of bone tumours (n = 412) to determine if these alterations could be used to distinguish GCT from other osteoclast-rich tumours such as aneurysmal bone cyst, nonossifying fibroma, giant cell granuloma, and osteoclast-rich malignant bone tumours and others. In addition, we explored the driver landscape of GCT through whole genome, exome and targeted sequencing (14 gene panel). We found that H3.3 mutations, namely mutations of glycine 34 in H3F3A, occur in 96% of GCT. We did not find additional driver mutations in GCT, including mutations in IDH1, IDH2, USP6, TP53. The genomes of GCT exhibited few somatic mutations, akin to the picture seen in CB. Overall our observations suggest that the presence of H3F3A p.Gly34 mutations does not entirely exclude malignancy in osteoclast-rich tumours. However, H3F3A p.Gly34 mutations appear to be an almost essential feature of GCT that will aid pathological evaluation of bone tumours, especially when confronted with small needle core biopsies. In the absence of H3F3A p.Gly34 mutations, a diagnosis of GCT should be made with caution. PMID:27499898

  18. Mutation rates, spectra, and genome-wide distribution of spontaneous mutations in mismatch repair deficient yeast.

    PubMed

    Lang, Gregory I; Parsons, Lance; Gammie, Alison E

    2013-09-01

    DNA mismatch repair is a highly conserved DNA repair pathway. In humans, germline mutations in hMSH2 or hMLH1, key components of mismatch repair, have been associated with Lynch syndrome, a leading cause of inherited cancer mortality. Current estimates of the mutation rate and the mutational spectra in mismatch repair defective cells are primarily limited to a small number of individual reporter loci. Here we use the yeast Saccharomyces cerevisiae to generate a genome-wide view of the rates, spectra, and distribution of mutation in the absence of mismatch repair. We performed mutation accumulation assays and next generation sequencing on 19 strains, including 16 msh2 missense variants implicated in Lynch cancer syndrome. The mutation rate for DNA mismatch repair null strains was approximately 1 mutation per genome per generation, 225-fold greater than the wild-type rate. The mutations were distributed randomly throughout the genome, independent of replication timing. The mutation spectra included insertions/deletions at homopolymeric runs (87.7%) and at larger microsatellites (5.9%), as well as transitions (4.5%) and transversions (1.9%). Additionally, repeat regions with proximal repeats are more likely to be mutated. A bias toward deletions at homopolymers and insertions at (AT)n microsatellites suggests a different mechanism for mismatch generation at these sites. Interestingly, 5% of the single base pair substitutions might represent double-slippage events that occurred at the junction of immediately adjacent repeats, resulting in a shift in the repeat boundary. These data suggest a closer scrutiny of tumor suppressors with homopolymeric runs with proximal repeats as the potential drivers of oncogenesis in mismatch repair defective cells. PMID:23821616

  19. The added value of using mutational profiling in addition to cytology in diagnosing aggressive pancreaticobiliary disease: review of clinical cases at a single center

    PubMed Central

    2014-01-01

    Background This study aimed to better understand the supporting role that mutational profiling (MP) of DNA from microdissected cytology slides and supernatant specimens may play in the diagnosis of malignancy in fine-needle aspirates (FNA) and biliary brushing specimens from patients with pancreaticobiliary masses. Methods Cytology results were examined in a total of 30 patients with associated surgical (10) or clinical (20) outcomes. MP of DNA from microdissected cytology slides and from discarded supernatant fluid was analyzed in 26 patients with atypical, negative or indeterminate cytology. Results Cytology correctly diagnosed aggressive disease in 4 patients. Cytological diagnoses for the remaining 26 were as follows: 16 negative (9 false negative), 9 atypical, 1 indeterminate. MP correctly determined aggressive disease in 1 false negative cytology case and confirmed a negative cytology diagnosis in 7 of 7 cases of non-aggressive disease. Of the 9 atypical cytology cases, MP correctly diagnosed 7 as positive and 1 as negative for aggressive disease. One specimen that was indeterminate by cytology was correctly diagnosed as non-aggressive by MP. When first line malignant (positive) cytology results were combined with positive second line MP results, 12/21 cases of aggressive disease were identified, compared to 4/21 cases identified by positive cytology alone. Conclusions When first line cytology results were uncertain (atypical), questionable (negative), or not possible (non-diagnostic/indeterminate), MP provided additional information regarding the presence of aggressive disease. When used in conjunction with first line cytology, MP increased detection of aggressive disease without compromising specificity in patients that were difficult to diagnose by cytology alone. PMID:25084836

  20. Transposon Mutagenesis Screen Identifies Potential Lung Cancer Drivers and CUL3 as a Tumor Suppressor

    PubMed Central

    Dorr, Casey; Janik, Callie; Weg, Madison; Been, Raha A.; Bader, Justin; Kang, Ryan; Ng, Brandon; Foran, Lindsey; Landman, Sean R.; O’Sullivan, M. Gerard; Steinbach, Michael; Sarver, Aaron L.; Silverstein, Kevin A. T.; Largaespada, David A.

    2015-01-01

    Non-small cell lung cancers (NSCLCs) harbor thousands of passenger events that hide genetic drivers. Even highly recurrent events in NSCLC, such as mutations in PTEN, EGFR, KRAS, and ALK, are only detected in, at most, 30% of patients. Thus, many unidentified low-penetrant events are causing a significant portion of lung cancers. To detect low-penetrance drivers of NSCLC a forward genetic screen was performed in mice using the Sleeping Beauty (SB) DNA transposon as a random mutagen to generate lung tumors in a Pten deficient background. SB mutations coupled with Pten deficiency were sufficient to produce lung tumors in 29% of mice. Pten deficiency alone, without SB mutations, resulted in lung tumors in 11% of mice, while the rate in control mice was ~3%. In addition, thyroid cancer and other carcinomas as well as the presence of bronchiolar and alveolar epithelialization in mice deficient for Pten were also identified. Analysis of common transposon insertion sites identified 76 candidate cancer driver genes. These genes are frequently dysregulated in human lung cancers and implicate several signaling pathways. Cullin3 (Cul3), a member of an ubiquitin ligase complex that plays a role in the oxidative stress response pathway, was identified in the screen and evidence demonstrates that Cul3 functions as a tumor suppressor. PMID:25995385

  1. 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. PMID:8153752

  2. Cancer3D: understanding cancer mutations through protein structures

    PubMed Central

    Porta-Pardo, Eduard; Hrabe, Thomas; Godzik, Adam

    2015-01-01

    The new era of cancer genomics is providing us with extensive knowledge of mutations and other alterations in cancer. The Cancer3D database at http://www.cancer3d.org gives an open and user-friendly way to analyze cancer missense mutations in the context of structures of proteins in which they are found. The database also helps users analyze the distribution patterns of the mutations as well as their relationship to changes in drug activity through two algorithms: e-Driver and e-Drug. These algorithms use knowledge of modular structure of genes and proteins to separately study each region. This approach allows users to find novel candidate driver regions or drug biomarkers that cannot be found when similar analyses are done on the whole-gene level. The Cancer3D database provides access to the results of such analyses based on data from The Cancer Genome Atlas (TCGA) and the Cancer Cell Line Encyclopedia (CCLE). In addition, it displays mutations from over 14 700 proteins mapped to more than 24 300 structures from PDB. This helps users visualize the distribution of mutations and identify novel three-dimensional patterns in their distribution. PMID:25392415

  3. Driver behaviour at roadworks.

    PubMed

    Walker, Guy; Calvert, Malcolm

    2015-11-01

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

  4. Driver behaviour at roadworks.

    PubMed

    Walker, Guy; Calvert, Malcolm

    2015-11-01

    There is an incompatibility between how transport engineers think drivers behave in roadworks and how they actually behave. As a result of this incompatibility we are losing approximately a lane's worth of capacity in addition to those closed by the roadworks themselves. The problem would have little significance were it not for the fact a lane of motorway costs approx. £30 m per mile to construct and £43 k a year to maintain, and that many more roadworks are planned as infrastructure constructed 40 or 50 years previously reaches a critical stage in its lifecycle. Given current traffic volumes, and the sensitivity of road networks to congestion, the effects of roadworks need to be accurately assessed. To do this requires a new ergonomic approach. A large-scale observational study of real traffic conditions was used to identify the issues and impacts, which were then mapped to the ergonomic knowledge-base on driver behaviour, and combined to developed practical guidelines to help in modelling future roadworks scenarios with greater behavioural accuracy. Also stemming from the work are novel directions for the future ergonomic design of roadworks themselves. PMID:26154200

  5. LANL GPIB Driver

    SciTech Connect

    2004-04-15

    This driver code adds a GPIB infrastructure and API features to 2.6 series Linux kernels. Currently supported hardware is National Instruments PCI-GPIB cards built on either the TNT4882 controller chip, or the TNT5004 controller chip. This driver is an improvement over previous GPIB drivers in Linux because it has all the features of the GPL, high performance DMA, supports Linux 2.6 and the new driver model, and has a cleaner API than the previous drivers. GPIB is the "general purpose interface bus", commonly used to control oscilloscopes, digital multimeters, function generators, and other electronic test equipment.

  6. LANL GPIB Driver

    2004-04-15

    This driver code adds a GPIB infrastructure and API features to 2.6 series Linux kernels. Currently supported hardware is National Instruments PCI-GPIB cards built on either the TNT4882 controller chip, or the TNT5004 controller chip. This driver is an improvement over previous GPIB drivers in Linux because it has all the features of the GPL, high performance DMA, supports Linux 2.6 and the new driver model, and has a cleaner API than the previous drivers.more » GPIB is the "general purpose interface bus", commonly used to control oscilloscopes, digital multimeters, function generators, and other electronic test equipment.« less

  7. Non-coding recurrent mutations in chronic lymphocytic leukaemia.

    PubMed

    Puente, Xose S; Beà, Silvia; Valdés-Mas, Rafael; Villamor, Neus; Gutiérrez-Abril, Jesús; Martín-Subero, José I; Munar, Marta; Rubio-Pérez, Carlota; Jares, Pedro; Aymerich, Marta; Baumann, Tycho; Beekman, Renée; Belver, Laura; Carrio, Anna; Castellano, Giancarlo; Clot, Guillem; Colado, Enrique; Colomer, Dolors; Costa, Dolors; Delgado, Julio; Enjuanes, Anna; Estivill, Xavier; Ferrando, Adolfo A; Gelpí, Josep L; González, Blanca; González, Santiago; González, Marcos; Gut, Marta; Hernández-Rivas, Jesús M; López-Guerra, Mónica; Martín-García, David; Navarro, Alba; Nicolás, Pilar; Orozco, Modesto; Payer, Ángel R; Pinyol, Magda; Pisano, David G; Puente, Diana A; Queirós, Ana C; Quesada, Víctor; Romeo-Casabona, Carlos M; Royo, Cristina; Royo, Romina; Rozman, María; Russiñol, Nuria; Salaverría, Itziar; Stamatopoulos, Kostas; Stunnenberg, Hendrik G; Tamborero, David; Terol, María J; Valencia, Alfonso; López-Bigas, Nuria; Torrents, David; Gut, Ivo; López-Guillermo, Armando; López-Otín, Carlos; Campo, Elías

    2015-10-22

    Chronic lymphocytic leukaemia (CLL) is a frequent disease in which the genetic alterations determining the clinicobiological behaviour are not fully understood. Here we describe a comprehensive evaluation of the genomic landscape of 452 CLL cases and 54 patients with monoclonal B-lymphocytosis, a precursor disorder. We extend the number of CLL driver alterations, including changes in ZNF292, ZMYM3, ARID1A and PTPN11. We also identify novel recurrent mutations in non-coding regions, including the 3' region of NOTCH1, which cause aberrant splicing events, increase NOTCH1 activity and result in a more aggressive disease. In addition, mutations in an enhancer located on chromosome 9p13 result in reduced expression of the B-cell-specific transcription factor PAX5. The accumulative number of driver alterations (0 to ≥4) discriminated between patients with differences in clinical behaviour. This study provides an integrated portrait of the CLL genomic landscape, identifies new recurrent driver mutations of the disease, and suggests clinical interventions that may improve the management of this neoplasia. PMID:26200345

  8. Non-coding recurrent mutations in chronic lymphocytic leukaemia.

    PubMed

    Puente, Xose S; Beà, Silvia; Valdés-Mas, Rafael; Villamor, Neus; Gutiérrez-Abril, Jesús; Martín-Subero, José I; Munar, Marta; Rubio-Pérez, Carlota; Jares, Pedro; Aymerich, Marta; Baumann, Tycho; Beekman, Renée; Belver, Laura; Carrio, Anna; Castellano, Giancarlo; Clot, Guillem; Colado, Enrique; Colomer, Dolors; Costa, Dolors; Delgado, Julio; Enjuanes, Anna; Estivill, Xavier; Ferrando, Adolfo A; Gelpí, Josep L; González, Blanca; González, Santiago; González, Marcos; Gut, Marta; Hernández-Rivas, Jesús M; López-Guerra, Mónica; Martín-García, David; Navarro, Alba; Nicolás, Pilar; Orozco, Modesto; Payer, Ángel R; Pinyol, Magda; Pisano, David G; Puente, Diana A; Queirós, Ana C; Quesada, Víctor; Romeo-Casabona, Carlos M; Royo, Cristina; Royo, Romina; Rozman, María; Russiñol, Nuria; Salaverría, Itziar; Stamatopoulos, Kostas; Stunnenberg, Hendrik G; Tamborero, David; Terol, María J; Valencia, Alfonso; López-Bigas, Nuria; Torrents, David; Gut, Ivo; López-Guillermo, Armando; López-Otín, Carlos; Campo, Elías

    2015-10-22

    Chronic lymphocytic leukaemia (CLL) is a frequent disease in which the genetic alterations determining the clinicobiological behaviour are not fully understood. Here we describe a comprehensive evaluation of the genomic landscape of 452 CLL cases and 54 patients with monoclonal B-lymphocytosis, a precursor disorder. We extend the number of CLL driver alterations, including changes in ZNF292, ZMYM3, ARID1A and PTPN11. We also identify novel recurrent mutations in non-coding regions, including the 3' region of NOTCH1, which cause aberrant splicing events, increase NOTCH1 activity and result in a more aggressive disease. In addition, mutations in an enhancer located on chromosome 9p13 result in reduced expression of the B-cell-specific transcription factor PAX5. The accumulative number of driver alterations (0 to ≥4) discriminated between patients with differences in clinical behaviour. This study provides an integrated portrait of the CLL genomic landscape, identifies new recurrent driver mutations of the disease, and suggests clinical interventions that may improve the management of this neoplasia.

  9. Teenaged Drivers and Fatal Crash Responsibility. Preliminary Report.

    ERIC Educational Resources Information Center

    Williams, Allan F.; Karpf, Ronald S.

    According to data obtained for the year 1978 from the Fatal Accident Reporting System (FARS) and from state governments under contract to the National Highway Traffic Safety Administration, teenaged drivers (especially males) have much higher rates of fatal crash involvement than older drivers. In addition, teenaged drivers are more likely than…

  10. Genetic Mutations Associated With Cigarette Smoking in Pancreatic Cancer

    PubMed Central

    Blackford, Amanda; Parmigiani, Giovanni; Kensler, Thomas W.; Wolfgang, Christopher; Jones, Siân; Zhang, Xiaosong; Parsons, D. Willams; Lin, Jimmy Cheng-Ho; Leary, Rebecca J.; Eshleman, James R.; Goggins, Michael; Jaffee, Elizabeth M.; Iacobuzio-Donahue, Christine A.; Maitra, Anirban; Klein, Alison; Cameron, John L.; Olino, Kelly; Schulick, Richard; Winter, Jordan; Vogelstein, Bert; Velculescu, Victor E.; Kinzler, Kenneth W.; Hruban, Ralph H.

    2009-01-01

    Background Cigarette smoking doubles the risk of pancreatic cancer and smoking accounts for 20 to 25% of pancreatic cancers. The recent sequencing of the pancreatic cancer genome provides an unprecedented opportunity to identify mutational patterns associated with smoking. Design We previously sequenced over 750 million base pairs of DNA from 23,219 transcripts in 24 adenocarcinomas of the pancreas (“Discovery Screen”). In this previous study the 39 genes that were mutated more than once in the Discovery Screen were sequenced in an additional 90 adenocarcinomas of the pancreas (“Validation Screen”). Here we compared the somatic mutations in the cancers obtained from individuals who ever smoked cigarettes (n=64) to the somatic mutations in the cancers obtained from individuals who never smoked cigarettes (n=50). Results When adjusted for age and gender, analyses of the Discovery Screen revealed significantly more non-synonymous mutations in the carcinomas obtained from ever smokers (mean 53.1 mutations per tumor, SD 27.9) than in the carcinomas obtained from never smokers (mean 38.5, SD 11.1, p=0.04). The difference between smokers and non-smokers was not driven by mutations in known driver genes in pancreatic cancer (KRAS, TP53, p16/CDKN2A and SMAD4), but instead was predominantly observed in genes mutated at lower frequency. No differences were observed in mutations in carcinomas from the head vs. tail of the gland. Conclusion Pancreatic carcinomas from cigarette smokers harbor more mutations than do carcinomas from never smokers. The types and patterns of these mutations provide insight into the mechanisms by which cigarette smoking causes pancreatic cancer. PMID:19351817

  11. 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.

  12. 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. PMID:19540960

  13. The Mutational Landscape of Acute Promyelocytic Leukemia Reveals an Interacting Network of Co-Occurrences and Recurrent Mutations.

    PubMed

    Ibáñez, Mariam; Carbonell-Caballero, José; García-Alonso, Luz; Such, Esperanza; Jiménez-Almazán, Jorge; Vidal, Enrique; Barragán, Eva; López-Pavía, María; LLop, Marta; Martín, Iván; Gómez-Seguí, Inés; Montesinos, Pau; Sanz, Miguel A; Dopazo, Joaquín; Cervera, José

    2016-01-01

    Preliminary Acute Promyelocytic Leukemia (APL) whole exome sequencing (WES) studies have identified a huge number of somatic mutations affecting more than a hundred different genes mainly in a non-recurrent manner, suggesting that APL is a heterogeneous disease with secondary relevant changes not yet defined. To extend our knowledge of subtle genetic alterations involved in APL that might cooperate with PML/RARA in the leukemogenic process, we performed a comprehensive analysis of somatic mutations in APL combining WES with sequencing of a custom panel of targeted genes by next-generation sequencing. To select a reduced subset of high confidence candidate driver genes, further in silico analysis were carried out. After prioritization and network analysis we found recurrent deleterious mutations in 8 individual genes (STAG2, U2AF1, SMC1A, USP9X, IKZF1, LYN, MYCBP2 and PTPN11) with a strong potential of being involved in APL pathogenesis. Our network analysis of multiple mutations provides a reliable approach to prioritize genes for additional analysis, improving our knowledge of the leukemogenesis interactome. Additionally, we have defined a functional module in the interactome of APL. The hypothesis is that the number, or the specific combinations, of mutations harbored in each patient might not be as important as the disturbance caused in biological key functions, triggered by several not necessarily recurrent mutations. PMID:26886259

  14. The Mutational Landscape of Acute Promyelocytic Leukemia Reveals an Interacting Network of Co-Occurrences and Recurrent Mutations

    PubMed Central

    García-Alonso, Luz; Such, Esperanza; Jiménez-Almazán, Jorge; Vidal, Enrique; Barragán, Eva; López-Pavía, María; LLop, Marta; Martín, Iván; Gómez-Seguí, Inés; Montesinos, Pau; Sanz, Miguel A.; Dopazo, Joaquín; Cervera, José

    2016-01-01

    Preliminary Acute Promyelocytic Leukemia (APL) whole exome sequencing (WES) studies have identified a huge number of somatic mutations affecting more than a hundred different genes mainly in a non-recurrent manner, suggesting that APL is a heterogeneous disease with secondary relevant changes not yet defined. To extend our knowledge of subtle genetic alterations involved in APL that might cooperate with PML/RARA in the leukemogenic process, we performed a comprehensive analysis of somatic mutations in APL combining WES with sequencing of a custom panel of targeted genes by next-generation sequencing. To select a reduced subset of high confidence candidate driver genes, further in silico analysis were carried out. After prioritization and network analysis we found recurrent deleterious mutations in 8 individual genes (STAG2, U2AF1, SMC1A, USP9X, IKZF1, LYN, MYCBP2 and PTPN11) with a strong potential of being involved in APL pathogenesis. Our network analysis of multiple mutations provides a reliable approach to prioritize genes for additional analysis, improving our knowledge of the leukemogenesis interactome. Additionally, we have defined a functional module in the interactome of APL. The hypothesis is that the number, or the specific combinations, of mutations harbored in each patient might not be as important as the disturbance caused in biological key functions, triggered by several not necessarily recurrent mutations. PMID:26886259

  15. 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.

  16. The novel R347g pathogenic mutation of aromatic amino acid decarboxylase provides additional molecular insights into enzyme catalysis and deficiency.

    PubMed

    Montioli, Riccardo; Paiardini, Alessandro; Kurian, Manju A; Dindo, Mirco; Rossignoli, Giada; Heales, Simon J R; Pope, Simon; Voltattorni, Carla Borri; Bertoldi, Mariarita

    2016-06-01

    We report here a clinical case of a patient with a novel mutation (Arg347→Gly) in the gene encoding aromatic amino acid decarboxylase (AADC) that is associated with AADC deficiency. The variant R347G in the purified recombinant form exhibits, similarly to the pathogenic mutation R347Q previously studied, a 475-fold drop of kcat compared to the wild-type enzyme. In attempting to unravel the reason(s) for this catalytic defect, we have carried out bioinformatics analyses of the crystal structure of AADC-carbidopa complex with the modelled catalytic loop (residues 328-339). Arg347 appears to interact with Phe103, as well as with both Leu333 and Asp345. We have then prepared and characterized the artificial F103L, R347K and D345A mutants. F103L, D345A and R347K exhibit about 13-, 97-, and 345-fold kcat decrease compared to the wild-type AADC, respectively. However, unlike F103L, the R347G, R347K and R347Q mutants as well as the D345A variant appear to be more defective in catalysis than in protein folding. Moreover, the latter mutants, unlike the wild-type protein and the F103L variant, share a peculiar binding mode of dopa methyl ester consisting of formation of a quinonoid intermediate. This finding strongly suggests that their catalytic defects are mainly due to a misplacement of the substrate at the active site. Taken together, our results highlight the importance of the Arg347-Leu333-Asp345 hydrogen-bonds network in the catalysis of AADC and reveal the molecular basis for the pathogenicity of the variants R347. Following the above results, a therapeutic treatment for patients bearing the mutation R347G is proposed.

  17. A Linear Magnetic Field Scan Driver

    PubMed Central

    QUINE, RICHARD W.; CZECHOWSKI, TOMASZ; EATON, GARETH R.

    2009-01-01

    A linear magnetic field scan driver was developed to provide a rapidly scanning magnetic field for use in electron paramagnetic resonance (EPR) spectroscopy. The driver consists of two parts: a digitally synthesized ramp waveform generator and a power amplifier to drive the magnetic field coils. Additionally, the driver provides a trigger signal to a data collection digitizer that is synchronized to the ramp waveform. The driver can also drive an arbitrary current waveform supplied from an external source. The waveform generator is computer controlled through a serial data interface. Additional functions are controlled by the user from the driver front panel. The frequency and amplitude of the waveform are each separately controlled with 12-bit resolution (one part in 4,096). Several versions of the driver have been built with different frequency and amplitude ranges. Frequencies range from 500 to 20,000 Hz. Field sweep amplitudes range up to 80 Gpp. This article also gives a brief description of the field coils that are driven by the driver. PMID:19838315

  18. Profiling of somatic mutations in acute myeloid leukemia with FLT3-ITD at diagnosis and relapse.

    PubMed

    Garg, Manoj; Nagata, Yasunobu; Kanojia, Deepika; Mayakonda, Anand; Yoshida, Kenichi; Haridas Keloth, Sreya; Zang, Zhi Jiang; Okuno, Yusuke; Shiraishi, Yuichi; Chiba, Kenichi; Tanaka, Hiroko; Miyano, Satoru; Ding, Ling-Wen; Alpermann, Tamara; Sun, Qiao-Yang; Lin, De-Chen; Chien, Wenwen; Madan, Vikas; Liu, Li-Zhen; Tan, Kar-Tong; Sampath, Abhishek; Venkatesan, Subhashree; Inokuchi, Koiti; Wakita, Satoshi; Yamaguchi, Hiroki; Chng, Wee Joo; Kham, Shirley-Kow Yin; Yeoh, Allen Eng-Juh; Sanada, Masashi; Schiller, Joanna; Kreuzer, Karl-Anton; Kornblau, Steven M; Kantarjian, Hagop M; Haferlach, Torsten; Lill, Michael; Kuo, Ming-Chung; Shih, Lee-Yung; Blau, Igor-Wolfgang; Blau, Olga; Yang, Henry; Ogawa, Seishi; Koeffler, H Phillip

    2015-11-26

    Acute myeloid leukemia (AML) with an FLT3 internal tandem duplication (FLT3-ITD) mutation is an aggressive hematologic malignancy with a grave prognosis. To identify the mutational spectrum associated with relapse, whole-exome sequencing was performed on 13 matched diagnosis, relapse, and remission trios followed by targeted sequencing of 299 genes in 67 FLT3-ITD patients. The FLT3-ITD genome has an average of 13 mutations per sample, similar to other AML subtypes, which is a low mutation rate compared with that in solid tumors. Recurrent mutations occur in genes related to DNA methylation, chromatin, histone methylation, myeloid transcription factors, signaling, adhesion, cohesin complex, and the spliceosome. Their pattern of mutual exclusivity and cooperation among mutated genes suggests that these genes have a strong biological relationship. In addition, we identified mutations in previously unappreciated genes such as MLL3, NSD1, FAT1, FAT4, and IDH3B. Mutations in 9 genes were observed in the relapse-specific phase. DNMT3A mutations are the most stable mutations, and this DNMT3A-transformed clone can be present even in morphologic complete remissions. Of note, all AML matched trio samples shared at least 1 genomic alteration at diagnosis and relapse, suggesting common ancestral clones. Two types of clonal evolution occur at relapse: either the founder clone recurs or a subclone of the founder clone escapes from induction chemotherapy and expands at relapse by acquiring new mutations. Relapse-specific mutations displayed an increase in transversions. Functional assays demonstrated that both MLL3 and FAT1 exert tumor-suppressor activity in the FLT3-ITD subtype. An inhibitor of XPO1 synergized with standard AML induction chemotherapy to inhibit FLT3-ITD growth. This study clearly shows that FLT3-ITD AML requires additional driver genetic alterations in addition to FLT3-ITD alone.

  19. Profiling of somatic mutations in acute myeloid leukemia with FLT3-ITD at diagnosis and relapse.

    PubMed

    Garg, Manoj; Nagata, Yasunobu; Kanojia, Deepika; Mayakonda, Anand; Yoshida, Kenichi; Haridas Keloth, Sreya; Zang, Zhi Jiang; Okuno, Yusuke; Shiraishi, Yuichi; Chiba, Kenichi; Tanaka, Hiroko; Miyano, Satoru; Ding, Ling-Wen; Alpermann, Tamara; Sun, Qiao-Yang; Lin, De-Chen; Chien, Wenwen; Madan, Vikas; Liu, Li-Zhen; Tan, Kar-Tong; Sampath, Abhishek; Venkatesan, Subhashree; Inokuchi, Koiti; Wakita, Satoshi; Yamaguchi, Hiroki; Chng, Wee Joo; Kham, Shirley-Kow Yin; Yeoh, Allen Eng-Juh; Sanada, Masashi; Schiller, Joanna; Kreuzer, Karl-Anton; Kornblau, Steven M; Kantarjian, Hagop M; Haferlach, Torsten; Lill, Michael; Kuo, Ming-Chung; Shih, Lee-Yung; Blau, Igor-Wolfgang; Blau, Olga; Yang, Henry; Ogawa, Seishi; Koeffler, H Phillip

    2015-11-26

    Acute myeloid leukemia (AML) with an FLT3 internal tandem duplication (FLT3-ITD) mutation is an aggressive hematologic malignancy with a grave prognosis. To identify the mutational spectrum associated with relapse, whole-exome sequencing was performed on 13 matched diagnosis, relapse, and remission trios followed by targeted sequencing of 299 genes in 67 FLT3-ITD patients. The FLT3-ITD genome has an average of 13 mutations per sample, similar to other AML subtypes, which is a low mutation rate compared with that in solid tumors. Recurrent mutations occur in genes related to DNA methylation, chromatin, histone methylation, myeloid transcription factors, signaling, adhesion, cohesin complex, and the spliceosome. Their pattern of mutual exclusivity and cooperation among mutated genes suggests that these genes have a strong biological relationship. In addition, we identified mutations in previously unappreciated genes such as MLL3, NSD1, FAT1, FAT4, and IDH3B. Mutations in 9 genes were observed in the relapse-specific phase. DNMT3A mutations are the most stable mutations, and this DNMT3A-transformed clone can be present even in morphologic complete remissions. Of note, all AML matched trio samples shared at least 1 genomic alteration at diagnosis and relapse, suggesting common ancestral clones. Two types of clonal evolution occur at relapse: either the founder clone recurs or a subclone of the founder clone escapes from induction chemotherapy and expands at relapse by acquiring new mutations. Relapse-specific mutations displayed an increase in transversions. Functional assays demonstrated that both MLL3 and FAT1 exert tumor-suppressor activity in the FLT3-ITD subtype. An inhibitor of XPO1 synergized with standard AML induction chemotherapy to inhibit FLT3-ITD growth. This study clearly shows that FLT3-ITD AML requires additional driver genetic alterations in addition to FLT3-ITD alone. PMID:26438511

  20. Next generation sequencing in synovial sarcoma reveals novel gene mutations

    PubMed Central

    Vlenterie, Myrella; Hillebrandt-Roeffen, Melissa H.S.; Flucke, Uta E.; Groenen, Patricia J.T.A.; Tops, Bastiaan B.J.; Kamping, Eveline J.; Pfundt, Rolph; de Bruijn, Diederik R.H.; van Kessel, Ad H.M. Geurts; van Krieken, Han J.H.J.M.; van der Graaf, Winette T.A.; Versleijen-Jonkers, Yvonne M.H.

    2015-01-01

    Over 95% of all synovial sarcomas (SS) share a unique translocation, t(X;18), however, they show heterogeneous clinical behavior. We analyzed multiple SS to reveal additional genetic alterations besides the translocation. Twenty-six SS from 22 patients were sequenced for 409 cancer-related genes using the Comprehensive Cancer Panel (Life Technologies, USA) on an Ion Torrent platform. The detected variants were verified by Sanger sequencing and compared to matched normal DNAs. Copy number variation was assessed in six tumors using the Oncoscan array (Affymetrix, USA). In total, eight somatic mutations were detected in eight samples. These mutations have not been reported previously in SS. Two of these, in KRAS and CCND1, represent known oncogenic mutations in other malignancies. Additional mutations were detected in RNF213, SEPT9, KDR, CSMD3, MLH1 and ERBB4. DNA alterations occurred more often in adult tumors. A distinctive loss of 6q was found in a metastatic lesion progressing under pazopanib, but not in the responding lesion. Our results emphasize t(X;18) as a single initiating event in SS and as the main oncogenic driver. Our results also show the occurrence of additional genetic events, mutations or chromosomal aberrations, occurring more frequently in SS with an onset in adults. PMID:26415226

  1. Driver drowsiness detection using multimodal sensor fusion

    NASA Astrophysics Data System (ADS)

    Andreeva, Elena O.; Aarabi, Parham; Philiastides, Marios G.; Mohajer, Keyvan; Emami, Majid

    2004-04-01

    This paper proposes a multi-modal sensor fusion algorithm for the estimation of driver drowsiness. Driver sleepiness is believed to be responsible for more than 30% of passenger car accidents and for 4% of all accident fatalities. In commercial vehicles, drowsiness is blamed for 58% of single truck accidents and 31% of commercial truck driver fatalities. This work proposes an innovative automatic sleep-onset detection system. Using multiple sensors, the driver"s body is studied as a mechanical structure of springs and dampeners. The sleep-detection system consists of highly sensitive triple-axial accelerometers to monitor the driver"s upper body in 3-D. The subject is modeled as a linear time-variant (LTV) system. An LMS adaptive filter estimation algorithm generates the transfer function (i.e. weight coefficients) for this LTV system. Separate coefficients are generated for the awake and asleep states of the subject. These coefficients are then used to train a neural network. Once trained, the neural network classifies the condition of the driver as either awake or asleep. The system has been tested on a total of 8 subjects. The tests were conducted on sleep-deprived individuals for the sleep state and on fully awake individuals for the awake state. When trained and tested on the same subject, the system detected sleep and awake states of the driver with a success rate of 95%. When the system was trained on three subjects and then retested on a fourth "unseen" subject, the classification rate dropped to 90%. Furthermore, it was attempted to correlate driver posture and sleepiness by observing how car vibrations propagate through a person"s body. Eight additional subjects were studied for this purpose. The results obtained in this experiment proved inconclusive which was attributed to significant differences in the individual habitual postures.

  2. A Simple Wave Driver

    ERIC Educational Resources Information Center

    Temiz, Burak Kagan; Yavuz, Ahmet

    2015-01-01

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

  3. Help Wanted: Drivers.

    ERIC Educational Resources Information Center

    Hoober, Scott

    1999-01-01

    A booming economy and low unemployment make it harder than ever before to lure and retain good school-bus drivers. Lack of money for good wages has prompted some innovative recruitment and retention tactics. Chicago has turned to the rolls of people going off welfare as a source of bus-driver candidates. The Trans Group, headquartered in Chestnut…

  4. Synchrotron based proton drivers

    SciTech Connect

    Weiren Chou

    2002-09-19

    Proton drivers are the proton sources that produce intense short proton bunches. They have a wide range of applications. This paper discusses the proton drivers based on high-intensity proton synchrotrons. It gives a review of the high-intensity proton sources over the world and a brief report on recent developments in this field in the U.S. high-energy physics (HEP) community. The Fermilab Proton Driver is used as a case study for a number of challenging technical design issues.

  5. UV Signature Mutations

    PubMed Central

    2014-01-01

    Sequencing complete tumor genomes and exomes has sparked the cancer field's interest in mutation signatures for identifying the tumor's carcinogen. This review and meta-analysis discusses signatures and their proper use. We first distinguish between a mutagen's canonical mutations – deviations from a random distribution of base changes to create a pattern typical of that mutagen – and the subset of signature mutations, which are unique to that mutagen and permit inference backward from mutations to mutagen. To verify UV signature mutations, we assembled literature datasets on cells exposed to UVC, UVB, UVA, or solar simulator light (SSL) and tested canonical UV mutation features as criteria for clustering datasets. A confirmed UV signature was: ≥60% of mutations are C→T at a dipyrimidine site, with ≥5% CC→TT. Other canonical features such as a bias for mutations on the non-transcribed strand or at the 3' pyrimidine had limited application. The most robust classifier combined these features with criteria for the rarity of non-UV canonical mutations. In addition, several signatures proposed for specific UV wavelengths were limited to specific genes or species; non-signature mutations induced by UV may cause melanoma BRAF mutations; and the mutagen for sunlight-related skin neoplasms may vary between continents. PMID:25354245

  6. 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.

  7. 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.

  8. 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

  9. 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

  10. Identification of Variant-Specific Functions of PIK3CA by Rapid Phenotyping of Rare Mutations | Office of Cancer Genomics

    Cancer.gov

    Large-scale sequencing efforts are uncovering the complexity of cancer genomes, which are composed of causal "driver" mutations that promote tumor progression along with many more pathologically neutral "passenger" events. The majority of mutations, both in known cancer drivers and uncharacterized genes, are generally of low occurrence, highlighting the need to functionally annotate the long tail of infrequent mutations present in heterogeneous cancers.

  11. Driver Improvement Training and Evaluation.

    ERIC Educational Resources Information Center

    Whittenburg, John A.; And Others

    The last phase of the NHTSA-U.S. Coast Guard Driver Improvement Training and Evaluation Project is described. Begun in July 1970, the project had two basic objectives. The first was to determine whether or not driver training programs do, in fact, significantly reduce driver errors and accidents and improve overall driver efficiency. The second…

  12. 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.

  13. 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).

  14. Exome-Scale Discovery of Hotspot Mutation Regions in Human Cancer Using 3D Protein Structure.

    PubMed

    Tokheim, Collin; Bhattacharya, Rohit; Niknafs, Noushin; Gygax, Derek M; Kim, Rick; Ryan, Michael; Masica, David L; Karchin, Rachel

    2016-07-01

    The impact of somatic missense mutation on cancer etiology and progression is often difficult to interpret. One common approach for assessing the contribution of missense mutations in carcinogenesis is to identify genes mutated with statistically nonrandom frequencies. Even given the large number of sequenced cancer samples currently available, this approach remains underpowered to detect drivers, particularly in less studied cancer types. Alternative statistical and bioinformatic approaches are needed. One approach to increase power is to focus on localized regions of increased missense mutation density or hotspot regions, rather than a whole gene or protein domain. Detecting missense mutation hotspot regions in three-dimensional (3D) protein structure may also be beneficial because linear sequence alone does not fully describe the biologically relevant organization of codons. Here, we present a novel and statistically rigorous algorithm for detecting missense mutation hotspot regions in 3D protein structures. We analyzed approximately 3 × 10(5) mutations from The Cancer Genome Atlas (TCGA) and identified 216 tumor-type-specific hotspot regions. In addition to experimentally determined protein structures, we considered high-quality structural models, which increase genomic coverage from approximately 5,000 to more than 15,000 genes. We provide new evidence that 3D mutation analysis has unique advantages. It enables discovery of hotspot regions in many more genes than previously shown and increases sensitivity to hotspot regions in tumor suppressor genes (TSG). Although hotspot regions have long been known to exist in both TSGs and oncogenes, we provide the first report that they have different characteristic properties in the two types of driver genes. We show how cancer researchers can use our results to link 3D protein structure and the biologic functions of missense mutations in cancer, and to generate testable hypotheses about driver mechanisms. Our results

  15. Effectiveness evaluation of simulative workshops for newly licensed drivers.

    PubMed

    Rosenbloom, Tova; Eldror, Ehud

    2014-02-01

    The current study set to examine the effects of simulator use in driving instruction on newly licensed drivers, comparing the road safety knowledge and reported intended behavior, as well as the actual driving performance of new drivers. Participants consisted of 280 newly licensed driver, of which 140 whose drivers license training included additional simulator-based lessons, and 140 drivers whose training precluded simulator-based lessons. All drivers answered questionnaires pertaining to their intended safe driving behaviors (according to Ajzen's (2000) theory of planned behavior), and to their traffic safety knowledge. Of the initial sample, 40 drivers received actual driving performance evaluation by an expert driving instructor, as well as by in-vehicle data recorders (IVDRs). We assumed that safer drivers report safer driving intentions, demonstrate greater traffic safety knowledge, evaluated as safer drivers by the driving instructor, and display lower and stable driving parameters on the IVDRs. We hypothesized that theoretical driving studies combined with practical training on simulators will elevate the safety level of novices driving. Hierarchical regression analyses on driving intentions indicated that drivers who did not receive simulator-based lessons demonstrated safer driving intentions compared to drivers who received simulator-based lessons. This pattern possibly indicating the drivers who received simulator-based lessons felt more confident in their driving abilities compared to drivers who did not receive simulated training. No significant difference was found in traffic safety knowledge, or in the evaluation of the expert driving instructor. IDVR data comparisons indicated drivers who received simulator-based lessons braked more often and were less prone to headway events, suggesting a more responsive driving style. These findings do not point to any significant advantage or disadvantage of the current simulator-based driving training over

  16. Missing Drivers with Dementia: Antecedents and Recovery

    PubMed Central

    Rowe, Meredeth A.; Greenblum, Catherine A.; Boltz, Marie; Galvin, James E.

    2013-01-01

    OBJECTIVES To determine the circumstance in which persons with dementia become lost while driving, how missing drivers are found, and how Silver Alert notificationsare instrumental in those discoveries. DESIGN A retrospective, descriptive study. SETTING Retrospective record review. PARTICIPANTS Conducted using 156 records from the Florida Silver Alert program for the time period October, 2008 through May 2010. These alerts were issued in Florida for a missing driver with dementia. MEASUREMENTS Information derived from the reports on characteristics of the missing driver, antecedents to missing event and discovery of a missing driver. RESULTS and CONCLUSION The majority of missing drivers were males, with ages ranging from 58’94, who were being cared for by a spouse. Most drivers became lost on routine, caregiver-sanctioned trips to usual locations. Only 15% were in the act of driving when found with most being found in or near a parked car and the large majority were found by law enforcement officers. Only 40% were found in the county they went missing and 10% were found in a different state. Silver Alert notifications were most effective for law enforcement; citizen alerts resulted in a few discoveries. There was a 5% mortality rate in the study population with those living alone more likely to be found dead than alive. An additional 15% were found in dangerous situations such as stopped on railroad tracks. Thirty-two percent had documented driving or dangerous errors such as, driving thewrong way or into secluded areas, or walking in or near roadways. PMID:23134069

  17. Drinking histories of fatally injured drivers

    PubMed Central

    Baker, S; Braver, E; Chen, L; Li, G; Williams, A

    2002-01-01

    Context: About 30% of drivers killed in crashes have high blood alcohol concentrations (BACs) of 0.10+ g/dl. There is a question about whether these drivers primarily are problem drinkers who chronically drink and drive—the so-called hard core drinking drivers. Objective: To investigate drinking histories of fatally injured drivers in relation to their BACs. Design and participants: Retrospective cohort study of 818 fatally injured drivers who were included in the 1993 National Mortality Followback Survey (a national sample of US deaths in which next of kin were interviewed) and whose BACs were recorded by the Fatality Analysis Reporting System, a census of US traffic deaths. Main outcome measure: Problem drinking indicators. Results: At least one indicator of potential problem drinking, primarily heavy drinking, was reported for 68% of drivers with very high BACs (0.15+ g/dl), 41% with BACs of 0.10–0.14 g/dl, 32% with BACs of 0.01–0.09 g/dl, and 7% with zero BACs. Spouses provided more credible responses than other relatives: they were more likely to report at least occasional drinking and driving among deceased drivers with high BACs. For the most direct signs of problem drinking (described as a problem drinker during the last month of life or frequently driving after having five or more drinks), spousal reports suggested the prevalence of problem drinking among drivers with very high BACs was 22% (having both indicators), 32% (frequently driving after having five or more drinks), 44% (described as problem drinker), or 57% (having either indicator). Conclusions: Drivers with BACs of 0.10+ g/dl were far more likely than sober drivers to be described as having markers of problem drinking. However, many did not have indicators suggestive of problem drinking. In addition to programs focused on repeat offenders or problem drinkers, countermeasures such as sobriety checkpoints that target a broader spectrum of drinking drivers are appropriate. PMID:12226120

  18. CRAF R391W is a melanoma driver oncogene

    PubMed Central

    Atefi, Mohammad; Titz, Bjoern; Tsoi, Jennifer; Avramis, Earl; Le, Allison; Ng, Charles; Lomova, Anastasia; Lassen, Amanda; Friedman, Michael; Chmielowski, Bartosz; Ribas, Antoni; Graeber, Thomas G.

    2016-01-01

    Approximately 75% of melanomas have known driver oncogenic mutations in BRAF, NRAS, GNA11 or GNAQ, while the mutations providing constitutive oncogenic signaling in the remaining melanomas are not known. We established a melanoma cell line from a tumor with none of the common driver mutations. This cell line demonstrated a signaling profile similar to BRAF-mutants, but lacked sensitivity to the BRAF inhibitor vemurafenib. RNA-seq mutation data implicated CRAF R391W as the alternative driver mutation of this melanoma. CRAF R391W was homozygous and over expressed. These melanoma cells were highly sensitive to CRAF, but not BRAF knockdown. In reconstitution experiments, CRAF R391W, but not CRAF WT, transformed NIH3T3 cells in soft-agar colony formation assays, increased kinase activity in vitro, induced MAP kinase signaling and conferred vemurafenib resistance. MAP kinase inducing activity was dependent on CRAF dimerization. Thus, CRAF is a bona fide alternative oncogene for BRAF/NRAS/GNAQ/GNA11 wild type melanomas. PMID:27273450

  19. A multinomial choice model approach for dynamic driver vision transitions.

    PubMed

    Huang, Shih-Hsuan; Wong, Jinn-Tsai

    2015-01-01

    Exploring the continual process of drivers allocating their attention under varying conditions could be vital for preventing motor vehicle crashes. This study aims to model visual behaviors and to estimate the effects of various contributing factors on driver's vision transitions. A visual attention allocation framework, based on certain contributing attributes related to driving tasks and environmental conditions, has been developed. The associated logit type models for determining driver choices for focal points were successfully formulated and estimated by using naturalistic glance data from the 100-car event database. The results offer insights into driver visual behavior and patterns of visual attention allocation. The three focal points that drivers most frequently rely on and glance at are the forward, left and rear view mirror. The sample drivers were less likely to demonstrate troublesome transition patterns, particularly in mentally demanding situations. Additionally, instead of shifting vision directly between two non-forward focal points, the sample drivers frequently had an intermediate forward glance. Thus, seemingly unrelated paths could be grouped into explanatory patterns of driver attention allocation. Finally, in addition to the vision-transition patterns, the potential pitfalls of such patterns and possible countermeasures to improving safety are illustrated, focusing on situations when drivers are distracted, traveling at high speeds and approaching intersections.

  20. 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.

  1. Identification of novel candidate drivers connecting different dysfunctional levels for lung adenocarcinoma using protein-protein interactions and a shortest path approach

    PubMed Central

    Chen, Lei; Huang, Tao; Zhang, Yu-Hang; Jiang, Yang; Zheng, Mingyue; Cai, Yu-Dong

    2016-01-01

    Tumors are formed by the abnormal proliferation of somatic cells with disordered growth regulation under the influence of tumorigenic factors. Recently, the theory of “cancer drivers” connects tumor initiation with several specific mutations in the so-called cancer driver genes. According to the differentiation of four basic levels between tumor and adjacent normal tissues, the cancer drivers can be divided into the following: (1) Methylation level, (2) microRNA level, (3) mutation level, and (4) mRNA level. In this study, a computational method is proposed to identify novel lung adenocarcinoma drivers based on dysfunctional genes on the methylation, microRNA, mutation and mRNA levels. First, a large network was constructed using protein-protein interactions. Next, we searched all of the shortest paths connecting dysfunctional genes on different levels and extracted new candidate genes lying on these paths. Finally, the obtained candidate genes were filtered by a permutation test and an additional strict selection procedure involving a betweenness ratio and an interaction score. Several candidate genes remained, which are deemed to be related to two different levels of cancer. The analyses confirmed our assertions that some have the potential to contribute to the tumorigenesis process on multiple levels. PMID:27412431

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

    PubMed Central

    Tseng, Yuen-Yi; Oh, Coyin; Kim, Jaegil; Tyburczy, Magdalena E.; Chekaluk, Yvonne; Liu, Yang; Alesi, Nicola; Finlay, Geraldine A.; Wu, Chin-Lee; Signoretti, Sabina; Meyerson, Matthew; Getz, Gad; Kwiatkowski, David J.

    2016-01-01

    Renal angiomyolipoma is a kidney tumor in the perivascular epithelioid (PEComa) family that is common in patients with Tuberous Sclerosis Complex (TSC) and Lymphangioleiomyomatosis (LAM) but occurs rarely sporadically. Though histologically benign, renal angiomyolipoma can cause life-threatening hemorrhage and kidney failure. Both angiomyolipoma and LAM have mutations in TSC2 or TSC1. However, the frequency and contribution of other somatic events in tumor development is unknown. We performed whole exome sequencing in 32 resected tumor samples (n = 30 angiomyolipoma, n = 2 LAM) from 15 subjects, including three with TSC. Two germline and 22 somatic inactivating mutations in TSC2 were identified, and one germline TSC1 mutation. Twenty of 32 (62%) samples showed copy neutral LOH (CN-LOH) in TSC2 or TSC1 with at least 8 different LOH regions, and 30 of 32 (94%) had biallelic loss of either TSC2 or TSC1. Whole exome sequencing identified a median of 4 somatic non-synonymous coding region mutations (other than in TSC2/TSC1), a mutation rate lower than nearly all other cancer types. Three genes with mutations were known cancer associated genes (BAP1, ARHGAP35 and SPEN), but they were mutated in a single sample each, and were missense variants with uncertain functional effects. Analysis of sixteen angiomyolipomas from a TSC subject showed both second hit point mutations and CN-LOH in TSC2, many of which were distinct, indicating that they were of independent clonal origin. However, three tumors had two shared mutations in addition to private somatic mutations, suggesting a branching evolutionary pattern of tumor development following initiating loss of TSC2. Our results indicate that TSC2 and less commonly TSC1 alterations are the primary essential driver event in angiomyolipoma/LAM, whereas other somatic mutations are rare and likely do not contribute to tumor development. PMID:27494029

  3. Seven Performance Drivers.

    ERIC Educational Resources Information Center

    Ross, Linda

    2003-01-01

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

  4. Assessment of older drivers.

    PubMed

    Reuben, D B

    1993-05-01

    As concern increases about the safety of the aging driver, it is clear that the principal goal of assessment is to identify the unsafe driver and provide effective medical and rehabilitative services to enable the resumption of safe driving. When adequate restorative therapy is not possible, it is necessary to restrict or revoke the privilege of driving. Assessment also can reassure the safe older driver that he or she can continue operating a motor vehicle without restrictions. The process of assessing the older driver is best accomplished through the collaboration of health professionals and governmental agencies. The former identify and treat, if possible, medical conditions that may pose threats to safe driving; the latter establish guidelines of competency for driving tasks. These roles are complementary, although the settings and methods for these assessments are different. Moreover, the responsibilities of the physician and other health care professionals extend beyond the decision regarding driving and must consider the individual needs for driving, as well as the ramifications associated with its cessation. PMID:8504391

  5. The Bicycle Driver's Guide.

    ERIC Educational Resources Information Center

    Pennsylvania State Dept. of Education, Harrisburg. Bureau of Curriculum Services.

    Designed to emphasize the concept of the bicycle driver vs. the popular term, bicycle rider, this manual contains guidelines on bicycle safety, addressing itself both to parents and children. The main section topics are: (1) parent responsibility; (2) choosing a bicycle, fitting it to the child, and learning to drive; (3) bicycle equipment,…

  6. Florida Driver Education Handbook.

    ERIC Educational Resources Information Center

    Mick, Susan H.

    This student edition contains the same basic information as the official Florida Driver Handbook, but the reading difficulty of the material has been sharply reduced. It also provides activity-oriented exercises and review tests on this material. Introductory materials include a complete listing of all activities given, some vocabulary exercises…

  7. Energy Efficiency Handbook for Driver's Education.

    ERIC Educational Resources Information Center

    Berlowitz, Dan; And Others

    Presented are suggestions to help the automobile driver attain the saving of fuel and money. Discussed are starting and stopping; anticipation of traffic conditions; use of accessories; trip planning; and accomodation of pedestrians and cyclists. Additional topics covered include systematic car maintenance and safety considerations. (RE)

  8. Exome-wide mutation profile in benzo[a]pyrene-derived post-stasis and immortal human mammary epithelial cells

    DOE PAGES

    Severson, Paul L.; Vrba, Lukas; Stampfer, Martha R.; Futscher, Bernard W.

    2014-11-04

    Genetic mutations are known to drive cancer progression and certain tumors have mutation signatures that reflect exposures to environmental carcinogens. Benzo[a]pyrene (BaP) has a known mutation signature and has proven capable of inducing changes to DNA sequence that drives normal pre-stasis human mammary epithelial cells (HMEC) past a first tumor suppressor barrier (stasis) and toward immortality. We analyzed normal, pre-stasis HMEC, three independent BaP-derived post-stasis HMEC strains (184Aa, 184Be, 184Ce) and two of their immortal derivatives(184A1 and 184BE1) by whole exome sequencing. The independent post-stasis strains exhibited between 93 and 233 BaP-induced mutations in exons. Seventy percent of the mutationsmore » were C:G>A:T transversions, consistent with the known mutation spectrum of BaP. Mutations predicted to impact protein function occurred in several known and putative cancer drivers including p16, PLCG1, MED12, TAF1 in 184Aa; PIK3CG, HSP90AB1, WHSC1L1, LCP1 in 184Be and FANCA, LPP in 184Ce. Biological processes that typically harbor cancer driver mutations such as cell cycle, regulation of cell death and proliferation, RNA processing, chromatin modification and DNA repair were found to have mutations predicted to impact function in each of the post-stasis strains. Spontaneously immortalized HMEC lines derived from two of the BaP-derived post-stasis strains shared greater than 95% of their BaP-induced mutations with their precursor cells. These immortal HMEC had 10 or fewer additional point mutations relative to their post-stasis precursors, but acquired chromosomal anomalies during immortalization that arose independent of BaP. In conclusion, the results of this study indicate that acute exposures of HMEC to high dose BaP recapitulate mutation patterns of human tumors and can induce mutations in a number of cancer driver genes.« less

  9. Road accidents caused by drivers falling asleep.

    PubMed

    Sagberg, F

    1999-11-01

    About 29600 Norwegian accident-involved drivers received a questionnaire about the last accident reported to their insurance company. About 9200 drivers (31%) returned the questionnaire. The questionnaire contained questions about sleep or fatigue as contributing factors to the accident. In addition, the drivers reported whether or not they had fallen asleep some time whilst driving. and what the consequences had been. Sleep or drowsiness was a contributing factor in 3.9% of all accidents, as reported by drivers who were at fault for the accident. This factor was strongly over-represented in night-time accidents (18.6%), in running-off-the-road accidents (8.3%), accidents after driving more than 150 km on one trip (8.1%), and personal injury accidents (7.3%). A logistic regression analysis showed that the following additional factors made significant and independent contributions to increasing the odds of sleep involvement in an accident: dry road, high speed limit, driving one's own car, not driving the car daily, high education, and few years of driving experience. More male than female drivers were involved in sleep-related accidents, but this seems largely to be explained by males driving relatively more than females on roads with high speed limits. A total of 10% of male drivers and 4% of females reported to have fallen asleep while driving during the last 12 months. A total of 4% of these events resulted in an accident. The most frequent consequence of falling asleep--amounting to more than 40% of the reported incidents--was crossing of the right edge-line before awaking, whereas crossing of the centreline was reported by 16%. Drivers' lack of awareness of important precursors of falling asleep--like highway hypnosis, driving without awareness, and similar phenomena--as well as a reluctance to discontinue driving despite feeling tired are pointed out as likely contributors to sleep-related accidents. More knowledge about the drivers' experiences immediately

  10. Mutation rates as adaptations.

    PubMed

    Maley, C

    1997-06-01

    In order to better understand life, it is helpful to look beyond the envelop of life as we know it. A simple model of coevolution was implemented with the addition of a gene for the mutation rate of the individual. This allowed the mutation rate itself to evolve in a lineage. The model shows that when the individuals interact in a sort of zero-sum game, the lineages maintain relatively high mutation rates. However, when individuals engage in interactions that have greater consequences for one individual in the interaction than the other, lineages tend to evolve relatively low mutation rates. This model suggests that one possible cause for differential mutation rates across genes may be the coevolutionary pressure of the various forms of interactions with other genes. PMID:9219670

  11. Drivers' perceptions and reactions to roadside memorials.

    PubMed

    Tay, Richard

    2009-07-01

    Despite their growing popularity in North America, little research has been conducted on understanding the effects of roadside memorials on drivers' behaviour. In this study, an online survey of 810 drivers found that public opinions on the policy options as well as drivers' self-reported reactions to the presence of roadside memorials were fairly divided. In addition, an on-road experiment was conducted to examine the short term effects of roadside memorials at two intersections. Our results showed that the number of red light violations was reduced by 16.7% in the 6 weeks after the installation of the mock memorials compared to the 6 weeks before whereas the number of violations at two comparison sites experienced an increase of 16.8%.

  12. Identifying potential cancer driver genes by genomic data integration

    NASA Astrophysics Data System (ADS)

    Chen, Yong; Hao, Jingjing; Jiang, Wei; He, Tong; Zhang, Xuegong; Jiang, Tao; Jiang, Rui

    2013-12-01

    Cancer is a genomic disease associated with a plethora of gene mutations resulting in a loss of control over vital cellular functions. Among these mutated genes, driver genes are defined as being causally linked to oncogenesis, while passenger genes are thought to be irrelevant for cancer development. With increasing numbers of large-scale genomic datasets available, integrating these genomic data to identify driver genes from aberration regions of cancer genomes becomes an important goal of cancer genome analysis and investigations into mechanisms responsible for cancer development. A computational method, MAXDRIVER, is proposed here to identify potential driver genes on the basis of copy number aberration (CNA) regions of cancer genomes, by integrating publicly available human genomic data. MAXDRIVER employs several optimization strategies to construct a heterogeneous network, by means of combining a fused gene functional similarity network, gene-disease associations and a disease phenotypic similarity network. MAXDRIVER was validated to effectively recall known associations among genes and cancers. Previously identified as well as novel driver genes were detected by scanning CNAs of breast cancer, melanoma and liver carcinoma. Three predicted driver genes (CDKN2A, AKT1, RNF139) were found common in these three cancers by comparative analysis.

  13. Identifying potential cancer driver genes by genomic data integration

    PubMed Central

    Chen, Yong; Hao, Jingjing; Jiang, Wei; He, Tong; Zhang, Xuegong; Jiang, Tao; Jiang, Rui

    2013-01-01

    Cancer is a genomic disease associated with a plethora of gene mutations resulting in a loss of control over vital cellular functions. Among these mutated genes, driver genes are defined as being causally linked to oncogenesis, while passenger genes are thought to be irrelevant for cancer development. With increasing numbers of large-scale genomic datasets available, integrating these genomic data to identify driver genes from aberration regions of cancer genomes becomes an important goal of cancer genome analysis and investigations into mechanisms responsible for cancer development. A computational method, MAXDRIVER, is proposed here to identify potential driver genes on the basis of copy number aberration (CNA) regions of cancer genomes, by integrating publicly available human genomic data. MAXDRIVER employs several optimization strategies to construct a heterogeneous network, by means of combining a fused gene functional similarity network, gene-disease associations and a disease phenotypic similarity network. MAXDRIVER was validated to effectively recall known associations among genes and cancers. Previously identified as well as novel driver genes were detected by scanning CNAs of breast cancer, melanoma and liver carcinoma. Three predicted driver genes (CDKN2A, AKT1, RNF139) were found common in these three cancers by comparative analysis. PMID:24346768

  14. Feasibility of a driver performance data acquisition system

    SciTech Connect

    Carter, R.J.; Spelt, P.F.; Goodman, M.J.

    1994-06-01

    The National Highway Traffic Safety Administration (NHTSA) envisions many future situations in which the effectiveness and consequences of new intelligent vehicle-highway systems technologies will need to be studied in actual production vehicles. Such studies will enable evaluations in vehicles which are familiar to drivers. These studies would be future enhanced by the availability of an instrumentation package that can be easily installed in these vehicles to enable specific vehicle configurations of interest to be evaluated, thereby increasing the variety of vehicle options that are available for study. Ideally, an approach is needed that would allow data collection from a variety of vehicle models and types, and would address the issue of driver familiarity. Such an approach is embodied in the concept of a driver performance data acquisition system that could be installed in a wide range of vehicles within a relatively short period of time. As a universally adaptable system, it would provide researchers with the ability to manually input data as well as directly record information on driver, vehicle, roadway, and environmental parameters. Furthermore, it would enable the measurement of driver performance in the driver`s own vehicle, thereby ensuring vehicle familiarity. In addition, it would be possible to measure driver performance in relation to any vehicle design characteristic at relatively little expense and effort, and would make it easy to update existing models of driver/vehicle behavior to reflect performance characteristics in vehicles of current manufacture.

  15. Recurrent inactivating RASA2 mutations in melanoma

    PubMed Central

    Arafeh, Rand; Qutob, Nouar; Emmanuel, Rafi; Keren-Paz, Alona; Madore, Jason; Elkahloun, Abdel; Wilmott, James S.; Gartner, Jared J.; Di Pizio, Antonella; Winograd-Katz, Sabina; Sindiri, Sivasish; Rotkopf, Ron; Dutton-Regester, Ken; Johansson, Peter; Pritchard, Antonia; Waddell, Nicola; Hill, Victoria K.; Lin, Jimmy C.; Hevroni, Yael; Rosenberg, Steven A.; Khan, Javed; Ben-Dor, Shifra; Niv, Masha Y.; Ulitsky, Igor; Mann, Graham J; Scolyer, Richard A.; Hayward, Nicholas K.; Samuels, Yardena

    2016-01-01

    Analysis of 501 melanoma exomes revealed RASA2, encoding a RasGAP, as a tumor-suppressor gene mutated in 5% of melanomas. Recurrent loss-of-function mutations in RASA2 were found to increase RAS activation, melanoma cell growth and migration. RASA2 expression was lost in ≥30% of human melanomas and was associated with reduced patient survival. These findings reveal RASA2 inactivation as a melanoma driver and highlight the importance of Ras GAPs in cancer. PMID:26502337

  16. 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

  17. Earning a driver's license.

    PubMed Central

    Williams, A F

    1997-01-01

    Teenage drivers in the United States have greatly elevated crash rates, primarily a result of qualities associated with immaturity and lack of driving experience. State licensing systems vary substantially, but most have allowed quick and easy access to driving with full privileges at a young age, contributing to the crash problem. Formal driver education has not been an effective crash prevention measure. Following the introduction of graduated licensing in New Zealand, Australia, and Canada, this system has been considered in many states and has been implemented in some. Graduated systems phase in full privilege driving, requiring initial experience to be gained under conditions of lower risk. The author describes the first five multistage graduated systems enacted in the United States in 1996 and 1997. Factors that will influence the acceptability and effectiveness of these new licensing systems are discussed. Images p[452]-a p454-a p456-a p457-a p460-a PMID:10822470

  18. Earning a driver's license.

    PubMed

    Williams, A F

    1997-01-01

    Teenage drivers in the United States have greatly elevated crash rates, primarily a result of qualities associated with immaturity and lack of driving experience. State licensing systems vary substantially, but most have allowed quick and easy access to driving with full privileges at a young age, contributing to the crash problem. Formal driver education has not been an effective crash prevention measure. Following the introduction of graduated licensing in New Zealand, Australia, and Canada, this system has been considered in many states and has been implemented in some. Graduated systems phase in full privilege driving, requiring initial experience to be gained under conditions of lower risk. The author describes the first five multistage graduated systems enacted in the United States in 1996 and 1997. Factors that will influence the acceptability and effectiveness of these new licensing systems are discussed.

  19. Drivers, Trends and Mitigation

    SciTech Connect

    Blanco, Arthur S.; Gerlagh, Reyer; Suh, Sangwon; Barrett, John A.; de Coninck, Heleen; Diaz Morejon, Cristobal Felix; Mathur, Ritu; Nakicenovic, Nebojsa; Ahenkorah, Alfred Ofosu; Pan, Jiahua; Pathak, Himanshu; Rice, Jake; Richels, Richard G.; Smith, Steven J.; Stern, David; Toth, Ferenc L.; Zhou, Peter

    2014-12-01

    Chapter 5 analyzes the anthropogenic greenhouse gas (GHG) emission trends until the present and the main drivers that explain those trends. The chapter uses different perspectives to analyze past GHG-emissions trends, including aggregate emissions flows and per capita emissions, cumulative emissions, sectoral emissions, and territory-based vs. consumption-based emissions. In all cases, global and regional trends are analyzed. Where appropriate, the emission trends are contextualized with long-term historic developments in GHG emissions extending back to 1750.

  20. Robotic Intelligence Kernel: Driver

    SciTech Connect

    2009-09-16

    The INL Robotic Intelligence Kernel-Driver is built on top of the RIK-A and implements a dynamic autonomy structure. The RIK-D is used to orchestrate hardware for sensing and action as well as software components for perception, communication, behavior and world modeling into a single cognitive behavior kernel that provides intrinsic intelligence for a wide variety of unmanned ground vehicle systems.

  1. Whole-genome sequencing reveals oncogenic mutations in mycosis fungoides

    PubMed Central

    McGirt, Laura Y.; Jia, Peilin; Baerenwald, Devin A.; Duszynski, Robert J.; Dahlman, Kimberly B.; Zic, John A.; Zwerner, Jeffrey P.; Hucks, Donald; Dave, Utpal; Zhao, Zhongming

    2015-01-01

    The pathogenesis of mycosis fungoides (MF), the most common cutaneous T-cell lymphoma (CTCL), is unknown. Although genetic alterations have been identified, none are considered consistently causative in MF. To identify potential drivers of MF, we performed whole-genome sequencing of MF tumors and matched normal skin. Targeted ultra-deep sequencing of MF samples and exome sequencing of CTCL cell lines were also performed. Multiple mutations were identified that affected the same pathways, including epigenetic, cell-fate regulation, and cytokine signaling, in MF tumors and CTCL cell lines. Specifically, interleukin-2 signaling pathway mutations, including activating Janus kinase 3 (JAK3) mutations, were detected. Treatment with a JAK3 inhibitor significantly reduced CTCL cell survival. Additionally, the mutation data identified 2 other potential contributing factors to MF, ultraviolet light, and a polymorphism in the tumor suppressor p53 (TP53). Therefore, genetic alterations in specific pathways in MF were identified that may be viable, effective new targets for treatment. PMID:26082451

  2. 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.

  3. There is a world beyond protein mutations: the role of non-coding RNAs in melanomagenesis.

    PubMed

    Swoboda, Rolf K; Herlyn, Meenhard

    2013-05-01

    Until recently, the general perception has been that mutations in protein-coding genes are responsible for tumorigenesis. With the discovery of (V600E)BRAF in about 50% of cutaneous melanomas, there was an increased effort to find additional mutations. However, mutations characterized in melanoma to date cannot account for the development of all melanomas. With the discovery of microRNAs as important players in melanomagenesis, protein mutations are no longer considered the sole drivers of tumors. Recent research findings have expanded the view for tumor initiation and progression to additional non-coding RNAs. The data suggest that tumorigenesis is likely an interplay between mutated proteins and deregulation of non-coding RNAs in the cell with an additional role of the tumor environment. With the exception of microRNAs, our knowledge of the role of non-coding RNAs in melanoma is in its infancy. Using few examples, we will summarize some of the roles of non-coding RNAs in tumorigenesis. Thus, there is a whole world beyond protein-coding sequences and microRNAs, which can cause melanoma.

  4. Displaceable Gear Torque Controlled Driver

    NASA Technical Reports Server (NTRS)

    Cook, Joseph S., Jr. (Inventor)

    1997-01-01

    Methods and apparatus are provided for a torque driver including a displaceable gear to limit torque transfer to a fastener at a precisely controlled torque limit. A biasing assembly biases a first gear into engagement with a second gear for torque transfer between the first and second gear. The biasing assembly includes a pressurized cylinder controlled at a constant pressure that corresponds to a torque limit. A calibrated gage and valve is used to set the desired torque limit. One or more coiled output linkages connect the first gear with the fastener adaptor which may be a socket for a nut. A gear tooth profile provides a separation force that overcomes the bias to limit torque at the desired torque limit. Multiple fasteners may be rotated simultaneously to a desired torque limit if additional output spur gears are provided. The torque limit is adjustable and may be different for fasteners within the same fastener configuration.

  5. Genome destabilizing mutator alleles drive specific mutational trajectories in Saccharomyces cerevisiae.

    PubMed

    Stirling, Peter C; Shen, Yaoqing; Corbett, Richard; Jones, Steven J M; Hieter, Philip

    2014-02-01

    In addition to environmental factors and intrinsic variations in base substitution rates, specific genome-destabilizing mutations can shape the mutational trajectory of genomes. How specific alleles influence the nature and position of accumulated mutations in a genomic context is largely unknown. Understanding the impact of genome-destabilizing alleles is particularly relevant to cancer genomes where biased mutational signatures are identifiable. We first created a more complete picture of cellular pathways that impact mutation rate using a primary screen to identify essential Saccharomyces cerevisiae gene mutations that cause mutator phenotypes. Drawing primarily on new alleles identified in this resource, we measure the impact of diverse mutator alleles on mutation patterns directly by whole-genome sequencing of 68 mutation-accumulation strains derived from wild-type and 11 parental mutator genotypes. The accumulated mutations differ across mutator strains, displaying base-substitution biases, allele-specific mutation hotspots, and break-associated mutation clustering. For example, in mutants of POLα and the Cdc13-Stn1-Ten1 complex, we find a distinct subtelomeric bias for mutations that we show is independent of the target sequence. Together our data suggest that specific genome-instability mutations are sufficient to drive discrete mutational signatures, some of which share properties with mutation patterns seen in tumors. Thus, in a population of cells, genome-instability mutations could influence clonal evolution by establishing discrete mutational trajectories for genomes.

  6. Genome Destabilizing Mutator Alleles Drive Specific Mutational Trajectories in Saccharomyces cerevisiae

    PubMed Central

    Stirling, Peter C.; Shen, Yaoqing; Corbett, Richard; Jones, Steven J. M.; Hieter, Philip

    2014-01-01

    In addition to environmental factors and intrinsic variations in base substitution rates, specific genome-destabilizing mutations can shape the mutational trajectory of genomes. How specific alleles influence the nature and position of accumulated mutations in a genomic context is largely unknown. Understanding the impact of genome-destabilizing alleles is particularly relevant to cancer genomes where biased mutational signatures are identifiable. We first created a more complete picture of cellular pathways that impact mutation rate using a primary screen to identify essential Saccharomyces cerevisiae gene mutations that cause mutator phenotypes. Drawing primarily on new alleles identified in this resource, we measure the impact of diverse mutator alleles on mutation patterns directly by whole-genome sequencing of 68 mutation-accumulation strains derived from wild-type and 11 parental mutator genotypes. The accumulated mutations differ across mutator strains, displaying base-substitution biases, allele-specific mutation hotspots, and break-associated mutation clustering. For example, in mutants of POLα and the Cdc13–Stn1–Ten1 complex, we find a distinct subtelomeric bias for mutations that we show is independent of the target sequence. Together our data suggest that specific genome-instability mutations are sufficient to drive discrete mutational signatures, some of which share properties with mutation patterns seen in tumors. Thus, in a population of cells, genome-instability mutations could influence clonal evolution by establishing discrete mutational trajectories for genomes. PMID:24336748

  7. Hypothesis: Obesity Is Associated with a Lower Mutation Threshold in Colon Cancer

    PubMed Central

    Bordonaro, Michael; Lazarova, Darina

    2015-01-01

    Neoplastic progression requires accumulation of several mutations (mutation threshold). We hypothesize that obesity raises the risk of microsatellite stable (MSS) colon cancer (CC) at least in part by decreasing the mutation threshold. Thus, we posit that obese patients require fewer mutations, particularly driver mutations, compared to their normal BMI counterparts. Further, we suggest that the reduced number of required mutations in obese patients could be due to several factors, including the high levels of cytokines that accompany obesity. Cytokine-activated ERK, AKT, and JAK/STAT signaling could synergize with CC-initiating mutations to promote intestinal neoplastic development. Therefore, driver mutations that induce these specific pathways may not be “required” for neoplastic development in obesity; alteration in cell signaling consequent to obesity can substitute for some driver mutations in neoplastic progression. This hypothesis is supported by preliminary analyses of data from The Cancer Genome Atlas (TCGA). Thus, we observed that, compared to normal weight patients, cancer genomes of obese MSS CC patients exhibit fewer somatic mutations, and correspondingly lower numbers of mutations in driver genes (P = 0.026).The most striking observation was the lower number of KRAS mutations detected in patients with high body-mass index (BMI). These intriguing observations require further validation with increased number of patients, taking into account all possible confounding factors. If the hypothesis is confirmed, future studies should also address several possible explanations for the observed lower mutation threshold in obese MSS CC patients. PMID:26284133

  8. Rapid growth of a hepatocellular carcinoma and the driving mutations revealed by cell-population genetic analysis of whole-genome data.

    PubMed

    Tao, Yong; Ruan, Jue; Yeh, Shiou-Hwei; Lu, Xuemei; Wang, Yu; Zhai, Weiwei; Cai, Jun; Ling, Shaoping; Gong, Qiang; Chong, Zecheng; Qu, Zhengzhong; Li, Qianqian; Liu, Jiang; Yang, Jin; Zheng, Caihong; Zeng, Changqing; Wang, Hurng-Yi; Zhang, Jing; Wang, Sheng-Han; Hao, Lingtong; Dong, Lili; Li, Wenjie; Sun, Min; Zou, Wei; Yu, Caixia; Li, Chaohua; Liu, Guojing; Jiang, Lan; Xu, Jin; Huang, Huanwei; Li, Chunyan; Mi, Shuangli; Zhang, Bing; Chen, Baoxian; Zhao, Wenming; Hu, Songnian; Zhuang, Shi-Mei; Shen, Yang; Shi, Suhua; Brown, Christopher; White, Kevin P; Chen, Ding-Shinn; Chen, Pei-Jer; Wu, Chung-I

    2011-07-19

    We present the analysis of the evolution of tumors in a case of hepatocellular carcinoma. This case is particularly informative about cancer growth dynamics and the underlying driving mutations. We sampled nine different sections from three tumors and seven more sections from the adjacent nontumor tissues. Selected sections were subjected to exon as well as whole-genome sequencing. Putative somatic mutations were then individually validated across all 9 tumor and 7 nontumor sections. Among the mutations validated, 24 were amino acid changes; in addition, 22 large indels/copy number variants (>1 Mb) were detected. These somatic mutations define four evolutionary lineages among tumor cells. Separate evolution and expansion of these lineages were recent and rapid, each apparently having only one lineage-specific protein-coding mutation. Hence, by using a cell-population genetic definition, this approach identified three coding changes (CCNG1, P62, and an indel/fusion gene) as tumor driver mutations. These three mutations, affecting cell cycle control and apoptosis, are functionally distinct from mutations that accumulated earlier, many of which are involved in inflammation/immunity or cell anchoring. These distinct functions of mutations at different stages may reflect the genetic interactions underlying tumor growth.

  9. Sandia Material Model Driver

    2005-09-28

    The Sandia Material Model Driver (MMD) software package allows users to run material models from a variety of different Finite Element Model (FEM) codes in a standalone fashion, independent of the host codes. The MMD software is designed to be run on a variety of different operating system platforms as a console application. Initial development efforts have resulted in a package that has been shown to be fast, convenient, and easy to use, with substantialmore » growth potential.« less

  10. The RIA driver linac.

    SciTech Connect

    Shepard, K. W.

    2002-09-23

    The driver linac for the U.S. RIA project will be a 1.4 GV superconducting linac capable of accelerating the full mass range of ions from 900 MeV protons to 400 MeV/u uranium, and delivering a cw beam of 400 kW shared by at least two targets simultaneously. Elements of the linac are being developed at several U.S. laboratories. The current status of linac design and development is reviewed with emphasis on changes in the baseline design since the last linac conference.

  11. A novel active heads-up display for driver assistance.

    PubMed

    Doshi, Anup; Cheng, Shinko Yuanhsien; Trivedi, Mohan Manubhai

    2009-02-01

    In this paper, we introduce a novel laser-based wide-area heads-up windshield display which is capable of actively interfacing with a human as part of a driver assistance system. The dynamic active display (DAD) is a unique prototype interface that presents safety-critical visual icons to the driver in a manner that minimizes the deviation of his or her gaze direction without adding to unnecessary visual clutter. As part of an automotive safety system, the DAD presents alerts in the field of view of the driver only if necessary, which is based upon the state and pose of the driver, vehicle, and environment. This paper examines the effectiveness of DAD through a comprehensive comparative experimental evaluation of a speed compliance driver assistance system, which is implemented on a vehicular test bed. Three different types of display protocols for assisting a driver to comply with speed limits are tested on actual roadways, and these are compared with a conventional dashboard display. Given the inclination, drivers who are given an overspeed warning alert reduced the time required to slow down to the speed limit by 38% (p < 0.01) as compared with the drivers not given the alert. Additionally, certain alerts decreased distraction levels by reducing the time spent looking away from the road by 63% (p < 0.01). Ultimately, these alerts demonstrate the utility and promise of the DAD system.

  12. Hazard prediction discriminates between novice and experienced drivers.

    PubMed

    Crundall, David

    2016-01-01

    Typical hazard perception tests often confound multiple processes in their responses. The current study tested hazard prediction in isolation to assess whether this component can discriminate between novice and experienced drivers. A variant of the hazard perception test, based on the Situation Awareness Global Assessment Technique, found experienced drivers to outperform novices across three experiments suggesting that the act of predicting an imminent hazard is a crucial part of the hazard-perception process. Furthermore three additional hypotheses were tested in these experiments. First, performance was compared across clips of different length. There was marginal evidence that novice drivers' performance suffered with the longest clips, but experienced drivers' performance did not, suggesting that experienced drivers find hazard prediction less effortful. Secondly, predictive accuracy was found to be dependent on the temporal proximity of visual precursors to the hazard. Thirdly the relationship between the hazard and its precursor was found to be important, with less obvious precursors improving the discrimination between novice and experience drivers. These findings demonstrate that a measure of hazard prediction, which is less confounded by the influence of risk appraisal than simple response time measures, can still discriminate between novice and experienced drivers. Application of this methodology under different conditions can produce insights into the underlying processes that may be at work, whilst also providing an alternative test of driver skill in relation to the detection of hazards. PMID:26513336

  13. Determining older driver crash responsibility from police and insurance data.

    PubMed

    Langford, Jim; Koppel, Sjaanie; Andrea, Dale; Fildes, Brian

    2006-12-01

    This study aimed to determine the extent to which older drivers can be considered responsible for their crashes, to identify key factors in those crashes for which older drivers have been judged responsible, and to assess the extent to which older drivers' extra crash responsibility contributes to the road toll. Insurance claims from the State of Tasmania, Australia, for 1998-2002 were linked with police records for crashes involving drivers aged either 41-55 years or 65 years or older. Insurance and police data sets contained independent judgments of crash responsibility. There was a high level of agreement between the two sets of judgments, with older drivers judged around 1.5 times more likely to be responsible for their crashes than middle-aged drivers and, conversely, older drivers were around 0.6 as likely to be absolved from crash responsibility. It was concluded that older drivers' additional crash responsibility while valuable in explaining "what went wrong," currently makes only a small contribution to the overall road toll.

  14. Mechanisms responsible for the chromosome and gene mutations driving carcinogenesis: Implications for dose-response characteristics of mutagenic carcinogens

    EPA Science Inventory

    Through the use of high throughput DNA sequencing techniques, it has been possible to characterize a number of tumor types at the molcular level. This has led to the concept that there are "driver" mutations and "passenger" mutations, with an estimate of the number of the driver...

  15. SF3B1 mutations constitute a novel therapeutic target in breast cancer

    PubMed Central

    Maguire, Sarah L; Leonidou, Andri; Wai, Patty; Marchiò, Caterina; Ng, Charlotte KY; Sapino, Anna; Salomon, Anne-Vincent; Reis-Filho, Jorge S; Weigelt, Britta; Natrajan, Rachael C

    2015-01-01

    Mutations in genes encoding proteins involved in RNA splicing have been found to occur at relatively high frequencies in several tumour types including myelodysplastic syndromes, chronic lymphocytic leukaemia, uveal melanoma, and pancreatic cancer, and at lower frequencies in breast cancer. To investigate whether dysfunction in RNA splicing is implicated in the pathogenesis of breast cancer, we performed a re-analysis of published exome and whole genome sequencing data. This analysis revealed that mutations in spliceosomal component genes occurred in 5.6% of unselected breast cancers, including hotspot mutations in the SF3B1 gene, which were found in 1.8% of unselected breast cancers. SF3B1 mutations were significantly associated with ER-positive disease, AKT1 mutations, and distinct copy number alterations. Additional profiling of hotspot mutations in a panel of special histological subtypes of breast cancer showed that 16% and 6% of papillary and mucinous carcinomas of the breast harboured the SF3B1 K700E mutation. RNA sequencing identified differentially spliced events expressed in tumours with SF3B1 mutations including the protein coding genes TMEM14C, RPL31, DYNL11, UQCC, and ABCC5, and the long non-coding RNA CRNDE. Moreover, SF3B1 mutant cell lines were found to be sensitive to the SF3b complex inhibitor spliceostatin A and treatment resulted in perturbation of the splicing signature. Albeit rare, SF3B1 mutations result in alternative splicing events, and may constitute drivers and a novel therapeutic target in a subset of breast cancers. © 2014 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland. PMID:25424858

  16. Counter-driver shock tube

    NASA Astrophysics Data System (ADS)

    Tamba, T.; Nguyen, T. M.; Takeya, K.; Harasaki, T.; Iwakawa, A.; Sasoh, A.

    2015-11-01

    A "counter-driver" shock tube was developed. In this device, two counter drivers are actuated with an appropriate delay time to generate the interaction between a shock wave and a flow in the opposite direction which is induced by another shock wave. The conditions for the counter drivers can be set independently. Each driver is activated by a separate electrically controlled diaphragm rupture device, in which a pneumatic piston drives a rupture needle with a temporal jitter of better than 1.1 ms. Operation demonstrations were conducted to evaluate the practical performance.

  17. Novel recurrently mutated genes in African American colon cancers

    PubMed Central

    Guda, Kishore; Veigl, Martina L.; Varadan, Vinay; Nosrati, Arman; Ravi, Lakshmeswari; Lutterbaugh, James; Beard, Lydia; Willson, James K. V.; Sedwick, W. David; Wang, Zhenghe John; Molyneaux, Neil; Miron, Alexander; Adams, Mark D.; Elston, Robert C.; Markowitz, Sanford D.; Willis, Joseph E.

    2015-01-01

    We used whole-exome and targeted sequencing to characterize somatic mutations in 103 colorectal cancers (CRC) from African Americans, identifying 20 new genes as significantly mutated in CRC. Resequencing 129 Caucasian derived CRCs confirmed a 15-gene set as a preferential target for mutations in African American CRCs. Two predominant genes, ephrin type A receptor 6 (EPHA6) and folliculin (FLCN), with mutations exclusive to African American CRCs, are by genetic and biological criteria highly likely African American CRC driver genes. These previously unsuspected differences in the mutational landscapes of CRCs arising among individuals of different ethnicities have potential to impact on broader disparities in cancer behaviors. PMID:25583493

  18. Novel recurrently mutated genes in African American colon cancers.

    PubMed

    Guda, Kishore; Veigl, Martina L; Varadan, Vinay; Nosrati, Arman; Ravi, Lakshmeswari; Lutterbaugh, James; Beard, Lydia; Willson, James K V; Sedwick, W David; Wang, Zhenghe John; Molyneaux, Neil; Miron, Alexander; Adams, Mark D; Elston, Robert C; Markowitz, Sanford D; Willis, Joseph E

    2015-01-27

    We used whole-exome and targeted sequencing to characterize somatic mutations in 103 colorectal cancers (CRC) from African Americans, identifying 20 new genes as significantly mutated in CRC. Resequencing 129 Caucasian derived CRCs confirmed a 15-gene set as a preferential target for mutations in African American CRCs. Two predominant genes, ephrin type A receptor 6 (EPHA6) and folliculin (FLCN), with mutations exclusive to African American CRCs, are by genetic and biological criteria highly likely African American CRC driver genes. These previously unsuspected differences in the mutational landscapes of CRCs arising among individuals of different ethnicities have potential to impact on broader disparities in cancer behaviors. PMID:25583493

  19. Fast SCR Thyratron Driver

    SciTech Connect

    Nguyen, M.N.; /SLAC

    2007-06-18

    As part of an improvement project on the linear accelerator at SLAC, it was necessary to replace the original thyratron trigger generator, which consisted of two chassis, two vacuum tubes, and a small thyratron. All solid-state, fast rise, and high voltage thyratron drivers, therefore, have been developed and built for the 244 klystron modulators. The rack mounted, single chassis driver employs a unique way to control and generate pulses through the use of an asymmetric SCR, a PFN, a fast pulse transformer, and a saturable reactor. The resulting output pulse is 2 kV peak into 50 {Omega} load with pulse duration of 1.5 {mu}s FWHM at 180 Hz. The pulse risetime is less than 40 ns with less than 1 ns jitter. Various techniques are used to protect the SCR from being damaged by high voltage and current transients due to thyratron breakdowns. The end-of-line clipper (EOLC) detection circuit is also integrated into this chassis to interrupt the modulator triggering in the event a high percentage of line reflections occurred.

  20. Square pulse linear transformer driver

    NASA Astrophysics Data System (ADS)

    Kim, A. A.; Mazarakis, M. G.; Sinebryukhov, V. A.; Volkov, S. N.; Kondratiev, S. S.; Alexeenko, V. M.; Bayol, F.; Demol, G.; Stygar, W. A.

    2012-04-01

    The linear transformer driver (LTD) technological approach can result in relatively compact devices that can deliver fast, high current, and high-voltage pulses straight out of the LTD cavity without any complicated pulse forming and pulse compression network. Through multistage inductively insulated voltage adders, the output pulse, increased in voltage amplitude, can be applied directly to the load. The usual LTD architecture [A. A. Kim, M. G. Mazarakis, V. A. Sinebryukhov, B. M. Kovalchuk, V. A. Vizir, S. N Volkov, F. Bayol, A. N. Bastrikov, V. G. Durakov, S. V. Frolov, V. M. Alexeenko, D. H. McDaniel, W. E. Fowler, K. LeCheen, C. Olson, W. A. Stygar, K. W. Struve, J. Porter, and R. M. Gilgenbach, Phys. Rev. ST Accel. Beams 12, 050402 (2009)PRABFM1098-440210.1103/PhysRevSTAB.12.050402; M. G. Mazarakis, W. E. Fowler, A. A. Kim, V. A. Sinebryukhov, S. T. Rogowski, R. A. Sharpe, D. H. McDaniel, C. L. Olson, J. L. Porter, K. W. Struve, W. A. Stygar, and J. R. Woodworth, Phys. Rev. ST Accel. Beams 12, 050401 (2009)PRABFM1098-440210.1103/PhysRevSTAB.12.050401] provides sine shaped output pulses that may not be well suited for some applications like z-pinch drivers, flash radiography, high power microwaves, etc. A more suitable power pulse would have a flat or trapezoidal (rising or falling) top. In this paper, we present the design and first test results of an LTD cavity that generates such a type of output pulse by including within its circular array a number of third harmonic bricks in addition to the main bricks. A voltage adder made out of a square pulse cavity linear array will produce the same shape output pulses provided that the timing of each cavity is synchronized with the propagation of the electromagnetic pulse.

  1. Braf Mutations Initiate the Development of Rat Gliomas Induced by Postnatal Exposure to N-Ethyl-N-Nitrosourea.

    PubMed

    Wang, Qi; Satomi, Kaishi; Oh, Ji Eun; Hutter, Barbara; Brors, Benedikt; Diessl, Nicolle; Liu, Hai-Kun; Wolf, Stephan; Wiestler, Otmar; Kleihues, Paul; Koelsch, Bernd; Kindler-Röhrborn, Andrea; Ohgaki, Hiroko

    2016-10-01

    A single dose of N-ethyl-N-nitrosourea (ENU) during late prenatal or early postnatal development induces a high incidence of malignant schwannomas and gliomas in rats. Although T->A mutations in the transmembrane domain of the Neu (c-ErbB-2) gene are the driver mutations in ENU-induced malignant schwannomas, the molecular basis of ENU-induced gliomas remains enigmatic. We performed whole-genome sequencing of gliomas that developed in three BDIV and two BDIX rats exposed to a single dose of 80 mg ENU/kg body weight on postnatal day one. T:A->A:T and T:A->C:G mutations, which are typical for ENU-induced mutagenesis, were predominant (41% to 55% of all somatic single nucleotide mutations). T->A mutations were identified in all five rat gliomas at Braf codon 545 (V545E), which corresponds to the human BRAF V600E. Additional screening revealed that 33 gliomas in BDIV rats and 12 gliomas in BDIX rats all carried a Braf V545E mutation, whereas peritumoral brain tissue of either strain had the wild-type sequence. The gliomas were immunoreactive to BRAF V600E antibody. These results indicate that Braf mutation is a frequent early event in the development of rat gliomas caused by a single dose of ENU. PMID:27658714

  2. Sparse expression bases in cancer reveal tumor drivers.

    PubMed

    Logsdon, Benjamin A; Gentles, Andrew J; Miller, Chris P; Blau, C Anthony; Becker, Pamela S; Lee, Su-In

    2015-02-18

    We define a new category of candidate tumor drivers in cancer genome evolution: 'selected expression regulators' (SERs)-genes driving dysregulated transcriptional programs in cancer evolution. The SERs are identified from genome-wide tumor expression data with a novel method, namely SPARROW ( SPAR: se selected exp R: essi O: n regulators identified W: ith penalized regression). SPARROW uncovers a previously unknown connection between cancer expression variation and driver events, by using a novel sparse regression technique. Our results indicate that SPARROW is a powerful complementary approach to identify candidate genes containing driver events that are hard to detect from sequence data, due to a large number of passenger mutations and lack of comprehensive sequence information from a sufficiently large number of samples. SERs identified by SPARROW reveal known driver mutations in multiple human cancers, along with known cancer-associated processes and survival-associated genes, better than popular methods for inferring gene expression networks. We demonstrate that when applied to acute myeloid leukemia expression data, SPARROW identifies an apoptotic biomarker (PYCARD) for an investigational drug obatoclax. The PYCARD and obatoclax association is validated in 30 AML patient samples.

  3. Sparse expression bases in cancer reveal tumor drivers

    PubMed Central

    Logsdon, Benjamin A.; Gentles, Andrew J.; Miller, Chris P.; Blau, C. Anthony; Becker, Pamela S.; Lee, Su-In

    2015-01-01

    We define a new category of candidate tumor drivers in cancer genome evolution: ‘selected expression regulators’ (SERs)—genes driving dysregulated transcriptional programs in cancer evolution. The SERs are identified from genome-wide tumor expression data with a novel method, namely SPARROW (SPARse selected expRessiOn regulators identified With penalized regression). SPARROW uncovers a previously unknown connection between cancer expression variation and driver events, by using a novel sparse regression technique. Our results indicate that SPARROW is a powerful complementary approach to identify candidate genes containing driver events that are hard to detect from sequence data, due to a large number of passenger mutations and lack of comprehensive sequence information from a sufficiently large number of samples. SERs identified by SPARROW reveal known driver mutations in multiple human cancers, along with known cancer-associated processes and survival-associated genes, better than popular methods for inferring gene expression networks. We demonstrate that when applied to acute myeloid leukemia expression data, SPARROW identifies an apoptotic biomarker (PYCARD) for an investigational drug obatoclax. The PYCARD and obatoclax association is validated in 30 AML patient samples. PMID:25583238

  4. A Pan-Cancer Catalogue of Cancer Driver Protein Interaction Interfaces.

    PubMed

    Porta-Pardo, Eduard; Garcia-Alonso, Luz; Hrabe, Thomas; Dopazo, Joaquin; Godzik, Adam

    2015-10-01

    Despite their importance in maintaining the integrity of all cellular pathways, the role of mutations on protein-protein interaction (PPI) interfaces as cancer drivers has not been systematically studied. Here we analyzed the mutation patterns of the PPI interfaces from 10,028 proteins in a pan-cancer cohort of 5,989 tumors from 23 projects of The Cancer Genome Atlas (TCGA) to find interfaces enriched in somatic missense mutations. To that end we use e-Driver, an algorithm to analyze the mutation distribution of specific protein functional regions. We identified 103 PPI interfaces enriched in somatic cancer mutations. 32 of these interfaces are found in proteins coded by known cancer driver genes. The remaining 71 interfaces are found in proteins that have not been previously identified as cancer drivers even that, in most cases, there is an extensive literature suggesting they play an important role in cancer. Finally, we integrate these findings with clinical information to show how tumors apparently driven by the same gene have different behaviors, including patient outcomes, depending on which specific interfaces are mutated. PMID:26485003

  5. A Pan-Cancer Catalogue of Cancer Driver Protein Interaction Interfaces

    PubMed Central

    Hrabe, Thomas; Dopazo, Joaquin; Godzik, Adam

    2015-01-01

    Despite their importance in maintaining the integrity of all cellular pathways, the role of mutations on protein-protein interaction (PPI) interfaces as cancer drivers has not been systematically studied. Here we analyzed the mutation patterns of the PPI interfaces from 10,028 proteins in a pan-cancer cohort of 5,989 tumors from 23 projects of The Cancer Genome Atlas (TCGA) to find interfaces enriched in somatic missense mutations. To that end we use e-Driver, an algorithm to analyze the mutation distribution of specific protein functional regions. We identified 103 PPI interfaces enriched in somatic cancer mutations. 32 of these interfaces are found in proteins coded by known cancer driver genes. The remaining 71 interfaces are found in proteins that have not been previously identified as cancer drivers even that, in most cases, there is an extensive literature suggesting they play an important role in cancer. Finally, we integrate these findings with clinical information to show how tumors apparently driven by the same gene have different behaviors, including patient outcomes, depending on which specific interfaces are mutated. PMID:26485003

  6. Testing a structural model of young driver willingness to uptake Smartphone Driver Support Systems.

    PubMed

    Kervick, Aoife A; Hogan, Michael J; O'Hora, Denis; Sarma, Kiran M

    2015-10-01

    There is growing interest in the potential value of using phone applications that can monitor driver behaviour (Smartphone Driver Support Systems, 'SDSSs') in mitigating risky driving by young people. However, their value in this regard will only be realised if young people are willing to use this technology. This paper reports the findings of a study in which a novel structural model of willingness to use SDSSs was tested. Grounded in the driver monitoring and Technology Acceptance (TA) research literature, the model incorporates the perceived risks and gains associated with potential SDSS usage and additional social cognitive factors, including perceived usability and social influences. A total of 333 smartphone users, aged 18-24, with full Irish driving licenses completed an online questionnaire examining willingness or Behavioural Intention (BI) to uptake a SDSS. Following exploratory and confirmatory factor analyses, structural equation modelling indicated that perceived gains and social influence factors had significant direct effects on BI. Perceived risks and social influence also had significant indirect effects on BI, as mediated by perceived gains. Overall, this model accounted for 72.5% of the variance in willingness to uptake SDSSs. Multi-group structural models highlighted invariance of effects across gender, high and low risk drivers, and those likely or unlikely to adopt novel phone app technologies. These findings have implications for our understanding of the willingness of young drivers to adopt and use SDSSs, and highlight potential factors that could be targeted in behavioural change interventions seeking to improve usage rates. PMID:26277411

  7. Testing a structural model of young driver willingness to uptake Smartphone Driver Support Systems.

    PubMed

    Kervick, Aoife A; Hogan, Michael J; O'Hora, Denis; Sarma, Kiran M

    2015-10-01

    There is growing interest in the potential value of using phone applications that can monitor driver behaviour (Smartphone Driver Support Systems, 'SDSSs') in mitigating risky driving by young people. However, their value in this regard will only be realised if young people are willing to use this technology. This paper reports the findings of a study in which a novel structural model of willingness to use SDSSs was tested. Grounded in the driver monitoring and Technology Acceptance (TA) research literature, the model incorporates the perceived risks and gains associated with potential SDSS usage and additional social cognitive factors, including perceived usability and social influences. A total of 333 smartphone users, aged 18-24, with full Irish driving licenses completed an online questionnaire examining willingness or Behavioural Intention (BI) to uptake a SDSS. Following exploratory and confirmatory factor analyses, structural equation modelling indicated that perceived gains and social influence factors had significant direct effects on BI. Perceived risks and social influence also had significant indirect effects on BI, as mediated by perceived gains. Overall, this model accounted for 72.5% of the variance in willingness to uptake SDSSs. Multi-group structural models highlighted invariance of effects across gender, high and low risk drivers, and those likely or unlikely to adopt novel phone app technologies. These findings have implications for our understanding of the willingness of young drivers to adopt and use SDSSs, and highlight potential factors that could be targeted in behavioural change interventions seeking to improve usage rates.

  8. Voltage-Boosting Driver For Switching Regulator

    NASA Technical Reports Server (NTRS)

    Trump, Ronald C.

    1990-01-01

    Driver circuit assures availability of 10- to 15-V gate-to-source voltage needed to turn on n-channel metal oxide/semiconductor field-effect transistor (MOSFET) acting as switch in switching voltage regulator. Includes voltage-boosting circuit efficiently providing gate voltage 10 to 15 V above supply voltage. Contains no exotic parts and does not require additional power supply. Consists of NAND gate and dual voltage booster operating in conjunction with pulse-width modulator part of regulator.

  9. 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;…

  10. Resonant gate driver with efficient gate energy recovery and switching loss reduction

    NASA Astrophysics Data System (ADS)

    Kim, I.-G.; Kwak, S.-S.

    2016-04-01

    This article describes a novel resonant gate driver for charging the gate capacitor of power metal-oxide semiconductor field-effect-transistors (MOSFETs) that operate at a high switching frequency in power converters. The proposed resonant gate driver is designed with three small MOSFETs to build up the inductor current in addition to an inductor for temporary energy storage. The proposed resonant gate driver recovers the CV2 gate loss, which is the largest loss dissipated in the gate resistance in conventional gate drivers. In addition, the switching loss is reduced at the instants of turn on and turn off in the power MOSFETs of power converters by using the proposed gate driver. Mathematical analyses of the total loss appearing in the gate driver circuit and the switching loss reduction in the power switch of power converters are discussed. Finally, the proposed resonant gate driver is verified with experimental results at a switching frequency of 1 MHz.

  11. Lung cancer with concurrent EGFR mutation and ROS1 rearrangement: a case report and review of the literature.

    PubMed

    Zhu, You-Cai; Xu, Chun-Wei; Ye, Xiao-Qian; Yin, Man-Xiang; Zhang, Jin-Xian; Du, Kai-Qi; Zhang, Zhi-Hao; Hu, Jian

    2016-01-01

    ROS1 rearrangement has recently emerged as a new molecular subtype in non-small cell lung cancer, and is predominantly found in lung adenocarcinomas compared with other oncogenes such as EGFR, KRAS, or ALK. Patients who have both mutations are extremely rare. Here we report a 50-year-old female diagnosed with adenocarcinoma with sarcomatoid differentiation, who was shown to have EGFR and ROS1 mutations. The patient was treated surgically and received three cycles of adjuvant postoperative chemotherapy. In addition, we reviewed the previously reported cases and related literature. This presentation will provide further understanding of the underlying molecular biology and optimal treatment for non-small cell lung cancer patients with more than one driver mutation. PMID:27486332

  12. Lung cancer with concurrent EGFR mutation and ROS1 rearrangement: a case report and review of the literature

    PubMed Central

    Zhu, You-cai; Xu, Chun-wei; Ye, Xiao-qian; Yin, Man-xiang; Zhang, Jin-xian; Du, Kai-qi; Zhang, Zhi-hao; Hu, Jian

    2016-01-01

    ROS1 rearrangement has recently emerged as a new molecular subtype in non-small cell lung cancer, and is predominantly found in lung adenocarcinomas compared with other oncogenes such as EGFR, KRAS, or ALK. Patients who have both mutations are extremely rare. Here we report a 50-year-old female diagnosed with adenocarcinoma with sarcomatoid differentiation, who was shown to have EGFR and ROS1 mutations. The patient was treated surgically and received three cycles of adjuvant postoperative chemotherapy. In addition, we reviewed the previously reported cases and related literature. This presentation will provide further understanding of the underlying molecular biology and optimal treatment for non-small cell lung cancer patients with more than one driver mutation. PMID:27486332

  13. Improving School Bus Driver Performance.

    ERIC Educational Resources Information Center

    Farmer, Ernest

    This reference source is intended to assist the school bus driver training instructor in course preparation. Instructional units for program planning each contain pertinent course questions, a summary, and evaluation questions. Unit 1, "Introduction to the School Bus Driver Training Program," focuses on basic course objectives and requirements and…

  14. The older adult driver.

    PubMed

    Carr, D B

    2000-01-01

    More adults aged 65 and older will be driving in the next few decades. Many older drivers are safe behind the wheel and do not need intensive testing for license renewal. Others, however, have physiologic or cognitive impairments that can affect their mobility and driving safety. When an older patient's driving competency is questioned, a comprehensive, step-by-step assessment is recommended. Many diseases that impair driving ability can be detected and treated effectively by family physicians. Physicians should take an active role in assessing and reducing the risk for injury in a motor vehicle and, when possible, prevent or delay driving cessation in their patients. Referral to other health care professionals, such as an occupational or physical therapist, may be helpful for evaluation and treatment. When an older patient is no longer permitted or able to drive, the physician should counsel the patient about using alternative methods of transportation. PMID:10643955

  15. e-Driver: a novel method to identify protein regions driving cancer

    PubMed Central

    Porta-Pardo, Eduard; Godzik, Adam

    2014-01-01

    Motivation: Most approaches used to identify cancer driver genes focus, true to their name, on entire genes and assume that a gene, treated as one entity, has a specific role in cancer. This approach may be correct to describe effects of gene loss or changes in gene expression; however, mutations may have different effects, including their relevance to cancer, depending on which region of the gene they affect. Except for rare and well-known exceptions, there are not enough data for reliable statistics for individual positions, but an intermediate level of analysis, between an individual position and the entire gene, may give us better statistics than the former and better resolution than the latter approach. Results: We have developed e-Driver, a method that exploits the internal distribution of somatic missense mutations between the protein’s functional regions (domains or intrinsically disordered regions) to find those that show a bias in their mutation rate as compared with other regions of the same protein, providing evidence of positive selection and suggesting that these proteins may be actual cancer drivers. We have applied e-Driver to a large cancer genome dataset from The Cancer Genome Atlas and compared its performance with that of four other methods, showing that e-Driver identifies novel candidate cancer drivers and, because of its increased resolution, provides deeper insights into the potential mechanism of cancer driver genes identified by other methods. Availability and implementation: A Perl script with e-Driver and the files to reproduce the results described here can be downloaded from https://github.com/eduardporta/e-Driver.git Contact: adam@godziklab.org or eppardo@sanfordburnham.org Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25064568

  16. Modelling mutational landscapes of human cancers in vitro

    NASA Astrophysics Data System (ADS)

    Olivier, Magali; Weninger, Annette; Ardin, Maude; Huskova, Hana; Castells, Xavier; Vallée, Maxime P.; McKay, James; Nedelko, Tatiana; Muehlbauer, Karl-Rudolf; Marusawa, Hiroyuki; Alexander, John; Hazelwood, Lee; Byrnes, Graham; Hollstein, Monica; Zavadil, Jiri

    2014-03-01

    Experimental models that recapitulate mutational landscapes of human cancers are needed to decipher the rapidly expanding data on human somatic mutations. We demonstrate that mutation patterns in immortalised cell lines derived from primary murine embryonic fibroblasts (MEFs) exposed in vitro to carcinogens recapitulate key features of mutational signatures observed in human cancers. In experiments with several cancer-causing agents we obtained high genome-wide concordance between human tumour mutation data and in vitro data with respect to predominant substitution types, strand bias and sequence context. Moreover, we found signature mutations in well-studied human cancer driver genes. To explore endogenous mutagenesis, we used MEFs ectopically expressing activation-induced cytidine deaminase (AID) and observed an excess of AID signature mutations in immortalised cell lines compared to their non-transgenic counterparts. MEF immortalisation is thus a simple and powerful strategy for modelling cancer mutation landscapes that facilitates the interpretation of human tumour genome-wide sequencing data.

  17. Impact of mandating a driving lesson for older drivers at license renewal in Japan.

    PubMed

    Ichikawa, Masao; Nakahara, Shinji; Inada, Haruhiko

    2015-02-01

    In Japan, a driving lesson consisting of a lecture, a driver aptitude test, on-road driving assessment and a discussion session was added to the driving license renewal procedure for drivers aged 75 years or older in 1998 and for drivers aged 70 years or older in 2002. We investigated whether these additions contributed to a reduction in at-fault motor vehicle collisions (MVCs) by examining the trend of the at-fault MVC rates per licensed driver and the rate ratios of the older drivers relative to those aged 65-69 years for the years 1986-2011. All data were derived from nationwide traffic statistics. If the introduction of the lesson was effective in reducing at-fault MVCs of older drivers, the rate ratio should have declined, given that the lesson targeted only the older drivers. We found this was not the case, i.e., there was no declining trend in the at-fault MVC rate ratios of both drivers aged 75 years or older and drivers aged 70 years or older, relative to drivers aged 65-69 years, after the driving lesson at license renewal became mandatory for these older drivers. Therefore, the mandatory lesson for the older drivers at license renewal needs to be reconsidered. PMID:25460091

  18. Impact of mandating a driving lesson for older drivers at license renewal in Japan.

    PubMed

    Ichikawa, Masao; Nakahara, Shinji; Inada, Haruhiko

    2015-02-01

    In Japan, a driving lesson consisting of a lecture, a driver aptitude test, on-road driving assessment and a discussion session was added to the driving license renewal procedure for drivers aged 75 years or older in 1998 and for drivers aged 70 years or older in 2002. We investigated whether these additions contributed to a reduction in at-fault motor vehicle collisions (MVCs) by examining the trend of the at-fault MVC rates per licensed driver and the rate ratios of the older drivers relative to those aged 65-69 years for the years 1986-2011. All data were derived from nationwide traffic statistics. If the introduction of the lesson was effective in reducing at-fault MVCs of older drivers, the rate ratio should have declined, given that the lesson targeted only the older drivers. We found this was not the case, i.e., there was no declining trend in the at-fault MVC rate ratios of both drivers aged 75 years or older and drivers aged 70 years or older, relative to drivers aged 65-69 years, after the driving lesson at license renewal became mandatory for these older drivers. Therefore, the mandatory lesson for the older drivers at license renewal needs to be reconsidered.

  19. Predictive and Prognostic Roles of BRAF Mutation in Stage III Colon Cancer: Results from Intergroup Trial CALGB 89803

    PubMed Central

    Ogino, Shuji; Shima, Kaori; Meyerhardt, Jeffrey A.; McCleary, Nadine J.; Ng, Kimmie; Hollis, Donna; Saltz, Leonard B.; Mayer, Robert J.; Schaefer, Paul; Whittom, Renaud; Hantel, Alexander; Benson, Al B.; Spiegelman, Donna; Goldberg, Richard M.; Bertagnolli, Monica M.; Fuchs, Charles S.

    2011-01-01

    Purpose Alterations in the RAS-RAF-MAP2K (MEK)-MAPK signaling pathway are major drivers in colon and rectal carcinogenesis. In colorectal cancer, BRAF mutation is associated with microsatellite instability (MSI), and typically predicts inferior prognosis. We examined the effect of BRAF mutation on survival and treatment efficacy in patients with stage III colon cancer. Methods We assessed status of BRAF c.1799T>A (p.V600E) mutation and MSI in 506 stage III colon cancer patients enrolled in a randomized adjuvant chemotherapy trial [5-fluorouracil and leucovorin (FU/LV) vs. irinotecan (CPT11), FU and LV (IFL); CALGB 89803]. Cox proportional hazards model was used to assess the prognostic role of BRAF mutation, adjusting for clinical features, adjuvant chemotherapy arm and MSI status. Results Compared to 431 BRAF-wild-type patients, 75 BRAF-mutated patients experienced significantly worse overall survival [OS; log-rank p=0.015; multivariate hazard ratio (HR)=1.66; 95% confidence interval (CI), 1.05-2.63]. By assessing combined status of BRAF and MSI, it appeared that BRAF-mutated MSS (microsatellite stable) tumor was an unfavorable subtype, while BRAF-wild-type MSI-high tumor was a favorable subtype, and BRAF-mutated MSI-high tumor and BRAF-wild-type MSS tumor were intermediate subtypes. Among patients with BRAF-mutated tumors, a non-significant trend toward improved OS was observed for IFL vs. FU/LV arm (multivariate HR=0.52; 95% CI, 0.25-1.10). Among patients with BRAF-wild-type cancer, IFL conferred no suggestion of benefit beyond FU/LV alone (multivariate HR=1.02; 95% CI, 0.72-1.46). Conclusions BRAF mutation is associated with inferior survival in stage III colon cancer. Additional studies are necessary to assess whether there is any predictive role of BRAF mutation for irinotecan-based therapy. PMID:22147942

  20. Deciphering intra-tumor heterogeneity of lung adenocarcinoma confirms that dominant, branching, and private gene mutations occur within individual tumor nodules.

    PubMed

    Pelosi, Giuseppe; Pellegrinelli, Alessio; Fabbri, Alessandra; Tamborini, Elena; Perrone, Federica; Settanni, Giulio; Busico, Adele; Picciani, Benedetta; Testi, Maria Adele; Militti, Lucia; Maisonneuve, Patrick; Valeri, Barbara; Sonzogni, Angelica; Proto, Claudia; Garassino, Marina; De Braud, Filippo; Pastorino, Ugo

    2016-06-01

    While pulmonary adenocarcinoma (ADC) is morphologically heterogeneous, little is known about intra-tumor gene mutation heterogeneity (ITH). We therefore subjected 20 ADC nodules, 5 mutated for EGFR and 5 for KRAS, 5 with an ALK translocation, and 5 wild type (WT) for these alterations, to unsupervised next-generation sequencing of tumor regions from diverse architectural patterns. When 2 or more different gene mutations were found in a single tumor, this fulfilled the criteria for ITH. In the 84 studied tumor regions with diverse architecture, 71 gene mutations and 34 WT profiles were found. ITH was observed in 9/15 (60 %) ADC, 3 with an EGFR, 3 with a KRAS, and 3 with an ALK aberration, as reflected in 5, 6, and 9 additional mutations, respectively, detected in these tumors. EGFR mutations were observed in 21/22 and KRAS mutations in 18/22 tumor regions, suggesting that they appear early and have a driver role (dominant or trunk mutations). Branching mutations (in EZH2, PIK3CA, TP53, and EGFR exon 18) occurred in two or more regions, while private mutations (in ABL1, ALK, BRAF, HER2, KDR, LKB1, PTEN, MET, SMAD4, SMARCB1, and SRC) were confined to unique tumor samples of individual lesions, suggesting that they occurred later on during tumor progression. Patients with a tumor showing branching mutations ran a worse clinical course, independent of confounding factors. We conclude that in ADC, ITH exists in a pattern suggesting spatial and temporal hierarchy with dominant, branching, and private mutations. This is consistent with diverse intra-tumor clonal evolution, which has potential implications for patient prognosis or development of secondary therapy resistance.

  1. Deciphering intra-tumor heterogeneity of lung adenocarcinoma confirms that dominant, branching, and private gene mutations occur within individual tumor nodules.

    PubMed

    Pelosi, Giuseppe; Pellegrinelli, Alessio; Fabbri, Alessandra; Tamborini, Elena; Perrone, Federica; Settanni, Giulio; Busico, Adele; Picciani, Benedetta; Testi, Maria Adele; Militti, Lucia; Maisonneuve, Patrick; Valeri, Barbara; Sonzogni, Angelica; Proto, Claudia; Garassino, Marina; De Braud, Filippo; Pastorino, Ugo

    2016-06-01

    While pulmonary adenocarcinoma (ADC) is morphologically heterogeneous, little is known about intra-tumor gene mutation heterogeneity (ITH). We therefore subjected 20 ADC nodules, 5 mutated for EGFR and 5 for KRAS, 5 with an ALK translocation, and 5 wild type (WT) for these alterations, to unsupervised next-generation sequencing of tumor regions from diverse architectural patterns. When 2 or more different gene mutations were found in a single tumor, this fulfilled the criteria for ITH. In the 84 studied tumor regions with diverse architecture, 71 gene mutations and 34 WT profiles were found. ITH was observed in 9/15 (60 %) ADC, 3 with an EGFR, 3 with a KRAS, and 3 with an ALK aberration, as reflected in 5, 6, and 9 additional mutations, respectively, detected in these tumors. EGFR mutations were observed in 21/22 and KRAS mutations in 18/22 tumor regions, suggesting that they appear early and have a driver role (dominant or trunk mutations). Branching mutations (in EZH2, PIK3CA, TP53, and EGFR exon 18) occurred in two or more regions, while private mutations (in ABL1, ALK, BRAF, HER2, KDR, LKB1, PTEN, MET, SMAD4, SMARCB1, and SRC) were confined to unique tumor samples of individual lesions, suggesting that they occurred later on during tumor progression. Patients with a tumor showing branching mutations ran a worse clinical course, independent of confounding factors. We conclude that in ADC, ITH exists in a pattern suggesting spatial and temporal hierarchy with dominant, branching, and private mutations. This is consistent with diverse intra-tumor clonal evolution, which has potential implications for patient prognosis or development of secondary therapy resistance. PMID:27056568

  2. Towards an understanding of driver inattention: taxonomy and theory.

    PubMed

    Regan, Michael A; Strayer, David L

    2014-01-01

    There is little agreement in the scientific literature about what the terms "driver distraction" and "driver inattention" mean, and what the relationship is between them. In 2011, Regan, Hallett and Gordon proposed a taxonomy of driver inattention in which driver distraction is conceptualized as just one of several processes that give rise to driver inattention. Since publication of that paper, two other papers have emerged that bear on the taxonomy. In one, the Regan et al taxonomy was used, for the first time, to classify data from an in-depth crash investigation in Australia. In the other, another taxonomy of driver inattention was proposed and described. In this paper we revisit the original taxonomy proposed by Regan et al. in light of these developments, and make recommendations for how the original taxonomy might be improved to make it more useful as a tool for classifying and coding crash and critical incident data. In addition, we attempt to characterize, theoretically, the processes within each category of the original taxonomy that are assumed to give rise to driver inattention. Recommendations are made for several lines of research: to further validate the original taxonomy; to understand the impact of each category of inattention in the taxonomy on driving performance, crash type and crash risk; and to revise and align with the original taxonomy existing crash and incident investigation protocols, so that they provide more comprehensive, reliable and consistent information regarding the contribution of inattention to crashes of all types.

  3. Towards an Understanding of Driver Inattention: Taxonomy and Theory

    PubMed Central

    Regan, Michael. A.; Strayer, David. L.

    2014-01-01

    There is little agreement in the scientific literature about what the terms “driver distraction” and “driver inattention” mean, and what the relationship is between them. In 2011, Regan, Hallett and Gordon proposed a taxonomy of driver inattention in which driver distraction is conceptualized as just one of several processes that give rise to driver inattention. Since publication of that paper, two other papers have emerged that bear on the taxonomy. In one, the Regan et al taxonomy was used, for the first time, to classify data from an in-depth crash investigation in Australia. In the other, another taxonomy of driver inattention was proposed and described. In this paper we revisit the original taxonomy proposed by Regan et al. in light of these developments, and make recommendations for how the original taxonomy might be improved to make it more useful as a tool for classifying and coding crash and critical incident data. In addition, we attempt to characterize, theoretically, the processes within each category of the original taxonomy that are assumed to give rise to driver inattention. Recommendations are made for several lines of research: to further validate the original taxonomy; to understand the impact of each category of inattention in the taxonomy on driving performance, crash type and crash risk; and to revise and align with the original taxonomy existing crash and incident investigation protocols, so that they provide more comprehensive, reliable and consistent information regarding the contribution of inattention to crashes of all types. PMID:24776222

  4. What happens when drivers face hazards on the road?

    PubMed

    Ventsislavova, Petya; Gugliotta, Andres; Peña-Suarez, Elsa; Garcia-Fernandez, Pedro; Eisman, Eduardo; Crundall, David; Castro, Candida

    2016-06-01

    The current study aims to obtain knowledge about the nature of the processes involved in Hazard Perception, using measurement techniques to separate and independently quantify these suspected sub-processes: Sensation, Situation Awareness (recognition, location and projection) and decision-making. It applies Signal Detection Theory analysis to Hazard Perception and Prediction Tasks. To enable the calculation of Signal Detection Theory parameters, video-recorded hazardous vs. quasi-hazardous situations were presented to the participants. In the hazardous situations it is necessary to perform an evasive action, for instance, braking or swerving abruptly, while the quasi-hazardous situations do not require the driver to make any evasive manoeuvre, merely to carry on driving at the same speed and following the same trajectory. A first Multiple Choice Hazard Perception and Prediction test was created to measure participants' performance in a What Happens Next? Task. The sample comprised 143 participants, 47 females and 94 males. Groups of non-offender drivers (learner, novice and experienced) and offender drivers (novice and experienced) were recruited. The Multiple Choice Hazard Perception and Prediction test succeeded in finding differences between drivers according to their driving experience. In fact, differences exist with regard to the level of hazard discrimination (d' prime) by drivers with different experience (learner, novice and experienced drivers) and profile (offenders and non-offenders) and these differences emerge from Signal Detection Theory analysis. In addition, it was found that experienced drivers show higher Situation Awareness than learner or novice drivers. On the other hand, although offenders do worse than non-offenders on the hazard identification question, they do just as well when their Situation Awareness is probed (in fact, they are as aware as non-offenders of what the obstacles on the road are, where they are and what will happen next

  5. 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. PMID:16595327

  6. Prevalence of drug use in commercial tractor-trailer drivers.

    PubMed

    Couper, Fiona J; Pemberton, Melissa; Jarvis, Anjanette; Hughes, Marty; Logan, Barry K

    2002-05-01

    An enforcement emphasis project, "Operation Trucker Check," was established in order to determine the extent to which commercial tractor-trailer drivers were operating their vehicles while impaired by drugs. A total of 1079 drivers and their vehicles were assessed for driver and equipment violations, and drivers additionally underwent preliminary field sobriety tests conducted by drug recognition expert (DRE) officers. Anonymous urine specimens for drug analysis were requested, and 822 urine specimens were obtained in total. Compliance with the drug-testing portion was voluntary, and there was a 19% refusal rate. Overall, 21% of the urine specimens tested positive for either illicit, prescription, and/or over-the-counter drugs, and 7% tested positive for more than one drug. Excluding caffeine and nicotine, the largest number of positive findings (9.5%) were for CNS stimulants, such as methamphetamine, amphetamine, phentermine, ephedrine/pseudoephedrine, and cocaine. The second most frequently encountered drug class were the cannabinoids, with 4.3% of drivers testing positive for marijuana metabolites. Only 11 drivers (1.3%) were positive for alcohol. Sixteen truck drivers (1.6%) were charged with driving under the influence of drugs after a full DRE evaluation was conducted. The results indicate that in spite of comprehensive drug testing in the trucking industry, some tractor-trailer drivers are continuing to take illicit and other drugs with the potential of having a negative effect on their driving ability. On the other hand, only a few drivers were, in fact, deemed to be under the influence of drugs at the time of driving when evaluated by DRE officers.

  7. Prevalence of drug use in commercial tractor-trailer drivers.

    PubMed

    Couper, Fiona J; Pemberton, Melissa; Jarvis, Anjanette; Hughes, Marty; Logan, Barry K

    2002-05-01

    An enforcement emphasis project, "Operation Trucker Check," was established in order to determine the extent to which commercial tractor-trailer drivers were operating their vehicles while impaired by drugs. A total of 1079 drivers and their vehicles were assessed for driver and equipment violations, and drivers additionally underwent preliminary field sobriety tests conducted by drug recognition expert (DRE) officers. Anonymous urine specimens for drug analysis were requested, and 822 urine specimens were obtained in total. Compliance with the drug-testing portion was voluntary, and there was a 19% refusal rate. Overall, 21% of the urine specimens tested positive for either illicit, prescription, and/or over-the-counter drugs, and 7% tested positive for more than one drug. Excluding caffeine and nicotine, the largest number of positive findings (9.5%) were for CNS stimulants, such as methamphetamine, amphetamine, phentermine, ephedrine/pseudoephedrine, and cocaine. The second most frequently encountered drug class were the cannabinoids, with 4.3% of drivers testing positive for marijuana metabolites. Only 11 drivers (1.3%) were positive for alcohol. Sixteen truck drivers (1.6%) were charged with driving under the influence of drugs after a full DRE evaluation was conducted. The results indicate that in spite of comprehensive drug testing in the trucking industry, some tractor-trailer drivers are continuing to take illicit and other drugs with the potential of having a negative effect on their driving ability. On the other hand, only a few drivers were, in fact, deemed to be under the influence of drugs at the time of driving when evaluated by DRE officers. PMID:12051337

  8. Mutations in Lettuce Improvement

    PubMed Central

    Mou, Beiquan

    2011-01-01

    Lettuce is a major vegetable in western countries. Mutations generated genetic variations and played an important role in the domestication of the crop. Many traits derived from natural and induced mutations, such as dwarfing, early flowering, male sterility, and chlorophyll deficiency, are useful in physiological and genetic studies. Mutants were also used to develop new lettuce products including miniature and herbicide-tolerant cultivars. Mutant analysis was critical in lettuce genomic studies including identification and cloning of disease-resistance genes. Mutagenesis combined with genomic technology may provide powerful tools for the discovery of novel gene alleles. In addition to radiation and chemical mutagens, unconventional approaches such as tissue or protoplast culture, transposable elements, and space flights have been utilized to generate mutants in lettuce. Since mutation breeding is considered nontransgenic, it is more acceptable to consumers and will be explored more in the future for lettuce improvement. PMID:22287955

  9. Proton driver power supply system

    SciTech Connect

    C. Jach and D. Wolff

    2002-06-03

    This paper describes magnet power supply system for a proposed Proton Driver at Fermilab. The magnet power supply system consists of resonant dipole/quadrupole power supply system, quadrupole tracking, dipole correction (horizontal and vertical) and sextupole power supply systems. This paper also describes preliminary design of the power distribution system supplying 13.8 kV power to all proton Driver electrical systems.

  10. Causal influence of car mass and size on driver fatality risk.

    PubMed Central

    Evans, L

    2001-01-01

    OBJECTIVES: This study estimated how adding mass, in the form of a passenger, to a car crashing head-on into another car affects fatality risks to both drivers. The study distinguished the causal roles of mass and size. METHODS: Head-on crashes between 2 cars, one with a right-front passenger and the other with only a driver, were examined with Fatality Analysis Reporting System data. RESULTS: Adding a passenger to a car led to a 14.5% reduction in driver risk ratio (risk to one driver divided by risk to the other). To divide this effect between the individual drivers, the author developed equations that express each driver's risk as a function of causal contributions from the mass and size of both involved cars. Adding a passenger reduced a driver's frontal crash fatality risk by 7.5% but increased the risk to the other driver by 8.1%. CONCLUSIONS: The presence of a passenger reduces a driver's frontal crash fatality risk but increases the risk to the driver of the other car. The findings are applicable to some single-car crashes, in which the driver risk decrease is not offset by any increase in harm to others. When all cars carry the same additional cargo, total population risk is reduced. PMID:11441734

  11. How do drivers overtake cyclists?

    PubMed

    Dozza, Marco; Schindler, Ron; Bianchi-Piccinini, Giulio; Karlsson, Johan

    2016-03-01

    In Europe, the number of road crashes is steadily decreasing every year. However, the incidence of bicycle crashes is not declining as fast as that of car crashes. In Sweden, cyclists are the most frequently injured road users. Collisions between bicycles and motorized vehicles are of particular concern because the high speed and large mass of motorized vehicles create a high risk of serious injury to cyclists. In Sweden's urban areas, bicycle lanes keep bicycles separated from motorized vehicles, but on rural roads bicycle lanes are often absent, requiring drivers to interact with cyclists-usually by overtaking them. During this maneuver, drivers regulate speed and lateral position, negotiating with potential oncoming traffic to stay within their comfort zones while approaching and passing cyclists. In this study an instrumented bicycle recorded 145 overtaking maneuvers performed by car and truck drivers on public rural roads in Sweden. The bicycle was equipped with a LIDAR and two cameras to assess how drivers approached and circumvented the bicycle. The collected data allowed us to identify four overtaking phases and quantify the corresponding driver comfort zones. The presence of an oncoming vehicle was the factor that most influenced the maneuver, whereas neither vehicle speed, lane width, shoulder width nor posted speed limit significantly affected the driver comfort zone or the overtaking dynamics. PMID:26717348

  12. How do drivers overtake cyclists?

    PubMed

    Dozza, Marco; Schindler, Ron; Bianchi-Piccinini, Giulio; Karlsson, Johan

    2016-03-01

    In Europe, the number of road crashes is steadily decreasing every year. However, the incidence of bicycle crashes is not declining as fast as that of car crashes. In Sweden, cyclists are the most frequently injured road users. Collisions between bicycles and motorized vehicles are of particular concern because the high speed and large mass of motorized vehicles create a high risk of serious injury to cyclists. In Sweden's urban areas, bicycle lanes keep bicycles separated from motorized vehicles, but on rural roads bicycle lanes are often absent, requiring drivers to interact with cyclists-usually by overtaking them. During this maneuver, drivers regulate speed and lateral position, negotiating with potential oncoming traffic to stay within their comfort zones while approaching and passing cyclists. In this study an instrumented bicycle recorded 145 overtaking maneuvers performed by car and truck drivers on public rural roads in Sweden. The bicycle was equipped with a LIDAR and two cameras to assess how drivers approached and circumvented the bicycle. The collected data allowed us to identify four overtaking phases and quantify the corresponding driver comfort zones. The presence of an oncoming vehicle was the factor that most influenced the maneuver, whereas neither vehicle speed, lane width, shoulder width nor posted speed limit significantly affected the driver comfort zone or the overtaking dynamics.

  13. A study of the mutational landscape of pediatric-type follicular lymphoma and pediatric nodal marginal zone lymphoma

    PubMed Central

    Ozawa, Michael G; Bhaduri, Aparna; Chisholm, Karen M; Baker, Steven A; Ma, Lisa; Zehnder, James L; Luna-Fineman, Sandra; Link, Michael P; Merker, Jason D; Arber, Daniel A; Ohgami, Robert S

    2016-01-01

    Pediatric-type follicular lymphoma and pediatric marginal zone lymphoma are two of the rarest B-cell lymphomas. These lymphomas occur predominantly in the pediatric population and show features distinct from their more common counterparts in adults: adult-type follicular lymphoma and adult-type nodal marginal zone lymphoma. Here we report a detailed whole-exome deep sequencing analysis of a cohort of pediatric-type follicular lymphomas and pediatric marginal zone lymphomas. This analysis revealed a recurrent somatic variant encoding p.Lys66Arg in the transcription factor interferon regulatory factor 8 (IRF8) in 3 of 6 cases (50%) of pediatric-type follicular lymphoma. This specific point mutation was not detected in pediatric marginal zone lymphoma or in adult-type follicular lymphoma. Additional somatic point mutations in pediatric-type follicular lymphoma were observed in genes involved in transcription, intracellular signaling, and cell proliferation. In pediatric marginal zone lymphoma, no recurrent mutation was identified; however, somatic point mutations were observed in genes involved in cellular adhesion, cytokine regulatory elements, and cellular proliferation. A somatic variant in AMOTL1, a recurrently mutated gene in splenic marginal zone lymphoma, was also identified in a case of pediatric marginal zone lymphoma. The overall non-synonymous mutational burden was low in both pediatric-type follicular lymphoma and pediatric marginal zone lymphoma (4.6 mutations per exome). Altogether, these findings support a distinctive genetic basis for pediatric-type follicular lymphoma and pediatric marginal zone lymphoma when compared with adult subtypes and to one another. Moreover, identification of a recurrent point mutation in IRF8 provides insight into a potential driver mutation in the pathogenesis of pediatric-type follicular lymphoma with implications for novel diagnostic or therapeutic strategies. PMID:27338637

  14. 49 CFR 380.109 - Driver testing.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ....109 Driver testing. (a) Testing methods. The driver-student must pass knowledge and skills tests in... an LCV driver-training program as specified in subpart B of this part. The written knowledge test may be administered by any qualified driver-instructor. The skills tests, based on actual operation of...

  15. Accelerating Mutational Load Is Not Due to Synergistic Epistasis or Mutator Alleles in Mutation Accumulation Lines of Yeast.

    PubMed

    Jasmin, Jean-Nicolas; Lenormand, Thomas

    2016-02-01

    Much of our knowledge about the fitness effects of new mutations has been gained from mutation accumulation (MA) experiments. Yet the fitness effect of single mutations is rarely measured in MA experiments. This raises several issues, notably for inferring epistasis for fitness. The acceleration of fitness decline in MA lines has been taken as evidence for synergistic epistasis, but establishing the role of epistasis requires measuring the fitness of genotypes carrying known numbers of mutations. Otherwise, accelerating fitness loss could be explained by increased genetic mutation rates. Here we segregated mutations accumulated over 4800 generations in haploid and diploid MA lines of the yeast Saccharomyces cerevisiae. We found no correspondence between an accelerated fitness decline and synergistic epistasis among deleterious mutations in haploid lines. Pairs of mutations showed no overall epistasis. Furthermore, several lines of evidence indicate that genetic mutation rates did not increase in the MA lines. Crucially, segregant fitness analyses revealed that MA accelerated in both haploid and diploid lines, even though the fitness of diploid lines was nearly constant during the MA experiment. This suggests that the accelerated fitness decline in haploids was caused by cryptic environmental factors that increased mutation rates in all lines during the last third of the lines' transfers. In addition, we provide new estimates of deleterious mutation rates, including lethal mutations, and highlight that nearly all the mutational load we observed was due to one or two mutations having a large effect on fitness.

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

    PubMed

    Chen, Ying; McGee, Jeremy; Chen, Xianming; Doman, Thompson N; Gong, Xueqian; Zhang, Youyan; Hamm, Nicole; Ma, Xiwen; Higgs, Richard E; Bhagwat, Shripad V; Buchanan, Sean; Peng, Sheng-Bin; Staschke, Kirk A; Yadav, Vipin; Yue, Yong; Kouros-Mehr, Hosein

    2014-01-01

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

  17. Using Multiplexed Assays of Oncogenic Drivers in Lung Cancers to Select Targeted Drugs

    PubMed Central

    Kris, Mark G.; Johnson, Bruce E.; Berry, Lynne D.; Kwiatkowski, David J.; Iafrate, A. John; Wistuba, Ignacio I.; Varella-Garcia, Marileila; Franklin, Wilbur A.; Aronson, Samuel L.; Su, Pei-Fang; Shyr, Yu; Camidge, D. Ross; Sequist, Lecia V.; Glisson, Bonnie S.; Khuri, Fadlo R.; Garon, Edward B.; Pao, William; Rudin, Charles; Schiller, Joan; Haura, Eric B.; Socinski, Mark; Shirai, Keisuke; Chen, Heidi; Giaccone, Giuseppe; Ladanyi, Marc; Kugler, Kelly; Minna, John D.; Bunn, Paul A.

    2014-01-01

    IMPORTANCE Targeting oncogenic drivers (genomic alterations critical to cancer development and maintenance) has transformed the care of patients with lung adenocarcinomas. The Lung Cancer Mutation Consortium was formed to perform multiplexed assays testing adenocarcinomas of the lung for drivers in 10 genes to enable clinicians to select targeted treatments and enroll patients into clinical trials. OBJECTIVES To determine the frequency of oncogenic drivers in patients with lung adenocarcinomas and to use the data to select treatments targeting the identified driver(s) and measure survival. DESIGN, SETTING, AND PARTICIPANTS From 2009 through 2012, 14 sites in the United States enrolled patients with metastatic lung adenocarcinomas and a performance status of 0 through 2 and tested their tumors for 10 drivers. Information was collected on patients, therapies, and survival. INTERVENTIONS Tumors were tested for 10 oncogenic drivers, and results were used to select matched targeted therapies. MAIN OUTCOMES AND MEASURES Determination of the frequency of oncogenic drivers, the proportion of patients treated with genotype-directed therapy, and survival. RESULTS From 2009 through 2012, tumors from 1007 patients were tested for at least 1 gene and 733 for 10 genes (patients with full genotyping). An oncogenic driver was found in 466 of 733 patients (64%). Among these 733 tumors, 182 tumors (25%) had the KRAS driver; sensitizing EGFR, 122 (17%); ALK rearrangements, 57 (8%); other EGFR, 29 (4%); 2 or more genes, 24 (3%); ERBB2 (formerly HER2), 19 (3%); BRAF, 16 (2%); PIK3CA, 6 (<1%); MET amplification, 5 (<1%); NRAS, 5 (<1%); MEK1, 1 (<1%); AKT1, 0. Results were used to select a targeted therapy or trial in 275 of 1007 patients (28%). The median survival was 3.5 years (interquartile range [IQR], 1.96-7.70) for the 260 patients with an oncogenic driver and genotype-directed therapy compared with 2.4 years (IQR, 0.88-6.20) for the 318 patients with any oncogenic driver(s) who

  18. Proteogenomics connects somatic mutations to signalling in breast cancer.

    PubMed

    Mertins, Philipp; Mani, D R; Ruggles, Kelly V; Gillette, Michael A; Clauser, Karl R; Wang, Pei; Wang, Xianlong; Qiao, Jana W; Cao, Song; Petralia, Francesca; Kawaler, Emily; Mundt, Filip; Krug, Karsten; Tu, Zhidong; Lei, Jonathan T; Gatza, Michael L; Wilkerson, Matthew; Perou, Charles M; Yellapantula, Venkata; Huang, Kuan-lin; Lin, Chenwei; McLellan, Michael D; Yan, Ping; Davies, Sherri R; Townsend, R Reid; Skates, Steven J; Wang, Jing; Zhang, Bing; Kinsinger, Christopher R; Mesri, Mehdi; Rodriguez, Henry; Ding, Li; Paulovich, Amanda G; Fenyö, David; Ellis, Matthew J; Carr, Steven A

    2016-06-01

    Somatic mutations have been extensively characterized in breast cancer, but the effects of these genetic alterations on the proteomic landscape remain poorly understood. Here we describe quantitative mass-spectrometry-based proteomic and phosphoproteomic analyses of 105 genomically annotated breast cancers, of which 77 provided high-quality data. Integrated analyses provided insights into the somatic cancer genome including the consequences of chromosomal loss, such as the 5q deletion characteristic of basal-like breast cancer. Interrogation of the 5q trans-effects against the Library of Integrated Network-based Cellular Signatures, connected loss of CETN3 and SKP1 to elevated expression of epidermal growth factor receptor (EGFR), and SKP1 loss also to increased SRC tyrosine kinase. Global proteomic data confirmed a stromal-enriched group of proteins in addition to basal and luminal clusters, and pathway analysis of the phosphoproteome identified a G-protein-coupled receptor cluster that was not readily identified at the mRNA level. In addition to ERBB2, other amplicon-associated highly phosphorylated kinases were identified, including CDK12, PAK1, PTK2, RIPK2 and TLK2. We demonstrate that proteogenomic analysis of breast cancer elucidates the functional consequences of somatic mutations, narrows candidate nominations for driver genes within large deletions and amplified regions, and identifies therapeutic targets. PMID:27251275

  19. Recurrent inactivating RASA2 mutations in melanoma.

    PubMed

    Arafeh, Rand; Qutob, Nouar; Emmanuel, Rafi; Keren-Paz, Alona; Madore, Jason; Elkahloun, Abdel; Wilmott, James S; Gartner, Jared J; Di Pizio, Antonella; Winograd-Katz, Sabina; Sindiri, Sivasish; Rotkopf, Ron; Dutton-Regester, Ken; Johansson, Peter; Pritchard, Antonia L; Waddell, Nicola; Hill, Victoria K; Lin, Jimmy C; Hevroni, Yael; Rosenberg, Steven A; Khan, Javed; Ben-Dor, Shifra; Niv, Masha Y; Ulitsky, Igor; Mann, Graham J; Scolyer, Richard A; Hayward, Nicholas K; Samuels, Yardena

    2015-12-01

    Analysis of 501 melanoma exomes identified RASA2, encoding a RasGAP, as a tumor-suppressor gene mutated in 5% of melanomas. Recurrent loss-of-function mutations in RASA2 were found to increase RAS activation, melanoma cell growth and migration. RASA2 expression was lost in ≥30% of human melanomas and was associated with reduced patient survival. These findings identify RASA2 inactivation as a melanoma driver and highlight the importance of RasGAPs in cancer. PMID:26502337

  20. Point mutation instability (PIN) mutator phenotype as model for true back mutations seen in hereditary tyrosinemia type 1 - a hypothesis.

    PubMed

    van Dyk, Etresia; Pretorius, Pieter J

    2012-05-01

    Hereditary tyrosinemia type 1 (HT1) is an autosomal recessive disorder affecting fumarylacetoacetate hydrolase (FAH), the last enzyme in the tyrosine catabolism pathway. The liver mosaicism observed in HT1 patients is due to the reversion to the wild type of one allele of the original point mutation in fah. It is generally accepted that these reversions are true back mutations; however, the mechanism is still unresolved. Previous reports excluded intragenic recombination, mitotic recombination, or homologous recombination with a pseudogene as possible mechanisms of mutation reversion in HT1. Sequence analysis did not reveal DNA motifs, tandem repeats or other sequence peculiarities that may be involved in mutation reversion. We propose the hypothesis that a point mutation instability mutator (PIN) phenotype brought about by the sustained stress environment created by the accumulating metabolites in the cell is the driver of the true back mutations in HT1. The metabolites accumulating in HT1 create a sustained stress environment by activating the extracellular signal-regulated kinase (ERK) and AKT survival pathways, inducing aberrant mitosis and development of death resistant cells, depleting glutathione, and impairing DNA ligase IV and possibly DNA polymerases δ and ε. This continual production of proliferative and stress-related survival signals in the cellular environment coupled with the mutagenicity of FAA, may instigate a mutator phenotype and could end in tumorigenesis and/or mutation reversion. The establishment of a PIN-mutator phenotype therefore not only seems to be a possible mechanism underlying the true back mutations, but also contributes to explaining the clinical heterogeneity seen in hereditary tyrosinemia type 1.

  1. Increased plasma homocysteine levels in shift working bus drivers

    PubMed Central

    Martins, P; D'Almeida, V; Vergani, N; Perez, A; Tufik, S

    2003-01-01

    Background: Previous studies have indicated an association between shift work and cardiovascular disease. There is also considerable epidemiological evidence that hyperhomocysteinemia is an independent risk factor for cardiovascular disorders. Aims: To analyse plasma homocysteine levels in shift work bus drivers, and to investigate possible relations with sleep parameters and other biochemical factors. Methods: Blood samples were collected from 30 male shift working long-haul bus drivers in a Brazilian sample and analysed for plasma levels of homocysteine, folic acid, vitamin B12, and serum lipids. A group of 22 daytime workers, matched for age and body mass index served as controls. The incidence of mutations in the gene coding for methylene tetrahydrofolate, an enzyme which is related to hyperhomocysteinemia, was also assessed. Polysomnographic recordings were obtained from the target group. Results: Bus drivers showed significantly higher levels of plasma homocysteine than the control group (18.57 v 9.43 µM). Most of the other biochemical, behavioural, and molecular parameters did not differ between groups. Likewise, sleep parameters appeared to be within the normal range. Conclusions: The significantly increased plasma homocysteine levels in long-haul bus drivers did not appear to be secondary to other biochemical or behavioural problems in this group. These results suggest that hyperhomocysteinemia may be involved in the increased incidence of cardiovascular diseases observed in shift workers. PMID:12937187

  2. Identification of Oncogenic Mutations and Gene Fusions in the Follicular Variant of Papillary Thyroid Carcinoma

    PubMed Central

    Dias-Santagata, Dora; Sadow, Peter M.; Lynch, Kerry D.; Lubitz, Carrie; Donovan, Samuel E.; Zheng, Zongli; Le, Long; Iafrate, A. J.; Daniels, Gilbert H.

    2014-01-01

    Background: The diagnosis of the follicular variant of papillary thyroid carcinoma (FVPTC) is increasingly common. Recent studies have suggested that FVPTC is heterogeneous and comprises multiple tumor types with distinct biological behaviors and underlying genetics. Objectives: The purpose of this work was to identify the prevalence of mutations and gene fusions in known oncogenes in a panel representative of the common spectrum of FVPTC diagnosed at an academic medical center and correlate the clinical and pathological features obtained at the initial diagnosis with the tumor genotype. Materials and Methods: We performed SNaPshot genotyping on a panel of 129 FVPTCs of ≥1 cm for 90 point mutations or small deletions in known oncogenes and tumor suppressors and identified gene fusions using an anchored multiplex PCR assay targeting a panel of rearranged oncogenes. Results: We identified a mutation or gene fusion in 70% (89 of 127) of cases. Mutations targeting the RAS family of oncogenes were the most frequently observed class of alterations, present in 36% (46 of 127) of cases, followed by BRAF mutation, present in 30% (38 of 127). We also detected oncogenic rearrangements not previously associated with FVPTC, including TFG-ALK and CREB3L2-PPARγ. BRAF mutation was significantly associated with unencapsulated tumor status. Conclusions: These data support the hypothesis that FVPTC is composed of distinct biological entities, with one class being identified by BRAF mutation and support the use of clinical genotyping assays that detect a diverse array of rearrangements involving ALK and PPARγ. Additional studies are necessary to identify genetic drivers in the 30% of FVPTCs with no known oncogenic alteration and to better predict behavior in tumors with known genotypes. PMID:25148236

  3. CRAC channels, calcium, and cancer in light of the driver and passenger concept.

    PubMed

    Hoth, Markus

    2016-06-01

    Advances in next-generation sequencing allow very comprehensive analyses of large numbers of cancer genomes leading to an increasingly better characterization and classification of cancers. Comparing genomic data predicts candidate genes driving development, growth, or metastasis of cancer. Cancer driver genes are defined as genes whose mutations are causally implicated in oncogenesis whereas passenger mutations are defined as not being oncogenic. Currently, a list of several hundred cancer driver mutations is discussed including prominent members like TP53, BRAF, NRAS, or NF1. According to the vast literature on Ca(2+) and cancer, Ca(2+) signals and the underlying Ca(2+) channels and transporters certainly influence the development, growth, and metastasis of many cancers. In this review, I focus on the calcium release-activated calcium (CRAC) channel genes STIM and Orai and their role for cancer development, growth, and metastasis. STIM and Orai genes are being discussed in the context of current cancer concepts with a focus on the driver-passenger hypothesis. One result of this discussion is the hypothesis that a driver analysis of Ca(2+) homeostasis-related genes should not be carried out by looking at isolated genes. Rather a pool of “Ca(2+) genes” might be considered to act as one potential cancer driver. This article is part of a Special Issue entitled: Calcium and Cell Fate. Guest Editors: Jacques Haiech, Claus Heizmann, Joachim Krebs, Thierry Capiod and Olivier Mignen.

  4. Oncogenically active MYD88 mutations in human lymphoma

    PubMed Central

    Ngo, Vu N.; Young, Ryan M.; Schmitz, Roland; Jhavar, Sameer; Xiao, Wenming; Lim, Kian-Huat; Kohlhammer, Holger; Xu, Weihong; Yang, Yandan; Zhao, Hong; Shaffer, Arthur L.; Romesser, Paul; Wright, George; Powell, John; Rosenwald, Andreas; Muller-Hermelink, Hans Konrad; Ott, German; Gascoyne, Randy D.; Connors, Joseph M.; Rimsza, Lisa M.; Campo, Elias; Jaffe, Elaine S.; Delabie, Jan; Smeland, Erlend B.; Fisher, Richard I.; Braziel, Rita M.; Tubbs, Raymond R.; Cook, J. R.; Weisenburger, Denny D.; Chan, Wing C.; Staudt, Louis M.

    2016-01-01

    The activated B-cell-like (ABC) subtype of diffuse large B-cell lymphoma (DLBCL) remains the least curable form of this malignancy despite recent advances in therapy1. Constitutive nuclear factor (NF)-κB and JAK kinase signalling promotes malignant cell survival in these lymphomas, but the genetic basis for this signalling is incompletely understood. Here we describe the dependence of ABC DLBCLs on MYD88, an adaptor protein that mediates toll and interleukin (IL)-1 receptor signalling2,3, and the discovery of highly recurrent oncogenic mutations affecting MYD88 in ABC DLBCL tumours. RNA interference screening revealed that MYD88 and the associated kinases IRAK1 and IRAK4 are essential for ABC DLBCL survival. High-throughput RNA resequencing uncovered MYD88 mutations in ABC DLBCL lines. Notably, 29% of ABC DLBCL tumours harboured the same amino acid substitution, L265P, in the MYD88 Toll/IL-1 receptor (TIR) domain at an evolutionarily invariant residue in its hydrophobic core. This mutation was rare or absent in other DLBCL subtypes and Burkitt’s lymphoma, but was observed in 9% of mucosa-associated lymphoid tissue lymphomas. At a lower frequency, additional mutations were observed in the MYD88 TIR domain, occurring in both the ABC and germinal centre B-cell-like (GCB) DLBCL subtypes. Survival of ABC DLBCL cells bearing the L265P mutation was sustained by the mutant but not the wild-type MYD88 isoform, demonstrating that L265P is a gain-of-function driver mutation. The L265P mutant promoted cell survival by spontaneously assembling a protein complex containing IRAK1 and IRAK4, leading to IRAK4 kinase activity, IRAK1 phosphorylation, NF-κB signalling, JAK kinase activation of STAT3, and secretion of IL-6, IL-10 and interferon-β. Hence, theMYD88 signalling pathway is integral to the pathogenesis of ABC DLBCL, supporting the development of inhibitors of IRAK4 kinase and other components of this pathway for the treatment of tumours bearing oncogenic MYD88 mutations

  5. Augmented reality cues to assist older drivers with gap estimation for left-turns.

    PubMed

    Rusch, Michelle L; Schall, Mark C; Lee, John D; Dawson, Jeffrey D; Rizzo, Matthew

    2014-10-01

    The objective of this study was to assess the effects of augmented reality (AR) cues designed to assist middle-aged and older drivers with a range of UFOV impairments, judging when to make left-turns across oncoming traffic. Previous studies have shown that AR cues can help middle-aged and older drivers respond to potential roadside hazards by increasing hazard detection without interfering with other driving tasks. Intersections pose a critical challenge for cognitively impaired drivers, prone to misjudge time-to-contact with oncoming traffic. We investigated whether AR cues improve or interfere with hazard perception in left-turns across oncoming traffic for drivers with age-related cognitive decline. Sixty-four middle-aged and older drivers with a range of UFOV impairment judged when it would be safe to turn left across oncoming traffic approaching the driver from the opposite direction in a rural stop-sign controlled intersection scenario implemented in a static base driving simulator. Outcome measures used to evaluate the effectiveness of AR cueing included: Time-to-Contact (TTC), Gap Time Variation (GTV), Response Rate, and Gap Response Variation (GRV). All drivers estimated TTCs were shorter in cued than in uncued conditions. In addition, drivers responded more often in cued conditions than in uncued conditions and GRV decreased for all drivers in scenarios that contained AR cues. For both TTC and response rate, drivers also appeared to adjust their behavior to be consistent with the cues, especially drivers with the poorest UFOV scores (matching their behavior to be close to middle-aged drivers). Driver ratings indicated that cueing was not considered to be distracting. Further, various conditions of reliability (e.g., 15% miss rate) did not appear to affect performance or driver ratings.

  6. AUGMENTED REALITY CUES TO ASSIST OLDER DRIVERS WITH GAP ESTIMATION FOR LEFT-TURNS

    PubMed Central

    Rusch, Michelle L.; Schall, Mark C.; Lee, John D.; Dawson, Jeffrey D.; Rizzo, Matthew

    2014-01-01

    The objective of this study was to assess the effects of augmented reality (AR) cues designed to assist middle-aged and older drivers with a range of UFOV impairments, judging when to make left-turns across oncoming traffic. Previous studies have shown that AR cues can help middle-aged and older drivers respond to potential roadside hazards by increasing hazard detection without interfering with other driving tasks. Intersections pose a critical challenge for cognitively impaired drivers, prone to misjudge time-to-contact with oncoming traffic. We investigated whether AR cues improve or interfere with hazard perception in left-turns across oncoming traffic for drivers with age-related cognitive decline. Sixty-four middle-aged and older drivers with a range of UFOV impairment judged when it would be safe to turn left across oncoming traffic approaching the driver from the opposite direction in a rural stop-sign controlled intersection scenario implemented in a static base driving simulator. Outcome measures used to evaluate the effectiveness of AR cueing included: Time-to-Contact (TTC), Gap Time Variation (GTV), Response Rate, and Gap Response Variation (GRV). All drivers estimated TTCs were shorter in cued than in uncued conditions. In addition, drivers responded more often in cued conditions than in uncued conditions and GRV decreased for all drivers in scenarios that contained AR cues. For both TTC and response rate, drivers also appeared to adjust their behavior to be consistent with the cues, especially drivers with the poorest UFOV scores (matching their behavior to be close to middle-aged drivers). Driver ratings indicated that cueing was not considered to be distracting. Further, various conditions of reliability (e.g., 15% miss rate) did not appear to affect performance or driver ratings. PMID:24950128

  7. Designing Fatigue Warning Systems: The perspective of professional drivers.

    PubMed

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

    2016-03-01

    Professional drivers have been characterized as experiencing heavy fatigue resulting from long driving time in their daily work. This study aimed to explore the potential demand of Fatigue Warning Systems (FWSs) among professional drivers as a means of reducing the danger of fatigue driving and to examine their opinions regarding the design of FWSs. Six focus groups with 35 participants and a questionnaire survey with 600 respondents were conducted among Chinese truck and taxi drivers to collect qualitative and quantitative data concerning the current situation of fatigue driving and opinions regarding the design of FWSs. The results revealed that both truck and taxi drivers had a positive attitude toward FWSs, and they hoped this system could not only monitor and warn them regarding their fatigue but also somewhat relieve their fatigue before they could stop and rest. As for warning signals, participants preferred auditory warnings, as opposed to visual, vibrotactile or electric stimuli. Interestingly, it was proposed that verbal warnings involving the information regarding consequences of fatigue driving or the wishes of drivers' family members would be more effective. Additionally, different warning patterns, including graded, single and continuous warnings, were discussed in the focus group. Finally, the participants proposed many other suggestions, as well as their concerns regarding FWSs, which will provide valuable information for companies who wish to develop FWSs for professional drivers. PMID:26482894

  8. Designing Fatigue Warning Systems: The perspective of professional drivers.

    PubMed

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

    2016-03-01

    Professional drivers have been characterized as experiencing heavy fatigue resulting from long driving time in their daily work. This study aimed to explore the potential demand of Fatigue Warning Systems (FWSs) among professional drivers as a means of reducing the danger of fatigue driving and to examine their opinions regarding the design of FWSs. Six focus groups with 35 participants and a questionnaire survey with 600 respondents were conducted among Chinese truck and taxi drivers to collect qualitative and quantitative data concerning the current situation of fatigue driving and opinions regarding the design of FWSs. The results revealed that both truck and taxi drivers had a positive attitude toward FWSs, and they hoped this system could not only monitor and warn them regarding their fatigue but also somewhat relieve their fatigue before they could stop and rest. As for warning signals, participants preferred auditory warnings, as opposed to visual, vibrotactile or electric stimuli. Interestingly, it was proposed that verbal warnings involving the information regarding consequences of fatigue driving or the wishes of drivers' family members would be more effective. Additionally, different warning patterns, including graded, single and continuous warnings, were discussed in the focus group. Finally, the participants proposed many other suggestions, as well as their concerns regarding FWSs, which will provide valuable information for companies who wish to develop FWSs for professional drivers.

  9. A load driver device for engineering modularity in biological networks.

    PubMed

    Mishra, Deepak; Rivera, Phillip M; Lin, Allen; Del Vecchio, Domitilla; Weiss, Ron

    2014-12-01

    The behavior of gene modules in complex synthetic circuits is often unpredictable. After joining modules to create a circuit, downstream elements (such as binding sites for a regulatory protein) apply a load to upstream modules that can negatively affect circuit function. Here we devised a genetic device named a load driver that mitigates the impact of load on circuit function, and we demonstrate its behavior in Saccharomyces cerevisiae. The load driver implements the design principle of timescale separation: inclusion of the load driver's fast phosphotransfer processes restores the capability of a slower transcriptional circuit to respond to time-varying input signals even in the presence of substantial load. Without the load driver, we observed circuit behavior that suffered from a 76% delay in response time and a 25% decrease in system bandwidth due to load. With the addition of a load driver, circuit performance was almost completely restored. Load drivers will serve as fundamental building blocks in the creation of complex, higher-level genetic circuits.

  10. Musculoskeletal Symptoms among Drivers of All-Terrain Vehicles

    NASA Astrophysics Data System (ADS)

    REHN, B.; BERGDAHL, I. A.; AHLGREN, C.; FROM, C.; JÄRVHOLM, B.; LUNDSTRÖM, R.; NILSSON, T.; SUNDELIN, G.

    2002-05-01

    The aim of this cross-sectional study was to characterize the risk of experiencing musculoskeletal symptoms in the region of the neck, shoulders and upper and lower back for professional drivers of various categories of all-terrain vehicles and to assess the association between symptoms and duration of exposure to whole-body vibration (WBV) and shock from driving all-terrain vehicles. The study group consisted of 215 drivers of forest machines, 137 drivers of snowmobiles and 79 drivers of snowgroomers and a control group of 167 men randomly selected from the general population. The subjects were all from one of the four most northern counties in Sweden and they were all men. Musculoskeletal symptoms were assessed by use of a standardized questionnaire. In addition, the questionnaire held items about the driving time with all-terrain vehicles and a subjective estimation of exposure to unpleasant movements (shock, jolt, irregular sway). The job strain was measured according to Karasek's demands/control model. The prevalence ratios were adjusted for age, smoking and job strain. Among drivers, significantly increased prevalence ratios within the range of 1∂5-2·9 were revealed for symptoms from the neck-shoulder and thoracic regions during the previous year. None of the driver categories had a statistically significantly increased risk of low back pain. Forest vehicles were those most reported to cause unpleasant movements. In conclusion, drivers of all-terrain vehicles exhibit an increased risk of symptoms of musculoskeletal disorders in the neck-shoulder and thoracic regions. The increased risk is suggested to be related to physical factors such as exposure to whole-body vibration (WBV) and shock, static overload or extreme body postures. However, since symptoms of low back pain were not significantly increased, it appears that factors other than WBV would explain the occurrence of symptoms in the group of all-terrain drivers.

  11. Does attention capacity moderate the effect of driver distraction in older drivers?

    PubMed

    Cuenen, Ariane; Jongen, Ellen M M; Brijs, Tom; Brijs, Kris; Lutin, Mark; Van Vlierden, Karin; Wets, Geert

    2015-04-01

    With age, a decline in attention capacity may occur and this may impact driving performance especially while distracted. Although the effect of distraction on driving performance of older drivers has been investigated, the moderating effect of attention capacity on driving performance during distraction has not been investigated yet. Therefore, the aim was to investigate whether attention capacity has a moderating effect on older drivers' driving performance during visual distraction (experiment 1) and cognitive distraction (experiment 2). In a fixed-based driving simulator, older drivers completed a driving task without and with visual distraction (experiment 1, N=17, mean age 78 years) or cognitive distraction (experiment 2, N=35, mean age 76 years). Several specific driving measures of varying complexity (i.e., speed, lane keeping, following distance, braking behavior, and crashes) were investigated. In addition to these objective driving measures, subjective measures of workload and driving performance were also included. In experiment 1, crash occurrence increased with visual distraction and was negatively related to attention capacity. In experiment 2, complete stops at stop signs decreased, initiation of braking at pedestrian crossings was later, and crash occurrence increased with cognitive distraction. Interestingly, for a measure of lane keeping (i.e., standard deviation of lateral lane position (SDLP)), effects of both types of distraction were moderated by attention capacity. Despite the decrease of driving performance with distraction, participants estimated their driving performance during distraction as good. These results imply that attention capacity is important for driving. Driver assessment and training programs might therefore focus on attention capacity. Nonetheless, it is crucial to eliminate driver distraction as much as possible given the deterioration of performance on several driving measures in those with low and high attention capacity.

  12. MUFFINN: cancer gene discovery via network analysis of somatic mutation data.

    PubMed

    Cho, Ara; Shim, Jung Eun; Kim, Eiru; Supek, Fran; Lehner, Ben; Lee, Insuk

    2016-01-01

    A major challenge for distinguishing cancer-causing driver mutations from inconsequential passenger mutations is the long-tail of infrequently mutated genes in cancer genomes. Here, we present and evaluate a method for prioritizing cancer genes accounting not only for mutations in individual genes but also in their neighbors in functional networks, MUFFINN (MUtations For Functional Impact on Network Neighbors). This pathway-centric method shows high sensitivity compared with gene-centric analyses of mutation data. Notably, only a marginal decrease in performance is observed when using 10 % of TCGA patient samples, suggesting the method may potentiate cancer genome projects with small patient populations. PMID:27333808

  13. Recurrent PTPRB and PLCG1 mutations in angiosarcoma

    PubMed Central

    Martincorena, Inigo; Van Loo, Peter; Gundem, Gunes; Wedge, David C; Ramakrishna, Manasa; Cooke, Susanna L; Pillay, Nischalan; Vollan, Hans Kristian M; Papaemmanuil, Elli; Koss, Hans; Bunney, Tom D; Hardy, Claire; Joseph, Olivia R; Martin, Sancha; Mudie, Laura; Butler, Adam; Teague, Jon W; Patil, Meena; Steers, Graham; Cao, Yu; Gumbs, Curtis; Ingram, Davis; Lazar, Alexander J; Little, Latasha; Mahadeshwar, Harshad; Protopopov, Alexei; Al Sannaa, Ghadah A; Seth, Sahil; Song, Xingzhi; Tang, Jiabin; Zhang, Jianhua; Ravi, Vinod; Torres, Keila E; Khatri, Bhavisha; Halai, Dina; Roxanis, Ioannis; Baumhoer, Daniel; Tirabosco, Roberto; Amary, M Fernanda; Boshoff, Chris; McDermott, Ultan; Katan, Matilda; Stratton, Michael R; Futreal, P Andrew; Flanagan, Adrienne M; Harris, Adrian; Campbell, Peter J

    2014-01-01

    Angiosarcoma is an aggressive malignancy that arises spontaneously or secondarily to ionising radiation or chronic lymphoedema1. Previous work has identified aberrant angiogenesis, including occasional somatic mutations in angiogenesis signalling genes, as a key driver of angiosarcoma1. Here, we employed whole genome, exome, and targeted sequencing to study the somatic changes underpinning primary and secondary angiosarcoma. We identified recurrent mutations in two genes, PTPRB and PLCG1, which are intimately linked to angiogenesis. The endothelial phosphatase PTPRB, a negative regulator of vascular growth factor tyrosine kinases, harboured predominantly truncating mutations in 10/39 (26%) tumours. PLCG1, a signal transducer of tyrosine kinases, presented with a recurrent, likely activating R707Q missense variant in 3/34 cases (9%). Overall, 15/39 (38%) tumours harboured at least one driver mutation in angiogenesis signalling genes. Our findings inform and reinforce current therapeutic efforts to target angiogenesis signalling in angiosarcoma. PMID:24633157

  14. Efficiency of carcinogenesis: is the mutator phenotype inevitable?

    PubMed

    Beckman, Robert A

    2010-10-01

    Cancer development requires multiple oncogenic mutations. Pathogenic mechanisms which accelerate this process may be favored carcinogenic pathways. Mutator mutations are mutations in genetic stability genes, and increase the mutation rate, speeding up the accumulation of oncogenic mutations. The mutator hypothesis states that mutator mutations play a critical role in carcinogenesis. Alternatively, tumors might arise by mutations occurring at the normal rate followed by selection and expansion of various premalignant lineages on the path to cancer. This alternative pathway is a significant argument against the mutator hypothesis. Mutator mutations may also lead to accumulation of deleterious mutations, which could lead to extinction of premalignant lineages before they become cancerous, another argument against the mutator hypothesis. Finally, the need for acquisition of a mutator mutation imposes an additional step on the carcinogenic process. Accordingly, the mutator hypothesis has been a seminal but controversial idea for several decades despite considerable experimental and theoretical work. To resolve this debate, the concept of efficiency has been introduced as a metric for comparing carcinogenic mechanisms, and a new theoretical approach of focused quantitative modeling has been applied. The results demonstrate that, given what is already known, the predominance of mutator mechanisms is likely inevitable, as they overwhelm less efficient non-mutator pathways to cancer.

  15. Efficiency of carcinogenesis: is the mutator phenotype inevitable?

    PubMed

    Beckman, Robert A

    2010-10-01

    Cancer development requires multiple oncogenic mutations. Pathogenic mechanisms which accelerate this process may be favored carcinogenic pathways. Mutator mutations are mutations in genetic stability genes, and increase the mutation rate, speeding up the accumulation of oncogenic mutations. The mutator hypothesis states that mutator mutations play a critical role in carcinogenesis. Alternatively, tumors might arise by mutations occurring at the normal rate followed by selection and expansion of various premalignant lineages on the path to cancer. This alternative pathway is a significant argument against the mutator hypothesis. Mutator mutations may also lead to accumulation of deleterious mutations, which could lead to extinction of premalignant lineages before they become cancerous, another argument against the mutator hypothesis. Finally, the need for acquisition of a mutator mutation imposes an additional step on the carcinogenic process. Accordingly, the mutator hypothesis has been a seminal but controversial idea for several decades despite considerable experimental and theoretical work. To resolve this debate, the concept of efficiency has been introduced as a metric for comparing carcinogenic mechanisms, and a new theoretical approach of focused quantitative modeling has been applied. The results demonstrate that, given what is already known, the predominance of mutator mechanisms is likely inevitable, as they overwhelm less efficient non-mutator pathways to cancer. PMID:20934514

  16. Sexual behavior among truck drivers.

    PubMed

    Singh, Rajiv Kumar; Joshi, Hari Shankar

    2012-01-01

    A cross-sectional study was conducted on Lucknow highway in Bareilly district of Uttar Pradesh to study the knowledge of truck drivers about HIV transmission and prevention and to study the sexual behaviour of these drivers with reference to HIV/AIDS. Age, marital status, education, income, drinking alcohol, length of stay away from home, knowledge about transmission and prevention of HIV, and HIV-prone behavior of truck drivers were studied. Chi-square, mean, and SD were calculated. In all, 289 (97.6%) drivers had heard about HIV/AIDS. Only 242 (81.8%) were aware of HIV transmission by heterosexual route. Misconceptions such as HIV transmission by mosquito bites, living in same room, shaking hands, and sharing food were found. Out of 174 (58.8%) who visited Commercial Sex Workers (CSW), 146 (83.9%) used a condom. 38 (12.8%) visited more than 5 CSW in the last 3 months. Time away from home on the road, marital status, alcohol use, and income class were associated with visiting CSW. High-risk behavior was established in the study population. Safe sex and use of condoms need to be promoted among the truck drivers and better condom availability needs to be assured on highways.

  17. Identification of Variant-Specific Functions of PIK3CA by Rapid Phenotyping of Rare Mutations.

    PubMed

    Dogruluk, Turgut; Tsang, Yiu Huen; Espitia, Maribel; Chen, Fengju; Chen, Tenghui; Chong, Zechen; Appadurai, Vivek; Dogruluk, Armel; Eterovic, Agna Karina; Bonnen, Penelope E; Creighton, Chad J; Chen, Ken; Mills, Gordon B; Scott, Kenneth L

    2015-12-15

    Large-scale sequencing efforts are uncovering the complexity of cancer genomes, which are composed of causal "driver" mutations that promote tumor progression along with many more pathologically neutral "passenger" events. The majority of mutations, both in known cancer drivers and uncharacterized genes, are generally of low occurrence, highlighting the need to functionally annotate the long tail of infrequent mutations present in heterogeneous cancers. Here we describe a mutation assessment pipeline enabled by high-throughput engineering of molecularly barcoded gene variant expression clones identified by tumor sequencing. We first used this platform to functionally assess tail mutations observed in PIK3CA, which encodes the catalytic subunit alpha of the phosphatidylinositol-4,5-bisphosphate 3-kinase (PI3K) frequently mutated in cancer. Orthogonal screening for PIK3CA variant activity using in vitro and in vivo cell growth and transformation assays differentiated driver from passenger mutations, revealing that PIK3CA variant activity correlates imperfectly with its mutation frequency across breast cancer populations. Although PIK3CA mutations with frequencies above 5% were significantly more oncogenic than wild-type in all assays, mutations occurring at 0.07% to 5.0% included those with and without oncogenic activities that ranged from weak to strong in at least one assay. Proteomic profiling coupled with therapeutic sensitivity assays on PIK3CA variant-expressing cell models revealed variant-specific activation of PI3K signaling as well as other pathways that include the MEK1/2 module of mitogen-activated protein kinase pathway. Our data indicate that cancer treatments will need to increasingly consider the functional relevance of specific mutations in driver genes rather than considering all mutations in drivers as equivalent. PMID:26627007

  18. Signatures of mutational processes in human cancer

    PubMed Central

    Alexandrov, Ludmil B.; Nik-Zainal, Serena; Wedge, David C.; Aparicio, Samuel A.J.R.; Behjati, Sam; Biankin, Andrew V.; Bignell, Graham R.; Bolli, Niccolo; Borg, Ake; Børresen-Dale, Anne-Lise; Boyault, Sandrine; Burkhardt, Birgit; Butler, Adam P.; Caldas, Carlos; Davies, Helen R.; Desmedt, Christine; Eils, Roland; Eyfjörd, Jórunn Erla; Foekens, John A.; Greaves, Mel; Hosoda, Fumie; Hutter, Barbara; Ilicic, Tomislav; Imbeaud, Sandrine; Imielinsk, Marcin; Jäger, Natalie; Jones, David T.W.; Jones, David; Knappskog, Stian; Kool, Marcel; Lakhani, Sunil R.; López-Otín, Carlos; Martin, Sancha; Munshi, Nikhil C.; Nakamura, Hiromi; Northcott, Paul A.; Pajic, Marina; Papaemmanuil, Elli; Paradiso, Angelo; Pearson, John V.; Puente, Xose S.; Raine, Keiran; Ramakrishna, Manasa; Richardson, Andrea L.; Richter, Julia; Rosenstiel, Philip; Schlesner, Matthias; Schumacher, Ton N.; Span, Paul N.; Teague, Jon W.; Totoki, Yasushi; Tutt, Andrew N.J.; Valdés-Mas, Rafael; van Buuren, Marit M.; van ’t Veer, Laura; Vincent-Salomon, Anne; Waddell, Nicola; Yates, Lucy R.; Zucman-Rossi, Jessica; Futreal, P. Andrew; McDermott, Ultan; Lichter, Peter; Meyerson, Matthew; Grimmond, Sean M.; Siebert, Reiner; Campo, Elías; Shibata, Tatsuhiro; Pfister, Stefan M.; Campbell, Peter J.; Stratton, Michael R.

    2013-01-01

    All cancers are caused by somatic mutations. However, understanding of the biological processes generating these mutations is limited. The catalogue of somatic mutations from a cancer genome bears the signatures of the mutational processes that have been operative. Here, we analysed 4,938,362 mutations from 7,042 cancers and extracted more than 20 distinct mutational signatures. Some are present in many cancer types, notably a signature attributed to the APOBEC family of cytidine deaminases, whereas others are confined to a single class. Certain signatures are associated with age of the patient at cancer diagnosis, known mutagenic exposures or defects in DNA maintenance, but many are of cryptic origin. In addition to these genome-wide mutational signatures, hypermutation localized to small genomic regions, kataegis, is found in many cancer types. The results reveal the diversity of mutational processes underlying the development of cancer with potential implications for understanding of cancer etiology, prevention and therapy. PMID:23945592

  19. Signatures of mutational processes in human cancer.

    PubMed

    Alexandrov, Ludmil B; Nik-Zainal, Serena; Wedge, David C; Aparicio, Samuel A J R; Behjati, Sam; Biankin, Andrew V; Bignell, Graham R; Bolli, Niccolò; Borg, Ake; Børresen-Dale, Anne-Lise; Boyault, Sandrine; Burkhardt, Birgit; Butler, Adam P; Caldas, Carlos; Davies, Helen R; Desmedt, Christine; Eils, Roland; Eyfjörd, Jórunn Erla; Foekens, John A; Greaves, Mel; Hosoda, Fumie; Hutter, Barbara; Ilicic, Tomislav; Imbeaud, Sandrine; Imielinski, Marcin; Imielinsk, Marcin; Jäger, Natalie; Jones, David T W; Jones, David; Knappskog, Stian; Kool, Marcel; Lakhani, Sunil R; López-Otín, Carlos; Martin, Sancha; Munshi, Nikhil C; Nakamura, Hiromi; Northcott, Paul A; Pajic, Marina; Papaemmanuil, Elli; Paradiso, Angelo; Pearson, John V; Puente, Xose S; Raine, Keiran; Ramakrishna, Manasa; Richardson, Andrea L; Richter, Julia; Rosenstiel, Philip; Schlesner, Matthias; Schumacher, Ton N; Span, Paul N; Teague, Jon W; Totoki, Yasushi; Tutt, Andrew N J; Valdés-Mas, Rafael; van Buuren, Marit M; van 't Veer, Laura; Vincent-Salomon, Anne; Waddell, Nicola; Yates, Lucy R; Zucman-Rossi, Jessica; Futreal, P Andrew; McDermott, Ultan; Lichter, Peter; Meyerson, Matthew; Grimmond, Sean M; Siebert, Reiner; Campo, Elías; Shibata, Tatsuhiro; Pfister, Stefan M; Campbell, Peter J; Stratton, Michael R

    2013-08-22

    All cancers are caused by somatic mutations; however, understanding of the biological processes generating these mutations is limited. The catalogue of somatic mutations from a cancer genome bears the signatures of the mutational processes that have been operative. Here we analysed 4,938,362 mutations from 7,042 cancers and extracted more than 20 distinct mutational signatures. Some are present in many cancer types, notably a signature attributed to the APOBEC family of cytidine deaminases, whereas others are confined to a single cancer class. Certain signatures are associated with age of the patient at cancer diagnosis, known mutagenic exposures or defects in DNA maintenance, but many are of cryptic origin. In addition to these genome-wide mutational signatures, hypermutation localized to small genomic regions, 'kataegis', is found in many cancer types. The results reveal the diversity of mutational processes underlying the development of cancer, with potential implications for understanding of cancer aetiology, prevention and therapy.

  20. 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

  1. Drivers of the primate thalamus

    PubMed Central

    Rovó, Zita; Ulbert, István; Acsády, László

    2012-01-01

    The activity of thalamocortical neurons is largely determined by giant excitatory terminals, called drivers. These afferents may arise from neocortex or from subcortical centers; however their exact distribution, segregation or putative absence in given thalamic nuclei are unknown. To unravel the nucleus-specific composition of drivers, we mapped the entire macaque thalamus utilizing vesicular glutamate transporters 1 and 2 to label cortical and subcortical afferents, respectively. Large thalamic territories were innervated exclusively either by giant vGLUT2- or vGLUT1-positive boutons. Co-distribution of drivers with different origin was not abundant. In several thalamic regions, no giant terminals of any type could be detected at light microscopic level. Electron microscopic observation of these territories revealed either the complete absence of large multisynaptic excitatory terminals (basal ganglia-recipient nuclei) or the presence of both vGLUT1- and vGLUT2-positive terminals, which were significantly smaller than their giant counterparts (intralaminar nuclei, medial pulvinar). In the basal ganglia-recipient thalamus, giant inhibitory terminals replaced the excitatory driver inputs. The pulvinar and the mediodorsal nucleus displayed subnuclear heterogeneity in their driver assemblies. These results show that distinct thalamic territories can be under pure subcortical or cortical control; however there is significant variability in the composition of major excitatory inputs in several thalamic regions. Since thalamic information transfer depends on the origin and complexity of the excitatory inputs, this suggests that the computations performed by individual thalamic regions display considerable variability. Finally, the map of driver distribution may help to resolve the morphological basis of human diseases involving different parts of the thalamus. PMID:23223308

  2. Myopathies associated with β-tropomyosin mutations.

    PubMed

    Tajsharghi, H; Ohlsson, M; Palm, L; Oldfors, A

    2012-11-01

    Mutations in TPM2, encoding β-tropomyosin, have recently been found to cause a range of muscle disorders. We review the clinical and morphological expression of the previously reported mutations illustrating the heterogeneity of β-tropomyosin-associated diseases and describe an additional case with a novel mutation. The manifestations of mutations in TPM2 include non-specific congenital myopathy with type 1 fibre predominance, nemaline myopathy, cap disease and distal arthrogryposis. In addition, Escobar syndrome with nemaline myopathy is a manifestation of homozygous truncating β-tropomyosin mutation. Cap disease appears to be the most common morphological manifestation. A coarse intermyofibrillar network and jagged Z lines are additional frequent changes. The dominant β-tropomyosin mutations manifest either as congenital myopathy or distal arthrogryposis. The various congenital myopathies are usually associated with moderate muscle weakness and no congenital joint contractures. The distal arthrogryposis syndromes associated with TPM2 mutations include the less severe forms, with congenital contractures mainly of the hands and feet and mild or no muscle weakness. The dominant TPM2 mutations include amino acid deletions/insertions and missense mutations. There is no clear relation between the type of mutations or the localisation of the mutated residue in the β-tropomyosin molecule and the clinical and morphological phenotype. PMID:22749895

  3. Progress in heavy-ion drivers for inertial fusion

    SciTech Connect

    Friedman, A.; Bangerter, R.O.; Herrmannsfeldt, W.B.

    1994-12-22

    Heavy-ion induction accelerators are being developed as fusion drivers for ICF power production in the US Inertial Fusion Energy (IFE) program, in the Office of Fusion Energy of the US Department of Energy. In addition, they represent an attractive driver option for a high-yield microfusion facility for defense research. This paper describes recent progress in induction drivers for Heavy-Ion Fusion (HIF), and plans for future work. It presents research aimed at developing drivers having reduced cost and size, specifically advanced induction linacs and recirculating induction accelerators (recirculators). The goals and design of the Elise accelerator being built at Lawrence Berkeley Laboratory (LBL), as the first stage of the ILSE (Induction Linac Systems Experiments) program, are described. Elise will accelerate, for the first time, space-charge-dominated ion beams which are of full driver scale in line-charge density and diameter. Elise will be a platform on which the critical beam manipulations of the induction approach can be explored. An experimental program at Lawrence Livermore National Laboratory (LLNL) exploring the recirculator principle on a small scale is described in some detail; it is expected that these studies will result ultimately in an operational prototype recirculating induction accelerator. In addition, other elements of the US HIF program are described.

  4. UWB dual burst transmit driver

    SciTech Connect

    Dallum, Gregory E.; Pratt, Garth C.; Haugen, Peter C.; Zumstein, James M.; Vigars, Mark L.; Romero, Carlos E.

    2012-04-17

    A dual burst transmitter for ultra-wideband (UWB) communication systems generates a pair of precisely spaced RF bursts from a single trigger event. An input trigger pulse produces two oscillator trigger pulses, an initial pulse and a delayed pulse, in a dual trigger generator. The two oscillator trigger pulses drive a gated RF burst (power output) oscillator. A bias driver circuit gates the RF output oscillator on and off and sets the RF burst packet width. The bias driver also level shifts the drive signal to the level that is required for the RF output device.

  5. A new switched-capacitor frequency modulated driver for light emitting diodes.

    PubMed

    Feng, Weifeng; Shi, Frank G

    2007-11-01

    A new type of drivers for light emitting diodes (LEDs) is introduced based on the switched-capacitor frequency modulation. In contrast to conventional constant dc current drivers, the current pulse is provided by this new switched-capacitor LED driver. In the present driver, the charging capacitor is charged and discharged through a LED and the current flow direction is controlled by a metal oxide semiconductor switch. The input current (and thus the LED brightness) is proportional to the switch clock frequency at relatively low frequencies and becomes saturated at relatively high frequencies. This new driver circuit is simple and robust and maintains high efficiency for a wide range of input powers. In addition, the dimming control is easily realized by modulating clock frequency. Finally, this LED driver consumes no dc current and thus provides inherent protection to LED in standby mode. PMID:18052494

  6. 78 FR 30954 - Agency Information Collection Activities; Revision of a Currently Approved Collection: Driver...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-05-23

    .... The Agency's estimate of the number of drivers subject to these requirements has been revised to... addition, this revision request includes an updated estimate of the interstate drivers and an increase in the estimated annual burden hours for this ICR. The bulk of the increase in burden hours is the...

  7. Exome and deep sequencing of clinically aggressive neuroblastoma reveal somatic mutations that affect key pathways involved in cancer progression

    PubMed Central

    Lasorsa, Vito Alessandro; Formicola, Daniela; Pignataro, Piero; Cimmino, Flora; Calabrese, Francesco Maria; Mora, Jaume; Esposito, Maria Rosaria; Pantile, Marcella; Zanon, Carlo; De Mariano, Marilena; Longo, Luca; Hogarty, Michael D.; de Torres, Carmen; Tonini, Gian Paolo; Iolascon, Achille; Capasso, Mario

    2016-01-01

    The spectrum of somatic mutation of the most aggressive forms of neuroblastoma is not completely determined. We sought to identify potential cancer drivers in clinically aggressive neuroblastoma. Whole exome sequencing was conducted on 17 germline and tumor DNA samples from high-risk patients with adverse events within 36 months from diagnosis (HR-Event3) to identify somatic mutations and deep targeted sequencing of 134 genes selected from the initial screening in additional 48 germline and tumor pairs (62.5% HR-Event3 and high-risk patients), 17 HR-Event3 tumors and 17 human-derived neuroblastoma cell lines. We revealed 22 significantly mutated genes, many of which implicated in cancer progression. Fifteen genes (68.2%) were highly expressed in neuroblastoma supporting their involvement in the disease. CHD9, a cancer driver gene, was the most significantly altered (4.0% of cases) after ALK. Other genes (PTK2, NAV3, NAV1, FZD1 and ATRX), expressed in neuroblastoma and involved in cell invasion and migration were mutated at frequency ranged from 4% to 2%. Focal adhesion and regulation of actin cytoskeleton pathways, were frequently disrupted (14.1% of cases) thus suggesting potential novel therapeutic strategies to prevent disease progression. Notably BARD1, CHEK2 and AXIN2 were enriched in rare, potentially pathogenic, germline variants. In summary, whole exome and deep targeted sequencing identified novel cancer genes of clinically aggressive neuroblastoma. Our analyses show pathway-level implications of infrequently mutated genes in leading neuroblastoma progression. PMID:27009842

  8. Exome and deep sequencing of clinically aggressive neuroblastoma reveal somatic mutations that affect key pathways involved in cancer progression.

    PubMed

    Lasorsa, Vito Alessandro; Formicola, Daniela; Pignataro, Piero; Cimmino, Flora; Calabrese, Francesco Maria; Mora, Jaume; Esposito, Maria Rosaria; Pantile, Marcella; Zanon, Carlo; De Mariano, Marilena; Longo, Luca; Hogarty, Michael D; de Torres, Carmen; Tonini, Gian Paolo; Iolascon, Achille; Capasso, Mario

    2016-04-19

    The spectrum of somatic mutation of the most aggressive forms of neuroblastoma is not completely determined. We sought to identify potential cancer drivers in clinically aggressive neuroblastoma.Whole exome sequencing was conducted on 17 germline and tumor DNA samples from high-risk patients with adverse events within 36 months from diagnosis (HR-Event3) to identify somatic mutations and deep targeted sequencing of 134 genes selected from the initial screening in additional 48 germline and tumor pairs (62.5% HR-Event3 and high-risk patients), 17 HR-Event3 tumors and 17 human-derived neuroblastoma cell lines.We revealed 22 significantly mutated genes, many of which implicated in cancer progression. Fifteen genes (68.2%) were highly expressed in neuroblastoma supporting their involvement in the disease. CHD9, a cancer driver gene, was the most significantly altered (4.0% of cases) after ALK.Other genes (PTK2, NAV3, NAV1, FZD1 and ATRX), expressed in neuroblastoma and involved in cell invasion and migration were mutated at frequency ranged from 4% to 2%.Focal adhesion and regulation of actin cytoskeleton pathways, were frequently disrupted (14.1% of cases) thus suggesting potential novel therapeutic strategies to prevent disease progression.Notably BARD1, CHEK2 and AXIN2 were enriched in rare, potentially pathogenic, germline variants.In summary, whole exome and deep targeted sequencing identified novel cancer genes of clinically aggressive neuroblastoma. Our analyses show pathway-level implications of infrequently mutated genes in leading neuroblastoma progression. PMID:27009842

  9. Children's Understanding of Drivers' Intentions

    ERIC Educational Resources Information Center

    Foot, Hugh C.; Thomson, James A.; Tolmie, Andrew K.; Whelan, Kirstie M.; Morrison, Sheila; Sarvary, Penelope

    2006-01-01

    To become more skilled as pedestrians, children need to acquire a view of the traffic environment as one in which road users are active agents with different intentions and objectives. This paper describes a simulation study designed to explore children's understanding of drivers' intentions. It also investigated the effect of training children's…

  10. Transporting Handicapped Students: Driver Manual.

    ERIC Educational Resources Information Center

    Turner, Dayton Ray

    The document offers guidelines for van or bus drivers transporting handicapped students to and from school. Part 1 offers an overview of adaptive transportation services and gives specifics on providing services to the blind/visually impaired, hearing impaired, mentally retarded, physically handicapped, behaviorally disordered, learning disabled,…

  11. Teaching French via Driver Education.

    ERIC Educational Resources Information Center

    Berwald, Jean-Pierre

    1980-01-01

    Driver instruction through the medium of a foreign language is useful in teaching vocabulary, grammar, and culture. The maps, driving manuals, and cars stimulate discussion and communication. Course techniques can include Asher's concept of Total Physical Response wherein students act in response to commands in the foreign language. (PMJ)

  12. Fuel-Cell Drivers Wanted

    ERIC Educational Resources Information Center

    Clark, Todd; Jones, Rick

    2004-01-01

    While the political climate seems favorable for the development of fuel-cell vehicles for personal transportation, the market's demand may not be so favorable. Nonetheless, middle level students will be the next generation of drivers and voters, and they need to be able to make informed decisions regarding the nation's energy and transportation…

  13. Older Drivers: A Closer Look.

    ERIC Educational Resources Information Center

    Goggin, Noreen L.; Keller, M. Jean

    1996-01-01

    Cognitive and decision-making capabilities and motor responses were assessed for 24 older adults using 15 videotaped driving scenarios. Older drivers performed better on the simulation than the written test. Men performed better, drove more miles per year, and did more highway driving, differences attributed to handgrip strength or sex-role…

  14. Identification of High-Impact cis-Regulatory Mutations Using Transcription Factor Specific Random Forest Models

    PubMed Central

    Svetlichnyy, Dmitry; Imrichova, Hana; Fiers, Mark; Kalender Atak, Zeynep; Aerts, Stein

    2015-01-01

    Cancer genomes contain vast amounts of somatic mutations, many of which are passenger mutations not involved in oncogenesis. Whereas driver mutations in protein-coding genes can be distinguished from passenger mutations based on their recurrence, non-coding mutations are usually not recurrent at the same position. Therefore, it is still unclear how to identify cis-regulatory driver mutations, particularly when chromatin data from the same patient is not available, thus relying only on sequence and expression information. Here we use machine-learning methods to predict functional regulatory regions using sequence information alone, and compare the predicted activity of the mutated region with the reference sequence. This way we define the Predicted Regulatory Impact of a Mutation in an Enhancer (PRIME). We find that the recently identified driver mutation in the TAL1 enhancer has a high PRIME score, representing a “gain-of-target” for MYB, whereas the highly recurrent TERT promoter mutation has a surprisingly low PRIME score. We trained Random Forest models for 45 cancer-related transcription factors, and used these to score variations in the HeLa genome and somatic mutations across more than five hundred cancer genomes. Each model predicts only a small fraction of non-coding mutations with a potential impact on the function of the encompassing regulatory region. Nevertheless, as these few candidate driver mutations are often linked to gains in chromatin activity and gene expression, they may contribute to the oncogenic program by altering the expression levels of specific oncogenes and tumor suppressor genes. PMID:26562774

  15. Food additives

    PubMed Central

    Spencer, Michael

    1974-01-01

    Food additives are discussed from the food technology point of view. The reasons for their use are summarized: (1) to protect food from chemical and microbiological attack; (2) to even out seasonal supplies; (3) to improve their eating quality; (4) to improve their nutritional value. The various types of food additives are considered, e.g. colours, flavours, emulsifiers, bread and flour additives, preservatives, and nutritional additives. The paper concludes with consideration of those circumstances in which the use of additives is (a) justified and (b) unjustified. PMID:4467857

  16. Alcohol and the driver. Council on Scientific Affairs.

    PubMed

    Scientific investigations have produced 50 years of accumulated evidence showing a direct relationship between increasing blood alcohol concentration (BAC) in drivers and increasing risk of a motor vehicle crash. There is scientific consensus that alcohol causes deterioration of driving skills beginning at 0.05% BAC or even lower, and progressively serious impairment at higher BACs. Drivers aged 16 to 24 years have the highest representation of all age groups in alcohol-related road crashes; young drivers involved in alcohol-related fatal crashes have lower average BACs than older drivers. Alcohol impairs driving skills by its effects on the central nervous system, acting like a general anesthetic. It renders slower and less efficient both information acquisition and information processing, making divided-attention tasks such as steering and braking more difficult to carry out without error. The influence of alcohol on emotions and attitudes may be a crash risk factor related to driving style in addition to driving skill. Biologic variability among humans produces substantial differences in alcohol influence and alcohol tolerance, making virtually useless any attempts to fix a "safe" drinking level for drivers. The American Medical Association supports a policy recommending (1) public education urging drivers not to drink, (2) adoption by all states of 0.05% BAC as per se evidence of alcohol-impaired driving, (3) 21 years as the legal drinking age in all states, (4) adoption by all states of administrative driver's license suspension in driving-under-the-influence cases, and (5) encouragement for the automobile industry to develop a safety module that thwarts operation of a motor vehicle by an intoxicated person.

  17. BINNING SOMATIC MUTATIONS BASED ON BIOLOGICAL KNOWLEDGE FOR PREDICTING SURVIVAL: AN APPLICATION IN RENAL CELL CARCINOMA

    PubMed Central

    Kim, Dokyoon; Li, Ruowang; Dudek, Scott M.; Wallace, John R.; Ritchie, Marylyn D.

    2014-01-01

    Enormous efforts of whole exome and genome sequencing from hundreds to thousands of patients have provided the landscape of somatic genomic alterations in many cancer types to distinguish between driver mutations and passenger mutations. Driver mutations show strong associations with cancer clinical outcomes such as survival. However, due to the heterogeneity of tumors, somatic mutation profiles are exceptionally sparse whereas other types of genomic data such as miRNA or gene expression contain much more complete data for all genomic features with quantitative values measured in each patient. To overcome the extreme sparseness of somatic mutation profiles and allow for the discovery of combinations of somatic mutations that may predict cancer clinical outcomes, here we propose a new approach for binning somatic mutations based on existing biological knowledge. Through the analysis using renal cell carcinoma dataset from The Cancer Genome Atlas (TCGA), we identified combinations of somatic mutation burden based on pathways, protein families, evolutionary conversed regions, and regulatory regions associated with survival. Due to the nature of heterogeneity in cancer, using a binning strategy for somatic mutation profiles based on biological knowledge will be valuable for improved prognostic biomarkers and potentially for tailoring therapeutic strategies by identifying combinations of driver mutations. PMID:25592572

  18. Landscape of somatic mutations in 560 breast cancer whole-genome sequences

    DOE PAGES

    Nik-Zainal, Serena; Davies, Helen; Staaf, Johan; Ramakrishna, Manasa; Glodzik, Dominik; Zou, Xueqing; Martincorena, Inigo; Alexandrov, Ludmil B.; Martin, Sancha; Wedge, David C.; et al

    2016-05-02

    Here, we analysed whole-genome sequences of 560 breast cancers to advance understanding of the driver mutations conferring clonal advantage and the mutational processes generating somatic mutations. We found that 93 protein-coding cancer genes carried probable driver mutations. Some non-coding regions exhibited high mutation frequencies, but most have distinctive structural features probably causing elevated mutation rates and do not contain driver mutations. Mutational signature analysis was extended to genome rearrangements and revealed twelve base substitution and six rearrangement signatures. Three rearrangement signatures, characterized by tandem duplications or deletions, appear associated with defective homologous-recombination-based DNA repair: one with deficient BRCA1 function, anothermore » with deficient BRCA1 or BRCA2 function, the cause of the third is unknown. This analysis of all classes of somatic mutation across exons, introns and intergenic regions highlights the repertoire of cancer genes and mutational processes operating, and progresses towards a comprehensive account of the somatic genetic basis of breast cancer.« less

  19. 49 CFR 380.109 - Driver testing.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... Transportation Other Regulations Relating to Transportation (Continued) FEDERAL MOTOR CARRIER SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION FEDERAL MOTOR CARRIER SAFETY REGULATIONS SPECIAL TRAINING....109 Driver testing. (a) Testing methods. The driver-student must pass knowledge and skills tests...

  20. 49 CFR 380.109 - Driver testing.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... Transportation Other Regulations Relating to Transportation (Continued) FEDERAL MOTOR CARRIER SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION FEDERAL MOTOR CARRIER SAFETY REGULATIONS SPECIAL TRAINING....109 Driver testing. (a) Testing methods. The driver-student must pass knowledge and skills tests...

  1. 49 CFR 380.109 - Driver testing.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... Transportation Other Regulations Relating to Transportation (Continued) FEDERAL MOTOR CARRIER SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION FEDERAL MOTOR CARRIER SAFETY REGULATIONS SPECIAL TRAINING....109 Driver testing. (a) Testing methods. The driver-student must pass knowledge and skills tests...

  2. 49 CFR 380.109 - Driver testing.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... Transportation Other Regulations Relating to Transportation (Continued) FEDERAL MOTOR CARRIER SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION FEDERAL MOTOR CARRIER SAFETY REGULATIONS SPECIAL TRAINING....109 Driver testing. (a) Testing methods. The driver-student must pass knowledge and skills tests...

  3. Driver training interests of a Spanish sample of young drivers and its relationship with their self-assessment skills concerning risky driving behavior.

    PubMed

    Molina, J Gabriel; Sanmartín, Jaime; Keskinen, Esko

    2013-03-01

    Poor driving self-assessment skills (e.g., over-confidence) have been pointed out as an important explanatory factor behind young drivers' accident involvement. This paper explores (1) what young drivers miss in their training as drivers in order to analyze whether an assessment of one's own driving skills plays an important role in their desire to improve as drivers, and (2) how these training interests are related to an estimate of their self-assessment skills concerning risky driving behavior. For this purpose, a study was conducted using a survey with a blocked sampling design of novice drivers. The survey solicited respondents' self-report about (1) the contents of training courses that they feel would improve their driving, (2) their risky driving behavior, and (3) their likelihood of being involved in a risky driving situation. From the initial sample invited to participate, of nearly 1300 people, we finally obtained complete data from 321 young Spanish drivers. Two main results were apparent from our data analysis: (1) the novice drivers were mainly interested in improving their ability to recognize their strengths and weaknesses as drivers (i.e., self-assessment skills); (2) a significant relationship was found between novice drivers' interests and their current self-assessment skills concerning risky driving behavior. Specifically, there was greater general interest expressed in post-license training by the under-confident self-assessors than the over-confident ones. These results provide a relevant input which should be taken into account when designing driver training programs for novice drivers. Moreover, the relationship between their training interests and their risky driving self-assessment skills introduces an additional factor to be considered in the implementation of these training programs.

  4. Analytics For Distracted Driver Behavior Modeling in Dilemma Zone

    SciTech Connect

    Li, Jan-Mou; Malikopoulos, Andreas; Thakur, Gautam; Vatsavai, Raju

    2014-01-01

    In this paper, we present the results obtained and insights gained through the analysis of TRB contest data. We used exploratory analysis, regression, and clustering models for gaining insights into the driver behavior in a dilemma zone while driving under distraction. While simple exploratory analysis showed the distinguishing driver behavior patterns among different popu- lation groups in the dilemma zone, regression analysis showed statically signification relationships between groups of variables. In addition to analyzing the contest data, we have also looked into the possible impact of distracted driving on the fuel economy.

  5. Addition of a UL5 helicase-primase subunit point mutation eliminates bursal-thymic atrophy of Marek's disease virus ∆Meq recombinant virus but reduces vaccinal protection.

    PubMed

    Hildebrandt, Evin; Dunn, John R; Cheng, Hans H

    2015-01-01

    Marek's disease virus (MDV) is an oncogenic alphaherpesvirus and the causative agent of Marek's disease (MD), characterized by immunosuppression, paralysis, nerve enlargement and induction of T-cell lymphomas in chickens. Despite widespread usage of vaccines since the 1970s to control MD, more virulent field strains of MDV have emerged that overcome vaccinal protection, necessitating the development of new and more protective MD vaccines. The ∆Meq virus, a recombinant Md5 strain MDV lacking the viral oncogene Meq, is one candidate MD vaccine with great potential but unfortunately it also causes bursal-thymic atrophy (BTA) in maternal antibody negative chickens, raising concerns that impede commercial use as a vaccine. Previously, we identified a point mutation within UL5 that reduced in vivo replication in attenuated viruses. We proposed that introduction of the UL5 point mutation into the ∆Meq virus would reduce in vivo replication and eliminate BTA yet potentially retain high protective abilities. In birds, the ∆Meq+UL5 recombinant MDV had reduced replication compared to the original ∆Meq virus, while weights of lymphoid organs indicated that ∆Meq+UL5 did not induce BTA, supporting the hypothesis that reduction of in vivo replication would also abolish BTA. Vaccine trials of the ∆Meq+UL5 virus compared to other ∆Meq-based viruses and commercial vaccines show that, while the ∆Meq+UL5 does provide vaccinal protection, this protection was also reduced compared to the original ∆Meq virus. Therefore, it appears that a very delicate balance is required between levels of replication able to induce high vaccinal protection, yet not so high as to induce BTA.

  6. Systematic analysis of somatic mutations impacting gene expression in 12 tumour types

    PubMed Central

    Ding, Jiarui; McConechy, Melissa K.; Horlings, Hugo M.; Ha, Gavin; Chun Chan, Fong; Funnell, Tyler; Mullaly, Sarah C.; Reimand, Jüri; Bashashati, Ali; Bader, Gary D.; Huntsman, David; Aparicio, Samuel; Condon, Anne; Shah, Sohrab P.

    2015-01-01

    We present a novel hierarchical Bayes statistical model, xseq, to systematically quantify the impact of somatic mutations on expression profiles. We establish the theoretical framework and robust inference characteristics of the method using computational benchmarking. We then use xseq to analyse thousands of tumour data sets available through The Cancer Genome Atlas, to systematically quantify somatic mutations impacting expression profiles. We identify 30 novel cis-effect tumour suppressor gene candidates, enriched in loss-of-function mutations and biallelic inactivation. Analysis of trans-effects of mutations and copy number alterations with xseq identifies mutations in 150 genes impacting expression networks, with 89 novel predictions. We reveal two important novel characteristics of mutation impact on expression: (1) patients harbouring known driver mutations exhibit different downstream gene expression consequences; (2) expression patterns for some mutations are stable across tumour types. These results have critical implications for identification and interpretation of mutations with consequent impact on transcription in cancer. PMID:26436532

  7. Eaton AF5000+Genesis Communication Driver

    1995-05-25

    Communication driver allows the Genesis Control Series software to interact with Eaton AF5000+ frequency drives via RS-232 communications. All Eaton AF5000+ parameters that support communications are supported by the Genesis driver. Multidrop addressing to multiple units is available with the Genesis communication driver.

  8. Driver Education and the Learning Disabled.

    ERIC Educational Resources Information Center

    Wirths, Claudine G.; Leonard, Steven

    1982-01-01

    A project of the University of Maryland has developed a driver education curriculum for the learning disabled. Several states are making efforts to improve driver education, including rewriting materials and providing oral tests for drivers' licenses. Options for future safety programs include parent-student seminars, multidiscipline teaching, and…

  9. Driver perceptions of the safety implications of quiet electric vehicles.

    PubMed

    Cocron, Peter; Krems, Josef F

    2013-09-01

    Previous research on the safety implications of quiet electric vehicles (EVs) has mostly focused on pedestrians' acoustic perception of EVs, and suggests that EVs are more difficult for pedestrians to hear and, therefore, compromise traffic safety. The two German field studies presented here examine the experiences of 70 drivers with low noise emissions of EVs and the drivers' long-term evaluation of the issue. Participants were surveyed via interviews and questionnaires before driving an EV for the first time, after 3 months of driving, and in the first study, again after 6 months. Based on participants' reports, a catalogue of safety-relevant incidents was composed in Study 1. The catalogue revealed that low noise-related critical incidents only rarely occur, and mostly take place in low-speed environments. The degree of hazard related to these incidents was rated as low to medium. In Study 1, driver concern for vulnerable road users as a result of low noise diminished with increasing driving experience, while perceived comfort due to this feature increased. These results were replicated in Study 2. In the second study, it was additionally examined, if drivers adjust their perceived risk of harming other road users over time. Results show that the affective assessment of risk also decreased with increased driving experience. Based on individual experience, drivers adjust their evaluation of noise-related hazards, suggesting that dangers associated with low noise emissions might be less significant than previously expected.

  10. Keep the driver in control: Automating automobiles of the future.

    PubMed

    Banks, Victoria A; Stanton, Neville A

    2016-03-01

    Automated automobiles will be on our roads within the next decade but the role of the driver has not yet been formerly recognised or designed. Rather, the driver is often left in a passive monitoring role until they are required to reclaim control from the vehicle. This research aimed to test the idea of driver-initiated automation, in which the automation offers decision support that can be either accepted or ignored. The test case examined a combination of lateral and longitudinal control in addition to an auto-overtake system. Despite putting the driver in control of the automated systems by enabling them to accept or ignore behavioural suggestions (e.g. overtake), there were still issues associated with increased workload and decreased trust. These issues are likely to have arisen due to the way in which the automated system has been designed. Recommendations for improvements in systems design have been made which are likely to improve trust and make the role of the driver more transparent concerning their authority over the automated system.

  11. Keep the driver in control: Automating automobiles of the future.

    PubMed

    Banks, Victoria A; Stanton, Neville A

    2016-03-01

    Automated automobiles will be on our roads within the next decade but the role of the driver has not yet been formerly recognised or designed. Rather, the driver is often left in a passive monitoring role until they are required to reclaim control from the vehicle. This research aimed to test the idea of driver-initiated automation, in which the automation offers decision support that can be either accepted or ignored. The test case examined a combination of lateral and longitudinal control in addition to an auto-overtake system. Despite putting the driver in control of the automated systems by enabling them to accept or ignore behavioural suggestions (e.g. overtake), there were still issues associated with increased workload and decreased trust. These issues are likely to have arisen due to the way in which the automated system has been designed. Recommendations for improvements in systems design have been made which are likely to improve trust and make the role of the driver more transparent concerning their authority over the automated system. PMID:26141907

  12. Comprehensive mutation profiling of mucinous gastric carcinoma.

    PubMed

    Rokutan, Hirofumi; Hosoda, Fumie; Hama, Natsuko; Nakamura, Hiromi; Totoki, Yasushi; Furukawa, Eisaku; Arakawa, Erika; Ohashi, Shoko; Urushidate, Tomoko; Satoh, Hironori; Shimizu, Hiroko; Igarashi, Keiko; Yachida, Shinichi; Katai, Hitoshi; Taniguchi, Hirokazu; Fukayama, Masashi; Shibata, Tatsuhiro

    2016-10-01

    Mucinous gastric carcinoma (MGC) is a unique subtype of gastric cancer with a poor survival outcome. Comprehensive molecular profiles and putative therapeutic targets of MGC remain undetermined. We subjected 16 tumour-normal tissue pairs to whole-exome sequencing (WES) and an expanded set of 52 tumour-normal tissue pairs to subsequent targeted sequencing. The latter focused on 114 genes identified by WES. Twenty-two histologically differentiated MGCs (D-MGCs) and 46 undifferentiated MGCs (U-MGCs) were analysed. Chromatin modifier genes, including ARID1A (21%), MLL2 (19%), MLL3 (15%), and KDM6A (7%), were frequently mutated (47%) in MGC. We also identified mutations in potential therapeutic target genes, including MTOR (9%), BRCA2 (9%), BRCA1 (7%), and ERBB3 (6%). RHOA mutation was detected only in 4% of U-MGCs and in no D-MGCs. MYH9 was recurrently (13%) mutated in MGC, with all these being of the U-MGC subtype (p = 0.023). Three U-MGCs harboured MYH9 nonsense mutations. MYH9 knockdown enhanced cell migration and induced intracytoplasmic mucin and cellular elongation. BCOR mutation was associated with improved survival. In U-MGCs, the MLH1 expression status and combined mutation status (TP53/BCL11B or TP53/MLL2) were prognostic factors. A comparative analysis of driver genes revealed that the mutation profile of D-MGC was similar to that of intestinal-type gastric cancer, whereas U-MGC was a distinct entity, harbouring a different mutational profile to intestinal- and diffuse-type gastric cancers. Copyright © 2016 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. PMID:27313181

  13. KRAS mutation testing in clinical practice.

    PubMed

    Perincheri, Sudhir; Hui, Pei

    2015-03-01

    Activating mutation of KRAS plays a significant role in the pathogenesis of common human malignancies and molecular testing of KRAS mutation has emerged as an essential biomarker in the current practice of clinical oncology. The presence of KRAS mutation is generally associated with clinical aggressiveness of the cancer and reduced survival of the patient. Therapeutically, KRAS mutation testing has maximum utility in stratifying metastatic colorectal carcinoma and lung cancer patients for treatment with targeted therapy. Diagnostically, KRAS mutation testing is useful in the workup of pancreaticobiliary and thyroid cancers, particularly using cytological specimens. In the era of precision medicine, the role of KRAS mutation testing is poised to expand, likely in a setting of combinatorial therapeutic strategy and requiring additional mutation testing of its upstream and/or downstream effectors.

  14. Driver's lane keeping ability with eyes off road: Insights from a naturalistic study.

    PubMed

    Peng, Yiyun; Boyle, Linda Ng; Hallmark, Shauna L

    2013-01-01

    Many studies have shown that driver inattention can influence lane-keeping ability. The majority of studies on lane keeping have been conducted in controlled on-road networks or in simulated environments. However, few studies have examined lane-keeping ability in naturalistic settings for the same purpose. In this current study, the relationship between driver inattention and lane keeping ability was examined using naturalistic data for 24 drivers. Driver inattention was placed into two categories based on whether drivers were looking forward toward the roadway (inattention with eyes-on-road) or not looking forward (inattention with eyes-off-road) while engaged in a secondary task. Repeated measures regression models were used to account for within-subject correlations. The results showed that, after accounting for driving speed and lane width, the eyes-off-road significantly increased the standard deviation of lane position (SDLP). The findings from this study are consistent with other studies that show that the amount of time drivers spend looking away from the road can impact drivers' ability to maintain their lane position. Additionally, this paper demonstrates how driver inattention can be examined with real world data while accounting for the roadway, environment, and driver behavior.

  15. Factors Contributing to Crashes among Young Drivers.

    PubMed

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

    2014-08-01

    Young drivers are the group of drivers most likely to crash. There are a number of factors that contribute to the high crash risk experienced by these drivers. While some of these factors are intrinsic to the young driver, such as their age, gender or driving skill, others relate to social factors and when and how often they drive. This article reviews the factors that affect the risk of young drivers crashing to enable a fuller understanding of why this risk is so high in order to assist in developing effective countermeasures.

  16. Visualization drivers for Geant4

    SciTech Connect

    Beretvas, Andy; /Fermilab

    2005-10-01

    This document is on Geant4 visualization tools (drivers), evaluating pros and cons of each option, including recommendations on which tools to support at Fermilab for different applications. Four visualization drivers are evaluated. They are OpenGL, HepRep, DAWN and VRML. They all have good features, OpenGL provides graphic output without an intermediate file. HepRep provides menus to assist the user. DAWN provides high quality plots and even for large files produces output quickly. VRML uses the smallest disk space for intermediate files. Large experiments at Fermilab will want to write their own display. They should proceed to make this display graphics independent. Medium experiment will probably want to use HepRep because of it's menu support. Smaller scale experiments will want to use OpenGL in the spirit of having immediate response, good quality output and keeping things simple.

  17. 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

  18. The drivers of tropical speciation.

    PubMed

    Smith, Brian Tilston; McCormack, John E; Cuervo, Andrés M; Hickerson, Michael J; Aleixo, Alexandre; Cadena, Carlos Daniel; Pérez-Emán, Jorge; Burney, Curtis W; Xie, Xiaoou; Harvey, Michael G; Faircloth, Brant C; Glenn, Travis C; Derryberry, Elizabeth P; Prejean, Jesse; Fields, Samantha; Brumfield, Robb T

    2014-11-20

    Since the recognition that allopatric speciation can be induced by large-scale reconfigurations of the landscape that isolate formerly continuous populations, such as the separation of continents by plate tectonics, the uplift of mountains or the formation of large rivers, landscape change has been viewed as a primary driver of biological diversification. This process is referred to in biogeography as vicariance. In the most species-rich region of the world, the Neotropics, the sundering of populations associated with the Andean uplift is ascribed this principal role in speciation. An alternative model posits that rather than being directly linked to landscape change, allopatric speciation is initiated to a greater extent by dispersal events, with the principal drivers of speciation being organism-specific abilities to persist and disperse in the landscape. Landscape change is not a necessity for speciation in this model. Here we show that spatial and temporal patterns of genetic differentiation in Neotropical birds are highly discordant across lineages and are not reconcilable with a model linking speciation solely to landscape change. Instead, the strongest predictors of speciation are the amount of time a lineage has persisted in the landscape and the ability of birds to move through the landscape matrix. These results, augmented by the observation that most species-level diversity originated after episodes of major Andean uplift in the Neogene period, suggest that dispersal and differentiation on a matrix previously shaped by large-scale landscape events was a major driver of avian speciation in lowland Neotropical rainforests.

  19. The drivers of tropical speciation.

    PubMed

    Smith, Brian Tilston; McCormack, John E; Cuervo, Andrés M; Hickerson, Michael J; Aleixo, Alexandre; Cadena, Carlos Daniel; Pérez-Emán, Jorge; Burney, Curtis W; Xie, Xiaoou; Harvey, Michael G; Faircloth, Brant C; Glenn, Travis C; Derryberry, Elizabeth P; Prejean, Jesse; Fields, Samantha; Brumfield, Robb T

    2014-11-20

    Since the recognition that allopatric speciation can be induced by large-scale reconfigurations of the landscape that isolate formerly continuous populations, such as the separation of continents by plate tectonics, the uplift of mountains or the formation of large rivers, landscape change has been viewed as a primary driver of biological diversification. This process is referred to in biogeography as vicariance. In the most species-rich region of the world, the Neotropics, the sundering of populations associated with the Andean uplift is ascribed this principal role in speciation. An alternative model posits that rather than being directly linked to landscape change, allopatric speciation is initiated to a greater extent by dispersal events, with the principal drivers of speciation being organism-specific abilities to persist and disperse in the landscape. Landscape change is not a necessity for speciation in this model. Here we show that spatial and temporal patterns of genetic differentiation in Neotropical birds are highly discordant across lineages and are not reconcilable with a model linking speciation solely to landscape change. Instead, the strongest predictors of speciation are the amount of time a lineage has persisted in the landscape and the ability of birds to move through the landscape matrix. These results, augmented by the observation that most species-level diversity originated after episodes of major Andean uplift in the Neogene period, suggest that dispersal and differentiation on a matrix previously shaped by large-scale landscape events was a major driver of avian speciation in lowland Neotropical rainforests. PMID:25209666

  20. Genetics Home Reference: familial acute myeloid leukemia with mutated CEBPA

    MedlinePlus

    ... N. A family harboring a germ-line N-terminal C/EBPalpha mutation and development of acute myeloid leukemia with an additional somatic C-terminal C/EBPalpha mutation. Genes Chromosomes Cancer. 2010 Mar; ...

  1. Somatic CTNNB1 mutation in hepatoblastoma from a patient with Simpson-Golabi-Behmel syndrome and germline GPC3 mutation.

    PubMed

    Kosaki, Rika; Takenouchi, Toshiki; Takeda, Noriko; Kagami, Masayo; Nakabayashi, Kazuhiko; Hata, Kenichiro; Kosaki, Kenjiro

    2014-04-01

    Simpson-Golabi-Behmel syndrome is a rare overgrowth syndrome caused by the GPC3 mutation at Xq26 and is clinically characterized by multiple congenital abnormalities, intellectual disability, pre/postnatal overgrowth, distinctive craniofacial features, macrocephaly, and organomegaly. Although this syndrome is known to be associated with a risk for embryonal tumors, similar to other overgrowth syndromes, the pathogenetic basis of this mode of tumorigenesis remains largely unknown. Here, we report a boy with Simpson-Golabi-Behmel syndrome who had a germline loss-of function mutation in GPC3. At 9 months of age, he developed hepatoblastoma. A comparison of exome analysis results for the germline genome and for the tumor genome revealed a somatic mutation, p.Ile35Ser, within the degradation targeting box of β-catenin. The same somatic mutation in CTNNB1 has been repeatedly reported in hepatoblastoma and other cancers. This finding suggested that the CTNNB1 mutation in the tumor tissue represents a driver mutation and that both the GPC3 and the CTNNB1 mutations contributed to tumorigenesis in a clearly defined sequential manner in the propositus. The current observation of a somatic CTNNB1 mutation in a hepatoblastoma from a patient with a germline GPC3 mutation supports the notion that the mutation in GPC3 may influence one of the initial steps in tumorigenesis and the progression to hepatoblastoma. PMID:24459012

  2. Somatic CTNNB1 mutation in hepatoblastoma from a patient with Simpson-Golabi-Behmel syndrome and germline GPC3 mutation.

    PubMed

    Kosaki, Rika; Takenouchi, Toshiki; Takeda, Noriko; Kagami, Masayo; Nakabayashi, Kazuhiko; Hata, Kenichiro; Kosaki, Kenjiro

    2014-04-01

    Simpson-Golabi-Behmel syndrome is a rare overgrowth syndrome caused by the GPC3 mutation at Xq26 and is clinically characterized by multiple congenital abnormalities, intellectual disability, pre/postnatal overgrowth, distinctive craniofacial features, macrocephaly, and organomegaly. Although this syndrome is known to be associated with a risk for embryonal tumors, similar to other overgrowth syndromes, the pathogenetic basis of this mode of tumorigenesis remains largely unknown. Here, we report a boy with Simpson-Golabi-Behmel syndrome who had a germline loss-of function mutation in GPC3. At 9 months of age, he developed hepatoblastoma. A comparison of exome analysis results for the germline genome and for the tumor genome revealed a somatic mutation, p.Ile35Ser, within the degradation targeting box of β-catenin. The same somatic mutation in CTNNB1 has been repeatedly reported in hepatoblastoma and other cancers. This finding suggested that the CTNNB1 mutation in the tumor tissue represents a driver mutation and that both the GPC3 and the CTNNB1 mutations contributed to tumorigenesis in a clearly defined sequential manner in the propositus. The current observation of a somatic CTNNB1 mutation in a hepatoblastoma from a patient with a germline GPC3 mutation supports the notion that the mutation in GPC3 may influence one of the initial steps in tumorigenesis and the progression to hepatoblastoma.

  3. Battery electric vehicles - implications for the driver interface.

    PubMed

    Neumann, Isabel; Krems, Josef F

    2016-03-01

    The current study examines the human-machine interface of a battery electric vehicle (BEV) from a user-perspective, focussing on the evaluation of BEV-specific displays, the relevance of provided information and challenges for drivers due to the concept of electricity in a road vehicle. A sample of 40 users drove a BEV for 6 months. Data were gathered at three points of data collection. Participants perceived the BEV-specific displays as only moderately reliable and helpful for estimating the displayed parameters. This was even less the case after driving the BEV for 3 months. A taxonomy of user requirements was compiled revealing the need for improved and additional information, especially regarding energy consumption and efficiency. Drivers had difficulty understanding electrical units and the energy consumption of the BEV. On the background of general principles for display design, results provide implications how to display relevant information and how to facilitate drivers' understanding of energy consumption in BEVs. Practitioner Summary: Battery electric vehicle (BEV) displays need to incorporate new information. A taxonomy of user requirements was compiled revealing the need for improved and additional information in the BEV interface. Furthermore, drivers had trouble understanding electrical units and energy consumption; therefore, appropriate assistance is required. Design principles which are specifically important in the BEV context are discussed. PMID:26444273

  4. Battery electric vehicles - implications for the driver interface.

    PubMed

    Neumann, Isabel; Krems, Josef F

    2016-03-01

    The current study examines the human-machine interface of a battery electric vehicle (BEV) from a user-perspective, focussing on the evaluation of BEV-specific displays, the relevance of provided information and challenges for drivers due to the concept of electricity in a road vehicle. A sample of 40 users drove a BEV for 6 months. Data were gathered at three points of data collection. Participants perceived the BEV-specific displays as only moderately reliable and helpful for estimating the displayed parameters. This was even less the case after driving the BEV for 3 months. A taxonomy of user requirements was compiled revealing the need for improved and additional information, especially regarding energy consumption and efficiency. Drivers had difficulty understanding electrical units and the energy consumption of the BEV. On the background of general principles for display design, results provide implications how to display relevant information and how to facilitate drivers' understanding of energy consumption in BEVs. Practitioner Summary: Battery electric vehicle (BEV) displays need to incorporate new information. A taxonomy of user requirements was compiled revealing the need for improved and additional information in the BEV interface. Furthermore, drivers had trouble understanding electrical units and energy consumption; therefore, appropriate assistance is required. Design principles which are specifically important in the BEV context are discussed.

  5. Distinct clinical characteristics of myeloproliferative neoplasms with calreticulin mutations

    PubMed Central

    Andrikovics, Hajnalka; Krahling, Tunde; Balassa, Katalin; Halm, Gabriella; Bors, Andras; Koszarska, Magdalena; Batai, Arpad; Dolgos, Janos; Csomor, Judit; Egyed, Miklos; Sipos, Andrea; Remenyi, Peter; Tordai, Attila; Masszi, Tamas

    2014-01-01

    Somatic insertions/deletions in the calreticulin gene have recently been discovered to be causative alterations in myeloproliferative neoplasms. A combination of qualitative and quantitative allele-specific polymerase chain reaction, fragment-sizing, high resolution melting and Sanger-sequencing was applied for the detection of three driver mutations (in Janus kinase 2, calreticulin and myeloproliferative leukemia virus oncogene genes) in 289 cases of essential thrombocythemia and 99 cases of primary myelofibrosis. In essential thrombocythemia, 154 (53%) Janus kinase 2 V617F, 96 (33%) calreticulin, 9 (3%) myeloproliferative leukemia virus oncogene gene mutation-positive and 30 triple-negative (11%) cases were identified, while in primary myelofibrosis 56 (57%) Janus kinase 2 V617F, 25 (25%) calreticulin, 7 (7%) myeloproliferative leukemia virus oncogene gene mutation-positive and 11 (11%) triple-negative cases were identified. Patients positive for the calreticulin mutation were younger and had higher platelet counts compared to Janus kinase 2 mutation-positive counterparts. Calreticulin mutation-positive patients with essential thrombocythemia showed a lower risk of developing venous thrombosis, but no difference in overall survival. Calreticulin mutation-positive patients with primary myelofibrosis had a better overall survival compared to that of the Janus kinase 2 mutation-positive (P=0.04) or triple-negative cases (P=0.01). Type 2 calreticulin mutation occurred more frequently in essential thrombocythemia than in primary myelofibrosis (P=0.049). In essential thrombocythemia, the calreticulin mutational load was higher than the Janus kinase 2 mutational load (P<0.001), and increased gradually in advanced stages. Calreticulin mutational load influenced blood counts even at the time point of diagnosis in essential thrombocythemia. We confirm that calreticulin mutation is associated with distinct clinical characteristics and explored relationships between mutation

  6. Mutations affecting enzymatic activity in liver arginase

    SciTech Connect

    Vockley, J.G.; Tabor, D.E.; Goodman, B.K.

    1994-09-01

    The hydrolysis of arginine to ornithine and urea is catalyzed by arginase in the last step of the urea cycle. We examined a group of arginase deficient patients by PCR-SSCP analysis to characterize the molecular basis of this disorder. A heterogeneous population of nonsense mutations, microdeletions, and missense mutations has been identified in our cohort. Microdeletions which introduce premature stop codons downstream of the deletion and nonsense mutations result in no arginase activity. These mutations occur randomly along the gene. The majority of missense mutations identified appear to occur in regions of high cross-species homology. To test the effect of these missense mutations on arginase activity, site-directed mutagenesis was used to re-create the patient mutations for in vivo expression studies in a prokaryotic fusion-protein expression system. Of 4 different missense mutations identified in 6 individuals, only one was located outside of a conserved region. The three substitution mutations within the conserved regions had a significant effect on enzymatic activity (0-3.1 nmole/30min, normal is 1300-1400 nmoles/30min, as determined by in vitro arginase assay), while the fourth mutation, a T to S substitution, did not. In addition, site-directed mutagenesis was utilized to create mutations not in residues postulated to play a significant role in the enzymatic function or active site formation in manganese-binding proteins such as arginase. We have determined that the substitution of glycine for a histidine residue, located in a very highly conserved region of exon 3, and the substitution of a histidine and an aspartic acid residue within a similarly conserved region in exon 4, totally abolishes enzymatic activity. Mutations substituting glycine for an additional histidine and aspartic acid residue in exon 4 and two aspartic acid residues in exon 7 have also been created. We are currently in the process of characterizing these mutations.

  7. Car drivers' attitudes towards motorcyclists: a survey.

    PubMed

    Crundall, David; Bibby, Peter; Clarke, David; Ward, Patrick; Bartle, Craig

    2008-05-01

    Motorcyclists are over-represented in UK traffic accident statistics. Many car-motorcycle accidents are however due to the inappropriate actions of car drivers. It is predicted that car drivers at risk of collision with motorcycles have divergent attitudes and beliefs about motorcyclists compared to safer drivers, which may lead to a deficient mental model guiding their interactions with motorcyclists. To assess car drivers' attitudes towards motorcyclists, a survey was undertaken. Respondents filled in 26 general and motorcycle-related items and the 24 items of the reduced Driver Behaviour Questionnaire. Compared to an experienced dual driver group (who both drive cars and ride motorcycles), all other drivers showed divergent beliefs and attitudes. Four factors were extracted from the motorcycle items: negative attitudes, empathic attitudes, awareness of perceptual problems, and spatial understanding. Car drivers with a moderate amount of experience (between 2 and 10 years driving) held the most negative views and reported the most violations. The results have lead to several suggestions for interventions aimed at decreasing the divergence between drivers' perceptions of motorcyclists, and the perceptions of experienced dual drivers.

  8. Experimental Study on Forward Collision Warning System Adapted for Driver Characteristics

    NASA Astrophysics Data System (ADS)

    Kamada, Takayoshi; Miyoshi, Noboru; Nagai, Masao

    This paper describes forward-collision warning system adapted for individual driver characteristics. Conventional forward-collision warning system has the problem to output warning signals excessively though the driver intends to stop the vehicle. The driver feels irritated by these useless warnings. The objective of this study is to develop an algorithm which solves this problem. In this algorithm, the warning output timing is determined to a value that the driver conducts braking action for possible collision avoidance when looking aside. In addition, the warning output timing is changed by foot position of the driver. From experimental result by young and elderly subjects using driving simulator, excessive output of warning signal was reduced without collision.

  9. TERT promoter mutations in sinonasal malignant melanoma: a study of 49 cases.

    PubMed

    Jangard, Mattias; Zebary, Abdlsattar; Ragnarsson-Olding, Boel; Hansson, Johan

    2015-06-01

    Sinonasal malignant melanoma (SNMM) comprises less than 1% of all melanomas and is located in the nasal cavity and the paranasal sinuses. The majority of SNMMs have unknown underlying oncogenic driver mutations. The recent identification of a high frequency of driver mutations in the promoter of the telomerase reverse transcriptase (TERT) gene in cutaneous melanoma led us to investigate whether these mutations also occur in SNMM. Our aim was to determine the TERT promoter mutation frequencies in primary SNMMs. Laser capture microdissection and manual dissection were used to isolate tumour cells from 49 formalin-fixed paraffin-embedded tissues. The tumours were screened for TERT promoter mutations by direct Sanger sequencing. Information on NRAS, BRAF and KIT mutation was available from an earlier study. Overall, 8% (4/49) of SNMMs harboured TERT promoter mutations. One of these mutated tumours had a coexistent NRAS mutation and one had a BRAF mutation. Our findings show that TERT promoter mutations are present in a moderate proportion of SNMM. No conclusion can be drawn on their potential influence on the clinical outcome or tumour progression. PMID:25746036

  10. Phosphazene additives

    DOEpatents

    Harrup, Mason K; Rollins, Harry W

    2013-11-26

    An additive comprising a phosphazene compound that has at least two reactive functional groups and at least one capping functional group bonded to phosphorus atoms of the phosphazene compound. One of the at least two reactive functional groups is configured to react with cellulose and the other of the at least two reactive functional groups is configured to react with a resin, such as an amine resin of a polycarboxylic acid resin. The at least one capping functional group is selected from the group consisting of a short chain ether group, an alkoxy group, or an aryloxy group. Also disclosed are an additive-resin admixture, a method of treating a wood product, and a wood product.

  11. Potlining Additives

    SciTech Connect

    Rudolf Keller

    2004-08-10

    In this project, a concept to improve the performance of aluminum production cells by introducing potlining additives was examined and tested. Boron oxide was added to cathode blocks, and titanium was dissolved in the metal pool; this resulted in the formation of titanium diboride and caused the molten aluminum to wet the carbonaceous cathode surface. Such wetting reportedly leads to operational improvements and extended cell life. In addition, boron oxide suppresses cyanide formation. This final report presents and discusses the results of this project. Substantial economic benefits for the practical implementation of the technology are projected, especially for modern cells with graphitized blocks. For example, with an energy savings of about 5% and an increase in pot life from 1500 to 2500 days, a cost savings of $ 0.023 per pound of aluminum produced is projected for a 200 kA pot.

  12. [HPV-associated head and neck cancer : mutational signature and genomic aberrations].

    PubMed

    Wagner, S; Würdemann, N; Hübbers, C; Reuschenbach, M; Prigge, E-S; Wichmann, G; Hess, J; Dietz, A; Dürst, M; Tinhofer, I; von Knebel-Döberitz, M; Wittekindt, C; Klussmann, J P

    2015-11-01

    A significantly increasing proportion of oropharyngeal head and neck carcinomas (OSCC) in North America and Europe are associated with human papillomavirus (HPV) infections. HPV-related OSCC is regarded as a distinct tumor type with regard to its cellular, biologic, and clinical characteristics. Patients with HPV-related OSCC have significantly better local control, but higher rates of regional lymph node and distant metastases as compared to patients with HPV-negative OSCC. Classical molecular genetic investigations demonstrated specific chromosomal aberration signatures in HPV-related OSCC, and recent developments in next generation sequencing (NGS) technology have rendered possible the sequencing of entire genomes, and thus detection of specific mutations, in just a few days. Initial data from The Cancer Genome Atlas (TCGA) project obtained by using genome-wide high throughput methods have confirmed that HPV-related OSCC contain fewer, albeit more specific mutations than HPV-negative tumors. Additionally, these data revealed the presence of specific-potentially therapeutically targetable-activating driver mutations in subgroups of HPV-positive OSCC, some of which have a prognostic impact. Specific targeted NGS technologies provide new possibilities for identification of diagnostic, prognostic, and predictive biomarkers and the development of personalized cancer treatment. Patients with HPV-positive tumors are likely to profit from these developments in the future, since the genetic alterations are relatively homogenous and frequently lead to signal pathway activation. There is an urgent need for network research activities to carry out the necessary basic research in prospective cohort studies.

  13. Recent developments in mass drivers

    NASA Technical Reports Server (NTRS)

    Oneill, G. K.

    1981-01-01

    In the past eight months a new mass driver concept has been explored through calculation and inductance model verification. It retains the linear synchronous principle and freedom from arcs, plasmas or physical contact between the accelerated bucket and accelerator. However, it discards passive magnetic flight and obtains transverse focussing from strong off-axis restoring forces produced by drive coils operating in a pull-only mode. This paper gives the reasoning on which the new concept is based, and applies the concept to a lunar catapult design.

  14. Optical flow and driver's kinematics analysis for state of alert sensing.

    PubMed

    Jiménez-Pinto, Javier; Torres-Torriti, Miguel

    2013-01-01

    Road accident statistics from different countries show that a significant number of accidents occur due to driver's fatigue and lack of awareness to traffic conditions. In particular, about 60% of the accidents in which long haul truck and bus drivers are involved are attributed to drowsiness and fatigue. It is thus fundamental to improve non-invasive systems for sensing a driver's state of alert. One of the main challenges to correctly resolve the state of alert is measuring the percentage of eyelid closure over time (PERCLOS), despite the driver's head and body movements. In this paper, we propose a technique that involves optical flow and driver's kinematics analysis to improve the robustness of the driver's alert state measurement under pose changes using a single camera with near-infrared illumination. The proposed approach infers and keeps track of the driver's pose in 3D space in order to ensure that eyes can be located correctly, even after periods of partial occlusion, for example, when the driver stares away from the camera. Our experiments show the effectiveness of the approach with a correct eyes detection rate of 99.41%, on average. The results obtained with the proposed approach in an experiment involving fifteen persons under different levels of sleep deprivation also confirm the discriminability of the fatigue levels. In addition to the measurement of fatigue and drowsiness, the pose tracking capability of the proposed approach has potential applications in distraction assessment and alerting of machine operators. PMID:23539029

  15. Optical Flow and Driver's Kinematics Analysis for State of Alert Sensing

    PubMed Central

    Jiménez-Pinto, Javier; Torres-Torriti, Miguel

    2013-01-01

    Road accident statistics from different countries show that a significant number of accidents occur due to driver's fatigue and lack of awareness to traffic conditions. In particular, about 60% of the accidents in which long haul truck and bus drivers are involved are attributed to drowsiness and fatigue. It is thus fundamental to improve non-invasive systems for sensing a driver's state of alert. One of the main challenges to correctly resolve the state of alert is measuring the percentage of eyelid closure over time (PERCLOS), despite the driver's head and body movements. In this paper, we propose a technique that involves optical flow and driver's kinematics analysis to improve the robustness of the driver's alert state measurement under pose changes using a single camera with near-infrared illumination. The proposed approach infers and keeps track of the driver's pose in 3D space in order to ensure that eyes can be located correctly, even after periods of partial occlusion, for example, when the driver stares away from the camera. Our experiments show the effectiveness of the approach with a correct eyes detection rate of 99.41%, on average. The results obtained with the proposed approach in an experiment involving fifteen persons under different levels of sleep deprivation also confirm the discriminability of the fatigue levels. In addition to the measurement of fatigue and drowsiness, the pose tracking capability of the proposed approach has potential applications in distraction assessment and alerting of machine operators. PMID:23539029

  16. Drug use by tractor-trailer drivers.

    PubMed

    Lund, A K; Preusser, D F; Blomberg, R D; Williams, A F

    1988-05-01

    Blood or urine samples or both were obtained from 317 of 359 randomly selected tractor-trailer drivers asked to participate in a driver health survey conducted at a truck weighing station on Interstate 40 in Tennessee. Altogether, 29% of the drivers had evidence of alcohol, marijuana, cocaine, prescription or nonprescription stimulants, or some combination of these, in either blood or urine. Cannabinoids were found in 15% of the drivers' blood or urine; nonprescription stimulants such as phenylpropanolamine were found in 12%; prescription stimulants such as amphetamine were found in 5%; cocaine metabolites were found in 2%; and alcohol was found in less than 1%. These results provide the first objective information about the use of potentially abusive drugs by tractor-trailer drivers. The extent of driver impairment attributable to the observed drugs is uncertain because of the complex relationship between performance and drug concentrations.

  17. Monitoring Car Drivers' Condition Using Image Processing

    NASA Astrophysics Data System (ADS)

    Adachi, Kazumasa; Yamamto, Nozomi; Yamamoto, Osami; Nakano, Tomoaki; Yamamoto, Shin

    We have developed a car driver monitoring system for measuring drivers' consciousness, with which we aim to reduce car accidents caused by drowsiness of drivers. The system consists of the following three subsystems: an image capturing system with a pulsed infrared CCD camera, a system for detecting blinking waveform by the images using a neural network with which we can extract images of face and eye areas, and a system for measuring drivers' consciousness analyzing the waveform with a fuzzy inference technique and others. The third subsystem extracts three factors from the waveform first, and analyzed them with a statistical method, while our previous system used only one factor. Our experiments showed that the three-factor method we used this time was more effective to measure drivers' consciousness than the one-factor method we described in the previous paper. Moreover, the method is more suitable for fitting parameters of the system to each individual driver.

  18. Too Many Mutants with Multiple Mutations

    PubMed Central

    Drake, John W.

    2007-01-01

    It has recently become clear that the classical notion of the random nature of mutation does not hold for the distribution of mutations among genes: most collections of mutants contain more isolates with two or more mutations than predicted by the mutant frequency on the assumption of a random distribution of mutations. Excesses of multiples are seen in a wide range of organisms, including riboviruses, DNA viruses, prokaryotes, yeasts, and higher eukaryotic cell lines and tissues. In addition, such excesses are produced by DNA polymerases in vitro. These “multiples” appear to be generated by transient, localized hypermutation rather than by heritable mutator mutations. The components of multiples are sometimes scattered at random and sometimes display an excess of smaller distances between mutations. As yet, almost nothing is known about the mechanisms that generate multiples, but such mutations have the capacity to accelerate those evolutionary pathways that require multiple mutations where the individual mutations are neutral or deleterious. Examples that impinge on human health may include carcinogenesis and the adaptation of microbial pathogens as they move between individual hosts. PMID:17687667

  19. Ordering of mutations in preinvasive disease stages of esophageal carcinogenesis

    PubMed Central

    Forshew, Tim; Barbera, Mariagnese; Murtaza, Muhammed; Ong, Chin-Ann J.; Lao-Sirieix, Pierre; Dunning, Mark J; Smith, Laura; Smith, Mike L.; Anderson, Charlotte L.; Carvalho, Benilton; O’Donovan, Maria; Underwood, Timothy J.; May, Andrew P; Grehan, Nicola; Hardwick, Richard; Davies, Jim; Oloumi, Arusha; Aparicio, Sam; Caldas, Carlos; Eldridge, Matthew D.; Edwards, Paul A.W.; Rosenfeld, Nitzan; Tavaré, Simon; Fitzgerald, Rebecca C

    2014-01-01

    Cancer genome sequencing studies have identified numerous driver genes but the relative timing of mutations in carcinogenesis remains unclear. The gradual progression from pre-malignant Barrett’s esophagus to esophageal adenocarcinoma (EAC) provides an ideal model to study the ordering of somatic mutations. We identified recurrently-mutated genes and assessed clonal structure using whole-genome sequencing and amplicon-resequencing of 112 EACs. We next screened a cohort of 109 biopsies from two key transition points in the development of malignancy; benign metaplastic never-dysplastic Barrett’s esophagus (NDBE, n=66), and high-grade dysplasia (HGD, n=43). Unexpectedly, the majority of recurrently mutated genes in EAC were also mutated in NDBE. Only TP53 and SMAD4 were stage-specific, confined to HGD and EAC, respectively. Finally, we applied this knowledge to identify high-risk Barrett’s esophagus in a novel non-endoscopic test. In conclusion, mutations in EAC driver genes generally occur exceptionally early in disease development with profound implications for diagnostic and therapeutic strategies. PMID:24952744

  20. Chromatin accessibility contributes to simultaneous mutations of cancer genes

    PubMed Central

    Shi, Yi; Su, Xian-Bin; He, Kun-Yan; Wu, Bing-Hao; Zhang, Bo-Yu; Han, Ze-Guang

    2016-01-01

    Somatic mutations of many cancer genes tend to co-occur (termed co-mutations) in certain patterns during tumor initiation and progression. However, the genetic and epigenetic mechanisms that contribute to the co-mutations of these cancer genes have yet to be explored. Here, we systematically investigated the association between the somatic co-mutations of cancer genes and high-order chromatin conformation. Significantly, somatic point co-mutations in protein-coding genes were closely associated with high-order spatial chromatin folding. We propose that these regions be termed Spatial Co-mutation Hotspots (SCHs) and report their occurrence in different cancer types. The conserved mutational signatures and DNA sequences flanking these point co-mutations, as well as CTCF-binding sites, are also enriched within the SCH regions. The genetic alterations that are harboured in the same SCHs tend to disrupt cancer driver genes involved in multiple signalling pathways. The present work demonstrates that high-order spatial chromatin organisation may contribute to the somatic co-mutations of certain cancer genes during tumor development. PMID:27762310

  1. EGFR kinase domain duplication (EGFR-KDD) is a novel oncogenic driver in lung cancer that is clinically responsive to afatinib

    PubMed Central

    Gallant, Jean-Nicolas; Sheehan, Jonathan H.; Shaver, Timothy M.; Bailey, Mark; Lipson, Doron; Chandramohan, Raghu; Brewer, Monica Red; York, Sally J.; Kris, Mark G.; Pietenpol, Jennifer A.; Ladanyi, Marc; Miller, Vincent A.; Ali, Siraj M.; Meiler, Jens; Lovly, Christine M.

    2015-01-01

    Oncogenic EGFR mutations are found in 10-35% of lung adenocarcinomas. Such mutations, which present most commonly as small in-frame deletions in exon 19 or point mutations in exon 21 (L858R), confer sensitivity to EGFR tyrosine kinase inhibitors (TKIs). In analyzing the tumor from a 33-year-old male never smoker, we identified a novel EGFR alteration in lung cancer: EGFR exon 18-25 kinase domain duplication (EGFR-KDD). Through analysis of a larger cohort of tumor samples, we detected additional cases of EGFR-KDD in lung, brain, and other cancers. In vitro, EGFR-KDD is constitutively active, and computational modeling provides potential mechanistic support for its auto-activation. EGFR-KDD-transformed cells are sensitive to EGFR TKIs and, consistent with these in vitro findings, the index patient had a partial response to the EGFR TKI, afatinib. The patient eventually progressed, at which time, re-sequencing revealed an EGFR-dependent mechanism of acquired resistance to afatinib, thereby validating EGFR-KDD as a driver alteration and therapeutic target. PMID:26286086

  2. Economic drivers of mineral supply

    USGS Publications Warehouse

    Wagner, Lorie A.; Sullivan, Daniel E.; Sznopek, John L.

    2003-01-01

    The debate over the adequacy of future supplies of mineral resources continues in light of the growing use of mineral-based materials in the United States. According to the U.S. Geological Survey, the quantity of new materials utilized each year has dramatically increased from 161 million tons2 in 1900 to 3.2 billion tons in 2000. Of all the materials used during the 20th century in the United States, more than half were used in the last 25 years. With the Earth?s endowment of natural resources remaining constant, and increased demand for resources, economic theory states that as depletion approaches, prices rise. This study shows that many economic drivers (conditions that create an economic incentive for producers to act in a particular way) such as the impact of globalization, technological improvements, productivity increases, and efficient materials usage are at work simultaneously to impact minerals markets and supply. As a result of these economic drivers, the historical price trend of mineral prices3 in constant dollars has declined as demand has risen. When price is measured by the cost in human effort, the price trend also has been almost steadily downward. Although the United States economy continues its increasing mineral consumption trend, the supply of minerals has been able to keep pace. This study shows that in general supply has grown faster than demand, causing a declining trend in mineral prices.

  3. Evaluating the within-host fitness effects of mutations fixed during virus adaptation to different ecotypes of a new host.

    PubMed

    Hillung, Julia; Cuevas, José M; Elena, Santiago F

    2015-08-19

    The existence of genetic variation for resistance in host populations is assumed to be essential to the spread of an emerging virus. Models predict that the rate of spread slows down with the increasing frequency and higher diversity of resistance alleles in the host population. We have been using the experimental pathosystem Arabidopsis thaliana-tobacco etch potyvirus (TEV) to explore the interplay between genetic variation in host's susceptibility and virus diversity. We have recently shown that TEV populations evolving in A. thaliana ecotypes that differ in susceptibility to infection gained within-host fitness, virulence and infectivity in a manner compatible with a gene-for-gene model of host-parasite interactions: hard-to-infect ecotypes were infected by generalist viruses, whereas easy-to-infect ecotypes were infected by every virus. We characterized the genomes of the evolved viruses and found cases of host-driven convergent mutations. To gain further insights in the mechanistic basis of this gene-for-gene model, we have generated all viral mutations individually as well as in specific combinations and tested their within-host fitness effects across ecotypes. Most of these mutations were deleterious or neutral in their local ecotype and only a very reduced number had a host-specific beneficial effect. We conclude that most of the mutations fixed during the evolution experiment were so by drift or by selective sweeps along with the selected driver mutation. In addition, we evaluated the ruggedness of the underlying adaptive fitness landscape and found that mutational effects were mostly multiplicative, with few cases of significant epistasis. PMID:26150658

  4. Evaluating the within-host fitness effects of mutations fixed during virus adaptation to different ecotypes of a new host

    PubMed Central

    Hillung, Julia; Cuevas, José M.; Elena, Santiago F.

    2015-01-01

    The existence of genetic variation for resistance in host populations is assumed to be essential to the spread of an emerging virus. Models predict that the rate of spread slows down with the increasing frequency and higher diversity of resistance alleles in the host population. We have been using the experimental pathosystem Arabidopsis thaliana—tobacco etch potyvirus (TEV) to explore the interplay between genetic variation in host's susceptibility and virus diversity. We have recently shown that TEV populations evolving in A. thaliana ecotypes that differ in susceptibility to infection gained within-host fitness, virulence and infectivity in a manner compatible with a gene-for-gene model of host–parasite interactions: hard-to-infect ecotypes were infected by generalist viruses, whereas easy-to-infect ecotypes were infected by every virus. We characterized the genomes of the evolved viruses and found cases of host-driven convergent mutations. To gain further insights in the mechanistic basis of this gene-for-gene model, we have generated all viral mutations individually as well as in specific combinations and tested their within-host fitness effects across ecotypes. Most of these mutations were deleterious or neutral in their local ecotype and only a very reduced number had a host-specific beneficial effect. We conclude that most of the mutations fixed during the evolution experiment were so by drift or by selective sweeps along with the selected driver mutation. In addition, we evaluated the ruggedness of the underlying adaptive fitness landscape and found that mutational effects were mostly multiplicative, with few cases of significant epistasis. PMID:26150658

  5. Emergence of constitutively active estrogen receptor-α mutations in pretreated advanced estrogen receptor positive breast cancer

    PubMed Central

    Meric-Bernstam, Funda; Gonzalez-Angulo, Ana Maria; Ferrer-Lozano, Jaime; Perez-Fidalgo, Jose A.; Cristofanilli, Massimo; Gómez, Henry; Arteaga, Carlos L.; Giltnane, Jennifer; Balko, Justin M.; Cronin, Maureen T; Jarosz, Mirna; Sun, James; Hawryluk, Matthew; Lipson, Doron; Otto, Geoff; Ross, Jeffrey S; Dvir, Addie; Soussan-Gutman, Lior; Wolf, Ido; Rubinek, Tamar; Gilmore, Lauren; Schnitt, Stuart; Come, Steven E.; Pusztai, Lajos; Stephens, Philip; Brown, Myles; Miller, Vincent A.

    2014-01-01

    Purpose We undertook this study to determine the prevalence of estrogen receptor (ER) α (ESR1) mutations throughout the natural history of hormone dependent breast cancer and to delineate the functional roles of the most commonly detected alterations. Experimental Design We studied a total of 249 tumor specimens from 208 patients. The specimens include 134 ER positive (ER+/HER2–) and, as controls, 115 ER negative (ER−) tumors. The ER+ samples consist of 58 primary breast cancers and 76 metastatic samples. All tumors were sequenced to high unique coverage using next generation sequencing targeting the coding sequence of the estrogen receptor and an additional 182 cancer-related genes. Results Recurring somatic mutations in codons 537 and 538 within the ligand-binding domain of ER were detected in ER+ metastatic disease. Overall, the frequency of these mutations was 12% (9/76, 95% CI 6%-21%) in metastatic tumors and in a subgroup of patients who received an average of 7 lines of treatment the frequency was 20% (5/25, 95% CI 7%-41%). These mutations were not detected in primary or treatment naïve ER+ cancer or in any stage of ER− disease. Functional studies in cell line models demonstrate that these mutations render estrogen receptor constitutive activity and confer partial resistance to currently available endocrine treatments. Conclusions In this study we show evidence for the temporal selection of functional ESR1 mutations as potential drivers of endocrine resistance during the progression of ER positive breast cancer. PMID:24398047

  6. TAD disruption as oncogenic driver.

    PubMed

    Valton, Anne-Laure; Dekker, Job

    2016-02-01

    Topologically Associating Domains (TADs) are conserved during evolution and play roles in guiding and constraining long-range regulation of gene expression. Disruption of TAD boundaries results in aberrant gene expression by exposing genes to inappropriate regulatory elements. Recent studies have shown that TAD disruption is often found in cancer cells and contributes to oncogenesis through two mechanisms. One mechanism locally disrupts domains by deleting or mutating a TAD boundary leading to fusion of the two adjacent TADs. The other mechanism involves genomic rearrangements that break up TADs and creates new ones without directly affecting TAD boundaries. Understanding the mechanisms by which TADs form and control long-range chromatin interactions will therefore not only provide insights into the mechanism of gene regulation in general, but will also reveal how genomic rearrangements and mutations in cancer genomes can lead to misregulation of oncogenes and tumor suppressors. PMID:27111891

  7. Police referral of drivers to the Maryland Motor Vehicle Administration's Medical Advisory Board.

    PubMed

    Soderstrom, Carl A; Scottino, Mary Anne; Joyce, John J; Burch, Cynthia; Ho, Shiu M; Kerns, Timothy J

    2009-10-01

    In the 50 United States and the District of Columbia law enforcement medical referrals are accepted by licensing agencies. This study assessed driving actions, medical concerns, and medical conditions in 486 police referrals to the Medical Advisory Board of the Maryland Motor Vehicle Administration during a 25-month period. Driving actions, medical concerns, and medical conditions were grouped into categories and entered into a database. These elements were analyzed relative to driver age and sex. In addition, the issuance of citations for driving violations was studied relative to age and sex. A greater percentage of drivers 60 years of age or greater (senior adults) were referred compared to the general population of licensed drivers that age, being 71.4% vs 20.6% (p <0.01). Crashing, the most common driving action, was not associated with age or sex. Among driving actions frequently mentioned relative to older drivers, only confusion of pedals was associated with senior adults drivers as compared to younger drivers (6.1% vs 0.1%, p <0.01). Of the most frequently mentioned medical concerns, confusion/disorientation was associated with being a senior adult (p <0.01), while loss of consciousness was associated with younger drivers (p <0.01). The most frequently mentioned medical conditions, diabetes and seizure, were associated with being under 60 years of age. All mentions of dementia were in senior adult drivers. Compared with younger drivers, drivers 60 years of age or older, were less often summoned for driving violations, being 33.0% vs 53.5% (p <0.01), respectively. The threshold for the issuance of fewer citations was lower for men (40 to 59 years of age) compared to women (60 years of age or greater). Studies are needed to correlate specific traffic violations and/or crashes to specific medical conditions.

  8. U.S. Truck Driver Anthropometric Study and Multivariate Anthropometric Models for Cab Designs

    PubMed Central

    Guan, Jinhua; Hsiao, Hongwei; Bradtmiller, Bruce; Kau, Tsui-Ying; Reed, Matthew R.; Jahns, Steven K.; Loczi, Josef; Hardee, H. Lenora; Piamonte, Dominic Paul T.

    2015-01-01

    Objective This study presents data from a large-scale anthropometric study of U.S. truck drivers and the multivariate anthropometric models developed for the design of next-generation truck cabs. Background Up-to-date anthropometric information of the U.S. truck driver population is needed for the design of safe and ergonomically efficient truck cabs. Method We collected 35 anthropometric dimensions for 1,950 truck drivers (1,779 males and 171 females) across the continental United States using a sampling plan designed to capture the appropriate ethnic, gender, and age distributions of the truck driver population. Results Truck drivers are heavier than the U.S. general population, with a difference in mean body weight of 13.5 kg for males and 15.4 kg for females. They are also different in physique from the U.S. general population. In addition, the current truck drivers are heavier and different in physique compared to their counterparts of 25 to 30 years ago. Conclusion The data obtained in this study provide more accurate anthropometric information for cab designs than do the current U.S. general population data or truck driver data collected 25 to 30 years ago. Multivariate anthropometric models, spanning 95% of the current truck driver population on the basis of a set of 12 anthropometric measurements, have been developed to facilitate future cab designs. Application The up-to-date truck driver anthropometric data and multivariate anthropometric models will benefit the design of future truck cabs which, in turn, will help promote the safety and health of the U.S. truck drivers. PMID:23156628

  9. PDII- Additional discussion of the dynamic aperture

    SciTech Connect

    Norman M. Gelfand

    2002-07-23

    This note is in the nature of an addition to the dynamic aperture calculations found in the report on the Proton Driver, FERMILAB-TM-2169. A extensive discussion of the Proton Driver lattice, as well as the nomenclature used to describe it can be found in TM-2169. Basically the proposed lattice is a racetrack design with the two arcs joined by two long straight sections. The straight sections are dispersion free. Tracking studies were undertaken with the objective of computing the dynamic aperture for the lattice and some of the results have been incorporated into TM-2169. This note is a more extensive report of those calculations.

  10. HPMV: human protein mutation viewer - relating sequence mutations to protein sequence architecture and function changes.

    PubMed

    Sherman, Westley Arthur; Kuchibhatla, Durga Bhavani; Limviphuvadh, Vachiranee; Maurer-Stroh, Sebastian; Eisenhaber, Birgit; Eisenhaber, Frank

    2015-10-01

    Next-generation sequencing advances are rapidly expanding the number of human mutations to be analyzed for causative roles in genetic disorders. Our Human Protein Mutation Viewer (HPMV) is intended to explore the biomolecular mechanistic significance of non-synonymous human mutations in protein-coding genomic regions. The tool helps to assess whether protein mutations affect the occurrence of sequence-architectural features (globular domains, targeting signals, post-translational modification sites, etc.). As input, HPMV accepts protein mutations - as UniProt accessions with mutations (e.g. HGVS nomenclature), genome coordinates, or FASTA sequences. As output, HPMV provides an interactive cartoon showing the mutations in relation to elements of the sequence architecture. A large variety of protein sequence architectural features were selected for their particular relevance to mutation interpretation. Clicking a sequence feature in the cartoon expands a tree view of additional information including multiple sequence alignments of conserved domains and a simple 3D viewer mapping the mutation to known PDB structures, if available. The cartoon is also correlated with a multiple sequence alignment of similar sequences from other organisms. In cases where a mutation is likely to have a straightforward interpretation (e.g. a point mutation disrupting a well-understood targeting signal), this interpretation is suggested. The interactive cartoon can be downloaded as standalone viewer in Java jar format to be saved and viewed later with only a standard Java runtime environment. The HPMV website is: http://hpmv.bii.a-star.edu.sg/ .

  11. Mutation testing for directing upfront targeted therapy and post-progression combination therapy strategies in lung adenocarcinoma

    PubMed Central

    Salgia, Ravi

    2016-01-01

    ABSTRACT Introduction: Advances in the biology of non-small-cell lung cancer, especially adenocarcinoma, reveal multiple molecular subtypes driving oncogenesis. Accordingly, individualized targeted therapeutics are based on mutational diagnostics. Areas covered: Advances in strategies and techniques for individualized treatment, particularly of adenocarcinoma, are described through literature review. Approved therapies are established for some molecular subsets, with new driver mutations emerging that represent increasing proportions of patients. Actionable mutations are de novo oncogenic drivers or acquired resistance mediators, and mutational profiling is important for directing therapy. Patients should be monitored for emerging actionable resistance mutations. Liquid biopsy and associated multiplex diagnostics will be important means to monitor patients during treatment. Expert commentary: Outcomes with targeted agents may be improved by integrating mutation screens during treatment to optimize subsequent therapy. In order for this to be translated into impactful patient benefit, appropriate platforms and strategies need to be optimized and then implemented universally. PMID:27139190

  12. Molecular methods for somatic mutation testing in lung adenocarcinoma: EGFR and beyond

    PubMed Central

    Rogers, Toni-Maree; Fellowes, Andrew; Bell, Anthony; Fox, Stephen

    2015-01-01

    Somatic mutational profiling in cancer has revolutionized the practice of clinical oncology. The discovery of driver mutations in non-small cell lung cancer (NSCLC) is an example of this. Molecular testing of lung adenocarcinoma is now considered standard of care and part of the diagnostic algorithm. This article provides an overview of the workflow of molecular testing in a clinical diagnostic laboratory discussing in particular novel assays that are currently in use for somatic mutation detection in NSCLC focussing on epidermal growth factor receptor (EGFR) mutations and anaplastic lymphoma kinase (ALK), ROS1 and RET rearrangements. PMID:25870795

  13. Predictions of Geospace Drivers By the Probability Distribution Function Model

    NASA Astrophysics Data System (ADS)

    Bussy-Virat, C.; Ridley, A. J.

    2014-12-01

    Geospace drivers like the solar wind speed, interplanetary magnetic field (IMF), and solar irradiance have a strong influence on the density of the thermosphere and the near-Earth space environment. This has important consequences on the drag on satellites that are in low orbit and therefore on their position. One of the basic problems with space weather prediction is that these drivers can only be measured about one hour before they affect the environment. In order to allow for adequate planning for some members of the commercial, military, or civilian communities, reliable long-term space weather forecasts are needed. The study presents a model for predicting geospace drivers up to five days in advance. This model uses the same general technique to predict the solar wind speed, the three components of the IMF, and the solar irradiance F10.7. For instance, it uses Probability distribution functions (PDFs) to relate the current solar wind speed and slope to the future solar wind speed, as well as the solar wind speed to the solar wind speed one solar rotation in the future. The PDF Model has been compared to other models for predictions of the speed. It has been found that it is better than using the current solar wind speed (i.e., persistence), and better than the Wang-Sheeley-Arge Model for prediction horizons of 24 hours. Once the drivers are predicted, and the uncertainty on the drivers are specified, the density in the thermosphere can be derived using various models of the thermosphere, such as the Global Ionosphere Thermosphere Model. In addition, uncertainties on the densities can be estimated, based on ensembles of simulations. From the density and uncertainty predictions, satellite positions, as well as the uncertainty in those positions can be estimated. These can assist operators in determining the probability of collisions between objects in low Earth orbit.

  14. ERBB activation modulates sensitivity to MEK1/2 inhibition in a subset of driver-negative melanoma

    PubMed Central

    Hutchinson, Katherine E.; Johnson, Douglas B.; Johnson, Adam S.; Sanchez, Violeta; Kuba, Maria; Lu, Pengcheng; Chen, Xi; Kelley, Mark C.; Wang, Qingguo; Zhao, Zhongming; Kris, Mark; Berger, Michael F.; Sosman, Jeffrey A.; Pao, William

    2015-01-01

    Melanomas are characterized by activating “driver” mutations in BRAF, NRAS, KIT, GNAQ, and GNA11. Resultant mitogen-activated protein kinase (MAPK) pathway signaling makes some melanomas susceptible to BRAF (BRAF V600 mutations), MEK1/2 (BRAF V600, L597, fusions; NRAS mutations), or other kinase inhibitors (KIT), respectively. Among driver-negative (“pan-negative”) patients, an unexplained heterogeneity of response to MEK1/2 inhibitors has been observed. Analysis of 16 pan-negative melanoma cell lines revealed that 8 (50%; termed Class I) are sensitive to the MEK1/2 inhibitor, trametinib, similar to BRAF V600E melanomas. A second set (termed Class II) display reduced trametinib sensitivity, paradoxical activation of MEK1/2 and basal activation of ERBBs 1, 2, and 3 (4 lines, 25%). In 3 of these lines, PI3K/AKT and MAPK pathway signaling is abrogated using the ERBB inhibitor, afatinib, and proliferation is even further reduced upon the addition of trametinib. A potential mechanism of ERBB activation in Class II melanomas is minimal expression of the ERK1/2 phosphatase, DUSP4, as ectopic restoration of DUSP4 attenuated ERBB signaling through potential modulation of the ERBB ligand, amphiregulin (AREG). Consistent with these data, immunohistochemical analysis of patient melanomas revealed a trend towards lower overall DUSP4 expression in pan-negative versus BRAF- and NRAS-mutant tumors. This study is the first to demonstrate that differential ERBB activity in pan-negative melanoma may modulate sensitivity to clinically-available MEK1/2 inhibitors and provides rationale for the use of ERBB inhibitors, potentially in combination with MEK1/2 inhibitors, in subsets of this disease. PMID:26084293

  15. Graduated Driver Licensing: The New Zealand Experience.

    ERIC Educational Resources Information Center

    Begg, Dorothy; Stephenson, Shaun

    2003-01-01

    Evaluates the graduated driver-licensing (GDL) system in New Zealand. Describes driver licensing and crash fatality rates before and after the implementation of GDL in 1987. Reports that GDL has contributed to a reduction in crashes among young people. (Contains 2 figures and 6 references.) (AUTHOR/WFA)

  16. Tractor Trailer Driver's Training Programs. Performance Report.

    ERIC Educational Resources Information Center

    New Hampshire Vocational Technical Coll., Nashua.

    This document describes a project to develop a 320-hour tractor trailer driver training program and a 20-hour commercial driver licensing upgrade training program. Of 34 graduates from the training program, 28 secured employment in the trucking industry. From August 1989 to June 1990, 725 students were trained in the upgrade training program with…

  17. New method of designing CCD driver

    NASA Astrophysics Data System (ADS)

    Yu, Wei; Yu, Daoyin; Zhang, Yimo

    1993-04-01

    A new method of designing CCD driver circuits is introduced in this paper. Some kinds of programmable logic device (PLD) chips including generic array logic (GAL) and EPROM are used to drive a CCD sensor. The driver runs stably and reliably. It is widely applied in many fields with its good interchangeability, small size, and low cost.

  18. School Bus Driver Instructional Program. Instructor's Guide.

    ERIC Educational Resources Information Center

    Department of Transportation, Washington, DC. National Highway Safety Bureau.

    A standardized and comprehensive school bus driver instructional program has been developed under contract with the Federal Government. The course has been organized to provide in one package a program for developing the minimum skills and knowledge needed by the school bus driver instructor, as well as those supplemental skills and knowledge…

  19. Prevalence of hypertension in bus drivers.

    PubMed

    Ragland, D R; Winkleby, M A; Schwalbe, J; Holman, B L; Morse, L; Syme, S L; Fisher, J M

    1987-06-01

    This paper reports the results of a cross-sectional study conducted to evaluate the prevalence of hypertension in 1500 black and white male bus drivers from a large urban transit system in the US. Data for this study were compiled from the files of an occupational health clinic which conducts biennial medical examinations for drivers' license renewal. To test whether prevalence of hypertension was higher among bus drivers than among employed individuals in general, drivers were compared to three groups: individuals from both a national and local health survey and individuals undergoing baseline health examinations prior to employment as bus drivers. After adjustment for age and race, hypertension rates for bus drivers were significantly greater than rates for each of the three comparison groups. These findings support previous results from international studies of bus drivers suggesting that exposure to the occupation of driving a bus may carry increased health risk. This research has expanded into an on-going study which has the goals of clarifying the extent of hypertension in bus drivers and identifying specific behavioural and occupational factors that may be responsible for increased risk of cardiovascular disease.

  20. California's Bus Driver's Training Course. Instructor's Manual.

    ERIC Educational Resources Information Center

    California State Dept. of Education, Sacramento.

    This instructor's manual was designed to help graduates of the California Bus Driver Instructor Course provide effective instruction to school bus driver trainees. It contains enough material for 20-30 hours of classroom training. The information is organized in 12 instructional units that cover the following topics: introduction to the course;…

  1. Hallways to Highways. Driver Education 1982.

    ERIC Educational Resources Information Center

    Oklahoma State Dept. of Education, Oklahoma City.

    The purpose of this guide is to provide direction and assistance to driver education instructors and school administrators as they plan and implement quality programs of traffic safety instruction. Materials are divided into seven chapters conveying: (1) the organization and administration of driver and traffic safety education, (2) the driving…

  2. Evaluation of Driver Education and Training Programs.

    ERIC Educational Resources Information Center

    Harman, Harry H.; And Others

    What contributions do driver education and training programs make to the Nation's highway safety program? An answer to this question was sought through a synthesis of four feasibility studies concerning the effectiveness of current or proposed driver education programs. These preliminary investigations failed to identify any clear proof that…

  3. Physics at an upgraded Fermilab proton driver

    SciTech Connect

    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.

  4. High-acceleration mass drivers

    NASA Technical Reports Server (NTRS)

    Oneill, G. K.; Kolm, H. H.

    1979-01-01

    High-acceleration mass drivers are discussed including the MD2 model of axial geometry, with individually powered drive coils of 13.1 cm diameter. Timing is derived through the interruption of light beams by the moving armature (bucket). Electric power is provided by the resonant discharge of sector capacitor banks through silicon-controlled rectifiers in a two-phase, quadrature circuit. The bucket flies in vacuum, guided by passive dynamic eddy-current magnetic forces, those currents flowing in strip conductors lining the inside of a nonconducting vacuum pipe. Quantitative measurements are obtained with a solid bucket carrying two superconducting coils with a current density of 25 kA/sq cm. A cryogenic station for cooling the bucket to liquid helium temperature is connected to the vacuum pipe.

  5. Mutational signatures of ionizing radiation in second malignancies.

    PubMed

    Behjati, Sam; Gundem, Gunes; Wedge, David C; Roberts, Nicola D; Tarpey, Patrick S; Cooke, Susanna L; Van Loo, Peter; Alexandrov, Ludmil B; Ramakrishna, Manasa; Davies, Helen; Nik-Zainal, Serena; Hardy, Claire; Latimer, Calli; Raine, Keiran M; Stebbings, Lucy; Menzies, Andy; Jones, David; Shepherd, Rebecca; Butler, Adam P; Teague, Jon W; Jorgensen, Mette; Khatri, Bhavisha; Pillay, Nischalan; Shlien, Adam; Futreal, P Andrew; Badie, Christophe; McDermott, Ultan; Bova, G Steven; Richardson, Andrea L; Flanagan, Adrienne M; Stratton, Michael R; Campbell, Peter J

    2016-01-01

    Ionizing radiation is a potent carcinogen, inducing cancer through DNA damage. The signatures of mutations arising in human tissues following in vivo exposure to ionizing radiation have not been documented. Here, we searched for signatures of ionizing radiation in 12 radiation-associated second malignancies of different tumour types. Two signatures of somatic mutation characterize ionizing radiation exposure irrespective of tumour type. Compared with 319 radiation-naive tumours, radiation-associated tumours carry a median extra 201 deletions genome-wide, sized 1-100 base pairs often with microhomology at the junction. Unlike deletions of radiation-naive tumours, these show no variation in density across the genome or correlation with sequence context, replication timing or chromatin structure. Furthermore, we observe a significant increase in balanced inversions in radiation-associated tumours. Both small deletions and inversions generate driver mutations. Thus, ionizing radiation generates distinctive mutational signatures that explain its carcinogenic potential. PMID:27615322

  6. Mutational signatures of ionizing radiation in second malignancies

    PubMed Central

    Behjati, Sam; Gundem, Gunes; Wedge, David C.; Roberts, Nicola D.; Tarpey, Patrick S.; Cooke, Susanna L.; Van Loo, Peter; Alexandrov, Ludmil B.; Ramakrishna, Manasa; Davies, Helen; Nik-Zainal, Serena; Hardy, Claire; Latimer, Calli; Raine, Keiran M.; Stebbings, Lucy; Menzies, Andy; Jones, David; Shepherd, Rebecca; Butler, Adam P.; Teague, Jon W.; Jorgensen, Mette; Khatri, Bhavisha; Pillay, Nischalan; Shlien, Adam; Futreal, P. Andrew; Badie, Christophe; Cooper, Colin S.; Eeles, Rosalind A.; Easton, Douglas; Foster, Christopher; Neal, David E.; Brewer, Daniel S.; Hamdy, Freddie; Lu, Yong-Jie; Lynch, Andrew G.; Massi, Charlie E.; Ng, Anthony; Whitaker, Hayley C.; Yu, Yongwei; Zhang, Hongwei; Bancroft, Elizabeth; Berney, Dan; Camacho, Niedzica; Corbishley, Cathy; Dadaev, Tokhir; Dennis, Nening; Dudderidge, Tim; Edwards, Sandra; Fisher, Cyril; Ghori, Jilur; Gnanapragasam, Vincent J.; Greenman, Christopher; Hawkins, Steve; Hazell, Steven; Howat, Will; Karaszi, Katalin; Kay, Jonathan; Kote-Jarai, Zsofia; Kremeyer, Barbara; Kumar, Pardeep; Lambert, Adam; Leongamornlert, Daniel; Livni, Naomi; Luxton, Hayley; Matthews, Lucy; Mayer, Erik; Merson, Susan; Nicol, David; Ogden, Christopher; O'Meara, Sarah; Pelvender, Gill; Shah, Nimish C.; Tavare, Simon; Thomas, Sarah; Thompson, Alan; Verrill, Claire; Warren, Anne; Zamora, Jorge; McDermott, Ultan; Bova, G. Steven; Richardson, Andrea L.; Flanagan, Adrienne M.; Stratton, Michael R.; Campbell, Peter J.

    2016-01-01

    Ionizing radiation is a potent carcinogen, inducing cancer through DNA damage. The signatures of mutations arising in human tissues following in vivo exposure to ionizing radiation have not been documented. Here, we searched for signatures of ionizing radiation in 12 radiation-associated second malignancies of different tumour types. Two signatures of somatic mutation characterize ionizing radiation exposure irrespective of tumour type. Compared with 319 radiation-naive tumours, radiation-associated tumours carry a median extra 201 deletions genome-wide, sized 1–100 base pairs often with microhomology at the junction. Unlike deletions of radiation-naive tumours, these show no variation in density across the genome or correlation with sequence context, replication timing or chromatin structure. Furthermore, we observe a significant increase in balanced inversions in radiation-associated tumours. Both small deletions and inversions generate driver mutations. Thus, ionizing radiation generates distinctive mutational signatures that explain its carcinogenic potential. PMID:27615322

  7. Stability analysis of automobile driver steering control

    NASA Technical Reports Server (NTRS)

    Allen, R. W.

    1981-01-01

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

  8. The Mutational Robustness of Influenza A Virus.

    PubMed

    Visher, Elisa; Whitefield, Shawn E; McCrone, John T; Fitzsimmons, William; Lauring, Adam S

    2016-08-01

    A virus' mutational robustness is described in terms of the strength and distribution of the mutational fitness effects, or MFE. The distribution of MFE is central to many questions in evolutionary theory and is a key parameter in models of molecular evolution. Here we define the mutational fitness effects in influenza A virus by generating 128 viruses, each with a single nucleotide mutation. In contrast to mutational scanning approaches, this strategy allowed us to unambiguously assign fitness values to individual mutations. The presence of each desired mutation and the absence of additional mutations were verified by next generation sequencing of each stock. A mutation was considered lethal only after we failed to rescue virus in three independent transfections. We measured the fitness of each viable mutant relative to the wild type by quantitative RT-PCR following direct competition on A549 cells. We found that 31.6% of the mutations in the genome-wide dataset were lethal and that the lethal fraction did not differ appreciably between the HA- and NA-encoding segments and the rest of the genome. Of the viable mutants, the fitness mean and standard deviation were 0.80 and 0.22 in the genome-wide dataset and best modeled as a beta distribution. The fitness impact of mutation was marginally lower in the segments coding for HA and NA (0.88 ± 0.16) than in the other 6 segments (0.78 ± 0.24), and their respective beta distributions had slightly different shape parameters. The results for influenza A virus are remarkably similar to our own analysis of CirSeq-derived fitness values from poliovirus and previously published data from other small, single stranded DNA and RNA viruses. These data suggest that genome size, and not nucleic acid type or mode of replication, is the main determinant of viral mutational fitness effects. PMID:27571422

  9. The Mutational Robustness of Influenza A Virus

    PubMed Central

    McCrone, John T.; Lauring, Adam S.

    2016-01-01

    A virus’ mutational robustness is described in terms of the strength and distribution of the mutational fitness effects, or MFE. The distribution of MFE is central to many questions in evolutionary theory and is a key parameter in models of molecular evolution. Here we define the mutational fitness effects in influenza A virus by generating 128 viruses, each with a single nucleotide mutation. In contrast to mutational scanning approaches, this strategy allowed us to unambiguously assign fitness values to individual mutations. The presence of each desired mutation and the absence of additional mutations were verified by next generation sequencing of each stock. A mutation was considered lethal only after we failed to rescue virus in three independent transfections. We measured the fitness of each viable mutant relative to the wild type by quantitative RT-PCR following direct competition on A549 cells. We found that 31.6% of the mutations in the genome-wide dataset were lethal and that the lethal fraction did not differ appreciably between the HA- and NA-encoding segments and the rest of the genome. Of the viable mutants, the fitness mean and standard deviation were 0.80 and 0.22 in the genome-wide dataset and best modeled as a beta distribution. The fitness impact of mutation was marginally lower in the segments coding for HA and NA (0.88 ± 0.16) than in the other 6 segments (0.78 ± 0.24), and their respective beta distributions had slightly different shape parameters. The results for influenza A virus are remarkably similar to our own analysis of CirSeq-derived fitness values from poliovirus and previously published data from other small, single stranded DNA and RNA viruses. These data suggest that genome size, and not nucleic acid type or mode of replication, is the main determinant of viral mutational fitness effects. PMID:27571422

  10. Design and analysis issues in genome-wide somatic mutation studies of cancer.

    PubMed

    Parmigiani, Giovanni; Boca, Simina; Lin, Jimmy; Kinzler, Kenneth W; Velculescu, Victor; Vogelstein, Bert

    2009-01-01

    The availability of the human genome sequence and progress in sequencing and bioinformatic technologies have enabled genome-wide investigation of somatic mutations in human cancers. This article briefly reviews challenges arising in the statistical analysis of mutational data of this kind. A first challenge is that of designing studies that efficiently allocate sequencing resources. We show that this can be addressed by two-stage designs and demonstrate via simulations that even relatively small studies can produce lists of candidate cancer genes that are highly informative for future research efforts. A second challenge is to distinguish mutated genes that are selected for by cancer (drivers) from mutated genes that have no role in the development of cancer and simply happened to mutate (passengers). We suggest that this question is best approached as a classification problem and discuss some of the difficulties of more traditional testing-based approaches. A third challenge is to identify biologic processes affected by the driver genes. This can be pursued by gene set analyses. These can reliably identify functional groups and pathways that are enriched for mutated genes even when the individual genes involved in those pathways or sets are not mutated at sufficient frequencies to provide conclusive evidence as drivers.

  11. Identification of significantly mutated regions across cancer types highlights a rich landscape of functional molecular alterations

    PubMed Central

    Araya, Carlos L.; Cenik, Can; Reuter, Jason A.; Kiss, Gert; Pande, Vijay S.; Snyder, Michael P.; Greenleaf, William J.

    2015-01-01

    Cancer sequencing studies have primarily identified cancer-driver genes by the accumulation of protein-altering mutations. An improved method would be annotation-independent, sensitive to unknown distributions of functions within proteins, and inclusive of non-coding drivers. We employed density-based clustering methods in 21 tumor types to detect variably-sized significantly mutated regions (SMRs). SMRs reveal recurrent alterations across a spectrum of coding and non-coding elements, including transcription factor binding sites and untranslated regions mutated in up to ∼15% of specific tumor types. SMRs reveal spatial clustering of mutations at molecular domains and interfaces, often with associated changes in signaling. Mutation frequencies in SMRs demonstrate that distinct protein regions are differentially mutated among tumor types, as exemplified by a linker region of PIK3CA in which biophysical simulations suggest mutations affect regulatory interactions. The functional diversity of SMRs underscores both the varied mechanisms of oncogenic misregulation and the advantage of functionally-agnostic driver identification. PMID:26691984

  12. Mutations driving CLL and their evolution in progression and relapse.

    PubMed

    Landau, Dan A; Tausch, Eugen; Taylor-Weiner, Amaro N; Stewart, Chip; Reiter, Johannes G; Bahlo, Jasmin; Kluth, Sandra; Bozic, Ivana; Lawrence, Mike; Böttcher, Sebastian; Carter, Scott L; Cibulskis, Kristian; Mertens, Daniel; Sougnez, Carrie L; Rosenberg, Mara; Hess, Julian M; Edelmann, Jennifer; Kless, Sabrina; Kneba, Michael; Ritgen, Matthias; Fink, Anna; Fischer, Kirsten; Gabriel, Stacey; Lander, Eric S; Nowak, Martin A; Döhner, Hartmut; Hallek, Michael; Neuberg, Donna; Getz, Gad; Stilgenbauer, Stephan; Wu, Catherine J

    2015-10-22

    Which genetic alterations drive tumorigenesis and how they evolve over the course of disease and therapy are central questions in cancer biology. Here we identify 44 recurrently mutated genes and 11 recurrent somatic copy number variations through whole-exome sequencing of 538 chronic lymphocytic leukaemia (CLL) and matched germline DNA samples, 278 of which were collected in a prospective clinical trial. These include previously unrecognized putative cancer drivers (RPS15, IKZF3), and collectively identify RNA processing and export, MYC activity, and MAPK signalling as central pathways involved in CLL. Clonality analysis of this large data set further enabled reconstruction of temporal relationships between driver events. Direct comparison between matched pre-treatment and relapse samples from 59 patients demonstrated highly frequent clonal evolution. Thus, large sequencing data sets of clinically informative samples enable the discovery of novel genes associated with cancer, the network of relationships between the driver events, and their impact on disease relapse and clinical outcome. PMID:26466571

  13. Identification of drivers from cancer genome diversity in hepatocellular carcinoma.

    PubMed

    Takai, Atsushi; Dang, Hien T; Wang, Xin W

    2014-01-01

    Hepatocellular carcinoma (HCC) is one of the most common cancers with a dismal outcome. The complicated molecular pathogenesis of HCC caused by tumor heterogeneity makes it difficult to identify druggable targets useful for treating HCC patients. One approach that has a potential for the improvement of patient prognosis is the identification of cancer driver genes that play a critical role in the development of HCC. Recent technological advances of high-throughput methods, such as gene expression profiles, DNA copy number alterations and somatic mutations, have expanded our understanding of the comprehensive genetic profiles of HCC. Integrative analysis of these omics profiles enables us to classify the molecular subgroups of HCC patients. As each subgroup classified according to genetic profiles has different clinical features, such as recurrence rate and prognosis, the tumor subclassification tools are useful in clinical practice. Furthermore, a global genetic analysis, including genome-wide RNAi functional screening, makes it possible to identify cancer vulnerable genes. Identification of common cancer driver genes in HCC leads to the development of an effective molecular target therapy.

  14. Tissue-specific mutation accumulation in human adult stem cells during life

    NASA Astrophysics Data System (ADS)

    Blokzijl, Francis; de Ligt, Joep; Jager, Myrthe; Sasselli, Valentina; Roerink, Sophie; Sasaki, Nobuo; Huch, Meritxell; Boymans, Sander; Kuijk, Ewart; Prins, Pjotr; Nijman, Isaac J.; Martincorena, Inigo; Mokry, Michal; Wiegerinck, Caroline L.; Middendorp, Sabine; Sato, Toshiro; Schwank, Gerald; Nieuwenhuis, Edward E. S.; Verstegen, Monique M. A.; van der Laan, Luc J. W.; de Jonge, Jeroen; Ijzermans, Jan N. M.; Vries, Robert G.; van de Wetering, Marc; Stratton, Michael R.; Clevers, Hans; Cuppen, Edwin; van Boxtel, Ruben

    2016-10-01

    The gradual accumulation of genetic mutations in human adult stem cells (ASCs) during life is associated with various age-related diseases, including cancer. Extreme variation in cancer risk across tissues was recently proposed to depend on the lifetime number of ASC divisions, owing to unavoidable random mutations that arise during DNA replication. However, the rates and patterns of mutations in normal ASCs remain unknown. Here we determine genome-wide mutation patterns in ASCs of the small intestine, colon and liver of human donors with ages ranging from 3 to 87 years by sequencing clonal organoid cultures derived from primary multipotent cells. Our results show that mutations accumulate steadily over time in all of the assessed tissue types, at a rate of approximately 40 novel mutations per year, despite the large variation in cancer incidence among these tissues. Liver ASCs, however, have different mutation spectra compared to those of the colon and small intestine. Mutational signature analysis reveals that this difference can be attributed to spontaneous deamination of methylated cytosine residues in the colon and small intestine, probably reflecting their high ASC division rate. In liver, a signature with an as-yet-unknown underlying mechanism is predominant. Mutation spectra of driver genes in cancer show high similarity to the tissue-specific ASC mutation spectra, suggesting that intrinsic mutational processes in ASCs can initiate tumorigenesis. Notably, the inter-individual variation in mutation rate and spectra are low, suggesting tissue-specific activity of common mutational processes throughout life.

  15. Phenotypic clustering in MPZ mutations.

    PubMed

    Shy, Michael E; Jáni, Agnes; Krajewski, Karen; Grandis, Marina; Lewis, Richard A; Li, Jun; Shy, Rosemary R; Balsamo, Janne; Lilien, Jack; Garbern, James Y; Kamholz, John

    2004-02-01

    Myelin protein zero (MPZ) is a member of the immunoglobulin gene superfamily with single extracellular, transmembrane and cytoplasmic domains. Homotypic interactions between extracellular domains of MPZ adhere adjacent myelin wraps to each other. MPZ is also necessary for myelin compaction since mice which lack MPZ develop severe dysmyelinating neuropathies in which compaction is dramatically disrupted. MPZ mutations in humans cause the inherited demyelinating neuropathy CMT1B. Some mutations cause the severe neuropathies of infancy designated as Dejerine-Sottas disease, while others cause a 'classical' Charcot-Marie-Tooth (CMT) disease Type 1B (CMT1B) phenotype with normal early milestones but development of disability during the first two decades of life. Still other mutations cause a neuropathy that presents in adults, with normal nerve conduction velocities, designated as a 'CMT2' form of CMT1B. To correlate the phenotype of patients with MPZ mutations with their genotype, we identified and evaluated 13 patients from 12 different families with eight different MPZ mutations. In addition, we re-analysed the clinical data from 64 cases of CMT1B from the literature. Contrary to our expectations, we found that most patients presented with either an early onset neuropathy with signs and symptoms prior to the onset of walking or a late onset neuropathy with signs and symptoms at around age 40 years. Only occasional patients presented with a 'classical' CMT phenotype. Correlation of specific MPZ mutations with their phenotypes demonstrated that addition of either a charged amino acid or altering a cysteine residue in the extracellular domain caused a severe early onset neuropathy. Severe neuropathy was also caused by truncation of the cytoplasmic domain or alteration of an evolutionarily conserved amino acid. Taken together, these data suggest that early onset neuropathy is caused by MPZ mutations that significantly disrupt the tertiary structure of MPZ and thus

  16. Electron holes appear to trigger cancer-implicated mutations

    NASA Astrophysics Data System (ADS)

    Miller, John; Villagran, Martha

    Malignant tumors are caused by mutations, which also affect their subsequent growth and evolution. We use a novel approach, computational DNA hole spectroscopy [M.Y. Suarez-Villagran & J.H. Miller, Sci. Rep. 5, 13571 (2015)], to compute spectra of enhanced hole probability based on actual sequence data. A hole is a mobile site of positive charge created when an electron is removed, for example by radiation or contact with a mutagenic agent. Peaks in the hole spectrum depict sites where holes tend to localize and potentially trigger a base pair mismatch during replication. Our studies of reveal a correlation between hole spectrum peaks and spikes in human mutation frequencies. Importantly, we also find that hole peak positions that do not coincide with large variant frequencies often coincide with cancer-implicated mutations and/or (for coding DNA) encoded conserved amino acids. This enables combining hole spectra with variant data to identify critical base pairs and potential cancer `driver' mutations. Such integration of DNA hole and variance spectra could also prove invaluable for pinpointing critical regions, and sites of driver mutations, in the vast non-protein-coding genome. Supported by the State of Texas through the Texas Ctr. for Superconductivity.

  17. Mutational landscape of yeast mutator strains.

    PubMed

    Serero, Alexandre; Jubin, Claire; Loeillet, Sophie; Legoix-Né, Patricia; Nicolas, Alain G

    2014-02-01

    The acquisition of mutations is relevant to every aspect of genetics, including cancer and evolution of species on Darwinian selection. Genome variations arise from rare stochastic imperfections of cellular metabolism and deficiencies in maintenance genes. Here, we established the genome-wide spectrum of mutations that accumulate in a WT and in nine Saccharomyces cerevisiae mutator strains deficient for distinct genome maintenance processes: pol32Δ and rad27Δ (replication), msh2Δ (mismatch repair), tsa1Δ (oxidative stress), mre11Δ (recombination), mec1Δ tel1Δ (DNA damage/S-phase checkpoints), pif1Δ (maintenance of mitochondrial genome and telomere length), cac1Δ cac3Δ (nucleosome deposition), and clb5Δ (cell cycle progression). This study reveals the diversity, complexity, and ultimate unique nature of each mutational spectrum, composed of punctual mutations, chromosomal structural variations, and/or aneuploidies. The mutations produced in clb5Δ/CCNB1, mec1Δ/ATR, tel1Δ/ATM, and rad27Δ/FEN1 strains extensively reshape the genome, following a trajectory dependent on previous events. It comprises the transmission of unstable genomes that lead to colony mosaicisms. This comprehensive analytical approach of mutator defects provides a model to understand how genome variations might accumulate during clonal evolution of somatic cell populations, including tumor cells.

  18. Mutation accumulation and fitness in mutator subpopulations of Escherichia coli.

    PubMed

    Maharjan, Ram P; Liu, Bin; Li, Yang; Reeves, Peter R; Wang, Lei; Ferenci, Thomas

    2013-02-23

    Bacterial populations in clinical and laboratory settings contain a significant proportion of mutants with elevated mutation rates (mutators). Mutators have a particular advantage when multiple beneficial mutations are needed for fitness, as in antibiotic resistance. Nevertheless, high mutation rates potentially lead to increasing numbers of deleterious mutations and subsequently to the decreased fitness of mutators. To test how fitness changed with mutation accumulation, genome sequencing and fitness assays of nine Escherichia coli mutY mutators were undertaken in an evolving chemostat population at three time points. Unexpectedly, the fitness in members of the mutator subpopulation became constant despite a growing number of mutations over time. To test if the accumulated mutations affected fitness, we replaced each of the known beneficial mutations with wild-type alleles in a mutator isolate. We found that the other 25 accumulated mutations were not deleterious. Our results suggest that isolates with deleterious mutations are eliminated by competition in a continuous culture, leaving mutators with mostly neutral mutations. Interestingly, the mutator-non-mutator balance in the population reversed after the fitness plateau of mutators was reached, suggesting that the mutator-non-mutator ratio in populations has more to do with competition between members of the population than the accumulation of deleterious mutations.

  19. Generation of desired signals from acoustic drivers. [for aircraft engine internal noise propagation experiment

    NASA Technical Reports Server (NTRS)

    Ramakrishnan, R.; Salikuddin, M.; Ahuja, K. K.

    1982-01-01

    A procedure to control transient signal generation is developed for the study of internal noise propagation from aircraft engines. A simple algorithm incorporating transform techniques is used to produce signals of any desired waveform from acoustic drivers. The accurate driver response is then calculated, and from this the limiting frequency characteristics are determined and the undesirable frequencies where the driver response is poor are eliminated from the analysis. A synthesized signal is then produced by convolving the inverse of the response function with the desired signal. Although the shape of the synthesized signal is in general quite awkward, the driver generates the desired signal when the distorted signal is fed into the driver. The results of operating the driver in two environments, in a free field and in a duct, are presented in order to show the impedance matching effect of the driver. In addition, results using a high frequency cut-off value as a parameter is presented in order to demonstrate the extent of the applicability of the synthesis procedure. It is concluded that the desired signals can be generated through the signal synthesis procedure.

  20. Whole-genome mutational landscape and characterization of noncoding and structural mutations in liver cancer.

    PubMed

    Fujimoto, Akihiro; Furuta, Mayuko; Totoki, Yasushi; Tsunoda, Tatsuhiko; Kato, Mamoru; Shiraishi, Yuichi; Tanaka, Hiroko; Taniguchi, Hiroaki; Kawakami, Yoshiiku; Ueno, Masaki; Gotoh, Kunihito; Ariizumi, Shun-Ichi; Wardell, Christopher P; Hayami, Shinya; Nakamura, Toru; Aikata, Hiroshi; Arihiro, Koji; Boroevich, Keith A; Abe, Tetsuo; Nakano, Kaoru; Maejima, Kazuhiro; Sasaki-Oku, Aya; Ohsawa, Ayako; Shibuya, Tetsuo; Nakamura, Hiromi; Hama, Natsuko; Hosoda, Fumie; Arai, Yasuhito; Ohashi, Shoko; Urushidate, Tomoko; Nagae, Genta; Yamamoto, Shogo; Ueda, Hiroki; Tatsuno, Kenji; Ojima, Hidenori; Hiraoka, Nobuyoshi; Okusaka, Takuji; Kubo, Michiaki; Marubashi, Shigeru; Yamada, Terumasa; Hirano, Satoshi; Yamamoto, Masakazu; Ohdan, Hideki; Shimada, Kazuaki; Ishikawa, Osamu; Yamaue, Hiroki; Chayama, Kazuki; Miyano, Satoru; Aburatani, Hiroyuki; Shibata, Tatsuhiro; Nakagawa, Hidewaki

    2016-05-01

    Liver cancer, which is most often associated with virus infection, is prevalent worldwide, and its underlying etiology and genomic structure are heterogeneous. Here we provide a whole-genome landscape of somatic alterations in 300 liver cancers from Japanese individuals. Our comprehensive analysis identified point mutations, structural variations (STVs), and virus integrations, in noncoding and coding regions. We discovered mutational signatures related to liver carcinogenesis and recurrently mutated coding and noncoding regions, such as long intergenic noncoding RNA genes (NEAT1 and MALAT1), promoters, CTCF-binding sites, and regulatory regions. STV analysis found a significant association with replication timing and identified known (CDKN2A, CCND1, APC, and TERT) and new (ASH1L, NCOR1, and MACROD2) cancer-related genes that were recurrently affected by STVs, leading to altered expression. These results emphasize the value of whole-genome sequencing analysis in discovering cancer driver mutations and understanding comprehensive molecular profiles of liver cancer, especially with regard to STVs and noncoding mutations. PMID:27064257

  1. Comparison of teen and adult driver crash scenarios in a nationally representative sample of serious crashes.

    PubMed

    McDonald, Catherine C; Curry, Allison E; Kandadai, Venk; Sommers, Marilyn S; Winston, Flaura K

    2014-11-01

    Motor vehicle crashes are the leading cause of death and acquired disability during the first four decades of life. While teen drivers have the highest crash risk, few studies examine the similarities and differences in teen and adult driver crashes. We aimed to: (1) identify and compare the most frequent crash scenarios-integrated information on a vehicle's movement prior to crash, immediate pre-crash event, and crash configuration-for teen and adult drivers involved in serious crashes, and (2) for the most frequent scenarios, explore whether the distribution of driver critical errors differed for teens and adult drivers. We analyzed data from the National Motor Vehicle Crash Causation Survey, a nationally representative study of serious crashes conducted by the U.S. National Highway Traffic Safety Administration from 2005 to 2007. Our sample included 642 16- to 19-year-old and 1167 35- to 54-year-old crash-involved drivers (weighted n=296,482 and 439,356, respectively) who made a critical error that led to their crash's critical pre-crash event (i.e., event that made the crash inevitable). We estimated prevalence ratios (PR) and 95% confidence intervals (CI) to compare the relative frequency of crash scenarios and driver critical errors. The top five crash scenarios among teen drivers, accounting for 37.3% of their crashes, included: (1) going straight, other vehicle stopped, rear end; (2) stopped in traffic lane, turning left at intersection, turn into path of other vehicle; (3) negotiating curve, off right edge of road, right roadside departure; (4) going straight, off right edge of road, right roadside departure; and (5) stopped in lane, turning left at intersection, turn across path of other vehicle. The top five crash scenarios among adult drivers, accounting for 33.9% of their crashes, included the same scenarios as the teen drivers with the exception of scenario (3) and the addition of going straight, crossing over an intersection, and continuing on a

  2. Whole-exome sequencing identifies recurrent AKT1 mutations in sclerosing hemangioma of lung

    PubMed Central

    Jung, Seung-Hyun; Kim, Min Sung; Lee, Sung-Hak; Park, Hyun-Chun; Choi, Hyun Joo; Maeng, Leeso; Min, Ki Ouk; Kim, Jeana; Park, Tae In; Shin, Ok Ran; Kim, Tae-Jung; Xu, Haidong; Lee, Kyo Young; Kim, Tae-Min; Song, Sang Yong; Lee, Charles; Chung, Yeun-Jun; Lee, Sug Hyung

    2016-01-01

    Pulmonary sclerosing hemangioma (PSH) is a benign tumor with two cell populations (epithelial and stromal cells), for which genomic profiles remain unknown. We conducted exome sequencing of 44 PSHs and identified recurrent somatic mutations of AKT1 (43.2%) and β-catenin (4.5%). We used a second subset of 24 PSHs to confirm the high frequency of AKT1 mutations (overall 31/68, 45.6%; p.E17K, 33.8%) and recurrent β-catenin mutations (overall 3 of 68, 4.4%). Of the PSHs without AKT1 mutations, two exhibited AKT1 copy gain. AKT1 mutations existed in both epithelial and stromal cells. In two separate PSHs from one patient, we observed two different AKT1 mutations, indicating they were not disseminated but independent arising tumors. Because the AKT1 mutations were not found to co-occur with β-catenin mutations (or any other known driver alterations) in any of the PSHs studied, we speculate that this may be the single-most common driver alteration to develop PSHs. Our study revealed genomic differences between PSHs and lung adenocarcinomas, including a high rate of AKT1 mutation in PSHs. These genomic features of PSH identified in the present study provide clues to understanding the biology of PSH and for differential genomic diagnosis of lung tumors. PMID:27601661

  3. Whole-exome sequencing identifies recurrent AKT1 mutations in sclerosing hemangioma of lung.

    PubMed

    Jung, Seung-Hyun; Kim, Min Sung; Lee, Sung-Hak; Park, Hyun-Chun; Choi, Hyun Joo; Maeng, Leeso; Min, Ki Ouk; Kim, Jeana; Park, Tae In; Shin, Ok Ran; Kim, Tae-Jung; Xu, Haidong; Lee, Kyo Young; Kim, Tae-Min; Song, Sang Yong; Lee, Charles; Chung, Yeun-Jun; Lee, Sug Hyung

    2016-09-20

    Pulmonary sclerosing hemangioma (PSH) is a benign tumor with two cell populations (epithelial and stromal cells), for which genomic profiles remain unknown. We conducted exome sequencing of 44 PSHs and identified recurrent somatic mutations of AKT1 (43.2%) and β-catenin (4.5%). We used a second subset of 24 PSHs to confirm the high frequency of AKT1 mutations (overall 31/68, 45.6%; p.E17K, 33.8%) and recurrent β-catenin mutations (overall 3 of 68, 4.4%). Of the PSHs without AKT1 mutations, two exhibited AKT1 copy gain. AKT1 mutations existed in both epithelial and stromal cells. In two separate PSHs from one patient, we observed two different AKT1 mutations, indicating they were not disseminated but independent arising tumors. Because the AKT1 mutations were not found to co-occur with β-catenin mutations (or any other known driver alterations) in any of the PSHs studied, we speculate that this may be the single-most common driver alteration to develop PSHs. Our study revealed genomic differences between PSHs and lung adenocarcinomas, including a high rate of AKT1 mutation in PSHs. These genomic features of PSH identified in the present study provide clues to understanding the biology of PSH and for differential genomic diagnosis of lung tumors. PMID:27601661

  4. Displaceable spur gear torque controlled driver and method

    NASA Technical Reports Server (NTRS)

    Cook, Joseph S., Jr. (Inventor)

    1994-01-01

    Methods and apparatus are provided for a torque driver including a laterally displaceable gear support member to carry an output spur gear. A biasing assembly biases the output spur gear into engagement with a pinion to which is applied an input torque greater than a desired output torque limit for a threaded fastener such as a nut or screw. A coiled output linkage connects the output spur gear with a fastener adaptor which may be a socket for a nut. A gear tooth profile provides a separation force that overcomes the bias to limit torque at the desired torque limit. Multiple fasteners may be rotated simultaneously to a desired torque limit if additional output spur gears are provided. A gauged selector mechanism is provided to laterally displace multiple driver members for fasteners arranged in differing configurations. The torque limit is selectably adjustable and may be different for fasteners within the same fastener configuration.

  5. Evaluation of Driver Stress Using Motor-vehicle Driving Simulator

    NASA Astrophysics Data System (ADS)

    Deguchi, Mitsuo; Wakasugi, Junichi; Ikegami, Tatsuya; Nanba, Shinji; Yamaguchi, Masaki

    This paper proposes a method for evaluating driver stress using a motor-vehicle driving simulator and a biomarker as an index of stress. Software has been developed, which can deliberately control driving tasks, in addition to analyzing driving information, such as frequency of the use of accelerator and/or brakes and the degree of deviation from the driving course. Sympathetic nervous activity was noninvasively evaluated using a hand-held monitor of salivary amylase activity, which chemically measured a biomarker every few minutes. Using healthy 20 female adults, the appropriateness of the proposed method was evaluated in vivo. The experimental results showed that the driving stress might be caused to the drivers in only 20 minutes by adding more severe driving tasks than normally experienced by the subjects without endangering them. Furthermore, the result indicate that frequent measurements of sympathetic nervous activity were possible without putting the subjects under restraint by using salivary amylase activity as the index.

  6. 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.

  7. Does advanced driver training improve situational awareness?

    PubMed

    Walker, Guy H; Stanton, Neville A; Kazi, Tara A; Salmon, Paul M; Jenkins, Daniel P

    2009-07-01

    Over 70 years of experiential evidence suggests that a specific form of advanced driver training, one based on an explicit system of car control, improves driver situation awareness (SA). Five experimental hypotheses are developed. They propose that advanced driving should increase the number of information elements in the driver's working memory, increase the interconnection between those elements, increase the amount of 'new' information in memory as well as the prominence of existing information, and that finally, it should stimulate behaviours that help drivers evolve better situations to be aware of. An approach to SA based on Neisser's perceptual cycle theory is anchored to a network based methodology. This is applied within the context of a longitudinal on-road study involving three groups of 25 drivers, all of whom were measured pre- and post-intervention. One experimental group was subject to advanced driver training and two further groups provided control for time and for being accompanied whilst driving. Empirical support is found for all five hypotheses. Advanced driving does improve driver SA but not necessarily in the way that existing situation focused, closed loop models of the concept might predict. PMID:18675387

  8. MutationAligner: a resource of recurrent mutation hotspots in protein domains in cancer

    PubMed Central

    Gauthier, Nicholas Paul; Reznik, Ed; Gao, Jianjiong; Sumer, Selcuk Onur; Schultz, Nikolaus; Sander, Chris; Miller, Martin L.

    2016-01-01

    The MutationAligner web resource, available at http://www.mutationaligner.org, enables discovery and exploration of somatic mutation hotspots identified in protein domains in currently (mid-2015) more than 5000 cancer patient samples across 22 different tumor types. Using multiple sequence alignments of protein domains in the human genome, we extend the principle of recurrence analysis by aggregating mutations in homologous positions across sets of paralogous genes. Protein domain analysis enhances the statistical power to detect cancer-relevant mutations and links mutations to the specific biological functions encoded in domains. We illustrate how the MutationAligner database and interactive web tool can be used to explore, visualize and analyze mutation hotspots in protein domains across genes and tumor types. We believe that MutationAligner will be an important resource for the cancer research community by providing detailed clues for the functional importance of particular mutations, as well as for the design of functional genomics experiments and for decision support in precision medicine. MutationAligner is slated to be periodically updated to incorporate additional analyses and new data from cancer genomics projects. PMID:26590264

  9. Mutational screening of the RB1 gene in Italian patients with retinoblastoma reveals 11 novel mutations.

    PubMed

    Sampieri, Katia; Hadjistilianou, Theodora; Mari, Francesca; Speciale, Caterina; Mencarelli, Maria Antonietta; Cetta, Francesco; Manoukian, Siranoush; Peissel, Bernard; Giachino, Daniela; Pasini, Barbara; Acquaviva, Antonio; Caporossi, Aldo; Frezzotti, Renato; Renieri, Alessandra; Bruttini, Mirella

    2006-01-01

    Retinoblastoma (RB, OMIM#180200) is the most common intraocular tumour in infancy and early childhood. Constituent mutations in the RB1 gene predispose individuals to RB development. We performed a mutational screening of the RB1 gene in Italian patients affected by RB referred to the Medical Genetics of the University of Siena. In 35 unrelated patients, we identified germline RB1 mutations in 6 out of 9 familial cases (66%) and in 7 out of 26 with no family history of RB (27%). Using the single-strand conformational polymorphism (SSCP) technique, 11 novel mutations were detected, including 3 nonsense, 5 frameshift and 4 splice-site mutations. Only two of these mutations (1 splice site and 1 missense) were previously reported. The mutation spectrum reflects the published literature, encompassing predominately nonsense or frameshift and splicing mutations. RB1 germline mutation was detected in 37% of our cases. Gross rearrangements outside the investigated region, altered DNA methylation, or mutations in non-coding regions, may be the cause of disease in the remainder of the patients. Some cases, e.g. a case of incomplete penetrance, or variable expressivity ranging from retinoma to multiple tumours, are discussed in detail. In addition, a case of pre-conception genetic counselling resolved by rescue of banked cordonal blood of the affected deceased child is described.

  10. [Drivers license qualification for epileptics].

    PubMed

    Egli, M; Hartmann, H; Hess, R

    1977-03-26

    The question whether a person with epilepsy qualified for a driving licence must be examined from the point of view of the individual as well as that of the community. The general public should be protected against unduly high risks from epileptic drivers, whereas the patient has a right to live as normal a life as possible, which includes driving an automobile. Too rigid criteria for obtaining the license increase the number of persons who evade medical control and drive "illegally". To require physicians to report their epileptic patients to the authorities would be counterproductive; it would also destroy the personal confidence between physician and patient which is so essential for successful treatment. Epileptic persons endanger safety on the road only slightly: 0.1-0.3% of all traffic accidents are due to epileptic seizures. In contrast, abuse of alcohol plays a major role in 6-9% of all accidents, whereas 80-90% are attributable to evident mistakes by the driver. Epileptic patients under regular medical supervision who are licenced on grounds of approved criteria do not cause more accidents than the general population. A dangerous group are, however, those with mental alterations (organic or reactive) and particularly patients with aggressive and expansive-compensatory traits, as well as those driving without permission. Prognostic criteria as to the further course of the disease are paramount for the assessment of qualification for the licence. The following rules have proved their worth: 2 years freedom from seizures (with or without therapy), no abnormalities specific for epilepsy in the EEG, no serious mental changes, regular medical supervision and treatment mus be guaranteed. Departures from these rules should be confined to exceptional cases with the consent of a physician specialized in epileptology. The same holds for admission to higher categories of driving licence, the only practical eventuality being category D (lorries), and even this only in

  11. Measurement of driver calibration and the impact of feedback on drivers' estimates of performance.

    PubMed

    Roberts, Shannon C; Horrey, William J; Liang, Yulan

    2016-03-01

    Recent studies focused on driver calibration show that drivers are often miscalibrated, either over confident or under confident, and the magnitude of this miscalibration changes under different conditions. Previous work has demonstrated behavioral and performance benefits of feedback, yet these studies have not explicitly examined the issue of calibration. The objective of this study was to examine driver calibration, i.e., the degree to which drivers are accurately aware of their performance, and determine whether feedback alters driver calibration. Twenty-four drivers completed a series of driving tasks (pace clocks, traffic light, speed maintenance, and traffic cones) on a test track. Drivers drove three different blocks around the test track: (1) baseline block, where no participants received feedback; (2) feedback block, where half of the participants received performance feedback while the other half received no feedback; (3) a no feedback block, where no participants received feedback. Results indicated that across two different calibration measures, drivers were sufficiently calibrated to the pace clocks, traffic light, and traffic cone tasks. Drivers were not accurately aware of their performance regarding speed maintenance, though receiving feedback on this task improved calibration. Proper and accurate measurements of driver calibration are needed before designing performance feedback to improve calibration as these feedback systems may not always yield the intended results.

  12. Camera-based driver assistance systems

    NASA Astrophysics Data System (ADS)

    Grimm, Michael

    2013-04-01

    In recent years, camera-based driver assistance systems have taken an important step: from laboratory setup to series production. This tutorial gives a brief overview on the technology behind driver assistance systems, presents the most significant functionalities and focuses on the processes of developing camera-based systems for series production. We highlight the critical points which need to be addressed when camera-based driver assistance systems are sold in their thousands, worldwide - and the benefit in terms of safety which results from it.

  13. A parametric duration model of the reaction times of drivers distracted by mobile phone conversations.

    PubMed

    Haque, Md Mazharul; Washington, Simon

    2014-01-01

    The use of mobile phones while driving is more prevalent among young drivers-a less experienced cohort with elevated crash risk. The objective of this study was to examine and better understand the reaction times of young drivers to a traffic event originating in their peripheral vision whilst engaged in a mobile phone conversation. The CARRS-Q advanced driving simulator was used to test a sample of young drivers on various simulated driving tasks, including an event that originated within the driver's peripheral vision, whereby a pedestrian enters a zebra crossing from a sidewalk. Thirty-two licensed drivers drove the simulator in three phone conditions: baseline (no phone conversation), hands-free and handheld. In addition to driving the simulator each participant completed questionnaires related to driver demographics, driving history, usage of mobile phones while driving, and general mobile phone usage history. The participants were 21-26 years old and split evenly by gender. Drivers' reaction times to a pedestrian in the zebra crossing were modelled using a parametric accelerated failure time (AFT) duration model with a Weibull distribution. Also tested where two different model specifications to account for the structured heterogeneity arising from the repeated measures experimental design. The Weibull AFT model with gamma heterogeneity was found to be the best fitting model and identified four significant variables influencing the reaction times, including phone condition, driver's age, license type (provisional license holder or not), and self-reported frequency of usage of handheld phones while driving. The reaction times of drivers were more than 40% longer in the distracted condition compared to baseline (not distracted). Moreover, the impairment of reaction times due to mobile phone conversations was almost double for provisional compared to open license holders. A reduction in the ability to detect traffic events in the periphery whilst distracted

  14. Food consumption trends and drivers

    PubMed Central

    Kearney, John

    2010-01-01

    A picture of food consumption (availability) trends and projections to 2050, both globally and for different regions of the world, along with the drivers largely responsible for these observed consumption trends are the subject of this review. Throughout the world, major shifts in dietary patterns are occurring, even in the consumption of basic staples towards more diversified diets. Accompanying these changes in food consumption at a global and regional level have been considerable health consequences. Populations in those countries undergoing rapid transition are experiencing nutritional transition. The diverse nature of this transition may be the result of differences in socio-demographic factors and other consumer characteristics. Among other factors including urbanization and food industry marketing, the policies of trade liberalization over the past two decades have implications for health by virtue of being a factor in facilitating the ‘nutrition transition’ that is associated with rising rates of obesity and chronic diseases such as cardiovascular disease and cancer. Future food policies must consider both agricultural and health sectors, thereby enabling the development of coherent and sustainable policies that will ultimately benefit agriculture, human health and the environment. PMID:20713385

  15. Generalized drivers in the mammalian endangerment process.

    PubMed

    González-Suárez, Manuela; Revilla, Eloy

    2014-01-01

    An important challenge for conservation today is to understand the endangerment process and identify any generalized patterns in how threats occur and aggregate across taxa. Here we use a global database describing main current external threats in mammals to evaluate the prevalence of distinct threatening processes, primarily of anthropogenic origin, and to identify generalized drivers of extinction and their association with vulnerability status and intrinsic species' traits. We detect several primary threat combinations that are generally associated with distinct species. In particular, large and widely distributed mammals are affected by combinations of direct exploitation and threats associated with increasing landscape modification that go from logging to intense human land-use. Meanwhile, small, narrowly distributed species are affected by intensifying levels of landscape modification but are not directly exploited. In general more vulnerable species are affected by a greater number of threats, suggesting increased extinction risk is associated with the accumulation of external threats. Overall, our findings show that endangerment in mammals is strongly associated with increasing habitat loss and degradation caused by human land-use intensification. For large and widely distributed mammals there is the additional risk of being hunted.

  16. Global coccolithophore diversity: Drivers and future change

    NASA Astrophysics Data System (ADS)

    O'Brien, Colleen J.; Vogt, Meike; Gruber, Nicolas

    2016-01-01

    We use the MAREDAT global compilation of coccolithophore species distribution and combine them with observations of climatological environmental conditions to determine the global-scale distribution of coccolithophore species diversity, its underlying drivers, and potential future changes. To this end, we developed a feed-forward neural network, which predicts 78% of the observed variance in coccolithophore diversity from environmental input variables (temperature, PAR, nitrate, silicic acid, mixed layer depth, excess phosphate (P∗) and chlorophyll). Light and temperature are the strongest predictors of coccolithophore diversity. Coccolithophore diversity is highest in the low latitudes, where coccolithophores are a relatively dominant component of the total phytoplankton community. Particularly high diversity is predicted in the western equatorial Pacific and the southern Indian Ocean, with additional peaks at approximately 30°N and 30°S. The global, zonal mean pattern is dominated by the Pacific Ocean, which shows a clear latitudinal gradient with diversity peaking at the equator, whereas in the Atlantic Ocean diversity is highest in the subtropics. We find a unimodal relationship between coccolithophore diversity and biomass, as has previously been observed for total phytoplankton assemblages. In contrast, diversity shows a negative relationship with total chlorophyll. Applying our diversity model to projections from the CMIP5 climate models, we project an increase in the diversity of coccolithophore assemblages by the end of this century.

  17. Generalized drivers in the mammalian endangerment process.

    PubMed

    González-Suárez, Manuela; Revilla, Eloy

    2014-01-01

    An important challenge for conservation today is to understand the endangerment process and identify any generalized patterns in how threats occur and aggregate across taxa. Here we use a global database describing main current external threats in mammals to evaluate the prevalence of distinct threatening processes, primarily of anthropogenic origin, and to identify generalized drivers of extinction and their association with vulnerability status and intrinsic species' traits. We detect several primary threat combinations that are generally associated with distinct species. In particular, large and widely distributed mammals are affected by combinations of direct exploitation and threats associated with increasing landscape modification that go from logging to intense human land-use. Meanwhile, small, narrowly distributed species are affected by intensifying levels of landscape modification but are not directly exploited. In general more vulnerable species are affected by a greater number of threats, suggesting increased extinction risk is associated with the accumulation of external threats. Overall, our findings show that endangerment in mammals is strongly associated with increasing habitat loss and degradation caused by human land-use intensification. For large and widely distributed mammals there is the additional risk of being hunted. PMID:24587315

  18. Biomass burning a driver for global change

    SciTech Connect

    Levine, J.S.; Cofer, W.R. III; Cahoon, D.R. Jr.; Winstead, E.L.

    1995-03-01

    Recent research has identified another biospheric process that has instantaneous and longer term effects on the production of atmospheric gases: biomass burning. Biomass burning includes the burning of the world`s vegetation-forests, savannas. and agricultural lands, to clear the land and change its use. Only in the past decade have researchers realized the important contributions of biomass burning to the global budgets of many radiatively and chemically active gases - carbon dioxide, methane, nitric oxide, tropospheric ozone, methyl chloride - and elemental carbon particulates. International field experiments and satellite data are yielding a clearer understanding of this important global source of atmospheric gases and particulates. It is seen that in addition to being a significant instantaneous global source of atmospheric gases and particulates, burning enhances the biogenic emissions of nitric oxide and nitrous oxide from the world`s soils. Biomass burning affects the reflectivity and emissivity of the Earth`s surface as well as the hydrological cycle by changing rates of land evaporation and water runoff. For these reasons, it appears that biomass burning is a significant driver of global change. 20 refs., 4 figs., 2 tabs.

  19. Generalized Drivers in the Mammalian Endangerment Process

    PubMed Central

    González-Suárez, Manuela; Revilla, Eloy

    2014-01-01

    An important challenge for conservation today is to understand the endangerment process and identify any generalized patterns in how threats occur and aggregate across taxa. Here we use a global database describing main current external threats in mammals to evaluate the prevalence of distinct threatening processes, primarily of anthropogenic origin, and to identify generalized drivers of extinction and their association with vulnerability status and intrinsic species' traits. We detect several primary threat combinations that are generally associated with distinct species. In particular, large and widely distributed mammals are affected by combinations of direct exploitation and threats associated with increasing landscape modification that go from logging to intense human land-use. Meanwhile, small, narrowly distributed species are affected by intensifying levels of landscape modification but are not directly exploited. In general more vulnerable species are affected by a greater number of threats, suggesting increased extinction risk is associated with the accumulation of external threats. Overall, our findings show that endangerment in mammals is strongly associated with increasing habitat loss and degradation caused by human land-use intensification. For large and widely distributed mammals there is the additional risk of being hunted. PMID:24587315

  20. Validation of Deleterious Mutations in Vorderwald Cattle

    PubMed Central

    Reinartz, Sina; Distl, Ottmar

    2016-01-01

    In Montbéliarde cattle two candidate mutations on bovine chromosomes 19 and 29 responsible for embryonic lethality have been detected. Montbéliarde bulls have been introduced into Vorderwald cattle to improve milk and fattening performance. Due to the small population size of Vorderwald cattle and the wide use of a few Montbéliarde bulls through artificial insemination, inbreeding on Montbéliarde bulls in later generations was increasing. Therefore, we genotyped an aborted fetus which was inbred on Montbéliarde as well as Vorderwald x Montbéliarde crossbred bulls for both deleterious mutations. The abortion was observed in an experimental herd of Vorderwald cattle. The objectives of the present study were to prove if one or both lethal mutations may be assumed to have caused this abortion and to show whether these deleterious mutations have been introduced into the Vorderwald cattle population through Montbéliarde bulls. The aborted fetus was homozygous for the SLC37A2:g.28879810C>T mutation (ss2019324563) on BTA29 and both parents as well as the paternal and maternal grandsire were heterozygous for this mutation. In addition, the parents and the paternal grandsire were carriers of the MH2-haplotype linked with the T-allele of the SLC37A2:g.28879810C>T mutation. For the SHBG:g.27956790C>T mutation (rs38377500) on BTA19 (MH1), the aborted fetus and its sire were heterozygous. Among all further 341 Vorderwald cattle genotyped we found 27 SLC37A2:g.28879810C>T heterozygous animals resulting in an allele frequency of 0.0396. Among the 120 male Vorderwald cattle, there were 12 heterozygous with an allele frequency of 0.05. The SLC37A2:g.28879810C>T mutation could not be found in further nine cattle breeds nor in Vorderwald cattle with contributions from Ayrshire bulls. In 69 Vorderwald cattle without genes from Montbéliarde bulls the mutated allele of SLC37A2:g.28879810C>T could not be detected. The SHBG:g.27956790C>T mutation appeared unlikely to be responsible

  1. Validation of Deleterious Mutations in Vorderwald Cattle.

    PubMed

    Reinartz, Sina; Distl, Ottmar

    2016-01-01

    In Montbéliarde cattle two candidate mutations on bovine chromosomes 19 and 29 responsible for embryonic lethality have been detected. Montbéliarde bulls have been introduced into Vorderwald cattle to improve milk and fattening performance. Due to the small population size of Vorderwald cattle and the wide use of a few Montbéliarde bulls through artificial insemination, inbreeding on Montbéliarde bulls in later generations was increasing. Therefore, we genotyped an aborted fetus which was inbred on Montbéliarde as well as Vorderwald x Montbéliarde crossbred bulls for both deleterious mutations. The abortion was observed in an experimental herd of Vorderwald cattle. The objectives of the present study were to prove if one or both lethal mutations may be assumed to have caused this abortion and to show whether these deleterious mutations have been introduced into the Vorderwald cattle population through Montbéliarde bulls. The aborted fetus was homozygous for the SLC37A2:g.28879810C>T mutation (ss2019324563) on BTA29 and both parents as well as the paternal and maternal grandsire were heterozygous for this mutation. In addition, the parents and the paternal grandsire were carriers of the MH2-haplotype linked with the T-allele of the SLC37A2:g.28879810C>T mutation. For the SHBG:g.27956790C>T mutation (rs38377500) on BTA19 (MH1), the aborted fetus and its sire were heterozygous. Among all further 341 Vorderwald cattle genotyped we found 27 SLC37A2:g.28879810C>T heterozygous animals resulting in an allele frequency of 0.0396. Among the 120 male Vorderwald cattle, there were 12 heterozygous with an allele frequency of 0.05. The SLC37A2:g.28879810C>T mutation could not be found in further nine cattle breeds nor in Vorderwald cattle with contributions from Ayrshire bulls. In 69 Vorderwald cattle without genes from Montbéliarde bulls the mutated allele of SLC37A2:g.28879810C>T could not be detected. The SHBG:g.27956790C>T mutation appeared unlikely to be responsible

  2. Quantifying the mutational meltdown in diploid populations.

    PubMed

    Coron, Camille; Méléard, Sylvie; Porcher, Emmanuelle; Robert, Alexandre

    2013-05-01

    Mutational meltdown, in which demographic and genetic processes mutually reinforce one another to accelerate the extinction of small populations, has been poorly quantified despite its potential importance in conservation biology. Here we present a model-based framework to study and quantify the mutational meltdown in a finite diploid population that is evolving continuously in time and subject to resource competition. We model slightly deleterious mutations affecting the population demographic parameters and study how the rate of mutation fixation increases as the genetic load increases, a process that we investigate at two timescales: an ecological scale and a mutational scale. Unlike most previous studies, we treat population size as a random process in continuous time. We show that as deleterious mutations accumulate, the decrease in mean population size accelerates with time relative to a null model with a constant mean fixation time. We quantify this mutational meltdown via the change in the mean fixation time after each new mutation fixation, and we show that the meltdown appears less severe than predicted by earlier theoretical work. We also emphasize that mean population size alone can be a misleading index of the risk of population extinction, which could be better evaluated with additional information on demographic parameters.

  3. The role of mutation of metabolism-related genes in genomic hypermethylation.

    PubMed

    Waterfall, Joshua J; Killian, J Keith; Meltzer, Paul S

    2014-12-01

    Genetic mutations, metabolic dysfunction, and epigenetic misregulation are commonly considered to play distinct roles in tumor development and maintenance. However, intimate relationships between these mechanisms are now emerging. In particular, mutations in genes for the core metabolic enzymes IDH, SDH, and FH are significant drivers of diverse tumor types. In each case, the resultant accumulation of particular metabolites inhibits TET enzymes responsible for oxidizing 5-methylcytosine, leading to pervasive DNA hypermethylation. PMID:25111818

  4. The role of mutation of metabolism-related genes in genomic hypermethylation.

    PubMed

    Waterfall, Joshua J; Killian, J Keith; Meltzer, Paul S

    2014-12-01

    Genetic mutations, metabolic dysfunction, and epigenetic misregulation are commonly considered to play distinct roles in tumor development and maintenance. However, intimate relationships between these mechanisms are now emerging. In particular, mutations in genes for the core metabolic enzymes IDH, SDH, and FH are significant drivers of diverse tumor types. In each case, the resultant accumulation of particular metabolites inhibits TET enzymes responsible for oxidizing 5-methylcytosine, leading to pervasive DNA hypermethylation.

  5. 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.

  6. The choice to text and drive in younger drivers: behavior may shape attitude.

    PubMed

    Atchley, Paul; Atwood, Stephanie; Boulton, Aaron

    2011-01-01

    Following a previous study that reported a large number of young adult drivers text and drive, the current study investigated this behavior by looking at patterns of use and driver assessment of the risk of the behavior. The data from the current study converge with and extended the previous work showing 70% of the 348 young adult drivers surveyed report initiating texts while driving while higher numbers reply to texts (81%) and read texts (92%) while driving. Additional drivers also report doing these behaviors, but only while stopped in traffic, showing only 2% never text and drive under any circumstances. The drivers indicated that they perceived these behaviors to be very risky and riskier than talking on a cell phone while driving, but perception of risk was a very weak predictor of behavior (for initiating texts) or had no effect on texting (for replying or reading texts while driving). In addition, a factor analysis of the perception of road conditions while texting revealed that making the choice to engage in texting (initiating) led drivers to perceive road conditions as being safer than if they replied to a text or read a text, suggesting that choosing to engage in the behavior itself changes attitudes toward risk. PMID:21094307

  7. SOX10 mutations mimic isolated hearing loss.

    PubMed

    Pingault, V; Faubert, E; Baral, V; Gherbi, S; Loundon, N; Couloigner, V; Denoyelle, F; Noël-Pétroff, N; Ducou Le Pointe, H; Elmaleh-Bergès, M; Bondurand, N; Marlin, S

    2015-10-01

    Ninety genes have been identified to date that are involved in non-syndromic hearing loss, and more than 300 different forms of syndromic hearing impairment have been described. Mutations in SOX10, one of the genes contributing to syndromic hearing loss, induce a large range of phenotypes, including several subtypes of Waardenburg syndrome and Kallmann syndrome with deafness. In addition, rare mutations have been identified in patients with isolated signs of these diseases. We used the recent characterization of temporal bone imaging aspects in patients with SOX10 mutations to identify possible patients with isolated hearing loss due to SOX10 mutation. We selected 21 patients with isolated deafness and temporal bone morphological defects for mutational screening. We identified two SOX10 mutations and found that both resulted in a non-functional protein in vitro. Re-evaluation of the two affected patients showed that both had previously undiagnosed olfactory defects. Diagnosis of anosmia or hyposmia in young children is challenging, and particularly in the absence of magnetic resonance imaging (MRI), SOX10 mutations can mimic non-syndromic hearing impairment. MRI should complete temporal bones computed tomographic scan in the management of congenital deafness as it can detect brain anomalies, cochlear nerve defects, and olfactory bulb malformation in addition to inner ear malformations.

  8. Timing, rates and spectra of human germline mutation

    PubMed Central

    Lindsay, Sarah J.; Hardwick, Robert J.; Alexandrov, Ludmil B.; Turki, Saeed Al; Dominiczak, Anna; Morris, Andrew; Porteous, David; Smith, Blair; Stratton, Michael R.; Hurles, Matthew E.

    2015-01-01

    Germline mutations are a driving force behind genome evolution and genetic disease. We investigated genome-wide mutation rates and spectra in multi-sibling families. Mutation rate increased with paternal age in all families, but the number of additional mutations per year differed more than two-fold between families. Meta-analysis of 6,570 mutations showed that germline methylation influences mutation rates. In contrast to somatic mutations, we found remarkable consistency of germline mutation spectra between the sexes and at different paternal ages. 3.8% of mutations were mosaic in the parental germline, resulting in 1.3% of mutations being shared between siblings. The number of these shared mutations varied significantly between families. Our data suggest that the mutation rate per cell division is higher during both early embryogenesis and differentiation of primordial germ cells, but is reduced substantially during post-pubertal spermatogenesis. These findings have important consequences for the recurrence risks of disorders caused by de novo mutations. PMID:26656846

  9. Driver circuit for solid state light sources

    DOEpatents

    Palmer, Fred; Denvir, Kerry; Allen, Steven

    2016-02-16

    A driver circuit for a light source including one or more solid state light sources, a luminaire including the same, and a method of so driving the solid state light sources are provided. The driver circuit includes a rectifier circuit that receives an alternating current (AC) input voltage and provides a rectified AC voltage. The driver circuit also includes a switching converter circuit coupled to the light source. The switching converter circuit provides a direct current (DC) output to the light source in response to the rectified AC voltage. The driver circuit also includes a mixing circuit, coupled to the light source, to switch current through at least one solid state light source of the light source in response to each of a plurality of consecutive half-waves of the rectified AC voltage.

  10. Top 3 Mistakes Teen Drivers Make

    MedlinePlus

    ... those crashes, according to the American Automobile Association (AAA). "Involved parents really can help save lives, so ... to avoid other common mistakes," Bill Van Tassel, AAA's manager of driver training operations, said in a ...

  11. Physics at a new Fermilab proton driver

    SciTech Connect

    Geer, Steve; /Fermilab

    2006-04-01

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

  12. A Superconducting Linac Proton Driver at Fermilab

    NASA Astrophysics Data System (ADS)

    Foster, G. William

    2004-05-01

    A proton driver has emerged as the leading candidate for Fermilab's next near-term accelerator project. The preferred technical solution is an 8 GeV superconducting linac based on technology developed for TESLA and the Spallation Neutron Source (SNS). Its primary mission is to serve as a single-stage H- injector to prepare 2 MW "Super-Beams" for Neutrino experiments using the Fermilab Main Injector. The linac can also accelerate electrons, protons, and relativistic muons, permitting future applications such as a driver for an FEL, a long-pulse spallation source, the driver for an intense 8 GeV neutrino or kaon program, and potential applications to a neutrino factory or muon collider. The technical design of the 8 GeV linac, as well as the design of an alternative synchrotron based proton driver, will be described along with plans for project proposal and construction.

  13. Drivers of desertification and their impact

    NASA Astrophysics Data System (ADS)

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

    2012-04-01

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

  14. Electron cloud considerations for HIF drivers

    NASA Astrophysics Data System (ADS)

    Cohen, R. H.

    2014-01-01

    We review some previous results on electron-cloud dynamics and accumulation and the impact of electron clouds on ion beam dynamics, and assess these in the context of a magnetic-quadrupole-based heavy-ion fusion driver. We present a new analysis which exploits analytic solution of linearized envelope equations between accelerating gaps to derive a set of mapping equations which we use to extrapolate from previously obtained particle-simulation results for a beam transport system to an HIF driver.

  15. Driving Decisions when Leaving Electronic Music Dance Events: Driver, Passenger, and Group Effects

    PubMed Central

    Johnson, Mark B.; Voas, Robert B.; Miller, Brenda A.

    2013-01-01

    Objectives The goal of this paper was to identify characteristics of drivers and passengers that predicted peer-groups whose drivers exit dance clubs with alcohol levels indicative of impairment (BAC ≥ .05 grams per deciliter ([g/dL]). Methods We used the portal survey methodology to randomly sample groups of 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 blood alcohol concentration (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. Results Although drivers drank less than passengers, one driver in five groups had a BAC indicative of elevated crash risk (BAC ≥ .05 g/dL). Groups of drivers and/or passengers with a recent history of binge drinking were more likely to have drivers with BACs ≥ .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 ≥ .05 g/dL. Additionally, we found that groups with all female passengers were at greater risk for having a driver whose BAC was ≥ .05 g/dL. Conclusions Some group characteristics predicted drivers who exit clubs with BACs ≥ .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, as 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 .05 g/dL, and new intervention efforts should be particularly directed to these at-risk groups. PMID:23137088

  16. S-Band POSIX Device Drivers for RTEMS

    NASA Technical Reports Server (NTRS)

    Lux, James P.; Lang, Minh; Peters, Kenneth J.; Taylor, Gregory H.

    2011-01-01

    This is a set of POSIX device driver level abstractions in the RTEMS RTOS (Real-Time Executive for Multiprocessor Systems real-time operating system) to SBand radio hardware devices that have been instantiated in an FPGA (field-programmable gate array). These include A/D (analog-to-digital) sample capture, D/A (digital-to-analog) sample playback, PLL (phase-locked-loop) tuning, and PWM (pulse-width-modulation)-controlled gain. This software interfaces to Sband radio hardware in an attached Xilinx Virtex-2 FPGA. It uses plug-and-play device discovery to map memory to device IDs. Instead of interacting with hardware devices directly, using direct-memory mapped access at the application level, this driver provides an application programming interface (API) offering that easily uses standard POSIX function calls. This simplifies application programming, enables portability, and offers an additional level of protection to the hardware. There are three separate device drivers included in this package: sband_device (ADC capture and DAC playback), pll_device (RF front end PLL tuning), and pwm_device (RF front end AGC control).

  17. Consistent drivers of plant biodiversity across managed ecosystems.

    PubMed

    Minden, Vanessa; Scherber, Christoph; Cebrián Piqueras, Miguel A; Trinogga, Juliane; Trenkamp, Anastasia; Mantilla-Contreras, Jasmin; Lienin, Patrick; Kleyer, Michael

    2016-05-19

    Ecosystems managed for production of biomass are often characterized by low biodiversity because management aims to optimize single ecosystem functions (i.e. yield) involving deliberate selection of species or cultivars. In consequence, considerable differences in observed plant species richness and productivity remain across systems, and the drivers of these differences have remained poorly resolved so far. In addition, it has remained unclear if species richness feeds back on ecosystem functions such as yield in real-world systems. Here, we establish N = 360 experimental plots across a broad range of managed ecosystems in several European countries, and use structural equation models to unravel potential drivers of plant species richness. We hypothesize that the relationships between productivity, total biomass and observed species richness are affected by management intensity, and that these effects differ between habitat types (dry grasslands, grasslands, and wetlands). We found that local management was an important driver of species richness across systems. Management caused system disturbance, resulting in reduced productivity yet enhanced total biomass. Plant species richness was directly and positively driven by management, with consistently negative effects of total biomass. Productivity effects on richness were positive, negative or neutral. Our study shows that management and total biomass drive plant species richness across real-world managed systems.

  18. Consistent drivers of plant biodiversity across managed ecosystems.

    PubMed

    Minden, Vanessa; Scherber, Christoph; Cebrián Piqueras, Miguel A; Trinogga, Juliane; Trenkamp, Anastasia; Mantilla-Contreras, Jasmin; Lienin, Patrick; Kleyer, Michael

    2016-05-19

    Ecosystems managed for production of biomass are often characterized by low biodiversity because management aims to optimize single ecosystem functions (i.e. yield) involving deliberate selection of species or cultivars. In consequence, considerable differences in observed plant species richness and productivity remain across systems, and the drivers of these differences have remained poorly resolved so far. In addition, it has remained unclear if species richness feeds back on ecosystem functions such as yield in real-world systems. Here, we establish N = 360 experimental plots across a broad range of managed ecosystems in several European countries, and use structural equation models to unravel potential drivers of plant species richness. We hypothesize that the relationships between productivity, total biomass and observed species richness are affected by management intensity, and that these effects differ between habitat types (dry grasslands, grasslands, and wetlands). We found that local management was an important driver of species richness across systems. Management caused system disturbance, resulting in reduced productivity yet enhanced total biomass. Plant species richness was directly and positively driven by management, with consistently negative effects of total biomass. Productivity effects on richness were positive, negative or neutral. Our study shows that management and total biomass drive plant species richness across real-world managed systems. PMID:27114585

  19. Aberrant driving behaviors: a study of drivers in Beijing.

    PubMed

    Shi, Jing; Bai, Yun; Ying, Xiwen; Atchley, Paul

    2010-07-01

    The addition of massive numbers of new drivers with varied driving experience to roads in China suggests it is important to understand the nature of aberrant driving behaviors for this new set of drivers. A paper-based and an Internet survey were administered. Factor analysis produced a five-factor structure for each survey. The distinction between violations and errors indicated in previous studies was confirmed. The violations included emotional violations, risky violations and self-willed violations, and the errors included inexperience errors and distraction errors. In contrast to previous work, age was not found to be a good predictor of violations though driving experience was. Contrary to expectations, non-automotive (bicycle) roadway experience or level of driving training failed to predict poor driving behavior. On-road experience is the key to risk for China's drivers. Good agreement between the paper-based and Internet surveys indicate online surveys to be a feasible way to conduct research of driving behavior at low cost. PMID:20441810

  20. License plate confiscation for persistent alcohol impaired drivers.

    PubMed

    Ross, H L; Simon, S; Cleary, J

    1996-01-01

    Minnesota cancels the registrations and confiscates the license plates of vehicles driven by repeat drinking drivers in a procedure which prior research has demonstrated to be effective in reducing subsequent recidivism. The research reported here concerns the problems experienced in the functioning of this law. Samples of officials and repeat driving under the influence (DUI) offenders were interviewed in Minnesota and in the neighboring state of Iowa, chosen for comparison because its laws also provide for plate confiscation, but using a judicial rather than an administrative procedure. In addition, representative samples of the driving and vehicle registration records of convicted drunk drivers and of routine traffic offenders were analyzed. The research found that evasion of plate impoundment orders by drivers, though apparently easy to accomplish, appeared to be rare. However, the orders were themselves not issued in a large proportion of cases where they were prescribed by statute, potentially weakening the effectiveness of the law. The reasons, with possible countermeasures, are explored in this report.

  1. SSL Luminaire with Novel Driver Architecture

    SciTech Connect

    Heikman, Sten; Robinson, Clark

    2011-07-07

    Cree has developed a new high-efficiency light emitting diode (LED) technology platform capable of providing low-cost, high performance luminaires that can be adopted across a variety of SSL applications. This development is built on Cree’s high brightness LED platform to design a novel LED chip that enables a high-efficiency driver architecture to improve the overall luminaire system efficacy. These system efficiency gains were realized using an integrated approach tailoring the LED chip characteristics to allow for the high-efficiency driver technology platform. The reliability of the new LED design was robust at the component level under accelerated testing conditions. Luminaires were assembled integrating the novel LED and driver technology to demonstrate the system improvement. Cree has successfully completed this project by developing a novel LED architecture that enables a new driver design with 93% efficiency. This technology was showcased in an LED luminaire that produced 725 lumens at an efficacy of 87.4 lumens per watt (LPW). The correlated color temperature (CCT) of the luminaire was 2708 K with a color rendering index (CRI) of 91. The novel LEDs and driver led to a 9% system performance improvement compared to the standard LEDs and driver scheme.

  2. BRAF mutations in non-small cell lung cancer: has finally Janus opened the door?

    PubMed

    Caparica, Rafael; de Castro, Gilberto; Gil-Bazo, Ignacio; Caglevic, Christian; Calogero, Raffaele; Giallombardo, Marco; Santos, Edgardo S; Raez, Luis E; Rolfo, Christian

    2016-05-01

    B-Raf mutations occur in about 1-2% of non-small cell lung cancers (NSCLC). These mutations generate a permanent activation of the mitogen activated protein kinase (MAPK) pathway, which promotes tumor growth and proliferation. In the present review, we discuss B-Raf mutation epidemiology, diagnostic methods to detect B-Raf mutations, the role of B-Raf as a driver mutation and a potential therapeutic target in NSCLC. The results of clinical trials involving B-Raf or MAPK pathway inhibitors for the treatment of NSCLC are also discussed. Clinical trials evaluating B-Raf inhibitors in BRAF mutated NSCLC patients have shown promising results, and larger prospective studies are warranted to validate these findings. Enrollment of these patients in clinical trials is an interesting strategy to offer a potentially more effective and less toxic targeted therapy.

  3. BRAF mutations in non-small cell lung cancer: has finally Janus opened the door?

    PubMed

    Caparica, Rafael; de Castro, Gilberto; Gil-Bazo, Ignacio; Caglevic, Christian; Calogero, Raffaele; Giallombardo, Marco; Santos, Edgardo S; Raez, Luis E; Rolfo, Christian

    2016-05-01

    B-Raf mutations occur in about 1-2% of non-small cell lung cancers (NSCLC). These mutations generate a permanent activation of the mitogen activated protein kinase (MAPK) pathway, which promotes tumor growth and proliferation. In the present review, we discuss B-Raf mutation epidemiology, diagnostic methods to detect B-Raf mutations, the role of B-Raf as a driver mutation and a potential therapeutic target in NSCLC. The results of clinical trials involving B-Raf or MAPK pathway inhibitors for the treatment of NSCLC are also discussed. Clinical trials evaluating B-Raf inhibitors in BRAF mutated NSCLC patients have shown promising results, and larger prospective studies are warranted to validate these findings. Enrollment of these patients in clinical trials is an interesting strategy to offer a potentially more effective and less toxic targeted therapy. PMID:26960735

  4. 77 FR 60956 - State Graduated Driver Licensing Incentive Grant

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-10-05

    ... the minimum qualification criteria for the State Graduated Driver Licensing (GDL) Incentive Grant... grants for States that implement multi-stage licensing systems that require novice drivers younger than... multi-staged process for issuing driver's licenses to young, novice drivers. During the first stage,...

  5. Workshop on transport for a common ion driver

    SciTech Connect

    Olson, C.C.; Lee, E.; Langdon, B.

    1994-12-31

    This report contains research in the following areas related to beam transport for a common ion driver: multi-gap acceleration; neutralization with electrons; gas neutralization; self-pinched transport; HIF and LIF transport, and relevance to common ion driver; LIF and HIF reactor concepts and relevance to common ion driver; atomic physics for common ion driver; code capabilities and needed improvement.

  6. 49 CFR 391.63 - Multiple-employer drivers.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 5 2010-10-01 2010-10-01 false Multiple-employer drivers. 391.63 Section 391.63... AND LONGER COMBINATION VEHICLE (LCV) DRIVER INSTRUCTORS Limited Exemptions § 391.63 Multiple-employer drivers. (a) If a motor carrier employs a person as a multiple-employer driver (as defined in § 390.5...

  7. 49 CFR 395.8 - Driver's record of duty status.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... shall be shown on the driver's record of duty status. (g) Graph grid. The following graph grid must be... 49 Transportation 5 2014-10-01 2014-10-01 false Driver's record of duty status. 395.8 Section 395... SERVICE OF DRIVERS § 395.8 Driver's record of duty status. (a) Except for a private motor carrier...

  8. 49 CFR 395.8 - Driver's record of duty status.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... shall be shown on the driver's record of duty status. (g) Graph grid. The following graph grid must be... 49 Transportation 5 2011-10-01 2011-10-01 false Driver's record of duty status. 395.8 Section 395... SERVICE OF DRIVERS § 395.8 Driver's record of duty status. (a) Except for a private motor carrier...

  9. 49 CFR 395.8 - Driver's record of duty status.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... shall be shown on the driver's record of duty status. (g) Graph grid. The following graph grid must be... 49 Transportation 5 2013-10-01 2013-10-01 false Driver's record of duty status. 395.8 Section 395... SERVICE OF DRIVERS § 395.8 Driver's record of duty status. (a) Except for a private motor carrier...

  10. 49 CFR 395.8 - Driver's record of duty status.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... shall be shown on the driver's record of duty status. (g) Graph grid. The following graph grid must be... 49 Transportation 5 2012-10-01 2012-10-01 false Driver's record of duty status. 395.8 Section 395... SERVICE OF DRIVERS § 395.8 Driver's record of duty status. (a) Except for a private motor carrier...

  11. Accumulation of Deleterious Passenger Mutations Is Associated with the Progression of Hepatocellular Carcinoma.

    PubMed

    Budzinska, Magdalena A; Tu, Thomas; d'Avigdor, William M H; McCaughan, Geoffrey W; Luciani, Fabio; Shackel, Nicholas A

    2016-01-01

    In hepatocellular carcinoma (HCC), somatic genome-wide DNA mutations are numerous, universal and heterogeneous. Some of these somatic mutations are drivers of the malignant process but the vast majority are passenger mutations. These passenger mutations can be deleterious to individual protein function but are tolerated by the cell or are offset by a survival advantage conferred by driver mutations. It is unknown if these somatic deleterious passenger mutations (DPMs) develop in the precancerous state of cirrhosis or if it is confined to HCC. Therefore, we studied four whole-exome sequencing datasets, including patients with non-cirrhotic liver (n = 12), cirrhosis without HCC (n = 6) and paired HCC with surrounding non-HCC liver (n = 74 paired samples), to identify DPMs. After filtering out putative germline mutations, we identified 187±22 DPMs per non-diseased tissue. DPMs number was associated with liver disease progressing to HCC, independent of the number of exonic mutations. Tumours contained significantly more DPMs compared to paired non-tumour tissue (258-293 per HCC exome). Cirrhosis- and HCC-associated DPMs do not occur predominantly in specific genes, chromosomes or biological pathways and the effect on tumour biology is presently unknown. Importantly, for the first time we have shown a significant increase in DPMs with HCC. PMID:27631787

  12. Accumulation of Deleterious Passenger Mutations Is Associated with the Progression of Hepatocellular Carcinoma

    PubMed Central

    d’Avigdor, William M. H.; McCaughan, Geoffrey W.; Luciani, Fabio; Shackel, Nicholas A.

    2016-01-01

    In hepatocellular carcinoma (HCC), somatic genome-wide DNA mutations are numerous, universal and heterogeneous. Some of these somatic mutations are drivers of the malignant process but the vast majority are passenger mutations. These passenger mutations can be deleterious to individual protein function but are tolerated by the cell or are offset by a survival advantage conferred by driver mutations. It is unknown if these somatic deleterious passenger mutations (DPMs) develop in the precancerous state of cirrhosis or if it is confined to HCC. Therefore, we studied four whole-exome sequencing datasets, including patients with non-cirrhotic liver (n = 12), cirrhosis without HCC (n = 6) and paired HCC with surrounding non-HCC liver (n = 74 paired samples), to identify DPMs. After filtering out putative germline mutations, we identified 187±22 DPMs per non-diseased tissue. DPMs number was associated with liver disease progressing to HCC, independent of the number of exonic mutations. Tumours contained significantly more DPMs compared to paired non-tumour tissue (258–293 per HCC exome). Cirrhosis- and HCC-associated DPMs do not occur predominantly in specific genes, chromosomes or biological pathways and the effect on tumour biology is presently unknown. Importantly, for the first time we have shown a significant increase in DPMs with HCC. PMID:27631787

  13. Validation of selected temperament and personality questionnaires for diagnosing drivers' aptitude for safe driving. A Polish study.

    PubMed

    Łuczak, Anna; Tarnowski, Adam

    2014-09-01

    This paper presents the results of a study aimed at validating psychological questionnaires evaluating temperamental and personality features. It discusses their usefulness in diagnosing drivers' aptitude for safe driving and working as professional drivers. Three psychological questionnaires were validated: the Formal Characteristics of Behaviour - Temperament Inventory (FCB-TI), the Eysenck Personality Questionnaire - Revised and Short Scale (EPQ-R (S)) and the Impulsiveness Questionnaire (IVE). Three groups of drivers (n=246) aged 19-75 participated in the study. Group I (professional drivers; n=96) and Group II (nonprofessional drivers; n=75) had never been involved in road crashes, whereas Group III (nonprofessional drivers; n=75) were offenders involved in fatal injury road crashes. Criterion-related validity, Cronbach's alpha and Guttman split-half reliability coefficient were in assessing the psychometric properties of the questionnaires. There were some significant differences between Groups II and III for most traits. However, contrary to expectations, higher Emotional Reactivity, Perseveration and lower Endurance as well as higher Neuroticism, Impulsiveness and Venturesomeness were determined for Group II than for Group III. Additionally, the temperament and personality profile of Group II turned out to be less fitted to the profile of safe drivers than that of Group III, whose profile was actually similar to that of Group I. This seems to result from a high tendency for a positive self-presentation among Group I and Group III (a significantly higher result on the Lie scale in comparison with Group II). The results suggest that if psychological tests are to decide on whether a person may be a professional driver or may drive vehicles, the three questionnaires (FCB-TI, EPQ-R(S) and IVE) do not provide a valid diagnosis of professional drivers' aptitude because of drivers' high tendency for positive self-presentation. However, they can be used in job

  14. Characteristics of Designated Drivers and their Passengers from the 2007 National Roadside Survey in the United States

    PubMed Central

    Bergen, Gwen; Yao, Jie; Shults, Ruth A.; Romano, Eduardo; Lacey, John

    2015-01-01

    Objective The objectives of this study were to estimate the prevalence of designated driving in the United States, compare these results with those from the 1996 National Roadside Survey, and explore the demographic, drinking, and trip characteristics of both designated drivers and their passengers. Methods The data used were from the 2007 National Roadside Survey which randomly stopped drivers, administered breath tests for alcohol, and administered a questionnaire to drivers and front seat passengers. Results Almost a third (30%) of nighttime drivers reported being designated drivers, with 84% of them having a blood alcohol concentration of zero. Drivers who were more likely to be designated drivers were those with a blood alcohol concentration that was over zero but still legal, who were under 35 years of age, who were African-American, Hispanic or Asian, and whose driving trip originated at a bar, tavern, or club. Over a third of passengers of designated drivers reported consuming an alcoholic drink the day of the survey compared with a fifth of passengers of non-designated drivers. One-fifth of designated driver passengers who reported drinking consumed five or more drinks that day. Conclusions Designated driving is widely used in the United States, with the majority of designated drivers abstaining from drinking alcohol. However as designated driving separates drinking from driving for passengers in a group travelling together, this may encourage passengers to binge drink, which is associated with many adverse health consequences in addition to those arising from alcohol-impaired driving. Designated driving programs and campaigns, although not proven to be effective when used alone, can complement proven effective interventions to help reduce excessive drinking and alcohol-impaired driving. PMID:24372499

  15. Effect of long term driving on driver discomfort and its relationship with seat fidgets and movements (SFMs).

    PubMed

    Sammonds, George M; Fray, Mike; Mansfield, Neil J

    2017-01-01

    Discomfort in vehicle seats is a multifactorial problem with large increases in discomfort occurring during extended duration driving. Due to the nature of driver discomfort, previous research has found it difficult to accurately quantify long term driver discomfort via the use of objective measures. This paper reports a laboratory study that investigates a novel objective measure of long term driver discomfort and its correlation with subjective discomfort ratings. Analysis of driver's seat fidgets and movements was conducted over the duration of a 140 min drive on a driving simulator in addition to collecting subjective ratings of discomfort. It is shown that as subjects' subjective discomfort increases, the frequency of subjects' seat fidgets and movements increases congruently. A large correlation is observed between the subjective and objective measures of driver discomfort and provides the opportunity for long term discomfort evaluations to be made via remote monitoring; removing the need for subjective assessment. PMID:27633204

  16. Effect of long term driving on driver discomfort and its relationship with seat fidgets and movements (SFMs).

    PubMed

    Sammonds, George M; Fray, Mike; Mansfield, Neil J

    2017-01-01

    Discomfort in vehicle seats is a multifactorial problem with large increases in discomfort occurring during extended duration driving. Due to the nature of driver discomfort, previous research has found it difficult to accurately quantify long term driver discomfort via the use of objective measures. This paper reports a laboratory study that investigates a novel objective measure of long term driver discomfort and its correlation with subjective discomfort ratings. Analysis of driver's seat fidgets and movements was conducted over the duration of a 140 min drive on a driving simulator in addition to collecting subjective ratings of discomfort. It is shown that as subjects' subjective discomfort increases, the frequency of subjects' seat fidgets and movements increases congruently. A large correlation is observed between the subjective and objective measures of driver discomfort and provides the opportunity for long term discomfort evaluations to be made via remote monitoring; removing the need for subjective assessment.

  17. The somatic mutation profiles of 2,433 breast cancers refines their genomic and transcriptomic landscapes

    PubMed Central

    Pereira, Bernard; Chin, Suet-Feung; Rueda, Oscar M.; Vollan, Hans-Kristian Moen; Provenzano, Elena; Bardwell, Helen A.; Pugh, Michelle; Jones, Linda; Russell, Roslin; Sammut, Stephen-John; Tsui, Dana W. Y.; Liu, Bin; Dawson, Sarah-Jane; Abraham, Jean; Northen, Helen; Peden, John F.; Mukherjee, Abhik; Turashvili, Gulisa; Green, Andrew R.; McKinney, Steve; Oloumi, Arusha; Shah, Sohrab; Rosenfeld, Nitzan; Murphy, Leigh; Bentley, David R.; Ellis, Ian O.; Purushotham, Arnie; Pinder, Sarah E.; Børresen-Dale, Anne-Lise; Earl, Helena M.; Pharoah, Paul D.; Ross, Mark T.; Aparicio, Samuel; Caldas, Carlos

    2016-01-01

    The genomic landscape of breast cancer is complex, and inter- and intra-tumour heterogeneity are important challenges in treating the disease. In this study, we sequence 173 genes in 2,433 primary breast tumours that have copy number aberration (CNA), gene expression and long-term clinical follow-up data. We identify 40 mutation-driver (Mut-driver) genes, and determine associations between mutations, driver CNA profiles, clinical-pathological parameters and survival. We assess the clonal states of Mut-driver mutations, and estimate levels of intra-tumour heterogeneity using mutant-allele fractions. Associations between PIK3CA mutations and reduced survival are identified in three subgroups of ER-positive cancer (defined by amplification of 17q23, 11q13–14 or 8q24). High levels of intra-tumour heterogeneity are in general associated with a worse outcome, but highly aggressive tumours with 11q13–14 amplification have low levels of intra-tumour heterogeneity. These results emphasize the importance of genome-based stratification of breast cancer, and have important implications for designing therapeutic strategies. PMID:27161491

  18. Hotspot activating PRKD1 somatic mutations in polymorphous low-grade adenocarcinomas of the salivary glands.

    PubMed

    Weinreb, Ilan; Piscuoglio, Salvatore; Martelotto, Luciano G; Waggott, Daryl; Ng, Charlotte K Y; Perez-Ordonez, Bayardo; Harding, Nicholas J; Alfaro, Javier; Chu, Kenneth C; Viale, Agnes; Fusco, Nicola; da Cruz Paula, Arnaud; Marchio, Caterina; Sakr, Rita A; Lim, Raymond; Thompson, Lester D R; Chiosea, Simion I; Seethala, Raja R; Skalova, Alena; Stelow, Edward B; Fonseca, Isabel; Assaad, Adel; How, Christine; Wang, Jianxin; de Borja, Richard; Chan-Seng-Yue, Michelle; Howlett, Christopher J; Nichols, Anthony C; Wen, Y Hannah; Katabi, Nora; Buchner, Nicholas; Mullen, Laura; Kislinger, Thomas; Wouters, Bradly G; Liu, Fei-Fei; Norton, Larry; McPherson, John D; Rubin, Brian P; Clarke, Blaise A; Weigelt, Britta; Boutros, Paul C; Reis-Filho, Jorge S

    2014-11-01

    Polymorphous low-grade adenocarcinoma (PLGA) is the second most frequent type of malignant tumor of the minor salivary glands. We identified PRKD1 hotspot mutations encoding p.Glu710Asp in 72.9% of PLGAs but not in other salivary gland tumors. Functional studies demonstrated that this kinase-activating alteration likely constitutes a driver of PLGA.

  19. Gestational mutations in radiation carcinogenesis

    NASA Astrophysics Data System (ADS)

    Meza, R.; Luebeck, G.; Moolgavkar, S.

    Mutations in critical genes during gestation could increase substantially the risk of cancer. We examine the consequences of such mutations using the Luebeck-Moolgavkar model for colorectal cancer and the Lea-Coulson modification of the Luria-Delbruck model for the accumulation of mutations during gestation. When gestational mutation rates are high, such mutations make a significant contribution to cancer risk even for adult tumors. Furthermore, gestational mutations ocurring at distinct times during emryonic developmemt lead to substantially different numbers of mutated cells at birth, with early mutations leading to a large number (jackpots) of mutated cells at birth and mutation occurring late leading to only a few mutated cells. Thus gestational mutations could confer considerable heterogeneity of the risk of cancer. If the fetus is exposed to an environmental mutagen, such as ionizing radiation, the gestational mutation rate would be expected to increase. We examine the consequences of such exposures during gestation on the subsequent development of cancer.

  20. GNAS gene mutation may be present only transiently during colorectal tumorigenesis

    PubMed Central

    Zauber, Peter; Marotta, Stephen P; Sabbath-Solitare, Marlene

    2016-01-01

    Mutations of the gene GNAS have been shown to activate the adenylate cyclase gene and lead to constitutive cAMP signaling. Several preliminary reports have suggested a role for GNAS gene mutations during colorectal carcinogenesis, particularly mucinous carcinomas. The aim of this study was to clarify the incidence of GNAS mutations in adenomas (tubular, tubulovillous, and villous), carcinomas with residual adenoma, and carcinomas, and to relate these findings to mutations of the KRAS gene and to the mucinous status of the tumors. We used standard PCR techniques and direct gene sequencing to evaluate tumors for gene mutations. No GNAS mutations were identified in 25 tubular adenomas, but were present in 6.4% of tubulovillous adenomas and 11.2% of villous adenomas. A GNAS mutation was found in 9.7% of the benign portion of carcinoma with residual adenoma, but in none of 86 carcinomas. A similar trend was seen for KRAS mutation across the five groups of tumors. GNAS mutations may function as an important driver mutation during certain phases of colorectal carcinogenesis, but may then be lost once the biological advantage gained by the mutated gene is no longer necessary to sustain or advance tumor development. PMID:27186325

  1. Protein Domain-Level Landscape of Cancer-Type-Specific Somatic Mutations

    PubMed Central

    Yang, Fan; Petsalaki, Evangelia; Rolland, Thomas; Hill, David E.; Vidal, Marc; Roth, Frederick P.

    2015-01-01

    Identifying driver mutations and their functional consequences is critical to our understanding of cancer. Towards this goal, and because domains are the functional units of a protein, we explored the protein domain-level landscape of cancer-type-specific somatic mutations. Specifically, we systematically examined tumor genomes from 21 cancer types to identify domains with high mutational density in specific tissues, the positions of mutational hotspots within these domains, and the functional and structural context where possible. While hotspots corresponding to specific gain-of-function mutations are expected for oncoproteins, we found that tumor suppressor proteins also exhibit strong biases toward being mutated in particular domains. Within domains, however, we observed the expected patterns of mutation, with recurrently mutated positions for oncogenes and evenly distributed mutations for tumor suppressors. For example, we identified both known and new endometrial cancer hotspots in the tyrosine kinase domain of the FGFR2 protein, one of which is also a hotspot in breast cancer, and found new two hotspots in the Immunoglobulin I-set domain in colon cancer. Thus, to prioritize cancer mutations for further functional studies aimed at more precise cancer treatments, we have systematically correlated mutations and cancer types at the protein domain level. PMID:25794154

  2. What factors influence drivers' response time for evasive maneuvers in real traffic?

    PubMed

    Dozza, Marco

    2013-09-01

    Distraction and inattention contribute to 80% of traffic accidents by delaying or hindering driver responses. However, distraction and inattention are not the only factors increasing response times. In addition, the extent to which different factors-related to the driver, the vehicle, or the environment-influence response times in real traffic is still uncertain. Such knowledge may significantly help the development of countermeasures to distraction and inattention. Naturalistic driving data promises to help determine the causes of distraction and inattention by understanding driver behavior in real traffic. Further, large naturalistic datasets are now publically available from a few sources such as UMTRI (University of Michigan Transportation Institute) and VTTI (Virginia Tech Transportation Institute). However, analysis of such data is made difficult by the intrinsic nature of the data: it is large and complex and the variables of interest are hard to control. This study used the public 100-car and 8-truck naturalistic data from VTTI to show how the NatWare toolkit developed at SAFER (Vehicle and Traffic Safety Center at Chalmers) can be used to determine the influence of several factors on response time. Among these factors, attendance to secondary tasks and eyes-off-road, which are indicators of driver's distraction and inattention, significantly delayed response times; the type of incident and response maneuver also affected response times; and finally, truck drivers responded more quickly than car drivers.

  3. Non-small Cell Lung Cancer with Concomitant EGFR, KRAS, and ALK Mutation: Clinicopathologic Features of 12 Cases

    PubMed Central

    Lee, Taebum; Lee, Boram; Choi, Yoon-La; Han, Joungho; Ahn, Myung-Ju; Um, Sang-Won

    2016-01-01

    Background: Although epidermal growth factor receptor (EGFR), v-Ki-ras2 Kirsten rat sarcoma viral oncogene (KRAS), and anaplastic lymphoma kinase (ALK) mutations in non-small cell lung cancer (NSCLC) were thought to be mutually exclusive, some tumors harbor concomitant mutations. Discovering a driver mutation on the basis of morphologic features and therapeutic responses with mutation analysis can be used to understand pathogenesis and predict resistance in targeted therapy. Methods: In 6,637 patients with NSCLC, 12 patients who had concomitant mutations were selected and clinicopathologic features were reviewed. Clinical characteristics included sex, age, smoking history, previous treatment, and targeted therapy with response and disease-free survival. Histologic features included dominant patterns, nuclear and cytoplasmic features. Results: All patients were diagnosed with adenocarcinoma and had an EGFR mutation. Six patients had concomitant KRAS mutations and the other six had KRAS mutations. Five of six EGFR-KRAS mutation patients showed papillary and acinar histologic patterns with hobnail cells. Three of six received EGFR tyrosine kinase inhibitor (TKI) and showed partial response for 7–29 months. All six EGFR-ALK mutation patients showed solid or cribriform patterns and three had signet ring cells. Five of six EGFR-ALK mutation patients received EGFR TKI and/or ALK inhibitor and four showed partial response or stable disease, except for one patient who had acquired an EGFR mutation. Conclusions: EGFR and ALK mutations play an important role as driver mutations in double mutated NSCLC, and morphologic analysis can be used to predict treatment response. PMID:27086595

  4. Increased risk of driver fatality due to unrestrained rear-seat passengers in severe frontal crashes.

    PubMed

    Bose, Dipan; Arregui-Dalmases, Carlos; Sanchez-Molina, David; Velazquez-Ameijide, Juan; Crandall, Jeff

    2013-04-01

    While belt usage among rear-seat passengers is disproportionately lower than their front-seat counterpart, this may have serious consequences in the event of a crash not only for the unbelted rear-seat passenger but also for the front-seat passengers as well. To quantify that effect, the objective of the study is to evaluate the increased likelihood of driver fatality in the presence of unrestrained rear-seat passengers in a severe frontal collision. U.S.-based census data from 2001 to 2009 fatal motor vehicle crashes was used to enroll frontal crashes which involved 1998 or later year vehicle models with belted drivers and at least one adult passenger in the rear left seat behind the driver. Results using multivariate logistic regression analysis indicated that the odds of a belt restrained driver sustaining a fatal injury was 137% (95% CI=95%, 189%) higher when the passenger behind the driver was unbelted in comparison to a belted case while the effects of driver age, sex, speed limit, vehicle body type, airbag deployment and driver ejection were controlled in the model. The likelihood of driver fatality due to an unrestrained rear left passenger increased further (119-197%) in the presence of additional unrestrained rear seat passengers in the rear middle or right seats. The results from the study highlight the fact that future advances to front row passive safety systems (e.g. multi-stage airbag deployment) must be adapted to take into account the effect of unrestrained rear-seat passengers. PMID:23411155

  5. Parents' and peers' contribution to risky driving of male teen drivers.

    PubMed

    Taubman - Ben-Ari, Orit; Kaplan, Sigal; Lotan, Tsippy; Prato, Carlo Giacomo

    2015-05-01

    The current study joins efforts devoted to understanding the associations of parents' personality, attitude, and behavior, and to evaluating the added contribution of peers to the driving behavior of young drivers during their solo driving. The study combines data gathered using in-vehicle data recorders from actual driving of parents and their male teen driver with data collected from self-report questionnaires completed by the young drivers. The sample consists of 121 families, who participated in the study for 12 months, beginning with the licensure of the teen driver. The current examination concentrates on the last 3 months of this first year of driving. The experimental design was based on a random control assignment into three treatment groups (with different forms of feedback) and a control group (with no feedback). Findings indicate that the parents' (especially the fathers') sensation seeking, anxiety, and aggression, as well as their risky driving events rate were positively associated with higher risky driving of the young driver. In addition, parents' involvement in the intervention, either by feedback or by training, led to lower risky driving events rate of young drivers compared to the control group. Finally, higher cohesion and adaptability mitigated parents' model for risky driving, and peers norms' of risky driving were associated with higher risk by the teen drivers. We conclude by claiming that there is an unequivocal need to look at a full and complex set of antecedents in parents' personality, attitudes, and behavior, together with the contribution of peers to the young drivers' reckless driving, and address the practical implications for road safety.

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

    PubMed

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

    2016-08-01

    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.

  7. 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

  8. 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.

  9. WT1 mutations in T-ALL.

    PubMed

    Tosello, Valeria; Mansour, Marc R; Barnes, Kelly; Paganin, Maddalena; Sulis, Maria Luisa; Jenkinson, Sarah; Allen, Christopher G; Gale, Rosemary E; Linch, David C; Palomero, Teresa; Real, Pedro; Murty, Vundavalli; Yao, Xiaopan; Richards, Susan M; Goldstone, Anthony; Rowe, Jacob; Basso, Giuseppe; Wiernik, Peter H; Paietta, Elisabeth; Pieters, Rob; Horstmann, Martin; Meijerink, Jules P P; Ferrando, Adolfo A

    2009-07-30

    The molecular mechanisms involved in disease progression and relapse in T-cell acute lymphoblastic leukemia (T-ALL) are poorly understood. We used single nucleotide polymorphism array analysis to analyze paired diagnostic and relapsed T-ALL samples to identify recurrent genetic alterations in T-ALL. This analysis showed that diagnosis and relapsed cases have common genetic alterations, but also that relapsed samples frequently lose chromosomal markers present at diagnosis, suggesting that relapsed T-ALL emerges from an ancestral clone different from the major leukemic population at diagnosis. In addition, we identified deletions and associated mutations in the WT1 tumor suppressor gene in 2 of 9 samples. Subsequent analysis showed WT1 mutations in 28 of 211 (13.2%) of pediatric and 10 of 85 (11.7%) of adult T-ALL cases. WT1 mutations present in T-ALL are predominantly heterozygous frameshift mutations resulting in truncation of the C-terminal zinc finger domains of this transcription factor. WT1 mutations are most prominently found in T-ALL cases with aberrant rearrangements of the oncogenic TLX1, TLX3, and HOXA transcription factor oncogenes. Survival analysis demonstrated that WT1 mutations do not confer adverse prognosis in pediatric and adult T-ALL. Overall, these results identify the presence of WT1 mutations as a recurrent genetic alteration in T-ALL. PMID:19494353

  10. Muller's ratchet, epistasis and mutation effects.

    PubMed

    Butcher, D

    1995-09-01

    In this study, computer simulation is used to show that despite synergistic epistasis for fitness, Muller's ratchet can lead to lethal fitness loss in a population of asexuals through the accumulation of deleterious mutations. This result contradicts previous work that indicated that epistasis will halt the ratchet. The present results show that epistasis will not halt the ratchet provided that rather than a single deleterious mutation effect, there is a distribution of deleterious mutation effects with sufficient density near zero. In addition to epistasis and mutation distribution, the ability of Muller's ratchet to lead to the extinction of an asexual population under epistasis for fitness depends strongly on the expected number of offspring that survive to reproductive age. This strong dependence is not present in the nonepistatic model and suggests that interpreting the population growth parameter as fecundity is inadequate. Because a continuous distribution of mutation effects is used in this model, an emphasis is placed on the dynamics of the mutation effect distribution rather than on the dynamics of the number of least mutation loaded individuals. This perspective suggests that current models of gene interaction are too simple to apply directly to long-term prediction for populations undergoing the ratchet.

  11. New mutations in CMT 1 and HNPP

    SciTech Connect

    Vandenberghe, A.; Boucherat, M.; Bonnebouche, C.

    1994-09-01

    The majority of mutations in CMT 1 (Charcot-Marie-Tooth disease type 1) are due to a duplication of a 1.5 Mb fragment from chromosome 17 containing the PMP22 myelin gene. In addition, micromutations are found in the genes for PMP22 and myelin Po. We collected data from over one hundred families with a duplication in 17p11.2. In about 10% of these families, a de novo mutation was observed. All parents were clinically examined as normal and correct paternity was confirmed. Some families were informative for polymorphic probes located in the duplicated region, and we could deduce a majority of new mutations to be from paternal origin. HNPP (hereditary neuropathy with liability to pressure palsies) is believed to be the reciprocal product of an unequal crossing over underlying the CMT 1 mutation and is due to a deletion of the 1.5 Mb fragment. One new HNPP mutation was found among 7 deleted HNPP families. This mutation is of paternal origin. Clinically assigned CMT 1 patients without a duplication are screened for micromutations applying the SSCP technique. In one family, a de novo mutation was found in the gene for Po.

  12. Proliferation of mutators in A cell population.

    PubMed Central

    Mao, E F; Lane, L; Lee, J; Miller, J H

    1997-01-01

    A Lac- strain of Escherichia coli that reverts by the addition of a G to a G-G-G-G-G-G sequence was used to study the proliferation of mutators in a bacterial culture. Selection for the Lac+ phenotype, which is greatly stimulated in mismatch repair-deficient strains, results in an increase in the percentage of mutators in the selected population from less than 1 per 100,000 cells to 1 per 200 cells. All the mutators detected were deficient in the mismatch repair system. Mutagenesis results in a similar increase in the percentage of mutators. Mutagenesis combined with a single selection can result in a population of more than 50% mutators when a sample of several thousand cells is grown out and selected. Mutagenesis combined with two or more successive selections can generate a population that is 100% mutator. These experiments are discussed in relation to ideas that an early step in carcinogenesis is the creation of a mutator phenotype. PMID:8990293

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

    PubMed

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

    2014-10-01

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

  14. Mutation and premating isolation.

    PubMed

    Woodruff, R C; Thompson, J N

    2002-11-01

    While premating isolation might be traceable to different genetic mechanisms in different species, evidence supports the idea that as few as one or two genes may often be sufficient to initiate isolation. Thus, new mutation can theoretically play a key role in the process. But it has long been thought that a new isolation mutation would fail, because there would be no other individuals for the isolation-mutation-carrier to mate with. We now realize that premeiotic mutations are very common and will yield a cluster of progeny carrying the same new mutant allele. In this paper, we discuss the evidence for genetically simple premating isolation barriers and the role that clusters of an isolation mutation may play in initiating allopatric, and even sympatric, species divisions.

  15. Multiplex detection of mutations.

    PubMed

    Perlin, David S; Balashov, Sergey; Park, Steven

    2008-01-01

    Rapid and reliable detection of mutations at the genetic level is an integral part of modern molecular diagnostics. These mutations can range from dominant single nucleotide polymorphisms within specific loci to codominant heterozygotic insertions and they present considerable challenges to investigators in developing rapid nucleic acid-based amplification assays that can distinguish wild-type from mutant alleles. The recent improvements of real-time polymerase chain reaction (PCR) using self-reporting fluorescence probes have given researchers a powerful tool in developing assays for mutation detection that can be multiplexed for high-throughput screening of multiple mutations and cost effectiveness. Here we describe an application of a multiplexed real-time PCR assay using Molecular Beacon probes for the detection of mutations in codon 54 of the CYP51A gene in Aspergillus fumigatus conferring triazole resistance.

  16. Mutation and premating isolation

    NASA Technical Reports Server (NTRS)

    Woodruff, R. C.; Thompson, J. N. Jr

    2002-01-01

    While premating isolation might be traceable to different genetic mechanisms in different species, evidence supports the idea that as few as one or two genes may often be sufficient to initiate isolation. Thus, new mutation can theoretically play a key role in the process. But it has long been thought that a new isolation mutation would fail, because there would be no other individuals for the isolation-mutation-carrier to mate with. We now realize that premeiotic mutations are very common and will yield a cluster of progeny carrying the same new mutant allele. In this paper, we discuss the evidence for genetically simple premating isolation barriers and the role that clusters of an isolation mutation may play in initiating allopatric, and even sympatric, species divisions.

  17. Conceptual Drivers for an Exploration Medical System

    NASA Technical Reports Server (NTRS)

    Antonsen, Erik; Hanson, Andrea; Shah, Ronak; Reed, Rebekah; Canga, Michael

    2016-01-01

    Interplanetary spaceflight, such as NASA's proposed three-year mission to Mars, provides unique and novel challenges when compared with human spaceflight to date. Extended distance and multi-year missions introduce new elements of operational complexity and additional risk. These elements include: inability to resupply medications and consumables, inability to evacuate injured or ill crew, uncharted psychosocial conditions, and communication delays that create a requirement for some level of autonomous medical capability. Because of these unique challenges, the approaches used in prior programs have limited application to a Mars mission. On a Mars mission, resource limitations will significantly constrain available medical capabilities, and require a paradigm shift in the approach to medical system design and risk mitigation for crew health. To respond to this need for a new paradigm, the Exploration Medical Capability (ExMC) Element is assessing each Mars mission phase-transit, surface stay, rendezvous, extravehicular activity, and return-to identify and prioritize medical needs for the journey beyond low Earth orbit (LEO). ExMC is addressing both planned medical operations, and unplanned contingency medical operations that meld clinical needs and research needs into a single system. This assessment is being used to derive a gap analysis and studies to support meaningful medical capabilities trades. These trades, in turn, allow the exploration medical system design to proceed from both a mission centric and ethics-based approach, and to manage the risks associated with the medical limitations inherent in an exploration class mission. This paper outlines the conceptual drivers used to derive medical system and vehicle needs from an integrated vision of how medical care will be provided within this paradigm. Keywords: (Max 6 keywords: exploration, medicine, spaceflight, Mars, research, NASA)

  18. Long survival in a child with a mutated K27M-H3.3 pilocytic astrocytoma.

    PubMed

    Hochart, Audrey; Escande, Fabienne; Rocourt, Nathalie; Grill, Jacques; Koubi-Pick, Valérie; Beaujot, Juliette; Meignan, Samuel; Vinchon, Matthieu; Maurage, Claude Alain; Leblond, Pierre

    2015-04-01

    We report the first case of a child with a H3F3A K27M mutated pilocytic astrocytoma, who presented with a 10 years survival, and underwent spontaneous malignant transformation. The complex tumoral chromosomal rearrangements were consistent for genomic instability and for the histopathological features of malignant transformation into glioblastoma. H3F3A K27M mutations are rarely observed in benign neoplasms and may be associated with an adverse outcome. This mutation might not be the major driver that led to the onset of tumorigenesis, and we could consider that the associated TP53 mutation, would be required for malignant transformation. PMID:25909089

  19. Long survival in a child with a mutated K27M-H3.3 pilocytic astrocytoma

    PubMed Central

    Hochart, Audrey; Escande, Fabienne; Rocourt, Nathalie; Grill, Jacques; Koubi-Pick, Valérie; Beaujot, Juliette; Meignan, Samuel; Vinchon, Matthieu; Maurage, Claude Alain; Leblond, Pierre

    2015-01-01

    We report the first case of a child with a H3F3A K27M mutated pilocytic astrocytoma, who presented with a 10 years survival, and underwent spontaneous malignant transformation. The complex tumoral chromosomal rearrangements were consistent for genomic instability and for the histopathological features of malignant transformation into glioblastoma. H3F3A K27M mutations are rarely observed in benign neoplasms and may be associated with an adverse outcome. This mutation might not be the major driver that led to the onset of tumorigenesis, and we could consider that the associated TP53 mutation, would be required for malignant transformation. PMID:25909089

  20. Lung Cancer Mutations and Use of Targeted Agents in Hispanics

    PubMed Central

    Cress, W. Douglas; Chiappori, Alberto; Santiago, Pedro; Muñoz-Antonia, Teresita

    2015-01-01

    Hispanic/Latinos (H/L) are expected to grow to over 24% of the USA population by 2050 and lung cancer is the number one cause of cancer death among H/L men. Due to the information that is becoming available via genetic testing, lung cancer molecular profiling is allowing for increasing application of personalized lung cancer therapies. However, to benefit the most people, development of these therapies and genetic tests must include research on as many racial and ethnic groups as possible. The purpose of this review is to bring attention to the fact that the mutations driving lung cancer in H/Ls differ in frequency and nature relative to the non-Hispanic White (WNH) majority that dominate current databases and participate in clinical trials that test new therapies. Clinical trials using new agents targeting genetic alterations (driver mutations) in lung cancer have demonstrated significant improvements in patient outcomes (for example, gefitinib, erlotinib or crizotinib for lung adenocarcinomas harboring EGFR mutations or EML4-ALK fusions, respectively). The nature and frequencies of some lung cancer driver mutations have been shown to be considerably different among racial and ethnic groups. This is particularly true for H/Ls. For example, several reports suggest a dramatic shift in the mutation pattern from predominantly KRAS in a WNH population to predominantly EGFR in multiple H/L populations. However, these studies are limited, and the effects of racial and ethnic differences on the incidence of mutations in lung cancer remain incompletely understood. This review serves as a call to address this problem. PMID:25626064

  1. Lung cancer mutations and use of targeted agents in Hispanics.

    PubMed

    Cress, W Douglas; Chiappori, Alberto; Santiago, Pedro; Muñoz-Antonia, Teresita

    2014-01-01

    Hispanic/Latinos (H/L) are expected to grow to over 24% of the USA population by 2050 and lung cancer is the number one cause of cancer death among H/L men. Due to the information that is becoming available via genetic testing, lung cancer molecular profiling is allowing for increasing application of personalized lung cancer therapies. However, to benefit the most people, development of these therapies and genetic tests must include research on as many racial and ethnic groups as possible. The purpose of this review is to bring attention to the fact that the mutations driving lung cancer in H/Ls differ in frequency and nature relative to the non-Hispanic White (WNH) majority that dominate current databases and participate in clinical trials that test new therapies. Clinical trials using new agents targeting genetic alterations (driver mutations) in lung cancer have demonstrated significant improvements in patient outcomes (for example, gefitinib, erlotinib or crizotinib for lung adenocarcinomas harboring EGFR mutations or EML4-ALK fusions, respectively). The nature and frequencies of some lung cancer driver mutations have been shown to be considerably different among racial and ethnic groups. This is particularly true for H/Ls. For example, several reports suggest a dramatic shift in the mutation pattern from predominantly KRAS in a WNH population to predominantly EGFR in multiple H/L populations. However, these studies are limited, and the effects of racial and ethnic differences on the incidence of mutations in lung cancer remain incompletely understood. This review serves as a call to address this problem.

  2. 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. PMID:1615108

  3. Drivers of the virtual water trade

    NASA Astrophysics Data System (ADS)

    Tamea, S.; Carr, J. A.; Laio, F.; Ridolfi, L.

    2014-01-01

    Through the international trade of food commodities, countries virtually export or import the water used for food production, known as "virtual water." The international trade network thus implies a network of virtual water flows from exporting to importing countries. The purpose of this study is to identify some controlling factors of the virtual water network by means of multivariate regression analyses, or gravity laws, as often named in economics. Starting from the FAOSTAT database, we reconstruct 25 years (1986-2010) of international virtual water trade values; we then analyze the dependence of the exchanged fluxes on: population, gross domestic product, arable land, virtual water embedded in agricultural production and dietary demand, and geographical distance between countries. Significant drivers are identified for each country considering separately export and import fluxes; temporal trends are outlined and the relative importance of drivers is assessed by a commonality analysis. Results indicate that population, gross domestic product and geographical distance are the major drivers of virtual water fluxes, with a minor (nonnegligible) contribution given by the agricultural production of exporting countries. Such drivers have become relevant for an increasing number of countries throughout the years, with an increasing variance explained by the distance between countries and a decreasing role of the gross domestic product. The worldwide adjusted coefficient of determination of fitted gravity-law model is 0.57 (in 2010), and it has increased in time, confirming the good descriptive capability of selected drivers for the virtual water trade.

  4. Driver Module for Noise Cancellation System

    NASA Astrophysics Data System (ADS)

    Shirvani, Mir S.

    2002-12-01

    The Driver module is an integral part of the noise cancellation system, which was my primary objective to research, design, and prototype during the tenure in NASA Langley research center. The function of the driver module is to actuate a panel that is constructed with a smart material and invented in NASA-LaRC. The bandwidth and amplitude of the actuation of the panel correlates the undesirable structural bandwidth and amplitude of the applied object. The undesirable structural bandwidth is relatively narrow and the undesirable amplitude is relatively large. A highly stable, low distortion, linear monolithic integrated circuit was used as a variable frequency and amplitude function generator. In order to elevate the amplitude of the output waveform of the generator to a sufficient magnitude a pair of high voltage monolithic MOSFET operational amplifiers were implemented. The amplifiers connected in a bipolar bridge configuration for a higher efficiency. In order to reduce the required external Supply voltages and make the driver capable to be operated by a battery a pair of ultra miniature high-output voltage dc to dc converters are also used. The driver module tested with the noise cancellation panel, the required data was acquired, and the result was promising. After examining all the options the driver module was designed and prototyped.

  5. Directing driver attention with augmented reality cues

    PubMed Central

    Rusch, Michelle L.; Schall, Mark C.; Gavin, Patrick; Lee, John D.; Dawson, Jeffrey D.; Vecera, Shaun; Rizzo, Matthew

    2013-01-01

    This simulator study evaluated the effects of augmented reality (AR) cues designed to direct the attention of experienced drivers to roadside hazards. Twenty-seven healthy middle-aged licensed drivers with a range of attention capacity participated in a 54 mile (1.5 hour) drive in an interactive fixed-base driving simulator. Each participant received AR cues to potential roadside hazards in six simulated straight (9 mile long) rural roadway segments. Drivers were evaluated on response time for detecting a potentially hazardous event, detection accuracy for target (hazard) and non-target objects, and headway with respect to the hazards. Results showed no negative outcomes associated with interference. AR cues did not impair perception of non-target objects, including for drivers with lower attentional capacity. Results showed near significant response time benefits for AR cued hazards. AR cueing increased response rate for detecting pedestrians and warning signs but not vehicles. AR system false alarms and misses did not impair driver responses to potential hazards. PMID:24436635

  6. 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. PMID:23201756

  7. The androgen receptor gene mutations database.

    PubMed

    Gottlieb, B; Trifiro, M; Lumbroso, R; Pinsky, L

    1997-01-01

    The current version of the androgen receptor (AR) gene mutations database is described. The total number of reported mutations has risen from 212 to 272. We have expanded the database: (i) by adding a large amount of new data on somatic mutations in prostatic cancer tissue; (ii) by defining a new constitutional phenotype, mild androgen insensitivity (MAI); (iii) by placing additional relevant information on an internet site (http://www.mcgill.ca/androgendb/ ). The database has allowed us to examine the contribution of CpG sites to the multiplicity of reports of the same mutation in different families. The database is also available from EMBL (ftp.ebi.ac.uk/pub/databases/androgen) or as a Macintosh Filemaker Pro or Word file (MC33@musica,mcgill.ca)

  8. Mutations in GNAL cause primary torsion dystonia

    PubMed Central

    Fuchs, Tania; Saunders-Pullman, Rachel; Masuho, Ikuo; Luciano, Marta San; Raymond, Deborah; Factor, Stewart; Lang, Anthony E.; Liang, Tsao-Wei; Trosch, Richard M.; White, Sierra; Ainehsazan, Edmond; Herve, Denis; Sharma, Nutan; Ehrlich, Michelle E.; Martemyanov, Kirill A.; Bressman, Susan B.; Ozelius, Laurie J.

    2012-01-01

    Dystonia is a movement disorder characterized by repetitive twisting muscle contractions and postures1,2. Its molecular pathophysiology is poorly understood, in part due to limited knowledge of the genetic basis of the disorder. Only three genes for primary torsion dystonia (PTD), TOR1A (DYT1)3, THAP1 (DYT6)4, and CIZ15 have been identified. Using exome sequencing in two PTD families we identified a novel causative gene, GNAL, with a nonsense p.S293X mutation resulting in premature stop codon in one family and a missense p.V137M mutation in the other. Screening of GNAL in 39 PTD families, revealed six additional novel mutations in this gene. Impaired function of several of the mutations was shown by bioluminescence resonance energy transfer (BRET) assays. PMID:23222958

  9. Novel recurrently mutated genes and a prognostic mutation signature in colorectal cancer

    PubMed Central

    Yu, Jun; Wu, William K K; Li, Xiangchun; He, Jun; Li, Xiao-Xing; Ng, Simon S M; Yu, Chang; Gao, Zhibo; Yang, Jie; Li, Miao; Wang, Qiaoxiu; Liang, Qiaoyi; Pan, Yi; Tong, Joanna H; To, Ka F; Wong, Nathalie; Zhang, Ning; Chen, Jie; Lu, Youyong; Lai, Paul B S; Chan, Francis K L; Li, Yingrui; Kung, Hsiang-Fu; Yang, Huanming; Wang, Jun; Sung, Joseph J Y

    2015-01-01

    Background Characterisation of colorectal cancer (CRC) genomes by next-generation sequencing has led to the discovery of novel recurrently mutated genes. Nevertheless, genomic data has not yet been used for CRC prognostication. Objective To identify recurrent somatic mutations with prognostic significance in patients with CRC. Method Exome sequencing was performed to identify somatic mutations in tumour tissues of 22 patients with CRC, followed by validation of 187 recurrent and pathway-related genes using targeted capture sequencing in additional 160 cases. Results Seven significantly mutated genes, including four reported (APC, TP53, KRAS and SMAD4) and three novel recurrently mutated genes (CDH10, FAT4 and DOCK2), exhibited high mutation prevalence (6–14% for novel cancer genes) and higher-than-expected number of non-silent mutations in our CRC cohort. For prognostication, a five-gene-signature (CDH10, COL6A3, SMAD4, TMEM132D, VCAN) was devised, in which mutation(s) in one or more of these genes was significantly associated with better overall survival independent of tumor-node-metastasis (TNM) staging. The median survival time was 80.4 months in the mutant group versus 42.4 months in the wild type group (p=0.0051). The prognostic significance of this signature was successfully verified using the data set from the Cancer Genome Atlas study. Conclusions The application of next-generation sequencing has led to the identification of three novel significantly mutated genes in CRC and a mutation signature that predicts survival outcomes for stratifying patients with CRC independent of TNM staging. PMID:24951259

  10. Reverse mutations in fragile X syndrome

    SciTech Connect

    Brown, W.T.; Nolin, S.; Houck, G.E.

    1994-09-01

    The fragile X syndrome is the most common inherited form of mental retardation. Yet new mutations have not been described and no affected child has been born to a carrier mother having less than 60 FMR-1 CGG triplet repeats. Reverse mutations also appear to be very rare. We have previously identified the daughter of a premutation mother (95 CGGs) who inherited a normal repeat size of 35 as a reverse mutation. In the process of carrier testing by PCR, we have now identified two additional females with reverse mutations. All three of these reverse mutation women were previously tested by linkage as part of known fragile X families (subsequently confirmed by direct analysis), and assigned a > 99% risk as a carrier. In the second family, the mother carries a premutation allele of 95 repeats and the daughter inherited a 43 repeat allele. Prior to direct DNA testing, she had a positive prenatal diagnosis by linkage (> 99% risk) and cytogenetics with 3/450 cells apparently positive. Subsequent retesting of the products of conception by PCR now reveals a 43 repeat allele from her carrier mother with an 82 repeat allele. Testing with close CA markers (FRAXAC1 and DXS548) confirmed that these women inherited the same chromosome and their full mutation brothers. Further analysis is pending. These examples of reverse mutations are the only ones we have identified in our study of offspring of more than 200 carriers (400+ meioses) examined to date. Therefore, we conclude the frequency of fragile X back mutations is likely to be less than 1%. Retesting of linkage positive carriers is recommended to detect reverse mutations and assure accurate genetic counseling.

  11. Patient-specific driver gene prediction and risk assessment through integrated network analysis of cancer omics profiles

    PubMed Central

    Bertrand, Denis; Chng, Kern Rei; Sherbaf, Faranak Ghazi; Kiesel, Anja; Chia, Burton K. H.; Sia, Yee Yen; Huang, Sharon K.; Hoon, Dave S.B.; Liu, Edison T.; Hillmer, Axel; Nagarajan, Niranjan

    2015-01-01

    Extensive and multi-dimensional data sets generated from recent cancer omics profiling projects have presented new challenges and opportunities for unraveling the complexity of cancer genome landscapes. In particular, distinguishing the unique complement of genes that drive tumorigenesis in each patient from a sea of passenger mutations is necessary for translating the full benefit of cancer genome sequencing into the clinic. We address this need by presenting a data integration framework (OncoIMPACT) to nominate patient-specific driver genes based on their phenotypic impact. Extensive in silico and in vitro validation helped establish OncoIMPACT's robustness, improved precision over competing approaches and verifiable patient and cell line specific predictions (2/2 and 6/7 true positives and negatives, respectively). In particular, we computationally predicted and experimentally validated the gene TRIM24 as a putative novel amplified driver in a melanoma patient. Applying OncoIMPACT to more than 1000 tumor samples, we generated patient-specific driver gene lists in five different cancer types to identify modes of synergistic action. We also provide the first demonstration that computationally derived driver mutation signatures can be overall superior to single gene and gene expression based signatures in enabling patient stratification and prognostication. Source code and executables for OncoIMPACT are freely available from http://sourceforge.net/projects/oncoimpact. PMID:25572314

  12. Patient-specific driver gene prediction and risk assessment through integrated network analysis of cancer omics profiles.

    PubMed

    Bertrand, Denis; Chng, Kern Rei; Sherbaf, Faranak Ghazi; Kiesel, Anja; Chia, Burton K H; Sia, Yee Yen; Huang, Sharon K; Hoon, Dave S B; Liu, Edison T; Hillmer, Axel; Nagarajan, Niranjan

    2015-04-20

    Extensive and multi-dimensional data sets generated from recent cancer omics profiling projects have presented new challenges and opportunities for unraveling the complexity of cancer genome landscapes. In particular, distinguishing the unique complement of genes that drive tumorigenesis in each patient from a sea of passenger mutations is necessary for translating the full benefit of cancer genome sequencing into the clinic. We address this need by presenting a data integration framework (OncoIMPACT) to nominate patient-specific driver genes based on their phenotypic impact. Extensive in silico and in vitro validation helped establish OncoIMPACT's robustness, improved precision over competing approaches and verifiable patient and cell line specific predictions (2/2 and 6/7 true positives and negatives, respectively). In particular, we computationally predicted and experimentally validated the gene TRIM24 as a putative novel amplified driver in a melanoma patient. Applying OncoIMPACT to more than 1000 tumor samples, we generated patient-specific driver gene lists in five different cancer types to identify modes of synergistic action. We also provide the first demonstration that computationally derived driver mutation signatures can be overall superior to single gene and gene expression based signatures in enabling patient stratification and prognostication. Source code and executables for OncoIMPACT are freely available from http://sourceforge.net/projects/oncoimpact. PMID:25572314

  13. 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. PMID:26982104

  14. 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

  15. Linear transformer driver for pulse generation

    DOEpatents

    Kim, Alexander A; Mazarakis, Michael G; Sinebryukhov, Vadim A; Volkov, Sergey N; Kondratiev, Sergey S; Alexeenko, Vitaly M; Bayol, Frederic; Demol, Gauthier; Stygar, William A

    2015-04-07

    A linear transformer driver includes at least one ferrite ring positioned to accept a load. The linear transformer driver also includes a first power delivery module that includes a first charge storage devices and a first switch. The first power delivery module sends a first energy in the form of a first pulse to the load. The linear transformer driver also includes a second power delivery module including a second charge storage device and a second switch. The second power delivery module sends a second energy in the form of a second pulse to the load. The second pulse has a frequency that is approximately three times the frequency of the first pulse. The at least one ferrite ring is positioned to force the first pulse and the second pulse to the load by temporarily isolating the first pulse and the second pulse from an electrical ground.

  16. A model of Beijing drivers' scrambling behaviors.

    PubMed

    Shi, Jing; Bai, Yun; Tao, Li; Atchley, Paul

    2011-07-01

    A major, but unstudied, cause of crashes in China is drivers that "scramble" to gain the right of way in violation of traffic regulations. The motivation of this study is to explore the features of drivers' scrambling behaviors and the attitudes and driving skills that influence them. In this study, we established a scrambling behavior scale, and developed a driving attitude scale and a driving skill scale using factor analysis of an Internet survey of 486 drivers in Beijing. A structural equation model of scrambling behavior toward cars and pedestrians/cyclists was developed with attitudes and skills as predictors of behavior. Skills and attitudes of approval toward violations of traffic rules did not predict scrambling behaviors, while the motivation for safety and attitudes against violating traffic rules led to reduced scrambling behaviors. The current work highlights this peculiar aspect of Chinese roads and suggests methods to reduce the behavior.

  17. Nonadaptive mutations occur on the F' episome during adaptive mutation conditions in Escherichia coli.

    PubMed Central

    Foster, P L

    1997-01-01

    One of the most studied examples of adaptive mutation is a strain of Escherichia coli, FC40, that cannot utilize lactose (Lac-) but that readily reverts to lactose utilization (Lac+) when lactose is its sole carbon source. Adaptive reversion to Lac+ occurs at a high rate when the Lac- allele is on an F' episome and conjugal functions are expressed. It was previously shown that nonselected mutations on the chromosome did not appear in the Lac- population while episomal Lac+ mutations accumulated, but it remained possible that nonselected mutations might occur on the episome. To investigate this possibility, a second mutational target was created on the Lac- episome by mutation of a Tn1O element, which encodes tetracycline resistance (Tetr), to tetracycline sensitivity (Tets). Reversion rates to Tetr during normal growth and during lactose selection were measured. The results show that nonselected Tetr mutations do accumulate in Lac- cells when those cells are under selection to become Lac+. Thus, reversion to Lac+ in FC40 does not appear to be adaptive in the narrow sense of the word. In addition, the results suggest that during lactose selection, both Lac+ and Tetr mutations are created or preserved by the same recombination-dependent mechanism. PMID:9045812

  18. Living dangerously: driver distraction at high speed.

    PubMed

    Johnson, Mark B; Voas, Robert B; Lacey, John H; McKnight, A Scott; Lange, James E

    2004-03-01

    Recent research indicates that cell phone use can distract drivers from safe vehicle operation. However, estimates of the prevalence of cell phone use while driving have been limited to daytime hours and low-speed roadways. This paper describes the results of a study to estimate rates of cell phone use and other distractions by examining approximately 40,000 high-quality digital photographs of vehicles and drivers on the New Jersey Turnpike. The photographs, which originally were collected as part of a separate study, were taken both during the day and during the night and at different locations across the span of the Turnpike. A radar gun linked to the camera recorded the speeds of vehicles as they passed. This provided us with the speeds of every vehicle photographed, and allowed us to determine population counts of vehicles. A panel of three trained coders examined each photograph and recorded the presence of cell phone use by the drivers or any other distracting behavior. Demographic information on the driver was obtained during previous examinations of the photographs for an unrelated study. A rating was considered reliable when two out of the three coders agreed. Population estimates (and confidence intervals) of cell phone use and other distractions were estimated by weighting the cases by the inverse probability of vehicle selection. Logistic regression was used to predict cell phone use from demographic and situational factors. The results indicated that the most frequent distraction was cell phone use: 1.5% of the drivers on the Turnpike were using cell phones compared to the 3 to 4% use rates reported in the National Occupant Protection Use Survey (NOPUS) surveys conducted during the daytime on lower speed roadways. The Turnpike survey indicated that cell phones were used less on weekends and at night, and when the driver was exceeding the speed limit or had a passenger in the car.

  19. Activating STAT6 mutations in follicular lymphoma

    PubMed Central

    Yildiz, Mehmet; Li, Hongxiu; Bernard, Denzil; Amin, Nisar A.; Ouillette, Peter; Jones, Siân; Saiya-Cork, Kamlai; Parkin, Brian; Jacobi, Kathryn; Shedden, Kerby; Wang, Shaomeng; Chang, Alfred E.; Kaminski, Mark S.

    2015-01-01

    Follicular lymphoma (FL) is the second most common non-Hodgkin lymphoma in the Western world. FL cell-intrinsic and cell-extrinsic factors influence FL biology and clinical outcome. To further our understanding of the genetic basis of FL, we performed whole-exome sequencing of 23 highly purified FL cases and 1 transformed FL case and expanded findings to a combined total of 114 FLs. We report recurrent mutations in the transcription factor STAT6 in 11% of FLs and identified the STAT6 amino acid residue 419 as a novel STAT6 mutation hotspot (p.419D/G, p.419D/A, and p.419D/H). FL-associated STAT6 mutations were activating, as evidenced by increased transactivation in HEK293T cell–based transfection/luciferase reporter assays, heightened interleukin-4 (IL-4) –induced activation of target genes in stable STAT6 transfected lymphoma cell lines, and elevated baseline expression levels of STAT6 target genes in primary FL B cells harboring mutant STAT6. Mechanistically, FL-associated STAT6 mutations facilitated nuclear residency of STAT6, independent of IL-4–induced STAT6-Y641 phosphorylation. Structural modeling of STAT6 based on the structure of the STAT1-DNA complex revealed that most FL-associated STAT6 mutants locate to the STAT6-DNA interface, potentially facilitating heightened interactions. The genetic and functional data combined strengthen the recognition of the IL-4/JAK/STAT6 axis as a driver of FL pathogenesis. PMID:25428220

  20. Concealing their communication: exploring psychosocial predictors of young drivers' intentions and engagement in concealed texting.

    PubMed

    Gauld, Cassandra S; Lewis, Ioni; White, Katherine M

    2014-01-01

    Making a conscious effort to hide the fact that you are texting while driving (i.e., concealed texting) is a deliberate and risky behaviour involving attention diverted away from the road. As the most frequent users of text messaging services and mobile phones while driving, young people appear at heightened risk of crashing from engaging in this behaviour. This study investigated the phenomenon of concealed texting while driving, and utilised an extended Theory of Planned Behaviour (TPB) including the additional predictors of moral norm, mobile phone involvement, and anticipated regret to predict young drivers' intentions and subsequent behaviour. Participants (n=171) were aged 17-25 years, owned a mobile phone, and had a current driver's licence. Participants completed a questionnaire measuring their intention to conceal texting while driving, and a follow-up questionnaire a week later to report their behavioural engagement. The results of hierarchical multiple regression analyses showed overall support for the predictive utility of the TPB with the standard constructs accounting for 69% of variance in drivers' intentions, and the extended predictors contributing an additional 6% of variance in intentions over and above the standard constructs. Attitude, subjective norm, PBC, moral norm, and mobile phone involvement emerged as significant predictors of intentions; and intention was the only significant predictor of drivers' self-reported behaviour. These constructs can provide insight into key focal points for countermeasures including advertising and other public education strategies aimed at influencing young drivers to reconsider their engagement in this risky behaviour. PMID:24211560

  1. Concealing their communication: exploring psychosocial predictors of young drivers' intentions and engagement in concealed texting.

    PubMed

    Gauld, Cassandra S; Lewis, Ioni; White, Katherine M

    2014-01-01

    Making a conscious effort to hide the fact that you are texting while driving (i.e., concealed texting) is a deliberate and risky behaviour involving attention diverted away from the road. As the most frequent users of text messaging services and mobile phones while driving, young people appear at heightened risk of crashing from engaging in this behaviour. This study investigated the phenomenon of concealed texting while driving, and utilised an extended Theory of Planned Behaviour (TPB) including the additional predictors of moral norm, mobile phone involvement, and anticipated regret to predict young drivers' intentions and subsequent behaviour. Participants (n=171) were aged 17-25 years, owned a mobile phone, and had a current driver's licence. Participants completed a questionnaire measuring their intention to conceal texting while driving, and a follow-up questionnaire a week later to report their behavioural engagement. The results of hierarchical multiple regression analyses showed overall support for the predictive utility of the TPB with the standard constructs accounting for 69% of variance in drivers' intentions, and the extended predictors contributing an additional 6% of variance in intentions over and above the standard constructs. Attitude, subjective norm, PBC, moral norm, and mobile phone involvement emerged as significant predictors of intentions; and intention was the only significant predictor of drivers' self-reported behaviour. These constructs can provide insight into key focal points for countermeasures including advertising and other public education strategies aimed at influencing young drivers to reconsider their engagement in this risky behaviour.

  2. Communications Interface Driver (CID) test plan

    NASA Astrophysics Data System (ADS)

    Bratton, Thomas; Davis, James; Dudas, Charles; Livings, Jeffrey G.; Schoenthal, Mark

    1990-09-01

    This test plan for the Communications Interface Driver (CID) systems will be used to evaluate and accept the CID. The CID system is a test tool whose purpose is to supply or receive a capacity level of communication (comm) messages to and from the air traffic control (ATC) and non-ATC ports of the Mode Select (Mode S) sensor. The primary concern of the CID test plan is written to establish the detailed test requirements, criteria, and methods to achieve the evaluation of the CID against the requirements set forth in the report, Functional Requirements of the Communications Interface Driver (CID), DOT/FAA/CT-TN87/41.

  3. LHON: Mitochondrial Mutations and More.

    PubMed

    Kirches, E

    2011-03-01

    Leber's hereditary optic neuropathy (LHON) is a mitochondrial disorder leading to severe visual impairment or even blindness by death of retinal ganglion cells (RGCs). The primary cause of the disease is usually a mutation of the mitochondrial genome (mtDNA) causing a single amino acid exchange in one of the mtDNA-encoded subunits of NADH:ubiquinone oxidoreductase, the first complex of the electron transport chain. It was thus obvious to accuse neuronal energy depletion as the most probable mediator of neuronal death. The group of Valerio Carelli and other authors have nicely shown that energy depletion shapes the cell fate in a LHON cybrid cell model. However, the cybrids used were osteosarcoma cells, which do not fully model neuronal energy metabolism. Although complex I mutations may cause oxidative stress, a potential pathogenetic role of the latter was less taken into focus. The hypothesis of bioenergetic failure does not provide a simple explanation for the relatively late disease onset and for the incomplete penetrance, which differs remarkably between genders. It is assumed that other genetic and environmental factors are needed in addition to the 'primary LHON mutations' to elicit RGC death. Relevant nuclear modifier genes have not been identified so far. The review discusses the unresolved problems of a pathogenetic hypothesis based on ATP decline and/or ROS-induced apoptosis in RGCs.

  4. Homologous Mutation to Human BRAF V600E is Common in Naturally Occurring Canine Bladder Cancer—Evidence for a Relevant Model System and Urine-based Diagnostic Test

    PubMed Central

    Decker, Brennan; Parker, Heidi G.; Dhawan, Deepika; Kwon, Erika M.; Karlins, Eric; Davis, Brian W.; Ramos-Vara, José A.; Bonney, Patty L.; McNiel, Elizabeth A.; Knapp, Deborah W.; Ostrander, Elaine A.

    2015-01-01

    Targeted cancer therapies offer great clinical promise, but treatment resistance is common, and basic research aimed at overcoming this challenge is limited by reduced genomic and biological complexity in artificially induced rodent tumors compared to their human counterparts. Animal models that more faithfully recapitulate genotype-specific human pathology could improve the predictive value of these investigations. Here, a newly identified animal model for oncogenic BRAF-driven cancers is described. With 20,000 new cases in the United States each year, canine invasive transitional cell carcinoma of the bladder (InvTCC) is a common, naturally occurring malignancy that shares significant histological, biological, and clinical phenotypes with human muscle invasive bladder cancer. In order to identify somatic drivers of canine InvTCC, the complete transcriptome for multiple tumors was determined by RNAseq. All tumors harbored a somatic mutation that is homologous to the human BRAF(V600E) mutation, and an identical mutation was present in 87% of 62 additional canine InvTCC tumors. The mutation was also detectable in the urine sediments of all dogs tested with mutation-positive tumors. Functional experiments suggest that, like human tumors, canine activating BRAF mutations potently stimulate the mitogen activated protein kinase (MAPK) pathway. Cell lines with the mutation have elevated levels of phosphorylated MEK, compared to a line with wild type BRAF. This effect can be diminished through application of the BRAF(V600E) inhibitor vemurafenib. These findings set the stage for canine InvTCC as a powerful system to evaluate BRAF-targeted therapies, as well as therapies designed to overcome resistance, which could enhance treatment of both human and canine cancers PMID:25767210

  5. Validation of the Driver Behaviour Questionnaire in a representative sample of drivers in Australia.

    PubMed

    Stephens, A N; Fitzharris, M

    2016-01-01

    The Driver Behaviour Questionnaire (DBQ) is a widely used measure of driving behaviours that may increase a driver's risk of crash involvement. However, there are several different versions of the DBQ varying in terms of number of items and factor structure. The aim of the current research was to assess the construct validity of the popular 28-item four-factor DBQ solution in a representative sample of drivers in Australia. A further aim was to test the factorial invariance of the measure across gender, age and also between fleet and non-fleet drivers using multigroup confirmatory factor analyses. Data on a range of attitudes towards road safety were collected using an online survey. A stratified sampling procedure was undertaken to ensure the age, gender and location distributions of participants were representative of the Australian population. A total of 2771 responses were obtained from fully licensed motor vehicle drivers (male: 46%). Confirmatory factor analysis supported the 28-item four-factor DBQ in the Australian sample. The DBQ was also found to be gender-invariant and strong partial measurement invariance was found for drivers aged from 26 to 64, but not for younger (17-25) or older (65-75) drivers. Modifications to the DBQ suggest how the DBQ can be improved for use in these two age groups. PMID:26584016

  6. Genomic confirmation of nutrient-dependent mutability of mutators in Escherichia coli.

    PubMed

    Tsuru, Saburo; Ishizawa, Yuuka; Shibai, Atsushi; Takahashi, Yusuke; Motooka, Daisuke; Nakamura, Shota; Yomo, Tetsuya

    2015-12-01

    Mutators with increased mutation rates are prevalent in various environments and have important roles in accelerating adaptive evolution. Previous studies on mutator strains of microorganisms have shown that some mutators have constant mutation rates, whereas others exhibit switchable mutation rates depending on nutritional conditions. This suggests that the contributions of mutators on evolution vary with fluctuating nutritional conditions. However, such conditional mutability has been unclear at the genomic level. In addition, it is still unknown why mutation rates change with nutritional condition. Here, we used two mutator strains of Escherichia coli to explore the nutrient dependence of mutation rates at the genomic level. These strains were transferred repeatedly under different nutritional conditions for hundreds of generations to accumulate mutations. Whole-genome sequencing of the offspring showed that the nutrient dependence of the mutation rates was pervasive at the genomic scale. Neutrality in the mutation accumulation processes and constancy in the mutational bias suggested that nutrient dependence was not derived from conditional selective purges or from shifts of mutational bias. Some mutators could simply switch their mutation rates for both transitions and transversions in response to nutritional shifts.

  7. Next Generation Sequencing of Cytokeratin 20-Negative Merkel Cell Carcinoma Reveals Ultraviolet Signature Mutations and Recurrent TP53 and RB1 Inactivation

    PubMed Central

    Harms, Paul W.; Collie, Angela M. B.; Hovelson, Daniel H.; Cani, Andi K.; Verhaegen, Monique E.; Patel, Rajiv M.; Fullen, Douglas R.; Omata, Kei; Dlugosz, Andrzej A.; Tomlins, Scott A.; Billings, Steven D.

    2016-01-01

    Merkel cell carcinoma is a rare but highly aggressive cutaneous neuroendocrine carcinoma. Cytokeratin-20 (CK20) is expressed in approximately 95% of Merkel cell carcinomas and is useful for distinction from morphologically similar entities including metastatic small cell lung carcinoma. Lack of CK20 expression may make diagnosis of Merkel cell carcinoma more challenging, and has unknown biological significance. Approximately 80% of CK20-positive Merkel cell carcinomas are associated with the oncogenic Merkel cell polyomavirus. Merkel cell carcinomas lacking Merkel cell polyomavirus display distinct genetic changes from Merkel cell polyomavirus-positive Merkel cell carcinoma, including RB1 inactivating mutations. Unlike CK20-positive Merkel cell carcinoma, the majority of CK20-negative Merkel cell carcinomas are Merkel cell polyomavirus-negative, suggesting CK20-negative Merkel cell carcinomas predominantly arise through virus-independent pathway(s) and may harbor additional genetic differences from conventional Merkel cell carcinoma. Hence, we analyzed 15 CK20-negative Merkel cell carcinoma tumors (ten Merkel cell polyomavirus-negative, four Merkel cell polyomavirus-positive, and one undetermined) using the Ion Ampliseq Comprehensive Cancer Panel, which assesses copy number alterations and mutations in 409 cancer-relevant genes. Twelve tumors displayed prioritized high-level chromosomal gains or losses (average 1.9 per tumor). Non-synonymous high confidence somatic mutations were detected in 14 tumors (average 11.9 per tumor). Assessing all somatic coding mutations, an ultraviolet-signature mutational profile was present, and more prevalent in Merkel cell polyomavirus-negative tumors. Recurrent deleterious tumor suppressor mutations affected TP53 (9/15, 60%), RB1 (3/15, 20%), and BAP1 (2/15, 13%). Oncogenic activating mutations included PIK3CA (3/15, 20%), AKT1 (1/15, 7%)) and EZH2 (1/15, 7%). In conclusion, CK20-negative Merkel cell carcinoma display overlapping

  8. Weaver syndrome and EZH2 mutations: Clarifying the clinical phenotype.

    PubMed

    Tatton-Brown, Katrina; Murray, Anne; Hanks, Sandra; Douglas, Jenny; Armstrong, Ruth; Banka, Siddharth; Bird, Lynne M; Clericuzio, Carol L; Cormier-Daire, Valerie; Cushing, Tom; Flinter, Frances; Jacquemont, Marie-Line; Joss, Shelagh; Kinning, Esther; Lynch, Sally Ann; Magee, Alex; McConnell, Vivienne; Medeira, Ana; Ozono, Keiichi; Patton, Michael; Rankin, Julia; Shears, Debbie; Simon, Marleen; Splitt, Miranda; Strenger, Volker; Stuurman, Kyra; Taylor, Clare; Titheradge, Hannah; Van Maldergem, Lionel; Temple, I Karen; Cole, Trevor; Seal, Sheila; Rahman, Nazneen

    2013-12-01

    Weaver syndrome, first described in 1974, is characterized by tall stature, a typical facial appearance, and variable intellectual disability. In 2011, mutations in the histone methyltransferase, EZH2, were shown to cause Weaver syndrome. To date, we have identified 48 individuals with EZH2 mutations. The mutations were primarily missense mutations occurring throughout the gene, with some clustering in the SET domain (12/48). Truncating mutations were uncommon (4/48) and only identified in the final exon, after the SET domain. Through analyses of clinical data and facial photographs of EZH2 mutation-positive individuals, we have shown that the facial features can be subtle and the clinical diagnosis of Weaver syndrome is thus challenging, especially in older individuals. However, tall stature is very common, reported in >90% of affected individuals. Intellectual disability is also common, present in ~80%, but is highly variable and frequently mild. Additional clinical features which may help in stratifying individuals to EZH2 mutation testing include camptodactyly, soft, doughy skin, umbilical hernia, and a low, hoarse cry. Considerable phenotypic overlap between Sotos and Weaver syndromes is also evident. The identification of an EZH2 mutation can therefore provide an objective means of confirming a subtle presentation of Weaver syndrome and/or distinguishing Weaver and Sotos syndromes. As mutation testing becomes increasingly accessible and larger numbers of EZH2 mutation-positive individuals are identified, knowledge of the clinical spectrum and prognostic implications of EZH2 mutations should improve.

  9. Weaver syndrome and EZH2 mutations: Clarifying the clinical phenotype.

    PubMed

    Tatton-Brown, Katrina; Murray, Anne; Hanks, Sandra; Douglas, Jenny; Armstrong, Ruth; Banka, Siddharth; Bird, Lynne M; Clericuzio, Carol L; Cormier-Daire, Valerie; Cushing, Tom; Flinter, Frances; Jacquemont, Marie-Line; Joss, Shelagh; Kinning, Esther; Lynch, Sally Ann; Magee, Alex; McConnell, Vivienne; Medeira, Ana; Ozono, Keiichi; Patton, Michael; Rankin, Julia; Shears, Debbie; Simon, Marleen; Splitt, Miranda; Strenger, Volker; Stuurman, Kyra; Taylor, Clare; Titheradge, Hannah; Van Maldergem, Lionel; Temple, I Karen; Cole, Trevor; Seal, Sheila; Rahman, Nazneen

    2013-12-01

    Weaver syndrome, first described in 1974, is characterized by tall stature, a typical facial appearance, and variable intellectual disability. In 2011, mutations in the histone methyltransferase, EZH2, were shown to cause Weaver syndrome. To date, we have identified 48 individuals with EZH2 mutations. The mutations were primarily missense mutations occurring throughout the gene, with some clustering in the SET domain (12/48). Truncating mutations were uncommon (4/48) and only identified in the final exon, after the SET domain. Through analyses of clinical data and facial photographs of EZH2 mutation-positive individuals, we have shown that the facial features can be subtle and the clinical diagnosis of Weaver syndrome is thus challenging, especially in older individuals. However, tall stature is very common, reported in >90% of affected individuals. Intellectual disability is also common, present in ~80%, but is highly variable and frequently mild. Additional clinical features which may help in stratifying individuals to EZH2 mutation testing include camptodactyly, soft, doughy skin, umbilical hernia, and a low, hoarse cry. Considerable phenotypic overlap between Sotos and Weaver syndromes is also evident. The identification of an EZH2 mutation can therefore provide an objective means of confirming a subtle presentation of Weaver syndrome and/or distinguishing Weaver and Sotos syndromes. As mutation testing becomes increasingly accessible and larger numbers of EZH2 mutation-positive individuals are identified, knowledge of the clinical spectrum and prognostic implications of EZH2 mutations should improve. PMID:24214728

  10. MUTATION RATES OF BACTERIA IN STEADY STATE POPULATIONS

    PubMed Central

    Fox, Maurice S.

    1955-01-01

    The breeder and the chemostat have been used to measure mutation rates for two mutations under a variety of steady state growth conditions. These rates have been found to be higher in complex medium than in minimal (F) medium. The effects of changes in nutritional conditions on these high rates have been described. In addition, the mutation rates at short generation times, in complex medium, have been shown to decrease with increasing generation time. PMID:13271726

  11. Mutations in man

    SciTech Connect

    Obe, G.

    1984-01-01

    This book contains 13 selections that cover some of the following topics: DNA repair, gene or point mutations, aspects of nondisjunction, origin and significance of chromosomal alterations, structure and organization of the human genome, and mutagenic activity of cigarette smoke.

  12. 49 CFR 177.816 - Driver training.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... employee who will operate a motor vehicle has been trained in the applicable requirements of 49 CFR parts... 49 CFR part 383. Specialized training shall include the following: (1) Operation of emergency control... 49 Transportation 2 2010-10-01 2010-10-01 false Driver training. 177.816 Section...

  13. 49 CFR 177.816 - Driver training.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... cause to be transported, a hazardous material unless each hazmat employee who will operate a motor vehicle has been trained in the applicable requirements of 49 CFR parts 390 through 397 and the procedures... have the appropriate State-issued commercial driver's license required by 49 CFR part 383....

  14. Driver Education Program. Administrative and Curriculum Guide.

    ERIC Educational Resources Information Center

    Hawaii State Dept. of Education, Honolulu. Office of Instructional Services.

    This administrative and curriculum guide is designed for use in establishing and teaching a driver education course for high school students. The first section of the guide, a discussion of program administration, deals with various aspects of program management as well as the roles and responsibilities of the key practitioners involved in driver…

  15. Wisconsin Bicycle Driver Training Course. Instructor's Handbook.

    ERIC Educational Resources Information Center

    Thompson, Ronald L.

    Designed for use by trained and certified instructors of a voluntary bicycle driver training course, this handbook provides materials for eight one-hour sessions for beginners or experienced bicyclists. Part 1, Instructor's Guidelines, discusses course objectives, organization, and content; instruction methods; and audiovisual materials. Part 2…

  16. Who's Driving This Bus Anyway? Empowering Drivers.

    ERIC Educational Resources Information Center

    Allen, J. D.

    1997-01-01

    In 1977, a school transportation director developed a policy giving school bus drivers authority to discipline unruly student behavior via a system of graduated warnings and suspension of riding privileges. Most parents have been supportive and expect their kids to behave on the bus. In the interest of safety, school administrators should support…

  17. Toms River Drivers Manual 1984-1985.

    ERIC Educational Resources Information Center

    Thomas, Patricia

    The procedures in this manual are designed to establish stability and continuity within the student transportation department of the Toms River Regional Schools in New Jersey. The manual is divided into three sections. Section 1 provides driver and aide specific information. It includes directives related to time clock, spare buses, and…

  18. What Are Drivers for Informal Learning?

    ERIC Educational Resources Information Center

    Schürmann, Eva; Beausaert, Simon

    2016-01-01

    Purpose: The topic of informal learning at work has received increasing attention in the past years. The purpose of this study is to explore in which informal learning activities employees engage and what are the drivers for informal learning. Design/Methodology/Approach: Semi-structured interviews were taken from ten human resources (HR) and ten…

  19. Mathematical model to predict drivers' reaction speeds.

    PubMed

    Long, Benjamin L; Gillespie, A Isabella; Tanaka, Martin L

    2012-02-01

    Mental distractions and physical impairments can increase the risk of accidents by affecting a driver's ability to control the vehicle. In this article, we developed a linear mathematical model that can be used to quantitatively predict drivers' performance over a variety of possible driving conditions. Predictions were not limited only to conditions tested, but also included linear combinations of these tests conditions. Two groups of 12 participants were evaluated using a custom drivers' reaction speed testing device to evaluate the effect of cell phone talking, texting, and a fixed knee brace on the components of drivers' reaction speed. Cognitive reaction time was found to increase by 24% for cell phone talking and 74% for texting. The fixed knee brace increased musculoskeletal reaction time by 24%. These experimental data were used to develop a mathematical model to predict reaction speed for an untested condition, talking on a cell phone with a fixed knee brace. The model was verified by comparing the predicted reaction speed to measured experimental values from an independent test. The model predicted full braking time within 3% of the measured value. Although only a few influential conditions were evaluated, we present a general approach that can be expanded to include other types of distractions, impairments, and environmental conditions. PMID:22431214

  20. Levitation With a Single Acoustic Driver

    NASA Technical Reports Server (NTRS)

    Barmatz, M. B.; Gaspar, M. S.; Allen, J. L.

    1986-01-01

    Pair of reports describes acoustic-levitation systems in which only one acoustic resonance mode excited, and only one driver needed. Systems employ levitation chambers of rectangular and cylindrical geometries. Reports first describe single mode concept and indicate which modes used to levitate sample without rotation. Reports then describe systems in which controlled rotation of sample introduced.

  1. Multi-Phase Driver Education Teaching Guide.

    ERIC Educational Resources Information Center

    Hurst-Euless-Bedford Independent School District, Hurst, TX.

    For use in planning and conducting functional multi-phase driver education programs, this teacher's guide consists of four phases of instruction: classroom activities, simulated application, in-car range practice, and in-car public practice. Contents are divided into three instructional sections, with the first combining the classroom activities…

  2. Evasive and Emergency Curriculum for Driver Education.

    ERIC Educational Resources Information Center

    1976

    An advanced course to increase the student's driving ability and knowledge of the automobile is presented in this curriculum guide for use by high school driver education instructors. The course is designed for students who have been driving for 6 to 12 months or who have mastered basic driving skills. Focus is on advanced driving techniques,…

  3. Driver and Traffic Safety Education Policies.

    ERIC Educational Resources Information Center

    New York State Education Dept., Albany. Div. of General Education.

    The policy statement outlines New York State standards regarding: (1) the driver's education program; (2) vehicles in the program; (3) administration, supervision, and organization of summer school programs; (4) teachers in the program; and (5) pupils in the program. A glossary defines terms and instructional objectives. Program policies…

  4. Driver Education for Motorcycle Operation. Final Report.

    ERIC Educational Resources Information Center

    Council, Forrest M.; And Others

    A three-year pilot project was conducted to evaluate the feasibility of implementing a statewide off-road motorcycle training program for beginning drivers in North Carolina. The first year of the program involved approximately 422 students from five locations, the second year involved seven sites across the State. The three basic criteria for the…

  5. Mathematical model to predict drivers' reaction speeds.

    PubMed

    Long, Benjamin L; Gillespie, A Isabella; Tanaka, Martin L

    2012-02-01

    Mental distractions and physical impairments can increase the risk of accidents by affecting a driver's ability to control the vehicle. In this article, we developed a linear mathematical model that can be used to quantitatively predict drivers' performance over a variety of possible driving conditions. Predictions were not limited only to conditions tested, but also included linear combinations of these tests conditions. Two groups of 12 participants were evaluated using a custom drivers' reaction speed testing device to evaluate the effect of cell phone talking, texting, and a fixed knee brace on the components of drivers' reaction speed. Cognitive reaction time was found to increase by 24% for cell phone talking and 74% for texting. The fixed knee brace increased musculoskeletal reaction time by 24%. These experimental data were used to develop a mathematical model to predict reaction speed for an untested condition, talking on a cell phone with a fixed knee brace. The model was verified by comparing the predicted reaction speed to measured experimental values from an independent test. The model predicted full braking time within 3% of the measured value. Although only a few influential conditions were evaluated, we present a general approach that can be expanded to include other types of distractions, impairments, and environmental conditions.

  6. Comparing Mutational Variabilities

    PubMed Central

    Houle, D.; Morikawa, B.; Lynch, M.

    1996-01-01

    We have reviewed the available data on V(M), the amount of genetic variation in phenotypic traits produced each generation by mutation. We use these data to make several qualitative tests of the mutation-selection balance hypothesis for the maintenance of genetic variance (MSB). To compare V(M) values, we use three dimensionless quantities: mutational heritability, V(M)/V(E); the mutational coefficient of variation, CV(M); and the ratio of the standing genetic variance to V(M), V(G)/V(M). Since genetic coefficients of variation for life history traits are larger than those for morphological traits, we predict that under MSB, life history traits should also have larger CV(M). This is confirmed; life history traits have a median CV(M) value more than six times higher than that for morphological traits. V(G)/V(M) approximates the persistence time of mutations under MSB in an infinite population. In order for MSB to hold, V(G)/V(M) must be small, substantially less than 1000, and life history traits should have smaller values than morphological traits. V(G)/V(M) averages about 50 generations for life history traits and 100 generations for morphological traits. These observations are all consistent with the predictions of a mutation-selection balance model. PMID:8807316

  7. Diploid yeast cells yield homozygous spontaneous mutations

    NASA Technical Reports Server (NTRS)

    Esposito, M. S.; Bruschi, C. V.; Brushi, C. V. (Principal Investigator)

    1993-01-01

    A leucine-requiring hybrid of Saccharomyces cerevisiae, homoallelic at the LEU1 locus (leu1-12/leu1-12) and heterozygous for three chromosome-VII genetic markers distal to the LEU1 locus, was employed to inquire: (1) whether spontaneous gene mutation and mitotic segregation of heterozygous markers occur in positive nonrandom association and (2) whether homozygous LEU1/LEU1 mutant diploids are generated. The results demonstrate that gene mutation of leu1-12 to LEU1 and mitotic segregation of heterozygous chromosome-VII markers occur in strong positive nonrandom association, suggesting that the stimulatory DNA lesion is both mutagenic and recombinogenic. In addition, genetic analysis of diploid Leu+ revertants revealed that approximately 3% of mutations of leu1-12 to LEU1 result in LEU1/LEU1 homozygotes. Red-white sectored Leu+ colonies exhibit genotypes that implicate post-replicational chromatid breakage and exchange near the site of leu1-12 reversion, chromosome loss, and subsequent restitution of diploidy, in the sequence of events leading to mutational homozygosis. By analogy, diploid cell populations can yield variants homozygous for novel recessive gene mutations at biologically significant rates. Mutational homozygosis may be relevant to both carcinogenesis and the evolution of asexual diploid organisms.

  8. Towards a general theory of driver behaviour.

    PubMed

    Fuller, Ray

    2005-05-01

    Taylor [Taylor, D.H., 1964. Drivers' galvanic skin response and the risk of accident. Ergonomics 7, 439-451] argued that drivers attempt to maintain a constant level of anxiety when driving which Wilde [Wilde, G.J.S., 1982. The theory of risk homeostasis: implications for safety and health. Risk Anal. 2, 209-225] interpreted to be coupled to subjective estimates of the probability of collision. This theoretical paper argues that what drivers attempt to maintain is a level of task difficulty. Naatanen and Summala [Naatanen, R., Summala, H., 1976. Road User Behaviour and Traffic Accidents. North Holland/Elsevier, Amsterdam, New York] similarly rejected the concept of statistical risk as a determinant of driver behaviour, but in so doing fell back on the learning process to generate a largely automatised selection of appropriate safety margins. However it is argued here that driver behaviour cannot be acquired and executed principally in such S-R terms. The concept of task difficulty is elaborated within the framework of the task-capability interface (TCI) model, which describes the dynamic interaction between the determinants of task demand and driver capability. It is this interaction which produces different levels of task difficulty. Implications of the model are discussed regarding variation in performance, resource allocation, hierarchical decision-making and the interdependence of demand and capability. Task difficulty homeostasis is proposed as a key sub-goal in driving and speed choice is argued to be the primary solution to the problem of keeping task difficulty within selected boundaries. The relationship between task difficulty and mental workload and calibration is clarified. Evidence is cited in support of the TCI model, which clearly distinguishes task difficulty from estimates of statistical risk. However, contrary to expectation, ratings of perceived risk depart from ratings of statistical risk but track difficulty ratings almost perfectly. It now

  9. 77 FR 30919 - Commercial Driver's License Testing and Commercial Learner's Permit Standards

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-24

    ... and to qualify to transport the range of cargo they normally handle. The Agency includes in this... vehicle.'' The change required additional drivers, primarily those transporting certain tanks temporarily... minimum Federal standards for States to issue the commercial learner's permit (CLP) (73 FR 19282). On...

  10. Driving styles among young novice drivers--the contribution of parental driving styles and personal characteristics.

    PubMed

    Miller, Gila; Taubman-Ben-Ari, Orit

    2010-03-01

    As part of the effort to ascertain why young drivers are more at risk for car crashes, attention has recently turned to the effects of family, including the intergenerational transmission of driving styles from parents to offspring. The current study sought to further understanding of the nature and aspects of the family influence with the help of Bowen's family systems theory. In Phase 1 of the prospective study, 130 young driving students completed questionnaires tapping personal and personality measures, and their parents completed driving-related instruments. In Phase 2, a year after the young drivers had obtained their driver's license, they were administered the same questionnaires their parents had previously completed. The results show significant correlations between the parents' driving styles and those of their offspring a year after licensure. Furthermore, differentiation of self and self-efficacy in newly acquired driving skills were found to moderate or heighten the similarity between the driving styles of parents and their offspring. For young drivers reporting anxiety in Phase 1, this was associated with a reported anxious driving style a year later. Among young female drivers, anxiety was also associated with a reckless and careless style. Higher sensation seeking was related to higher reckless driving among young male drivers. The findings are discussed in the context of adolescence and the role of the study variables in the development and intergenerational transmission of driving styles. In addition to its theoretical contribution to the realms of intergenerational transmission in general, and young drivers in particular, the study may have practical implications for both family therapy and the design of driving interventions. PMID:20159080

  11. How countries link REDD+ interventions to drivers in their readiness plans: implications for monitoring systems

    NASA Astrophysics Data System (ADS)

    Salvini, G.; Herold, M.; De Sy, V.; Kissinger, G.; Brockhaus, M.; Skutsch, M.

    2014-07-01

    Countries participating in the REDD+ scheme are in the readiness phase, designing policy interventions to address drivers of deforestation and forest degradation (DD). In order for REDD+ interventions to be effective, it is essential that they take into account the specific drivers that they aim to address. Moreover it is crucial to design systems that monitor the effectiveness of the planned interventions. In this article we provide a comprehensive and comparative assessment of interventions proposed by 43 REDD+ countries in 98 readiness documents. We summarize the types of interventions and assess if they are formulated referring to the drivers of DD that they are aiming to address. Based on this assessment we consider the implications for systems for monitoring effectiveness of proposed interventions. Most countries reviewed link proposed interventions to specific drivers of DD. The majority of the countries making this link have better driver data quality, in particularly those that present their data in ratio or ordinal terms. Proposed interventions focus not only on activities to reduce deforestation, but also on other forest related REDD+ activities such as sustainable forest management, which reduce forest degradation and enhance forest stocks. Moreover, driver-specific interventions often relate to drivers not only inside but also outside the forest sector. Hence we suggest that monitoring systems need to assess not only deforestation rates through remote sensing, but also degradation and other carbon stock changes within the forest, using more detailed ground level surveys and measurements. In addition, the performance of interventions outside the forest need to be monitored, even if the impacts of these cannot be linked to specific changes in forest carbon stock in specific locations.

  12. Driving styles among young novice drivers--the contribution of parental driving styles and personal characteristics.

    PubMed

    Miller, Gila; Taubman-Ben-Ari, Orit

    2010-03-01

    As part of the effort to ascertain why young drivers are more at risk for car crashes, attention has recently turned to the effects of family, including the intergenerational transmission of driving styles from parents to offspring. The current study sought to further understanding of the nature and aspects of the family influence with the help of Bowen's family systems theory. In Phase 1 of the prospective study, 130 young driving students completed questionnaires tapping personal and personality measures, and their parents completed driving-related instruments. In Phase 2, a year after the young drivers had obtained their driver's license, they were administered the same questionnaires their parents had previously completed. The results show significant correlations between the parents' driving styles and those of their offspring a year after licensure. Furthermore, differentiation of self and self-efficacy in newly acquired driving skills were found to moderate or heighten the similarity between the driving styles of parents and their offspring. For young drivers reporting anxiety in Phase 1, this was associated with a reported anxious driving style a year later. Among young female drivers, anxiety was also associated with a reckless and careless style. Higher sensation seeking was related to higher reckless driving among young male drivers. The findings are discussed in the context of adolescence and the role of the study variables in the development and intergenerational transmission of driving styles. In addition to its theoretical contribution to the realms of intergenerational transmission in general, and young drivers in particular, the study may have practical implications for both family therapy and the design of driving interventions.

  13. Prefrontal Cortex Activation and Young Driver Behaviour: A fNIRS Study

    PubMed Central

    Foy, Hannah J.; Runham, Patrick; Chapman, Peter

    2016-01-01

    Road traffic accidents consistently show a significant over-representation for young, novice and particularly male drivers. This research examines the prefrontal cortex activation of young drivers and the changes in activation associated with manipulations of mental workload and inhibitory control. It also considers the explanation that a lack of prefrontal cortex maturation is a contributing factor to the higher accident risk in this young driver population. The prefrontal cortex is associated with a number of factors including mental workload and inhibitory control, both of which are also related to road traffic accidents. This experiment used functional near infrared spectroscopy to measure prefrontal cortex activity during five simulated driving tasks: one following task and four overtaking tasks at varying traffic densities which aimed to dissociate workload and inhibitory control. Age, experience and gender were controlled for throughout the experiment. The results showed that younger drivers had reduced prefrontal cortex activity compared to older drivers. When both mental workload and inhibitory control increased prefrontal cortex activity also increased, however when inhibitory control alone increased there were no changes in activity. Along with an increase in activity during overtaking manoeuvres, these results suggest that prefrontal cortex activation is more indicative of workload in the current task. There were no differences in the number of overtakes completed by younger and older drivers but males overtook significantly more than females. We conclude that prefrontal cortex activity is associated with the mental workload required for overtaking. We additionally suggest that the reduced activation in younger drivers may be related to a lack of prefrontal maturation which could contribute to the increased crash risk seen in this population. PMID:27227990

  14. 77 FR 12361 - Qualification of Drivers; Exemption Applications; Vision

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-02-29

    ... Federal Motor Carrier Safety Administration Qualification of Drivers; Exemption Applications; Vision... Federal vision standard applicable to interstate truck and bus drivers and the reasons for the denials. FMCSA has statutory authority to exempt individuals from the vision requirement if the...

  15. 75 FR 22175 - Qualification of Drivers; Exemption Applications; Vision

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-04-27

    ... Federal Motor Carrier Safety Administration Qualification of Drivers; Exemption Applications; Vision... Federal vision standard applicable to interstate truck and bus drivers and the reasons for the denials. FMCSA has statutory authority to exempt individuals from the vision requirement if the...

  16. 76 FR 25763 - Qualification of Drivers; Exemption Applications; Vision

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-05

    ... Federal Motor Carrier Safety Administration Qualification of Drivers; Exemption Applications; Vision... Federal vision standard applicable to interstate truck and bus drivers and the reasons for the denials. FMCSA has statutory authority to exempt individuals from the vision requirement if the...

  17. 78 FR 76394 - Qualification of Drivers; Exemption Applications; Vision

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-12-17

    ... Federal Motor Carrier Safety Administration Qualification of Drivers; Exemption Applications; Vision... Federal vision standard applicable to interstate truck and bus drivers and the reasons for the denials. FMCSA has statutory authority to exempt individuals from the vision requirement if the...

  18. A UNIX device driver for a Translink II Transputer board

    SciTech Connect

    Wiley, J.C.

    1991-01-01

    A UNIX device driver for a TransLink II Transputer board is described. A complete listing of the code is presented. The device driver allows a transputer array to be used with the A/UX operating system.

  19. 78 FR 63295 - Qualification of Drivers; Exemption Applications; Diabetes Mellitus

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-10-23

    ... individuals for exemptions from the prohibition against persons with insulin- treated diabetes mellitus (ITDM... individual assessment of drivers with diabetes mellitus, and be consistent with the criteria described in... Federal Motor Carrier Safety Administration Qualification of Drivers; Exemption Applications;...

  20. 78 FR 63280 - Qualification of Drivers; Exemption Applications; Diabetes Mellitus

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-10-23

    ... exemptions from the prohibition against persons with insulin- treated diabetes mellitus (ITDM) operating... drivers with diabetes mellitus, and be consistent with the criteria described in section 4018 of the... Federal Motor Carrier Safety Administration Qualification of Drivers; Exemption Applications;...

  1. 78 FR 63298 - Qualification of Drivers; Exemption Applications; Diabetes Mellitus

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-10-23

    ... individuals for exemptions from the prohibition against persons with insulin- treated diabetes mellitus (ITDM... must provide for individual assessment of drivers with diabetes mellitus, and be consistent with the... Federal Motor Carrier Safety Administration Qualification of Drivers; Exemption Applications;...

  2. Calreticulin (CALR) mutation in myeloproliferative neoplasms (MPNs)

    PubMed Central

    Luo, Wenyi

    2015-01-01

    As a heterogeneous group of disease, myeloproliferative neoplasms (MPNs) have confused hematologists and hematopathologists with their protean clinical presentations and myriads of morphologies. A thought of classifying MPNs based on molecular alterations has gained popularity because there is increasing evidence that molecular or chromosomal alterations have a better correlation with clinical presentation, response to therapies, and prognosis than conventional morphological classification. This type of efforts has been facilitated by the advancement of molecular technologies. A significant number of gene mutations have been identified in MPNs with JAK2 and MPL being the major ones. However, a significant gap is present in that many cases of MPNs do not harbor any of these mutations. This gap is recently filled by the discovery of Calreticulin (CALR) mutation in MPNs without JAK2 or MPL mutation and since then, the clinical and molecular correlation in MPNs has become a hot research topic. There seems to be a fairly consistent correlation between CALR mutation and certain hematological parameters such as a high platelet count and a better prognosis in MPNs with CALR mutation. However, controversies are present regarding the risks of thrombosis, interactions of CALR with other gene mutation, the role of CALR in the pathogenesis, and the optimal treatment strategies. In addition, there are many questions remain to be answered, which all boiled down to the molecular mechanisms by which CALR causes or contributes to MPNs. Here, we summarized current published literatures on CALR mutations in MPNs with an emphasis on the clinical-molecular correlation. We also discussed the controversies and questions remain to be answered. PMID:27358884

  3. Cardiovascular Risk Factors of Taxi Drivers.

    PubMed

    Elshatarat, Rami Azmi; Burgel, Barbara J

    2016-06-01

    In the United States (U.S.), cardiovascular disease (CVD) is a major leading cause of death. Despite the high mortality rate related to CVD, little is known about CVD risk factors among urban taxi drivers in the U.S. A cross-sectional design was used to identify the predictors of high cardiovascular risk factors among taxi drivers. Convenience sampling method was used to recruit 130 taxi drivers. A structured questionnaire was used to obtain the data. The sample was male (94 %), age mean (45 ± 10.75) years, married (54 %), born outside of the USA (55 %), had some college or below (61.5 %), night drivers (50.8 %), and driving on average 9.7 years and 41 h/week. About 79 % of them were eligible for CVD prevention, and 35.4 % had high CVD risk factors (4-9 risk factors). A CVD high-risk profile had a significant relationship with the subjects who were ≥55 years old; had hypertension, diabetes, or hyperlipidemia; were drinking alcohol ≥2 times/week; and had insufficient physical activity. Subjects who worked as a taxi driver for more than 10 years (OR 4.37; 95 % CI 1.82, 10.50) and had mental exertion from cab driving >5 out of 10 (OR 2.63; 95 % CI 1.05, 6.57) were more likely to have a CVD high-risk profile. As a conclusion, system-level or worksite interventions include offering healthy food at taxi dispatching locations, creating a work culture of frequent walking breaks, and interventions focusing on smoking, physical activity, and weight management. Improving health insurance coverage for this group of workers is recommended. PMID:27151321

  4. 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.

  5. Leading to distraction: Driver distraction, lead car, and road environment.

    PubMed

    Kountouriotis, G K; Merat, N

    2016-04-01

    Driver distraction is strongly associated with crashes and near-misses, and despite the attention this topic has received in recent years, the effect of different types of distracting task on driving performance remains unclear. In the case of non-visual distractions, such as talking on the phone or other engaging verbal tasks that do not require a visual input, a common finding is reduced lateral variability in steering and gaze patterns where participants concentrate their gaze towards the centre of the road and their steering control is less variable. In the experiments presented here, we examined whether this finding is more pronounced in the presence of a lead car (which may provide a focus point for gaze) and whether the behaviour of the lead car has any influence on the driver's steering control. In addition, both visual and non-visual distraction tasks were used, and their effect on different road environments (straight and curved roadways) was assessed. Visual distraction was found to increase variability in both gaze patterns and steering control, non-visual distraction reduced gaze and steering variability in conditions without a lead car; in the conditions where a lead car was present there was no significant difference from baseline. The lateral behaviour of the lead car did