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  1. Fine-scale maps of recombination rates and hotspots in the mouse genome.

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    Brunschwig, Hadassa; Levi, Liat; Ben-David, Eyal; Williams, Robert W; Yakir, Benjamin; Shifman, Sagiv

    2012-07-01

    Recombination events are not uniformly distributed and often cluster in narrow regions known as recombination hotspots. Several studies using different approaches have dramatically advanced our understanding of recombination hotspot regulation. Population genetic data have been used to map and quantify hotspots in the human genome. Genetic variation in recombination rates and hotspots usage have been explored in human pedigrees, mouse intercrosses, and by sperm typing. These studies pointed to the central role of the PRDM9 gene in hotspot modulation. In this study, we used single nucleotide polymorphisms (SNPs) from whole-genome resequencing and genotyping studies of mouse inbred strains to estimate recombination rates across the mouse genome and identified 47,068 historical hotspots--an average of over 2477 per chromosome. We show by simulation that inbred mouse strains can be used to identify positions of historical hotspots. Recombination hotspots were found to be enriched for the predicted binding sequences for different alleles of the PRDM9 protein. Recombination rates were on average lower near transcription start sites (TSS). Comparing the inferred historical recombination hotspots with the recent genome-wide mapping of double-strand breaks (DSBs) in mouse sperm revealed a significant overlap, especially toward the telomeres. Our results suggest that inbred strains can be used to characterize and study the dynamics of historical recombination hotspots. They also strengthen previous findings on mouse recombination hotspots, and specifically the impact of sequence variants in Prdm9.

  2. Regulatory hotspots in the malaria parasite genome dictate transcriptional variation.

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    Joseph M Gonzales

    2008-09-01

    Full Text Available The determinants of transcriptional regulation in malaria parasites remain elusive. The presence of a well-characterized gene expression cascade shared by different Plasmodium falciparum strains could imply that transcriptional regulation and its natural variation do not contribute significantly to the evolution of parasite drug resistance. To clarify the role of transcriptional variation as a source of stain-specific diversity in the most deadly malaria species and to find genetic loci that dictate variations in gene expression, we examined genome-wide expression level polymorphisms (ELPs in a genetic cross between phenotypically distinct parasite clones. Significant variation in gene expression is observed through direct co-hybridizations of RNA from different P. falciparum clones. Nearly 18% of genes were regulated by a significant expression quantitative trait locus. The genetic determinants of most of these ELPs resided in hotspots that are physically distant from their targets. The most prominent regulatory locus, influencing 269 transcripts, coincided with a Chromosome 5 amplification event carrying the drug resistance gene, pfmdr1, and 13 other genes. Drug selection pressure in the Dd2 parental clone lineage led not only to a copy number change in the pfmdr1 gene but also to an increased copy number of putative neighboring regulatory factors that, in turn, broadly influence the transcriptional network. Previously unrecognized transcriptional variation, controlled by polymorphic regulatory genes and possibly master regulators within large copy number variants, contributes to sweeping phenotypic evolution in drug-resistant malaria parasites.

  3. ARG-walker: inference of individual specific strengths of meiotic recombination hotspots by population genomics analysis.

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    Chen, Hao; Yang, Peng; Guo, Jing; Kwoh, Chee Keong; Przytycka, Teresa M; Zheng, Jie

    2015-01-01

    Meiotic recombination hotspots play important roles in various aspects of genomics, but the underlying mechanisms for regulating the locations and strengths of recombination hotspots are not yet fully revealed. Most existing algorithms for estimating recombination rates from sequence polymorphism data can only output average recombination rates of a population, although there is evidence for the heterogeneity in recombination rates among individuals. For genome-wide association studies (GWAS) of recombination hotspots, an efficient algorithm that estimates the individualized strengths of recombination hotspots is highly desirable. In this work, we propose a novel graph mining algorithm named ARG-walker, based on random walks on ancestral recombination graphs (ARG), to estimate individual-specific recombination hotspot strengths. Extensive simulations demonstrate that ARG-walker is able to distinguish the hot allele of a recombination hotspot from the cold allele. Integrated with output of ARG-walker, we performed GWAS on the phased haplotype data of the 22 autosome chromosomes of the HapMap Asian population samples of Chinese and Japanese (JPT+CHB). Significant cis-regulatory signals have been detected, which is corroborated by the enrichment of the well-known 13-mer motif CCNCCNTNNCCNC of PRDM9 protein. Moreover, two new DNA motifs have been identified in the flanking regions of the significantly associated SNPs (single nucleotide polymorphisms), which are likely to be new cis-regulatory elements of meiotic recombination hotspots of the human genome. Our results on both simulated and real data suggest that ARG-walker is a promising new method for estimating the individual recombination variations. In the future, it could be used to uncover the mechanisms of recombination regulation and human diseases related with recombination hotspots.

  4. Drosophila duplication hotspots are associated with late-replicating regions of the genome.

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    Margarida Cardoso-Moreira

    2011-11-01

    Full Text Available Duplications play a significant role in both extremes of the phenotypic spectrum of newly arising mutations: they can have severe deleterious effects (e.g. duplications underlie a variety of diseases but can also be highly advantageous. The phenotypic potential of newly arisen duplications has stimulated wide interest in both the mutational and selective processes shaping these variants in the genome. Here we take advantage of the Drosophila simulans-Drosophila melanogaster genetic system to further our understanding of both processes. Regarding mutational processes, the study of two closely related species allows investigation of the potential existence of shared duplication hotspots, and the similarities and differences between the two genomes can be used to dissect its underlying causes. Regarding selection, the difference in the effective population size between the two species can be leveraged to ask questions about the strength of selection acting on different classes of duplications. In this study, we conducted a survey of duplication polymorphisms in 14 different lines of D. simulans using tiling microarrays and combined it with an analogous survey for the D. melanogaster genome. By integrating the two datasets, we identified duplication hotspots conserved between the two species. However, unlike the duplication hotspots identified in mammalian genomes, Drosophila duplication hotspots are not associated with sequences of high sequence identity capable of mediating non-allelic homologous recombination. Instead, Drosophila duplication hotspots are associated with late-replicating regions of the genome, suggesting a link between DNA replication and duplication rates. We also found evidence supporting a higher effectiveness of selection on duplications in D. simulans than in D. melanogaster. This is also true for duplications segregating at high frequency, where we find evidence in D. simulans that a sizeable fraction of these mutations is

  5. Identification of coding and non-coding mutational hotspots in cancer genomes.

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    Piraino, Scott W; Furney, Simon J

    2017-01-05

    The identification of mutations that play a causal role in tumour development, so called "driver" mutations, is of critical importance for understanding how cancers form and how they might be treated. Several large cancer sequencing projects have identified genes that are recurrently mutated in cancer patients, suggesting a role in tumourigenesis. While the landscape of coding drivers has been extensively studied and many of the most prominent driver genes are well characterised, comparatively less is known about the role of mutations in the non-coding regions of the genome in cancer development. The continuing fall in genome sequencing costs has resulted in a concomitant increase in the number of cancer whole genome sequences being produced, facilitating systematic interrogation of both the coding and non-coding regions of cancer genomes. To examine the mutational landscapes of tumour genomes we have developed a novel method to identify mutational hotspots in tumour genomes using both mutational data and information on evolutionary conservation. We have applied our methodology to over 1300 whole cancer genomes and show that it identifies prominent coding and non-coding regions that are known or highly suspected to play a role in cancer. Importantly, we applied our method to the entire genome, rather than relying on predefined annotations (e.g. promoter regions) and we highlight recurrently mutated regions that may have resulted from increased exposure to mutational processes rather than selection, some of which have been identified previously as targets of selection. Finally, we implicate several pan-cancer and cancer-specific candidate non-coding regions, which could be involved in tumourigenesis. We have developed a framework to identify mutational hotspots in cancer genomes, which is applicable to the entire genome. This framework identifies known and novel coding and non-coding mutional hotspots and can be used to differentiate candidate driver regions from

  6. Genomic features shaping the landscape of meiotic double-strand-break hotspots in maize.

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    He, Yan; Wang, Minghui; Dukowic-Schulze, Stefanie; Zhou, Adele; Tiang, Choon-Lin; Shilo, Shay; Sidhu, Gaganpreet K; Eichten, Steven; Bradbury, Peter; Springer, Nathan M; Buckler, Edward S; Levy, Avraham A; Sun, Qi; Pillardy, Jaroslaw; Kianian, Penny M A; Kianian, Shahryar F; Chen, Changbin; Pawlowski, Wojciech P

    2017-11-14

    Meiotic recombination is the most important source of genetic variation in higher eukaryotes. It is initiated by formation of double-strand breaks (DSBs) in chromosomal DNA in early meiotic prophase. The DSBs are subsequently repaired, resulting in crossovers (COs) and noncrossovers (NCOs). Recombination events are not distributed evenly along chromosomes but cluster at recombination hotspots. How specific sites become hotspots is poorly understood. Studies in yeast and mammals linked initiation of meiotic recombination to active chromatin features present upstream from genes, such as absence of nucleosomes and presence of trimethylation of lysine 4 in histone H3 (H3K4me3). Core recombination components are conserved among eukaryotes, but it is unclear whether this conservation results in universal characteristics of recombination landscapes shared by a wide range of species. To address this question, we mapped meiotic DSBs in maize, a higher eukaryote with a large genome that is rich in repetitive DNA. We found DSBs in maize to be frequent in all chromosome regions, including sites lacking COs, such as centromeres and pericentromeric regions. Furthermore, most DSBs are formed in repetitive DNA, predominantly Gypsy retrotransposons, and only one-quarter of DSB hotspots are near genes. Genic and nongenic hotspots differ in several characteristics, and only genic DSBs contribute to crossover formation. Maize hotspots overlap regions of low nucleosome occupancy but show only limited association with H3K4me3 sites. Overall, maize DSB hotspots exhibit distribution patterns and characteristics not reported previously in other species. Understanding recombination patterns in maize will shed light on mechanisms affecting dynamics of the plant genome.

  7. Genome-wide signatures of 'rearrangement hotspots' within segmental duplications in humans.

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    Mohammed Uddin

    Full Text Available The primary objective of this study was to create a genome-wide high resolution map (i.e., >100 bp of 'rearrangement hotspots' which can facilitate the identification of regions capable of mediating de novo deletions or duplications in humans. A hierarchical method was employed to fragment segmental duplications (SDs into multiple smaller SD units. Combining an end space free pairwise alignment algorithm with a 'seed and extend' approach, we have exhaustively searched 409 million alignments to detect complex structural rearrangements within the reference-guided assembly of the NA18507 human genome (18× coverage, including the previously identified novel 4.8 Mb sequence from de novo assembly within this genome. We have identified 1,963 rearrangement hotspots within SDs which encompass 166 genes and display an enrichment of duplicated gene nucleotide variants (DNVs. These regions are correlated with increased non-allelic homologous recombination (NAHR event frequency which presumably represents the origin of copy number variations (CNVs and pathogenic duplications/deletions. Analysis revealed that 20% of the detected hotspots are clustered within the proximal and distal SD breakpoints flanked by the pathogenic deletions/duplications that have been mapped for 24 NAHR-mediated genomic disorders. FISH Validation of selected complex regions revealed 94% concordance with in silico localization of the highly homologous derivatives. Other results from this study indicate that intra-chromosomal recombination is enhanced in genic compared with agenic duplicated regions, and that gene desert regions comprising SDs may represent reservoirs for creation of novel genes. The generation of genome-wide signatures of 'rearrangement hotspots', which likely serve as templates for NAHR, may provide a powerful approach towards understanding the underlying mutational mechanism(s for development of constitutional and acquired diseases.

  8. Seeds as emerging hotspot for maintenance of genome stability

    Czech Academy of Sciences Publication Activity Database

    Diaz, Mariana; Pečinka, Aleš

    2017-01-01

    Roč. 82, č. 5 (2017), s. 467-470 ISSN 0011-4545 Institutional support: RVO:61389030 Keywords : Chromatin * Chromosome * DNA damage repair * Genome stability * Seed * Structural maintenance of chromosome Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Genetics and heredity (medical genetics to be 3) Impact factor: 0.913, year: 2016

  9. Distribution of recombination hotspots in the human genome--a comparison of computer simulations with real data.

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    Dorota Mackiewicz

    Full Text Available Recombination is the main cause of genetic diversity. Thus, errors in this process can lead to chromosomal abnormalities. Recombination events are confined to narrow chromosome regions called hotspots in which characteristic DNA motifs are found. Genomic analyses have shown that both recombination hotspots and DNA motifs are distributed unevenly along human chromosomes and are much more frequent in the subtelomeric regions of chromosomes than in their central parts. Clusters of motifs roughly follow the distribution of recombination hotspots whereas single motifs show a negative correlation with the hotspot distribution. To model the phenomena related to recombination, we carried out computer Monte Carlo simulations of genome evolution. Computer simulations generated uneven distribution of hotspots with their domination in the subtelomeric regions of chromosomes. They also revealed that purifying selection eliminating defective alleles is strong enough to cause such hotspot distribution. After sufficiently long time of simulations, the structure of chromosomes reached a dynamic equilibrium, in which number and global distribution of both hotspots and defective alleles remained statistically unchanged, while their precise positions were shifted. This resembles the dynamic structure of human and chimpanzee genomes, where hotspots change their exact locations but the global distributions of recombination events are very similar.

  10. Distribution of Recombination Hotspots in the Human Genome – A Comparison of Computer Simulations with Real Data

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    Mackiewicz, Dorota; de Oliveira, Paulo Murilo Castro; Moss de Oliveira, Suzana; Cebrat, Stanisław

    2013-01-01

    Recombination is the main cause of genetic diversity. Thus, errors in this process can lead to chromosomal abnormalities. Recombination events are confined to narrow chromosome regions called hotspots in which characteristic DNA motifs are found. Genomic analyses have shown that both recombination hotspots and DNA motifs are distributed unevenly along human chromosomes and are much more frequent in the subtelomeric regions of chromosomes than in their central parts. Clusters of motifs roughly follow the distribution of recombination hotspots whereas single motifs show a negative correlation with the hotspot distribution. To model the phenomena related to recombination, we carried out computer Monte Carlo simulations of genome evolution. Computer simulations generated uneven distribution of hotspots with their domination in the subtelomeric regions of chromosomes. They also revealed that purifying selection eliminating defective alleles is strong enough to cause such hotspot distribution. After sufficiently long time of simulations, the structure of chromosomes reached a dynamic equilibrium, in which number and global distribution of both hotspots and defective alleles remained statistically unchanged, while their precise positions were shifted. This resembles the dynamic structure of human and chimpanzee genomes, where hotspots change their exact locations but the global distributions of recombination events are very similar. PMID:23776462

  11. Genome Mutational and Transcriptional Hotspots Are Traps for Duplicated Genes and Sources of Adaptations.

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    Fares, Mario A; Sabater-Muñoz, Beatriz; Toft, Christina

    2017-05-01

    Gene duplication generates new genetic material, which has been shown to lead to major innovations in unicellular and multicellular organisms. A whole-genome duplication occurred in the ancestor of Saccharomyces yeast species but 92% of duplicates returned to single-copy genes shortly after duplication. The persisting duplicated genes in Saccharomyces led to the origin of major metabolic innovations, which have been the source of the unique biotechnological capabilities in the Baker's yeast Saccharomyces cerevisiae. What factors have determined the fate of duplicated genes remains unknown. Here, we report the first demonstration that the local genome mutation and transcription rates determine the fate of duplicates. We show, for the first time, a preferential location of duplicated genes in the mutational and transcriptional hotspots of S. cerevisiae genome. The mechanism of duplication matters, with whole-genome duplicates exhibiting different preservation trends compared to small-scale duplicates. Genome mutational and transcriptional hotspots are rich in duplicates with large repetitive promoter elements. Saccharomyces cerevisiae shows more tolerance to deleterious mutations in duplicates with repetitive promoter elements, which in turn exhibit higher transcriptional plasticity against environmental perturbations. Our data demonstrate that the genome traps duplicates through the accelerated regulatory and functional divergence of their gene copies providing a source of novel adaptations in yeast. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  12. The Impact of Recombination Hotspots on Genome Evolution of a Fungal Plant Pathogen.

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    Croll, Daniel; Lendenmann, Mark H; Stewart, Ethan; McDonald, Bruce A

    2015-11-01

    Recombination has an impact on genome evolution by maintaining chromosomal integrity, affecting the efficacy of selection, and increasing genetic variability in populations. Recombination rates are a key determinant of the coevolutionary dynamics between hosts and their pathogens. Historic recombination events created devastating new pathogens, but the impact of ongoing recombination in sexual pathogens is poorly understood. Many fungal pathogens of plants undergo regular sexual cycles, and sex is considered to be a major factor contributing to virulence. We generated a recombination map at kilobase-scale resolution for the haploid plant pathogenic fungus Zymoseptoria tritici. To account for intraspecific variation in recombination rates, we constructed genetic maps from two independent crosses. We localized a total of 10,287 crossover events in 441 progeny and found that recombination rates were highly heterogeneous within and among chromosomes. Recombination rates on large chromosomes were inversely correlated with chromosome length. Short accessory chromosomes often lacked evidence for crossovers between parental chromosomes. Recombination was concentrated in narrow hotspots that were preferentially located close to telomeres. Hotspots were only partially conserved between the two crosses, suggesting that hotspots are short-lived and may vary according to genomic background. Genes located in hotspot regions were enriched in genes encoding secreted proteins. Population resequencing showed that chromosomal regions with high recombination rates were strongly correlated with regions of low linkage disequilibrium. Hence, genes in pathogen recombination hotspots are likely to evolve faster in natural populations and may represent a greater threat to the host. Copyright © 2015 by the Genetics Society of America.

  13. The red queen model of recombination hotspots evolution in the light of archaic and modern human genomes.

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    Yann Lesecque

    2014-11-01

    Full Text Available Recombination is an essential process in eukaryotes, which increases diversity by disrupting genetic linkage between loci and ensures the proper segregation of chromosomes during meiosis. In the human genome, recombination events are clustered in hotspots, whose location is determined by the PRDM9 protein. There is evidence that the location of hotspots evolves rapidly, as a consequence of changes in PRDM9 DNA-binding domain. However, the reasons for these changes and the rate at which they occur are not known. In this study, we investigated the evolution of human hotspot loci and of PRDM9 target motifs, both in modern and archaic human lineages (Denisovan to quantify the dynamic of hotspot turnover during the recent period of human evolution. We show that present-day human hotspots are young: they have been active only during the last 10% of the time since the divergence from chimpanzee, starting to be operating shortly before the split between Denisovans and modern humans. Surprisingly, however, our analyses indicate that Denisovan recombination hotspots did not overlap with modern human ones, despite sharing similar PRDM9 target motifs. We further show that high-affinity PRDM9 target motifs are subject to a strong self-destructive drive, known as biased gene conversion (BGC, which should lead to the loss of the majority of them in the next 3 MYR. This depletion of PRDM9 genomic targets is expected to decrease fitness, and thereby to favor new PRDM9 alleles binding different motifs. Our refined estimates of the age and life expectancy of human hotspots provide empirical evidence in support of the Red Queen hypothesis of recombination hotspots evolution.

  14. The red queen model of recombination hotspots evolution in the light of archaic and modern human genomes.

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    Lesecque, Yann; Glémin, Sylvain; Lartillot, Nicolas; Mouchiroud, Dominique; Duret, Laurent

    2014-11-01

    Recombination is an essential process in eukaryotes, which increases diversity by disrupting genetic linkage between loci and ensures the proper segregation of chromosomes during meiosis. In the human genome, recombination events are clustered in hotspots, whose location is determined by the PRDM9 protein. There is evidence that the location of hotspots evolves rapidly, as a consequence of changes in PRDM9 DNA-binding domain. However, the reasons for these changes and the rate at which they occur are not known. In this study, we investigated the evolution of human hotspot loci and of PRDM9 target motifs, both in modern and archaic human lineages (Denisovan) to quantify the dynamic of hotspot turnover during the recent period of human evolution. We show that present-day human hotspots are young: they have been active only during the last 10% of the time since the divergence from chimpanzee, starting to be operating shortly before the split between Denisovans and modern humans. Surprisingly, however, our analyses indicate that Denisovan recombination hotspots did not overlap with modern human ones, despite sharing similar PRDM9 target motifs. We further show that high-affinity PRDM9 target motifs are subject to a strong self-destructive drive, known as biased gene conversion (BGC), which should lead to the loss of the majority of them in the next 3 MYR. This depletion of PRDM9 genomic targets is expected to decrease fitness, and thereby to favor new PRDM9 alleles binding different motifs. Our refined estimates of the age and life expectancy of human hotspots provide empirical evidence in support of the Red Queen hypothesis of recombination hotspots evolution.

  15. Platform comparison for evaluation of ALK protein immunohistochemical expression, genomic copy number and hotspot mutation status in neuroblastomas.

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    Benedict Yan

    Full Text Available ALK is an established causative oncogenic driver in neuroblastoma, and is likely to emerge as a routine biomarker in neuroblastoma diagnostics. At present, the optimal strategy for clinical diagnostic evaluation of ALK protein, genomic and hotspot mutation status is not well-studied. We evaluated ALK immunohistochemical (IHC protein expression using three different antibodies (ALK1, 5A4 and D5F3 clones, ALK genomic status using single-color chromogenic in situ hybridization (CISH, and ALK hotspot mutation status using conventional Sanger sequencing and a next-generation sequencing platform (Ion Torrent Personal Genome Machine (IT-PGM, in archival formalin-fixed, paraffin-embedded neuroblastoma samples. We found a significant difference in IHC results using the three different antibodies, with the highest percentage of positive cases seen on D5F3 immunohistochemistry. Correlation with ALK genomic and hotspot mutational status revealed that the majority of D5F3 ALK-positive cases did not possess either ALK genomic amplification or hotspot mutations. Comparison of sequencing platforms showed a perfect correlation between conventional Sanger and IT-PGM sequencing. Our findings suggest that D5F3 immunohistochemistry, single-color CISH and IT-PGM sequencing are suitable assays for evaluation of ALK status in future neuroblastoma clinical trials.

  16. LDSplitDB: a database for studies of meiotic recombination hotspots in MHC using human genomic data.

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    Guo, Jing; Chen, Hao; Yang, Peng; Lee, Yew Ti; Wu, Min; Przytycka, Teresa M; Kwoh, Chee Keong; Zheng, Jie

    2018-04-20

    Meiotic recombination happens during the process of meiosis when chromosomes inherited from two parents exchange genetic materials to generate chromosomes in the gamete cells. The recombination events tend to occur in narrow genomic regions called recombination hotspots. Its dysregulation could lead to serious human diseases such as birth defects. Although the regulatory mechanism of recombination events is still unclear, DNA sequence polymorphisms have been found to play crucial roles in the regulation of recombination hotspots. To facilitate the studies of the underlying mechanism, we developed a database named LDSplitDB which provides an integrative and interactive data mining and visualization platform for the genome-wide association studies of recombination hotspots. It contains the pre-computed association maps of the major histocompatibility complex (MHC) region in the 1000 Genomes Project and the HapMap Phase III datasets, and a genome-scale study of the European population from the HapMap Phase II dataset. Besides the recombination profiles, related data of genes, SNPs and different types of epigenetic modifications, which could be associated with meiotic recombination, are provided for comprehensive analysis. To meet the computational requirement of the rapidly increasing population genomics data, we prepared a lookup table of 400 haplotypes for recombination rate estimation using the well-known LDhat algorithm which includes all possible two-locus haplotype configurations. To the best of our knowledge, LDSplitDB is the first large-scale database for the association analysis of human recombination hotspots with DNA sequence polymorphisms. It provides valuable resources for the discovery of the mechanism of meiotic recombination hotspots. The information about MHC in this database could help understand the roles of recombination in human immune system. DATABASE URL: http://histone.scse.ntu.edu.sg/LDSplitDB.

  17. Genomic analysis and selected molecular pathways in rare cancers

    International Nuclear Information System (INIS)

    Liu, Stephen V; Lenkiewicz, Elizabeth; Evers, Lisa; Holley, Tara; Kiefer, Jeffrey; Demeure, Michael J; Ramanathan, Ramesh K; Von Hoff, Daniel D; Barrett, Michael T; Ruiz, Christian; Glatz, Katharina; Bubendorf, Lukas; Eng, Cathy

    2012-01-01

    It is widely accepted that many cancers arise as a result of an acquired genomic instability and the subsequent evolution of tumor cells with variable patterns of selected and background aberrations. The presence and behaviors of distinct neoplastic cell populations within a patient's tumor may underlie multiple clinical phenotypes in cancers. A goal of many current cancer genome studies is the identification of recurring selected driver events that can be advanced for the development of personalized therapies. Unfortunately, in the majority of rare tumors, this type of analysis can be particularly challenging. Large series of specimens for analysis are simply not available, allowing recurring patterns to remain hidden. In this paper, we highlight the use of DNA content-based flow sorting to identify and isolate DNA-diploid and DNA-aneuploid populations from tumor biopsies as a strategy to comprehensively study the genomic composition and behaviors of individual cancers in a series of rare solid tumors: intrahepatic cholangiocarcinoma, anal carcinoma, adrenal leiomyosarcoma, and pancreatic neuroendocrine tumors. We propose that the identification of highly selected genomic events in distinct tumor populations within each tumor can identify candidate driver events that can facilitate the development of novel, personalized treatment strategies for patients with cancer. (paper)

  18. Quantile-Based Permutation Thresholds for Quantitative Trait Loci Hotspots

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    Neto, Elias Chaibub; Keller, Mark P.; Broman, Andrew F.; Attie, Alan D.; Jansen, Ritsert C.; Broman, Karl W.; Yandell, Brian S.; Borevitz, J.

    Quantitative trait loci (QTL) hotspots (genomic locations affecting many traits) are a common feature in genetical genomics studies and are biologically interesting since they may harbor critical regulators. Therefore, statistical procedures to assess the significance of hotspots are of key

  19. Genomic hotspots for adaptation: the population genetics of Müllerian mimicry in Heliconius erato.

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    Brian A Counterman

    2010-02-01

    Full Text Available Wing pattern evolution in Heliconius butterflies provides some of the most striking examples of adaptation by natural selection. The genes controlling pattern variation are classic examples of Mendelian loci of large effect, where allelic variation causes large and discrete phenotypic changes and is responsible for both convergent and highly divergent wing pattern evolution across the genus. We characterize nucleotide variation, genotype-by-phenotype associations, linkage disequilibrium (LD, and candidate gene expression patterns across two unlinked genomic intervals that control yellow and red wing pattern variation among mimetic forms of Heliconius erato. Despite very strong natural selection on color pattern, we see neither a strong reduction in genetic diversity nor evidence for extended LD across either patterning interval. This observation highlights the extent that recombination can erase the signature of selection in natural populations and is consistent with the hypothesis that either the adaptive radiation or the alleles controlling it are quite old. However, across both patterning intervals we identified SNPs clustered in several coding regions that were strongly associated with color pattern phenotype. Interestingly, coding regions with associated SNPs were widely separated, suggesting that color pattern alleles may be composed of multiple functional sites, conforming to previous descriptions of these loci as "supergenes." Examination of gene expression levels of genes flanking these regions in both H. erato and its co-mimic, H. melpomene, implicate a gene with high sequence similarity to a kinesin as playing a key role in modulating pattern and provides convincing evidence for parallel changes in gene regulation across co-mimetic lineages. The complex genetic architecture at these color pattern loci stands in marked contrast to the single casual mutations often identified in genetic studies of adaptation, but may be more indicative

  20. The substantial first impact of bottom fishing on rare biodiversity hotspots: a dilemma for evidence-based conservation.

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    Cook, Robert; Fariñas-Franco, Jose M; Gell, Fiona R; Holt, Rohan H F; Holt, Terry; Lindenbaum, Charles; Porter, Joanne S; Seed, Ray; Skates, Lucie R; Stringell, Thomas B; Sanderson, William G

    2013-01-01

    This study describes the impact of the first passage of two types of bottom-towed fishing gear on rare protected shellfish-reefs formed by the horse mussel Modiolus modiolus (L.). One of the study sites was trawled and the other was scallop-dredged. Divers collected HD video imagery of epifauna from quadrats at the two study sites and directed infaunal samples from one site. The total number of epifaunal organisms was significantly reduced following a single pass of a trawl (90%) or scallop dredge (59%), as was the diversity of the associated community and the total number of M. modiolus at the trawled site. At both sites declines in anthozoans, hydrozoans, bivalves, echinoderms and ascidians accounted for most of the change. A year later, no recovery was evident at the trawled site and significantly fewer infaunal taxa (polychaetes, malacostracans, bivalves and ophuroids) were recorded in the trawl track. The severity of the two types of impact reflected the undisturbed status of the habitats compared to previous studies. As a 'priority habitat' the nature of the impacts described on M. modiolus communities are important to the development of conservation management policy and indicators of condition in Marine Protected Areas (EU Habitats Directive) as well as indicators of 'Good Environmental Status' under the European Union Marine Strategy Framework Directive. Conservation managers are under pressure to support decisions with good quality evidence. Elsewhere, indirect studies have shown declines of M. modiolus biogenic communities in fishing grounds. However, given the protected status of the rare habitat, premeditated demonstration of direct impact is unethical or illegal in Marine Protected Areas. This study therefore provides a unique opportunity to investigate the impact from fishing gear whilst at the same time reflecting on the dilemma of evidence-based conservation management.

  1. The substantial first impact of bottom fishing on rare biodiversity hotspots: a dilemma for evidence-based conservation.

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    Robert Cook

    Full Text Available This study describes the impact of the first passage of two types of bottom-towed fishing gear on rare protected shellfish-reefs formed by the horse mussel Modiolus modiolus (L.. One of the study sites was trawled and the other was scallop-dredged. Divers collected HD video imagery of epifauna from quadrats at the two study sites and directed infaunal samples from one site. The total number of epifaunal organisms was significantly reduced following a single pass of a trawl (90% or scallop dredge (59%, as was the diversity of the associated community and the total number of M. modiolus at the trawled site. At both sites declines in anthozoans, hydrozoans, bivalves, echinoderms and ascidians accounted for most of the change. A year later, no recovery was evident at the trawled site and significantly fewer infaunal taxa (polychaetes, malacostracans, bivalves and ophuroids were recorded in the trawl track. The severity of the two types of impact reflected the undisturbed status of the habitats compared to previous studies. As a 'priority habitat' the nature of the impacts described on M. modiolus communities are important to the development of conservation management policy and indicators of condition in Marine Protected Areas (EU Habitats Directive as well as indicators of 'Good Environmental Status' under the European Union Marine Strategy Framework Directive. Conservation managers are under pressure to support decisions with good quality evidence. Elsewhere, indirect studies have shown declines of M. modiolus biogenic communities in fishing grounds. However, given the protected status of the rare habitat, premeditated demonstration of direct impact is unethical or illegal in Marine Protected Areas. This study therefore provides a unique opportunity to investigate the impact from fishing gear whilst at the same time reflecting on the dilemma of evidence-based conservation management.

  2. Performance of genotype imputation for low frequency and rare variants from the 1000 genomes.

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    Zheng, Hou-Feng; Rong, Jing-Jing; Liu, Ming; Han, Fang; Zhang, Xing-Wei; Richards, J Brent; Wang, Li

    2015-01-01

    Genotype imputation is now routinely applied in genome-wide association studies (GWAS) and meta-analyses. However, most of the imputations have been run using HapMap samples as reference, imputation of low frequency and rare variants (minor allele frequency (MAF) 1000 Genomes panel) are available to facilitate imputation of these variants. Therefore, in order to estimate the performance of low frequency and rare variants imputation, we imputed 153 individuals, each of whom had 3 different genotype array data including 317k, 610k and 1 million SNPs, to three different reference panels: the 1000 Genomes pilot March 2010 release (1KGpilot), the 1000 Genomes interim August 2010 release (1KGinterim), and the 1000 Genomes phase1 November 2010 and May 2011 release (1KGphase1) by using IMPUTE version 2. The differences between these three releases of the 1000 Genomes data are the sample size, ancestry diversity, number of variants and their frequency spectrum. We found that both reference panel and GWAS chip density affect the imputation of low frequency and rare variants. 1KGphase1 outperformed the other 2 panels, at higher concordance rate, higher proportion of well-imputed variants (info>0.4) and higher mean info score in each MAF bin. Similarly, 1M chip array outperformed 610K and 317K. However for very rare variants (MAF ≤ 0.3%), only 0-1% of the variants were well imputed. We conclude that the imputation of low frequency and rare variants improves with larger reference panels and higher density of genome-wide genotyping arrays. Yet, despite a large reference panel size and dense genotyping density, very rare variants remain difficult to impute.

  3. Rare and common regulatory variation in population-scale sequenced human genomes.

    Directory of Open Access Journals (Sweden)

    Stephen B Montgomery

    2011-07-01

    Full Text Available Population-scale genome sequencing allows the characterization of functional effects of a broad spectrum of genetic variants underlying human phenotypic variation. Here, we investigate the influence of rare and common genetic variants on gene expression patterns, using variants identified from sequencing data from the 1000 genomes project in an African and European population sample and gene expression data from lymphoblastoid cell lines. We detect comparable numbers of expression quantitative trait loci (eQTLs when compared to genotypes obtained from HapMap 3, but as many as 80% of the top expression quantitative trait variants (eQTVs discovered from 1000 genomes data are novel. The properties of the newly discovered variants suggest that mapping common causal regulatory variants is challenging even with full resequencing data; however, we observe significant enrichment of regulatory effects in splice-site and nonsense variants. Using RNA sequencing data, we show that 46.2% of nonsynonymous variants are differentially expressed in at least one individual in our sample, creating widespread potential for interactions between functional protein-coding and regulatory variants. We also use allele-specific expression to identify putative rare causal regulatory variants. Furthermore, we demonstrate that outlier expression values can be due to rare variant effects, and we approximate the number of such effects harboured in an individual by effect size. Our results demonstrate that integration of genomic and RNA sequencing analyses allows for the joint assessment of genome sequence and genome function.

  4. Functional annotation of rare gene aberration drivers of pancreatic cancer | Office of Cancer Genomics

    Science.gov (United States)

    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).

  5. Investigation of common, low-frequency and rare genome-wide variation in anorexia nervosa

    Science.gov (United States)

    Huckins, L M; Hatzikotoulas, K; Southam, L; Thornton, L M; Steinberg, J; Aguilera-McKay, F; Treasure, J; Schmidt, U; Gunasinghe, C; Romero, A; Curtis, C; Rhodes, D; Moens, J; Kalsi, G; Dempster, D; Leung, R; Keohane, A; Burghardt, R; Ehrlich, S; Hebebrand, J; Hinney, A; Ludolph, A; Walton, E; Deloukas, P; Hofman, A; Palotie, A; Palta, P; van Rooij, F J A; Stirrups, K; Adan, R; Boni, C; Cone, R; Dedoussis, G; van Furth, E; Gonidakis, F; Gorwood, P; Hudson, J; Kaprio, J; Kas, M; Keski-Rahonen, A; Kiezebrink, K; Knudsen, G-P; Slof-Op 't Landt, M C T; Maj, M; Monteleone, A M; Monteleone, P; Raevuori, A H; Reichborn-Kjennerud, T; Tozzi, F; Tsitsika, A; van Elburg, A; Adan, R A H; Alfredsson, L; Ando, T; Andreassen, O A; Aschauer, H; Baker, J H; Barrett, J C; Bencko, V; Bergen, A W; Berrettini, W H; Birgegard, A; Boni, C; Boraska Perica, V; Brandt, H; Breen, G; Bulik, C M; Carlberg, L; Cassina, M; Cichon, S; Clementi, M; Cohen-Woods, S; Coleman, J; Cone, R D; Courtet, P; Crawford, S; Crow, S; Crowley, J; Danner, U N; Davis, O S P; de Zwaan, M; Dedoussis, G; Degortes, D; DeSocio, J E; Dick, D M; Dikeos, D; Dina, C; Ding, B; Dmitrzak-Weglarz, M; Docampo, E; Duncan, L; Egberts, K; Ehrlich, S; Escaramís, G; Esko, T; Espeseth, T; Estivill, X; Favaro, A; Fernández-Aranda, F; Fichter, M M; Finan, C; Fischer, K; Floyd, J A B; Foretova, L; Forzan, M; Franklin, C S; Gallinger, S; Gambaro, G; Gaspar, H A; Giegling, I; Gonidakis, F; Gorwood, P; Gratacos, M; Guillaume, S; Guo, Y; Hakonarson, H; Halmi, K A; Hatzikotoulas, K; Hauser, J; Hebebrand, J; Helder, S; Herms, S; Herpertz-Dahlmann, B; Herzog, W; Hilliard, C E; Hinney, A; Hübel, C; Huckins, L M; Hudson, J I; Huemer, J; Inoko, H; Janout, V; Jiménez-Murcia, S; Johnson, C; Julià, A; Juréus, A; Kalsi, G; Kaminska, D; Kaplan, A S; Kaprio, J; Karhunen, L; Karwautz, A; Kas, M J H; Kaye, W; Kennedy, J L; Keski-Rahkonen, A; Kiezebrink, K; Klareskog, L; Klump, K L; Knudsen, G P S; Koeleman, B P C; Koubek, D; La Via, M C; Landén, M; Le Hellard, S; Levitan, R D; Li, D; Lichtenstein, P; Lilenfeld, L; Lissowska, J; Lundervold, A; Magistretti, P; Maj, M; Mannik, K; Marsal, S; Martin, N; Mattingsdal, M; McDevitt, S; McGuffin, P; Merl, E; Metspalu, A; Meulenbelt, I; Micali, N; Mitchell, J; Mitchell, K; Monteleone, P; Monteleone, A M; Mortensen, P; Munn-Chernoff, M A; Navratilova, M; Nilsson, I; Norring, C; Ntalla, I; Ophoff, R A; O'Toole, J K; Palotie, A; Pante, J; Papezova, H; Pinto, D; Rabionet, R; Raevuori, A; Rajewski, A; Ramoz, N; Rayner, N W; Reichborn-Kjennerud, T; Ripatti, S; Roberts, M; Rotondo, A; Rujescu, D; Rybakowski, F; Santonastaso, P; Scherag, A; Scherer, S W; Schmidt, U; Schork, N J; Schosser, A; Slachtova, L; Sladek, R; Slagboom, P E; Slof-Op 't Landt, M C T; Slopien, A; Soranzo, N; Southam, L; Steen, V M; Strengman, E; Strober, M; Sullivan, P F; Szatkiewicz, J P; Szeszenia-Dabrowska, N; Tachmazidou, I; Tenconi, E; Thornton, L M; Tortorella, A; Tozzi, F; Treasure, J; Tsitsika, A; Tziouvas, K; van Elburg, A A; van Furth, E F; Wagner, G; Walton, E; Watson, H; Wichmann, H-E; Widen, E; Woodside, D B; Yanovski, J; Yao, S; Yilmaz, Z; Zeggini, E; Zerwas, S; Zipfel, S; Collier, D A; Sullivan, P F; Breen, G; Bulik, C M; Zeggini, E

    2018-01-01

    Anorexia nervosa (AN) is a complex neuropsychiatric disorder presenting with dangerously low body weight, and a deep and persistent fear of gaining weight. To date, only one genome-wide significant locus associated with AN has been identified. We performed an exome-chip based genome-wide association studies (GWAS) in 2158 cases from nine populations of European origin and 15 485 ancestrally matched controls. Unlike previous studies, this GWAS also probed association in low-frequency and rare variants. Sixteen independent variants were taken forward for in silico and de novo replication (11 common and 5 rare). No findings reached genome-wide significance. Two notable common variants were identified: rs10791286, an intronic variant in OPCML (P=9.89 × 10−6), and rs7700147, an intergenic variant (P=2.93 × 10−5). No low-frequency variant associations were identified at genome-wide significance, although the study was well-powered to detect low-frequency variants with large effect sizes, suggesting that there may be no AN loci in this genomic search space with large effect sizes. PMID:29155802

  6. Hotspot advance speed - hotspot size/core-hotspot distance relation ...

    African Journals Online (AJOL)

    We examined the evolution of extragalactic radio sources using the observed corehotspot distance and hotspot size. Analysis indicates a fairly strong positive correlation in the ratio of core-hotspot distance to hotspot size between that of the approaching arm and the receding arm with a correlation coefficient of r ~ 0.7.

  7. Inclusion and exclusion in the globalisation of genomics; the case of rare genetic disease in Brazil

    Science.gov (United States)

    Gibbon, Sahra

    2018-01-01

    ABSTRACT Within the context of a globalising agenda for genetic research where ‘global health’ is increasingly seen as necessarily informed by and having to account for genomics, the focus on rare genetic diseases is becoming prominent. Drawing from ethnographic research carried out separately by both authors in Brazil, this paper examines how an emerging focus on two different arenas of rare genetic disease, cancer genetics and a class of degenerative neurological diseases known as Ataxias, is subject to and a product of the dynamics of inclusion and exclusion as this concerns participation in research and access to health care. It examines how in these different cases ‘rarenesss’ has been diversely situated and differently politicised and how clinicians, patients and their families grapple with the slippery boundaries between research, rights to health and the limits of care, therapy or prevention. It illustrates how attention to rare genetic disease in Brazil emerges at the intersection of a particular history of genetic research and public health infrastructure, densely complicated feedback loops between clinical care and research, patient mobilisation around the ‘judicialisation’ of health and recent state legislation regarding rare disease in Brazil. It highlights the relevance of local configurations in the way rare genetic disease is being made relevant for and by different communities. PMID:29533091

  8. Inclusion and exclusion in the globalisation of genomics; the case of rare genetic disease in Brazil.

    Science.gov (United States)

    Gibbon, Sahra; Aureliano, Waleska

    2018-04-01

    Within the context of a globalising agenda for genetic research where 'global health' is increasingly seen as necessarily informed by and having to account for genomics, the focus on rare genetic diseases is becoming prominent. Drawing from ethnographic research carried out separately by both authors in Brazil, this paper examines how an emerging focus on two different arenas of rare genetic disease, cancer genetics and a class of degenerative neurological diseases known as Ataxias, is subject to and a product of the dynamics of inclusion and exclusion as this concerns participation in research and access to health care. It examines how in these different cases 'rarenesss' has been diversely situated and differently politicised and how clinicians, patients and their families grapple with the slippery boundaries between research, rights to health and the limits of care, therapy or prevention. It illustrates how attention to rare genetic disease in Brazil emerges at the intersection of a particular history of genetic research and public health infrastructure, densely complicated feedback loops between clinical care and research, patient mobilisation around the 'judicialisation' of health and recent state legislation regarding rare disease in Brazil. It highlights the relevance of local configurations in the way rare genetic disease is being made relevant for and by different communities.

  9. A genome-wide study reveals rare CNVs exclusive to extreme phenotypes of Alzheimer disease.

    Science.gov (United States)

    Rovelet-Lecrux, Anne; Legallic, Solenn; Wallon, David; Flaman, Jean-Michel; Martinaud, Olivier; Bombois, Stéphanie; Rollin-Sillaire, Adeline; Michon, Agnès; Le Ber, Isabelle; Pariente, Jérémie; Puel, Michèle; Paquet, Claire; Croisile, Bernard; Thomas-Antérion, Catherine; Vercelletto, Martine; Lévy, Richard; Frébourg, Thierry; Hannequin, Didier; Campion, Dominique

    2012-06-01

    Studying rare extreme forms of Alzheimer disease (AD) may prove to be a useful strategy in identifying new genes involved in monogenic determinism of AD. Amyloid precursor protein (APP), PSEN1, and PSEN2 mutations account for only 85% of autosomal dominant early-onset AD (ADEOAD) families. We hypothesised that rare copy number variants (CNVs) could be involved in ADEOAD families without mutations in known genes, as well as in rare sporadic young-onset AD cases. Using high-resolution array comparative genomic hybridisation, we assessed the presence of rare CNVs in 21 unrelated ADEOAD cases, having no alteration on known genes, and 12 sporadic AD cases, with an age of onset younger than 55 years. The analysis revealed the presence of 7 singleton CNVs (4 in ADEOAD and 3 in sporadic cases) absent in 1078 controls and 912 late-onset AD cases. Strikingly, 4 out of 7 rearrangements target genes (KLK6, SLC30A3, MEOX2, and FPR2) encoding proteins that are tightly related to amyloid-β peptide metabolism or signalling. Although these variants are individually rare and restricted to particular subgroups of patients, these findings support the causal role, in human pathology, of a set of genes coding for molecules suspected for a long time to modify Aβ metabolism or signalling, and for which animal or cellular models have already been developed.

  10. Genome sequence of a diabetes-prone rodent reveals a mutation hotspot around the ParaHox gene cluster

    DEFF Research Database (Denmark)

    Hargreaves, Adam D.; Zhou, Long; Christensen, Josef

    2017-01-01

    The sand rat Psammomys obesus is a gerbil species native to deserts of North Africa and the Middle East, and is constrained in its ecology because high carbohydrate diets induce obesity and type II diabetes that, in extreme cases, can lead to pancreatic failure and death. We report the sequencing...... Pdx1 has been grossly affected by GC-biased mutation, leading to the highest divergence observed for this gene across the Bilateria. In addition to genomic insights into restricted caloric intake in a desert species, the discovery of a localized chromosomal region subject to elevated mutation suggests...

  11. Protein Determinants of Meiotic DNA Break Hotspots

    Science.gov (United States)

    Fowler, Kyle R.; Gutiérrez-Velasco, Susana

    2013-01-01

    SUMMARY Meiotic recombination, crucial for proper chromosome segregation and genome evolution, is initiated by programmed DNA double-strand breaks (DSBs) in yeasts and likely all sexually reproducing species. In fission yeast, DSBs occur up to hundreds of times more frequently at special sites, called hotspots, than in other regions of the genome. What distinguishes hotspots from cold regions is an unsolved problem, although transcription factors determine some hotspots. We report the discovery that three coiled-coil proteins – Rec25, Rec27, and Mug20 – bind essentially all hotspots with unprecedented specificity even without DSB formation. These small proteins are components of linear elements, are related to synaptonemal complex proteins, and are essential for nearly all DSBs at most hotspots. Our results indicate these hotspot determinants activate or stabilize the DSB-forming protein Rec12 (Spo11 homolog) rather than promote its binding to hotspots. We propose a new paradigm for hotspot determination and crossover control by linear element proteins. PMID:23395004

  12. Genomic Resources of Three Pulsatilla Species Reveal Evolutionary Hotspots, Species-Specific Sites and Variable Plastid Structure in the Family Ranunculaceae.

    Science.gov (United States)

    Szczecińska, Monika; Sawicki, Jakub

    2015-09-15

    The European continent is presently colonized by nine species of the genus Pulsatilla, five of which are encountered only in mountainous regions of southwest and south-central Europe. The remaining four species inhabit lowlands in the north-central and eastern parts of the continent. Most plants of the genus Pulsatilla are rare and endangered, which is why most research efforts focused on their biology, ecology and hybridization. The objective of this study was to develop genomic resources, including complete plastid genomes and nuclear rRNA clusters, for three sympatric Pulsatilla species that are most commonly found in Central Europe. The results will supply valuable information about genetic variation, which can be used in the process of designing primers for population studies and conservation genetics research. The complete plastid genomes together with the nuclear rRNA cluster can serve as a useful tool in hybridization studies. Six complete plastid genomes and nuclear rRNA clusters were sequenced from three species of Pulsatilla using the Illumina sequencing technology. Four junctions between single copy regions and inverted repeats and junctions between the identified locally-collinear blocks (LCB) were confirmed by Sanger sequencing. Pulsatilla genomes of 120 unique genes had a total length of approximately 161-162 kb, and 21 were duplicated in the inverted repeats (IR) region. Comparative plastid genomes of newly-sequenced Pulsatilla and the previously-identified plastomes of Aconitum and Ranunculus species belonging to the family Ranunculaceae revealed several variations in the structure of the genome, but the gene content remained constant. The nuclear rRNA cluster (18S-ITS1-5.8S-ITS2-26S) of studied Pulsatilla species is 5795 bp long. Among five analyzed regions of the rRNA cluster, only Internal Transcribed Spacer 2 (ITS2) enabled the molecular delimitation of closely-related Pulsatilla patens and Pulsatilla vernalis. The determination of complete

  13. Klebsiella pneumoniae asparagine tDNAs are integration hotspots for different genomic islands encoding microcin E492 production determinants and other putative virulence factors present in hypervirulent strains

    Directory of Open Access Journals (Sweden)

    Andrés Esteban Marcoleta

    2016-06-01

    Full Text Available Due to the developing of multi-resistant and invasive hypervirulent strains, Klebsiella pneumoniae has become one of the most urgent bacterial pathogen threats in the last years. Genomic comparison of a growing number of sequenced isolates has allowed the identification of putative virulence factors, proposed to be acquirable mainly through horizontal gene transfer. In particular, those related with synthesizing the antibacterial peptide microcin E492 (MccE492 and salmochelin siderophores were found to be highly prevalent among hypervirulent strains. The determinants for the production of both molecules were first reported as part of a 13-kbp segment of K. pneumoniae RYC492 chromosome, and were cloned and characterized in E. coli. However, the genomic context of this segment in K. pneumoniae remained uncharacterized.In this work we provided experimental and bioinformatics evidence indicating that the MccE492 cluster is part of a highly conserved 23-kbp genomic island (GI named GIE492, that was integrated in a specific asparagine-tRNA gene (asn-tDNA and was found in a high proportion of isolates from liver abscesses sampled around the world. This element resulted to be unstable and its excision frequency increased after treating bacteria with mytomicin C and upon the overexpression of the island-encoded integrase. Besides the MccE492 genetic cluster, it invariably included an integrase-coding gene, at least 7 protein-coding genes of unknown function, and a putative transfer origin that possibly allows this GI to be mobilized through conjugation. In addition, we analyzed the asn-tDNA loci of all the available K. pneumoniae assembled chromosomes to evaluate them as GI-integration sites. Remarkably, 73% of the strains harbored at least one GI integrated in one of the four asn-tDNA present in this species, confirming them as integration hotspots. Each of these tDNAs was occupied with different frequencies, although they were 100% identical. Also, we

  14. Live hot, die young: transmission distortion in recombination hotspots.

    Directory of Open Access Journals (Sweden)

    Graham Coop

    2007-03-01

    Full Text Available There is strong evidence that hotspots of meiotic recombination in humans are transient features of the genome. For example, hotspot locations are not shared between human and chimpanzee. Biased gene conversion in favor of alleles that locally disrupt hotspots is a possible explanation of the short lifespan of hotspots. We investigate the implications of such a bias on human hotspots and their evolution. Our results demonstrate that gene conversion bias is a sufficiently strong force to produce the observed lack of sharing of intense hotspots between species, although sharing may be much more common for weaker hotspots. We investigate models of how hotspots arise, and find that only models in which hotspot alleles do not initially experience drive are consistent with observations of rather hot hotspots in the human genome. Mutations acting against drive cannot successfully introduce such hotspots into the population, even if there is direct selection for higher recombination rates, such as to ensure correct segregation during meiosis. We explore the impact of hotspot alleles on patterns of haplotype variation, and show that such alleles mask their presence in population genetic data, making them difficult to detect.

  15. The spatial regulation of meiotic recombination hotspots: are all DSB hotspots crossover hotspots?

    Science.gov (United States)

    Serrentino, Maria-Elisabetta; Borde, Valérie

    2012-07-15

    A key step for the success of meiosis is programmed homologous recombination, during which crossovers, or exchange of chromosome arms, take place. Crossovers increase genetic diversity but their main function is to ensure accurate chromosome segregation. Defects in crossover number and position produce aneuploidies that represent the main cause of miscarriages and chromosomal abnormalities such as Down's syndrome. Recombination is initiated by the formation of programmed double strand breaks (DSBs), which occur preferentially at places called DSB hotspots. Among all DSBs generated, only a small fraction is repaired by crossover, the other being repaired by other homologous recombination pathways. Crossover maps have been generated in a number of organisms, defining crossover hotspots. With the availability of genome-wide maps of DSBs as well as the ability to measure genetically the repair outcome at several hotspots, it is becoming more and more clear that not all DSB hotspots behave the same for crossover formation, suggesting that chromosomal features distinguish different types of hotspots. Copyright © 2012. Published by Elsevier Inc.

  16. Efficient utilization of rare variants for detection of disease-related genomic regions.

    Directory of Open Access Journals (Sweden)

    Lei Zhang

    2010-12-01

    Full Text Available When testing association between rare variants and diseases, an efficient analytical approach involves considering a set of variants in a genomic region as the unit of analysis. One factor complicating this approach is that the vast majority of rare variants in practical applications are believed to represent background neutral variation. As a result, analyzing a single set with all variants may not represent a powerful approach. Here, we propose two alternative strategies. In the first, we analyze the subsets of rare variants exhaustively. In the second, we categorize variants selectively into two subsets: one in which variants are overrepresented in cases, and the other in which variants are overrepresented in controls. When the proportion of neutral variants is moderate to large we show, by simulations, that the both proposed strategies improve the statistical power over methods analyzing a single set with total variants. When applied to a real sequencing association study, the proposed methods consistently produce smaller p-values than their competitors. When applied to another real sequencing dataset to study the difference of rare allele distributions between ethnic populations, the proposed methods detect the overrepresentation of variants between the CHB (Chinese Han in Beijing and YRI (Yoruba people of Ibadan populations with small p-values. Additional analyses suggest that there is no difference between the CHB and CHD (Chinese Han in Denver datasets, as expected. Finally, when applied to the CHB and JPT (Japanese people in Tokyo populations, existing methods fail to detect any difference, while it is detected by the proposed methods in several regions.

  17. Rare genomic structural variants in complex disease: lessons from the replication of associations with obesity.

    Directory of Open Access Journals (Sweden)

    Robin G Walters

    Full Text Available The limited ability of common variants to account for the genetic contribution to complex disease has prompted searches for rare variants of large effect, to partly explain the 'missing heritability'. Analyses of genome-wide genotyping data have identified genomic structural variants (GSVs as a source of such rare causal variants. Recent studies have reported multiple GSV loci associated with risk of obesity. We attempted to replicate these associations by similar analysis of two familial-obesity case-control cohorts and a population cohort, and detected GSVs at 11 out of 18 loci, at frequencies similar to those previously reported. Based on their reported frequencies and effect sizes (OR≥25, we had sufficient statistical power to detect the large majority (80% of genuine associations at these loci. However, only one obesity association was replicated. Deletion of a 220 kb region on chromosome 16p11.2 has a carrier population frequency of 2×10(-4 (95% confidence interval [9.6×10(-5-3.1×10(-4]; accounts overall for 0.5% [0.19%-0.82%] of severe childhood obesity cases (P = 3.8×10(-10; odds ratio = 25.0 [9.9-60.6]; and results in a mean body mass index (BMI increase of 5.8 kg.m(-2 [1.8-10.3] in adults from the general population. We also attempted replication using BMI as a quantitative trait in our population cohort; associations with BMI at or near nominal significance were detected at two further loci near KIF2B and within FOXP2, but these did not survive correction for multiple testing. These findings emphasise several issues of importance when conducting rare GSV association, including the need for careful cohort selection and replication strategy, accurate GSV identification, and appropriate correction for multiple testing and/or control of false discovery rate. Moreover, they highlight the potential difficulty in replicating rare CNV associations across different populations. Nevertheless, we show that such studies are potentially

  18. SequenceLDhot: detecting recombination hotspots.

    Science.gov (United States)

    Fearnhead, Paul

    2006-12-15

    There is much local variation in recombination rates across the human genome--with the majority of recombination occurring in recombination hotspots--short regions of around approximately 2 kb in length that have much higher recombination rates than neighbouring regions. Knowledge of this local variation is important, e.g. in the design and analysis of association studies for disease genes. Population genetic data, such as that generated by the HapMap project, can be used to infer the location of these hotspots. We present a new, efficient and powerful method for detecting recombination hotspots from population data. We compare our method with four current methods for detecting hotspots. It is orders of magnitude quicker, and has greater power, than two related approaches. It appears to be more powerful than HotspotFisher, though less accurate at inferring the precise positions of the hotspot. It was also more powerful than LDhot in some situations: particularly for weaker hotspots (10-40 times the background rate) when SNP density is lower (maths.lancs.ac.uk/~fearnhea/Hotspot.

  19. Insights from early experience of a Rare Disease Genomic Medicine Multidisciplinary Team: a qualitative study.

    Science.gov (United States)

    Ormondroyd, Elizabeth; Mackley, Michael P; Blair, Edward; Craft, Jude; Knight, Julian C; Taylor, John; Taylor, Jenny C; Wilkie, Andrew Om; Watkins, Hugh

    2017-06-01

    Whole-exome/whole-genome sequencing (WES/WGS) has the potential to enhance genetic diagnosis of rare disease, and is increasingly becoming part of routine clinical care in mainstream medicine. Effective translation will require ongoing efforts in a number of areas including: selection of appropriate patients, provision of effective consent, pre- and post-test genetic counselling, improving variant interpretation algorithms and practices, and management of secondary findings including those found incidentally and those actively sought. Allied to this is the need for an effective education programme for all members of clinical teams involved in care of patients with rare disease, as well as to maintain public confidence in the use of these technologies. We established a Genomic Medicine Multidisciplinary Team (GM-MDT) in 2014 to build on the experiences of earlier successful research-based WES/WGS studies, to address these needs and to review results including pertinent and secondary findings. Here we report on a qualitative study of decision-making in the GM-MDT combined with analysis of semi-structured interviews with GM-MDT members. Study findings show that members appreciate the clinical and scientific diversity of the GM-MDT and value it for education and oversight. To date, discussions have focussed on case selection including the extent and interpretation of clinical and family history information required to establish likely monogenic aetiology and inheritance model. Achieving a balance between effective use of WES/WGS - prioritising cases in a diverse and highly complex patient population where WES/WGS will be tractable - and meeting the recruitment targets of a large project is considered challenging.

  20. Genome-wide assessment of the association of rare and common copy number variations to testicular germ cell cancer

    DEFF Research Database (Denmark)

    Edsgard, Stefan Daniel; Dalgaard, Marlene Danner; Weinhold, Nils

    2013-01-01

    Testicular germ cell cancer (TGCC) is one of the most heritable forms of cancer. Previous genome-wide association studies have focused on single nucleotide polymorphisms, largely ignoring the influence of copy number variants (CNVs). Here we present a genome-wide study of CNV on a cohort of 212...... of rare CNVs related to cell migration (false-discovery rate = 0.021, 1.8% of cases and 1.1% of controls). Dysregulation during migration of primordial germ cells has previously been suspected to be a part of TGCC development and this set of multiple rare variants may thereby have a minor contribution...

  1. Genomic Resources of Three Pulsatilla Species Reveal Evolutionary Hotspots, Species-Specific Sites and Variable Plastid Structure in the Family Ranunculaceae

    Directory of Open Access Journals (Sweden)

    Monika Szczecińska

    2015-09-01

    Full Text Available Background: The European continent is presently colonized by nine species of the genus Pulsatilla, five of which are encountered only in mountainous regions of southwest and south-central Europe. The remaining four species inhabit lowlands in the north-central and eastern parts of the continent. Most plants of the genus Pulsatilla are rare and endangered, which is why most research efforts focused on their biology, ecology and hybridization. The objective of this study was to develop genomic resources, including complete plastid genomes and nuclear rRNA clusters, for three sympatric Pulsatilla species that are most commonly found in Central Europe. The results will supply valuable information about genetic variation, which can be used in the process of designing primers for population studies and conservation genetics research. The complete plastid genomes together with the nuclear rRNA cluster can serve as a useful tool in hybridization studies. Methodology/principal findings: Six complete plastid genomes and nuclear rRNA clusters were sequenced from three species of Pulsatilla using the Illumina sequencing technology. Four junctions between single copy regions and inverted repeats and junctions between the identified locally-collinear blocks (LCB were confirmed by Sanger sequencing. Pulsatilla genomes of 120 unique genes had a total length of approximately 161–162 kb, and 21 were duplicated in the inverted repeats (IR region. Comparative plastid genomes of newly-sequenced Pulsatilla and the previously-identified plastomes of Aconitum and Ranunculus species belonging to the family Ranunculaceae revealed several variations in the structure of the genome, but the gene content remained constant. The nuclear rRNA cluster (18S-ITS1-5.8S-ITS2-26S of studied Pulsatilla species is 5795 bp long. Among five analyzed regions of the rRNA cluster, only Internal Transcribed Spacer 2 (ITS2 enabled the molecular delimitation of closely-related Pulsatilla

  2. Identifying Rare Variation in Cases of Schizophrenia in the Isolated Population of the Faroe Islands using Whole-genome Sequencing

    DEFF Research Database (Denmark)

    Als, Thomas Damm; Lescai, Francesco; Dahl, Hans

    to map risk variants involved in complex traits. We aim at utilizing samples of cases and controls of the isolated population of the Faroe Islands to conduct whole-genome-sequence analysis in order to identify rare genetic variants associated with schizophrenia. We will search for rare genetic variants...... of developing SZ. However, these studies are designed to examining only “the common variant” proportion of the genomic landscape of SZ. Due to increased genetic drift during founding and potential bottlenecks, followed by population expansion, isolated populations may be particularly useful in identifying rare...... disease variants, that may appear at higher frequencies and/or within a more clearly distinct haplotype structure compared to outbred populations. Small isolated populations also typically show reduced phenotypic, genetic and environmental heterogeneity, thus making them advantageous in studies aiming...

  3. Integrative analysis of functional genomic annotations and sequencing data to identify rare causal variants via hierarchical modeling

    Directory of Open Access Journals (Sweden)

    Marinela eCapanu

    2015-05-01

    Full Text Available Identifying the small number of rare causal variants contributing to disease has beena major focus of investigation in recent years, but represents a formidable statisticalchallenge due to the rare frequencies with which these variants are observed. In thiscommentary we draw attention to a formal statistical framework, namely hierarchicalmodeling, to combine functional genomic annotations with sequencing data with theobjective of enhancing our ability to identify rare causal variants. Using simulations weshow that in all configurations studied, the hierarchical modeling approach has superiordiscriminatory ability compared to a recently proposed aggregate measure of deleteriousness,the Combined Annotation-Dependent Depletion (CADD score, supportingour premise that aggregate functional genomic measures can more accurately identifycausal variants when used in conjunction with sequencing data through a hierarchicalmodeling approach

  4. Novel and rare functional genomic variants in multiple autoimmune syndrome and Sjögren's syndrome.

    Science.gov (United States)

    Johar, Angad S; Mastronardi, Claudio; Rojas-Villarraga, Adriana; Patel, Hardip R; Chuah, Aaron; Peng, Kaiman; Higgins, Angela; Milburn, Peter; Palmer, Stephanie; Silva-Lara, Maria Fernanda; Velez, Jorge I; Andrews, Dan; Field, Matthew; Huttley, Gavin; Goodnow, Chris; Anaya, Juan-Manuel; Arcos-Burgos, Mauricio

    2015-06-02

    Multiple autoimmune syndrome (MAS), an extreme phenotype of autoimmune disorders, is a very well suited trait to tackle genomic variants of these conditions. Whole exome sequencing (WES) is a widely used strategy for detection of protein coding and splicing variants associated with inherited diseases. The DNA of eight patients affected by MAS [all of whom presenting with Sjögren's syndrome (SS)], four patients affected by SS alone and 38 unaffected individuals, were subject to WES. Filters to identify novel and rare functional (pathogenic-deleterious) homozygous and/or compound heterozygous variants in these patients and controls were applied. Bioinformatics tools such as the Human gene connectome as well as pathway and network analysis were applied to test overrepresentation of genes harbouring these variants in critical pathways and networks involved in autoimmunity. Eleven novel and rare functional variants were identified in cases but not in controls, harboured in: MACF1, KIAA0754, DUSP12, ICA1, CELA1, LRP1/STAT6, GRIN3B, ANKLE1, TMEM161A, and FKRP. These were subsequently subject to network analysis and their functional relatedness to genes already associated with autoimmunity was evaluated. Notably, the LRP1/STAT6 novel mutation was homozygous in one MAS affected patient and heterozygous in another. LRP1/STAT6 disclosed the strongest plausibility for autoimmunity. LRP1/STAT6 are involved in extracellular and intracellular anti-inflammatory pathways that play key roles in maintaining the homeostasis of the immune system. Further; networks, pathways, and interaction analyses showed that LRP1 is functionally related to the HLA-B and IL10 genes and it has a substantial impact within immunological pathways and/or reaction to bacterial and other foreign proteins (phagocytosis, regulation of phospholipase A2 activity, negative regulation of apoptosis and response to lipopolysaccharides). Further, ICA1 and STAT6 were also closely related to AIRE and IRF5, two very

  5. Rare Genome-Wide Copy Number Variation and Expression of Schizophrenia in 22q11.2 Deletion Syndrome.

    Science.gov (United States)

    Bassett, Anne S; Lowther, Chelsea; Merico, Daniele; Costain, Gregory; Chow, Eva W C; van Amelsvoort, Therese; McDonald-McGinn, Donna; Gur, Raquel E; Swillen, Ann; Van den Bree, Marianne; Murphy, Kieran; Gothelf, Doron; Bearden, Carrie E; Eliez, Stephan; Kates, Wendy; Philip, Nicole; Sashi, Vandana; Campbell, Linda; Vorstman, Jacob; Cubells, Joseph; Repetto, Gabriela M; Simon, Tony; Boot, Erik; Heung, Tracy; Evers, Rens; Vingerhoets, Claudia; van Duin, Esther; Zackai, Elaine; Vergaelen, Elfi; Devriendt, Koen; Vermeesch, Joris R; Owen, Michael; Murphy, Clodagh; Michaelovosky, Elena; Kushan, Leila; Schneider, Maude; Fremont, Wanda; Busa, Tiffany; Hooper, Stephen; McCabe, Kathryn; Duijff, Sasja; Isaev, Karin; Pellecchia, Giovanna; Wei, John; Gazzellone, Matthew J; Scherer, Stephen W; Emanuel, Beverly S; Guo, Tingwei; Morrow, Bernice E; Marshall, Christian R

    2017-11-01

    Chromosome 22q11.2 deletion syndrome (22q11.2DS) is associated with a more than 20-fold increased risk for developing schizophrenia. The aim of this study was to identify additional genetic factors (i.e., "second hits") that may contribute to schizophrenia expression. Through an international consortium, the authors obtained DNA samples from 329 psychiatrically phenotyped subjects with 22q11.2DS. Using a high-resolution microarray platform and established methods to assess copy number variation (CNV), the authors compared the genome-wide burden of rare autosomal CNV, outside of the 22q11.2 deletion region, between two groups: a schizophrenia group and those with no psychotic disorder at age ≥25 years. The authors assessed whether genes overlapped by rare CNVs were overrepresented in functional pathways relevant to schizophrenia. Rare CNVs overlapping one or more protein-coding genes revealed significant between-group differences. For rare exonic duplications, six of 19 gene sets tested were enriched in the schizophrenia group; genes associated with abnormal nervous system phenotypes remained significant in a stepwise logistic regression model and showed significant interactions with 22q11.2 deletion region genes in a connectivity analysis. For rare exonic deletions, the schizophrenia group had, on average, more genes overlapped. The additional rare CNVs implicated known (e.g., GRM7, 15q13.3, 16p12.2) and novel schizophrenia risk genes and loci. The results suggest that additional rare CNVs overlapping genes outside of the 22q11.2 deletion region contribute to schizophrenia risk in 22q11.2DS, supporting a multigenic hypothesis for schizophrenia. The findings have implications for understanding expression of psychotic illness and herald the importance of whole-genome sequencing to appreciate the overall genomic architecture of schizophrenia.

  6. Dynamic malaria hotspots in an open cohort in western Kenya.

    Science.gov (United States)

    Platt, Alyssa; Obala, Andrew A; MacIntyre, Charlie; Otsyula, Barasa; Meara, Wendy Prudhomme O'

    2018-01-12

    Malaria hotspots, defined as areas where transmission intensity exceeds the average level, become more pronounced as transmission declines. Targeting hotspots may accelerate reductions in transmission and could be pivotal for malaria elimination. Determinants of hotspot location, particularly of their movement, are poorly understood. We used spatial statistical methods to identify foci of incidence of self-reported malaria in a large census population of 64,000 people, in 8,290 compounds over a 2.5-year study period. Regression models examine stability of hotspots and identify static and dynamic correlates with their location. Hotspot location changed over short time-periods, rarely recurring in the same area. Hotspots identified in spring versus fall season differed in their stability. Households located in a hotspot in the fall were more likely to be located in a hotspot the following fall (RR = 1.77, 95% CI: 1.66-1.89), but the opposite was true for compounds in spring hotspots (RR = 0.15, 95% CI: 0.08-0.28). Location within a hotspot was related to environmental and static household characteristics such as distance to roads or rivers. Human migration into a household was correlated with risk of hotspot membership, but the direction of the association differed based on the origin of the migration event.

  7. Epigenetic functions enriched in transcription factors binding to mouse recombination hotspots.

    Science.gov (United States)

    Wu, Min; Kwoh, Chee-Keong; Przytycka, Teresa M; Li, Jing; Zheng, Jie

    2012-06-21

    The regulatory mechanism of recombination is a fundamental problem in genomics, with wide applications in genome-wide association studies, birth-defect diseases, molecular evolution, cancer research, etc. In mammalian genomes, recombination events cluster into short genomic regions called "recombination hotspots". Recently, a 13-mer motif enriched in hotspots is identified as a candidate cis-regulatory element of human recombination hotspots; moreover, a zinc finger protein, PRDM9, binds to this motif and is associated with variation of recombination phenotype in human and mouse genomes, thus is a trans-acting regulator of recombination hotspots. However, this pair of cis and trans-regulators covers only a fraction of hotspots, thus other regulators of recombination hotspots remain to be discovered. In this paper, we propose an approach to predicting additional trans-regulators from DNA-binding proteins by comparing their enrichment of binding sites in hotspots. Applying this approach on newly mapped mouse hotspots genome-wide, we confirmed that PRDM9 is a major trans-regulator of hotspots. In addition, a list of top candidate trans-regulators of mouse hotspots is reported. Using GO analysis we observed that the top genes are enriched with function of histone modification, highlighting the epigenetic regulatory mechanisms of recombination hotspots.

  8. Hotspots Definition Study

    International Nuclear Information System (INIS)

    De Pater, F.; Brinkman, S.; Schellekens, E.

    2010-03-01

    In the Dutch research programme Climate changes Spatial Planning (CcSP) many scientific projects are carried out. They often take a multidisciplinary approach to the climate issue. However, more attention needed to be given to embedding the programme into practice. Therefore, the board decided to start a hotspot programme. A hotspot was defined as a pilot project in a sector, place or region in which spatial planning and climate change play an important role in the physical shape and land use of the area and where conflicts of interest are found between these and other factors. The hotspot programme started with a definition study. This report is the result of this study. The goal of the study was to identify, describe and evaluate possible hotspots. In two workshops with policy-makers from national and regional governments, consultancy firms and nature conservation organizations, a large number of potential hotspots were identified. Fifteen were selected after the workshops took place and described in detail. The selection was done using a set of conditional criteria, criteria that all had to be met. Two potential hotspots were withdrawn after the selection. Since the Board of the CcSP programme expressed its interest in financing six to seven hotspots, a prioritization was made, using prioritizing criteria. Also the potential hotspots were assessed looking at regional distribution, thematic coverage and target groups. After this assessment and an analysis of the hotspots taking some other factors into account (eg. some hotspots were very similar or one could easily be incorporated in another one) five hotspots were selected: Kampen, Biesbosch-Haringvliet, Zuidplaspolder, Delta Waters and Tilburg. Options to fill the last two places were: Grounds for Change, Noordoostpolder, Oude Vaart Valley and Arnhem/Nijmegen (KAN). For these remaining potential hotspots draft terms of reference were drawn as basis for a project proposals. These terms of reference are added to

  9. Genome-wide Polygenic Burden of Rare Deleterious Variants in Sudden Unexpected Death in Epilepsy

    Directory of Open Access Journals (Sweden)

    Costin Leu

    2015-09-01

    Full Text Available Sudden unexpected death in epilepsy (SUDEP represents the most severe degree of the spectrum of epilepsy severity and is the commonest cause of epilepsy-related premature mortality. The precise pathophysiology and the genetic architecture of SUDEP remain elusive. Aiming to elucidate the genetic basis of SUDEP, we analysed rare, protein-changing variants from whole-exome sequences of 18 people who died of SUDEP, 87 living people with epilepsy and 1479 non-epilepsy disease controls. Association analysis revealed a significantly increased genome-wide polygenic burden per individual in the SUDEP cohort when compared to epilepsy (P = 5.7 × 10−3 and non-epilepsy disease controls (P = 1.2 × 10−3. The polygenic burden was driven both by the number of variants per individual, and over-representation of variants likely to be deleterious in the SUDEP cohort. As determined by this study, more than a thousand genes contribute to the observed polygenic burden within the framework of this study. Subsequent gene-based association analysis revealed five possible candidate genes significantly associated with SUDEP or epilepsy, but no one single gene emerges as common to the SUDEP cases. Our findings provide further evidence for a genetic susceptibility to SUDEP, and suggest an extensive polygenic contribution to SUDEP causation. Thus, an overall increased burden of deleterious variants in a highly polygenic background might be important in rendering a given individual more susceptible to SUDEP. Our findings suggest that exome sequencing in people with epilepsy might eventually contribute to generating SUDEP risk estimates, promoting stratified medicine in epilepsy, with the eventual aim of reducing an individual patient's risk of SUDEP.

  10. Genome-wide Polygenic Burden of Rare Deleterious Variants in Sudden Unexpected Death in Epilepsy.

    Science.gov (United States)

    Leu, Costin; Balestrini, Simona; Maher, Bridget; Hernández-Hernández, Laura; Gormley, Padhraig; Hämäläinen, Eija; Heggeli, Kristin; Schoeler, Natasha; Novy, Jan; Willis, Joseph; Plagnol, Vincent; Ellis, Rachael; Reavey, Eleanor; O'Regan, Mary; Pickrell, William O; Thomas, Rhys H; Chung, Seo-Kyung; Delanty, Norman; McMahon, Jacinta M; Malone, Stephen; Sadleir, Lynette G; Berkovic, Samuel F; Nashef, Lina; Zuberi, Sameer M; Rees, Mark I; Cavalleri, Gianpiero L; Sander, Josemir W; Hughes, Elaine; Helen Cross, J; Scheffer, Ingrid E; Palotie, Aarno; Sisodiya, Sanjay M

    2015-09-01

    Sudden unexpected death in epilepsy (SUDEP) represents the most severe degree of the spectrum of epilepsy severity and is the commonest cause of epilepsy-related premature mortality. The precise pathophysiology and the genetic architecture of SUDEP remain elusive. Aiming to elucidate the genetic basis of SUDEP, we analysed rare, protein-changing variants from whole-exome sequences of 18 people who died of SUDEP, 87 living people with epilepsy and 1479 non-epilepsy disease controls. Association analysis revealed a significantly increased genome-wide polygenic burden per individual in the SUDEP cohort when compared to epilepsy (P = 5.7 × 10(- 3)) and non-epilepsy disease controls (P = 1.2 × 10(- 3)). The polygenic burden was driven both by the number of variants per individual, and over-representation of variants likely to be deleterious in the SUDEP cohort. As determined by this study, more than a thousand genes contribute to the observed polygenic burden within the framework of this study. Subsequent gene-based association analysis revealed five possible candidate genes significantly associated with SUDEP or epilepsy, but no one single gene emerges as common to the SUDEP cases. Our findings provide further evidence for a genetic susceptibility to SUDEP, and suggest an extensive polygenic contribution to SUDEP causation. Thus, an overall increased burden of deleterious variants in a highly polygenic background might be important in rendering a given individual more susceptible to SUDEP. Our findings suggest that exome sequencing in people with epilepsy might eventually contribute to generating SUDEP risk estimates, promoting stratified medicine in epilepsy, with the eventual aim of reducing an individual patient's risk of SUDEP.

  11. Global MLST of Salmonella Typhi Revisited in Post-Genomic Era: Genetic conservation, Population Structure and Comparative genomics of rare sequence types

    Directory of Open Access Journals (Sweden)

    Kien-Pong eYap

    2016-03-01

    Full Text Available Typhoid fever, caused by Salmonella enterica serovar Typhi, remains an important public health burden in Southeast Asia and other endemic countries. Various genotyping methods have been applied to study the genetic variations of this human-restricted pathogen. Multilocus Sequence Typing (MLST is one of the widely accepted methods, and recently, there is a growing interest in the re-application of MLST in the post-genomic era. In this study, we provide the global MLST distribution of S. Typhi utilizing both publicly available 1,826 S. Typhi genome sequences in addition to performing conventional MLST on S. Typhi strains isolated from various endemic regions spanning over a century. Our global MLST analysis confirms the predominance of two sequence types (ST1 and ST2 co-existing in the endemic regions. Interestingly, S. Typhi strains with ST8 are currently confined within the African continent. Comparative genomic analyses of ST8 and other rare STs with genomes of ST1/ST2 revealed unique mutations in important virulence genes such as flhB, sipC and tviD that may explain the variations that differentiate between seemingly successful (widespread and unsuccessful (poor dissemination S. Typhi populations. Large scale whole-genome phylogeny demonstrated evidence of phylogeographical structuring and showed that ST8 may have diverged from the earlier ancestral population of ST1 and ST2, which later lost some of its fitness advantages, leading to poor worldwide dissemination. In response to the unprecedented increase in genomic data, this study demonstrates and highlights the utility of large-scale genome-based MLST as a quick and effective approach to narrow the scope of in-depth comparative genomic analysis and consequently provide new insights into the fine scale of pathogen evolution and population structure.

  12. Taksonomi i et hotspot

    DEFF Research Database (Denmark)

    Balslev, Henrik

    2016-01-01

    Op mod halvdelen af alle jordens plantearter findes koncentreret på kun 1,4 % af jordoverfladen. Langt de fleste af disse hotspots for biodiversitet befinder sig i de tropiske egne, hvor vores viden om antallet af arter er mangelfuld. Thailand er placeret i centrum af jordens største hotspot, som...

  13. Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

    DEFF Research Database (Denmark)

    Albertsen, Mads; Hugenholtz, Philip; Skarshewski, Adam

    2013-01-01

    Reference genomes are required to understand the diverse roles of microorganisms in ecology, evolution, human and animal health, but most species remain uncultured. Here we present a sequence composition–independent approach to recover high-quality microbial genomes from deeply sequenced metageno......Reference genomes are required to understand the diverse roles of microorganisms in ecology, evolution, human and animal health, but most species remain uncultured. Here we present a sequence composition–independent approach to recover high-quality microbial genomes from deeply sequenced...

  14. A scan statistic to extract causal gene clusters from case-control genome-wide rare CNV data

    Directory of Open Access Journals (Sweden)

    Scherer Stephen W

    2011-05-01

    Full Text Available Abstract Background Several statistical tests have been developed for analyzing genome-wide association data by incorporating gene pathway information in terms of gene sets. Using these methods, hundreds of gene sets are typically tested, and the tested gene sets often overlap. This overlapping greatly increases the probability of generating false positives, and the results obtained are difficult to interpret, particularly when many gene sets show statistical significance. Results We propose a flexible statistical framework to circumvent these problems. Inspired by spatial scan statistics for detecting clustering of disease occurrence in the field of epidemiology, we developed a scan statistic to extract disease-associated gene clusters from a whole gene pathway. Extracting one or a few significant gene clusters from a global pathway limits the overall false positive probability, which results in increased statistical power, and facilitates the interpretation of test results. In the present study, we applied our method to genome-wide association data for rare copy-number variations, which have been strongly implicated in common diseases. Application of our method to a simulated dataset demonstrated the high accuracy of this method in detecting disease-associated gene clusters in a whole gene pathway. Conclusions The scan statistic approach proposed here shows a high level of accuracy in detecting gene clusters in a whole gene pathway. This study has provided a sound statistical framework for analyzing genome-wide rare CNV data by incorporating topological information on the gene pathway.

  15. Bayesian inference of shared recombination hotspots between humans and chimpanzees.

    Science.gov (United States)

    Wang, Ying; Rannala, Bruce

    2014-12-01

    Recombination generates variation and facilitates evolution. Recombination (or lack thereof) also contributes to human genetic disease. Methods for mapping genes influencing complex genetic diseases via association rely on linkage disequilibrium (LD) in human populations, which is influenced by rates of recombination across the genome. Comparative population genomic analyses of recombination using related primate species can identify factors influencing rates of recombination in humans. Such studies can indicate how variable hotspots for recombination may be both among individuals (or populations) and over evolutionary timescales. Previous studies have suggested that locations of recombination hotspots are not conserved between humans and chimpanzees. We made use of the data sets from recent resequencing projects and applied a Bayesian method for identifying hotspots and estimating recombination rates. We also reanalyzed SNP data sets for regions with known hotspots in humans using samples from the human and chimpanzee. The Bayes factors (BF) of shared recombination hotspots between human and chimpanzee across regions were obtained. Based on the analysis of the aligned regions of human chromosome 21, locations where the two species show evidence of shared recombination hotspots (with high BFs) were identified. Interestingly, previous comparative studies of human and chimpanzee that focused on the known human recombination hotspots within the β-globin and HLA regions did not find overlapping of hotspots. Our results show high BFs of shared hotspots at locations within both regions, and the estimated locations of shared hotspots overlap with the locations of human recombination hotspots obtained from sperm-typing studies. Copyright © 2014 by the Genetics Society of America.

  16. Meiotic recombination hotspots - a comparative view.

    Science.gov (United States)

    Choi, Kyuha; Henderson, Ian R

    2015-07-01

    During meiosis homologous chromosomes pair and undergo reciprocal genetic exchange, termed crossover. Meiotic recombination has a profound effect on patterns of genetic variation and is an important tool during crop breeding. Crossovers initiate from programmed DNA double-stranded breaks that are processed to form single-stranded DNA, which can invade a homologous chromosome. Strand invasion events mature into double Holliday junctions that can be resolved as crossovers. Extensive variation in the frequency of meiotic recombination occurs along chromosomes and is typically focused in narrow hotspots, observed both at the level of DNA breaks and final crossovers. We review methodologies to profile hotspots at different steps of the meiotic recombination pathway that have been used in different eukaryote species. We then discuss what these studies have revealed concerning specification of hotspot locations and activity and the contributions of both genetic and epigenetic factors. Understanding hotspots is important for interpreting patterns of genetic variation in populations and how eukaryotic genomes evolve. In addition, manipulation of hotspots will allow us to accelerate crop breeding, where meiotic recombination distributions can be limiting. © 2015 The Authors The Plant Journal © 2015 John Wiley & Sons Ltd.

  17. Mitochondrial genome sequences illuminate maternal lineages of conservation concern in a rare carnivore

    Science.gov (United States)

    Brian J. Knaus; Richard Cronn; Aaron Liston; Kristine Pilgrim; Michael K. Schwartz

    2011-01-01

    Science-based wildlife management relies on genetic information to infer population connectivity and identify conservation units. The most commonly used genetic marker for characterizing animal biodiversity and identifying maternal lineages is the mitochondrial genome. Mitochondrial genotyping figures prominently in conservation and management plans, with much of the...

  18. Warfare in biodiversity hotspots.

    Science.gov (United States)

    Hanson, Thor; Brooks, Thomas M; Da Fonseca, Gustavo A B; Hoffmann, Michael; Lamoreux, John F; Machlis, Gary; Mittermeier, Cristina G; Mittermeier, Russell A; Pilgrim, John D

    2009-06-01

    Conservation efforts are only as sustainable as the social and political context within which they take place. The weakening or collapse of sociopolitical frameworks during wartime can lead to habitat destruction and the erosion of conservation policies, but in some cases, may also confer ecological benefits through altered settlement patterns and reduced resource exploitation. Over 90% of the major armed conflicts between 1950 and 2000 occurred within countries containing biodiversity hotspots, and more than 80% took place directly within hotspot areas. Less than one-third of the 34 recognized hotspots escaped significant conflict during this period, and most suffered repeated episodes of violence. This pattern was remarkably consistent over these 5 decades. Evidence from the war-torn Eastern Afromontane hotspot suggests that biodiversity conservation is improved when international nongovernmental organizations support local protected area staff and remain engaged throughout the conflict. With biodiversity hotspots concentrated in politically volatile regions, the conservation community must maintain continuous involvement during periods of war, and biodiversity conservation should be incorporated into military, reconstruction, and humanitarian programs in the world's conflict zones. ©2009 Society for Conservation Biology.

  19. Quantile-based permutation thresholds for quantitative trait loci hotspots.

    Science.gov (United States)

    Neto, Elias Chaibub; Keller, Mark P; Broman, Andrew F; Attie, Alan D; Jansen, Ritsert C; Broman, Karl W; Yandell, Brian S

    2012-08-01

    Quantitative trait loci (QTL) hotspots (genomic locations affecting many traits) are a common feature in genetical genomics studies and are biologically interesting since they may harbor critical regulators. Therefore, statistical procedures to assess the significance of hotspots are of key importance. One approach, randomly allocating observed QTL across the genomic locations separately by trait, implicitly assumes all traits are uncorrelated. Recently, an empirical test for QTL hotspots was proposed on the basis of the number of traits that exceed a predetermined LOD value, such as the standard permutation LOD threshold. The permutation null distribution of the maximum number of traits across all genomic locations preserves the correlation structure among the phenotypes, avoiding the detection of spurious hotspots due to nongenetic correlation induced by uncontrolled environmental factors and unmeasured variables. However, by considering only the number of traits above a threshold, without accounting for the magnitude of the LOD scores, relevant information is lost. In particular, biologically interesting hotspots composed of a moderate to small number of traits with strong LOD scores may be neglected as nonsignificant. In this article we propose a quantile-based permutation approach that simultaneously accounts for the number and the LOD scores of traits within the hotspots. By considering a sliding scale of mapping thresholds, our method can assess the statistical significance of both small and large hotspots. Although the proposed approach can be applied to any type of heritable high-volume "omic" data set, we restrict our attention to expression (e)QTL analysis. We assess and compare the performances of these three methods in simulations and we illustrate how our approach can effectively assess the significance of moderate and small hotspots with strong LOD scores in a yeast expression data set.

  20. cDNA Clones with Rare and Recurrent Mutations Found in Cancers | Office of Cancer Genomics

    Science.gov (United States)

    The CTD2 Center at UT- MD Anderson Cancer Center has developed High-Throughput Mutagenesis and Molecular Barcoding (HiTMMoB)1,2 pipeline to construct mutant alleles open reading frame expression clones that are either recurrent or rare in cancers. These barcoded genes can be used for context-specific functional validation, detection of novel biomarkers (pathway activation) and targets (drug sensitivity).

  1. Rare genomic rearrangement in a boy with Williams-Beuren syndrome associated to XYY syndrome and intriguing behavior.

    Science.gov (United States)

    Dutra, Roberta L; Piazzon, Flavia B; Zanardo, Évelin A; Costa, Thais Virginia Moura Machado; Montenegro, Marília M; Novo-Filho, Gil M; Dias, Alexandre T; Nascimento, Amom M; Kim, Chong Ae; Kulikowski, Leslie D

    2015-12-01

    Williams-Beuren syndrome (WBS) is caused by a hemizygous contiguous gene microdeletion of 1.55-1.84 Mb at 7q11.23 region. Approximately, 28 genes have been shown to contribute to classical phenotype of SWB with presence of dysmorphic facial features, supravalvular aortic stenosis (SVAS), intellectual disability, and overfriendliness. With the use of Microarray-based comparative genomic hybridization and other molecular cytogenetic techniques, is possible define with more accuracy partial or atypical deletion and refine the genotype-phenotype correlation. Here, we report on a rare genomic structural rearrangement in a boy with atypical deletion in 7q11.23 and XYY syndrome with characteristic clinical signs, but not sufficient for the diagnosis of WBS. Cytogenetic analysis of G-banding showed a karyotype 47,XYY. Analysis of DNA with the technique of MLPA (Multiplex Ligation-dependent Probe Amplification) using kits a combination of kits (P064, P036, P070, and P029) identified an atypical deletion on 7q11.23. In addition, high resolution SNP Oligonucleotide Microarray Analysis (SNP-array) confirmed the alterations found by MLPA and revealed others pathogenic CNVs, in the chromosomes 7 and X. The present report demonstrates an association not yet described in literature, between Williams-Beuren syndrome and 47,XYY. The identification of atypical deletion in 7q11.23 concomitant to additional pathogenic CNVs in others genomic regions allows a better comprehension of clinical consequences of atypical genomic rearrangements. © 2015 Wiley Periodicals, Inc.

  2. Hotspot swells revisited

    Science.gov (United States)

    King, Scott D.; Adam, Claudia

    2014-10-01

    The first attempts to quantify the width and height of hotspot swells were made more than 30 years ago. Since that time, topography, ocean-floor age, and sediment thickness datasets have improved considerably. Swell heights and widths have been used to estimate the heat flow from the core-mantle boundary, constrain numerical models of plumes, and as an indicator of the origin of hotspots. In this paper, we repeat the analysis of swell geometry and buoyancy flux for 54 hotspots, including the 37 considered by Sleep (1990) and the 49 considered by Courtillot et al. (2003), using the latest and most accurate data. We are able to calculate swell geometry for a number of hotspots that Sleep was only able to estimate by comparison with other swells. We find that in spite of the increased resolution in global bathymetry models there is significant uncertainty in our calculation of buoyancy fluxes due to differences in our measurement of the swells’ width and height, the integration method (volume integration or cross-sectional area), and the variations of the plate velocities between HS2-Nuvel1a (Gripp and Gordon, 1990) and HS3-Nuvel1a (Gripp and Gordon, 2002). We also note that the buoyancy flux for Pacific hotspots is in general larger than for Eurasian, North American, African and Antarctic hotspots. Considering that buoyancy flux is linearly related to plate velocity, we speculate that either the calculation of buoyancy flux using plate velocity over-estimates the actual vertical flow of material from the deep mantle or that convection in the Pacific hemisphere is more vigorous than the Atlantic hemisphere.

  3. Genomic diversity guides conservation strategies among rare terrestrial orchid species when taxonomy remains uncertain.

    Science.gov (United States)

    Ahrens, Collin W; Supple, Megan A; Aitken, Nicola C; Cantrill, David J; Borevitz, Justin O; James, Elizabeth A

    2017-06-01

    Species are often used as the unit for conservation, but may not be suitable for species complexes where taxa are difficult to distinguish. Under such circumstances, it may be more appropriate to consider species groups or populations as evolutionarily significant units (ESUs). A population genomic approach was employed to investigate the diversity within and among closely related species to create a more robust, lineage-specific conservation strategy for a nationally endangered terrestrial orchid and its relatives from south-eastern Australia. Four putative species were sampled from a total of 16 populations in the Victorian Volcanic Plain (VVP) bioregion and one population of a sub-alpine outgroup in south-eastern Australia. Morphological measurements were taken in situ along with leaf material for genotyping by sequencing (GBS) and microsatellite analyses. Species could not be differentiated using morphological measurements. Microsatellite and GBS markers confirmed the outgroup as distinct, but only GBS markers provided resolution of population genetic structure. The nationally endangered Diuris basaltica was indistinguishable from two related species ( D. chryseopsis and D. behrii ), while the state-protected D. gregaria showed genomic differentiation. Genomic diversity identified among the four Diuris species suggests that conservation of this taxonomically complex group will be best served by considering them as one ESU rather than separately aligned with species as currently recognized. This approach will maximize evolutionary potential among all species during increased isolation and environmental change. The methods used here can be applied generally to conserve evolutionary processes for groups where taxonomic uncertainty hinders the use of species as conservation units. © The Author 2017. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  4. Genomic comparison of invasive and rare non-invasive strains reveals Porphyromonas gingivalis genetic polymorphisms

    Directory of Open Access Journals (Sweden)

    Svetlana Dolgilevich

    2011-03-01

    Full Text Available Porphyromonas gingivalis strains are shown to invade human cells in vitro with different invasion efficiencies, varying by up to three orders of magnitude.We tested the hypothesis that invasion-associated interstrain genomic polymorphisms are present in P. gingivalis and that putative invasion-associated genes can contribute to P. gingivalis invasion.Using an invasive (W83 and the only available non-invasive P. gingivalis strain (AJW4 and whole genome microarrays followed by two separate software tools, we carried out comparative genomic hybridization (CGH analysis.We identified 68 annotated and 51 hypothetical open reading frames (ORFs that are polymorphic between these strains. Among these are surface proteins, lipoproteins, capsular polysaccharide biosynthesis enzymes, regulatory and immunoreactive proteins, integrases, and transposases often with abnormal GC content and clustered on the chromosome. Amplification of selected ORFs was used to validate the approach and the selection. Eleven clinical strains were investigated for the presence of selected ORFs. The putative invasion-associated ORFs were present in 10 of the isolates. The invasion ability of three isogenic mutants, carrying deletions in PG0185, PG0186, and PG0982 was tested. The PG0185 (ragA and PG0186 (ragB mutants had 5.1×103-fold and 3.6×103-fold decreased in vitro invasion ability, respectively.The annotation of divergent ORFs suggests deficiency in multiple genes as a basis for P. gingivalis non-invasive phenotype. Access the supplementary material to this article: Supplement, table (see Supplementary files under Reading Tools online.

  5. Systematic Functional Interrogation of Rare Cancer Variants Identifies Oncogenic Alleles | Office of Cancer Genomics

    Science.gov (United States)

    Cancer genome characterization efforts now provide an initial view of the somatic alterations in primary tumors. However, most point mutations occur at low frequency, and the function of these alleles remains undefined. We have developed a scalable systematic approach to interrogate the function of cancer-associated gene variants. We subjected 474 mutant alleles curated from 5,338 tumors to pooled in vivo tumor formation assays and gene expression profiling. We identified 12 transforming alleles, including two in genes (PIK3CB, POT1) that have not been shown to be tumorigenic.

  6. Rare genomic variants link bipolar disorder to CREB regulated intracellular signaling pathways

    Directory of Open Access Journals (Sweden)

    Berit eKerner

    2013-11-01

    Full Text Available Bipolar disorder is a common, complex, and severe psychiatric disorder with cyclical disturbances of mood and a high suicide rate. Here, we describe a family with four siblings, three affected females and one unaffected male. The disease course was characterized by early-onset bipolar disorder and co-morbid anxiety spectrum disorders that followed the onset of bipolar disorder. Genetic risk factors were suggested by the early onset of the disease, the severe disease course, including multiple suicide attempts, and lack of adverse prenatal or early life events. In particular, drug and alcohol abuse did not contribute to the disease onset. Exome sequencing identified very rare, heterozygous, and likely protein-damaging variants in eight brain-expressed genes: IQUB, JMJD1C, GADD45A, GOLGB1, PLSCR5, VRK2, MESDC2, and FGGY. The variants were shared among all three affected family members but absent in the unaffected sibling and in more than 200 controls. The genes encode proteins with significant regulatory roles in the ERK/MAPK and CREB-regulated intracellular signaling pathways. These pathways are central to neuronal and synaptic plasticity, cognition, affect regulation and response to chronic stress. In addition, proteins in these pathways are the target of commonly used mood stabilizing drugs, such as tricyclic antidepressants, lithium and valproic acid. The combination of multiple rare, damaging mutations in these central pathways could lead to reduced resilience and increased vulnerability to stressful life events. Our results support a new model for psychiatric disorders, in which multiple rare, damaging mutations in genes functionally related to a common signaling pathway contribute to the manifestation of bipolar disorder.

  7. Rare HIV-1 Subtype J Genomes and a New H/U/CRF02_AG Recombinant Genome Suggests an Ancient Origin of HIV-1 in Angola.

    Science.gov (United States)

    Bártolo, Inês; Calado, Rita; Borrego, Pedro; Leitner, Thomas; Taveira, Nuno

    2016-08-01

    Angola has an extremely diverse HIV-1 epidemic fueled in part by the frequent interchange of people with the Democratic Republic of Congo (DRC) and Republic of Congo (RC). Characterization of HIV-1 strains circulating in Angola should help to better understand the origin of HIV-1 subtypes and recombinant forms and their transmission dynamics. In this study we characterize the first near full-length HIV-1 genomic sequences from HIV-1 infected individuals from Angola. Samples were obtained in 1993 from three HIV-1 infected patients living in Cabinda, Angola. Near full-length genomic sequences were obtained from virus isolates. Maximum likelihood phylogenetic tree inference and analyses of potential recombination patterns were performed to evaluate the sequence classifications and origins. Phylogenetic and recombination analyses revealed that one virus was a pure subtype J, another mostly subtype J with a small uncertain region, and the final virus was classified as a H/U/CRF02_AG recombinant. Consistent with their epidemiological data, the subtype J sequences were more closely related to each other than to other J sequences previously published. Based on the env gene, taxa from Angola occur throughout the global subtype J phylogeny. HIV-1 subtypes J and H are present in Angola at low levels since at least 1993. Low transmission efficiency and/or high recombination potential may explain their limited epidemic success in Angola and worldwide. The high diversity of rare subtypes in Angola suggests that Angola was part of the early establishment of the HIV-1 pandemic.

  8. Dissecting genomic hotspots underlying seed protein, oil, and sucrose content in an interspecific mapping population of soybean using high-density linkage mapping.

    Science.gov (United States)

    Patil, Gunvant; Vuong, Tri D; Kale, Sandip; Valliyodan, Babu; Deshmukh, Rupesh; Zhu, Chengsong; Wu, Xiaolei; Bai, Yonghe; Yungbluth, Dennis; Lu, Fang; Kumpatla, Siva; Grover Shannon, J; Varshney, Rajeev K; Nguyen, Henry T

    2018-04-04

    The cultivated [Glycine max (L) Merr.] and wild [Glycine soja Siebold & Zucc.] soybean species comprise wide variation in seed composition traits. Compared to wild soybean, cultivated soybean contains low protein, high oil and high sucrose. In this study, an inter-specific population was derived from a cross between G. max (Williams 82) and G. soja (PI 483460B). This recombinant inbred line (RIL) population of 188 lines was sequenced at 0.3x depth. Based on 91,342 single nucleotide polymorphisms (SNPs), recombination events in RILs were defined, and a high-resolution bin map was developed (4,070 bins). In addition to bin mapping, QTL analysis for protein, oil and sucrose was performed using 3,343 polymorphic SNPs (3K-SNP), derived from Illumina Infinium BeadChip sequencing platform. The QTL regions from both platforms were compared and a significant concordance was observed between bin and 3K-SNP markers. Importantly, the bin map derived from next generation sequencing technology enhanced mapping resolution (from 1325 Kb to 50 Kb). A total of 5, 9 and 4 QTLs were identified for protein, oil and sucrose content, respectively and some of the QTLs coincided with soybean domestication related genomic loci. The major QTL for protein and oil was mapped on Chr. 20 (qPro_20) and suggested negative correlation between oil and protein. In terms of sucrose content, a novel and major QTL was identified on Chr. 8 (qSuc_08) and harbors putative genes involved in sugar transport. In addition, genome-wide association (GWAS) using 91,342 SNPs confirmed the genomic loci derived from QTL mapping. A QTL based haplotype using whole genome resequencing of 106 diverse soybean lines identified unique allelic variation in wild soybean that could be utilized to widen the genetic base in cultivated soybean. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  9. High coverage of the complete mitochondrial genome of the rare Gray's beaked whale (Mesoplodon grayi) using Illumina next generation sequencing.

    Science.gov (United States)

    Thompson, Kirsten F; Patel, Selina; Williams, Liam; Tsai, Peter; Constantine, Rochelle; Baker, C Scott; Millar, Craig D

    2016-01-01

    Using an Illumina platform, we shot-gun sequenced the complete mitochondrial genome of Gray's beaked whale (Mesoplodon grayi) to an average coverage of 152X. We performed a de novo assembly using SOAPdenovo2 and determined the total mitogenome length to be 16,347 bp. The nucleotide composition was asymmetric (33.3% A, 24.6% C, 12.6% G, 29.5% T) with an overall GC content of 37.2%. The gene organization was similar to that of other cetaceans with 13 protein-coding genes, 2 rRNAs (12S and 16S), 22 predicted tRNAs and 1 control region or D-loop. We found no evidence of heteroplasmy or nuclear copies of mitochondrial DNA in this individual. Beaked whales within the genus Mesoplodon are rarely seen at sea and their basic biology is poorly understood. These data will contribute to resolving the phylogeography and population ecology of this speciose group.

  10. Standardized analysis and sharing of genome-phenome data for neuromuscular and rare disease research through the RD-Connect platform

    OpenAIRE

    Thompson, Rachel; Beltran, Sergi; Papakonstantinou, Anastasios; Cañada, Andrés; Fernández, Jose Maria; Thompson, Mark; Kaliyaperumal, Rajaram; Lair, Séverine; Sernadela, Pedro; Girdea, Marta; Brudno, Michael; Blavier, André; Lochmüller, Hanns; Roos, Andreas; Straub, Volker

    2016-01-01

    Abstract: RD-Connect (rd-connect.eu) is an EU-funded project building an integrated platform to narrow the gaps in rare disease research, where patient populations, clinical expertise and research communities are small in number and highly fragmented. Guided by the needs of rare disease researchers and with neuromuscular and neurodegenerative researchers as its original collaborators, the RD-Connect platform securely integrates multiple types of omics data (genomics, proteomics and transcript...

  11. Hotspots in Hindsight

    Science.gov (United States)

    Julian, B. R.; Foulger, G. R.; Hatfield, O.; Jackson, S.; Simpson, E.; Einbeck, J.; Moore, A.

    2014-12-01

    Torsvik et al. [2006] suggest that the original locations of large igneous provinces ("LIPs") and kimberlites, and current locations of melting anomalies (hot-spots) lie preferentially above the margins of two Large Lower-Mantle Shear Velocity Provinces" (LLSVPs), at the base of the mantle, and that the correlation has a high significance level (> 99.9999%). They conclude the LLSVP margins are Plume-Generation Zones, and deep-mantle plumes cause hotspots and LIPs. This conclusion raises questions about what physical processes could be responsible, because, for example the LLSVPs are likely dense and not abnormally hot [Trampert et al., 2004]. The supposed LIP-hotspot-LLSVP correlations probably are examples of the "Hindsight Heresy" [Acton, 1959], of basing a statistical test upon the same data sample that led to the initial formulation of a hypothesis. In doing this, many competing hypotheses will have been considered and rejected, but this fact will not be taken into account in statistical assessments. Furthermore, probabilities will be computed for many subsets and combinations of the data, and the best-correlated cases will be cited, but this fact will not be taken into account either. Tests using independent hot-spot catalogs and mantle models suggest that the actual significance levels of the correlations are two or three orders of magnitude smaller than claimed. These tests also show that hot spots correlate well with presumably shallowly rooted features such as spreading plate boundaries. Consideration of the kimberlite dataset in the context of geological setting suggests that their apparent association with the LLSVP margins results from the fact that the Kaapvaal craton, the site of most of the kimberlites considered, lies in Southern Africa. These observations raise questions about the distinction between correlation and causation and underline the necessity to take geological factors into account. Fig: Left: Cumulative distributions of distances from

  12. Population Demographic History Can Cause the Appearance of Recombination Hotspots

    Science.gov (United States)

    Johnston, Henry R.; Cutler, David J.

    2012-01-01

    Although the prevailing view among geneticists suggests that recombination hotspots exist ubiquitously across the human genome, there is only limited experimental evidence from a few genomic regions to support the generality of this claim. A small number of true recombination hotspots are well supported experimentally, but the vast majority of hotspots have been identified on the basis of population genetic inferences from the patterns of linkage disequilibrium (LD) seen in the human population. These inferences are made assuming a particular model of human history, and one of the assumptions of that model is that the effective population size of humans has remained constant throughout our history. Our results show that relaxation of the constant population size assumption can create LD and variation patterns that are qualitatively and quantitatively similar to human populations without any need to invoke localized hotspots of recombination. In other words, apparent recombination hotspots could be an artifact of variable population size over time. Several lines of evidence suggest that the vast majority of hotspots identified on the basis of LD information are unlikely to have elevated recombination rates. PMID:22560089

  13. Using ecological niche modeling to determine avian richness hotspots

    Directory of Open Access Journals (Sweden)

    R. Mirzaei

    2017-04-01

    Full Text Available Understanding distributions of wildlife species is a key step towards identifying biodiversity hotspots and designing effective conservation strategies. In this paper, the spatial pattern of diversity of birds in Golestan Province, Iran was estimated. Ecological niche modeling was used to determine distributions of 144 bird species across the province using a maximum entropy algorithm. Richness maps across all birds, and separately for rare and threatened species, were prepared as approximations to hotspots. Results showed close similarity between hotspots for all birds and those for rare birds; hotspots were concentrated in the southern and especially the southwestern parts of the province. Hotspots for threatened birds tended more to the central and especially the western parts of the province, which include coastal habitats. Based on three criteria, it is clear that the western part is the most important area of the province in terms of bird Faunas. Despite some shortcomings, hotspot analysis for birds could be applied to guide conservation efforts and provide useful tool towards efficient conservation action.

  14. The potential of shifting recombination hotspots to increase genetic gain in livestock breeding.

    Science.gov (United States)

    Gonen, Serap; Battagin, Mara; Johnston, Susan E; Gorjanc, Gregor; Hickey, John M

    2017-07-04

    This study uses simulation to explore and quantify the potential effect of shifting recombination hotspots on genetic gain in livestock breeding programs. We simulated three scenarios that differed in the locations of quantitative trait nucleotides (QTN) and recombination hotspots in the genome. In scenario 1, QTN were randomly distributed along the chromosomes and recombination was restricted to occur within specific genomic regions (i.e. recombination hotspots). In the other two scenarios, both QTN and recombination hotspots were located in specific regions, but differed in whether the QTN occurred outside of (scenario 2) or inside (scenario 3) recombination hotspots. We split each chromosome into 250, 500 or 1000 regions per chromosome of which 10% were recombination hotspots and/or contained QTN. The breeding program was run for 21 generations of selection, after which recombination hotspot regions were kept the same or were shifted to adjacent regions for a further 80 generations of selection. We evaluated the effect of shifting recombination hotspots on genetic gain, genetic variance and genic variance. Our results show that shifting recombination hotspots reduced the decline of genetic and genic variance by releasing standing allelic variation in the form of new allele combinations. This in turn resulted in larger increases in genetic gain. However, the benefit of shifting recombination hotspots for increased genetic gain was only observed when QTN were initially outside recombination hotspots. If QTN were initially inside recombination hotspots then shifting them decreased genetic gain. Shifting recombination hotspots to regions of the genome where recombination had not occurred for 21 generations of selection (i.e. recombination deserts) released more of the standing allelic variation available in each generation and thus increased genetic gain. However, whether and how much increase in genetic gain was achieved by shifting recombination hotspots depended

  15. Transcription factor cooperativity in early adipogenic hotspots and super-enhancers

    DEFF Research Database (Denmark)

    Siersbæk, Rasmus; Rabiee, Atefeh; Nielsen, Ronni

    2014-01-01

    . Using a combination of advanced proteomics and genomics approaches, we identify ∼12,000 transcription factor hotspots (∼400 bp) in the early phase of adipogenesis, and we find evidence of both simultaneous and sequential binding of transcription factors at these regions. We demonstrate that hotspots...

  16. Rare copy number alterations and copy-neutral loss of heterozygosity revealed in ameloblastomas by high-density whole-genome microarray analysis.

    Science.gov (United States)

    Diniz, Marina Gonçalves; Duarte, Alessandra Pires; Villacis, Rolando A; Guimarães, Bruna V A; Duarte, Luiz Cláudio Pires; Rogatto, Sílvia R; Gomez, Ricardo Santiago; Gomes, Carolina Cavaliéri

    2017-05-01

    Ameloblastoma (unicystic, UA, or multicystic, MA) is a rare tumor associated with bone destruction and facial deformity. Its malignant counterpart is the ameloblastic carcinoma (AC). The BRAFV600E mutation is highly prevalent in all these tumors subtypes and cannot account for their different clinical behaviors. We assessed copy number alterations (CNAs) and copy-neutral loss of heterozygosity (cnLOH) in UA (n = 2), MA (n = 3), and AC (n = 1) using the CytoScan HD Array (Affymetrix) and the BRAFV600E status. RT-qPCR was applied in four selected genes (B4GALT1, BAG1, PKD1L2, and PPP2R5A) covered by rare alterations, also including three MA and four normal oral tissues. Fifty-seven CNAs and cnLOH were observed in the ameloblastomas and six CNAs in the AC. Seven of the CNAs were rare (six in UA and one in MA), four of them encompassing genes (gains of 7q11.21, 1q32.3, and 9p21.1 and loss of 16q23.2). We found positive correlation between rare CNA gene dosage and the expression of B4GALT1, BAG1, PKD1L2, and PPP2R5A. The AC and 1 UA were BRAF wild-type; however, this UA showed rare genomic alterations encompassing genes associated with RAF/MAPK activation. Ameloblastomas show rare CNAs and cnLOH, presenting a specific genomic profile with no overlapping of the rare alterations among UA, MA, and AC. These genomic changes might play a role in tumor evolution and in BRAFV600E-negative tumors. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  17. High resolution melting curve analysis targeting the HBB gene mutational hot-spot offers a reliable screening approach for all common as well as most of the rare beta-globin gene mutations in Bangladesh.

    Science.gov (United States)

    Islam, Md Tarikul; Sarkar, Suprovath Kumar; Sultana, Nusrat; Begum, Mst Noorjahan; Bhuyan, Golam Sarower; Talukder, Shezote; Muraduzzaman, A K M; Alauddin, Md; Islam, Mohammad Sazzadul; Biswas, Pritha Promita; Biswas, Aparna; Qadri, Syeda Kashfi; Shirin, Tahmina; Banu, Bilquis; Sadya, Salma; Hussain, Manzoor; Sarwardi, Golam; Khan, Waqar Ahmed; Mannan, Mohammad Abdul; Shekhar, Hossain Uddin; Chowdhury, Emran Kabir; Sajib, Abu Ashfaqur; Akhteruzzaman, Sharif; Qadri, Syed Saleheen; Qadri, Firdausi; Mannoor, Kaiissar

    2018-01-02

    Bangladesh lies in the global thalassemia belt, which has a defined mutational hot-spot in the beta-globin gene. The high carrier frequencies of beta-thalassemia trait and hemoglobin E-trait in Bangladesh necessitate a reliable DNA-based carrier screening approach that could supplement the use of hematological and electrophoretic indices to overcome the barriers of carrier screening. With this view in mind, the study aimed to establish a high resolution melting (HRM) curve-based rapid and reliable mutation screening method targeting the mutational hot-spot of South Asian and Southeast Asian countries that encompasses exon-1 (c.1 - c.92), intron-1 (c.92 + 1 - c.92 + 130) and a portion of exon-2 (c.93 - c.217) of the HBB gene which harbors more than 95% of mutant alleles responsible for beta-thalassemia in Bangladesh. Our HRM approach could successfully differentiate ten beta-globin gene mutations, namely c.79G > A, c.92 + 5G > C, c.126_129delCTTT, c.27_28insG, c.46delT, c.47G > A, c.92G > C, c.92 + 130G > C, c.126delC and c.135delC in heterozygous states from the wild type alleles, implying the significance of the approach for carrier screening as the first three of these mutations account for ~85% of total mutant alleles in Bangladesh. Moreover, different combinations of compound heterozygous mutations were found to generate melt curves that were distinct from the wild type alleles and from one another. Based on the findings, sixteen reference samples were run in parallel to 41 unknown specimens to perform direct genotyping of the beta-thalassemia specimens using HRM. The HRM-based genotyping of the unknown specimens showed 100% consistency with the sequencing result. Targeting the mutational hot-spot, the HRM approach could be successfully applied for screening of beta-thalassemia carriers in Bangladesh as well as in other countries of South Asia and Southeast Asia. The approach could be a useful supplement of hematological and

  18. Effectively identifying regulatory hotspots while capturing expression heterogeneity in gene expression studies

    Science.gov (United States)

    2014-01-01

    Expression quantitative trait loci (eQTL) mapping is a tool that can systematically identify genetic variation affecting gene expression. eQTL mapping studies have shown that certain genomic locations, referred to as regulatory hotspots, may affect the expression levels of many genes. Recently, studies have shown that various confounding factors may induce spurious regulatory hotspots. Here, we introduce a novel statistical method that effectively eliminates spurious hotspots while retaining genuine hotspots. Applied to simulated and real datasets, we validate that our method achieves greater sensitivity while retaining low false discovery rates compared to previous methods. PMID:24708878

  19. Generation of mutation hotspots in ageing bacterial colonies

    DEFF Research Database (Denmark)

    Sekowska, Agnieszka; Wendel, Sofie; Christian Fischer, Emil

    2016-01-01

    : most mutations were located in just a few hotspots in the genome, and over time, mutations increasingly were consistent with the involvement of 8-oxo-guanosine, formed exclusively on the transcribed strand. This work provides strong support for retromutagenesis as a general process creating adaptive...

  20. Geopolitical hotspots : Saudi Arabia

    International Nuclear Information System (INIS)

    Roberts, J.

    2004-01-01

    This presentation reviewed the geopolitics of energy in the Middle East, with particular reference to Saudi Arabia as a potential hotspot. The author examined the question of who actually governs Saudi Arabia and the core relationship between Crown Prince Abdullah and the interior Minister, Prince Nayef. Issues regarding the country's social stability were discussed with reference to the high unemployment rate. The financial security of Saudi Arabia was also discussed with reference to the need for economic and political reform. Expectations for Saudi petroleum output were outlined along with regional spurs for energy competition and OPEC participation

  1. Effects of Demographic History on the Detection of Recombination Hotspots from Linkage Disequilibrium.

    Science.gov (United States)

    Dapper, Amy L; Payseur, Bret A

    2018-02-01

    In some species, meiotic recombination is concentrated in small genomic regions. These "recombination hotspots" leave signatures in fine-scale patterns of linkage disequilibrium, raising the prospect that the genomic landscape of hotspots can be characterized from sequence variation. This approach has led to the inference that hotspots evolve rapidly in some species, but are conserved in others. Historic demographic events, such as population bottlenecks, are known to affect patterns of linkage disequilibrium across the genome, violating population genetic assumptions of this approach. Although such events are prevalent, demographic history is generally ignored when making inferences about the evolution of recombination hotspots. To determine the effect of demography on the detection of recombination hotspots, we use the coalescent to simulate haplotypes with a known recombination landscape. We measure the ability of popular linkage disequilibrium-based programs to detect hotspots across a range of demographic histories, including population bottlenecks, hidden population structure, population expansions, and population contractions. We find that demographic events have the potential to greatly reduce the power and increase the false positive rate of hotspot discovery. Neither the power nor the false positive rate of hotspot detection can be predicted without also knowing the demographic history of the sample. Our results suggest that ignoring demographic history likely overestimates the power to detect hotspots and therefore underestimates the degree of hotspot sharing between species. We suggest strategies for incorporating demographic history into population genetic inferences about recombination hotspots. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  2. Fish-derived nutrient hotspots shape coral reef benthic communities.

    Science.gov (United States)

    Shantz, Andrew A; Ladd, Mark C; Schrack, Elizabeth; Burkepile, Deron E

    2015-12-01

    Animal-derived nutrients play an important role in structuring nutrient regimes within and between ecosystems. When animals undergo repetitive, aggregating behavior through time, they can create nutrient hotspots where rates of biogeochemical activity are higher than those found in the surrounding environment. In turn, these hotspots can influence ecosystem processes and community structure. We examined the potential for reef fishes from the family Haemulidae (grunts) to create nutrient hotspots and the potential impact of these hotspots on reef communities. To do so, we tracked the schooling locations of diurnally migrating grunts, which shelter at reef sites during the day but forage off reef each night, and measured the impact of these fish schools on benthic communities. We found that grunt schools showed a high degree of site fidelity, repeatedly returning to the same coral heads. These aggregations created nutrient hotspots around coral heads where nitrogen and phosphorus delivery was roughly 10 and 7 times the respective rates of delivery to structurally similar sites that lacked schools of these fishes. In turn, grazing rates of herbivorous fishes at grunt-derived hotspots were approximately 3 times those of sites where grunts were rare. These differences in nutrient delivery and grazing led to distinct benthic communities with higher cover of crustose coralline algae and less total algal abundance at grunt aggregation sites. Importantly, coral growth was roughly 1.5 times greater at grunt hotspots, likely due to the important nutrient subsidy. Our results suggest that schooling reef fish and their nutrient subsidies play an important role in mediating community structure on coral reefs and that overfishing may have important negative consequences on ecosystem functions. As such, management strategies must consider mesopredatory fishes in addition to current protection often offered to herbivores and top-tier predators. Furthermore, our results suggest that

  3. Genetic recombination is directed away from functional genomic elements in mice.

    Science.gov (United States)

    Brick, Kevin; Smagulova, Fatima; Khil, Pavel; Camerini-Otero, R Daniel; Petukhova, Galina V

    2012-05-13

    Genetic recombination occurs during meiosis, the key developmental programme of gametogenesis. Recombination in mammals has been recently linked to the activity of a histone H3 methyltransferase, PR domain containing 9 (PRDM9), the product of the only known speciation-associated gene in mammals. PRDM9 is thought to determine the preferred recombination sites--recombination hotspots--through sequence-specific binding of its highly polymorphic multi-Zn-finger domain. Nevertheless, Prdm9 knockout mice are proficient at initiating recombination. Here we map and analyse the genome-wide distribution of recombination initiation sites in Prdm9 knockout mice and in two mouse strains with different Prdm9 alleles and their F(1) hybrid. We show that PRDM9 determines the positions of practically all hotspots in the mouse genome, with the exception of the pseudo-autosomal region (PAR)--the only area of the genome that undergoes recombination in 100% of cells. Surprisingly, hotspots are still observed in Prdm9 knockout mice, and as in wild type, these hotspots are found at H3 lysine 4 (H3K4) trimethylation marks. However, in the absence of PRDM9, most recombination is initiated at promoters and at other sites of PRDM9-independent H3K4 trimethylation. Such sites are rarely targeted in wild-type mice, indicating an unexpected role of the PRDM9 protein in sequestering the recombination machinery away from gene-promoter regions and other functional genomic elements.

  4. Specific modifications of histone tails, but not DNA methylation, mirror the temporal variation of mammalian recombination hotspots.

    Science.gov (United States)

    Zeng, Jia; Yi, Soojin V

    2014-10-16

    Recombination clusters nonuniformly across mammalian genomes at discrete genomic loci referred to as recombination hotspots. Despite their ubiquitous presence, individual hotspots rapidly lose their activities, and the molecular and evolutionary mechanisms underlying such frequent hotspot turnovers (the so-called "recombination hotspot paradox") remain unresolved. Even though some sequence motifs are significantly associated with hotspots, multiple lines of evidence indicate that factors other than underlying sequences, such as epigenetic modifications, may affect the evolution of recombination hotspots. Thus, identifying epigenetic factors that covary with recombination at fine-scale is a promising step for this important research area. It was previously reported that recombination rates correlate with indirect measures of DNA methylation in the human genome. Here, we analyze experimentally determined DNA methylation and histone modification of human sperms, and show that the correlation between DNA methylation and recombination in long-range windows does not hold with respect to the spatial and temporal variation of recombination at hotspots. On the other hand, two histone modifications (H3K4me3 and H3K27me3) overlap extensively with recombination hotspots. Similar trends were observed in mice. These results indicate that specific histone modifications rather than DNA methylation are associated with the rapid evolution of recombination hotspots. Furthermore, many human recombination hotspots occupy "bivalent" chromatin regions that harbor both active (H3K4me3) and repressive (H3K27me3) marks. This may explain why human recombination hotspots tend to occur in nongenic regions, in contrast to yeast and Arabidopsis hotspots that are characterized by generally active chromatins. Our results highlight the dynamic epigenetic underpinnings of recombination hotspot evolution. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for

  5. DNA Sequence-Mediated, Evolutionarily Rapid Redistribution of Meiotic Recombination Hotspots

    Science.gov (United States)

    Wahls, Wayne P.; Davidson, Mari K.

    2011-01-01

    Hotspots regulate the position and frequency of Spo11 (Rec12)-initiated meiotic recombination, but paradoxically they are suicidal and are somehow resurrected elsewhere in the genome. After the DNA sequence-dependent activation of hotspots was discovered in fission yeast, nearly two decades elapsed before the key realizations that (A) DNA site-dependent regulation is broadly conserved and (B) individual eukaryotes have multiple different DNA sequence motifs that activate hotspots. From our perspective, such findings provide a conceptually straightforward solution to the hotspot paradox and can explain other, seemingly complex features of meiotic recombination. We describe how a small number of single-base-pair substitutions can generate hotspots de novo and dramatically alter their distribution in the genome. This model also shows how equilibrium rate kinetics could maintain the presence of hotspots over evolutionary timescales, without strong selective pressures invoked previously, and explains why hotspots localize preferentially to intergenic regions and introns. The model is robust enough to account for all hotspots of humans and chimpanzees repositioned since their divergence from the latest common ancestor. PMID:22084420

  6. Methodology and software to detect viral integration site hot-spots

    Science.gov (United States)

    2011-01-01

    Background Modern gene therapy methods have limited control over where a therapeutic viral vector inserts into the host genome. Vector integration can activate local gene expression, which can cause cancer if the vector inserts near an oncogene. Viral integration hot-spots or 'common insertion sites' (CIS) are scrutinized to evaluate and predict patient safety. CIS are typically defined by a minimum density of insertions (such as 2-4 within a 30-100 kb region), which unfortunately depends on the total number of observed VIS. This is problematic for comparing hot-spot distributions across data sets and patients, where the VIS numbers may vary. Results We develop two new methods for defining hot-spots that are relatively independent of data set size. Both methods operate on distributions of VIS across consecutive 1 Mb 'bins' of the genome. The first method 'z-threshold' tallies the number of VIS per bin, converts these counts to z-scores, and applies a threshold to define high density bins. The second method 'BCP' applies a Bayesian change-point model to the z-scores to define hot-spots. The novel hot-spot methods are compared with a conventional CIS method using simulated data sets and data sets from five published human studies, including the X-linked ALD (adrenoleukodystrophy), CGD (chronic granulomatous disease) and SCID-X1 (X-linked severe combined immunodeficiency) trials. The BCP analysis of the human X-linked ALD data for two patients separately (774 and 1627 VIS) and combined (2401 VIS) resulted in 5-6 hot-spots covering 0.17-0.251% of the genome and containing 5.56-7.74% of the total VIS. In comparison, the CIS analysis resulted in 12-110 hot-spots covering 0.018-0.246% of the genome and containing 5.81-22.7% of the VIS, corresponding to a greater number of hot-spots as the data set size increased. Our hot-spot methods enable one to evaluate the extent of VIS clustering, and formally compare data sets in terms of hot-spot overlap. Finally, we show that the

  7. A recombination hotspot in a schizophrenia-associated region of GABRB2.

    Directory of Open Access Journals (Sweden)

    Siu-Kin Ng

    Full Text Available BACKGROUND: Schizophrenia is a major disorder with complex genetic mechanisms. Earlier, population genetic studies revealed the occurrence of strong positive selection in the GABRB2 gene encoding the beta(2 subunit of GABA(A receptors, within a segment of 3,551 bp harboring twenty-nine single nucleotide polymorphisms (SNPs and containing schizophrenia-associated SNPs and haplotypes. METHODOLOGY/PRINCIPAL FINDINGS: In the present study, the possible occurrence of recombination in this 'S1-S29' segment was assessed. The occurrence of hotspot recombination was indicated by high resolution recombination rate estimation, haplotype diversity, abundance of rare haplotypes, recurrent mutations and torsos in haplotype networks, and experimental haplotyping of somatic and sperm DNA. The sub-segment distribution of relative recombination strength, measured by the ratio of haplotype diversity (H(d over mutation rate (theta, was indicative of a human specific Alu-Yi6 insertion serving as a central recombining sequence facilitating homologous recombination. Local anomalous DNA conformation attributable to the Alu-Yi6 element, as suggested by enhanced DNase I sensitivity and obstruction to DNA sequencing, could be a contributing factor of the increased sequence diversity. Linkage disequilibrium (LD analysis yielded prominent low LD points that supported ongoing recombination. LD contrast revealed significant dissimilarity between control and schizophrenic cohorts. Among the large array of inferred haplotypes, H26 and H73 were identified to be protective, and H19 and H81 risk-conferring, toward the development of schizophrenia. CONCLUSIONS/SIGNIFICANCE: The co-occurrence of hotspot recombination and positive selection in the S1-S29 segment of GABRB2 has provided a plausible contribution to the molecular genetics mechanisms for schizophrenia. The present findings therefore suggest that genome regions characterized by the co-occurrence of positive selection and

  8. Clinical significance of rare copy number variations in epilepsy: a case-control survey using microarray-based comparative genomic hybridization.

    Science.gov (United States)

    Striano, Pasquale; Coppola, Antonietta; Paravidino, Roberta; Malacarne, Michela; Gimelli, Stefania; Robbiano, Angela; Traverso, Monica; Pezzella, Marianna; Belcastro, Vincenzo; Bianchi, Amedeo; Elia, Maurizio; Falace, Antonio; Gazzerro, Elisabetta; Ferlazzo, Edoardo; Freri, Elena; Galasso, Roberta; Gobbi, Giuseppe; Molinatto, Cristina; Cavani, Simona; Zuffardi, Orsetta; Striano, Salvatore; Ferrero, Giovanni Battista; Silengo, Margherita; Cavaliere, Maria Luigia; Benelli, Matteo; Magi, Alberto; Piccione, Maria; Dagna Bricarelli, Franca; Coviello, Domenico A; Fichera, Marco; Minetti, Carlo; Zara, Federico

    2012-03-01

    To perform an extensive search for genomic rearrangements by microarray-based comparative genomic hybridization in patients with epilepsy. Prospective cohort study. Epilepsy centers in Italy. Two hundred seventy-nine patients with unexplained epilepsy, 265 individuals with nonsyndromic mental retardation but no epilepsy, and 246 healthy control subjects were screened by microarray-based comparative genomic hybridization. Identification of copy number variations (CNVs) and gene enrichment. Rare CNVs occurred in 26 patients (9.3%) and 16 healthy control subjects (6.5%) (P = .26). The CNVs identified in patients were larger (P = .03) and showed higher gene content (P = .02) than those in control subjects. The CNVs larger than 1 megabase (P = .002) and including more than 10 genes (P = .005) occurred more frequently in patients than in control subjects. Nine patients (34.6%) among those harboring rare CNVs showed rearrangements associated with emerging microdeletion or microduplication syndromes. Mental retardation and neuropsychiatric features were associated with rare CNVs (P = .004), whereas epilepsy type was not. The CNV rate in patients with epilepsy and mental retardation or neuropsychiatric features is not different from that observed in patients with mental retardation only. Moreover, significant enrichment of genes involved in ion transport was observed within CNVs identified in patients with epilepsy. Patients with epilepsy show a significantly increased burden of large, rare, gene-rich CNVs, particularly when associated with mental retardation and neuropsychiatric features. The limited overlap between CNVs observed in the epilepsy group and those observed in the group with mental retardation only as well as the involvement of specific (ion channel) genes indicate a specific association between the identified CNVs and epilepsy. Screening for CNVs should be performed for diagnostic purposes preferentially in patients with epilepsy and mental retardation or

  9. Sequence requirement of the ade6-4095 meiotic recombination hotspot in Schizosaccharomyces pombe.

    Science.gov (United States)

    Foulis, Steven J; Fowler, Kyle R; Steiner, Walter W

    2018-02-01

    Homologous recombination occurs at a greatly elevated frequency in meiosis compared to mitosis and is initiated by programmed double-strand DNA breaks (DSBs). DSBs do not occur at uniform frequency throughout the genome in most organisms, but occur preferentially at a limited number of sites referred to as hotspots. The location of hotspots have been determined at nucleotide-level resolution in both the budding and fission yeasts, and while several patterns have emerged regarding preferred locations for DSB hotspots, it remains unclear why particular sites experience DSBs at much higher frequency than other sites with seemingly similar properties. Short sequence motifs, which are often sites for binding of transcription factors, are known to be responsible for a number of hotspots. In this study we identified the minimum sequence required for activity of one of such motif identified in a screen of random sequences capable of producing recombination hotspots. The experimentally determined sequence, GGTCTRGACC, closely matches the previously inferred sequence. Full hotspot activity requires an effective sequence length of 9.5 bp, whereas moderate activity requires an effective sequence length of approximately 8.2 bp and shows significant association with DSB hotspots. In combination with our previous work, this result is consistent with a large number of different sequence motifs capable of producing recombination hotspots, and supports a model in which hotspots can be rapidly regenerated by mutation as they are lost through recombination.

  10. VT Biodiversity Project - Biological Hotspots

    Data.gov (United States)

    Vermont Center for Geographic Information — (Link to Metadata) This dataset is the result of an effort to map biological "hotspots" in Vermont based on the "element occurrences" in the Nongame and Natural...

  11. HIV protein sequence hotspots for crosstalk with host hub proteins.

    Directory of Open Access Journals (Sweden)

    Mahdi Sarmady

    Full Text Available HIV proteins target host hub proteins for transient binding interactions. The presence of viral proteins in the infected cell results in out-competition of host proteins in their interaction with hub proteins, drastically affecting cell physiology. Functional genomics and interactome datasets can be used to quantify the sequence hotspots on the HIV proteome mediating interactions with host hub proteins. In this study, we used the HIV and human interactome databases to identify HIV targeted host hub proteins and their host binding partners (H2. We developed a high throughput computational procedure utilizing motif discovery algorithms on sets of protein sequences, including sequences of HIV and H2 proteins. We identified as HIV sequence hotspots those linear motifs that are highly conserved on HIV sequences and at the same time have a statistically enriched presence on the sequences of H2 proteins. The HIV protein motifs discovered in this study are expressed by subsets of H2 host proteins potentially outcompeted by HIV proteins. A large subset of these motifs is involved in cleavage, nuclear localization, phosphorylation, and transcription factor binding events. Many such motifs are clustered on an HIV sequence in the form of hotspots. The sequential positions of these hotspots are consistent with the curated literature on phenotype altering residue mutations, as well as with existing binding site data. The hotspot map produced in this study is the first global portrayal of HIV motifs involved in altering the host protein network at highly connected hub nodes.

  12. 'You should at least ask'. The expectations, hopes and fears of rare disease patients on large-scale data and biomaterial sharing for genomics research.

    Science.gov (United States)

    McCormack, Pauline; Kole, Anna; Gainotti, Sabina; Mascalzoni, Deborah; Molster, Caron; Lochmüller, Hanns; Woods, Simon

    2016-10-01

    Within the myriad articles about participants' opinions of genomics research, the views of a distinct group - people with a rare disease (RD) - are unknown. It is important to understand if their opinions differ from the general public by dint of having a rare disease and vulnerabilities inherent in this. Here we document RD patients' attitudes to participation in genomics research, particularly around large-scale, international data and biosample sharing. This work is unique in exploring the views of people with a range of rare disorders from many different countries. The authors work within an international, multidisciplinary consortium, RD-Connect, which has developed an integrated platform connecting databases, registries, biobanks and clinical bioinformatics for RD research. Focus groups were conducted with 52 RD patients from 16 countries. Using a scenario-based approach, participants were encouraged to raise topics relevant to their own experiences, rather than these being determined by the researcher. Issues include wide data sharing, and consent for new uses of historic samples and for children. Focus group members are positively disposed towards research and towards allowing data and biosamples to be shared internationally. Expressions of trust and attitudes to risk are often affected by the nature of the RD which they have experience of, as well as regulatory and cultural practices in their home country. Participants are concerned about data security and misuse. There is an acute recognition of the vulnerability inherent in having a RD and the possibility that open knowledge of this could lead to discrimination.

  13. MODIS Hotspot Validation over Thailand

    Directory of Open Access Journals (Sweden)

    Veerachai Tanpipat

    2009-11-01

    Full Text Available To ensure remote sensing MODIS hotspot (also known as active fire products or hotspots quality and precision in forest fire control and management in Thailand, an increased level of confidence is needed. Accuracy assessment of MODIS hotspots utilizing field survey data validation is described. A quantitative evaluation of MODIS hotspot products has been carried out since the 2007 forest fire season. The carefully chosen hotspots were scattered throughout the country and within the protected areas of the National Parks and Wildlife Sanctuaries. Three areas were selected as test sites for validation guidelines. Both ground and aerial field surveys were also conducted in this study by the Forest Fire Control Division, National Park, Wildlife and Plant Conversation Department, Ministry of Natural Resources and Environment, Thailand. High accuracy of 91.84 %, 95.60% and 97.53% for the 2007, 2008 and 2009 fire seasons were observed, resulting in increased confidence in the use of MODIS hotspots for forest fire control and management in Thailand.

  14. Detecting Recombination Hotspots from Patterns of Linkage Disequilibrium.

    Science.gov (United States)

    Wall, Jeffrey D; Stevison, Laurie S

    2016-08-09

    With recent advances in DNA sequencing technologies, it has become increasingly easy to use whole-genome sequencing of unrelated individuals to assay patterns of linkage disequilibrium (LD) across the genome. One type of analysis that is commonly performed is to estimate local recombination rates and identify recombination hotspots from patterns of LD. One method for detecting recombination hotspots, LDhot, has been used in a handful of species to further our understanding of the basic biology of recombination. For the most part, the effectiveness of this method (e.g., power and false positive rate) is unknown. In this study, we run extensive simulations to compare the effectiveness of three different implementations of LDhot. We find large differences in the power and false positive rates of these different approaches, as well as a strong sensitivity to the window size used (with smaller window sizes leading to more accurate estimation of hotspot locations). We also compared our LDhot simulation results with comparable simulation results obtained from a Bayesian maximum-likelihood approach for identifying hotspots. Surprisingly, we found that the latter computationally intensive approach had substantially lower power over the parameter values considered in our simulations. Copyright © 2016 Wall and Stevison.

  15. Applying Hotspot Detection Methods in Forestry: A Case Study of Chestnut Oak Regeneration

    International Nuclear Information System (INIS)

    Fei, S.

    2010-01-01

    Hotspot detection has been widely adopted in health sciences for disease surveillance, but rarely in natural resource disciplines. In this paper, two spatial scan statistics (SaT Scan and Cluster Seer) and a non spatial classification and regression trees method were evaluated as techniques for identifying chestnut oak (Quercus Montana) regeneration hotspots among 50 mixed-oak stands in the central Appalachian region of the eastern United States. Hotspots defined by the three methods had a moderate level of conformity and revealed similar chestnut oak regeneration site affinity. Chestnut oak regeneration hotspots were positively associated with the abundance of chestnut oak trees in the over story and a moderate cover of heather species (Vaccinium and Gaylussacia spp.) but were negatively associated with the abundance of hay scented fern (Dennstaedtia punctilobula) and mountain laurel (Kalmia latiforia). In general, hotspot detection is a viable tool for assisting natural resource managers with identifying areas possessing significantly high or low tree regeneration.

  16. Applying Hotspot Detection Methods in Forestry: A Case Study of Chestnut Oak Regeneration

    Directory of Open Access Journals (Sweden)

    Songlin Fei

    2010-01-01

    Full Text Available Hotspot detection has been widely adopted in health sciences for disease surveillance, but rarely in natural resource disciplines. In this paper, two spatial scan statistics (SaTScan and ClusterSeer and a nonspatial classification and regression trees method were evaluated as techniques for identifying chestnut oak (Quercus Montana regeneration hotspots among 50 mixed-oak stands in the central Appalachian region of the eastern United States. Hotspots defined by the three methods had a moderate level of conformity and revealed similar chestnut oak regeneration site affinity. Chestnut oak regeneration hotspots were positively associated with the abundance of chestnut oak trees in the overstory and a moderate cover of heather species (Vaccinium and Gaylussacia spp. but were negatively associated with the abundance of hayscented fern (Dennstaedtia punctilobula and mountain laurel (Kalmia latiforia. In general, hotspot detection is a viable tool for assisting natural resource managers with identifying areas possessing significantly high or low tree regeneration.

  17. Microbial micropatches within microbial hotspots

    Science.gov (United States)

    Smith, Renee J.; Tobe, Shanan S.; Paterson, James S.; Seymour, Justin R.; Oliver, Rod L.; Mitchell, James G.

    2018-01-01

    The spatial distributions of organism abundance and diversity are often heterogeneous. This includes the sub-centimetre distributions of microbes, which have ‘hotspots’ of high abundance, and ‘coldspots’ of low abundance. Previously we showed that 300 μl abundance hotspots, coldspots and background regions were distinct at all taxonomic levels. Here we build on these results by showing taxonomic micropatches within these 300 μl microscale hotspots, coldspots and background regions at the 1 μl scale. This heterogeneity among 1 μl subsamples was driven by heightened abundance of specific genera. The micropatches were most pronounced within hotspots. Micropatches were dominated by Pseudomonas, Bacteroides, Parasporobacterium and Lachnospiraceae incertae sedis, with Pseudomonas and Bacteroides being responsible for a shift in the most dominant genera in individual hotspot subsamples, representing up to 80.6% and 47.3% average abundance, respectively. The presence of these micropatches implies the ability these groups have to create, establish themselves in, or exploit heterogeneous microenvironments. These genera are often particle-associated, from which we infer that these micropatches are evidence for sub-millimetre aggregates and the aquatic polymer matrix. These findings support the emerging paradigm that the microscale distributions of planktonic microbes are numerically and taxonomically heterogeneous at scales of millimetres and less. We show that microscale microbial hotspots have internal structure within which specific local nutrient exchanges and cellular interactions might occur. PMID:29787564

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

    Science.gov (United States)

    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.

  19. Uncovering genomic causes of co-morbidity in epilepsy: gene-driven phenotypic characterization of rare microdeletions

    NARCIS (Netherlands)

    Kasperavičiūtė, Dalia; Catarino, Claudia B.; Chinthapalli, Krishna; Clayton, Lisa M. S.; Thom, Maria; Martinian, Lillian; Cohen, Hannah; Adalat, Shazia; Bockenhauer, Detlef; Pope, Simon A.; Lench, Nicholas; Koltzenburg, Martin; Duncan, John S.; Hammond, Peter; Hennekam, Raoul C. M.; Land, John M.; Sisodiya, Sanjay M.

    2011-01-01

    Patients with epilepsy often suffer from other important conditions. The existence of such co-morbidities is frequently not recognized and their relationship with epilepsy usually remains unexplained. We describe three patients with common, sporadic, non-syndromic epilepsies in whom large genomic

  20. Biodiversity hotspots house most undiscovered plant species.

    Science.gov (United States)

    Joppa, Lucas N; Roberts, David L; Myers, Norman; Pimm, Stuart L

    2011-08-09

    For most organisms, the number of described species considerably underestimates how many exist. This is itself a problem and causes secondary complications given present high rates of species extinction. Known numbers of flowering plants form the basis of biodiversity "hotspots"--places where high levels of endemism and habitat loss coincide to produce high extinction rates. How different would conservation priorities be if the catalog were complete? Approximately 15% more species of flowering plant are likely still undiscovered. They are almost certainly rare, and depending on where they live, suffer high risks of extinction from habitat loss and global climate disruption. By using a model that incorporates taxonomic effort over time, regions predicted to contain large numbers of undiscovered species are already conservation priorities. Our results leave global conservation priorities more or less intact, but suggest considerably higher levels of species imperilment than previously acknowledged.

  1. Highly polarized emission from the E-hotspot in DA240

    International Nuclear Information System (INIS)

    Tsien, S.C.; Saunders, R.

    1982-01-01

    The hotspot in the eastern lobe of the nearby giant radio galaxy DA240 (z=0.0356) provides a rare opportunity to examine the detailed polarization structure of a hotspot. Maps have been made with the Cambridge 5-km telescope at 2.7 and 5.0 GHz and the 5.0-GHz maps are shown here. The main characteristics are discussed briefly. (Auth.)

  2. Rare CNVs in Suicide Attempt include Schizophrenia-Associated Loci and Neurodevelopmental Genes: A Pilot Genome-Wide and Family-Based Study.

    Directory of Open Access Journals (Sweden)

    Marcus Sokolowski

    Full Text Available Suicidal behavior (SB has a complex etiology involving genes and environment. One of the genetic components in SB could be copy number variations (CNVs, as CNVs are implicated in neurodevelopmental disorders. However, a recently published genome-wide and case-control study did not observe any significant role of CNVs in SB. Here we complemented these initial observations by instead using a family-based trio-sample that is robust to control biases, having severe suicide attempt (SA in offspring as main outcome (n = 660 trios. We first tested for CNV associations on the genome-wide Illumina 1M SNP-array by using FBAT-CNV methodology, which allows for evaluating CNVs without reliance on CNV calling algorithms, analogous to a common SNP-based GWAS. We observed association of certain T-cell receptor markers, but this likely reflected inter-individual variation in somatic rearrangements rather than association with SA outcome. Next, we used the PennCNV software to call 385 putative rare (100 kb CNVs, observed in n = 225 SA offspring. Nine SA offspring had rare CNV calls in a set of previously schizophrenia-associated loci, indicating the importance of such CNVs in certain SA subjects. Several additional, very large (>1MB sized CNV calls in 15 other SA offspring also spanned pathogenic regions or other neural genes of interest. Overall, 45 SA had CNVs enriched for 65 medically relevant genes previously shown to be affected by CNVs, which were characterized by a neurodevelopmental biology. A neurodevelopmental implication was partly congruent with our previous SNP-based GWAS, but follow-up analysis here indicated that carriers of rare CNVs had a decreased burden of common SNP risk-alleles compared to non-carriers. In conclusion, while CNVs did not show genome-wide association by the FBAT-CNV methodology, our preliminary observations indicate rare pathogenic CNVs affecting neurodevelopmental functions in a subset of SA, who were distinct from SA having

  3. A large genome-wide association study of age-related macular degeneration highlights contributions of rare and common variants

    NARCIS (Netherlands)

    L.G. Fritsche (Lars); W. Igl (Wilmar); J.N. Cooke Bailey (Jessica N.); F. Grassmann (Felix); S. Sengupta (Sebanti); J.L. Bragg-Gresham (Jennifer L.); Burdon, K.P. (Kathryn P.); S.J. Hebbring (Scott J.); Wen, C. (Cindy); M. Gorski (Mathias); I.K. Kim (Ivana); Cho, D. (David); Zack, D. (Donald); E.H. Souied (Eric); H.P.N. Scholl (Hendrik); E. Bala (Elisa); ELee, K. (Kristine); D. Hunter (David); Sardell, R.J. (Rebecca J.); P. Mitchell (Paul); J.E. Merriam (Joanna); F. Cipriani (Francesco); Hoffman, J.D. (Joshua D.); T. Schick (Tina); Y.T.E. Lechanteur (Yara T. E.); R.H. Guymer (Robyn); M.P. Johnson (Matthew); Y. Jiang; C.M. Stanton (Chloe); G.H.S. Buitendijk (Gabrielle); X. Zhan (Xiaowei); Kwong, A.M. (Alan M.); A. Boleda (Alexis); M. Brooks (Matthew); L. Gieser (Linn); R. Ratna Priya (Rinki); K.E. Branham (Kari); Foerster, J.R. (Johanna R.); J.R. Heckenlively (John); M.I. Othman (Mohammad); B.J. Vote (Brendan J.); Liang, H.H. (Helena Hai); E. Souzeau (Emmanuelle); McAllister, I.L. (Ian L.); T. Isaacs (Timothy); Hall, J. (Janette); Lake, S. (Stewart); D.A. Mackey (David); Constable, I.J. (Ian J.); J.E. Craig (Jamie E.); T.E. Kitchner (Terrie E.); Yang, Z. (Zhenglin); Su, Z. (Zhiguang); Luo, H. (Hongrong); Chen, D. (Daniel); Ouyang, H. (Hong); K. Flagg (Ken); Lin, D. (Danni); Mao, G. (Guanping); H.A. Ferreyra (Henry); K. Stark (Klaus); C. von Strachwitz (Claudia); Wolf, A. (Armin); C. Brandl (Caroline); Rudolph, G. (Guenther); M. Olden (Matthias); M.A. Morrison (Margaux); D.J. Morgan (Denise); M. Schu (Matthew); Ahn, J. (Jeeyun); G. Silvestri (Giuliana); E.E. Tsironi (Evangelia); Park, K.H. (Kyu Hyung); L.A. Farrer (Lindsay); A. Orlin (Anton); Brucker, A. (Alexander); X. Li (Xiaohui); C.A. Curcio (Christine A.); Mohand-Sa'd, S. (Saddek); J.-A. Sahel (José-Alain); I. Audo (Isabelle); M. Benchaboune (Mustapha); A.J. Cree (Angela); Rennie, C.A. (Christina A.); Goverdhan, S.V. (Srinivas V.); M. Grunin (Michelle); S. Hagbi-Levi (Shira); B. Campochiaro (Betsy); N. Katsanis (Nicholas); J.-B. Holz; F. Blond (Frédéric); Blanché, H. (Hél'ne); Deleuze, J.-F. (Jean-Fran'ois); R.P. Igo Jr. (Robert); B.J. Truitt (Barbara); N.S. Peachey (Neal ); S.M. Meuer (Stacy); C.E. Myers (Chelsea); Moore, E.L. (Emily L.); R. Klein (Ronald); M.A. Hauser (Michael); E.A. Postel (Eric); M.D. Courtenay (Monique D.); S.M. Schwartz (Stephen); J.L. Kovach (Jaclyn); W.K. Scott (William); Liew, G. (Gerald); Tan, A.G. (Ava G.); B. Gopinath (Bamini); J.E. Merriam (Joanna); T. Smith (Tim); J.C. Khan (Jane); M. Shahid (Mohammad); A.T. Moore (Anthony); J.A. McGrath (J Allie); R. Laux (Reneé); M.A. Brantley (Milam); A. Agarwal (Anita); L. Ersoy (Lebriz); A. Caramoy (Albert); T. Langmann (Thomas); N.T.M. Saksens (Nicole T.); Jong, E.K. (Eiko Kde); C. Hoyng (Carel); M.S. Cain (Melinda); A.J. Richardson (Andrea); T.M. Martin (Tammy M.); J. Blangero (John); D.E. Weeks (Daniel); Dhillon, B. (Bal); C.M. van Duijn (Cornelia); K.F. Doheny (Kimberly); Romm, J. (Jane); C.C.W. Klaver (Caroline); C. Hayward (Caroline); Gorin, M.B. (Michael B.); M.L. Klein (Michael); P.N. Baird (Paul); A.I. Hollander (Anneke); Fauser, S. (Sascha); WYates, J.R. (John R.); R. Allikmets (Rando); J.J. Wang (Jie Jin); D.A. Schaumberg (Debra); B.E.K. Klein (Barbara); S.A. Hagstrom (Stephanie); Y. Chowers (Yehuda); A.J. Lotery (Andrew); T. Léveillard (Thierry); K. Zhang (Kang); M.H. Brilliant (Murray H.); A.W. Hewit (Alex); A. Swaroop (Anand); Chew, E.Y. (Emily Y.); M.A. Pericak-Vance (Margaret); M.M. DeAngelis (Margaret); D. Stambolian (Dwight); J.L. Haines (Jonathan); S.K. Iyengar (Sudha); B.H.F. Weber (Bernhard); G.R. Abecasis (Gonçalo); I.M. Heid (Iris)

    2016-01-01

    textabstractAdvanced age-related macular degeneration (AMD) is the leading cause of blindness in the elderly, with limited therapeutic options. Here we report on a study of >12 million variants, including 163,714 directly genotyped, mostly rare, protein-altering variants. Analyzing 16,144 patients

  4. A large genome-wide association study of age-related macular degeneration highlights contributions of rare and common variants

    NARCIS (Netherlands)

    Fritsche, L.G.; Igl, W.; Bailey, J.N.; Grassmann, F.; Sengupta, S; Bragg-Gresham, J.L.; Burdon, K.P.; Hebbring, S.J.; Wen, C.; Gorski, M.; Kim, I.K.; Cho, D.; Zack, D.; Souied, E.; Scholl, H.P.; Bala, E.; Lee, K.E.; Hunter, D.J.; Sardell, R.J.; Mitchell, P.; Merriam, J.E.; Cipriani, V.; Hoffman, J.D.; Schick, T.; Lechanteur, Y.T.; Guymer, R.H.; Johnson, M.P.; Jiang, Y.; Stanton, C.M.; Buitendijk, G.H.; Zhan, X.; Kwong, A.M.; Boleda, A.; Brooks, M.; Gieser, L.; Ratnapriya, R.; Branham, K.E.; Foerster, J.R.; Heckenlively, J.R.; Othman, M.I.; Vote, B.J.; Liang, H.H.; Souzeau, E.; McAllister, I.L.; Isaacs, T.; Hall, J.; Lake, S.; Mackey, D.A.; Constable, I.J.; Craig, J.E.; Kitchner, T.E.; Yang, Z; Su, Z.; Luo, H.; Chen, D.; Ouyang, H.; Flagg, K.; Lin, D.; Mao, G.; Ferreyra, H.; Stark, K.; Strachwitz, C.N. von; Wolf, A.; Brandl, C.; Rudolph, G.; Olden, M.; Morrison, M.A.; Morgan, D.J.; Schu, M.; Ahn, J.; Silvestri, G.; Tsironi, E.E.; Park, K.H.; Farrer, L.A.; Orlin, A.; Brucker, A.; Li, M.; Curcio, C.A.; Mohand-Said, S.; Sahel, J.A.; Audo, I.; Benchaboune, M.; Cree, A.J.; Rennie, C.A.; Goverdhan, S.V.; Grunin, M.; Hagbi-Levi, S.; Campochiaro, P.; Katsanis, N.; Holz, F.G.; Blond, F.; Blanche, H.; Deleuze, J.F.; Igo, R.P., Jr.; Truitt, B.; Peachey, N.S.; Meuer, S.M.; Myers, C.E.; Moore, E.L.; Klein, R.; Hollander, A.I. den; Saksens, N.T.M.; Hoyng, C.B.; Jong, E.K.; et al.,

    2016-01-01

    Advanced age-related macular degeneration (AMD) is the leading cause of blindness in the elderly, with limited therapeutic options. Here we report on a study of >12 million variants, including 163,714 directly genotyped, mostly rare, protein-altering variants. Analyzing 16,144 patients and 17,832

  5. Genomes

    National Research Council Canada - National Science Library

    Brown, T. A. (Terence A.)

    2002-01-01

    ... of genome expression and replication processes, and transcriptomics and proteomics. This text is richly illustrated with clear, easy-to-follow, full color diagrams, which are downloadable from the book's website...

  6. Uncovering genomic causes of co-morbidity in epilepsy: gene-driven phenotypic characterization of rare microdeletions.

    Directory of Open Access Journals (Sweden)

    Dalia Kasperavičiūtė

    Full Text Available Patients with epilepsy often suffer from other important conditions. The existence of such co-morbidities is frequently not recognized and their relationship with epilepsy usually remains unexplained.We describe three patients with common, sporadic, non-syndromic epilepsies in whom large genomic microdeletions were found during a study of genetic susceptibility to epilepsy. We performed detailed gene-driven clinical investigations in each patient. Disruption of the function of genes in the deleted regions can explain co-morbidities in these patients.Co-morbidities in patients with epilepsy can be part of a genomic abnormality even in the absence of (known congenital malformations or intellectual disabilities. Gene-driven phenotype examination can also reveal clinically significant unsuspected condition.

  7. Genomic hypomethylation in the human germline associates with selective structural mutability in the human genome.

    Directory of Open Access Journals (Sweden)

    Jian Li

    Full Text Available The hotspots of structural polymorphisms and structural mutability in the human genome remain to be explained mechanistically. We examine associations of structural mutability with germline DNA methylation and with non-allelic homologous recombination (NAHR mediated by low-copy repeats (LCRs. Combined evidence from four human sperm methylome maps, human genome evolution, structural polymorphisms in the human population, and previous genomic and disease studies consistently points to a strong association of germline hypomethylation and genomic instability. Specifically, methylation deserts, the ~1% fraction of the human genome with the lowest methylation in the germline, show a tenfold enrichment for structural rearrangements that occurred in the human genome since the branching of chimpanzee and are highly enriched for fast-evolving loci that regulate tissue-specific gene expression. Analysis of copy number variants (CNVs from 400 human samples identified using a custom-designed array comparative genomic hybridization (aCGH chip, combined with publicly available structural variation data, indicates that association of structural mutability with germline hypomethylation is comparable in magnitude to the association of structural mutability with LCR-mediated NAHR. Moreover, rare CNVs occurring in the genomes of individuals diagnosed with schizophrenia, bipolar disorder, and developmental delay and de novo CNVs occurring in those diagnosed with autism are significantly more concentrated within hypomethylated regions. These findings suggest a new connection between the epigenome, selective mutability, evolution, and human disease.

  8. Africa's hotspots of biodiversity redefined

    NARCIS (Netherlands)

    Küper, W.; Sommer, J.H.; Lovett, J.C.; Beentje, H.J.; Rompaey, van R.S.A.R.; Chatelain, C.; Sosef, M.S.M.; Barthlott, W.

    2004-01-01

    A key problem for conservation is the coincidence of regions of high biodiversity with regions of high human impact. Twenty-five of the most threatened centers of plant diversity were identified by Myers et al., and these "hotspots" play a crucial role in international conservation strategies. The

  9. Are hotspots of evolutionary potential adequately protected in southern California?

    Science.gov (United States)

    Vandergast, A.G.; Bohonak, A.J.; Hathaway, S.A.; Boys, J.; Fisher, R.N.

    2008-01-01

    Reserves are often designed to protect rare habitats, or "typical" exemplars of ecoregions and geomorphic provinces. This approach focuses on current patterns of organismal and ecosystem-level biodiversity, but typically ignores the evolutionary processes that control the gain and loss of biodiversity at these and other levels (e.g., genetic, ecological). In order to include evolutionary processes in conservation planning efforts, their spatial components must first be identified and mapped. We describe a GIS-based approach for explicitly mapping patterns of genetic divergence and diversity for multiple species (a "multi-species genetic landscape"). Using this approach, we analyzed mitochondrial DNA datasets from 21 vertebrate and invertebrate species in southern California to identify areas with common phylogeographic breaks and high intrapopulation diversity. The result is an evolutionary framework for southern California within which patterns of genetic diversity can be analyzed in the context of historical processes, future evolutionary potential and current reserve design. Our multi-species genetic landscapes pinpoint six hotspots where interpopulation genetic divergence is consistently high, five evolutionary hotspots within which genetic connectivity is high, and three hotspots where intrapopulation genetic diversity is high. These 14 hotspots can be grouped into eight geographic areas, of which five largely are unprotected at this time. The multi-species genetic landscape approach may provide an avenue to readily incorporate measures of evolutionary process into GIS-based systematic conservation assessment and land-use planning.

  10. Evaluating aggregate effects of rare and common variants in the 1000 Genomes Project exon sequencing data using latent variable structural equation modeling.

    Science.gov (United States)

    Nock, Nl; Zhang, Lx

    2011-11-29

    Methods that can evaluate aggregate effects of rare and common variants are limited. Therefore, we applied a two-stage approach to evaluate aggregate gene effects in the 1000 Genomes Project data, which contain 24,487 single-nucleotide polymorphisms (SNPs) in 697 unrelated individuals from 7 populations. In stage 1, we identified potentially interesting genes (PIGs) as those having at least one SNP meeting Bonferroni correction using univariate, multiple regression models. In stage 2, we evaluate aggregate PIG effects on trait, Q1, by modeling each gene as a latent construct, which is defined by multiple common and rare variants, using the multivariate statistical framework of structural equation modeling (SEM). In stage 1, we found that PIGs varied markedly between a randomly selected replicate (replicate 137) and 100 other replicates, with the exception of FLT1. In stage 1, collapsing rare variants decreased false positives but increased false negatives. In stage 2, we developed a good-fitting SEM model that included all nine genes simulated to affect Q1 (FLT1, KDR, ARNT, ELAV4, FLT4, HIF1A, HIF3A, VEGFA, VEGFC) and found that FLT1 had the largest effect on Q1 (βstd = 0.33 ± 0.05). Using replicate 137 estimates as population values, we found that the mean relative bias in the parameters (loadings, paths, residuals) and their standard errors across 100 replicates was on average, less than 5%. Our latent variable SEM approach provides a viable framework for modeling aggregate effects of rare and common variants in multiple genes, but more elegant methods are needed in stage 1 to minimize type I and type II error.

  11. Finding trans-regulatory genes and protein complexes modulating meiotic recombination hotspots of human, mouse and yeast.

    Science.gov (United States)

    Wu, Min; Kwoh, Chee-Keong; Li, Xiaoli; Zheng, Jie

    2014-09-11

    The regulatory mechanism of recombination is one of the most fundamental problems in genomics, with wide applications in genome wide association studies (GWAS), birth-defect diseases, molecular evolution, cancer research, etc. Recombination events cluster into short genomic regions called "recombination hotspots". Recently, a zinc finger protein PRDM9 was reported to regulate recombination hotspots in human and mouse genomes. In addition, a 13-mer motif contained in the binding sites of PRDM9 is found to be enriched in human hotspots. However, this 13-mer motif only covers a fraction of hotspots, indicating that PRDM9 is not the only regulator of recombination hotspots. Therefore, the challenge of discovering other regulators of recombination hotspots becomes significant. Furthermore, recombination is a complex process. Hence, multiple proteins acting as machinery, rather than individual proteins, are more likely to carry out this process in a precise and stable manner. Therefore, the extension of the prediction of individual trans-regulators to protein complexes is also highly desired. In this paper, we introduce a pipeline to identify genes and protein complexes associated with recombination hotspots. First, we prioritize proteins associated with hotspots based on their preference of binding to hotspots and coldspots. Second, using the above identified genes as seeds, we apply the Random Walk with Restart algorithm (RWR) to propagate their influences to other proteins in protein-protein interaction (PPI) networks. Hence, many proteins without DNA-binding information will also be assigned a score to implicate their roles in recombination hotspots. Third, we construct sub-PPI networks induced by top genes ranked by RWR for various species (e.g., yeast, human and mouse) and detect protein complexes in those sub-PPI networks. The GO term analysis show that our prioritizing methods and the RWR algorithm are capable of identifying novel genes associated with

  12. Hopping hotspots: global shifts in marine biodiversity.

    Science.gov (United States)

    Renema, W; Bellwood, D R; Braga, J C; Bromfield, K; Hall, R; Johnson, K G; Lunt, P; Meyer, C P; McMonagle, L B; Morley, R J; O'Dea, A; Todd, J A; Wesselingh, F P; Wilson, M E J; Pandolfi, J M

    2008-08-01

    Hotspots of high species diversity are a prominent feature of modern global biodiversity patterns. Fossil and molecular evidence is starting to reveal the history of these hotspots. There have been at least three marine biodiversity hotspots during the past 50 million years. They have moved across almost half the globe, with their timing and locations coinciding with major tectonic events. The birth and death of successive hotspots highlights the link between environmental change and biodiversity patterns. The antiquity of the taxa in the modern Indo-Australian Archipelago hotspot emphasizes the role of pre-Pleistocene events in shaping modern diversity patterns.

  13. Mammalian transcriptional hotspots are enriched for tissue specific enhancers near cell type specific highly expressed genes and are predicted to act as transcriptional activator hubs.

    Science.gov (United States)

    Joshi, Anagha

    2014-12-30

    Transcriptional hotspots are defined as genomic regions bound by multiple factors. They have been identified recently as cell type specific enhancers regulating developmentally essential genes in many species such as worm, fly and humans. The in-depth analysis of hotspots across multiple cell types in same species still remains to be explored and can bring new biological insights. We therefore collected 108 transcription-related factor (TF) ChIP sequencing data sets in ten murine cell types and classified the peaks in each cell type in three groups according to binding occupancy as singletons (low-occupancy), combinatorials (mid-occupancy) and hotspots (high-occupancy). The peaks in the three groups clustered largely according to the occupancy, suggesting priming of genomic loci for mid occupancy irrespective of cell type. We then characterized hotspots for diverse structural functional properties. The genes neighbouring hotspots had a small overlap with hotspot genes in other cell types and were highly enriched for cell type specific function. Hotspots were enriched for sequence motifs of key TFs in that cell type and more than 90% of hotspots were occupied by pioneering factors. Though we did not find any sequence signature in the three groups, the H3K4me1 binding profile had bimodal peaks at hotspots, distinguishing hotspots from mono-modal H3K4me1 singletons. In ES cells, differentially expressed genes after perturbation of activators were enriched for hotspot genes suggesting hotspots primarily act as transcriptional activator hubs. Finally, we proposed that ES hotspots might be under control of SetDB1 and not DNMT for silencing. Transcriptional hotspots are enriched for tissue specific enhancers near cell type specific highly expressed genes. In ES cells, they are predicted to act as transcriptional activator hubs and might be under SetDB1 control for silencing.

  14. PRDM9 drives evolutionary erosion of hotspots in Mus musculus through haplotype-specific initiation of meiotic recombination.

    Science.gov (United States)

    Baker, Christopher L; Kajita, Shimpei; Walker, Michael; Saxl, Ruth L; Raghupathy, Narayanan; Choi, Kwangbom; Petkov, Petko M; Paigen, Kenneth

    2015-01-01

    Meiotic recombination generates new genetic variation and assures the proper segregation of chromosomes in gametes. PRDM9, a zinc finger protein with histone methyltransferase activity, initiates meiotic recombination by binding DNA at recombination hotspots and directing the position of DNA double-strand breaks (DSB). The DSB repair mechanism suggests that hotspots should eventually self-destruct, yet genome-wide recombination levels remain constant, a conundrum known as the hotspot paradox. To test if PRDM9 drives this evolutionary erosion, we measured activity of the Prdm9Cst allele in two Mus musculus subspecies, M.m. castaneus, in which Prdm9Cst arose, and M.m. domesticus, into which Prdm9Cst was introduced experimentally. Comparing these two strains, we find that haplotype differences at hotspots lead to qualitative and quantitative changes in PRDM9 binding and activity. Using Mus spretus as an outlier, we found most variants affecting PRDM9Cst binding arose and were fixed in M.m. castaneus, suppressing hotspot activity. Furthermore, M.m. castaneus×M.m. domesticus F1 hybrids exhibit novel hotspots, with large haplotype biases in both PRDM9 binding and chromatin modification. These novel hotspots represent sites of historic evolutionary erosion that become activated in hybrids due to crosstalk between one parent's Prdm9 allele and the opposite parent's chromosome. Together these data support a model where haplotype-specific PRDM9 binding directs biased gene conversion at hotspots, ultimately leading to hotspot erosion.

  15. New Tests of the Fixed Hotspot Approximation

    Science.gov (United States)

    Gordon, R. G.; Andrews, D. L.; Horner-Johnson, B. C.; Kumar, R. R.

    2005-05-01

    We present new methods for estimating uncertainties in plate reconstructions relative to the hotspots and new tests of the fixed hotspot approximation. We find no significant motion between Pacific hotspots, on the one hand, and Indo-Atlantic hotspots, on the other, for the past ~ 50 Myr, but large and significant apparent motion before 50 Ma. Whether this motion is truly due to motion between hotspots or alternatively due to flaws in the global plate motion circuit can be tested with paleomagnetic data. These tests give results consistent with the fixed hotspot approximation and indicate significant misfits when a relative plate motion circuit through Antarctica is employed for times before 50 Ma. If all of the misfit to the global plate motion circuit is due to motion between East and West Antarctica, then that motion is 800 ± 500 km near the Ross Sea Embayment and progressively less along the Trans-Antarctic Mountains toward the Weddell Sea. Further paleomagnetic tests of the fixed hotspot approximation can be made. Cenozoic and Cretaceous paleomagnetic data from the Pacific plate, along with reconstructions of the Pacific plate relative to the hotspots, can be used to estimate an apparent polar wander (APW) path of Pacific hotspots. An APW path of Indo-Atlantic hotspots can be similarly estimated (e.g. Besse & Courtillot 2002). If both paths diverge in similar ways from the north pole of the hotspot reference frame, it would indicate that the hotspots have moved in unison relative to the spin axis, which may be attributed to true polar wander. If the two paths diverge from one another, motion between Pacific hotspots and Indo-Atlantic hotspots would be indicated. The general agreement of the two paths shows that the former is more important than the latter. The data require little or no motion between groups of hotspots, but up to ~10 mm/yr of motion is allowed within uncertainties. The results disagree, in particular, with the recent extreme interpretation of

  16. Hotspot uranium metallogenesis in south China

    International Nuclear Information System (INIS)

    Li Ziying

    2006-01-01

    The basic concepts of mantle plume and hotspots are expounded and the hotspots are classified into continental and oceanic types. The relationship between hotspots and metallogenesis are briefly discussed, and a new theory of uranium metallogenesis related to hotspots has been put forward. The geotectonism, magmatism, sedimentation, metamorphism and metallogenesis must be closely associated with deep geodynamics of mantle plume tectonics in Meso-Cenozoic period from 220 Ma to 50 Ma in South China. The eastern part of Guidong granite massif has been proved to be a Mesozoic hotspot from aspects of geological, geophysical and geochemical evidences and its correspondent relationship to uranium metallogenesis is discussed. Finally, the uranium metallogenetic prospect has been pointed out for hydrothermal uranium mineralization in South China from the view point of hotspot uranium metallogenesis. (authors)

  17. Global mammal distributions, biodiversity hotspots, and conservation.

    Science.gov (United States)

    Ceballos, Gerardo; Ehrlich, Paul R

    2006-12-19

    Hotspots, which have played a central role in the selection of sites for reserves, require careful rethinking. We carried out a global examination of distributions of all nonmarine mammals to determine patterns of species richness, endemism, and endangerment, and to evaluate the degree of congruence among hotspots of these three measures of diversity in mammals. We then compare congruence of hotspots in two animal groups (mammals and birds) to assess the generality of these patterns. We defined hotspots as the richest 2.5% of cells in a global equal-area grid comparable to 1 degrees latitude x 1 degrees longitude. Hotspots of species richness, "endemism," and extinction threat were noncongruent. Only 1% of cells and 16% of species were common to the three types of mammalian hotspots. Congruence increased with increases in both the geographic scope of the analysis and the percentage of cells defined as being hotspots. The within-mammal hotspot noncongruence was similar to the pattern recently found for birds. Thus, assigning global conservation priorities based on hotspots is at best a limited strategy.

  18. Evidence of hotspot paths below Arabia and the Horn of Africa and consequences on the Red Sea opening

    Science.gov (United States)

    Vicente de Gouveia, S.; Besse, J.; Frizon de Lamotte, D.; Greff-Lefftz, M.; Lescanne, M.; Gueydan, F.; Leparmentier, F.

    2018-04-01

    Rifts are often associated with ancient traces of hotspots, which are supposed to participate to the weakening of the lithosphere. We investigated the expected past trajectories followed by three hotspots (Afar, East-Africa and Lake-Victoria) located around the Red Sea. We used a hotspot reference frame to compute their location with respect to time, which is then compared to mantle tomography interpretations and geological features. Their tracks are frequently situated under continental crust, which is known to strongly filter plume activity. We looked for surface markers of their putative ancient existence, such as volcanism typology, doming, and heat-flow data from petroleum wells. Surface activity of the East-Africa hotspot is supported at 110 Ma, 90 Ma and 30 Ma by uplift, volcanic activity and rare gas isotopic signatures, reminiscent of a deep plume origin. The analysis of heat-flow data from petroleum wells under the Arabian plate shows a thermal anomaly that may correspond to the past impact of the Afar hotspot. According to derived hotspot trajectories, the Afar hotspot, situated (at 32 Ma) 1000 km north-east of the Ethiopian-Yemen traps, was probably too far away to be accountable for them. The trigger of the flood basalts would likely be linked to the East-Africa hotspot. The Lake-Victoria hotspot activity appears to have been more recent, attested only by Cenozoic volcanism in an uplifted area. Structural and thermal weakening of the lithosphere may have played a major role in the location of the rift systems. The Gulf of Aden is located on inherited Mesozoic extensional basins between two weak zones, the extremity of the Carlsberg Ridge and the present Afar triangle, previously impacted by the East-Africa hotspot. The Red Sea may have opened in the context of extension linked to Neo-Tethys slab-pull, along the track followed by the East Africa hotspot, suggesting an inherited thermal weakening.

  19. DNA barcoding the floras of biodiversity hotspots.

    Science.gov (United States)

    Lahaye, Renaud; van der Bank, Michelle; Bogarin, Diego; Warner, Jorge; Pupulin, Franco; Gigot, Guillaume; Maurin, Olivier; Duthoit, Sylvie; Barraclough, Timothy G; Savolainen, Vincent

    2008-02-26

    DNA barcoding is a technique in which species identification is performed by using DNA sequences from a small fragment of the genome, with the aim of contributing to a wide range of ecological and conservation studies in which traditional taxonomic identification is not practical. DNA barcoding is well established in animals, but there is not yet any universally accepted barcode for plants. Here, we undertook intensive field collections in two biodiversity hotspots (Mesoamerica and southern Africa). Using >1,600 samples, we compared eight potential barcodes. Going beyond previous plant studies, we assessed to what extent a "DNA barcoding gap" is present between intra- and interspecific variations, using multiple accessions per species. Given its adequate rate of variation, easy amplification, and alignment, we identified a portion of the plastid matK gene as a universal DNA barcode for flowering plants. Critically, we further demonstrate the applicability of DNA barcoding for biodiversity inventories. In addition, analyzing >1,000 species of Mesoamerican orchids, DNA barcoding with matK alone reveals cryptic species and proves useful in identifying species listed in Convention on International Trade of Endangered Species (CITES) appendixes.

  20. Coastal leatherback turtles reveal conservation hotspot

    Science.gov (United States)

    Robinson, Nathan J.; Morreale, Stephen J.; Nel, Ronel; Paladino, Frank V.

    2016-01-01

    Previous studies have shown that the world’s largest reptile – the leatherback turtle Dermochelys coriacea – conducts flexible foraging migrations that can cover thousands of kilometres between nesting sites and distant foraging areas. The vast distances that may be travelled by migrating leatherback turtles have greatly complicated conservation efforts for this species worldwide. However, we demonstrate, using a combination of satellite telemetry and stable isotope analysis, that approximately half of the nesting leatherbacks from an important rookery in South Africa do not migrate to distant foraging areas, but rather, forage in the coastal waters of the nearby Mozambique Channel. Moreover, this coastal cohort appears to remain resident year-round in shallow waters (turtles Caretta caretta. The rare presence of a resident coastal aggregation of leatherback turtles not only presents a unique opportunity for conservation, but alongside the presence of loggerhead turtles and other endangered marine megafauna in the Mozambique Channel, highlights the importance of this area as a marine biodiversity hotspot. PMID:27886262

  1. All Hazard Hotspots/Population Density

    Indian Academy of Sciences (India)

    This map shows hotspots of humanitarian risk for floods, cyclones, and drought overlaying a population density gradient. Blue areas with striped overlay represent areas of high population density that are also risk hotspots. These are at higher risk of future population displacement as a result of climate hazards.

  2. Microbial hotspots and hot moments in soil

    Science.gov (United States)

    Kuzyakov, Yakov; Blagodatskaya, Evgenia

    2015-04-01

    Soils are the most heterogeneous parts of the biosphere, with an extremely high differentiation of properties and processes within nano- to macroscales. The spatial and temporal heterogeneity of input of labile organics by plants creates microbial hotspots over short periods of time - the hot moments. We define microbial hotspots as small soil volumes with much faster process rates and much more intensive interactions compared to the average soil conditions. Such hotspots are found in the rhizosphere, detritusphere, biopores (including drilosphere) and on aggregate surfaces, but hotspots are frequently of mixed origin. Hot moments are short-term events or sequences of events inducing accelerated process rates as compared to the averaged rates. Thus, hotspots and hot moments are defined by dynamic characteristics, i.e. by process rates. For this hotspot concept we extensively reviewed and examined the localization and size of hotspots, spatial distribution and visualization approaches, transport of labile C to and from hotspots, lifetime and process intensities, with a special focus on process rates and microbial activities. The fraction of active microorganisms in hotspots is 2-20 times higher than in the bulk soil, and their specific activities (i.e. respiration, microbial growth, mineralization potential, enzyme activities, RNA/DNA ratio) may also be much higher. The duration of hot moments in the rhizosphere is limited and is controlled by the length of the input of labile organics. It can last a few hours up to a few days. In the detritusphere, however, the duration of hot moments is regulated by the output - by decomposition rates of litter - and lasts for weeks and months. Hot moments induce succession in microbial communities and intense intra- and interspecific competition affecting C use efficiency, microbial growth and turnover. The faster turnover and lower C use efficiency in hotspots counterbalances the high C inputs, leading to the absence of strong

  3. Fine-Scale Recombination Maps of Fungal Plant Pathogens Reveal Dynamic Recombination Landscapes and Intragenic Hotspots.

    Science.gov (United States)

    Stukenbrock, Eva H; Dutheil, Julien Y

    2018-03-01

    Meiotic recombination is an important driver of evolution. Variability in the intensity of recombination across chromosomes can affect sequence composition, nucleotide variation, and rates of adaptation. In many organisms, recombination events are concentrated within short segments termed recombination hotspots. The variation in recombination rate and positions of recombination hotspot can be studied using population genomics data and statistical methods. In this study, we conducted population genomics analyses to address the evolution of recombination in two closely related fungal plant pathogens: the prominent wheat pathogen Zymoseptoria tritici and a sister species infecting wild grasses Z. ardabiliae We specifically addressed whether recombination landscapes, including hotspot positions, are conserved in the two recently diverged species and if recombination contributes to rapid evolution of pathogenicity traits. We conducted a detailed simulation analysis to assess the performance of methods of recombination rate estimation based on patterns of linkage disequilibrium, in particular in the context of high nucleotide diversity. Our analyses reveal overall high recombination rates, a lack of suppressed recombination in centromeres, and significantly lower recombination rates on chromosomes that are known to be accessory. The comparison of the recombination landscapes of the two species reveals a strong correlation of recombination rate at the megabase scale, but little correlation at smaller scales. The recombination landscapes in both pathogen species are dominated by frequent recombination hotspots across the genome including coding regions, suggesting a strong impact of recombination on gene evolution. A significant but small fraction of these hotspots colocalize between the two species, suggesting that hotspot dynamics contribute to the overall pattern of fast evolving recombination in these species. Copyright © 2018 Stukenbrock and Dutheil.

  4. Evaluating Temporal Consistency in Marine Biodiversity Hotspots.

    Science.gov (United States)

    Piacenza, Susan E; Thurman, Lindsey L; Barner, Allison K; Benkwitt, Cassandra E; Boersma, Kate S; Cerny-Chipman, Elizabeth B; Ingeman, Kurt E; Kindinger, Tye L; Lindsley, Amy J; Nelson, Jake; Reimer, Jessica N; Rowe, Jennifer C; Shen, Chenchen; Thompson, Kevin A; Heppell, Selina S

    2015-01-01

    With the ongoing crisis of biodiversity loss and limited resources for conservation, the concept of biodiversity hotspots has been useful in determining conservation priority areas. However, there has been limited research into how temporal variability in biodiversity may influence conservation area prioritization. To address this information gap, we present an approach to evaluate the temporal consistency of biodiversity hotspots in large marine ecosystems. Using a large scale, public monitoring dataset collected over an eight year period off the US Pacific Coast, we developed a methodological approach for avoiding biases associated with hotspot delineation. We aggregated benthic fish species data from research trawls and calculated mean hotspot thresholds for fish species richness and Shannon's diversity indices over the eight year dataset. We used a spatial frequency distribution method to assign hotspot designations to the grid cells annually. We found no areas containing consistently high biodiversity through the entire study period based on the mean thresholds, and no grid cell was designated as a hotspot for greater than 50% of the time-series. To test if our approach was sensitive to sampling effort and the geographic extent of the survey, we followed a similar routine for the northern region of the survey area. Our finding of low consistency in benthic fish biodiversity hotspots over time was upheld, regardless of biodiversity metric used, whether thresholds were calculated per year or across all years, or the spatial extent for which we calculated thresholds and identified hotspots. Our results suggest that static measures of benthic fish biodiversity off the US West Coast are insufficient for identification of hotspots and that long-term data are required to appropriately identify patterns of high temporal variability in biodiversity for these highly mobile taxa. Given that ecological communities are responding to a changing climate and other

  5. The presence of two rare genomic syndromes, 1q21 deletion and Xq28 duplication, segregating independently in a family with intellectual disability.

    Science.gov (United States)

    Ha, Kyungsoo; Shen, Yiping; Graves, Tyler; Kim, Cheol-Hee; Kim, Hyung-Goo

    2016-01-01

    1q21 microdeletion syndrome is a rare contiguous gene deletion disorder with de novo or autosomal dominant inheritance patterns and its phenotypic features include intellectual disability, distinctive facial dysmorphism, microcephaly, cardiac abnormalities, and cataracts. MECP2 duplication syndrome is an X-linked recessive neurodevelopmental disorder characterized by intellectual disability, global developmental delay, and other neurological complications including late-onset seizures. Previously, these two different genetic syndromes have not been reported segregating independently in a same family. Here we describe two siblings carrying either a chromosome 1q21 microdeletion or a chromosome Xq28 duplication. Using a comparative genomic hybridization (CGH) array, we identified a 1.24 Mb heterozygous deletion at 1q21 resulting in the loss of 9 genes in a girl with learning disability, hypothyroidism, short stature, sensory integration disorder, and soft dysmorphic features including cupped ears and a unilateral ear pit. We also characterized a 508 kb Xq28 duplication encompassing MECP2 in her younger brother with hypotonia, poor speech, cognitive and motor impairment. The parental CGH and quantitative PCR (qPCR) analyses revealed that the 1q21 deletion in the elder sister is de novo , but the Xq28 duplication in the younger brother was originally inherited from the maternal grandmother through the mother, both of whom are asymptomatic carriers. RT-qPCR assays revealed that the affected brother has almost double the amount of MECP2 mRNA expression compared to other family members of both genders including maternal grandmother and mother who have the same Xq28 duplication with no phenotype. This suggests the X chromosome with an Xq28 duplication in the carrier females is preferentially silenced. From our understanding, this would be the first report showing the independent segregation of two genetically unrelated syndromes, 1q21 microdeletion and Xq28 duplication

  6. Investigating a rare methicillin-resistant Staphylococcus aureus strain: first description of genome sequencing and molecular characterization of CC15-MRSA

    Directory of Open Access Journals (Sweden)

    Senok AC

    2017-10-01

    Full Text Available Abiola C Senok,1 Ali M Somily,2 Peter Slickers,3,4 Muhabat A Raji,5 Ghada Garaween,5 Atef Shibl,5 Stefan Monecke,3,4,6 Ralf Ehricht3,4 1Department of Basic Science, College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates; 2Department of Pathology and Laboratory Medicine, College of Medicine, King Khalid University Hospital and King Saud University, Riyadh, Saudi Arabia; 3Alere Technologies GmbH, Jena, Germany, 4InfectoGnostics Research Campus, Jena, Germany; 5Department of Microbiology and Immunology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia; 6Institute for Medical Microbiology and Hygiene (IMMH, Technische Universität Dresden, Dresden, Germany Purpose: Methicillin resistant Staphylococcus aureus CC15 strains (CC15-MRSA have only been sporadically described in literature. This study was carried out to describe the genetic make-up for this rare MRSA strain.Methods: Four CC15-MRSA isolates collected in Riyadh, Saudi Arabia, between 2013 and 2014 were studied. Two isolates were from clinical infection and 2 from retail meat products. Whole genome sequencing was carried out using Illumina HiSeq2500 genome analyzer.Results: All the CC15-MRSA isolates had the multilocus sequence typing profile ST1535, 13–13-1–1-81-11-13, which is a single locus variant of ST15. Of the 6 contigs related to the SCC element, one comprised a recombinase gene ccrAA, ccrC-PM1, fusC and a helicase, another one included mvaS, dru, mecA and 1 had yobV and Q4LAG7. The SCC element had 5 transposase genes, namely 3 identical paralogs of tnpIS431 and 2 identical paralogs of tnpIS256. Two identical copies of a tnpIS256-based insertion element flank the aacA-aphD gene. Two copies of this insertion element were present with 1 located in the SCC element and another inserted into the sasC gene. A short 3 kb region, which lacks any bacteriophage structural genes and site-specific DNA integrase, was

  7. NIMS: hotspots on Io during G2

    Science.gov (United States)

    1996-01-01

    The Near Infrared Mapping Spectrometer (NIMS) on the Galileo spacecraft imaged Io at high spectral resolution at a range of 439,000 km (275,000 miles) during the G2 encounter on 7 September 1996. This image shows (on the right) Io as seen in the infrared by NIMS. The image on the left shows the same view from Voyager in 1979. This NIMS image can be compared to the NIMS images from the G1 orbit (June 1996) to monitor changes on Io. The NIMS image is at 4.9 microns, showing thermal emissions from the hotspots. The brightness of the pixels is a function of size and temperature.At least 10 hotspots have been identified and can be matched with surface features. An accurate determination of the position of the hotspot in the vicinity of Shamash Patera is pending. Hotspots are seen in the vicinity of Prometheus, Volund and Marduk, all sites of volcanic plume activity during the Galileo encounters, and also of active plumes in 1979. Temperatures and areas have been calculated for the hotspots shown. Temperatures range from 828 K (1031 F) to 210 K (- 81.4 F). The lowest temperature is significantly higher than the Io background (non-hotspot) surface temperature of about 100 K (-279 F). Hotspot areas range from 6.5 square km (2.5 sq miles) to 40,000 sq km (15,400 sq miles). The hottest hotspots have smallest areas, and the cooler hotspots have the largest areas. NIMS is continuing to observe Io to monitor volcanic activity throughout the Galileo mission.The Galileo mission is managed by the Jet Propulsion Laboratory for NASA's Office of Space Science, Washington, D.C.This image and other images and data received from Galileo are posted on the Galileo mission home page on the World Wide Web at http://galileo.jpl.nasa.gov.

  8. Capturing Hotspots For Constrained Indoor Movement

    DEFF Research Database (Denmark)

    Ahmed, Tanvir; Pedersen, Torben Bach; Lu, Hua

    2013-01-01

    Finding the hotspots in large indoor spaces is very important for getting overloaded locations, security, crowd management, indoor navigation and guidance. The tracking data coming from indoor tracking are huge in volume and not readily available for finding hotspots. This paper presents a graph......-based model for constrained indoor movement that can map the tracking records into mapping records which represent the entry and exit times of an object in a particular location. Then it discusses the hotspots extraction technique from the mapping records....

  9. Putting 'Local' Back into Public Wifi Hotspots

    DEFF Research Database (Denmark)

    Korn, Matthias; Klokmose, Clemens Nylandsted

    2012-01-01

    Public Wifi hotspots in cafes and public places are based on wireless local area network technology (WLAN). In contrast to the common understanding of connecting directly to the internet when connecting to a Wifi hotspot, we are proposing to bring the original notion of connecting to a local...... hotspot in cafes, bars, community centers, and other (semi-)public places in order to facilitate co-located activities for such varied purposes as fostering local community, civic participation, sociality in general, and entertainment. We propose a network locality that builds on local infrastructure...

  10. A micro-epidemiological analysis of febrile malaria in Coastal Kenya showing hotspots within hotspots.

    Science.gov (United States)

    Bejon, Philip; Williams, Thomas N; Nyundo, Christopher; Hay, Simon I; Benz, David; Gething, Peter W; Otiende, Mark; Peshu, Judy; Bashraheil, Mahfudh; Greenhouse, Bryan; Bousema, Teun; Bauni, Evasius; Marsh, Kevin; Smith, David L; Borrmann, Steffen

    2014-04-24

    Malaria transmission is spatially heterogeneous. This reduces the efficacy of control strategies, but focusing control strategies on clusters or 'hotspots' of transmission may be highly effective. Among 1500 homesteads in coastal Kenya we calculated (a) the fraction of febrile children with positive malaria smears per homestead, and (b) the mean age of children with malaria per homestead. These two measures were inversely correlated, indicating that children in homesteads at higher transmission acquire immunity more rapidly. This inverse correlation increased gradually with increasing spatial scale of analysis, and hotspots of febrile malaria were identified at every scale. We found hotspots within hotspots, down to the level of an individual homestead. Febrile malaria hotspots were temporally unstable, but 4 km radius hotspots could be targeted for 1 month following 1 month periods of surveillance.DOI: http://dx.doi.org/10.7554/eLife.02130.001. Copyright © 2014, Bejon et al.

  11. Ultraconfined Plasmonic Hotspots Inside Graphene Nanobubbles.

    Science.gov (United States)

    Fei, Z; Foley, J J; Gannett, W; Liu, M K; Dai, S; Ni, G X; Zettl, A; Fogler, M M; Wiederrecht, G P; Gray, S K; Basov, D N

    2016-12-14

    We report on a nanoinfrared (IR) imaging study of ultraconfined plasmonic hotspots inside graphene nanobubbles formed in graphene/hexagonal boron nitride (hBN) heterostructures. The volume of these plasmonic hotspots is more than one-million-times smaller than what could be achieved by free-space IR photons, and their real-space distributions are controlled by the sizes and shapes of the nanobubbles. Theoretical analysis indicates that the observed plasmonic hotspots are formed due to a significant increase of the local plasmon wavelength in the nanobubble regions. Such an increase is attributed to the high sensitivity of graphene plasmons to its dielectric environment. Our work presents a novel scheme for plasmonic hotspot formation and sheds light on future applications of graphene nanobubbles for plasmon-enhanced IR spectroscopy.

  12. Coral Reef Watch, Hotspots, 50 km

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NOAA Coral Reef Watch provides Coral Bleaching hotspot maps derived from NOAA's Polar Operational Environmental Satellites (POES). This data provides global area...

  13. Contrasted patterns of crossover and non-crossover at Arabidopsis thaliana meiotic recombination hotspots.

    Directory of Open Access Journals (Sweden)

    Jan Drouaud

    2013-11-01

    Full Text Available The vast majority of meiotic recombination events (crossovers (COs and non-crossovers (NCOs cluster in narrow hotspots surrounded by large regions devoid of recombinational activity. Here, using a new molecular approach in plants, called "pollen-typing", we detected and characterized hundreds of CO and NCO molecules in two different hotspot regions in Arabidopsis thaliana. This analysis revealed that COs are concentrated in regions of a few kilobases where their rates reach up to 50 times the genome average. The hotspots themselves tend to cluster in regions less than 8 kilobases in size with overlapping CO distribution. Non-crossover (NCO events also occurred in the two hotspots but at very different levels (local CO/NCO ratios of 1/1 and 30/1 and their track lengths were quite small (a few hundred base pairs. We also showed that the ZMM protein MSH4 plays a role in CO formation and somewhat unexpectedly we also found that it is involved in the generation of NCOs but with a different level of effect. Finally, factors acting in cis and in trans appear to shape the rate and distribution of COs at meiotic recombination hotspots.

  14. Was sind Biodiversity Hotspots - global, regional, lokal?

    OpenAIRE

    Hobohm, Carsten

    2005-01-01

    Das Konzept der Biodiversity Hotspots, das Ende der 1980er Jahre von Norman Myers entworfen wurde, gehört derzeit zu den wichtigen forschungsleitenden Ansätzen globaler Naturschutzstrategien. In der vorliegenden Arbeit geht es in erster Linie um die Frage, ob und inwiefern dieses Konzept auf die regionale und lokale Dimension Europas übertragen werden kann. Es wird ein Vorschlag unterbreitet, wie europäische Biodiversity Hotspots definiert und identifiziert werden können. Bei der Erforschung ...

  15. Evaluating Temporal Consistency in Marine Biodiversity Hotspots

    OpenAIRE

    Piacenza, Susan E.; Thurman, Lindsey L.; Barner, Allison K.; Benkwitt, Cassandra E.; Boersma, Kate S.; Cerny-Chipman, Elizabeth B.; Ingeman, Kurt E.; Kindinger, Tye L.; Lindsley, Amy J.; Nelson, Jake; Reimer, Jessica N.; Rowe, Jennifer C.; Shen, Chenchen; Thompson, Kevin A.; Heppell, Selina S.

    2015-01-01

    With the ongoing crisis of biodiversity loss and limited resources for conservation, the concept of biodiversity hotspots has been useful in determining conservation priority areas. However, there has been limited research into how temporal variability in biodiversity may influence conservation area prioritization. To address this information gap, we present an approach to evaluate the temporal consistency of biodiversity hotspots in large marine ecosystems. Using a large scale, public monito...

  16. Pollination decays in biodiversity hotspots.

    Science.gov (United States)

    Vamosi, Jana C; Knight, Tiffany M; Steets, Janette A; Mazer, Susan J; Burd, Martin; Ashman, Tia-Lynn

    2006-01-24

    As pollinators decline globally, competition for their services is expected to intensify, and this antagonism may be most severe where the number of plant species is the greatest. Using meta-analysis and comparative phylogenetic analysis, we provide a global-scale test of whether reproduction becomes more limited by pollen receipt (pollen limitation) as the number of coexisting plant species increases. As predicted, we find a significant positive relationship between pollen limitation and species richness. In addition, this pattern is particularly strong for species that are obligately outcrossing and for trees relative to herbs or shrubs. We suggest that plants occurring in species-rich communities may be more prone to pollen limitation because of interspecific competition for pollinators. As a consequence, plants in biodiversity hotspots may have a higher risk of extinction and/or experience increased selection pressure to specialize on certain pollinators or diversify into different phenological niches. The combination of higher pollen limitation and habitat destruction represents a dual risk to tropical plant species that has not been previously identified.

  17. Genetic and Rare Diseases Information Center (GARD)

    Data.gov (United States)

    Federal Laboratory Consortium — NCATS collaborates with the National Human Genome Research Institute (NHGRI) to support GARD, a center designed to provide comprehensive information about rare and...

  18. LDsplit: screening for cis-regulatory motifs stimulating meiotic recombination hotspots by analysis of DNA sequence polymorphisms.

    Science.gov (United States)

    Yang, Peng; Wu, Min; Guo, Jing; Kwoh, Chee Keong; Przytycka, Teresa M; Zheng, Jie

    2014-02-17

    As a fundamental genomic element, meiotic recombination hotspot plays important roles in life sciences. Thus uncovering its regulatory mechanisms has broad impact on biomedical research. Despite the recent identification of the zinc finger protein PRDM9 and its 13-mer binding motif as major regulators for meiotic recombination hotspots, other regulators remain to be discovered. Existing methods for finding DNA sequence motifs of recombination hotspots often rely on the enrichment of co-localizations between hotspots and short DNA patterns, which ignore the cross-individual variation of recombination rates and sequence polymorphisms in the population. Our objective in this paper is to capture signals encoded in genetic variations for the discovery of recombination-associated DNA motifs. Recently, an algorithm called "LDsplit" has been designed to detect the association between single nucleotide polymorphisms (SNPs) and proximal meiotic recombination hotspots. The association is measured by the difference of population recombination rates at a hotspot between two alleles of a candidate SNP. Here we present an open source software tool of LDsplit, with integrative data visualization for recombination hotspots and their proximal SNPs. Applying LDsplit on SNPs inside an established 7-mer motif bound by PRDM9 we observed that SNP alleles preserving the original motif tend to have higher recombination rates than the opposite alleles that disrupt the motif. Running on SNP windows around hotspots each containing an occurrence of the 7-mer motif, LDsplit is able to guide the established motif finding algorithm of MEME to recover the 7-mer motif. In contrast, without LDsplit the 7-mer motif could not be identified. LDsplit is a software tool for the discovery of cis-regulatory DNA sequence motifs stimulating meiotic recombination hotspots by screening and narrowing down to hotspot associated SNPs. It is the first computational method that utilizes the genetic variation of

  19. Human population in the biodiversity hotspots.

    Science.gov (United States)

    Cincotta, R P; Wisnewski, J; Engelman, R

    2000-04-27

    Biologists have identified 25 areas, called biodiversity hotspots, that are especially rich in endemic species and particularly threatened by human activities. The human population dynamics of these areas, however, are not well quantified. Here we report estimates of key demographic variables for each hotspot, and for three extensive tropical forest areas that are less immediately threatened. We estimate that in 1995 more than 1.1 billion people, nearly 20% of world population, were living within the hotspots, an area covering about 12% of Earth's terrestrial surface. We estimate that the population growth rate in the hotspots (1995-2000) is 1.8% yr(-1), substantially higher than the population growth rate of the world as a whole (1.3% yr(-1)) and above that of the developing countries (1.6% yr(-1)). These results suggest that substantial human-induced environmental changes are likely to continue in the hotspots and that demographic change remains an important factor in global biodiversity conservation. The results also underline the potential conservation significance of the continuing worldwide declines in human fertility and of policies and programs that influence human migration.

  20. Modeling Resource Hotspots: Critical Linkages and Processes

    Science.gov (United States)

    Daher, B.; Mohtar, R.; Pistikopoulos, E.; McCarl, B. A.; Yang, Y.

    2017-12-01

    Growing demands for interconnected resources emerge in the form of hotspots of varying characteristics. The business as usual allocation model cannot address the current, let alone anticipated, complex and highly interconnected resource challenges we face. A new paradigm for resource allocation must be adopted: one that identifies cross-sectoral synergies and, that moves away from silos to recognition of the nexus and integration of it. Doing so will result in new opportunities for business growth, economic development, and improved social well-being. Solutions and interventions must be multi-faceted; opportunities should be identified with holistic trade-offs in mind. No single solution fits all: different hotspots will require distinct interventions. Hotspots have varying resource constraints, stakeholders, goals and targets. The San Antonio region represents a complex resource hotspot with promising potential: its rapidly growing population, the Eagle Ford shale play, and the major agricultural activity there makes it a hotspot with many competing demands. Stakeholders need tools to allow them to knowledgeably address impending resource challenges. This study will identify contemporary WEF nexus questions and critical system interlinkages that will inform the modeling of the tightly interconnected resource systems and stresses using the San Antonio Region as a base; it will conceptualize a WEF nexus modeling framework, and develop assessment criteria to inform integrative planning and decision making.

  1. Evolutionary hotspots in the Mojave Desert

    Science.gov (United States)

    Vandergast, Amy G.; Inman, Richard D.; Barr, Kelly R.; Nussear, Kenneth E.; Esque, Todd C.; Hathaway, Stacie A.; Wood, Dustin A.; Medica, Philip A.; Breinholt, Jesse W.; Stephen, Catherine L.; Gottscho, Andrew D.; Marks, Sharyn B.; Jennings, W. Bryan; Fisher, Robert N.

    2013-01-01

    Genetic diversity within species provides the raw material for adaptation and evolution. Just as regions of high species diversity are conservation targets, identifying regions containing high genetic diversity and divergence within and among populations may be important to protect future evolutionary potential. When multiple co-distributed species show spatial overlap in high genetic diversity and divergence, these regions can be considered evolutionary hotspots. We mapped spatial population genetic structure for 17 animal species across the Mojave Desert, USA. We analyzed these in concurrence and located 10 regions of high genetic diversity, divergence or both among species. These were mainly concentrated along the western and southern boundaries where ecotones between mountain, grassland and desert habitat are prevalent, and along the Colorado River. We evaluated the extent to which these hotspots overlapped protected lands and utility-scale renewable energy development projects of the Bureau of Land Management. While 30–40% of the total hotspot area was categorized as protected, between 3–7% overlapped with proposed renewable energy project footprints, and up to 17% overlapped with project footprints combined with transmission corridors. Overlap of evolutionary hotspots with renewable energy development mainly occurred in 6 of the 10 identified hotspots. Resulting GIS-based maps can be incorporated into ongoing landscape planning efforts and highlight specific regions where further investigation of impacts to population persistence and genetic connectivity may be warranted.

  2. PRDM9 variation strongly influences recombination hot-spot activity and meiotic instability in humans.

    Science.gov (United States)

    Berg, Ingrid L; Neumann, Rita; Lam, Kwan-Wood G; Sarbajna, Shriparna; Odenthal-Hesse, Linda; May, Celia A; Jeffreys, Alec J

    2010-10-01

    PRDM9 has recently been identified as a likely trans regulator of meiotic recombination hot spots in humans and mice. PRDM9 contains a zinc finger array that, in humans, can recognize a short sequence motif associated with hot spots, with binding to this motif possibly triggering hot-spot activity via chromatin remodeling. We now report that human genetic variation at the PRDM9 locus has a strong effect on sperm hot-spot activity, even at hot spots lacking the sequence motif. Subtle changes within the zinc finger array can create hot-spot nonactivating or enhancing variants and can even trigger the appearance of a new hot spot, suggesting that PRDM9 is a major global regulator of hot spots in humans. Variation at the PRDM9 locus also influences aspects of genome instability-specifically, a megabase-scale rearrangement underlying two genomic disorders as well as minisatellite instability-implicating PRDM9 as a risk factor for some pathological genome rearrangements.

  3. Collimation of extragalactic jets: evidence from hotspots

    International Nuclear Information System (INIS)

    Banhatti, D.G.

    1984-01-01

    A linear relation with slope near unity is found between the logarithms of the hotspot size perpendicular to the source major axis and the distance from the core for 14 compact and/ or intense hotspots selected from a sample of 31 quasars having the largest angular sizes at various redshifts, as observed at 4.87 GHz with sub-arcsec resolution. A slope significantly less than 1 implies that the jet feeding the hotspot is laterally confined by the intergalactic medium, whereas a slope of 1 does not distinguish between a laterally confined jet and a free jet. The relation is found to have a slope near 1 implying a 0deg.1 jet confined within a cone of half-angle 15deg to 20deg or a 1deg-wide free jet. (author)

  4. HIV-1 vaccine-induced T-cell responses cluster in epitope hotspots that differ from those induced in natural infection with HIV-1.

    Science.gov (United States)

    Hertz, Tomer; Ahmed, Hasan; Friedrich, David P; Casimiro, Danilo R; Self, Steven G; Corey, Lawrence; McElrath, M Juliana; Buchbinder, Susan; Horton, Helen; Frahm, Nicole; Robertson, Michael N; Graham, Barney S; Gilbert, Peter

    2013-01-01

    Several recent large clinical trials evaluated HIV vaccine candidates that were based on recombinant adenovirus serotype 5 (rAd-5) vectors expressing HIV-derived antigens. These vaccines primarily elicited T-cell responses, which are known to be critical for controlling HIV infection. In the current study, we present a meta-analysis of epitope mapping data from 177 participants in three clinical trials that tested two different HIV vaccines: MRKAd-5 HIV and VRC-HIVAD014-00VP. We characterized the population-level epitope responses in these trials by generating population-based epitope maps, and also designed such maps using a large cohort of 372 naturally infected individuals. We used these maps to address several questions: (1) Are vaccine-induced responses randomly distributed across vaccine inserts, or do they cluster into immunodominant epitope hotspots? (2) Are the immunodominance patterns observed for these two vaccines in three vaccine trials different from one another? (3) Do vaccine-induced hotspots overlap with epitope hotspots induced by chronic natural infection with HIV-1? (4) Do immunodominant hotspots target evolutionarily conserved regions of the HIV genome? (5) Can epitope prediction methods be used to identify these hotspots? We found that vaccine responses clustered into epitope hotspots in all three vaccine trials and some of these hotspots were not observed in chronic natural infection. We also found significant differences between the immunodominance patterns generated in each trial, even comparing two trials that tested the same vaccine in different populations. Some of the vaccine-induced immunodominant hotspots were located in highly variable regions of the HIV genome, and this was more evident for the MRKAd-5 HIV vaccine. Finally, we found that epitope prediction methods can partially predict the location of vaccine-induced epitope hotspots. Our findings have implications for vaccine design and suggest a framework by which different

  5. The consequences of sequence erosion in the evolution of recombination hotspots.

    Science.gov (United States)

    Tiemann-Boege, Irene; Schwarz, Theresa; Striedner, Yasmin; Heissl, Angelika

    2017-12-19

    Meiosis is initiated by a double-strand break (DSB) introduced in the DNA by a highly controlled process that is repaired by recombination. In many organisms, recombination occurs at specific and narrow regions of the genome, known as recombination hotspots, which overlap with regions enriched for DSBs. In recent years, it has been demonstrated that conversions and mutations resulting from the repair of DSBs lead to a rapid sequence evolution at recombination hotspots eroding target sites for DSBs. We still do not fully understand the effect of this erosion in the recombination activity, but evidence has shown that the binding of trans -acting factors like PRDM9 is affected. PRDM9 is a meiosis-specific, multi-domain protein that recognizes DNA target motifs by its zinc finger domain and directs DSBs to these target sites. Here we discuss the changes in affinity of PRDM9 to eroded recognition sequences, and explain how these changes in affinity of PRDM9 can affect recombination, leading sometimes to sterility in the context of hybrid crosses. We also present experimental data showing that DNA methylation reduces PRDM9 binding in vitro Finally, we discuss PRDM9-independent hotspots, posing the question how these hotspots evolve and change with sequence erosion.This article is part of the themed issue 'Evolutionary causes and consequences of recombination rate variation in sexual organisms'. © 2017 The Authors.

  6. NIMS Observation of Hotspots on Io

    Science.gov (United States)

    1996-01-01

    Io has been imaged by the Near Infrared Mapping Spectrometer (NIMS) on Galileo. The image on the right shows for the first time the distribution of volcanic hotspots on the surface of Io, as seen by NIMS. Three of these hotspots are new discoveries, only detectable with the NIMS instrument. This image was taken during the G1 encounter on June 29 1996. The image on the left shows the same view of Io as seen by the Voyager spacecraft in 1979. At least one dozen hotspots have been identified from this NIMS image. Most of the hotspot locations can be matched with volcanic features on the surface of Io, including the vent area of the active Prometheus plume.The Jet Propulsion Laboratory, Pasadena, CA manages the mission for NASA's Office of Space Science, Washington, DC.This image and other images and data received from Galileo are posted on the World Wide Web, on the Galileo mission home page at URL http://galileo.jpl.nasa.gov.

  7. Eliminating "Hotspots" in Digital Image Processing

    Science.gov (United States)

    Salomon, P. M.

    1984-01-01

    Signals from defective picture elements rejected. Image processing program for use with charge-coupled device (CCD) or other mosaic imager augmented with algorithm that compensates for common type of electronic defect. Algorithm prevents false interpretation of "hotspots". Used for robotics, image enhancement, image analysis and digital television.

  8. Forecasting Hotspots-A Predictive Analytics Approach.

    Science.gov (United States)

    Maciejewski, R; Hafen, R; Rudolph, S; Larew, S G; Mitchell, M A; Cleveland, W S; Ebert, D S

    2011-04-01

    Current visual analytics systems provide users with the means to explore trends in their data. Linked views and interactive displays provide insight into correlations among people, events, and places in space and time. Analysts search for events of interest through statistical tools linked to visual displays, drill down into the data, and form hypotheses based upon the available information. However, current systems stop short of predicting events. In spatiotemporal data, analysts are searching for regions of space and time with unusually high incidences of events (hotspots). In the cases where hotspots are found, analysts would like to predict how these regions may grow in order to plan resource allocation and preventative measures. Furthermore, analysts would also like to predict where future hotspots may occur. To facilitate such forecasting, we have created a predictive visual analytics toolkit that provides analysts with linked spatiotemporal and statistical analytic views. Our system models spatiotemporal events through the combination of kernel density estimation for event distribution and seasonal trend decomposition by loess smoothing for temporal predictions. We provide analysts with estimates of error in our modeling, along with spatial and temporal alerts to indicate the occurrence of statistically significant hotspots. Spatial data are distributed based on a modeling of previous event locations, thereby maintaining a temporal coherence with past events. Such tools allow analysts to perform real-time hypothesis testing, plan intervention strategies, and allocate resources to correspond to perceived threats.

  9. Hotspot Mainport Schiphol : midterm review report

    NARCIS (Netherlands)

    Döpp, S.; Brink, van den P.; Hartogensis, O.K.; Jacobs, A.; Homan, C.; Sondij, J.

    2012-01-01

    The focus of Knowledge for Climate (KfC) research in Hotspot Schiphol Mainport is to optimize the contribution of meteorological services to a sustainable operation and reliable operation of Schiphol airport. Three research projects have been carried out in the first tranche of the Knowledge for

  10. The detection of thermophilous forest hotspots in Poland using geostatistical interpolation of plant richness

    Directory of Open Access Journals (Sweden)

    Marcin Kiedrzyński

    2014-07-01

    Full Text Available Attempts to study biodiversity hotspots on a regional scale should combine compositional and functionalist criteria. The detection of hotspots in this study uses one ecologically similar group of high conservation value species as hotspot indicators, as well as focal habitat indicators, to detect the distribution of suitable environmental conditions. The method is assessed with reference to thermophilous forests in Poland – key habitats for many rare and relict species. Twenty-six high conservation priority species were used as hotspot indicators, and ten plant taxa characteristic of the Quercetalia pubescenti-petraeae phytosociological order were used as focal habitat indicators. Species distribution data was based on a 10 × 10 km grid. The number of species per grid square was interpolated by the ordinary kriging geostatistical method. Our analysis largely determined the distribution of areas with concentration of thermophilous forest flora, but also regional disjunctions and geographical barriers. Indicator species richness can be interpreted as a reflection of the actual state of habitat conditions. It can also be used to determine the location of potential species refugia and possible past and future migration routes.

  11. Comparative analysis of Dendrobium plastomes and utility of plastomic mutational hotspots.

    Science.gov (United States)

    Zhitao, Niu; Shuying, Zhu; Jiajia, Pan; Ludan, Li; Jing, Sun; Xiaoyu, Ding

    2017-05-18

    Dendrobium is one of the largest genera in Orchidaceae, comprising about 800-1500 species mainly distributed in tropical Asia, Australasia, and Australia. There are 74 species and two varieties of this genus in China. Because of their ornamental and commercial value, Dendrobium orchids have been studied at low taxonomic levels. However, structural changes and effective mutational hotspots of Dendrobium plastomes have rarely been documented. Here, 30 Dendrobium plastomes were compared, comprising 25 newly sequenced in this study and five previously published. Except for their differences in NDH genes, these plastomes shared identical gene content and order. Comparative analyses revealed that the variation in size of Dendroubium plastomes was associated with dramatically changed length of InDels. Furthermore, ten loci were identified as the top-ten mutational hotspots, whose sequence variability was almost unchanged with more than 10 plastomes sampled, suggesting that they may be powerful markers for Dendrobium species. In addition, primer pairs of 47 polymorphic microsatellites were developed. After assessing the mean BS values of all combinations derived from the top-ten hotspots, we recommend that the combination of five hotspots-trnT-trnL, rpl32-trnL, clpP-psbB, trnL intron, and rps16-trnQ-should be used in the phylogenetic and identification studies of Dendrobium.

  12. Rare earths

    Energy Technology Data Exchange (ETDEWEB)

    Cranstone, D A

    1979-01-01

    Rare earth elements are commonly extracted from the minerals monazite, bastnaesite, and xenotine. New uses for these elements are constantly developing; they have found applications in glass polishing, television tube phosphors, high-strength low-alloy steels, magnets, catalysts, refractory ceramics, and hydrogen sponge alloys. In Canada, rare earths have been produced as byproducts of the uranium mining industry, but there was no production of rare earths in 1978 or 1979. The world sources of and markets for the rare earth elements are discussed.

  13. Rare copy number alterations and copy-neutral loss of heterozygosity revealed in ameloblastomas by high-density whole-genome microarray analysis

    DEFF Research Database (Denmark)

    Diniz, Marina Gonçalves; Duarte, Alessandra Pires; Villacis, Rolando A

    2017-01-01

    BACKGROUND: Ameloblastoma (unicystic, UA, or multicystic, MA) is a rare tumor associated with bone destruction and facial deformity. Its malignant counterpart is the ameloblastic carcinoma (AC). The BRAFV600E mutation is highly prevalent in all these tumors subtypes and cannot account for their d...

  14. The Use of Social Ecological Hotspots Mapping: Co-Developing Adaptation Strategies for Resource Management by Communities and Policy Makers

    Science.gov (United States)

    Alessa, L.

    2014-12-01

    Ultimately, adaptation is based on a set of trade-offs rather than optimal conditions, something that is rarely seen in messy social ecological systems (SES). In this talk, we discuss the role of spatial hot-spot mapping using social and biophysical data to understand the feedbacks in SES. We review the types of data needed, their means of acquisition and the analytic methods involved. In addition, we outline the challenges faced in co-developing this type of inquiry based on lessons learned from several long-term programs. Finally, we present the utility of SES hotspots in developing adaptation strategies on the ground by communities and policy makers.

  15. HOTSPOT Health Physics codes for the PC

    Energy Technology Data Exchange (ETDEWEB)

    Homann, S.G.

    1994-03-01

    The HOTSPOT Health Physics codes were created to provide Health Physics personnel with a fast, field-portable calculation tool for evaluating accidents involving radioactive materials. HOTSPOT codes are a first-order approximation of the radiation effects associated with the atmospheric release of radioactive materials. HOTSPOT programs are reasonably accurate for a timely initial assessment. More importantly, HOTSPOT codes produce a consistent output for the same input assumptions and minimize the probability of errors associated with reading a graph incorrectly or scaling a universal nomogram during an emergency. The HOTSPOT codes are designed for short-term (less than 24 hours) release durations. Users requiring radiological release consequences for release scenarios over a longer time period, e.g., annual windrose data, are directed to such long-term models as CAPP88-PC (Parks, 1992). Users requiring more sophisticated modeling capabilities, e.g., complex terrain; multi-location real-time wind field data; etc., are directed to such capabilities as the Department of Energy`s ARAC computer codes (Sullivan, 1993). Four general programs -- Plume, Explosion, Fire, and Resuspension -- calculate a downwind assessment following the release of radioactive material resulting from a continuous or puff release, explosive release, fuel fire, or an area contamination event. Other programs deal with the release of plutonium, uranium, and tritium to expedite an initial assessment of accidents involving nuclear weapons. Additional programs estimate the dose commitment from the inhalation of any one of the radionuclides listed in the database of radionuclides; calibrate a radiation survey instrument for ground-survey measurements; and screen plutonium uptake in the lung (see FIDLER Calibration and LUNG Screening sections).

  16. HOTSPOT Health Physics codes for the PC

    International Nuclear Information System (INIS)

    Homann, S.G.

    1994-03-01

    The HOTSPOT Health Physics codes were created to provide Health Physics personnel with a fast, field-portable calculation tool for evaluating accidents involving radioactive materials. HOTSPOT codes are a first-order approximation of the radiation effects associated with the atmospheric release of radioactive materials. HOTSPOT programs are reasonably accurate for a timely initial assessment. More importantly, HOTSPOT codes produce a consistent output for the same input assumptions and minimize the probability of errors associated with reading a graph incorrectly or scaling a universal nomogram during an emergency. The HOTSPOT codes are designed for short-term (less than 24 hours) release durations. Users requiring radiological release consequences for release scenarios over a longer time period, e.g., annual windrose data, are directed to such long-term models as CAPP88-PC (Parks, 1992). Users requiring more sophisticated modeling capabilities, e.g., complex terrain; multi-location real-time wind field data; etc., are directed to such capabilities as the Department of Energy's ARAC computer codes (Sullivan, 1993). Four general programs -- Plume, Explosion, Fire, and Resuspension -- calculate a downwind assessment following the release of radioactive material resulting from a continuous or puff release, explosive release, fuel fire, or an area contamination event. Other programs deal with the release of plutonium, uranium, and tritium to expedite an initial assessment of accidents involving nuclear weapons. Additional programs estimate the dose commitment from the inhalation of any one of the radionuclides listed in the database of radionuclides; calibrate a radiation survey instrument for ground-survey measurements; and screen plutonium uptake in the lung (see FIDLER Calibration and LUNG Screening sections)

  17. Transmission of infectious diseases en route to habitat hotspots.

    Science.gov (United States)

    Benavides, Julio; Walsh, Peter D; Meyers, Lauren Ancel; Raymond, Michel; Caillaud, Damien

    2012-01-01

    The spread of infectious diseases in wildlife populations is influenced by patterns of between-host contacts. Habitat "hotspots"--places attracting a large numbers of individuals or social groups--can significantly alter contact patterns and, hence, disease propagation. Research on the importance of habitat hotspots in wildlife epidemiology has primarily focused on how inter-individual contacts occurring at the hotspot itself increase disease transmission. However, in territorial animals, epidemiologically important contacts may primarily occur as animals cross through territories of conspecifics en route to habitat hotspots. So far, the phenomenon has received little attention. Here, we investigate the importance of these contacts in the case where infectious individuals keep visiting the hotspots and in the case where these individuals are not able to travel to the hotspot any more. We developed a simulation epidemiological model to investigate both cases in a scenario when transmission at the hotspot does not occur. We find that (i) hotspots still exacerbate epidemics, (ii) when infectious individuals do not travel to the hotspot, the most vulnerable individuals are those residing at intermediate distances from the hotspot rather than nearby, and (iii) the epidemiological vulnerability of a population is the highest when the number of hotspots is intermediate. By altering animal movements in their vicinity, habitat hotspots can thus strongly increase the spread of infectious diseases, even when disease transmission does not occur at the hotspot itself. Interestingly, when animals only visit the nearest hotspot, creating additional artificial hotspots, rather than reducing their number, may be an efficient disease control measure.

  18. Severe fluoropyrimidine toxicity due to novel and rare DPYD missense mutations, deletion and genomic amplification affecting DPD activity and mRNA splicing

    DEFF Research Database (Denmark)

    van Kuilenburg, André B P; Meijer, Judith; Maurer, Dirk

    2017-01-01

    Dihydropyrimidine dehydrogenase (DPD) is the initial and rate-limiting enzyme in the catabolism of 5-fluorouracil (5FU). Genetic variations in DPD have emerged as predictive risk factors for severe fluoropyrimidine toxicity. Here, we report novel and rare genetic variants underlying DPD deficiency...... in 9 cancer patients presenting with severe fluoropyrimidine-associated toxicity. All patients possessed a strongly reduced DPD activity, ranging from 9 to 53% of controls. Analysis of the DPD gene (DPYD) showed the presence of 21 variable sites including 4 novel and 4 very rare aberrations: 3 missense...... of exon 4 immediately upstream of the mutated splice-donor site in the process of DPD pre-mRNA splicing. A lethal toxicity in two DPD patients suggests that fluoropyrimidines combined with other therapies such as radiotherapy might be particularly toxic for DPD deficient patients. Our study advocates...

  19. Rare earths

    International Nuclear Information System (INIS)

    1984-01-01

    The conference was held from September 12 to 13, 1984 in Jetrichovice, Czechoslovakia. The participants heard 16 papers of which 4 were inputted in INIS. These papers dealt with industrial separation processes of rare earths, the use of chemical methods of separation from the concentrate of apatite and bastnesite, the effect of the relative permittivity of solvents in the elution of rare earth elements from a cation exchanger, and the determination of the content of different rare earth elements using X-ray fluorescence analysis and atomic absorption spectroscopy. (E.S.)

  20. The emergence of motives in liminal hotspots

    DEFF Research Database (Denmark)

    Nissen, Morten; Sørensen, Kathrine Solgaard

    2017-01-01

    The concept of “motivation” commonly constructs as a psychological essence what is really the paradoxical imposition of a required desire. While the resulting impasse blocked theoretical development for around four decades, pragmatic motivational techniques evolved regardless. These could...... motivation–resistance contradiction; then through pragmatic approaches in counseling, i.e., the prevalent cognitive-client-centered form and the “solution-focused brief therapy” approach—and finally as motives emergent in liminal hotspots....

  1. SPITZER OBSERVATIONS OF HOTSPOTS IN RADIO LOBES

    International Nuclear Information System (INIS)

    Werner, Michael W.; Murphy, David W.; Livingston, John H.; Gorjian, Varoujan; Jones, Dayton L.; Meier, David L.; Lawrence, Charles R.

    2012-01-01

    We have carried out a systematic search with Spitzer Warm Mission and archival data for infrared emission from the hotspots in radio lobes that have been described by Hardcastle et al. These hotspots have been detected with both radio and X-ray observations, but an observation at an intermediate frequency in the infrared can be critical to distinguish between competing models for particle acceleration and radiation processes in these objects. Between the archival and warm mission data, we report detections of 18 hotspots; the archival data generally include detections at all four IRAC bands, the Warm Mission data only at 3.6 μm. Using a theoretical formalism adopted from Godfrey et al., we fit both archival and warm mission spectral energy distributions (SEDs)—including radio, X-ray, and optical data from Hardcastle as well as the Spitzer data—with a synchrotron self-Compton (SSC) model, in which the X-rays are produced by Compton scattering of the radio frequency photons by the energetic electrons which radiate them. With one exception, an SSC model requires that the magnetic field be less or much less than the equipartition value which minimizes total energy and has comparable amounts of energy in the magnetic field and in the energetic particles. This conclusion agrees with those of comparable recent studies of hotspots, and with the analysis presented by Hardcastle et al. We also show that the infrared data rule out the simplest synchrotron-only models for the SEDs. We briefly discuss the implications of these results and of alternate interpretations of the data.

  2. Forecasting hotspots using predictive visual analytics approach

    Science.gov (United States)

    Maciejewski, Ross; Hafen, Ryan; Rudolph, Stephen; Cleveland, William; Ebert, David

    2014-12-30

    A method for forecasting hotspots is provided. The method may include the steps of receiving input data at an input of the computational device, generating a temporal prediction based on the input data, generating a geospatial prediction based on the input data, and generating output data based on the time series and geospatial predictions. The output data may be configured to display at least one user interface at an output of the computational device.

  3. Rare particles

    International Nuclear Information System (INIS)

    Kutschera, W.

    1984-01-01

    The use of Accelerator Mass Spectrometry (AMS) to search for hypothetical particles and known particles of rare processes is discussed. The hypothetical particles considered include fractionally charged particles, anomalously heavy isotopes, and superheavy elements. The known particles produced in rare processes discussed include doubly-charged negative ions, counting neutrino-produced atoms in detectors for solar neutrino detection, and the spontaneous emission of 14 C from 223 Ra. 35 references

  4. The history, hotspots, and trends of electrocardiogram.

    Science.gov (United States)

    Yang, Xiang-Lin; Liu, Guo-Zhen; Tong, Yun-Hai; Yan, Hong; Xu, Zhi; Chen, Qi; Liu, Xiang; Zhang, Hong-Hao; Wang, Hong-Bo; Tan, Shao-Hua

    2015-07-01

    The electrocardiogram (ECG) has broad applications in clinical diagnosis and prognosis of cardiovascular disease. Many researchers have contributed to its progressive development. To commemorate those pioneers, and to better study and promote the use of ECG, we reviewed and present here a systematic introduction about the history, hotspots, and trends of ECG. In the historical part, information including the invention, improvement, and extensive applications of ECG, such as in long QT syndrome (LQTS), angina, and myocardial infarction (MI), are chronologically presented. New technologies and applications from the 1990s are also introduced. In the second part, we use the bibliometric analysis method to analyze the hotspots in the field of ECG-related research. By using total citations and year-specific total citations as our main criteria, four key hotspots in ECG-related research were identified from 11 articles, including atrial fibrillation, LQTS, angina and MI, and heart rate variability. Recent studies in those four areas are also reported. In the final part, we discuss the future trends concerning ECG-related research. The authors believe that improvement of the ECG instrumentation, big data mining for ECG, and the accuracy of diagnosis and application will be areas of continuous concern.

  5. Whole genome sequencing of a rare rotavirus from archived stool sample demonstrates independent zoonotic origin of human G8P[14] strains in Hungary.

    Science.gov (United States)

    Marton, Szilvia; Dóró, Renáta; Fehér, Enikő; Forró, Barbara; Ihász, Katalin; Varga-Kugler, Renáta; Farkas, Szilvia L; Bányai, Krisztián

    2017-01-02

    Genotype P[14] rotaviruses in humans are thought to be zoonotic strains originating from bovine or ovine host species. Over the past 30 years only few genotype P[14] strains were identified in Hungary totalinghuman rotaviruses whose genotype had been determined. In this study we report the genome sequence and phylogenetic analysis of a human genotype G8P[14] strain, RVA/Human-wt/HUN/182-02/2001/G8P[14]. The whole genome constellation (G8-P[14]-I2-R2-C2-M2-A11-N2-T6-E2-H3) of this strain was shared with another Hungarian zoonotic G8P[14] strain, RVA/Human-wt/HUN/BP1062/2004/G8P[14], although phylogenetic analyses revealed the two rotaviruses likely had different progenitors. Overall, our findings indicate that human G8P[14] rotavirus detected in Hungary in the past originated from independent zoonotic events. Further studies are needed to assess the public health risk associated with infections by various animal rotavirus strains. Copyright © 2016. Published by Elsevier B.V.

  6. HOTSPOT: The Snake River Scientifi c Drilling Project— Tracking the Yellowstone Hotspot Through Space and Time

    Directory of Open Access Journals (Sweden)

    Douglas F. Williams

    2006-09-01

    Full Text Available The project “HOTSPOT: Scientifi c Drilling of the Snake River Plain” held its inaugural workshop in Twin Falls, Idaho, U.S.A. on 18–21 May 2006. This inter-disciplinary workshop, sponsored by the International Continental Scientifi c Drilling Program (ICDP, explored the major scientifi c and logistical issues central to a transect of boreholes along the hotspot track and addressing the geochemical evolution of continental lithosphere in response to interaction with deepseated mantle hotspots or plumes. A series of four to six bore holes is envisioned, each about 1.5–2.0 km deep and located along the axis of the Snake River Plain. The holes will specific ally target the origin and evolution of hotspot-related volcanism in space and time. To accomplish scientific and logistical planning, sixty scientists from six countries attended the workshop.

  7. Hot-spot KIF5A mutations cause familial ALS.

    Science.gov (United States)

    Brenner, David; Yilmaz, Rüstem; Müller, Kathrin; Grehl, Torsten; Petri, Susanne; Meyer, Thomas; Grosskreutz, Julian; Weydt, Patrick; Ruf, Wolfgang; Neuwirth, Christoph; Weber, Markus; Pinto, Susana; Claeys, Kristl G; Schrank, Berthold; Jordan, Berit; Knehr, Antje; Günther, Kornelia; Hübers, Annemarie; Zeller, Daniel; Kubisch, Christian; Jablonka, Sibylle; Sendtner, Michael; Klopstock, Thomas; de Carvalho, Mamede; Sperfeld, Anne; Borck, Guntram; Volk, Alexander E; Dorst, Johannes; Weis, Joachim; Otto, Markus; Schuster, Joachim; Del Tredici, Kelly; Braak, Heiko; Danzer, Karin M; Freischmidt, Axel; Meitinger, Thomas; Strom, Tim M; Ludolph, Albert C; Andersen, Peter M; Weishaupt, Jochen H

    2018-01-12

    Heterozygous missense mutations in the N-terminal motor or coiled-coil domains of the kinesin family member 5A (KIF5A) gene cause monogenic spastic paraplegia (HSP10) and Charcot-Marie-Tooth disease type 2 (CMT2). Moreover, heterozygous de novo frame-shift mutations in the C-terminal domain of KIF5A are associated with neonatal intractable myoclonus, a neurodevelopmental syndrome. These findings, together with the observation that many of the disease genes associated with amyotrophic lateral sclerosis disrupt cytoskeletal function and intracellular transport, led us to hypothesize that mutations in KIF5A are also a cause of amyotrophic lateral sclerosis. Using whole exome sequencing followed by rare variant analysis of 426 patients with familial amyotrophic lateral sclerosis and 6137 control subjects, we detected an enrichment of KIF5A splice-site mutations in amyotrophic lateral sclerosis (2/426 compared to 0/6137 in controls; P = 4.2 × 10-3), both located in a hot-spot in the C-terminus of the protein and predicted to affect splicing exon 27. We additionally show co-segregation with amyotrophic lateral sclerosis of two canonical splice-site mutations in two families. Investigation of lymphoblast cell lines from patients with KIF5A splice-site mutations revealed the loss of mutant RNA expression and suggested haploinsufficiency as the most probable underlying molecular mechanism. Furthermore, mRNA sequencing of a rare non-synonymous missense mutation (predicting p.Arg1007Gly) located in the C-terminus of the protein shortly upstream of the splice donor of exon 27 revealed defective KIF5A pre-mRNA splicing in respective patient-derived cell lines owing to abrogation of the donor site. Finally, the non-synonymous single nucleotide variant rs113247976 (minor allele frequency = 1.00% in controls, n = 6137), also located in the C-terminal region [p.(Pro986Leu) in exon 26], was significantly enriched in familial amyotrophic lateral sclerosis patients (minor allele

  8. Hot-spot KIF5A mutations cause familial ALS

    Science.gov (United States)

    Yilmaz, Rüstem; Müller, Kathrin; Grehl, Torsten; Petri, Susanne; Meyer, Thomas; Grosskreutz, Julian; Weydt, Patrick; Ruf, Wolfgang; Neuwirth, Christoph; Weber, Markus; Pinto, Susana; Claeys, Kristl G; Schrank, Berthold; Jordan, Berit; Knehr, Antje; Günther, Kornelia; Hübers, Annemarie; Zeller, Daniel; Kubisch, Christian; Jablonka, Sibylle; Klopstock, Thomas; de Carvalho, Mamede; Sperfeld, Anne; Borck, Guntram; Volk, Alexander E; Dorst, Johannes; Weis, Joachim; Otto, Markus; Schuster, Joachim; Del Tredici, Kelly; Braak, Heiko; Danzer, Karin M; Freischmidt, Axel; Meitinger, Thomas; Strom, Tim M; Ludolph, Albert C; Andersen, Peter M; Weishaupt, Jochen H; Weyen, Ute; Hermann, Andreas; Hagenacker, Tim; Koch, Jan Christoph; Lingor, Paul; Göricke, Bettina; Zierz, Stephan; Baum, Petra; Wolf, Joachim; Winkler, Andrea; Young, Peter; Bogdahn, Ulrich; Prudlo, Johannes; Kassubek., Jan

    2018-01-01

    Abstract Heterozygous missense mutations in the N-terminal motor or coiled-coil domains of the kinesin family member 5A (KIF5A) gene cause monogenic spastic paraplegia (HSP10) and Charcot-Marie-Tooth disease type 2 (CMT2). Moreover, heterozygous de novo frame-shift mutations in the C-terminal domain of KIF5A are associated with neonatal intractable myoclonus, a neurodevelopmental syndrome. These findings, together with the observation that many of the disease genes associated with amyotrophic lateral sclerosis disrupt cytoskeletal function and intracellular transport, led us to hypothesize that mutations in KIF5A are also a cause of amyotrophic lateral sclerosis. Using whole exome sequencing followed by rare variant analysis of 426 patients with familial amyotrophic lateral sclerosis and 6137 control subjects, we detected an enrichment of KIF5A splice-site mutations in amyotrophic lateral sclerosis (2/426 compared to 0/6137 in controls; P = 4.2 × 10−3), both located in a hot-spot in the C-terminus of the protein and predicted to affect splicing exon 27. We additionally show co-segregation with amyotrophic lateral sclerosis of two canonical splice-site mutations in two families. Investigation of lymphoblast cell lines from patients with KIF5A splice-site mutations revealed the loss of mutant RNA expression and suggested haploinsufficiency as the most probable underlying molecular mechanism. Furthermore, mRNA sequencing of a rare non-synonymous missense mutation (predicting p.Arg1007Gly) located in the C-terminus of the protein shortly upstream of the splice donor of exon 27 revealed defective KIF5A pre-mRNA splicing in respective patient-derived cell lines owing to abrogation of the donor site. Finally, the non-synonymous single nucleotide variant rs113247976 (minor allele frequency = 1.00% in controls, n = 6137), also located in the C-terminal region [p.(Pro986Leu) in exon 26], was significantly enriched in familial amyotrophic lateral sclerosis patients (minor

  9. Identifying species threat hotspots from global supply chains.

    Science.gov (United States)

    Moran, Daniel; Kanemoto, Keiichiro

    2017-01-04

    Identifying hotspots of species threat has been a successful approach for setting conservation priorities. One important challenge in conservation is that, in many hotspots, export industries continue to drive overexploitation. Conservation measures must consider not just the point of impact, but also the consumer demand that ultimately drives resource use. To understand which species threat hotspots are driven by which consumers, we have developed a new approach to link a set of biodiversity footprint accounts to the hotspots of threatened species on the IUCN Red List of Threatened Species. The result is a map connecting consumption to spatially explicit hotspots driven by production on a global scale. Locating biodiversity threat hotspots driven by consumption of goods and services can help to connect conservationists, consumers, companies and governments in order to better target conservation actions.

  10. Identifying the Species Threat Hotspots from Global Supply Chains

    OpenAIRE

    Moran, Daniel; Kanemoto, Keiichiro

    2016-01-01

    Identifying species threat hotspots has been a successful approach for setting conservation priorities. One major challenge in conservation is that in many hotspots export industries continue to drive overexploitation. Conservation measures must consider not just the point of impact, but also the consumer demand that ultimately drives resource use. To understand which species threat hotspots are driven by which consumers, we have developed a new approach to link a set of biodiversity footprin...

  11. Recombining without Hotspots: A Comprehensive Evolutionary Portrait of Recombination in Two Closely Related Species of Drosophila

    Science.gov (United States)

    Smukowski Heil, Caiti S.; Ellison, Chris; Dubin, Matthew; Noor, Mohamed A.F.

    2015-01-01

    Meiotic recombination rate varies across the genome within and between individuals, populations, and species in virtually all taxa studied. In almost every species, this variation takes the form of discrete recombination hotspots, determined in some mammals by a protein called PRDM9. Hotspots and their determinants have a profound effect on the genomic landscape, and share certain features that extend across the tree of life. Drosophila, in contrast, are anomalous in their absence of hotspots, PRDM9, and other species-specific differences in the determination of recombination. To better understand the evolution of meiosis and general patterns of recombination across diverse taxa, we present a truly comprehensive portrait of recombination across time, combining recently published cross-based contemporary recombination estimates from each of two sister species with newly obtained linkage-disequilibrium-based historic estimates of recombination from both of these species. Using Drosophila pseudoobscura and Drosophila miranda as a model system, we compare recombination rate between species at multiple scales, and we suggest that Drosophila replicate the pattern seen in human–chimpanzee in which recombination rate is conserved at broad scales. We also find evidence of a species-wide recombination modifier(s), resulting in both a present and historic genome-wide elevation of recombination rates in D. miranda, and identify broad scale effects on recombination from the presence of an inversion. Finally, we reveal an unprecedented view of the distribution of recombination in D. pseudoobscura, illustrating patterns of linked selection and where recombination is taking place. Overall, by combining these estimation approaches, we highlight key similarities and differences in recombination between Drosophila and other organisms. PMID:26430062

  12. Recombining without Hotspots: A Comprehensive Evolutionary Portrait of Recombination in Two Closely Related Species of Drosophila.

    Science.gov (United States)

    Smukowski Heil, Caiti S; Ellison, Chris; Dubin, Matthew; Noor, Mohamed A F

    2015-10-01

    Meiotic recombination rate varies across the genome within and between individuals, populations, and species in virtually all taxa studied. In almost every species, this variation takes the form of discrete recombination hotspots, determined in some mammals by a protein called PRDM9. Hotspots and their determinants have a profound effect on the genomic landscape, and share certain features that extend across the tree of life. Drosophila, in contrast, are anomalous in their absence of hotspots, PRDM9, and other species-specific differences in the determination of recombination. To better understand the evolution of meiosis and general patterns of recombination across diverse taxa, we present a truly comprehensive portrait of recombination across time, combining recently published cross-based contemporary recombination estimates from each of two sister species with newly obtained linkage-disequilibrium-based historic estimates of recombination from both of these species. Using Drosophila pseudoobscura and Drosophila miranda as a model system, we compare recombination rate between species at multiple scales, and we suggest that Drosophila replicate the pattern seen in human-chimpanzee in which recombination rate is conserved at broad scales. We also find evidence of a species-wide recombination modifier(s), resulting in both a present and historic genome-wide elevation of recombination rates in D. miranda, and identify broad scale effects on recombination from the presence of an inversion. Finally, we reveal an unprecedented view of the distribution of recombination in D. pseudoobscura, illustrating patterns of linked selection and where recombination is taking place. Overall, by combining these estimation approaches, we highlight key similarities and differences in recombination between Drosophila and other organisms. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  13. Nanoscale hotspots due to nonequilibrium thermal transport

    International Nuclear Information System (INIS)

    Sinha, Sanjiv; Goodson, Kenneth E.

    2004-01-01

    Recent experimental and modeling efforts have been directed towards the issue of temperature localization and hotspot formation in the vicinity of nanoscale heat generating devices. The nonequilibrium transport conditions which develop around these nanoscale devices results in elevated temperatures near the heat source which can not be predicted by continuum diffusion theory. Efforts to determine the severity of this temperature localization phenomena in silicon devices near and above room temperature are of technological importance to the development of microelectronics and other nanotechnologies. In this work, we have developed a new modeling tool in order to explore the magnitude of the additional thermal resistance which forms around nanoscale hotspots from temperatures of 100-1000K. The models are based on a two fluid approximation in which thermal energy is transferred between ''stationary'' optical phonons and fast propagating acoustic phonon modes. The results of the model have shown excellent agreement with experimental results of localized hotspots in silicon at lower temperatures. The model predicts that the effect of added thermal resistance due to the nonequilibrium phonon distribution is greatest at lower temperatures, but is maintained out to temperatures of 1000K. The resistance predicted by the numerical code can be easily integrated with continuum models in order to predict the temperature distribution around nanoscale heat sources with improved accuracy. Additional research efforts also focused on the measurements of the thermal resistance of silicon thin films at higher temperatures, with a focus on polycrystalline silicon. This work was intended to provide much needed experimental data on the thermal transport properties for micro and nanoscale devices built with this material. Initial experiments have shown that the exposure of polycrystalline silicon to high temperatures may induce recrystallization and radically increase the thermal

  14. A micro-epidemiological analysis of febrile malaria in Coastal Kenya showing hotspots within hotspots

    NARCIS (Netherlands)

    Bejon, P.; Williams, T.N.; Nyundo, C.; Hay, S.I.; Benz, D.; Gething, P.W.; Otiende, M.; Peshu, J.; Bashraheil, M.; Greenhouse, B.; Bousema, T.; Bauni, E.; Marsh, K.; Smith, D.L.; Borrmann, S.

    2014-01-01

    Malaria transmission is spatially heterogeneous. This reduces the efficacy of control strategies, but focusing control strategies on clusters or 'hotspots' of transmission may be highly effective. Among 1500 homesteads in coastal Kenya we calculated (a) the fraction of febrile children with positive

  15. Multimer Formation Explains Allelic Suppression of PRDM9 Recombination Hotspots.

    Science.gov (United States)

    Baker, Christopher L; Petkova, Pavlina; Walker, Michael; Flachs, Petr; Mihola, Ondrej; Trachtulec, Zdenek; Petkov, Petko M; Paigen, Kenneth

    2015-09-01

    Genetic recombination during meiosis functions to increase genetic diversity, promotes elimination of deleterious alleles, and helps assure proper segregation of chromatids. Mammalian recombination events are concentrated at specialized sites, termed hotspots, whose locations are determined by PRDM9, a zinc finger DNA-binding histone methyltransferase. Prdm9 is highly polymorphic with most alleles activating their own set of hotspots. In populations exhibiting high frequencies of heterozygosity, questions remain about the influences different alleles have in heterozygous individuals where the two variant forms of PRDM9 typically do not activate equivalent populations of hotspots. We now find that, in addition to activating its own hotspots, the presence of one Prdm9 allele can modify the activity of hotspots activated by the other allele. PRDM9 function is also dosage sensitive; Prdm9+/- heterozygous null mice have reduced numbers and less active hotspots and increased numbers of aberrant germ cells. In mice carrying two Prdm9 alleles, there is allelic competition; the stronger Prdm9 allele can partially or entirely suppress chromatin modification and recombination at hotspots of the weaker allele. In cell cultures, PRDM9 protein variants form functional heteromeric complexes which can bind hotspots sequences. When a heteromeric complex binds at a hotspot of one PRDM9 variant, the other PRDM9 variant, which would otherwise not bind, can still methylate hotspot nucleosomes. We propose that in heterozygous individuals the underlying molecular mechanism of allelic suppression results from formation of PRDM9 heteromers, where the DNA binding activity of one protein variant dominantly directs recombination initiation towards its own hotspots, effectively titrating down recombination by the other protein variant. In natural populations with many heterozygous individuals, allelic competition will influence the recombination landscape.

  16. Characterization and Prediction of Protein Phosphorylation Hotspots in Arabidopsis thaliana.

    Science.gov (United States)

    Christian, Jan-Ole; Braginets, Rostyslav; Schulze, Waltraud X; Walther, Dirk

    2012-01-01

    The regulation of protein function by modulating the surface charge status via sequence-locally enriched phosphorylation sites (P-sites) in so called phosphorylation "hotspots" has gained increased attention in recent years. We set out to identify P-hotspots in the model plant Arabidopsis thaliana. We analyzed the spacing of experimentally detected P-sites within peptide-covered regions along Arabidopsis protein sequences as available from the PhosPhAt database. Confirming earlier reports (Schweiger and Linial, 2010), we found that, indeed, P-sites tend to cluster and that distributions between serine and threonine P-sites to their respected closest next P-site differ significantly from those for tyrosine P-sites. The ability to predict P-hotspots by applying available computational P-site prediction programs that focus on identifying single P-sites was observed to be severely compromised by the inevitable interference of nearby P-sites. We devised a new approach, named HotSPotter, for the prediction of phosphorylation hotspots. HotSPotter is based primarily on local amino acid compositional preferences rather than sequence position-specific motifs and uses support vector machines as the underlying classification engine. HotSPotter correctly identified experimentally determined phosphorylation hotspots in A. thaliana with high accuracy. Applied to the Arabidopsis proteome, HotSPotter-predicted 13,677 candidate P-hotspots in 9,599 proteins corresponding to 7,847 unique genes. Hotspot containing proteins are involved predominantly in signaling processes confirming the surmised modulating role of hotspots in signaling and interaction events. Our study provides new bioinformatics means to identify phosphorylation hotspots and lays the basis for further investigating novel candidate P-hotspots. All phosphorylation hotspot annotations and predictions have been made available as part of the PhosPhAt database at http://phosphat.mpimp-golm.mpg.de.

  17. A Global Moving Hotspot Reference Frame: How well it fits?

    Science.gov (United States)

    Doubrovine, P. V.; Steinberger, B.; Torsvik, T. H.

    2010-12-01

    Since the early 1970s, when Jason Morgan proposed that hotspot tracks record motion of lithosphere over deep-seated mantle plumes, the concept of fixed hotspots has dominated the way we think about absolute plate reconstructions. In the last decade, with compelling evidence for southward drift of the Hawaiian hotspot from paleomagnetic studies, and for the relative motion between the Pacific and Indo-Atlantic hotspots from refined plate circuit reconstructions, the perception changed and a global moving hotspot reference frame (GMHRF) was introduced, in which numerical models of mantle convection and advection of plume conduits in the mantle flow were used to estimate hotspot motion. This reference frame showed qualitatively better performance in fitting hotspot tracks globally, but the error analysis and formal estimates of the goodness of fitted rotations were lacking in this model. Here we present a new generation of the GMHRF, in which updated plate circuit reconstructions and radiometric age data from the hotspot tracks were combined with numerical models of plume motion, and uncertainties of absolute plate rotations were estimated through spherical regression analysis. The overall quality of fit was evaluated using a formal statistical test, by comparing misfits produced by the model with uncertainties assigned to the data. Alternative plate circuit models linking the Pacific plate to the plates of Indo-Atlantic hemisphere were tested and compared to the fixed hotspot models with identical error budgets. Our results show that, with an appropriate choice of the Pacific plate circuit, it is possible to reconcile relative plate motions and modeled motions of mantle plumes globally back to Late Cretaceous time (80 Ma). In contrast, all fixed hotspot models failed to produce acceptable fits for Paleogene to Late Cretaceous time (30-80 Ma), highlighting significance of relative motion between the Pacific and Indo-Atlantic hotspots during this interval. The

  18. Geographic Hotspots of Critical National Infrastructure.

    Science.gov (United States)

    Thacker, Scott; Barr, Stuart; Pant, Raghav; Hall, Jim W; Alderson, David

    2017-12-01

    Failure of critical national infrastructures can result in major disruptions to society and the economy. Understanding the criticality of individual assets and the geographic areas in which they are located is essential for targeting investments to reduce risks and enhance system resilience. Within this study we provide new insights into the criticality of real-life critical infrastructure networks by integrating high-resolution data on infrastructure location, connectivity, interdependence, and usage. We propose a metric of infrastructure criticality in terms of the number of users who may be directly or indirectly disrupted by the failure of physically interdependent infrastructures. Kernel density estimation is used to integrate spatially discrete criticality values associated with individual infrastructure assets, producing a continuous surface from which statistically significant infrastructure criticality hotspots are identified. We develop a comprehensive and unique national-scale demonstration for England and Wales that utilizes previously unavailable data from the energy, transport, water, waste, and digital communications sectors. The testing of 200,000 failure scenarios identifies that hotspots are typically located around the periphery of urban areas where there are large facilities upon which many users depend or where several critical infrastructures are concentrated in one location. © 2017 Society for Risk Analysis.

  19. Rare Events

    Science.gov (United States)

    2009-10-01

    Limited Operational Exercise 1. 1A Limited Operational Exercise is a multiplayer experiment designed to exploit and study information sharing and...1.4 Summary of the Study The “rare event” of interest is an extreme, deliberate act of violence , destruction or socioeconomic disruption, such as an...connection with terrorism inves- tigations. The programs then use some combination of doctrinal revision and rewards to induce the people to abandon violence

  20. The problems with multi-species conservation: do hotspots, ideal ...

    African Journals Online (AJOL)

    South Africa urgently requires a national strategic plan for the conservation of the country's biodiversity. The for- mulation of such a plan would be relatively easy if centres (hotspots) of richness, endemism and rarity were con- gruent, both within and among many different taxa, if these hotspots captured a large proportion of ...

  1. The problems with multi-species conservation: do hotspots, ideal ...

    African Journals Online (AJOL)

    South Africa urgently requires a national strategic plan for the conservation of the country's biodiversity. The formulation of such a plan would be relatively easy if centres (hotspots) of richness, endemism and rarity were congruent, both within and among many different taxa, if these hotspots captured a large proportion of the ...

  2. Photothermal probing of plasmonic hotspots with nanomechanical resonator

    DEFF Research Database (Denmark)

    Schmid, Silvan; Wu, Kaiyu; Rindzevicius, Tomas

    2014-01-01

    Plasmonic nanostructures (hotspots) are key components e.g. in plasmon-enhanced spectroscopy, plasmonic solar cells, or as nano heat sources. The characterization of single hotspots is still challenging due to a lack of experimental tools. We present the direct photothermal probing and mapping...

  3. Hotspot relaxation dynamics in a current-carrying superconductor

    Science.gov (United States)

    Marsili, F.; Stevens, M. J.; Kozorezov, A.; Verma, V. B.; Lambert, Colin; Stern, J. A.; Horansky, R. D.; Dyer, S.; Duff, S.; Pappas, D. P.; Lita, A. E.; Shaw, M. D.; Mirin, R. P.; Nam, S. W.

    2016-03-01

    We experimentally studied the dynamics of optically excited hotspots in current-carrying WSi superconducting nanowires as a function of bias current, bath temperature, and excitation wavelength. We observed that the hotspot relaxation time depends on bias current, temperature, and wavelength. We explained this effect with a model based on quasiparticle recombination, which provides insight into the quasiparticle dynamics of superconductors.

  4. Hotspot Motion, Before and After the Hawaiian-Emperor Bend

    Science.gov (United States)

    Tarduno, J. A.; Bono, R. K.

    2014-12-01

    Hawaiian hotspot motion of >40 mm/yr is best documented by paleomagnetic investigations of basalt cores recovered by ocean drilling of the Emperor seamounts during ODP Leg 197 (Tarduno et al., 2003). These data indicate that the trend of the Emperor Seamounts dominantly records motion of the hotspot in the mantle, further suggesting that the great Hawaiian-Emperor bend (HEB) reflects mainly a change in hotspot motion. Data used for Pacific "absolute plate motion models" for times before the age of the HEB are also internally inconsistent with a fixed hotspot assumption; at present the best way to estimate Pacific absolute plate motion prior to the HEB bend is through use of predictions derived from plate circuits (e.g. Doubrovine and Tarduno, 2008). These analyses predict much less motion for the hotspot responsible for the Louisville Seamount chain, as has been observed by paleomagnetic analyses of cores recovered by IODP Expedition 330 (Koppers et al., 2012). Together, the ocean drilling data sets favor hotspot-specific processes to explain high drift rates, such as the model whereby the Hawaiian mantle plume was captured by a ridge in the Late Cretaceous, and subsequent changes in sub-Pacific mantle flow resulted in the trend of the Emperor Seamounts (Tarduno et al., 2009). However, the question of whether there is a smaller signal of motion between groups of hotspots remains. Plate circuit analyses yield a small discrepancy between predicted and actual hotspot locations for times between ca. 47 Ma and 10 Ma that could be a signal of continued southward migration of the Hawaiian hotspot. Alternatively, this could reflect the motion of the group of Indo-Atlantic hotspots relative to Hawaii. New paleomagnetic data from Midway Atoll (ca. 27 Ma) suggests little difference with the present-day latitude of the plume, indicating that the rate of motion of either the Hawaiian hotspot, or the Indo-Atlantic hotspot group, was about 15 mm/yr between 47 and 27 Ma. This

  5. Characteristics of suicide hotspots on the Belgian railway network.

    Science.gov (United States)

    Debbaut, Kevin; Krysinska, Karolina; Andriessen, Karl

    2014-01-01

    In 2004, railway suicide accounted for 5.3% of all suicides in Belgium. In 2008, Infrabel (Manager of the Belgian Railway Infrastructure) introduced a railway suicide prevention programme, including identification of suicide hotspots, i.e., areas of the railway network with an elevated incidence of suicide. The study presents an analysis of 43 suicide hotspots based on Infrabel data collected during field visits and semi-structured interviews conducted in mental health facilities in the vicinity of the hotspots. Three major characteristics of the hotspots were accessibility, anonymity, and vicinity of a mental health institution. The interviews identified several risk and protective factors for railway suicide, including the training of staff, introduction of a suicide prevention policy, and the role of the media. In conclusion, a comprehensive railway suicide prevention programme should continuously safeguard and monitor hotspots, and should be embedded in a comprehensive suicide prevention programme in the community.

  6. Imbalance aware lithography hotspot detection: a deep learning approach

    Science.gov (United States)

    Yang, Haoyu; Luo, Luyang; Su, Jing; Lin, Chenxi; Yu, Bei

    2017-07-01

    With the advancement of very large scale integrated circuits (VLSI) technology nodes, lithographic hotspots become a serious problem that affects manufacture yield. Lithography hotspot detection at the post-OPC stage is imperative to check potential circuit failures when transferring designed patterns onto silicon wafers. Although conventional lithography hotspot detection methods, such as machine learning, have gained satisfactory performance, with the extreme scaling of transistor feature size and layout patterns growing in complexity, conventional methodologies may suffer from performance degradation. For example, manual or ad hoc feature extraction in a machine learning framework may lose important information when predicting potential errors in ultra-large-scale integrated circuit masks. We present a deep convolutional neural network (CNN) that targets representative feature learning in lithography hotspot detection. We carefully analyze the impact and effectiveness of different CNN hyperparameters, through which a hotspot-detection-oriented neural network model is established. Because hotspot patterns are always in the minority in VLSI mask design, the training dataset is highly imbalanced. In this situation, a neural network is no longer reliable, because a trained model with high classification accuracy may still suffer from a high number of false negative results (missing hotspots), which is fatal in hotspot detection problems. To address the imbalance problem, we further apply hotspot upsampling and random-mirror flipping before training the network. Experimental results show that our proposed neural network model achieves comparable or better performance on the ICCAD 2012 contest benchmark compared to state-of-the-art hotspot detectors based on deep or representative machine leaning.

  7. Rare endocrine cancers have novel genetic alterations

    Science.gov (United States)

    A molecular characterization of adrenocortical carcinoma, a rare cancer of the adrenal cortex, analyzed 91 cases for alterations in the tumor genomes and identified several novel genetic mutations as likely mechanisms driving the disease as well as whole genome doubling as a probable driver of the disease.

  8. An underappreciated hotspot of antibiotic resistance

    DEFF Research Database (Denmark)

    Chen, Qing-Lin; Li, Hu; Zhou, Xin-Yuan

    2017-01-01

    Landfills are so far the most common practice for the disposals of municipal solid waste (MSW) worldwide. Since MSW landfill receives miscellaneous wastes, including unused/expired antibiotics and bioactive wastes, it gradually becomes a huge potential bioreactor for breeding antibiotic resistance....... Antibiotic resistance genes (ARGs) in landfill can flow to the environment through leakage of landfill leachate and pose a risk to public health. Using high throughput quantitative Polymerase Chain Reaction (HT-qPCR), we investigated the prevalence, diversity of ARGs and its association with various mobile...... be the potential hosts of ARGs. These findings provide evidence that groundwater near MSW landfill is an underappreciated hotspot of antibiotic resistance and contribute to the spread of ARGs via the flowing contaminated groundwater....

  9. Future hotspots of terrestrial mammal loss

    Science.gov (United States)

    Visconti, Piero; Pressey, Robert L.; Giorgini, Daniele; Maiorano, Luigi; Bakkenes, Michel; Boitani, Luigi; Alkemade, Rob; Falcucci, Alessandra; Chiozza, Federica; Rondinini, Carlo

    2011-01-01

    Current levels of endangerment and historical trends of species and habitats are the main criteria used to direct conservation efforts globally. Estimates of future declines, which might indicate different priorities than past declines, have been limited by the lack of appropriate data and models. Given that much of conservation is about anticipating and responding to future threats, our inability to look forward at a global scale has been a major constraint on effective action. Here, we assess the geography and extent of projected future changes in suitable habitat for terrestrial mammals within their present ranges. We used a global earth-system model, IMAGE, coupled with fine-scale habitat suitability models and parametrized according to four global scenarios of human development. We identified the most affected countries by 2050 for each scenario, assuming that no additional conservation actions other than those described in the scenarios take place. We found that, with some exceptions, most of the countries with the largest predicted losses of suitable habitat for mammals are in Africa and the Americas. African and North American countries were also predicted to host the most species with large proportional global declines. Most of the countries we identified as future hotspots of terrestrial mammal loss have little or no overlap with the present global conservation priorities, thus confirming the need for forward-looking analyses in conservation priority setting. The expected growth in human populations and consumption in hotspots of future mammal loss mean that local conservation actions such as protected areas might not be sufficient to mitigate losses. Other policies, directed towards the root causes of biodiversity loss, are required, both in Africa and other parts of the world. PMID:21844048

  10. Modelling Hotspots for Invasive Alien Plants in India.

    Science.gov (United States)

    Adhikari, Dibyendu; Tiwary, Raghuvar; Barik, Saroj Kanta

    2015-01-01

    Identification of invasion hotspots that support multiple invasive alien species (IAS) is a pre-requisite for control and management of invasion. However, till recently it remained a methodological challenge to precisely determine such invasive hotspots. We identified the hotspots of alien species invasion in India through Ecological Niche Modelling (ENM) using species occurrence data from the Global Biodiversity Information Facility (GBIF). The predicted area of invasion for selected species were classified into 4 categories based on number of model agreements for a region i.e. high, medium, low and very low. About 49% of the total geographical area of India was predicted to be prone to invasion at moderate to high levels of climatic suitability. The intersection of anthropogenic biomes and ecoregions with the regions of 'high' climatic suitability was classified as hotspot of alien plant invasion. Nineteen of 47 ecoregions of India, harboured such hotspots. Most ecologically sensitive regions of India, including the 'biodiversity hotspots' and coastal regions coincide with invasion hotspots, indicating their vulnerability to alien plant invasion. Besides demonstrating the usefulness of ENM and open source data for IAS management, the present study provides a knowledge base for guiding the formulation of an effective policy and management strategy for controlling the invasive alien species.

  11. Whole-exome sequencing of a rare case of familial childhood acute lymphoblastic leukemia reveals putative predisposing mutations in Fanconi anemia genes.

    Science.gov (United States)

    Spinella, Jean-François; Healy, Jasmine; Saillour, Virginie; Richer, Chantal; Cassart, Pauline; Ouimet, Manon; Sinnett, Daniel

    2015-07-23

    Acute lymphoblastic leukemia (ALL) is the most common pediatric cancer. While the multi-step model of pediatric leukemogenesis suggests interplay between constitutional and somatic genomes, the role of inherited genetic variability remains largely undescribed. Nonsyndromic familial ALL, although extremely rare, provides the ideal setting to study inherited contributions to ALL. Toward this goal, we sequenced the exomes of a childhood ALL family consisting of mother, father and two non-twinned siblings diagnosed with concordant pre-B hyperdiploid ALL and previously shown to have inherited a rare form of PRDM9, a histone H3 methyltransferase involved in crossing-over at recombination hotspots and Holliday junctions. We postulated that inheritance of additional rare disadvantaging variants in predisposing cancer genes could affect genomic stability and lead to increased risk of hyperdiploid ALL within this family. Whole exomes were captured using Agilent's SureSelect kit and sequenced on the Life Technologies SOLiD System. We applied a data reduction strategy to identify candidate variants shared by both affected siblings. Under a recessive disease model, we focused on rare non-synonymous or frame-shift variants in leukemia predisposing pathways. Though the family was nonsyndromic, we identified a combination of rare variants in Fanconi anemia (FA) genes FANCP/SLX4 (compound heterozygote - rs137976282/rs79842542) and FANCA (rs61753269) and a rare homozygous variant in the Holliday junction resolvase GEN1 (rs16981869). These variants, predicted to affect protein function, were previously identified in familial breast cancer cases. Based on our in-house database of 369 childhood ALL exomes, the sibs were the only patients to carry this particularly rare combination and only a single hyperdiploid patient was heterozygote at both FANCP/SLX4 positions, while no FANCA variant allele carriers were identified. FANCA is the most commonly mutated gene in FA and is essential for

  12. Phonon emission from self-heating hotspots into He II

    International Nuclear Information System (INIS)

    Schulze, H.-J.; Keck, K.

    1985-01-01

    Self-heating effects in superconducting films or whiskers can produce several hotspots distributed along the sample in the transition range between its superconducting and completely normal state. To obtain information about the temperature distribution along the film in this transition range and the emission of phonons from hotspots into the helium bath, we moved thin carbon filaments close to the film surfaces. By means of the data and the current-voltage characteristics of the films conclusions can be drawn about the number and the size of the hotspots. (author)

  13. Multiple Hotspot Mutations Scanning by Single Droplet Digital PCR.

    Science.gov (United States)

    Decraene, Charles; Silveira, Amanda B; Bidard, François-Clément; Vallée, Audrey; Michel, Marc; Melaabi, Samia; Vincent-Salomon, Anne; Saliou, Adrien; Houy, Alexandre; Milder, Maud; Lantz, Olivier; Ychou, Marc; Denis, Marc G; Pierga, Jean-Yves; Stern, Marc-Henri; Proudhon, Charlotte

    2018-02-01

    Progress in the liquid biopsy field, combined with the development of droplet digital PCR (ddPCR), has enabled noninvasive monitoring of mutations with high detection accuracy. However, current assays detect a restricted number of mutations per reaction. ddPCR is a recognized method for detecting alterations previously characterized in tumor tissues, but its use as a discovery tool when the mutation is unknown a priori remains limited. We established 2 ddPCR assays detecting all genomic alterations within KRAS exon 2 and EGFR exon 19 mutation hotspots, which are of clinical importance in colorectal and lung cancer, with use of a unique pair of TaqMan ® oligoprobes. The KRAS assay scanned for the 7 most common mutations in codons 12/13 but also all other mutations found in that region. The EGFR assay screened for all in-frame deletions of exon 19, which are frequent EGFR-activating events. The KRAS and EGFR assays were highly specific and both reached a limit of detection of <0.1% in mutant allele frequency. We further validated their performance on multiple plasma and formalin-fixed and paraffin-embedded tumor samples harboring a panel of different KRAS or EGFR mutations. This method presents the advantage of detecting a higher number of mutations with single-reaction ddPCRs while consuming a minimum of patient sample. This is particularly useful in the context of liquid biopsy because the amount of circulating tumor DNA is often low. This method should be useful as a discovery tool when the tumor tissue is unavailable or to monitor disease during therapy. © 2017 American Association for Clinical Chemistry.

  14. Polarization observations of DA240: structure of a hotspot

    International Nuclear Information System (INIS)

    Tsien, S.C.

    1982-01-01

    We present observations of the large-scale structure of the giant radio galaxy DA 240 at 0.15 and 1.4 GHz and high-resolution observations of the hotspot in its eastern lobe at 2.7 and 5.0 GHz. It is shown that the large-scale structure of DA 240 at 0.15 GHz is closely similar to that at 1.4 GHz. An age of about 4 x 10 7 yr is estimated from the spectral index. The hotspot contains a compact component of approximately 2 in size, and is strongly polarized, up to 50 to 60 per cent in its south-east region. The projected magnetic field in the hotspot runs nearly parallel to the two main elongated subcomponents. The thermal electron density in the hotspot is estimated to be -5 cm -3 . (author)

  15. The Manihiki Plateau—a key to missing hotspot tracks?

    Science.gov (United States)

    Pietsch, R.; Uenzelmann-Neben, G.

    2016-08-01

    A Neogene magmatic reactivation of the Manihiki Plateau, a large igneous province (LIP) in the central Pacific, is studied using seismic reflection data. Igneous diapirs have been identified exclusively within a narrow WNW-ESE striking corridor in the southern High Plateau (HP), which is parallel to the Neogene Pacific Plate motion and overlaps with an extrapolation of the Society Islands Hotspot (SIH) path. The igneous diapirs are characterized by a narrow width (>5 km), penetration of the Neogene sediments, and they become progressively younger towards the East (23-10 Ma). The magmatic source appears to be of small lateral extent, which leads to the conclusion that the diapirs represent Neogene hotspot volcanism within a LIP, and thus may be an older, previously unknown extension of the SIH track (>4.5 Ma). Comparing hotspot volcanism within oceanic and continental lithosphere, we further conclude that hotspot volcanism within LIP crust has similarities to tectonically faulted continental crust.

  16. Transportation conformity particulate matter hot-spot air quality modeling.

    Science.gov (United States)

    2013-07-01

    In light of the new development in particulate matter (PM) hot-spot regulations and Illinois Department : of Transportation (IDOT)s National Environmental Policy Act (NEPA) documentation requirements, : this project is intended to (1) perform and ...

  17. Ideas from the global climate change hotspot research | IDRC ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    2017-05-09

    May 9, 2017 ... Ideas from the global climate change hotspot research ... The Collaborative Adaptation Research Initiative in Africa and Asia (CARIAA) ... the decisions they need to make about investment choices and development options, ...

  18. Prdm9 Controls Activation of Mammalian Recombination Hotspots

    OpenAIRE

    Parvanov, Emil D.; Petkov, Petko M.; Paigen, Kenneth

    2009-01-01

    Mammalian meiotic recombination, which preferentially occurs at specialized sites called hotspots, assures the orderly segregation of meiotic chromosomes and creates genetic variation among offspring. A locus on mouse Chr 17, that controls activation of recombination at multiple distant hotspots, has been mapped within a 181 Kb interval, three of whose genes can be eliminated as candidates. The remaining gene, Prdm9, codes for a zinc finger containing histone H3K4 trimethylase that is uniquel...

  19. Investigating avian influenza infection hotspots in old-world shorebirds.

    Directory of Open Access Journals (Sweden)

    Nicolas Gaidet

    Full Text Available Heterogeneity in the transmission rates of pathogens across hosts or environments may produce disease hotspots, which are defined as specific sites, times or species associations in which the infection rate is consistently elevated. Hotspots for avian influenza virus (AIV in wild birds are largely unstudied and poorly understood. A striking feature is the existence of a unique but consistent AIV hotspot in shorebirds (Charadriiformes associated with a single species at a specific location and time (ruddy turnstone Arenaria interpres at Delaware Bay, USA, in May. This unique case, though a valuable reference, limits our capacity to explore and understand the general properties of AIV hotspots in shorebirds. Unfortunately, relatively few shorebirds have been sampled outside Delaware Bay and they belong to only a few shorebird families; there also has been a lack of consistent oropharyngeal sampling as a complement to cloacal sampling. In this study we looked for AIV hotspots associated with other shorebird species and/or with some of the larger congregation sites of shorebirds in the old world. We assembled and analysed a regionally extensive dataset of AIV prevalence from 69 shorebird species sampled in 25 countries across Africa and Western Eurasia. Despite this diverse and extensive coverage we did not detect any new shorebird AIV hotspots. Neither large shorebird congregation sites nor the ruddy turnstone were consistently associated with AIV hotspots. We did, however, find a low but widespread circulation of AIV in shorebirds that contrast with the absence of AIV previously reported in shorebirds in Europe. A very high AIV antibody prevalence coupled to a low infection rate was found in both first-year and adult birds of two migratory sandpiper species, suggesting the potential existence of an AIV hotspot along their migratory flyway that is yet to be discovered.

  20. A measurement concept for hot-spot BRDFs from space

    Energy Technology Data Exchange (ETDEWEB)

    Gerstl, S.A.W.

    1996-09-01

    Several concepts for canopy hot-spot measurements from space have been investigated. The most promising involves active illumination and bistatic detection that would allow hot-spot angular distribution (BRDF) measurements from space in a search-light mode. The concept includes a pointable illumination source, such as a laser operating at an atmospheric window wavelength, coupled with a number of high spatial-resolution detectors that are clustered around the illumination source in space, receiving photons nearly coaxial with the reto-reflection direction. Microwave control and command among the satellite cluster would allow orienting the direction of the laser beam as well as the focusing detectors simultaneously so that the coupled system can function like a search light with almost unlimited pointing capabilities. The concept is called the Hot-Spot Search-Light (HSSL) satellite. A nominal satellite altitude of 600 km will allow hot-spot BRDF measurements out to about 18 degrees phase angle. The distributed are taking radiometric measurements of the intensity wings of the hot-spot angular distribution without the need for complex imaging detectors. The system can be operated at night for increased signal-to-noise ratio. This way the hot-spot angular signatures can be quantified and parameterized in sufficient detail to extract the biophysical information content of plant architectures.

  1. A measurement concept for hot-spot BRDFs from space

    Science.gov (United States)

    Gerstl, S.A.W.

    1996-01-01

    Several concepts for canopy hot-spot measurements from space have been investigated. The most promising involves active illumination and bistatic detection that would allow hot-spot angular distribution (BRDF) measurements from space in a search-light mode. The concept includes a pointable illumination source, such as a laser operating at an atmospheric window wavelength, coupled with a number of high spatial-resolution detectors that are clustered around the illumination source in space, receiving photons nearly coaxial with the reto-reflection direction. Microwave control and command among the satellite cluster would allow orienting the direction of the laser beam as well as the focusing detectors simultaneously so that the coupled system can function like a search light with almost unlimited pointing capabilities. The concept is called the Hot-Spot Search-Light (HSSL) satellite. A nominal satellite altitude of 600 km will allow hot-spot BRDF measurements out to about 18 degrees phase angle. The distributed are taking radiometric measurements of the intensity wings of the hot-spot angular distribution without the need for complex imaging detectors. The system can be operated at night for increased signal-to-noise ratio. This way the hot-spot angular signatures can be quantified and parameterized in sufficient detail to extract the biophysical information content of plant architectures.

  2. HOTSPOT, Field Evaluation of Radiation Release from Nuclear Accident

    International Nuclear Information System (INIS)

    2001-01-01

    1 - Description of program or function: The HOTSPOT Health Physics codes were created to provide Health Physics personnel with a fast, field-portable calculational tool for evaluating accidents involving radioactive materials. HOTSPOT codes are a first-order approximation of the radiation effects associated with the atmospheric release of radioactive materials. HOTSPOT programs are reasonably accurate for a timely initial assessment. More importantly, HOTSPOT codes produce a consistent output for the same input assumptions and minimize the probability of errors associated with reading a graph incorrectly or scaling a universal nomogram during an emergency. Four general programs, PLUME, EXPLOSION, FIRE, and RESUSPENSION, calculate a downwind assessment following the release of radioactive material resulting from a continuous or puff release, explosive release, fuel fire, or an area contamination event. Other programs deal with the release of plutonium, uranium, and tritium to expedite an initial assessment of accidents involving nuclear weapons. Additional programs estimate the dose commitment from inhalation of any one of the radionuclides listed in the database of radionuclides, calibrate a radiation survey instrument for ground survey measurements, and screening of plutonium uptake in the lung. The HOTSPOT codes are fast, portable, easy to use, and fully documented. HOTSPOT supports color high resolution monitors and printers for concentration plots and contours. The codes have been extensively used by the DOS community since 1985. Version 8 allows users to add their own custom radionuclide library and to create custom radionuclide mixtures. It also includes wet deposition to approximate the enhanced plume depletion and ground deposition due to the effects of rain. Additional release geometry options for TRITIUM RELEASE and GENERAL PLUME were added, as well as several other enhancements and improvements. See info (f1) from the main HOTSPOT menu for additional

  3. Potential geographic "hotspots" for drug-injection related transmission of HIV and HCV and for initiation into injecting drug use in New York City, 2011-2015, with implications for the current opioid epidemic in the US.

    Science.gov (United States)

    Des Jarlais, D C; Cooper, H L F; Arasteh, K; Feelemyer, J; McKnight, C; Ross, Z

    2018-01-01

    We identified potential geographic "hotspots" for drug-injecting transmission of HIV and hepatitis C virus (HCV) among persons who inject drugs (PWID) in New York City. The HIV epidemic among PWID is currently in an "end of the epidemic" stage, while HCV is in a continuing, high prevalence (> 50%) stage. We recruited 910 PWID entering Mount Sinai Beth Israel substance use treatment programs from 2011-2015. Structured interviews and HIV/ HCV testing were conducted. Residential ZIP codes were used as geographic units of analysis. Potential "hotspots" for HIV and HCV transmission were defined as 1) having relatively large numbers of PWID 2) having 2 or more HIV (or HCV) seropositive PWID reporting transmission risk-passing on used syringes to others, and 3) having 2 or more HIV (or HCV) seronegative PWID reporting acquisition risk-injecting with previously used needles/syringes. Hotspots for injecting drug use initiation were defined as ZIP codes with 5 or more persons who began injecting within the previous 6 years. Among PWID, 96% injected heroin, 81% male, 34% White, 15% African-American, 47% Latinx, mean age 40 (SD = 10), 7% HIV seropositive, 62% HCV seropositive. Participants resided in 234 ZIP codes. No ZIP codes were identified as potential hotspots due to small numbers of HIV seropositive PWID reporting transmission risk. Four ZIP codes were identified as potential hotspots for HCV transmission. 12 ZIP codes identified as hotspots for injecting drug use initiation. For HIV, the lack of potential hotspots is further validation of widespread effectiveness of efforts to reduce injecting-related HIV transmission. Injecting-related HIV transmission is likely to be a rare, random event. HCV prevention efforts should include focus on potential hotspots for transmission and on hotspots for initiation into injecting drug use. We consider application of methods for the current opioid epidemic in the US.

  4. N2O emission hotspots at different spatial scales and governing factors for small scale hotspots

    International Nuclear Information System (INIS)

    Heuvel, R.N. van den; Hefting, M.M.; Tan, N.C.G.; Jetten, M.S.M.; Verhoeven, J.T.A.

    2009-01-01

    Chronically nitrate-loaded riparian buffer zones show high N 2 O emissions. Often, a large part of the N 2 O is emitted from small surface areas, resulting in high spatial variability in these buffer zones. These small surface areas with high N 2 O emissions (hotspots) need to be investigated to generate knowledge on the factors governing N 2 O emissions. In this study the N 2 O emission variability was investigated at different spatial scales. Therefore N 2 O emissions from three 32 m 2 grids were determined in summer and winter. Spatial variation and total emission were determined on three different scales (0.3 m 2 , 0.018 m 2 and 0.0013 m 2 ) at plots with different levels of N 2 O emissions. Spatial variation was high at all scales determined and highest at the smallest scale. To test possible factors inducing small scale hotspots, soil samples were collected for slurry incubation to determine responses to increased electron donor/acceptor availability. Acetate addition did increase N 2 O production, but nitrate addition failed to increase total denitrification or net N 2 O production. N 2 O production was similar in all soil slurries, independent of their origin from high or low emission soils, indicating that environmental conditions (including physical factors like gas diffusion) rather than microbial community composition governed N 2 O emission rates

  5. Burden analysis of rare microdeletions suggests a strong impact of neurodevelopmental genes in genetic generalised epilepsies

    DEFF Research Database (Denmark)

    Lal, Dennis; Ruppert, Ann-Kathrin; Trucks, Holger

    2015-01-01

    contribution of recurrent microdeletions at genomic rearrangement hotspots and non-recurrent microdeletions, and 3) identify potential candidate genes for GGE. We found a significant excess of microdeletions in 7.3% of GGE patients compared to 4.0% in controls (P = 1.8 x 10-7; OR = 1.9). Recurrent...

  6. Juniper Pollen Hotspots in the Southwest

    Science.gov (United States)

    Bunderson, L. D.; VandeWater, P.; Luvall, J.; Levetin, E.

    2013-01-01

    Rationale: Juniperus pollen is a major allergen in Texas, Oklahoma, and New Mexico. While the bulk of pollen may be released in rural areas, large amounts of pollen can be transported to urban areas. Major juniper species in the region include: Juniperus ashei, J. virginiana, J. pinchotii, and J. monosperma. Pollen release is virtually continuous beginning in late September with J. pinchotii and ending in May with J. monosperma. Urban areas in the region were evaluated for the potential of overlapping seasons in order to inform sensitive individuals. Methods: Burkard volumetric pollen traps were established for two consecutive spring seasons at 6 sites in northern New Mexico and 6 sites for two consecutive winter and fall seasons in Texas and Oklahoma Standard methods were used in the preparation and analysis of slides. Results: The Dallas-Fort Worth Metroplex is home to over 6 million people. It is adjacent to populations of J. pinchotii, J. virginiana, and J. ashei. Peak concentration near Dallas for J. ashei in 2011 was 5891 pollen grains/m3 in January 7th. The peak date for J. pinchotii at an upwind sampling location in San Marcos, TX was November 1, 2010 and peak for J. virginiana at a nearby station in Tulsa, OK was November 1, 2010 and peak for J. virginiana at a nearby station in Tulsa, OK was February 20, 2011. Amarillo, TX is adjacent to J. pinchotii, J. ashei, and J. monosperma populations and may be subject to juniper pollen from September through May. Conclusions: Considering the overlapping distributions of juniper trees and the overlapping temporal release of pollen, sensitive patients may benefit from avoiding hotspots.

  7. Hotspots on Io During the Ganymede 2 Encounter

    Science.gov (United States)

    1996-01-01

    The Near Infrared Mapping Spectrometer (NIMS) on the Galileo spacecraft imaged Io at high spectral resolution at a range of 439,000 km (275,000 miles) during the G2 encounter on 6 September 1996. This image shows, on the right, Io as seen by NIMS, centered on 150 W longitude. The image on the left shows the same view point from Voyager data (from the encounters in 1979 and 1980). The NIMS image can be compared to the NIMS hotspot image from the G1 orbit (June 1996) to monitor changes on Io. The most dramatic feature of the G2 image is the hotspot at Malik Patera. Preliminary analysis of the data yields a temperature of at least 1000 K (727 C) for this hotspot, an increase of more than 300 K from the G1 encounter. In the overlap area of the G1 and G2 images all the hotspots seen during the G1 encounter are also seen in the G2 image. Other hotspots were seen, including one at the Pele plume origin site. This image is at the 4 micron band to best view the Malik hotspot. Most of the other hotspots are best seen at longer wavelengths. NIMS is continuing to observe Io to monitor volcanic activity throughout the Galileo mission.The Jet Propulsion Laboratory, Pasadena, CA manages the mission for NASA's Office of Space Science, Washington, DC.This image and other images and data received from Galileo are posted on the World Wide Web, on the Galileo mission home page at URL http://galileo.jpl.nasa.gov.

  8. Borneo and Indochina are major evolutionary hotspots for Southeast Asian biodiversity.

    Science.gov (United States)

    de Bruyn, Mark; Stelbrink, Björn; Morley, Robert J; Hall, Robert; Carvalho, Gary R; Cannon, Charles H; van den Bergh, Gerrit; Meijaard, Erik; Metcalfe, Ian; Boitani, Luigi; Maiorano, Luigi; Shoup, Robert; von Rintelen, Thomas

    2014-11-01

    Tropical Southeast (SE) Asia harbors extraordinary species richness and in its entirety comprises four of the Earth's 34 biodiversity hotspots. Here, we examine the assembly of the SE Asian biota through time and space. We conduct meta-analyses of geological, climatic, and biological (including 61 phylogenetic) data sets to test which areas have been the sources of long-term biological diversity in SE Asia, particularly in the pre-Miocene, Miocene, and Plio-Pleistocene, and whether the respective biota have been dominated by in situ diversification, immigration and/or emigration, or equilibrium dynamics. We identify Borneo and Indochina, in particular, as major "evolutionary hotspots" for a diverse range of fauna and flora. Although most of the region's biodiversity is a result of both the accumulation of immigrants and in situ diversification, within-area diversification and subsequent emigration have been the predominant signals characterizing Indochina and Borneo's biota since at least the early Miocene. In contrast, colonization events are comparatively rare from younger volcanically active emergent islands such as Java, which show increased levels of immigration events. Few dispersal events were observed across the major biogeographic barrier of Wallace's Line. Accelerated efforts to conserve Borneo's flora and fauna in particular, currently housing the highest levels of SE Asian plant and mammal species richness, are critically required. © The Author(s) 2014. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  9. Can We Reconcile the TA Excess and Hotspot with Auger Observations?

    Energy Technology Data Exchange (ETDEWEB)

    Globus, Noemie; Piran, Tsvi [Racah Institute of Physics, The Hebrew University of Jerusalem, 91904 Jerusalem (Israel); Allard, Denis; Parizot, Etienne; Lachaud, Cyril [Laboratoire Astroparticule et Cosmologie, Université Paris Diderot/CNRS, 10 rue A. Domon et L. Duquet, F-75205 Paris Cedex 13 (France)

    2017-02-20

    The Telescope Array (TA) shows a 20° hotspot as well as an excess of ultra-high-energy cosmic-rays (UHECRs) above 50 EeV when compared with the Auger spectrum. We consider the possibility that both the TA excess and hotspot are due to a dominant source in the northern sky. We carry out detailed simulations of UHECR propagation in both the intergalactic medium and the Galaxy, using different values for the intergalactic magnetic field. We consider two general classes of sources: transients and steady, adopting a mixed UHECR composition that is consistent with the one found by Auger. The spatial location of the sources is drawn randomly. We generate Auger-like and TA-like data sets from which we determine the spectrum, the sky maps, and the level of anisotropy. We find that, while steady sources are favored over transients, it is unlikely to account for all the currently available observational data. While we reproduce fairly well the Auger spectrum for the vast majority of the simulated data sets, most of the simulated data sets with a spectrum compatible with that of TA (at most a few percent depending on density model tested) show a much stronger anisotropy than the one observed. We find that the rare cases in which both the spectrum and the anisotropy are consistent require a steady source within ∼10 Mpc, to account for the flux excess, and a strong extragalactic magnetic field ∼10 nG, to reduce the excessive anisotropy.

  10. Structured association analysis leads to insight into Saccharomyces cerevisiae gene regulation by finding multiple contributing eQTL hotspots associated with functional gene modules.

    Science.gov (United States)

    Curtis, Ross E; Kim, Seyoung; Woolford, John L; Xu, Wenjie; Xing, Eric P

    2013-03-21

    Association analysis using genome-wide expression quantitative trait locus (eQTL) data investigates the effect that genetic variation has on cellular pathways and leads to the discovery of candidate regulators. Traditional analysis of eQTL data via pairwise statistical significance tests or linear regression does not leverage the availability of the structural information of the transcriptome, such as presence of gene networks that reveal correlation and potentially regulatory relationships among the study genes. We employ a new eQTL mapping algorithm, GFlasso, which we have previously developed for sparse structured regression, to reanalyze a genome-wide yeast dataset. GFlasso fully takes into account the dependencies among expression traits to suppress false positives and to enhance the signal/noise ratio. Thus, GFlasso leverages the gene-interaction network to discover the pleiotropic effects of genetic loci that perturb the expression level of multiple (rather than individual) genes, which enables us to gain more power in detecting previously neglected signals that are marginally weak but pleiotropically significant. While eQTL hotspots in yeast have been reported previously as genomic regions controlling multiple genes, our analysis reveals additional novel eQTL hotspots and, more interestingly, uncovers groups of multiple contributing eQTL hotspots that affect the expression level of functional gene modules. To our knowledge, our study is the first to report this type of gene regulation stemming from multiple eQTL hotspots. Additionally, we report the results from in-depth bioinformatics analysis for three groups of these eQTL hotspots: ribosome biogenesis, telomere silencing, and retrotransposon biology. We suggest candidate regulators for the functional gene modules that map to each group of hotspots. Not only do we find that many of these candidate regulators contain mutations in the promoter and coding regions of the genes, in the case of the Ribi group

  11. The silent mass extinction of insect herbivores in biodiversity hotspots.

    Science.gov (United States)

    Fonseca, Carlos Roberto

    2009-12-01

    Habitat loss is silently leading numerous insects to extinction. Conservation efforts, however, have not been designed specifically to protect these organisms, despite their ecological and evolutionary significance. On the basis of species-host area equations, parameterized with data from the literature and interviews with botanical experts, I estimated the number of specialized plant-feeding insects (i.e., monophages) that live in 34 biodiversity hotspots and the number committed to extinction because of habitat loss. I estimated that 795,971-1,602,423 monophagous insect species live in biodiversity hotspots on 150,371 endemic plant species, which is 5.3-10.6 monophages per plant species. I calculated that 213,830-547,500 monophagous species are committed to extinction in biodiversity hotspots because of reduction of the geographic range size of their endemic hosts. I provided rankings of biodiversity hotspots on the basis of estimated richness of monophagous insects and on estimated number of extinctions of monophagous species. Extinction rates were predicted to be higher in biodiversity hotspots located along strong environmental gradients and on archipelagos, where high spatial turnover of monophagous species along the geographic distribution of their endemic plants is likely. The results strongly support the overall strategy of selecting priority conservation areas worldwide primarily on the basis of richness of endemic plants. To face the global decline of insect herbivores, one must expand the coverage of the network of protected areas and improve the richness of native plants on private lands.

  12. Global warming and extinctions of endemic species from biodiversity hotspots.

    Science.gov (United States)

    Malcolm, Jay R; Liu, Canran; Neilson, Ronald P; Hansen, Lara; Hannah, Lee

    2006-04-01

    Global warming is a key threat to biodiversity, but few researchers have assessed the magnitude of this threat at the global scale. We used major vegetation types (biomes) as proxies for natural habitats and, based on projected future biome distributions under doubled-CO2 climates, calculated changes in habitat areas and associated extinctions of endemic plant and vertebrate species in biodiversity hotspots. Because of numerous uncertainties in this approach, we undertook a sensitivity analysis of multiple factors that included (1) two global vegetation models, (2) different numbers of biome classes in our biome classification schemes, (3) different assumptions about whether species distributions were biome specific or not, and (4) different migration capabilities. Extinctions were calculated using both species-area and endemic-area relationships. In addition, average required migration rates were calculated for each hotspot assuming a doubled-CO2 climate in 100 years. Projected percent extinctions ranged from hotspots were the Cape Floristic Region, Caribbean, Indo-Burma, Mediterranean Basin, Southwest Australia, and Tropical Andes, where plant extinctions per hotspot sometimes exceeded 2000 species. Under the assumption that projected habitat changes were attained in 100 years, estimated global-warming-induced rates of species extinctions in tropical hotspots in some cases exceeded those due to deforestation, supporting suggestions that global warming is one of the most serious threats to the planet's biodiversity.

  13. Identifying Interactions that Determine Fragment Binding at Protein Hotspots.

    Science.gov (United States)

    Radoux, Chris J; Olsson, Tjelvar S G; Pitt, Will R; Groom, Colin R; Blundell, Tom L

    2016-05-12

    Locating a ligand-binding site is an important first step in structure-guided drug discovery, but current methods do little to suggest which interactions within a pocket are the most important for binding. Here we illustrate a method that samples atomic hotspots with simple molecular probes to produce fragment hotspot maps. These maps specifically highlight fragment-binding sites and their corresponding pharmacophores. For ligand-bound structures, they provide an intuitive visual guide within the binding site, directing medicinal chemists where to grow the molecule and alerting them to suboptimal interactions within the original hit. The fragment hotspot map calculation is validated using experimental binding positions of 21 fragments and subsequent lead molecules. The ligands are found in high scoring areas of the fragment hotspot maps, with fragment atoms having a median percentage rank of 97%. Protein kinase B and pantothenate synthetase are examined in detail. In each case, the fragment hotspot maps are able to rationalize a Free-Wilson analysis of SAR data from a fragment-based drug design project.

  14. Arago Seamount: The missing hotspot found in the Austral Islands

    Science.gov (United States)

    Bonneville, Alain; Le Suavé, Raymond; Audin, Laurence; Clouard, Valérie; Dosso, Laure; Yves Gillot, Pierre; Janney, Philip; Jordahl, Kelsey; Maamaatuaiahutapu, Keitapu

    2002-11-01

    The Austral archipelago, on the western side of the South Pacific superswell, is composed of several volcanic chains, corresponding to distinct events from 35 Ma to the present, and lies on oceanic crust created between 60 and 85 Ma. In 1982, Turner and Jarrard proposed that the two distinct volcanic stages found on Rurutu Island and dated as 12 Ma and 1 Ma could be due to two different hotspots, but no evidence of any recent aerial or submarine volcanic source has ever been found. In July 1999, expedition ZEPOLYF2 aboard the R/V L'Atalante conducted a geophysical survey of the northern part of the Austral volcanic archipelago. Thirty seamounts were mapped for the first time, including a very shallow one (French Navy ship that discovered its summit in 1993, is the missing hotspot in the Cook-Austral history. This interpretation adds a new hotspot to the already complicated geologic history of this region. We suggest that several hotspots have been active simultaneously on a region of the seafloor that does not exceed 2000 km in diameter and that each of them had a short lifetime (<20 m.y.). These short-lived and closely spaced hotspots cannot be the result of discrete deep-mantle plumes and are likely due to more local upwelling in the upper mantle strongly influenced by weaknesses in the lithosphere.

  15. Distribution, congruence, and hotspots of higher plants in China.

    Science.gov (United States)

    Zhao, Lina; Li, Jinya; Liu, Huiyuan; Qin, Haining

    2016-01-11

    Identifying biodiversity hotspots has become a central issue in setting up priority protection areas, especially as financial resources for biological diversity conservation are limited. Taking China's Higher Plants Red List (CHPRL), including Bryophytes, Ferns, Gymnosperms, Angiosperms, as the data source, we analyzed the geographic patterns of species richness, endemism, and endangerment via data processing at a fine grid-scale with an average edge length of 30 km based on three aspects of richness information: species richness, endemic species richness, and threatened species richness. We sought to test the accuracy of hotspots used in identifying conservation priorities with regard to higher plants. Next, we tested the congruence of the three aspects and made a comparison of the similarities and differences between the hotspots described in this paper and those in previous studies. We found that over 90% of threatened species in China are concentrated. While a high spatial congruence is observed among the three measures, there is a low congruence between two different sets of hotspots. Our results suggest that biodiversity information should be considered when identifying biological hotspots. Other factors, such as scales, should be included as well to develop biodiversity conservation plans in accordance with the region's specific conditions.

  16. Thermally-Driven Mantle Plumes Reconcile Hot-spot Observations

    Science.gov (United States)

    Davies, D.; Davies, J.

    2008-12-01

    Hot-spots are anomalous regions of magmatism that cannot be directly associated with plate tectonic processes (e.g. Morgan, 1972). They are widely regarded as the surface expression of upwelling mantle plumes. Hot-spots exhibit variable life-spans, magmatic productivity and fixity (e.g. Ito and van Keken, 2007). This suggests that a wide-range of upwelling structures coexist within Earth's mantle, a view supported by geochemical and seismic evidence, but, thus far, not reproduced by numerical models. Here, results from a new, global, 3-D spherical, mantle convection model are presented, which better reconcile hot-spot observations, the key modification from previous models being increased convective vigor. Model upwellings show broad-ranging dynamics; some drift slowly, while others are more mobile, displaying variable life-spans, intensities and migration velocities. Such behavior is consistent with hot-spot observations, indicating that the mantle must be simulated at the correct vigor and in the appropriate geometry to reproduce Earth-like dynamics. Thermally-driven mantle plumes can explain the principal features of hot-spot volcanism on Earth.

  17. Prdm9 controls activation of mammalian recombination hotspots.

    Science.gov (United States)

    Parvanov, Emil D; Petkov, Petko M; Paigen, Kenneth

    2010-02-12

    Mammalian meiotic recombination, which preferentially occurs at specialized sites called hotspots, ensures the orderly segregation of meiotic chromosomes and creates genetic variation among offspring. A locus on mouse chromosome 17, which controls activation of recombination at multiple distant hotspots, has been mapped within a 181-kilobase interval, three of whose genes can be eliminated as candidates. The remaining gene, Prdm9, codes for a zinc finger containing histone H3K4 trimethylase that is expressed in early meiosis and whose deficiency results in sterility in both sexes. Mus musculus exhibits five alleles of Prdm9; human populations exhibit two predominant alleles and multiple minor alleles. The identification of Prdm9 as a protein regulating mammalian recombination hotspots initiates molecular studies of this important biological control system.

  18. Interventions to reduce suicides at suicide hotspots: a systematic review.

    Science.gov (United States)

    Cox, Georgina R; Owens, Christabel; Robinson, Jo; Nicholas, Angela; Lockley, Anne; Williamson, Michelle; Cheung, Yee Tak Derek; Pirkis, Jane

    2013-03-09

    'Suicide hotspots' include tall structures (for example, bridges and cliffs), railway tracks, and isolated locations (for example, rural car parks) which offer direct means for suicide or seclusion that prevents intervention. We searched Medline for studies that could inform the following question: 'What interventions are available to reduce suicides at hotspots, and are they effective?' There are four main approaches: (a) restricting access to means (through installation of physical barriers); (b) encouraging help-seeking (by placement of signs and telephones); (c) increasing the likelihood of intervention by a third party (through surveillance and staff training); and (d) encouraging responsible media reporting of suicide (through guidelines for journalists). There is relatively strong evidence that reducing access to means can avert suicides at hotspots without substitution effects. The evidence is weaker for the other approaches, although they show promise. More well-designed intervention studies are needed to strengthen this evidence base.

  19. Energy efficient hotspot-targeted embedded liquid cooling of electronics

    International Nuclear Information System (INIS)

    Sharma, Chander Shekhar; Tiwari, Manish K.; Zimmermann, Severin; Brunschwiler, Thomas; Schlottig, Gerd; Michel, Bruno; Poulikakos, Dimos

    2015-01-01

    Highlights: • We present a novel concept for hotspot-targeted, energy efficient ELC for electronic chips. • Microchannel throttling zones distribute flow optimally without any external control. • Design is optimized for highly non-uniform multicore chip heat flux maps. • Optimized design minimizes chip temperature non-uniformity. • This is achieved with pumping power consumption less than 1% of total chip power. - Abstract: Large data centers today already account for nearly 1.31% of total electricity consumption with cooling responsible for roughly 33% of that energy consumption. This energy intensive cooling problem is exacerbated by the presence of hotspots in multicore microprocessors due to excess coolant flow requirement for thermal management. Here we present a novel liquid-cooling concept, for targeted, energy efficient cooling of hotspots through passively optimized microchannel structures etched into the backside of a chip (embedded liquid cooling or ELC architecture). We adopt an experimentally validated and computationally efficient modeling approach to predict the performance of our hotspot-targeted ELC design. The design is optimized for exemplar non-uniform chip power maps using Response Surface Methodology (RSM). For industrially acceptable limits of approximately 0.4 bar (40 kPa) on pressure drop and one percent of total chip power on pumping power, the optimized designs are computationally evaluated against a base, standard ELC design with uniform channel widths and uniform flow distribution. For an average steady-state heat flux of 150 W/cm 2 in core areas (hotspots) and 20 W/cm 2 over remaining chip area (background), the optimized design reduces the maximum chip temperature non-uniformity by 61% to 3.7 °C. For a higher average, steady-state hotspot heat flux of 300 W/cm 2 , the maximum temperature non-uniformity is reduced by 54% to 8.7 °C. It is shown that the base design requires a prohibitively high level of pumping power (about

  20. Hot-spots of radio sources in clusters of galaxies

    International Nuclear Information System (INIS)

    Saikia, D.J.

    1979-01-01

    A sample of extragalactic double radio sources is examined to test for a correlation between the prominence of compact hot-spots located at their outer edges and membership of clusters of galaxies. To minimize the effects of incompleteness in published catalogues of clusters, cluster classification is based on the number of galaxies in the neighbourhood of each source. After eliminating possible selection effects, it is found that sources in regions of high galactic density tend to have less prominent hot-spots. It is argued that the result is consistent with the 'continuous-flow' models of radio sources, but poses problems for the gravitational slingshot model. (author)

  1. The Complete Plastome Sequences of Four Orchid Species: Insights into the Evolution of the Orchidaceae and the Utility of Plastomic Mutational Hotspots

    Directory of Open Access Journals (Sweden)

    Zhitao Niu

    2017-05-01

    Full Text Available Orchidaceae (orchids is the largest family in the monocots, including about 25,000 species in 880 genera and five subfamilies. Many orchids are highly valued for their beautiful and long-lasting flowers. However, the phylogenetic relationships among the five orchid subfamilies remain unresolved. The major dispute centers on whether the three one-stamened subfamilies, Epidendroideae, Orchidoideae, and Vanilloideae, are monophyletic or paraphyletic. Moreover, structural changes in the plastid genome (plastome and the effective genetic loci at the species-level phylogenetics of orchids have rarely been documented. In this study, we compared 53 orchid plastomes, including four newly sequenced ones, that represent four remote genera: Dendrobium, Goodyera, Paphiopedilum, and Vanilla. These differ from one another not only in their lengths of inverted repeats and small single copy regions but also in their retention of ndh genes. Comparative analyses of the plastomes revealed that the expansion of inverted repeats in Paphiopedilum and Vanilla is associated with a loss of ndh genes. In orchid plastomes, mutational hotspots are genus specific. After having carefully examined the data, we propose that the three loci 5′trnK-rps16, trnS-trnG, and rps16-trnQ might be powerful markers for genera within Epidendroideae, and clpP-psbB and rps16-trnQ might be markers for genera within Cypripedioideae. After analyses of a partitioned dataset, we found that our plastid phylogenomic trees were congruent in a topology where two one-stamened subfamilies (i.e., Epidendroideae and Orchidoideae were sisters to a multi-stamened subfamily (i.e., Cypripedioideae rather than to the other one-stamened subfamily (Vanilloideae, suggesting that the living one-stamened orchids are paraphyletic.

  2. Efficient Assessment of Social Hotspots in the Supply Chains of 100 Product Categories Using the Social Hotspots Database

    Directory of Open Access Journals (Sweden)

    Catherine Benoît Norris

    2014-10-01

    Full Text Available Data collection, or the inventory step, is often the most labor-intensive phase of any Life Cycle Assessment (LCA study. The S-LCA Guidelines and numerous authors have recommended generic assessment in this first phase of an S-LCA. In an effort to identify the social hotspots in the supply chains of 100 product categories during just a few months’ time, adopting a streamlined approach was essential. The Social Hotspots Database system was developed by New Earth over 5 years. It includes a Global Input Output (IO model derived from the Global Trade Analysis Project, a Worker Hours Model constructed using annual wage payments and wage rates by country and sector, and Social Theme Tables covering 22 themes within five Social Impact Categories—Labor Rights and Decent Work, Health and Safety, Human Rights, Governance and Community Impacts. The data tables identify social risks for over 100 indicators. Both the ranking of worker hour intensity and the risk levels across multiple social themes for the Country Specific Sectors (CSS within a product category supply chain are used to calculate Social Hotspots Indexes (SHI using an additive weighting method. The CSS with the highest SHI are highlighted as social hotspots within the supply chain of the product in question. This system was tested in seven case studies in 2011. In order to further limit the number of hotspots, a set of prioritization rules was applied. This paper will review the method implemented to study the social hotspots of the 100 product categories and provide one detailed example. Limitations of the approach and recommended research avenues will be outlined.

  3. The genome of Eucalyptus grandis

    Energy Technology Data Exchange (ETDEWEB)

    Myburg, Alexander A.; Grattapaglia, Dario; Tuskan, Gerald A.; Hellsten, Uffe; Hayes, Richard D.; Grimwood, Jane; Jenkins, Jerry; Lindquist, Erika; Tice, Hope; Bauer, Diane; Goodstein, David M.; Dubchak, Inna; Poliakov, Alexandre; Mizrachi, Eshchar; Kullan, Anand R. K.; Hussey, Steven G.; Pinard, Desre; van der Merwe, Karen; Singh, Pooja; van Jaarsveld, Ida; Silva-Junior, Orzenil B.; Togawa, Roberto C.; Pappas, Marilia R.; Faria, Danielle A.; Sansaloni, Carolina P.; Petroli, Cesar D.; Yang, Xiaohan; Ranjan, Priya; Tschaplinski, Timothy J.; Ye, Chu-Yu; Li, Ting; Sterck, Lieven; Vanneste, Kevin; Murat, Florent; Soler, Marçal; Clemente, Hélène San; Saidi, Naijib; Cassan-Wang, Hua; Dunand, Christophe; Hefer, Charles A.; Bornberg-Bauer, Erich; Kersting, Anna R.; Vining, Kelly; Amarasinghe, Vindhya; Ranik, Martin; Naithani, Sushma; Elser, Justin; Boyd, Alexander E.; Liston, Aaron; Spatafora, Joseph W.; Dharmwardhana, Palitha; Raja, Rajani; Sullivan, Christopher; Romanel, Elisson; Alves-Ferreira, Marcio; Külheim, Carsten; Foley, William; Carocha, Victor; Paiva, Jorge; Kudrna, David; Brommonschenkel, Sergio H.; Pasquali, Giancarlo; Byrne, Margaret; Rigault, Philippe; Tibbits, Josquin; Spokevicius, Antanas; Jones, Rebecca C.; Steane, Dorothy A.; Vaillancourt, René E.; Potts, Brad M.; Joubert, Fourie; Barry, Kerrie; Pappas, Georgios J.; Strauss, Steven H.; Jaiswal, Pankaj; Grima-Pettenati, Jacqueline; Salse, Jérôme; Van de Peer, Yves; Rokhsar, Daniel S.; Schmutz, Jeremy

    2014-06-11

    Eucalypts are the world s most widely planted hardwood trees. Their broad adaptability, rich species diversity, fast growth and superior multipurpose wood, have made them a global renewable resource of fiber and energy that mitigates human pressures on natural forests. We sequenced and assembled >94% of the 640 Mbp genome of Eucalyptus grandis into its 11 chromosomes. A set of 36,376 protein coding genes were predicted revealing that 34% occur in tandem duplications, the largest proportion found thus far in any plant genome. Eucalypts also show the highest diversity of genes for plant specialized metabolism that act as chemical defence against biotic agents and provide unique pharmaceutical oils. Resequencing of a set of inbred tree genomes revealed regions of strongly conserved heterozygosity, likely hotspots of inbreeding depression. The resequenced genome of the sister species E. globulus underscored the high inter-specific genome colinearity despite substantial genome size variation in the genus. The genome of E. grandis is the first reference for the early diverging Rosid order Myrtales and is placed here basal to the Eurosids. This resource expands knowledge on the unique biology of large woody perennials and provides a powerful tool to accelerate comparative biology, breeding and biotechnology.

  4. Ecology and exploration of the rare biosphere.

    Science.gov (United States)

    Lynch, Michael D J; Neufeld, Josh D

    2015-04-01

    The profound influence of microorganisms on human life and global biogeochemical cycles underlines the value of studying the biogeography of microorganisms, exploring microbial genomes and expanding our understanding of most microbial species on Earth: that is, those present at low relative abundance. The detection and subsequent analysis of low-abundance microbial populations—the 'rare biosphere'—have demonstrated the persistence, population dynamics, dispersion and predation of these microbial species. We discuss the ecology of rare microbial populations, and highlight molecular and computational methods for targeting taxonomic 'blind spots' within the rare biosphere of complex microbial communities.

  5. Testing the Efficacy of Global Biodiversity Hotspots for Insect Conservation: The Case of South African Katydids

    OpenAIRE

    Bazelet, Corinna S.; Thompson, Aileen C.; Naskrecki, Piotr

    2016-01-01

    The use of endemism and vascular plants only for biodiversity hotspot delineation has long been contested. Few studies have focused on the efficacy of global biodiversity hotspots for the conservation of insects, an important, abundant, and often ignored component of biodiversity. We aimed to test five alternative diversity measures for hotspot delineation and examine the efficacy of biodiversity hotspots for conserving a non-typical target organism, South African katydids. Using a 1° fishnet...

  6. Seed plant features, distribution patterns, diversity hotspots, and conservation gaps in Xinjiang, China

    Directory of Open Access Journals (Sweden)

    Jihong Huang

    2018-06-01

    Full Text Available The flora in Xinjiang is unique. Decisions about biodiversity conservation and management based on seed plant diversity hotspots and conservation gaps in Xinjiang are essential to maintain this unique flora. Based on a species distribution dataset of seed plants, we measured seed plant diversity using species richness and phylogenetic diversity indices. Five percent of Xinjiang’s total land area with the highest biodiversity was used to identify hotspots for each index. In total, eight hotspots were identified. Most hotspots were located in mountainous areas, mainly in the Tianshan Mountains and Altai Mountains. Furthermore, we detected conservation gaps for Xinjiang’s seed flora hotspots by overlaying nature reserve maps on to maps of identified hotspots and we designated priority conservation gaps for hotspots by overlaying global biodiversity hotspot maps on to hotspot conservation gaps maps. Most of Xinjiang’s seed plant hotspots are poorly protected; only 10.45% of these hotspots were covered by nature reserves. We suggest that it is essential to promote network function of nature reserves within these hotspots in Xinjiang to conserve this unique flora.

  7. Prdm9, a major determinant of meiotic recombination hotspots, is not functional in dogs and their wild relatives, wolves and coyotes.

    Directory of Open Access Journals (Sweden)

    Violeta Muñoz-Fuentes

    Full Text Available Meiotic recombination is a fundamental process needed for the correct segregation of chromosomes during meiosis in sexually reproducing organisms. In humans, 80% of crossovers are estimated to occur at specific areas of the genome called recombination hotspots. Recently, a protein called PRDM9 was identified as a major player in determining the location of genome-wide meiotic recombination hotspots in humans and mice. The origin of this protein seems to be ancient in evolutionary time, as reflected by its fairly conserved structure in lineages that diverged over 700 million years ago. Despite its important role, there are many animal groups in which Prdm9 is absent (e.g. birds, reptiles, amphibians, diptera and it has been suggested to have disruptive mutations and thus to be a pseudogene in dogs. Because of the dog's history through domestication and artificial selection, we wanted to confirm the presence of a disrupted Prdm9 gene in dogs and determine whether this was exclusive of this species or whether it also occurred in its wild ancestor, the wolf, and in a close relative, the coyote. We sequenced the region in the dog genome that aligned to the last exon of the human Prdm9, containing the entire zinc finger domain, in 4 dogs, 17 wolves and 2 coyotes. Our results show that the three canid species possess mutations that likely make this gene non functional. Because these mutations are shared across the three species, they must have appeared prior to the split of the wolf and the coyote, millions of years ago, and are not related to domestication. In addition, our results suggest that in these three canid species recombination does not occur at hotspots or hotspot location is controlled through a mechanism yet to be determined.

  8. European hotspots as evidenced by the Palearctic distribution of songbirds

    NARCIS (Netherlands)

    Sluys, R.; Aliabadian, M.; Roselaar, C.S.; Zachos, F.E.; Habel, J.C.

    2011-01-01

    A database has been created of digitized equal area distribution maps of 2,401 phylogenetic species of songbirds endemic to the Palearctic Region. Geographic distribution of species richness delineated several hotspot regions in the Palearctic, mostly located in mountainous areas. The index of

  9. Identifying biodiversity hotspots for threatened mammal species in Iran

    NARCIS (Netherlands)

    Farashi, Azita; Shariati Najafabadi, Mitra; Hosseini, Mahshid

    2017-01-01

    Conservation biology has much more attention for biodiversity hot spots than before. In order to recognize the hotspots for Iranian terrestrial mammal species that are listed in any red list, nationally or globally, ten Species Distribution Models (SDMs) have been applied. The SDMs evaluation

  10. A Glance at Recombination Hotspots in the Domestic Cat.

    Directory of Open Access Journals (Sweden)

    Hasan Alhaddad

    Full Text Available Recombination has essential roles in increasing genetic variability within a population and in ensuring successful meiotic events. The objective of this study is to (i infer the population-scaled recombination rate (ρ, and (ii identify and characterize regions of increased recombination rate for the domestic cat, Felis silvestris catus. SNPs (n = 701 were genotyped in twenty-two East Asian feral cats (random bred. The SNPs covered ten different chromosomal regions (A1, A2, B3, C2, D1, D2, D4, E2, F2, X with an average region size of 850 Kb and an average SNP density of 70 SNPs/region. The Bayesian method in the program inferRho was used to infer regional population recombination rates and hotspots localities. The regions exhibited variable population recombination rates and four decisive recombination hotspots were identified on cat chromosome A2, D1, and E2 regions. As a description of the identified hotspots, no correlation was detected between the GC content and the locality of recombination spots, and the hotspots enclosed L2 LINE elements and MIR and tRNA-Lys SINE elements.

  11. Mortality hotspots: nitrogen cycling in forest soils during vertebrate decomposition

    Science.gov (United States)

    Decomposing plants and animals fundamentally transform their surrounding environments, and serve as a critical source of limiting nutrients for macro- and micro-fauna. Animal mortality hotspots alter soil biogeochemical cycles, and these natural ephemeral nutrient patches are important for maintaini...

  12. Molecular architecture of transcription factor hotspots in early adipogenesis

    DEFF Research Database (Denmark)

    Siersbæk, Rasmus; Baek, Songjoon; Rabiee, Atefeh

    2014-01-01

    motif on chromatin, and we suggest that this may be a general mechanism for integrating external signals on chromatin. Furthermore, we find evidence of extensive recruitment of transcription factors to hotspots through alternative mechanisms not involving their known motifs and demonstrate...

  13. Atmospheric gravity waves in the Red Sea: a new hotspot

    KAUST Repository

    Magalhaes, J. M.; Araú jo, I. B.; da Silva, J. C. B.; Grimshaw, R. H. J.; Davis, K.; Pineda, J.

    2011-01-01

    The region of the Middle East around the Red Sea (between 32° E and 44° E longitude and 12° N and 28° N latitude) is a currently undocumented hotspot for atmospheric gravity waves (AGWs). Satellite imagery shows evidence that this region is prone

  14. Threats from climate change to terrestrial vertebrate hotspots in Europe.

    Science.gov (United States)

    Maiorano, Luigi; Amori, Giovanni; Capula, Massimo; Falcucci, Alessandra; Masi, Monica; Montemaggiori, Alessandro; Pottier, Julien; Psomas, Achilleas; Rondinini, Carlo; Russo, Danilo; Zimmermann, Niklaus E; Boitani, Luigi; Guisan, Antoine

    2013-01-01

    We identified hotspots of terrestrial vertebrate species diversity in Europe and adjacent islands. Moreover, we assessed the extent to which by the end of the 21(st) century such hotspots will be exposed to average monthly temperature and precipitation patterns which can be regarded as extreme if compared to the climate experienced during 1950-2000. In particular, we considered the entire European sub-continent plus Turkey and a total of 1149 species of terrestrial vertebrates. For each species, we developed species-specific expert-based distribution models (validated against field data) which we used to calculate species richness maps for mammals, breeding birds, amphibians, and reptiles. Considering four global circulation model outputs and three emission scenarios, we generated an index of risk of exposure to extreme climates, and we used a bivariate local Moran's I to identify the areas with a significant association between hotspots of diversity and high risk of exposure to extreme climates. Our results outline that the Mediterranean basin represents both an important hotspot for biodiversity and especially for threatened species for all taxa. In particular, the Iberian and Italian peninsulas host particularly high species richness as measured over all groups, while the eastern Mediterranean basin is particularly rich in amphibians and reptiles; the islands (both Macaronesian and Mediterranean) host the highest richness of threatened species for all taxa occurs. Our results suggest that the main hotspots of biodiversity for terrestrial vertebrates may be extensively influenced by the climate change projected to occur over the coming decades, especially in the Mediterranean bioregion, posing serious concerns for biodiversity conservation.

  15. Evidence for positive selection and recombination hotspots in Deformed wing virus (DWV).

    Science.gov (United States)

    Dalmon, A; Desbiez, C; Coulon, M; Thomasson, M; Le Conte, Y; Alaux, C; Vallon, J; Moury, B

    2017-01-25

    Deformed wing virus (DWV) is considered one of the most damaging pests in honey bees since the spread of its vector, Varroa destructor. In this study, we sequenced the whole genomes of two virus isolates and studied the evolutionary forces that act on DWV genomes. The isolate from a Varroa-tolerant bee colony was characterized by three recombination breakpoints between DWV and the closely related Varroa destructor virus-1 (VDV-1), whereas the variant from the colony using conventional Varroa management was similar to the originally described DWV. From the complete sequence dataset, nine independent DWV-VDV-1 recombination breakpoints were detected, and recombination hotspots were found in the 5' untranslated region (5' UTR) and the conserved region encoding the helicase. Partial sequencing of the 5' UTR and helicase-encoding region in 41 virus isolates suggested that most of the French isolates were recombinants. By applying different methods based on the ratio between non-synonymous (dN) and synonymous (dS) substitution rates, we identified four positions that showed evidence of positive selection. Three of these positions were in the putative leader protein (Lp), and one was in the polymerase. These findings raise the question of the putative role of the Lp in viral evolution.

  16. The Red Queen model of recombination hot-spot evolution: a theoretical investigation.

    Science.gov (United States)

    Latrille, Thibault; Duret, Laurent; Lartillot, Nicolas

    2017-12-19

    In humans and many other species, recombination events cluster in narrow and short-lived hot spots distributed across the genome, whose location is determined by the Zn-finger protein PRDM9. To explain these fast evolutionary dynamics, an intra-genomic Red Queen model has been proposed, based on the interplay between two antagonistic forces: biased gene conversion, mediated by double-strand breaks, resulting in hot-spot extinction, followed by positive selection favouring new PRDM9 alleles recognizing new sequence motifs. Thus far, however, this Red Queen model has not been formalized as a quantitative population-genetic model, fully accounting for the intricate interplay between biased gene conversion, mutation, selection, demography and genetic diversity at the PRDM9 locus. Here, we explore the population genetics of the Red Queen model of recombination. A Wright-Fisher simulator was implemented, allowing exploration of the behaviour of the model (mean equilibrium recombination rate, diversity at the PRDM9 locus or turnover rate) as a function of the parameters (effective population size, mutation and erosion rates). In a second step, analytical results based on self-consistent mean-field approximations were derived, reproducing the scaling relations observed in the simulations. Empirical fit of the model to current data from the mouse suggests both a high mutation rate at PRDM9 and strong biased gene conversion on its targets.This article is part of the themed issue 'Evolutionary causes and consequences of recombination rate variation in sexual organisms'. © 2017 The Authors.

  17. Dynamic placement of plasmonic hotspots for super-resolution surface-enhanced Raman scattering.

    Science.gov (United States)

    Ertsgaard, Christopher T; McKoskey, Rachel M; Rich, Isabel S; Lindquist, Nathan C

    2014-10-28

    In this paper, we demonstrate dynamic placement of locally enhanced plasmonic fields using holographic laser illumination of a silver nanohole array. To visualize these focused "hotspots", the silver surface was coated with various biological samples for surface-enhanced Raman spectroscopy (SERS) imaging. Due to the large field enhancements, blinking behavior of the SERS hotspots was observed and processed using a stochastic optical reconstruction microscopy algorithm enabling super-resolution localization of the hotspots to within 10 nm. These hotspots were then shifted across the surface in subwavelength (hotspots. Using this technique, we also show that such subwavelength shifting and localization of plasmonic hotspots has potential for imaging applications. Interestingly, illuminating the surface with randomly shifting SERS hotspots was sufficient to completely fill in a wide field of view for super-resolution chemical imaging.

  18. Rare earth germanates

    International Nuclear Information System (INIS)

    Bondar', I.A.; Vinogradova, N.V.; Dem'yanets, L.N.

    1983-01-01

    Rare earth germanates attract close attention both as an independent class of compounds and analogues of a widely spread class of natural and synthetic minerals. The methods of rare earth germanate synthesis (solid-phase, hydrothermal) are considered. Systems on the basis of germanium and rare earth oxides, phase diagrams, phase transformations are studied. Using different chemical analysese the processes of rare earth germanate formation are investigated. IR spectra of alkali and rare earth metal germanates are presented, their comparative analysis being carried out. Crystal structures of the compounds, lattice parameters are studied. Fields of possible application of rare earth germanates are shown

  19. RARE DISEASES AND GENETIC DISCRIMINATION

    Directory of Open Access Journals (Sweden)

    Mariela Yaneva – Deliverska

    2011-04-01

    physicians (not enough physicians involved in rare diseases clinical trials, and the absence of treatment consensus recommendations.It is fundamental to realise that rare diseases can affect any family at any time. It is not just “something terrible that happens to other people”. It is a very cruel reality that can happen to anyone, either when having a child or in the course of one’s own life.In fact, the terminology “rare diseases” only highlights the characteristic of rarity of the complex and heterogeneous mosaic of an estimated 7,000 life-threatening and heavily debilitating conditions.The rare diseases for which a simple and effective preventive treatment is available are being screened for, as part of public health policy. But this is not enough, and it is essential for public authorities to consider rare diseases as a Public Health priority and take action to concretely support patients and families affected by rare diseases.As underlined in the Background Paper on Orphan Diseases for the World Health Organisation Report on Priority Medicines for Europe and the World, “despite the growing public awareness of rare diseases in the last one or two decades, there are still many gaps in knowledge related to the development of treatment for rare diseases. Policymakers have to realise that rare diseases are a crucial health issue for about 30 million people in the EU”.A good medication for rare disease patients is a medication that is both available in the country where they live and affordable. If one of these two factors is missing, the drug is of little use.Personalized medicine however is an emerging term for a medical philosophy that uses a person’s individual clinical, genetic, genomic, and environmental information to tailor a treatment plan that will maximize efficacy and safety for that individual. While the technology offers much promise, it also is also challenged by some ethical and social questions in both its clinical application and in its

  20. Twenty-First Century Diseases: Commonly Rare and Rarely Common?

    Science.gov (United States)

    Daunert, Sylvia; Sittampalam, Gurusingham Sitta; Goldschmidt-Clermont, Pascal J

    2017-09-20

    Alzheimer's drugs are failing at a rate of 99.6%, and success rate for drugs designed to help patients with this form of dementia is 47 times less than for drugs designed to help patients with cancers ( www.scientificamerican.com/article/why-alzheimer-s-drugs-keep-failing/2014 ). How can it be so difficult to produce a valuable drug for Alzheimer's disease? Each human has a unique genetic and epigenetic makeup, thus endowing individuals with a highly unique complement of genes, polymorphisms, mutations, RNAs, proteins, lipids, and complex sugars, resulting in distinct genome, proteome, metabolome, and also microbiome identity. This editorial is taking into account the uniqueness of each individual and surrounding environment, and stresses the point that a more accurate definition of a "common" disorder could be simply the amalgamation of a myriad of "rare" diseases. These rare diseases are being grouped together because they share a rather constant complement of common features and, indeed, generally respond to empirically developed treatments, leading to a positive outcome consistently. We make the case that it is highly unlikely that such treatments, despite their statistical success measured with large cohorts using standardized clinical research, will be effective on all patients until we increase the depth and fidelity of our understanding of the individual "rare" diseases that are grouped together in the "buckets" of common illnesses. Antioxid. Redox Signal. 27, 511-516.

  1. Diversity and host range of foliar fungal endophytes: are tropical leaves biodiversity hotspots?

    Science.gov (United States)

    Arnold, A Elizabeth; Lutzoni, F

    2007-03-01

    Fungal endophytes are found in asymptomatic photosynthetic tissues of all major lineages of land plants. The ubiquity of these cryptic symbionts is clear, but the scale of their diversity, host range, and geographic distributions are unknown. To explore the putative hyperdiversity of tropical leaf endophytes, we compared endophyte communities along a broad latitudinal gradient from the Canadian arctic to the lowland tropical forest of central Panama. Here, we use molecular sequence data from 1403 endophyte strains to show that endophytes increase in incidence, diversity, and host breadth from arctic to tropical sites. Endophyte communities from higher latitudes are characterized by relatively few species from many different classes of Ascomycota, whereas tropical endophyte assemblages are dominated by a small number of classes with a very large number of endophytic species. The most easily cultivated endophytes from tropical plants have wide host ranges, but communities are dominated by a large number of rare species whose host range is unclear. Even when only the most easily cultured species are considered, leaves of tropical trees represent hotspots of fungal species diversity, containing numerous species not yet recovered from other biomes. The challenge remains to recover and identify those elusive and rarely cultured taxa with narrower host ranges, and to elucidate the ecological roles of these little-known symbionts in tropical forests.

  2. Identification of chromosome aberrations in sporadic microsatellite stable and unstable colorectal cancers using array comparative genomic hybridization

    DEFF Research Database (Denmark)

    Jensen, Thomas Dyrsø; Li, Jian; Wang, Kai

    2011-01-01

    cancers constitute approximately 85% of sporadic cases, whereas microsatellite unstable (MSI) cases constitute the remaining 15%. In this study, we used array comparative genomic hybridization (aCGH) to identify genomic hotspot regions that harbor recurrent copy number changes. The study material...

  3. The Matchmaker Exchange: a platform for rare disease gene discovery

    NARCIS (Netherlands)

    Philippakis, A.A.; Azzariti, D.R.; Beltran, S.; Brookes, A.J.; Brownstein, C.A.; Brudno, M.; Brunner, H.G.; Buske, O.J.; Carey, K.; Doll, C.; Dumitriu, S.; Dyke, S.O.M.; Dunnen, J.T. den; Firth, H.V.; Gibbs, R.A.; Girdea, M.; Gonzalez, M.; Haendel, M.A.; Hamosh, A.; Holm, I.A.; Huang, L.; Hurles, M.E.; Hutton, B.; Krier, J.B.; Misyura, A.; Mungall, C.J.; Paschall, J.; Paten, B.; Robinson, P.N.; Schiettecatte, F.; Sobreira, N.L.; Swaminathan, G.J.; Taschner, P.E.M.; Terry, S.F.; Washington, N.L.; Zuchner, S.; Boycott, K.M.; Rehm, H.L.

    2015-01-01

    There are few better examples of the need for data sharing than in the rare disease community, where patients, physicians, and researchers must search for "the needle in a haystack" to uncover rare, novel causes of disease within the genome. Impeding the pace of discovery has been the existence of

  4. Mining with Rare Cases

    Science.gov (United States)

    Weiss, Gary M.

    Rare cases are often the most interesting cases. For example, in medical diagnosis one is typically interested in identifying relatively rare diseases, such as cancer, rather than more frequently occurring ones, such as the common cold. In this chapter we discuss the role of rare cases in Data Mining. Specific problems associated with mining rare cases are discussed, followed by a description of methods for addressing these problems.

  5. The prevalence of toxic hotspots in former Soviet countries.

    Science.gov (United States)

    Sharov, Petr; Dowling, Russell; Gogishvili, Megi; Jones, Barbara; Caravanos, Jack; McCartor, Andrew; Kashdan, Zachary; Fuller, Richard

    2016-04-01

    Using a global database of contaminated sites, toxic hotspots in eight former Soviet countries were analyzed to identify the prevalence, types and sources of toxic pollution, as well as their associated potential public health impacts. For this analysis, polluted sites in Armenia, Azerbaijan, Kazakhstan, Kyrgyzstan, Russia, Tajikistan, Ukraine, and Uzbekistan were compiled and analyzed. The levels of contamination of seven key pollutants were assessed in each country. 424 contaminated sites were identified using data from Blacksmith Institute. Pesticides, lead (Pb), radioactive metals, arsenic (As), mercury (Hg), chromium (Cr), and cadmium (Cd) were the most commonly identified key pollutants. Collectively, these sites pose health risks to an estimated 6.2 million residents. The existing data on toxic hotspots in former Soviet countries likely captures only a small percentage of actual contaminated sites, but suggests potentially severe public health consequences. Additional assessments are needed to understand the risks posed by toxic pollution in the region. Copyright © 2016. Published by Elsevier Ltd.

  6. Seismic Evidence for Lower Mantle Plume Under the Yellowstone Hotspot

    Science.gov (United States)

    Nelson, P.; Grand, S.

    2017-12-01

    The mantle plume hypothesis for the origin of intraplate volcanism has been controversial since its inception in the 1970s. The hypothesis proposes hot narrow upwelling of rock rooted at the core mantle boundary (CMB) rise through the mantle and interact with the base of the lithosphere forming linear volcanic systems such as Hawaii and Yellowstone. Recently, broad lower mantle (>500 km in diameter) slow velocity conduits, most likely thermochemical in origin, have been associated with some intraplate volcanic provinces (French and Romanowicz, 2015). However, the direct detection of a classical thin thermal plume in the lower mantle using travel time tomography has remained elusive (Anderson and Natland, 2014). Here we present a new shear wave tomography model for the mantle beneath the western United States that is optimized to find short wavelength, sub-vertical structures in the lower mantle. Our approach uses carefully measured SKS and SKKS travel times recorded by dense North American seismic networks in conjunction with finite frequency kernels to build on existing tomography models. We find the presence of a narrow ( 300 km diameter) well isolated cylindrically shaped slow anomaly in the lower most mantle which we associate with the Yellowstone Hotspot. The conduit has a 2% reduction in shear velocity and is rooted at the CMB near the California/Arizona/Nevada border. A cross sectional view through the anomaly shows that it is slightly tilted toward the north until about 1300 km depth where it appears to weaken and deflect toward the surficial positon of the hotspot. Given the anomaly's strength, proximity to the Yellowstone Hotspot, and morphology we argue that a thermal plume interpretation is the most reasonable. Our results provide strong support for a lower mantle plume origin of the Yellowstone hotspot and more importantly the existence of deep thermal plumes.

  7. European Atlantic: the hottest oil spill hotspot worldwide

    Science.gov (United States)

    Vieites, David R.; Nieto-Román, Sandra; Palanca, Antonio; Ferrer, Xavier; Vences, Miguel

    2004-11-01

    Oil spills caused by maritime transport of petroleum products are still an important source of ocean pollution, especially in main production areas and along major transport routes. We here provide a historical and geographic analysis of the major oil spills (>700 t) since 1960. Spills were recorded from several key marine ecosystems and marine biodiversity hotspots. The past four decades have been characterized by an overall decrease in the number of accidents and tonnes of oil spilled in the sea, but this trend was less distinct in the European Atlantic area. Recent black tides from the Erika and Prestige vessels provided new evidence for the high risk of accidents with serious ecological impact in this area, which according to our analysis is historically the most important oil spill hotspot worldwide. The English Channel and waters around Galicia in Spain were the areas with most accidents. Maritime transport in European Atlantic waters has been predicted to continue increasing. Together with our own results this suggests that, in addition to measures for increased traffic safety, deployment of emergency capacities in the spill hotspot areas may be crucial for a sustainable conservation of sea resources and ecosystems.

  8. Hotspot temperature calculation and quench analysis on ITER busbar

    International Nuclear Information System (INIS)

    Rong, J.; Huang, X.Y.; Song, Y.T.; Wu, S.T.

    2014-01-01

    Highlights: • The hotspot temperature is calculated in the case of different extra copper in this paper. • The MQE (minimum quench energy) is carried out as the external heating to trigger a quench in busbar. • The temperature changes after quench is analyzed by Gandalf code in the case of different extra copper and no helium. • The normal length is carried out in the case of different extra copper by Gandalf code. - Abstract: This paper describes the analysis of ITER feeder busbar, the hotspot temperature of busbar is calculated by classical method in the case of 0%, 50%, 75% and 100% extra copper (copper strands). The quench behavior of busbar is simulated by 1-D Gandalf code, and the MQE (minimum quench energy) is estimated in classical method as initial external heat in Gandalf input file. The temperature and the normal length of conductor are analyzed in the case of 0%, 50% and 100% extra copper and no helium. By hotspot temperature, conductor temperature and normal length are contrasted in different extra copper cases, it is shown that the extra copper play an important role in quench protecting

  9. Dynamics of Reactive Microbial Hotspots in Concentration Gradient.

    Science.gov (United States)

    Hubert, A.; Farasin, J.; Tabuteau, H.; Dufresne, A.; Meheust, Y.; Le Borgne, T.

    2017-12-01

    In subsurface environments, bacteria play a major role in controlling the kinetics of a broad range of biogeochemical reactions. In such environments, nutrients fluxes and solute concentrations needed for bacteria metabolism may be highly variable in space and intermittent in time. This can lead to the formation of reactive hotspots where and when conditions are favorable to particular microorganisms, hence inducing biogeochemical reaction kinetics that differ significantly from those measured in homogeneous model environments. To investigate the impact of chemical gradients on the spatial structure and temporal dynamics of subsurface microorganism populations, we develop microfluidic cells allowing for a precise control of flow and chemical gradient conditions, as well as quantitative monitoring of the bacteria's spatial distribution and biofilm development. Using the non-motile Escherichia coli JW1908-1 strain and Gallionella capsiferriformans ES-2 as model organisms, we investigate the behavior and development of bacteria over a range of single and double concentration gradients in the concentrations of nutrients, electron donors and electron acceptors. We measure bacterial activity and population growth locally in precisely known hydrodynamic and chemical environments. This approach allows time-resolved monitoring of the location and intensity of reactive hotspots in micromodels as a function of the flow and chemical gradient conditions. We compare reactive microbial hotspot dynamics in our micromodels to classic growth laws and well-known growth parameters for the laboratory model bacteria Escherichia coli.We also discuss consequences for the formation and temporal dynamics of biofilms in the subsurface.

  10. Towards biodiversity hotspots effective for conserving mammals with small geographic ranges

    Science.gov (United States)

    Carrara, Rodolfo; San Blas, Germán; Agrain, Federico; Roig-Juñent, Sergio

    2017-01-01

    The main goal of using global biodiversity hotspots for conservation purposes is to protect taxa with small geographic ranges because these are highly vulnerable to extinction. However, the extent to what different hotspots types are effective for meeting this goal remains controversial because hotspots have been previously defined as either the richest or most threatened and richest sites in terms of total, endemic or threatened species. In this regard, the use of species richness to set conservation priorities is widely discussed because strategies focused on this diversity measure tend to miss many of the taxa with small geographic ranges. Here we use data on global terrestrial mammal distributions to show that, hotspots of total species, endemism and threat defined in terms of species richness are effective in including 27%, 29% and 11% respectively, of the taxa with small geographic ranges. Whilst, the same hotspot types defined in terms of a simple diversity index, which is a function of species richness and range-size rarity, include 68%, 44% and 90% respectively, of these taxa. In addition, we demonstrate that index hotspot types are highly efficient because they conserve 79% of mammal species (21% more species than richness hotspot types), with 59% of species shared by three hotspot types (31% more than richness hotspot types). These results suggest that selection of different diversity measures to define hotspots may strongly affect the achievement of conservation goals.

  11. What makes labour and birth traumatic? A survey of intrapartum 'hotspots'.

    Science.gov (United States)

    Harris, Rachel; Ayers, Susan

    2012-01-01

    Evidence suggests between 1% and 6% of women develop post-traumatic stress disorder (PTSD) after childbirth. 'Hotspots' are moments of extreme distress during traumatising events that are implicated in symptoms of PTSD. This cross-sectional internet survey of hotspots examined (1) the content of intrapartum hotspots and (2) whether particular events, cognitions or emotions during hotspots are related to PTSD. Women (N = 675) who experienced a difficult or traumatic birth completed a questionnaire composed of a validated measure of PTSD, questions concerning the existence of hotspots, and a newly developed measure of emotions and cognitions during hotspots. The majority of women (67.4%) reported at least one hotspot during birth and 52.9% had re-experiencing symptoms of these hotspots. Women were more likely to have PTSD if hotspots involved fear and lack of control (odds ratio (OR) 1.30, 95% CI 1.17-1.43) or intrapartum dissociation (OR 1.12, 95% CI 1.05-1.19). Risk of PTSD was higher if hotspots concerned interpersonal difficulties (OR 4.34, 95% CI 2.15-8.77) or obstetric complications (OR 3.35, 95% CI 1.64-6.87) compared to complications with the baby.

  12. Forest and Land Fire Prevention Through the Hotspot Movement Pattern Approach

    Science.gov (United States)

    Turmudi, T.; Kardono, P.; Hartanto, P.; Ardhitasari, Y.

    2018-02-01

    Indonesia has experienced a great forest fire disaster in 2015. The losses incurred were enormous. But actually the incidence of forest and land fires occurs almost every year. Various efforts were made to cope with the fire disaster. The appearance of a hotspot becomes an early indication of the fire incident both location and time. By studying the location and time of the hotspot's appearance indicates that the hotspot has certain movement patterns from year to year. This study aims to show the pattern of movement of hotspots from year to year that can be used for the prevention of forest and land fires. The method used is time series analysis of land cover and hotspot distribution. The data used were land cover data from 2005 to 2016, hotspot data from 2005 to 2016. The location of this study is the territory of Meranti Kepulauan District. The results show that the highest hotspot is 425 hotspots occurs in the shrubs and bushes. From year to year, the pattern of hotspot movement occurs in the shrubs and bushes cover. The hotspot pattern follows the direction of unused land for cultivation and is dominated by shrubs. From these results, we need to pay more attentiont for the land with the cover of shrubs adjacent to the cultivated land.

  13. Rare earth sulfates

    International Nuclear Information System (INIS)

    Komissarova, L.N.; Shatskij, V.M.; Pokrovskij, A.N.; Chizhov, S.M.; Bal'kina, T.I.; Suponitskij, Yu.L.

    1986-01-01

    Results of experimental works on the study of synthesis conditions, structure and physico-chemical properties of rare earth, scandium and yttrium sulfates, have been generalized. Phase diagrams of solubility and fusibility, thermodynamic and crystallochemical characteristics, thermal stability of hydrates and anhydrous sulfates of rare earths, including normal, double (with cations of alkali and alkaline-earth metals), ternary and anion-mixed sulfates of rare earths, as well as their adducts, are considered. The state of ions of rare earths, scandium and yttrium in aqueous sulfuric acid solutions is discussed. Data on the use of rare earth sulfates are given

  14. Multiwavelength study of Cygnus A. V. The hotspots in the lobe

    Science.gov (United States)

    Pyrzas, S.; Steenbrugge, K. C.; Blundell, K. M.

    2015-02-01

    Context. The jets in Faranoff-Riley type II AGN are supposed come to an abrupt halt in hotspots on opposite sides of the nucleus. Quite commonly, two hotspots are observed in each lobe. The origin of the second hotspot is currently poorly understood. Aims: Our aims are to determine the origin of the secondary hotspot in the western lobe of Cygnus A from high resolution multifrequency radio images; to determine the minimum Lorentz factor of the electrons in the hotspots, often referred to as the low-energy turnover; and to study the magnetic field configuration of the hotspots. Methods: We used 151 MHz Merlin and 327 MHz, 1.4, 5, 8, 15, and 43 GHz VLA images to determine the centroid of the peak luminosity, the spectral shape, and polarization fraction of both hotspots in the western lobe of Cygnus A. Results: We find a spatial shift in peak luminosity between the lower and higher frequency images for both hotspots. We determine the minimum Lorentz factor of the electrons to be ~1000, and show that most of the emission from the primary hotspot is linearly polarized. The minimum energy magnetic field strength is found to range between ~0.14 and ~0.5 mG in both the primary and secondary hotspots. Conclusions: From the low polarization and the determined outflow velocity, we conclude that the secondary hotspot is no longer a strong shock, and is an expanding, and hence a fading hotspot. This hotspot has an age that is of the same order of magnitude as the jet precession period.

  15. Tolerance of Whole-Genome Doubling Propagates Chromosomal Instability and Accelerates Cancer Genome Evolution

    DEFF Research Database (Denmark)

    Dewhurst, Sally M.; McGranahan, Nicholas; Burrell, Rebecca A.

    2014-01-01

    The contribution of whole-genome doubling to chromosomal instability (CIN) and tumor evolution is unclear. We use long-term culture of isogenic tetraploid cells from a stable diploid colon cancer progenitor to investigate how a genome-doubling event affects genome stability over time. Rare cells...

  16. Implementing genomics and pharmacogenomics in the clinic: The National Human Genome Research Institute's genomic medicine portfolio.

    Science.gov (United States)

    Manolio, Teri A

    2016-10-01

    Increasing knowledge about the influence of genetic variation on human health and growing availability of reliable, cost-effective genetic testing have spurred the implementation of genomic medicine in the clinic. As defined by the National Human Genome Research Institute (NHGRI), genomic medicine uses an individual's genetic information in his or her clinical care, and has begun to be applied effectively in areas such as cancer genomics, pharmacogenomics, and rare and undiagnosed diseases. In 2011 NHGRI published its strategic vision for the future of genomic research, including an ambitious research agenda to facilitate and promote the implementation of genomic medicine. To realize this agenda, NHGRI is consulting and facilitating collaborations with the external research community through a series of "Genomic Medicine Meetings," under the guidance and leadership of the National Advisory Council on Human Genome Research. These meetings have identified and begun to address significant obstacles to implementation, such as lack of evidence of efficacy, limited availability of genomics expertise and testing, lack of standards, and difficulties in integrating genomic results into electronic medical records. The six research and dissemination initiatives comprising NHGRI's genomic research portfolio are designed to speed the evaluation and incorporation, where appropriate, of genomic technologies and findings into routine clinical care. Actual adoption of successful approaches in clinical care will depend upon the willingness, interest, and energy of professional societies, practitioners, patients, and payers to promote their responsible use and share their experiences in doing so. Published by Elsevier Ireland Ltd.

  17. Identifying hotspots and management of critical ecosystem services in rapidly urbanizing Yangtze River Delta Region, China.

    Science.gov (United States)

    Cai, Wenbo; Gibbs, David; Zhang, Lang; Ferrier, Graham; Cai, Yongli

    2017-04-15

    Rapid urbanization has altered many ecosystems, causing a decline in many ecosystem services, generating serious ecological crisis. To cope with these challenges, we presented a comprehensive framework comprising five core steps for identifying and managing hotspots of critical ecosystem services in a rapid urbanizing region. This framework was applied in the case study of the Yangtze River Delta (YRD) Region. The study showed that there was large spatial heterogeneity in the hotspots of ecosystem services in the region, hotspots of supporting services and regulating services aggregately distributing in the southwest mountainous areas while hotspots of provisioning services mainly in the northeast plain, and hotspots of cultural services widespread in the waterbodies and southwest mountainous areas. The regionalization of the critical ecosystem services was made through the hotspot analysis. This study provided valuable information for environmental planning and management in a rapid urbanizing region and helped improve China's ecological redlines policy at regional scale. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. A suggested classification and explanation for hotspots in some powerful radio sources

    International Nuclear Information System (INIS)

    Kronberg, P.P.; Jones, T.W.

    1982-01-01

    High resolution (1''→0.1') maps of the outer complexes of some ''well formed'' powerful radio sources suggest that we can now distinguish two physically distinct types of outer hotspots. The authors denote them as type ''A'' and ''B'' and describe them as follows: Type A hotspots, occur at the outer leading edge, and have a cusp-like, or otherwise elongated shape. This strongly suggests that their shape and energy density are determined by the ram-pressure interaction between the end of a beam or momentum flux ''pipeline'', and the ambient i.g.m. Type B hotspots generally lie off the A hotspot-galaxy/QSO axis, and are also behind the Type A hotspots. In at least some cases, they are compact and have a higher minimum energy density than the outer, Type A hotspots. (Auth.)

  19. Testing the Efficacy of Global Biodiversity Hotspots for Insect Conservation: The Case of South African Katydids.

    Directory of Open Access Journals (Sweden)

    Corinna S Bazelet

    Full Text Available The use of endemism and vascular plants only for biodiversity hotspot delineation has long been contested. Few studies have focused on the efficacy of global biodiversity hotspots for the conservation of insects, an important, abundant, and often ignored component of biodiversity. We aimed to test five alternative diversity measures for hotspot delineation and examine the efficacy of biodiversity hotspots for conserving a non-typical target organism, South African katydids. Using a 1° fishnet grid, we delineated katydid hotspots in two ways: (1 count-based: grid cells in the top 10% of total, endemic, threatened and/or sensitive species richness; vs. (2 score-based: grid cells with a mean value in the top 10% on a scoring system which scored each species on the basis of its IUCN Red List threat status, distribution, mobility and trophic level. We then compared katydid hotspots with each other and with recognized biodiversity hotspots. Grid cells within biodiversity hotspots had significantly higher count-based and score-based diversity than non-hotspot grid cells. There was a significant association between the three types of hotspots. Of the count-based measures, endemic species richness was the best surrogate for the others. However, the score-based measure out-performed all count-based diversity measures. Species richness was the least successful surrogate of all. The strong performance of the score-based method for hotspot prediction emphasizes the importance of including species' natural history information for conservation decision-making, and is easily adaptable to other organisms. Furthermore, these results add empirical support for the efficacy of biodiversity hotspots in conserving non-target organisms.

  20. Sampling effects on the identification of roadkill hotspots: Implications for survey design.

    Science.gov (United States)

    Santos, Sara M; Marques, J Tiago; Lourenço, André; Medinas, Denis; Barbosa, A Márcia; Beja, Pedro; Mira, António

    2015-10-01

    Although locating wildlife roadkill hotspots is essential to mitigate road impacts, the influence of study design on hotspot identification remains uncertain. We evaluated how sampling frequency affects the accuracy of hotspot identification, using a dataset of vertebrate roadkills (n = 4427) recorded over a year of daily surveys along 37 km of roads. "True" hotspots were identified using this baseline dataset, as the 500-m segments where the number of road-killed vertebrates exceeded the upper 95% confidence limit of the mean, assuming a Poisson distribution of road-kills per segment. "Estimated" hotspots were identified likewise, using datasets representing progressively lower sampling frequencies, which were produced by extracting data from the baseline dataset at appropriate time intervals (1-30 days). Overall, 24.3% of segments were "true" hotspots, concentrating 40.4% of roadkills. For different groups, "true" hotspots accounted from 6.8% (bats) to 29.7% (small birds) of road segments, concentrating from 60% (lizards, lagomorphs, carnivores) of roadkills. Spatial congruence between "true" and "estimated" hotspots declined rapidly with increasing time interval between surveys, due primarily to increasing false negatives (i.e., missing "true" hotspots). There were also false positives (i.e., wrong "estimated" hotspots), particularly at low sampling frequencies. Spatial accuracy decay with increasing time interval between surveys was higher for smaller-bodied (amphibians, reptiles, small birds, small mammals) than for larger-bodied species (birds of prey, hedgehogs, lagomorphs, carnivores). Results suggest that widely used surveys at weekly or longer intervals may produce poor estimates of roadkill hotspots, particularly for small-bodied species. Surveying daily or at two-day intervals may be required to achieve high accuracy in hotspot identification for multiple species. Copyright © 2015 Elsevier Ltd. All rights reserved.

  1. Temperature dependence of the current to sustain a normal hotspot in superconducting microbridges

    International Nuclear Information System (INIS)

    Yamaguchi, Y.; Ishii, C.

    1981-01-01

    A modification of the boundary condition to determine the SN boundary in the hotspot model of superconducting microbridges is proposed and successfully applied to the interpretation of recent measurements of the hotspot-sustaining current by Mizuno and Aomine. It is shown that suppression of the order parameter due to the applied current gives rise to an additional temperature dependence of the hotspot-sustaining current in the extreme vicinity of the transition temperature. (orig.)

  2. Testing the Efficacy of Global Biodiversity Hotspots for Insect Conservation: The Case of South African Katydids.

    Science.gov (United States)

    Bazelet, Corinna S; Thompson, Aileen C; Naskrecki, Piotr

    2016-01-01

    The use of endemism and vascular plants only for biodiversity hotspot delineation has long been contested. Few studies have focused on the efficacy of global biodiversity hotspots for the conservation of insects, an important, abundant, and often ignored component of biodiversity. We aimed to test five alternative diversity measures for hotspot delineation and examine the efficacy of biodiversity hotspots for conserving a non-typical target organism, South African katydids. Using a 1° fishnet grid, we delineated katydid hotspots in two ways: (1) count-based: grid cells in the top 10% of total, endemic, threatened and/or sensitive species richness; vs. (2) score-based: grid cells with a mean value in the top 10% on a scoring system which scored each species on the basis of its IUCN Red List threat status, distribution, mobility and trophic level. We then compared katydid hotspots with each other and with recognized biodiversity hotspots. Grid cells within biodiversity hotspots had significantly higher count-based and score-based diversity than non-hotspot grid cells. There was a significant association between the three types of hotspots. Of the count-based measures, endemic species richness was the best surrogate for the others. However, the score-based measure out-performed all count-based diversity measures. Species richness was the least successful surrogate of all. The strong performance of the score-based method for hotspot prediction emphasizes the importance of including species' natural history information for conservation decision-making, and is easily adaptable to other organisms. Furthermore, these results add empirical support for the efficacy of biodiversity hotspots in conserving non-target organisms.

  3. Rare lung cancers

    International Nuclear Information System (INIS)

    Berzinec, P.

    2013-01-01

    The RARECARE Project (Rare Cancers in the Europe) supported by the European Union defined the rare cancers by the incidence rate of less than 6/100 000. There are several variants of lung cancer which are rare according to this definition. From the clinical point of view the most interesting are the rare adenocarcinomas and large cell neuroendocrine carcinoma. There are important differences in the diagnostic probability of EGFR and ALK mutations in the mutinous and non-mucin ous adenocarcinomas, in the signet ring cell adenocarcinomas, and large cell carcinomas. The optimal chemotherapy for neuroendocrine large cell carcinomas remains undefined. There is only very limited number of clinical trials aimed on the rare lung cancers and actually none phase III trial. Rare lung cancers continue to be a challenge both for the laboratory and the clinical research. (author)

  4. 40 CFR 93.123 - Procedures for determining localized CO, PM10, and PM2.5 concentrations (hot-spot analysis).

    Science.gov (United States)

    2010-07-01

    ... CO, PM10, and PM2.5 concentrations (hot-spot analysis). 93.123 Section 93.123 Protection of... concentrations (hot-spot analysis). (a) CO hot-spot analysis. (1) The demonstrations required by § 93.116... make a categorical hot-spot finding that (93.116(a) is met without further hot-spot analysis for any...

  5. Towards Rare Itemset Mining

    OpenAIRE

    Szathmary , Laszlo; Napoli , Amedeo; Valtchev , Petko

    2007-01-01

    site de la conférence : http://ictai07.ceid.upatras.gr/; International audience; We describe here a general approach for rare itemset mining. While mining literature has been almost exclusively focused on frequent itemsets, in many practical situations rare ones are of higher interest (e.g., in medical databases, rare combinations of symptoms might provide useful insights for the physicians). Based on an examination of the relevant substructures of the mining space, our approach splits the ra...

  6. Rare earth octacyanomolybdates(4)

    International Nuclear Information System (INIS)

    Zubritskaya, D.I.; Sergeeva, A.N.; Pisak, Yu.V.

    1980-01-01

    Optimal conditions for synthesis of rare-earth octacyanomolybdates(4) of the Ln 4 [Mo(CN) 8 ] 3 xnH 2 O composition (where Ln is a rare-earth element, other than Pr, Pm, Lu, Tb) have been worked out. The synthesis has been accomplished by neutralization with octacianomolybdic acid with rare-earth carbonates. The composition and structure of the compounds synthesized have been studied by infrared-spectroscopy. It has been established that rare-earth octacyanomolybdates(4) form three isostructural groups

  7. Detecting Malaria Hotspots: A Comparison of Rapid Diagnostic Test, Microscopy, and Polymerase Chain Reaction.

    Science.gov (United States)

    Mogeni, Polycarp; Williams, Thomas N; Omedo, Irene; Kimani, Domtila; Ngoi, Joyce M; Mwacharo, Jedida; Morter, Richard; Nyundo, Christopher; Wambua, Juliana; Nyangweso, George; Kapulu, Melissa; Fegan, Gregory; Bejon, Philip

    2017-11-27

    Malaria control strategies need to respond to geographical hotspots of transmission. Detection of hotspots depends on the sensitivity of the diagnostic tool used. We conducted cross-sectional surveys in 3 sites within Kilifi County, Kenya, that had variable transmission intensities. Rapid diagnostic test (RDT), microscopy, and polymerase chain reaction (PCR) were used to detect asymptomatic parasitemia, and hotspots were detected using the spatial scan statistic. Eight thousand five hundred eighty-one study participants were surveyed in 3 sites. There were statistically significant malaria hotspots by RDT, microscopy, and PCR for all sites except by microscopy in 1 low transmission site. Pooled data analysis of hotspots by PCR overlapped with hotspots by microscopy at a moderate setting but not at 2 lower transmission settings. However, variations in degree of overlap were noted when data were analyzed by year. Hotspots by RDT were predictive of PCR/microscopy at the moderate setting, but not at the 2 low transmission settings. We observed long-term stability of hotspots by PCR and microscopy but not RDT. Malaria control programs may consider PCR testing to guide asymptomatic malaria hotspot detection once the prevalence of infection falls. © The Author 2017. Published by Oxford University Press for the Infectious Diseases Society of America.

  8. Resources, challenges and way forward in rare mitochondrial diseases research.

    Science.gov (United States)

    Rajput, Neeraj Kumar; Singh, Vipin; Bhardwaj, Anshu

    2015-01-01

    Over 300 million people are affected by about 7000 rare diseases globally. There are tremendous resource limitations and challenges in driving research and drug development for rare diseases. Hence, innovative approaches are needed to identify potential solutions. This review focuses on the resources developed over the past years for analysis of genome data towards understanding disease biology especially in the context of mitochondrial diseases, given that mitochondria are central to major cellular pathways and their dysfunction leads to a broad spectrum of diseases. Platforms for collaboration of research groups, clinicians and patients and the advantages of community collaborative efforts in addressing rare diseases are also discussed. The review also describes crowdsourcing and crowdfunding efforts in rare diseases research and how the upcoming initiatives for understanding disease biology including analyses of large number of genomes are also applicable to rare diseases.

  9. How hot are drosophila hotspots? examining recombination rate variation and associations with nucleotide diversity, divergence, and maternal age in Drosophila pseudoobscura.

    Directory of Open Access Journals (Sweden)

    Brenda Manzano-Winkler

    Full Text Available Fine scale meiotic recombination maps have uncovered a large amount of variation in crossover rate across the genomes of many species, and such variation in mammalian and yeast genomes is concentrated to <5kb regions of highly elevated recombination rates (10-100x the background rate called "hotspots." Drosophila exhibit substantial recombination rate heterogeneity across their genome, but evidence for these highly-localized hotspots is lacking. We assayed recombination across a 40Kb region of Drosophila pseudoobscura chromosome 2, with one 20kb interval assayed every 5Kb and the adjacent 20kb interval bisected into 10kb pieces. We found that recombination events across the 40kb stretch were relatively evenly distributed across each of the 5kb and 10kb intervals, rather than concentrated in a single 5kb region. This, in combination with other recent work, indicates that the recombination landscape of Drosophila may differ from the punctate recombination pattern observed in many mammals and yeast. Additionally, we found no correlation of average pairwise nucleotide diversity and divergence with recombination rate across the 20kb intervals, nor any effect of maternal age in weeks on recombination rate in our sample.

  10. Automated Selection of Hotspots (ASH): enhanced automated segmentation and adaptive step finding for Ki67 hotspot detection in adrenal cortical cancer.

    Science.gov (United States)

    Lu, Hao; Papathomas, Thomas G; van Zessen, David; Palli, Ivo; de Krijger, Ronald R; van der Spek, Peter J; Dinjens, Winand N M; Stubbs, Andrew P

    2014-11-25

    In prognosis and therapeutics of adrenal cortical carcinoma (ACC), the selection of the most active areas in proliferative rate (hotspots) within a slide and objective quantification of immunohistochemical Ki67 Labelling Index (LI) are of critical importance. In addition to intratumoral heterogeneity in proliferative rate i.e. levels of Ki67 expression within a given ACC, lack of uniformity and reproducibility in the method of quantification of Ki67 LI may confound an accurate assessment of Ki67 LI. We have implemented an open source toolset, Automated Selection of Hotspots (ASH), for automated hotspot detection and quantification of Ki67 LI. ASH utilizes NanoZoomer Digital Pathology Image (NDPI) splitter to convert the specific NDPI format digital slide scanned from the Hamamatsu instrument into a conventional tiff or jpeg format image for automated segmentation and adaptive step finding hotspots detection algorithm. Quantitative hotspot ranking is provided by the functionality from the open source application ImmunoRatio as part of the ASH protocol. The output is a ranked set of hotspots with concomitant quantitative values based on whole slide ranking. We have implemented an open source automated detection quantitative ranking of hotspots to support histopathologists in selecting the 'hottest' hotspot areas in adrenocortical carcinoma. To provide wider community easy access to ASH we implemented a Galaxy virtual machine (VM) of ASH which is available from http://bioinformatics.erasmusmc.nl/wiki/Automated_Selection_of_Hotspots . The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/13000_2014_216.

  11. Validation of Hotspots Detected by Satellites in Sentinel Asia

    Science.gov (United States)

    Kaku, K.; Kushida, K.; Fukuda, M.

    2008-12-01

    The Sentinel Asia (SA) initiative is a collaboration between space agencies and disaster management agencies, applying remote sensing and Web-GIS technologies to assist disaster management in the Asia- Pacific region. It aims to: "EImprove safety in society by ICT and space technology "EImprove speed and accuracy of disaster preparedness and early warning "EMinimize the number of victims and social/economic losses. SA is a voluntary initiative led by the Asia-Pacific Regional Space Agency Forum (APRSAF) to share disaster information in near-real-time across the Asia-Pacific region. Wildfire is a major and recurring phenomenon that has a serious impact on property and human health, affecting many countries in the Asia region. Compared to other disasters in the area, it does not necessarily cause many immediate fatalities. However, it causes serious impact on property and human health due to smoke. Furthermore, its effects are of great relevance both at a regional and global level, and accordingly bear substantial influence on global warming. Responding to requirements from Asian countries, under Sentinel Asia a dedicated Wildfire Working Group (WG) has been established to apply remote sensing technology to the management of wildfire. Having accurate information on the location and intensity of the fires, and subsequent control of wildfire, are therefore very important and urgent tasks across the region. SA primarily addresses the issue of near-real-time information distribution on wildfires in the region. Concerning hotspot data obtained by satellites, it is essential to validate and improve its accuracy. In the framework of Sentinel Asia Wildfire WG, various approaches to hotspot detection, including MOD14 algorithm for MODIS hotspots, were studied, and their validations were carried out, comparing them with active fires extracted from satellite imagery and ground truth data in Chiengmai, Thailand and in Kalimantan, Indonesia.

  12. Carnivore hotspots in Peninsular Malaysia and their landscape attributes

    Science.gov (United States)

    van Manen, Frank T.

    2018-01-01

    Mammalian carnivores play a vital role in ecosystem functioning. However, they are prone to extinction because of low population densities and growth rates, and high levels of persecution or exploitation. In tropical biodiversity hotspots such as Peninsular Malaysia, rapid conversion of natural habitats threatens the persistence of this vulnerable group of animals. Here, we carried out the first comprehensive literature review on 31 carnivore species reported to occur in Peninsular Malaysia and updated their probable distribution. We georeferenced 375 observations of 28 species of carnivore from 89 unique geographic locations using records spanning 1948 to 2014. Using the Getis-Ord Gi*statistic and weighted survey records by IUCN Red List status, we identified hotspots of species that were of conservation concern and built regression models to identify environmental and anthropogenic landscape factors associated with Getis-Ord Gi* z scores. Our analyses identified two carnivore hotspots that were spatially concordant with two of the peninsula’s largest and most contiguous forest complexes, associated with Taman Negara National Park and Royal Belum State Park. A cold spot overlapped with the southwestern region of the Peninsula, reflecting the disappearance of carnivores with higher conservation rankings from increasingly fragmented natural habitats. Getis-Ord Gi* z scores were negatively associated with elevation, and positively associated with the proportion of natural land cover and distance from the capital city. Malaysia contains some of the world’s most diverse carnivore assemblages, but recent rates of forest loss are some of the highest in the world. Reducing poaching and maintaining large, contiguous tracts of lowland forests will be crucial, not only for the persistence of threatened carnivores, but for many mammalian species in general. PMID:29617402

  13. Carnivore hotspots in Peninsular Malaysia and their landscape attributes.

    Science.gov (United States)

    Ratnayeke, Shyamala; van Manen, Frank T; Clements, Gopalasamy Reuben; Kulaimi, Noor Azleen Mohd; Sharp, Stuart P

    2018-01-01

    Mammalian carnivores play a vital role in ecosystem functioning. However, they are prone to extinction because of low population densities and growth rates, and high levels of persecution or exploitation. In tropical biodiversity hotspots such as Peninsular Malaysia, rapid conversion of natural habitats threatens the persistence of this vulnerable group of animals. Here, we carried out the first comprehensive literature review on 31 carnivore species reported to occur in Peninsular Malaysia and updated their probable distribution. We georeferenced 375 observations of 28 species of carnivore from 89 unique geographic locations using records spanning 1948 to 2014. Using the Getis-Ord Gi*statistic and weighted survey records by IUCN Red List status, we identified hotspots of species that were of conservation concern and built regression models to identify environmental and anthropogenic landscape factors associated with Getis-Ord Gi* z scores. Our analyses identified two carnivore hotspots that were spatially concordant with two of the peninsula's largest and most contiguous forest complexes, associated with Taman Negara National Park and Royal Belum State Park. A cold spot overlapped with the southwestern region of the Peninsula, reflecting the disappearance of carnivores with higher conservation rankings from increasingly fragmented natural habitats. Getis-Ord Gi* z scores were negatively associated with elevation, and positively associated with the proportion of natural land cover and distance from the capital city. Malaysia contains some of the world's most diverse carnivore assemblages, but recent rates of forest loss are some of the highest in the world. Reducing poaching and maintaining large, contiguous tracts of lowland forests will be crucial, not only for the persistence of threatened carnivores, but for many mammalian species in general.

  14. Carnivore hotspots in Peninsular Malaysia and their landscape attributes

    Science.gov (United States)

    Ratnayeke, Shyamala; van Manen, Frank T.; Clements, Gopalasamy Reuben; Mohd Kulaimi, Noor Azleen; Sharp, Stuart P.

    2018-01-01

    Mammalian carnivores play a vital role in ecosystem functioning. However, they are prone to extinction because of low population densities and growth rates, and high levels of persecution or exploitation. In tropical biodiversity hotspots such as Peninsular Malaysia, rapid conversion of natural habitats threatens the persistence of this vulnerable group of animals. Here, we carried out the first comprehensive literature review on 31 carnivore species reported to occur in Peninsular Malaysia and updated their probable distribution. We georeferenced 375 observations of 28 species of carnivore from 89 unique geographic locations using records spanning 1948 to 2014. Using the Getis-Ord Gi*statistic and weighted survey records by IUCN Red List status, we identified hotspots of species that were of conservation concern and built regression models to identify environmental and anthropogenic landscape factors associated with Getis-Ord Gi* z scores. Our analyses identified two carnivore hotspots that were spatially concordant with two of the peninsula’s largest and most contiguous forest complexes, associated with Taman Negara National Park and Royal Belum State Park. A cold spot overlapped with the southwestern region of the Peninsula, reflecting the disappearance of carnivores with higher conservation rankings from increasingly fragmented natural habitats. Getis-Ord Gi* z scores were negatively associated with elevation, and positively associated with the proportion of natural land cover and distance from the capital city. Malaysia contains some of the world’s most diverse carnivore assemblages, but recent rates of forest loss are some of the highest in the world. Reducing poaching and maintaining large, contiguous tracts of lowland forests will be crucial, not only for the persistence of threatened carnivores, but for many mammalian species in general.

  15. Coldspots and hotspots - Global tectonics and mantle dynamics of Venus

    Science.gov (United States)

    Bindschadler, Duane L.; Schubert, Gerald; Kaula, William M.

    1992-01-01

    Based on geologic observations provided by Magellan's first cycle of data collection and recent models of mantle convection in spherical shells and crustal deformation, the major topographic and geologic features of Venus are incorporated into a model of global mantle dynamics. Consideration is given to volcanic rises, such as Beta Regio and Atla Regio, plateau-shaped highlands dominated by complex ridged terrain (e.g., Ovda Regio and Alpha Regio), and circular lowland regions, such as Atalanta Planitia. Each of these features is related to either mantle plumes (hotspots) or mantle downwellings (coldspots).

  16. French Polynesia Hotspot Swells Explained By Dynamic Topography

    Science.gov (United States)

    Adam, C.; Yoshida, M.; Isse, T.; Suetsugu, D.; Shiobara, H.; Sugioka, H.; Kanazawa, T.; Fukao, Y.; Barruol, G.

    2007-12-01

    Situated on the South Pacific Superswell, French Polynesia is a region characterized by numerous geophysical anomalies among which a high volcanism concentration. Seven hotspots are required to explain the observed chains, volcanism ages and geochemical trends. Many open questions still remain on the origin of these hotspot chains: are they created by passive uplift of magma due to discontinuities in the structure of the lithosphere or by the ascent of mantle plumes? In this case, at which depth do these plumes initiate in the mantle? Many geophysical observations (bathymetry, gravity, magnetism, volcanism ages..) are used to understand the unique phenomenon occurring on this region. The most useful information may come from tomography models since they provide a 3D view of the mantle. Until recently, the tomography models over the region were quite inaccurate because of the sparse location of the seismic stations. The deployment of two new seismic stations networks (BBOBS and temporary island stations) has lately remedied this failing. The resulting tomography model obtained through the inversion of Rayleigh waves provides the most accurate view of the shallowest part of the mantle (depths ≤ 240 km) beneath French Polynesia. Indeed, for the first time the accuracy of a tomography model is good enough to provide information about plume phenomenology in this complex region. In order to quantify the plumes effect on the seafloor, we compute the dynamic topography through an instantaneous flow model. The general trend of the observed depths anomalies (highs and lows) is well recovered. For example the amplitude, location and extension of the swells associated with the Society, Macdonald and Rarotonga are accurately described by the dynamic model. We also find that dynamic uplift is associated with the Tuamotu archipelago which means that a part of the observed swell is due to the present day action of plumes. Since no volcanism ages are available over this chain

  17. A Method for Improving Hotspot Directional Signatures in BRDF Models Used for MODIS

    Science.gov (United States)

    Jiao, Ziti; Schaaf, Crystal B.; Dong, Yadong; Roman, Miguel; Hill, Michael J.; Chen, Jing M.; Wang, Zhuosen; Zhang, Hu; Saenz, Edward; Poudyal, Rajesh; hide

    2016-01-01

    The semi-empirical, kernel-driven, linear RossThick-LiSparseReciprocal (RTLSR) Bidirectional Reflectance Distribution Function (BRDF) model is used to generate the routine MODIS BRDFAlbedo product due to its global applicability and the underlying physics. A challenge of this model in regard to surface reflectance anisotropy effects comes from its underestimation of the directional reflectance signatures near the Sun illumination direction; also known as the hotspot effect. In this study, a method has been developed for improving the ability of the RTLSR model to simulate the magnitude and width of the hotspot effect. The method corrects the volumetric scattering component of the RTLSR model using an exponential approximation of a physical hotspot kernel, which recreates the hotspot magnitude and width using two free parameters (C(sub 1) and C(sub 2), respectively). The approach allows one to reconstruct, with reasonable accuracy, the hotspot effect by adjusting or using the prior values of these two hotspot variables. Our results demonstrate that: (1) significant improvements in capturing hotspot effect can be made to this method by using the inverted hotspot parameters; (2) the reciprocal nature allow this method to be more adaptive for simulating the hotspot height and width with high accuracy, especially in cases where hotspot signatures are available; and (3) while the new approach is consistent with the heritage RTLSR model inversion used to estimate intrinsic narrowband and broadband albedos, it presents some differences for vegetation clumping index (CI) retrievals. With the hotspot-related model parameters determined a priori, this method offers improved performance for various ecological remote sensing applications; including the estimation of canopy structure parameters.

  18. Pollination ecology and the possible impacts of environmental change in the Southwest Australian Biodiversity Hotspot.

    Science.gov (United States)

    Phillips, Ryan D; Hopper, Stephen D; Dixon, Kingsley W

    2010-02-12

    The Southwest Australian Biodiversity Hotspot contains an exceptionally diverse flora on an ancient, low-relief but edaphically diverse landscape. Since European colonization, the primary threat to the flora has been habitat clearance, though climate change is an impending threat. Here, we review (i) the ecology of nectarivores and biotic pollination systems in the region, (ii) the evidence that trends in pollination strategies are a consequence of characteristics of the landscape, and (iii) based on these discussions, provide predictions to be tested on the impacts of environmental change on pollination systems. The flora of southwestern Australia has an exceptionally high level of vertebrate pollination, providing the advantage of highly mobile, generalist pollinators. Nectarivorous invertebrates are primarily generalist foragers, though an increasing number of colletid bees are being recognized as being specialized at the level of plant family or more rarely genus. While generalist pollination strategies dominate among insect-pollinated plants, there are some cases of extreme specialization, most notably the multiple evolutions of sexual deception in the Orchidaceae. Preliminary data suggest that bird pollination confers an advantage of greater pollen movement and may represent a mechanism for minimizing inbreeding in naturally fragmented populations. The effects of future environmental change are predicted to result from a combination of the resilience of pollination guilds and changes in their foraging and dispersal behaviour.

  19. Avian Haemosporidian blood parasite infections at a migration hotspot in Eilat, Israel

    Directory of Open Access Journals (Sweden)

    Paperna Ilan

    2016-06-01

    Full Text Available Haemosporidian blood parasites are frequent amongst passerines. Though they often do not cause detectable consequences to host health, however, their presence or absence and also their prevalence across host populations may potentially carry meaningful information about the health, stress, body condition and viability of bird individuals or populations. The study of migratory birds captured in Eilat, Israel, allowed us to evaluate the prevalence of blood parasite infections in a wide range of both migrant and resident species in spring (N = 1,950 and autumn (N = 538 of 2004 and 2005. According to blood film microscopy, Haemoproteus spp. and Leucocytozoon spp. were more prevalent in the spring than in the autumn (0.289, 0.082 vs. 0.132, 0.033, respectively, whilst Plasmodium spp. exhibited a slight opposite trend (0.034, 0.056. All other parasites (such as trypanosomes, microfilaria and haemococcidians were rare. During the spring seasons, prevalences were significantly higher in migrant than in resident species, whilst this difference was only marginally significant in the autumn. Given that Eilat is a migration hotspot for several Palearctic passerine species, the present descriptive study may hopefully serve to set the baseline values for future long-term epidemiological monitoring.

  20. The research progress of genomic selection in livestock.

    Science.gov (United States)

    Li, Hong-wei; Wang, Rui-jun; Wang, Zhi-ying; Li, Xue-wu; Wang, Zhen-yu; Yanjun, Zhang; Rui, Su; Zhihong, Liu; Jinquan, Li

    2017-05-20

    With the development of gene chip and breeding technology, genomic selection in plants and animals has become research hotspots in recent years. Genomic selection has been extensively applied to all kinds of economic livestock, due to its high accuracy, short generation intervals and low breeding costs. In this review, we summarize genotyping technology and the methods for genomic breeding value estimation, the latter including the least square method, RR-BLUP, GBLUP, ssGBLUP, BayesA and BayesB. We also cover basic principles of genomic selection and compare their genetic marker ranges, genomic selection accuracy and operational speed. In addition, we list common indicators, methods and influencing factors that are related to genomic selection accuracy. Lastly, we discuss latest applications and the current problems of genomic selection at home and abroad. Importantly, we envision future status of genomic selection research, including multi-trait and multi-population genomic selection, as well as impact of whole genome sequencing and dominant effects on genomic selection. This review will provide some venues for other breeders to further understand genome selection.

  1. Preserving the evolutionary potential of floras in biodiversity hotspots.

    Science.gov (United States)

    Forest, Félix; Grenyer, Richard; Rouget, Mathieu; Davies, T Jonathan; Cowling, Richard M; Faith, Daniel P; Balmford, Andrew; Manning, John C; Procheş, Serban; van der Bank, Michelle; Reeves, Gail; Hedderson, Terry A J; Savolainen, Vincent

    2007-02-15

    One of the biggest challenges for conservation biology is to provide conservation planners with ways to prioritize effort. Much attention has been focused on biodiversity hotspots. However, the conservation of evolutionary process is now also acknowledged as a priority in the face of global change. Phylogenetic diversity (PD) is a biodiversity index that measures the length of evolutionary pathways that connect a given set of taxa. PD therefore identifies sets of taxa that maximize the accumulation of 'feature diversity'. Recent studies, however, concluded that taxon richness is a good surrogate for PD. Here we show taxon richness to be decoupled from PD, using a biome-wide phylogenetic analysis of the flora of an undisputed biodiversity hotspot--the Cape of South Africa. We demonstrate that this decoupling has real-world importance for conservation planning. Finally, using a database of medicinal and economic plant use, we demonstrate that PD protection is the best strategy for preserving feature diversity in the Cape. We should be able to use PD to identify those key regions that maximize future options, both for the continuing evolution of life on Earth and for the benefit of society.

  2. Seamounts are hotspots of pelagic biodiversity in the open ocean.

    Science.gov (United States)

    Morato, Telmo; Hoyle, Simon D; Allain, Valerie; Nicol, Simon J

    2010-05-25

    The identification of biodiversity hotspots and their management for conservation have been hypothesized as effective ways to protect many species. There has been a significant effort to identify and map these areas at a global scale, but the coarse resolution of most datasets masks the small-scale patterns associated with coastal habitats or seamounts. Here we used tuna longline observer data to investigate the role of seamounts in aggregating large pelagic biodiversity and to identify which pelagic species are associated with seamounts. Our analysis indicates that seamounts are hotspots of pelagic biodiversity. Higher species richness was detected in association with seamounts than with coastal or oceanic areas. Seamounts were found to have higher species diversity within 30-40 km of the summit, whereas for sets close to coastal habitat the diversity was lower and fairly constant with distance. Higher probability of capture and higher number of fish caught were detected for some shark, billfish, tuna, and other by-catch species. The study supports hypotheses that seamounts may be areas of special interest for management for marine pelagic predators.

  3. Can we detect oceanic biodiversity hotspots from space?

    Science.gov (United States)

    De Monte, Silvia; Soccodato, Alice; Alvain, Séverine; d'Ovidio, Francesco

    2013-10-01

    Understanding the variability of marine biodiversity is a central issue in microbiology. Current observational programs are based on in situ studies, but their implementation at the global scale is particularly challenging, owing to the ocean extent, its temporal variability and the heterogeneity of the data sources on which compilations are built. Here, we explore the possibility of identifying phytoplanktonic biodiversity hotspots from satellite. We define a Shannon entropy index based on patchiness in ocean color bio-optical anomalies. This index provides a high resolution (1 degree) global coverage. It shows a relation to temperature and mid-latitude maxima in accordance with those previously evidenced in microbiological biodiversity model and observational studies. Regional maxima are in remarkable agreement with several known biodiversity hotspots for plankton organisms and even for higher levels of the marine trophic chain, as well as with some in situ planktonic biodiversity estimates (from Atlantic Meridional Transect cruise). These results encourage to explore marine biodiversity with a coordinated effort of the molecular, ecological and remote sensing communities.

  4. What, When, Where, and Why of Secondary Hawaiian Hotspot Volcanism

    Science.gov (United States)

    Garcia, M. O.; Ito, G.; Applegate, B.; Weis, D.; Swinnard, L.; Flinders, A.; Hanano, D.; Nobre-Silva, I.; Bianco, T.; Naumann, T.; Geist, D.; Blay, C.; Sciaroni, L.; Maerschalk, C.; Harpp, K.; Christensen, B.

    2007-12-01

    Secondary hotspot volcanism occurs on most oceanic island groups (Hawaii, Canary, Society) but its origins remain enigmatic. A 28-day marine expedition used multibeam bathymetry and acoustic imagery to map the extent of submarine volcanic fields around the northern Hawaiian Islands (Kauai, Niihau and Kaula), and the JASON2 ROV to sample many volcanoes to characterize the petrology, geochemistry (major and trace elements, and isotopes) and ages of the lavas from these volcanoes. Our integrated geological, geochemical and geophysical study attempts to examine the what (compositions and source), where (distribution and volumes), when (ages), and why (mechanisms) of secondary volcanism on and around the northern Hawaiian Islands. A first-order objective was to establish how the submarine volcanism relates in space, time, volume, and composition to the nearby shield volcanoes and their associated onshore secondary volcanism. Our surveying and sampling revealed major fields of submarine volcanoes extending from the shallow slopes of these islands to more than 100 km offshore. These discoveries dramatically expand the volumetric importance, distribution and geodynamic framework for Hawaiian secondary volcanism. New maps and rock petrology on the samples collected will be used to evaluate currently proposed mechanisms for secondary volcanism and to consider new models such as small-scale mantle convection driven by thermal and melt-induced buoyancy to produce the huge volume of newly discovered lava. Our results seem to indicate substantial revisions are needed to our current perceptions of hotspot dynamics for Hawaii and possibly elsewhere.

  5. Hot-Spot Ignition Mechanisms for Explosives and Propellants

    Science.gov (United States)

    Field, J. E.; Bourne, N. K.; Palmer, S. J. P.; Walley, S. M.

    1992-05-01

    This paper describes the response of explosives to stress and impact and in particular the mechanisms of `hot-spot' production. Samples in the form of single crystals, powder layers, pressed pellets, gels, polymer bonded explosives (PBXs) and propellants have been studied. Techniques used include a drop-weight facility with transparent anvils which allows photography at microsecond framing intervals, an instrumented drop-weight machine, a miniaturized Hopkinson bar system for high strain rate property measurement, laser speckle for studying the deformation and fracture of PBXs, an automated system for analysing speckle patterns and heat sensitive film for recording the positions and temperatures of hot spots. Polishing and staining methods have been developed to observe the microstructure of PBXs and failure during quasi-static loading. Ignition, when it occurred, took place at local hot-spot sites. Evidence is discussed for a variety of ignition mechanisms including adiabatic shear of the explosive, adiabatic heating of trapped gases during cavity collapse, viscous flow, friction, fracture and shear of added particles and triboluminescent discharge.

  6. Biodiversity hotspots: A shortcut for a more complicated concept

    Directory of Open Access Journals (Sweden)

    Christian Marchese

    2015-01-01

    Full Text Available In an era of human activities, global environmental changes, habitat loss and species extinction, conservation strategies are a crucial step toward minimizing biodiversity loss. For instance, oceans acidification and land use are intensifying in many places with negative and often irreversible consequences for biodiversity. Biodiversity hotspots, despite some criticism, have become a tool for setting conservation priorities and play an important role in decision-making for cost-effective strategies to preserve biodiversity in terrestrial and, to some extent, marine ecosystems. This area-based approach can be applied to any geographical scale and it is considered to be one of the best approaches for maintaining a large proportion of the world’s biological diversity. However, delineating hotspots includes quantitative criteria along with subjective considerations and the risk is to neglect areas, such as coldspots, with other types of conservation value. Nowadays, it is widely acknowledged that biodiversity is much more than just the number of species in a region and a conservation strategy cannot be based merely on the number of taxa present in an ecosystem. Therefore, the idea that strongly emerges is the need to reconsider conservation priorities and to go toward an interdisciplinary approach through the creation of science-policy partnerships.

  7. The prevalence of toxic hotspots in former Soviet countries

    International Nuclear Information System (INIS)

    Sharov, Petr; Dowling, Russell; Gogishvili, Megi; Jones, Barbara; Caravanos, Jack; McCartor, Andrew; Kashdan, Zachary; Fuller, Richard

    2016-01-01

    Using a global database of contaminated sites, toxic hotspots in eight former Soviet countries were analyzed to identify the prevalence, types and sources of toxic pollution, as well as their associated potential public health impacts. For this analysis, polluted sites in Armenia, Azerbaijan, Kazakhstan, Kyrgyzstan, Russia, Tajikistan, Ukraine, and Uzbekistan were compiled and analyzed. The levels of contamination of seven key pollutants were assessed in each country. 424 contaminated sites were identified using data from Blacksmith Institute. Pesticides, lead (Pb), radioactive metals, arsenic (As), mercury (Hg), chromium (Cr), and cadmium (Cd) were the most commonly identified key pollutants. Collectively, these sites pose health risks to an estimated 6.2 million residents. The existing data on toxic hotspots in former Soviet countries likely captures only a small percentage of actual contaminated sites, but suggests potentially severe public health consequences. Additional assessments are needed to understand the risks posed by toxic pollution in the region. - Highlights: • Pollution in 8 former Soviet countries poses a health risk to 6.2 million residents. • The most commonly found key pollutants are pesticides, lead, arsenic, and cadmium. • The majority of sites can be traced to Soviet legacy pollution. - 424 sites were identified in the analysis. Pesticides, Pb, radioactive metals, As, Hg, Cr, and Cd were the most common key pollutants, collectively affecting 6.2 million people.

  8. Lack of visible change around active hotspots on Io

    Science.gov (United States)

    1996-01-01

    Detail of changes around two hotspots on Jupiter's moon Io as seen by Voyager 1 in April 1979 (left) and NASA's Galileo spacecraft on September 7th, 1996 (middle and right). The right frame was created with images from the Galileo Solid State Imaging system's near-infrared (756 nm), green, and violet filters. For better comparison, the middle frame mimics Voyager colors. The calderas at the top and at the lower right of the images correspond to the locations of hotspots detected by the Near Infrared Mapping Spectrometer aboard the Galileo spacecraft during its second orbit. There are no significant morphologic changes around these hot calderas; however, the diffuse red deposits, which are simply dark in the Voyager colors, appear to be associated with recent and/or ongoing volcanic activity. The three calderas range in size from approximately 100 kilometers to approximately 150 kilometers in diameter. The caldera in the lower right of each frame is named Malik. North is to the top of all frames.The Jet Propulsion Laboratory, Pasadena, CA manages the Galileo mission for NASA's Office of Space Science, Washington, DC. JPL is an operating division of California Institute of Technology (Caltech).This image and other images and data received from Galileo are posted on the World Wide Web, on the Galileo mission home page at URL http://galileo.jpl.nasa.gov. Background information and educational context for the images can be found at URL http://www.jpl.nasa.gov/galileo/sepo

  9. Are splash plumes the origin of minor hotspots?

    Science.gov (United States)

    Davies, J. H.; Bunge, H.-P.

    2006-05-01

    It has been claimed that focused hot cylindrical upwelling plumes cause many of the surface volcanic hotspots on Earth. It has also been argued that they must originate from thermal boundary layers. In this paper, we present spherical simulations of mantle circulation at close to Earth-like vigor with significant internal heating. These show, in addition to thermal boundary layer plumes, a new class of plumes that are not rooted in thermal boundary layers. These plumes develop as instabilities from the edge of bowls of hot mantle, which are produced by cold downwelling material deforming hot sheets of mantle. The resulting bowl and plume structure can look a bit like the “splash” of a water droplet. These splash plumes might provide an explanation for some hotspots that are not underlain by thermal boundary layer sourced plumes and not initiated by large igneous provinces. We suggest that in Earth's mantle, lithospheric instabilities or small pieces of subducting slab could play the role of the model downwelling material in initiating splash plumes. Splash plumes would have implications for interpreting ocean-island basalt geochemistry, plume fixity, excess plume temperature, and estimating core heat flux. Improved seismic imaging will ultimately test this hypothesis.

  10. Chronic kidney disease hotspots in developing countries in South Asia.

    Science.gov (United States)

    Abraham, Georgi; Varughese, Santosh; Thandavan, Thiagarajan; Iyengar, Arpana; Fernando, Edwin; Naqvi, S A Jaffar; Sheriff, Rezvi; Ur-Rashid, Harun; Gopalakrishnan, Natarajan; Kafle, Rishi Kumar

    2016-02-01

    In many developing countries in the South Asian region, screening for chronic diseases in the community has shown a widely varying prevalence. However, certain geographical regions have shown a high prevalence of chronic kidney disease (CKD) of unknown etiology. This predominantly affects the young and middle-aged population with a lower socioeconomic status. Here, we describe the hotspots of CKD of undiagnosed etiology in South Asian countries including the North, Central and Eastern provinces of Sri Lanka and the coastal region of the state of Andhra Pradesh in India. Screening of these populations has revealed cases of CKD in various stages. Race has also been shown to be a factor, with a much lower prevalence of CKD in whites compared to Asians, which could be related to the known influence of ethnicity on CKD development as well as environmental factors. The difference between developed and developing nations is most stark in the realm of healthcare, which translates into CKD hotspots in many regions of South Asian countries. Additionally, the burden of CKD stage G5 remains unknown due to the lack of registry reports, poor access to healthcare and lack of an organized chronic disease management program. The population receiving various forms of renal replacement therapy has dramatically increased in the last decade due to better access to point of care, despite the disproportionate increase in nephrology manpower. In this article we will discuss the nephrology care provided in various countries in South Asia, including India, Bangladesh, Pakistan, Nepal, Bhutan, Sri Lanka and Afghanistan.

  11. Tectonics, climate, and the rise and demise of continental aquatic species richness hotspots.

    Science.gov (United States)

    Neubauer, Thomas A; Harzhauser, Mathias; Georgopoulou, Elisavet; Kroh, Andreas; Mandic, Oleg

    2015-09-15

    Continental aquatic species richness hotspots are unevenly distributed across the planet. In present-day Europe, only two centers of biodiversity exist (Lake Ohrid on the Balkans and the Caspian Sea). During the Neogene, a wide variety of hotspots developed in a series of long-lived lakes. The mechanisms underlying the presence of richness hotspots in different geological periods have not been properly examined thus far. Based on Miocene to Recent gastropod distributions, we show that the existence and evolution of such hotspots in inland-water systems are tightly linked to the geodynamic history of the European continent. Both past and present hotspots are related to the formation and persistence of long-lived lake systems in geological basins or to isolation of existing inland basins and embayments from the marine realm. The faunal evolution within hotspots highly depends on warm climates and surface area. During the Quaternary icehouse climate and extensive glaciations, limnic biodiversity sustained a severe decline across the continent and most former hotspots disappeared. The Recent gastropod distribution is mainly a geologically young pattern formed after the Last Glacial Maximum (19 ky) and subsequent formation of postglacial lakes. The major hotspots today are related to long-lived lakes in preglacially formed, permanently subsiding geological basins.

  12. Biodiversity hotspots on the Dutch Continental Shelf: a marine strategy framework directive perspective

    NARCIS (Netherlands)

    Bos, O.G.; Witbaard, R.; Lavaleye, M.S.S.; Moorsel, G.W.N.M.; Teal, L.R.; Hal, van R.; Hammen, van der T.; Hofstede, ter R.; Bemmelen, van R.S.A.; Witte, R.H.; Geelhoed, S.C.V.; Dijkman, E.M.

    2011-01-01

    This report presenst hotspots of biodiversity for benthos, fish, birds, marine mammals and habitats on the Dutch Continental Shelf. These hotspots are based on a spatial application of biodiversity metrics developed in this study for the GES(Good Environmental Status)-descriptor 1 ‘Biological

  13. Hotspots in trauma memories and their relationship to successful trauma-focused psychotherapy: a pilot study.

    Science.gov (United States)

    Nijdam, Mirjam J; Baas, Melanie A M; Olff, Miranda; Gersons, Berthold P R

    2013-02-01

    Imaginal exposure is an essential element of trauma-focused psychotherapies for posttraumatic stress disorder (PTSD). Exposure should in particular focus on the "hotspots," the parts of trauma memories that cause high levels of emotional distress which are often reexperienced. Our aim was to investigate whether differences in the focus on hotspots differentiate between successful and unsuccessful trauma-focused psychotherapies. As part of a randomized trial, 45 PTSD patients completed brief eclectic psychotherapy for PTSD. We retrospectively assessed audio recordings of therapy sessions of 20 patients. Frequency of hotspots and the associated emotions, cognitions, and characteristics were compared for the most successful (n = 10) versus the least successful (n = 10) treatments. The mean number of unique hotspots per patient was 3.20, and this number did not differ between successful and unsuccessful treatments. In successful treatments, however, hotspots were more frequently addressed (r = .48), and they were accompanied by more characteristics of hotspots (r = .39), such as an audible change in affect, indicating medium- to large-sized effects. Repeatedly focusing on hotspots and looking for associated characteristics of hotspots may help clinicians to enhance the efficacy of imaginal exposure for patients who would otherwise show insufficient response to treatment. Copyright © 2013 International Society for Traumatic Stress Studies.

  14. Rare Disease Video Portal

    OpenAIRE

    Sánchez Bocanegra, Carlos Luis

    2011-01-01

    Rare Disease Video Portal (RD Video) is a portal web where contains videos from Youtube including all details from 12 channels of Youtube. Rare Disease Video Portal (RD Video) es un portal web que contiene los vídeos de Youtube incluyendo todos los detalles de 12 canales de Youtube. Rare Disease Video Portal (RD Video) és un portal web que conté els vídeos de Youtube i que inclou tots els detalls de 12 Canals de Youtube.

  15. Rare earth germanates

    International Nuclear Information System (INIS)

    Bondar', I.A.; Vinogradova, N.V.; Dem'yanets, L.N.

    1983-01-01

    From the viewpoint of structural chemistry and general regularities controlling formation reactions of compounds and phases in melts, solid and gaseous states, recent achievements in the chemistry of rare earth germanates are generalized. Methods of synthesizing germanates, systems on the base of germanium oxides and rare earths are considered. The data on crystallochemical characteristics are tabulated. Individual compounds of scandium germanate are also characterized. Processes of germanate formation using the data of IR-spectroscopy, X-ray phase analysis are studied. The structure and morphotropic series of rare earth germanates and silicates are determined. Fields of their present and possible future application are considered

  16. Paleo-drainage basin connectivity predicts evolutionary relationships across three Southeast Asian biodiversity hotspots.

    Science.gov (United States)

    de Bruyn, Mark; Rüber, Lukas; Nylinder, Stephan; Stelbrink, Björn; Lovejoy, Nathan R; Lavoué, Sébastien; Tan, Heok Hui; Nugroho, Estu; Wowor, Daisy; Ng, Peter K L; Siti Azizah, M N; Von Rintelen, Thomas; Hall, Robert; Carvalho, Gary R

    2013-05-01

    Understanding factors driving diversity across biodiversity hotspots is critical for formulating conservation priorities in the face of ongoing and escalating environmental deterioration. While biodiversity hotspots encompass a small fraction of Earth's land surface, more than half the world's plants and two-thirds of terrestrial vertebrate species are endemic to these hotspots. Tropical Southeast (SE) Asia displays extraordinary species richness, encompassing four biodiversity hotspots, though disentangling multiple potential drivers of species richness is confounded by the region's dynamic geological and climatic history. Here, we use multilocus molecular genetic data from dense multispecies sampling of freshwater fishes across three biodiversity hotspots, to test the effect of Quaternary climate change and resulting drainage rearrangements on aquatic faunal diversification. While Cenozoic geological processes have clearly shaped evolutionary history in SE Asian halfbeak fishes, we show that paleo-drainage re-arrangements resulting from Quaternary climate change played a significant role in the spatiotemporal evolution of lowland aquatic taxa, and provide priorities for conservation efforts.

  17. Peptides identify multiple hotspots within the ligand binding domain of the TNF receptor 2

    Directory of Open Access Journals (Sweden)

    Lennick Michael

    2003-01-01

    Full Text Available Abstract Background Hotspots are defined as the minimal functional domains involved in protein:protein interactions and sufficient to induce a biological response. Results Here we describe the use of complex and high diversity phage display libraries to isolate peptides (called Hotspot Ligands or HSPLs which sub-divide the ligand binding domain of the tumor necrosis factor receptor 2 (TNFR2; p75 into multiple hotspots. We have shown that these libraries could generate HSPLs which not only subdivide hotspots on protein and non-protein targets but act as agonists or antagonists. Using this approach, we generated peptides which were specific for human TNFR2, could be competed by the natural ligands, TNFα and TNFβ and induced an unexpected biological response in a TNFR2-specific manner. Conclusions To our knowledge, this is the first report describing the dissection of the TNFR2 into biologically active hotspots with the concomitant identification of a novel and unexpected biological activity.

  18. Diagnostic for determining the mix in inertial confinement fusion capsule hotspot

    Energy Technology Data Exchange (ETDEWEB)

    He, Shibei; Ding, Yongkun, E-mail: ding-yk@vip.sina.com; Miao, Wenyong; Zhang, Xing; Tu, Shaoyong; Yuan, Yongteng; Pu, Yudong; Yan, Ji; Wei, Minxi; Yin, Chuansheng [Research Center of Laser Fusion, China Academy of Engineering Physics, Mianyang 621900 (China)

    2016-07-15

    A diagnostic is developed for determining the hotspot mix in inertial confinement fusion experiments. A multi-channel pinhole camera measures Bremsstrahlung emissions from implosion capsules ranging from 6 keV to 30 keV and records an image of the hotspot. Meanwhile, a planar crystal spectrometer measures Ar line emissions used to deduce the electron density of the hotspot. An X-ray streaked camera records the burn duration. With the Bremsstrahlung spectrum, electron density, hotspot volume, and burn duration, the mix quantity is determined by solving a pair of linear equations. This inferred mix amount has an uncertainty due to the uncertainty of the electron density, but with the help of the measured neutron product, the most likely mix quantity value can be determined. This technique is applied to experimental images to infer the quantity of CH ablator mix into the hotspot.

  19. Diagnostic for determining the mix in inertial confinement fusion capsule hotspot

    International Nuclear Information System (INIS)

    He, Shibei; Ding, Yongkun; Miao, Wenyong; Zhang, Xing; Tu, Shaoyong; Yuan, Yongteng; Pu, Yudong; Yan, Ji; Wei, Minxi; Yin, Chuansheng

    2016-01-01

    A diagnostic is developed for determining the hotspot mix in inertial confinement fusion experiments. A multi-channel pinhole camera measures Bremsstrahlung emissions from implosion capsules ranging from 6 keV to 30 keV and records an image of the hotspot. Meanwhile, a planar crystal spectrometer measures Ar line emissions used to deduce the electron density of the hotspot. An X-ray streaked camera records the burn duration. With the Bremsstrahlung spectrum, electron density, hotspot volume, and burn duration, the mix quantity is determined by solving a pair of linear equations. This inferred mix amount has an uncertainty due to the uncertainty of the electron density, but with the help of the measured neutron product, the most likely mix quantity value can be determined. This technique is applied to experimental images to infer the quantity of CH ablator mix into the hotspot.

  20. Extreme genomes

    OpenAIRE

    DeLong, Edward F

    2000-01-01

    The complete genome sequence of Thermoplasma acidophilum, an acid- and heat-loving archaeon, has recently been reported. Comparative genomic analysis of this 'extremophile' is providing new insights into the metabolic machinery, ecology and evolution of thermophilic archaea.

  1. Analysis of rare categories

    CERN Document Server

    He, Jingrui

    2012-01-01

    This book focuses on rare category analysis where the majority classes have smooth distributions and the minority classes exhibit the compactness property. It focuses on challenging cases where the support regions of the majority and minority classes overlap.

  2. The characterization of twenty sequenced human genomes.

    Directory of Open Access Journals (Sweden)

    Kimberly Pelak

    2010-09-01

    Full Text Available We present the analysis of twenty human genomes to evaluate the prospects for identifying rare functional variants that contribute to a phenotype of interest. We sequenced at high coverage ten "case" genomes from individuals with severe hemophilia A and ten "control" genomes. We summarize the number of genetic variants emerging from a study of this magnitude, and provide a proof of concept for the identification of rare and highly-penetrant functional variants by confirming that the cause of hemophilia A is easily recognizable in this data set. We also show that the number of novel single nucleotide variants (SNVs discovered per genome seems to stabilize at about 144,000 new variants per genome, after the first 15 individuals have been sequenced. Finally, we find that, on average, each genome carries 165 homozygous protein-truncating or stop loss variants in genes representing a diverse set of pathways.

  3. SYMPOSIUM: Rare decays

    Energy Technology Data Exchange (ETDEWEB)

    Anon.

    1989-04-15

    Late last year, a symposium entitled 'Rare Decays' attracted 115 participants to a hotel in Vancouver, Canada. These participants were particle physicists interested in checking conventional selection rules to look for clues of possible new behaviour outside today's accepted 'Standard Model'. For physicists, 'rare decays' include processes that have so far not been seen, explicitly forbidden by the rules of the Standard Model, or processes highly suppressed because the decay is dominated by an easier route, or includes processes resulting from multiple transitions.

  4. Grass genomes

    OpenAIRE

    Bennetzen, Jeffrey L.; SanMiguel, Phillip; Chen, Mingsheng; Tikhonov, Alexander; Francki, Michael; Avramova, Zoya

    1998-01-01

    For the most part, studies of grass genome structure have been limited to the generation of whole-genome genetic maps or the fine structure and sequence analysis of single genes or gene clusters. We have investigated large contiguous segments of the genomes of maize, sorghum, and rice, primarily focusing on intergenic spaces. Our data indicate that much (>50%) of the maize genome is composed of interspersed repetitive DNAs, primarily nested retrotransposons that in...

  5. Cancer genomics

    DEFF Research Database (Denmark)

    Norrild, Bodil; Guldberg, Per; Ralfkiær, Elisabeth Methner

    2007-01-01

    Almost all cells in the human body contain a complete copy of the genome with an estimated number of 25,000 genes. The sequences of these genes make up about three percent of the genome and comprise the inherited set of genetic information. The genome also contains information that determines whe...

  6. The Snake River Plain Volcanic Province: Insights from Project Hotspot

    Science.gov (United States)

    Shervais, J. W.; Potter, K. E.; Hanan, B. B.; Jean, M. M.; Duncan, R. A.; Champion, D. E.; Vetter, S.; Glen, J. M. G.; Christiansen, E. H.; Miggins, D. P.; Nielson, D. L.

    2017-12-01

    The Snake River Plain (SRP) Volcanic Province is the best modern example of a time-transgressive hotspot track beneath continental crust. The SRP began 17 Ma with massive eruptions of Columbia River basalt and rhyolite. After 12 Ma volcanism progressed towards Yellowstone, with early rhyolite overlain by basalts that may exceed 2 km thick. The early rhyolites are anorogenic with dry phenocryst assemblages and eruption temperatures up to 950C. Tholeiitic basalts have major and trace element compositions similar to ocean island basalts (OIB). Project Hotspot cored three deep holes in the central and western Snake River Plain: Kimama (mostly basalt), Kimberly (mostly rhyolite), and Mountain Home (lake sediments and basaslt). The Kimberly core documents rhyolite ash flows up to 700 m thick, possibly filling a caldera or sag. Chemical stratigraphy in Kimama and other basalt cores document fractional crystallization in relatively shallow magma chambers with episodic magma recharge. Age-depth relations in the Kimama core suggest accumulation rates of roughly 305 m/Ma. Surface and subsurface basalt flows show systematic variations in Sr-Nd-Pb isotopes with distance from Yellowstone interpreted to reflect changes in the proportion of plume source and the underlying heterogeneous cratonic lithosphere, which varies in age, composition, and thickness from west to east. Sr-Nd-Pb isotopes suggest <5% lithospheric input into a system dominated by OIB-like plume-derived basalts. A major flare-up of basaltic volcanism occurred 75-780 ka throughout the entire SRP, from Yellowstone in the east to Boise in the west. The youngest western SRP basalts are transitional alkali basalts that range in age from circa 900 ka to 2 ka, with trace element and isotopic compositions similar to the plume component of Hawaiian basalts. These observations suggest that ancient SCLM was replaced by plume mantle after the North America passed over the hotspot in the western SRP, which triggered renewed

  7. A novel Bayesian hierarchical model for road safety hotspot prediction.

    Science.gov (United States)

    Fawcett, Lee; Thorpe, Neil; Matthews, Joseph; Kremer, Karsten

    2017-02-01

    In this paper, we propose a Bayesian hierarchical model for predicting accident counts in future years at sites within a pool of potential road safety hotspots. The aim is to inform road safety practitioners of the location of likely future hotspots to enable a proactive, rather than reactive, approach to road safety scheme implementation. A feature of our model is the ability to rank sites according to their potential to exceed, in some future time period, a threshold accident count which may be used as a criterion for scheme implementation. Our model specification enables the classical empirical Bayes formulation - commonly used in before-and-after studies, wherein accident counts from a single before period are used to estimate counterfactual counts in the after period - to be extended to incorporate counts from multiple time periods. This allows site-specific variations in historical accident counts (e.g. locally-observed trends) to offset estimates of safety generated by a global accident prediction model (APM), which itself is used to help account for the effects of global trend and regression-to-mean (RTM). The Bayesian posterior predictive distribution is exploited to formulate predictions and to properly quantify our uncertainty in these predictions. The main contributions of our model include (i) the ability to allow accident counts from multiple time-points to inform predictions, with counts in more recent years lending more weight to predictions than counts from time-points further in the past; (ii) where appropriate, the ability to offset global estimates of trend by variations in accident counts observed locally, at a site-specific level; and (iii) the ability to account for unknown/unobserved site-specific factors which may affect accident counts. We illustrate our model with an application to accident counts at 734 potential hotspots in the German city of Halle; we also propose some simple diagnostics to validate the predictive capability of our

  8. Genomic alterations detected by comparative genomic hybridization in ovarian endometriomas

    Directory of Open Access Journals (Sweden)

    L.C. Veiga-Castelli

    2010-08-01

    Full Text Available Endometriosis is a complex and multifactorial disease. Chromosomal imbalance screening in endometriotic tissue can be used to detect hot-spot regions in the search for a possible genetic marker for endometriosis. The objective of the present study was to detect chromosomal imbalances by comparative genomic hybridization (CGH in ectopic tissue samples from ovarian endometriomas and eutopic tissue from the same patients. We evaluated 10 ovarian endometriotic tissues and 10 eutopic endometrial tissues by metaphase CGH. CGH was prepared with normal and test DNA enzymatically digested, ligated to adaptors and amplified by PCR. A second PCR was performed for DNA labeling. Equal amounts of both normal and test-labeled DNA were hybridized in human normal metaphases. The Isis FISH Imaging System V 5.0 software was used for chromosome analysis. In both eutopic and ectopic groups, 4/10 samples presented chromosomal alterations, mainly chromosomal gains. CGH identified 11q12.3-q13.1, 17p11.1-p12, 17q25.3-qter, and 19p as critical regions. Genomic imbalances in 11q, 17p, 17q, and 19p were detected in normal eutopic and/or ectopic endometrium from women with ovarian endometriosis. These regions contain genes such as POLR2G, MXRA7 and UBA52 involved in biological processes that may lead to the establishment and maintenance of endometriotic implants. This genomic imbalance may affect genes in which dysregulation impacts both eutopic and ectopic endometrium.

  9. Hotspots in clinical management of severe liver diseases

    Directory of Open Access Journals (Sweden)

    LYU Jiayu

    2017-09-01

    Full Text Available Severe liver diseases such as liver failure and acute decompensated cirrhosis have critical conditions and high mortality rates, and the prognosis of such patients is closely associated with early warning, timely dynamic assessment, and comprehensive and effective therapy. The patients require a series of effective clinical management measures for elimination of causative factors, organ support, and prevention and treatment of complications. Medical treatment-artificial liver-liver transplantation is an important modality for severe liver diseases. Granulocyte colony-stimulating factor, stem cell therapy, and bioartificial liver have a promising future, while there are still controversies over non-selective β-blocker. This article reviews the hotspots in the clinical management of severe liver diseases.

  10. Future of endemic flora of biodiversity hotspots in India.

    Directory of Open Access Journals (Sweden)

    Vishwas Sudhir Chitale

    Full Text Available India is one of the 12 mega biodiversity countries of the world, which represents 11% of world's flora in about 2.4% of global land mass. Approximately 28% of the total Indian flora and 33% of angiosperms occurring in India are endemic. Higher human population density in biodiversity hotspots in India puts undue pressure on these sensitive eco-regions. In the present study, we predict the future distribution of 637 endemic plant species from three biodiversity hotspots in India; Himalaya, Western Ghats, Indo-Burma, based on A1B scenario for year 2050 and 2080. We develop individual variable based models as well as mixed models in MaxEnt by combining ten least co-related bioclimatic variables, two disturbance variables and one physiography variable as predictor variables. The projected changes suggest that the endemic flora will be adversely impacted, even under such a moderate climate scenario. The future distribution is predicted to shift in northern and north-eastern direction in Himalaya and Indo-Burma, while in southern and south-western direction in Western Ghats, due to cooler climatic conditions in these regions. In the future distribution of endemic plants, we observe a significant shift and reduction in the distribution range compared to the present distribution. The model predicts a 23.99% range reduction and a 7.70% range expansion in future distribution by 2050, while a 41.34% range reduction and a 24.10% range expansion by 2080. Integration of disturbance and physiography variables along with bioclimatic variables in the models improved the prediction accuracy. Mixed models provide most accurate results for most of the combinations of climatic and non-climatic variables as compared to individual variable based models. We conclude that a regions with cooler climates and higher moisture availability could serve as refugia for endemic plants in future climatic conditions; b mixed models provide more accurate results, compared to single

  11. Population growth, human development, and deforestation in biodiversity hotspots.

    Science.gov (United States)

    Jha, S; Bawa, K S

    2006-06-01

    Human population and development activities affect the rate of deforestation in biodiversity hotspots. We quantified the effect of human population growth and development on rates of deforestation and analyzed the relationship between these causal factors in the 1980s and 1990s. We compared the averages of population growth, human development index (HDI, which measures income, health, and education), and deforestation rate and computed correlations among these variables for countries that contain biodiversity hotspots. When population growth was high and HDI was low there was a high rate of deforestation, but when HDI was high, rate of deforestation was low, despite high population growth. The correlation among variables was significant for the 1990s but not for the 1980s. The relationship between population growth and HDI had a regional pattern that reflected the historical process of development. Based on the changes in HDI and deforestation rate over time, we identified two drivers of deforestation: policy choice and human-development constraints. Policy choices that disregard conservation may cause the loss of forests even in countries that are relatively developed. Lack of development in other countries, on the other hand, may increase the pressure on forests to meet the basic needs of the human population. Deforestation resulting from policy choices may be easier to fix than deforestation arising from human development constraints. To prevent deforestation in the countries that have such constraints, transfer of material and intellectual resources from developed countries may be needed. Popular interest in sustainable development in developed countries can facilitate the transfer of these resources.

  12. Future of endemic flora of biodiversity hotspots in India.

    Science.gov (United States)

    Chitale, Vishwas Sudhir; Behera, Mukund Dev; Roy, Partha Sarthi

    2014-01-01

    India is one of the 12 mega biodiversity countries of the world, which represents 11% of world's flora in about 2.4% of global land mass. Approximately 28% of the total Indian flora and 33% of angiosperms occurring in India are endemic. Higher human population density in biodiversity hotspots in India puts undue pressure on these sensitive eco-regions. In the present study, we predict the future distribution of 637 endemic plant species from three biodiversity hotspots in India; Himalaya, Western Ghats, Indo-Burma, based on A1B scenario for year 2050 and 2080. We develop individual variable based models as well as mixed models in MaxEnt by combining ten least co-related bioclimatic variables, two disturbance variables and one physiography variable as predictor variables. The projected changes suggest that the endemic flora will be adversely impacted, even under such a moderate climate scenario. The future distribution is predicted to shift in northern and north-eastern direction in Himalaya and Indo-Burma, while in southern and south-western direction in Western Ghats, due to cooler climatic conditions in these regions. In the future distribution of endemic plants, we observe a significant shift and reduction in the distribution range compared to the present distribution. The model predicts a 23.99% range reduction and a 7.70% range expansion in future distribution by 2050, while a 41.34% range reduction and a 24.10% range expansion by 2080. Integration of disturbance and physiography variables along with bioclimatic variables in the models improved the prediction accuracy. Mixed models provide most accurate results for most of the combinations of climatic and non-climatic variables as compared to individual variable based models. We conclude that a) regions with cooler climates and higher moisture availability could serve as refugia for endemic plants in future climatic conditions; b) mixed models provide more accurate results, compared to single variable based

  13. Hotspots, Lifelines, and the Safrr Haywired Earthquake Sequence

    Science.gov (United States)

    Ratliff, J. L.; Porter, K.

    2014-12-01

    Though California has experienced many large earthquakes (San Francisco, 1906; Loma Prieta, 1989; Northridge, 1994), the San Francisco Bay Area has not had a damaging earthquake for 25 years. Earthquake risk and surging reliance on smartphones and the Internet to handle everyday tasks raise the question: is an increasingly technology-reliant Bay Area prepared for potential infrastructure impacts caused by a major earthquake? How will a major earthquake on the Hayward Fault affect lifelines (roads, power, water, communication, etc.)? The U.S. Geological Survey Science Application for Risk Reduction (SAFRR) program's Haywired disaster scenario, a hypothetical two-year earthquake sequence triggered by a M7.05 mainshock on the Hayward Fault, addresses these and other questions. We explore four geographic aspects of lifeline damage from earthquakes: (1) geographic lifeline concentrations, (2) areas where lifelines pass through high shaking or potential ground-failure zones, (3) areas with diminished lifeline service demand due to severe building damage, and (4) areas with increased lifeline service demand due to displaced residents and businesses. Potential mainshock lifeline vulnerability and spatial demand changes will be discerned by superimposing earthquake shaking, liquefaction probability, and landslide probability damage thresholds with lifeline concentrations and with large-capacity shelters. Intersecting high hazard levels and lifeline clusters represent potential lifeline susceptibility hotspots. We will also analyze possible temporal vulnerability and demand changes using an aftershock shaking threshold. The results of this analysis will inform regional lifeline resilience initiatives and response and recovery planning, as well as reveal potential redundancies and weaknesses for Bay Area lifelines. Identified spatial and temporal hotspots can provide stakeholders with a reference for possible systemic vulnerability resulting from an earthquake sequence.

  14. Ecohydrological Interfaces as Dynamic Hotspots of Biogeochemical Cycling

    Science.gov (United States)

    Krause, Stefan; Lewandowski, Joerg; Hannah, David; McDonald, Karlie; Folegot, Silvia; Baranov, Victor

    2016-04-01

    Ecohydrological interfaces, represent the boundaries between water-dependent ecosystems that can alter substantially the fluxes of energy and matter. There is still a critical gap of understanding the organisational principles of the drivers and controls of spatially and temporally variable ecohydrological interface functions. This knowledge gap limits our capacity to efficiently quantify, predict and manage the services provided by complex ecosystems. Many ecohydrological interfaces are characterized by step changes in microbial metabolic activity, steep redox gradients and often even thermodynamic phase shifts, for instance at the interfaces between atmosphere and water or soil matrix and macro-pores interfaces. This paper integrates investigations from point scale laboratory microcosm experiments with reach and subcatchment scale tracer experiments and numerical modeling studies to elaborate similarities in the drivers and controls that constitute the enhanced biogeochemical activity of different types of ecohydrologica interfaces across a range of spatial and temporal scales. We therefore combine smart metabolic activity tracers to quantify the impact of bioturbating benthic fauna onto ecosystem respiration and oxygen consumption and investigate at larger scale, how microbial metabolic activity and carbon turnover at the water-sediment interface are controlled by sediment physical and chemical properties as well as water temperatures. Numerical modeling confirmed that experimentally identified hotspots of streambed biogeochemical cycling were controlled by patterns of physical properties such as hydraulic conductivities or bioavailability of organic matter, impacting on residence time distributions and hence reaction times. In contrast to previous research, our investigations thus confirmed that small-scale variability of physical and chemical interface properties had a major impact on biogeochemical processing at the investigated ecohydrological interfaces

  15. Rare earths and actinides

    International Nuclear Information System (INIS)

    Coqblin, B.

    1982-01-01

    This paper reviews the different properties of rare-earths and actinides, either as pure metals or as in alloys or compounds. Three different cases are considered: (i) First, in the case of 'normal' rare-earths which are characterized by a valence of 3, we discuss essentially the magnetic ordering, the coexistence between superconductivity and magnetism and the properties of amorphous rare-earth systems. (ii) Second, in the case of 'anomalous' rare-earths, we distinguish between either 'intermediate-valence' systems or 'Kondo' systems. Special emphasis is given to the problems of the 'Kondo lattice' (for compounds such as CeAl 2 ,CeAl 3 or CeB 6 ) or the 'Anderson lattice' (for compounds such as TmSe). The problem of neutron diffraction in these systems is also discussed. (iii) Third, in the case of actinides, we can separate between the d-f hybridized and almost magnetic metals at the beginning of the series and the rare-earth like the metals after americium. (orig.)

  16. Advanced in-production hotspot prediction and monitoring with micro-topography

    Science.gov (United States)

    Fanton, P.; Hasan, T.; Lakcher, A.; Le-Gratiet, B.; Prentice, C.; Simiz, J.-G.; La Greca, R.; Depre, L.; Hunsche, S.

    2017-03-01

    At 28nm technology node and below, hot spot prediction and process window control across production wafers have become increasingly critical to prevent hotspots from becoming yield-limiting defects. We previously established proof of concept for a systematic approach to identify the most critical pattern locations, i.e. hotspots, in a reticle layout by computational lithography and combining process window characteristics of these patterns with across-wafer process variation data to predict where hotspots may become yield impacting defects [1,2]. The current paper establishes the impact of micro-topography on a 28nm metal layer, and its correlation with hotspot best focus variations across a production chip layout. Detailed topography measurements are obtained from an offline tool, and pattern-dependent best focus (BF) shifts are determined from litho simulations that include mask-3D effects. We also establish hotspot metrology and defect verification by SEM image contour extraction and contour analysis. This enables detection of catastrophic defects as well as quantitative characterization of pattern variability, i.e. local and global CD uniformity, across a wafer to establish hotspot defect and variability maps. Finally, we combine defect prediction and verification capabilities for process monitoring by on-product, guided hotspot metrology, i.e. with sampling locations being determined from the defect prediction model and achieved prediction accuracy (capture rate) around 75%

  17. Hotspots for Nitrogen and Phosphorus Losses from Food Production in China: A County-Scale Analysis.

    Science.gov (United States)

    Wang, Mengru; Ma, Lin; Strokal, Maryna; Ma, Wenqi; Liu, Xuejun; Kroeze, Carolien

    2018-04-27

    Food production in China results in large losses of nitrogen (N) and phosphorus (P) to the environment. Our objective is to identify hotspots for N and P losses to the environment from food production in China at the county scale. To do this, we used the NUFER (Nutrient flows in Food chains, Environment and Resources use) model. Between 1990 and 2012, the hotspot area expanded by a factor of 3 for N, and 24 for P. In 2012 most hotspots were found in the North China Plain. Hotspots covered less than 10% of the Chinese land area, but contributed by more than half to N and P losses to the environment. Direct discharge of animal manure to rivers was an important cause of N and P losses. Food production was found to be more intensive in hotspots than in other counties. Synthetic fertilizer use and animal numbers in hotspots were a factor of 4-5 higher than in other counties in 2012. Also the number of people working in food production and the incomes of farmers are higher in hotspots than in other counties. This study concludes with suggestions for region-specific pollution control technologies for food production in China.

  18. Recombinational hotspot specific to female meiosis in the mouse major histocompatibility complex.

    Science.gov (United States)

    Shiroishi, T; Hanzawa, N; Sagai, T; Ishiura, M; Gojobori, T; Steinmetz, M; Moriwaki, K

    1990-01-01

    The wm7 haplotype of the major histocompatibility complex (MHC), derived from the Japanese wild mouse Mus musculus molossinus, enhances recombination specific to female meiosis in the K/A beta interval of the MHC. We have mapped crossover points of fifteen independent recombinants from genetic crosses of the wm7 and laboratory haplotypes. Most of them were confined to a short segment of approximately 1 kilobase (kb) of DNA between the A beta 3 and A beta 2 genes, indicating the presence of a female-specific recombinational hotspot. Its location overlaps with a sex-independent hotspot previously identified in the Mus musculus castaneus CAS3 haplotype. We have cloned and sequenced DNA fragments surrounding the hotspot from the wm7 haplotype and the corresponding regions from the hotspot-negative B10.A and C57BL/10 strains. There is no significant difference between the sequences of these three strains, or between these and the published sequences of the CAS3 and C57BL/6 strains. However, a comparison of this A beta 3/A beta 2 hotspot with a previously characterized hotspot in the E beta gene revealed that they have a very similar molecular organization. Each hotspot consists of two elements, the consensus sequence of the mouse middle repetitive MT family and the tetrameric repeated sequences, which are separated by 1 kb of DNA.

  19. Prediction of Protein Hotspots from Whole Protein Sequences by a Random Projection Ensemble System

    Directory of Open Access Journals (Sweden)

    Jinjian Jiang

    2017-07-01

    Full Text Available Hotspot residues are important in the determination of protein-protein interactions, and they always perform specific functions in biological processes. The determination of hotspot residues is by the commonly-used method of alanine scanning mutagenesis experiments, which is always costly and time consuming. To address this issue, computational methods have been developed. Most of them are structure based, i.e., using the information of solved protein structures. However, the number of solved protein structures is extremely less than that of sequences. Moreover, almost all of the predictors identified hotspots from the interfaces of protein complexes, seldom from the whole protein sequences. Therefore, determining hotspots from whole protein sequences by sequence information alone is urgent. To address the issue of hotspot predictions from the whole sequences of proteins, we proposed an ensemble system with random projections using statistical physicochemical properties of amino acids. First, an encoding scheme involving sequence profiles of residues and physicochemical properties from the AAindex1 dataset is developed. Then, the random projection technique was adopted to project the encoding instances into a reduced space. Then, several better random projections were obtained by training an IBk classifier based on the training dataset, which were thus applied to the test dataset. The ensemble of random projection classifiers is therefore obtained. Experimental results showed that although the performance of our method is not good enough for real applications of hotspots, it is very promising in the determination of hotspot residues from whole sequences.

  20. Hotspots for Nitrogen and Phosphorus Losses from Food Production in China: A County-Scale Analysis

    Science.gov (United States)

    2018-01-01

    Food production in China results in large losses of nitrogen (N) and phosphorus (P) to the environment. Our objective is to identify hotspots for N and P losses to the environment from food production in China at the county scale. To do this, we used the NUFER (Nutrient flows in Food chains, Environment and Resources use) model. Between 1990 and 2012, the hotspot area expanded by a factor of 3 for N, and 24 for P. In 2012 most hotspots were found in the North China Plain. Hotspots covered less than 10% of the Chinese land area, but contributed by more than half to N and P losses to the environment. Direct discharge of animal manure to rivers was an important cause of N and P losses. Food production was found to be more intensive in hotspots than in other counties. Synthetic fertilizer use and animal numbers in hotspots were a factor of 4–5 higher than in other counties in 2012. Also the number of people working in food production and the incomes of farmers are higher in hotspots than in other counties. This study concludes with suggestions for region-specific pollution control technologies for food production in China. PMID:29671326

  1. A Novel Approach for Identification and Ranking of Road Traffic Accident Hotspots

    Directory of Open Access Journals (Sweden)

    Zahran El-Said M.M.

    2017-01-01

    Full Text Available Road Traffic Accidents (RTA are known to be one of the main causes of fatalities worldwide. One usef ul approach to improve road safety is through the identification of RT A hotspots along a road, so they can be prioritised and treated. This paper introduces an approach based on Geographical Information System (GI S to identify and prioritise RTA hotspots along a road network using historical RTA data. One particular urban road in Brunei with a historically high rate of RT As, Jalan Gadong, was selected as a case study. Five years of historical RTA data were acquired from the relevant authorities and input into a GIS database. GI S analysis was then used to identify the spatial extension of the RT A hotspots. The RT A hotspots were ranked according to three different schemes: frequency, severity and socio-economic impact of RTAs. A composite ranking scheme was also developed to combine these schemes; this enabled the prioritisation and development of intervention and maintenance programmes of the identified RTA hotspots. A visualisation method of the RTA spatial distribution within each identified RTA hotspot was also developed to determine the most risky road stretches within each hotspot, which is important for treatment prioritisation when limited resources are available.

  2. HOTSPOTS DETECTION FROM TRAJECTORY DATA BASED ON SPATIOTEMPORAL DATA FIELD CLUSTERING

    Directory of Open Access Journals (Sweden)

    K. Qin

    2017-09-01

    Full Text Available City hotspots refer to the areas where residents visit frequently, and large traffic flow exist, which reflect the people travel patterns and distribution of urban function area. Taxi trajectory data contain abundant information about urban functions and citizen activities, and extracting interesting city hotspots from them can be of importance in urban planning, traffic command, public travel services etc. To detect city hotspots and discover a variety of changing patterns among them, we introduce a data field-based cluster analysis technique to the pick-up and drop-off points of taxi trajectory data and improve the method by introducing the time weight, which has been normalized to estimate the potential value in data field. Thus, in the light of the new potential function in data field, short distance and short time difference play a powerful role. So the region full of trajectory points, which is regarded as hotspots area, has a higher potential value, while the region with thin trajectory points has a lower potential value. The taxi trajectory data of Wuhan city in China on May 1, 6 and 9, 2015, are taken as the experimental data. From the result, we find the sustaining hotspots area and inconstant hotspots area in Wuhan city based on the spatiotemporal data field method. Further study will focus on optimizing parameter and the interaction among hotspots area.

  3. Monitoring the trajectory of urban nighttime light hotspots using a Gaussian volume model

    Science.gov (United States)

    Zheng, Qiming; Jiang, Ruowei; Wang, Ke; Huang, Lingyan; Ye, Ziran; Gan, Muye; Ji, Biyong

    2018-03-01

    Urban nighttime light hotspot is an ideal representation of the spatial heterogeneity of human activities within a city, which is sensitive to regional urban expansion pattern. However, most of previous studies related to nighttime light imageries focused on extracting urban extent, leaving the spatial variation of radiance intensity insufficiently explored. With the help of global radiance calibrated DMSP-OLS datasets (NTLgrc), we proposed an innovative framework to explore the spatio-temporal trajectory of polycentric urban nighttime light hotspots. Firstly, NTLgrc was inter-annually calibrated to improve the consistency. Secondly, multi-resolution segmentation and region-growing SVM classification were employed to remove blooming effect and to extract potential clusters. At last, the urban hotspots were identified by a Gaussian volume model, and the resulting parameters were used to quantitatively depict hotspot features (i.e., intensity, morphology and centroid dynamics). The result shows that our framework successfully captures hotspots in polycentric urban area, whose Ra2 are over 0.9. Meanwhile, the spatio-temporal dynamics of the hotspot features intuitively reveal the impact of the regional urban growth pattern and planning strategies on human activities. Compared to previous studies, our framework is more robust and offers an effective way to describe hotspot pattern. Also, it provides a more comprehensive and spatial-explicit understanding regarding the interaction between urbanization pattern and human activities. Our findings are expected to be beneficial to governors in term of sustainable urban planning and decision making.

  4. Application of GIS to predict malaria hotspots based on Anopheles arabiensis habitat suitability in Southern Africa

    Science.gov (United States)

    Gwitira, Isaiah; Murwira, Amon; Zengeya, Fadzai M.; Shekede, Munyaradzi Davis

    2018-02-01

    Malaria remains a major public health problem and a principal cause of morbidity and mortality in most developing countries. Although malaria still presents health problems, significant successes have been recorded in reducing deaths resulting from the disease. As malaria transmission continues to decline, control interventions will increasingly depend on the ability to define high-risk areas known as malaria hotspots. Therefore, there is urgent need to use geospatial tools such as geographic information system to detect spatial patterns of malaria and delineate disease hot spots for better planning and management. Thus, accurate mapping and prediction of seasonality of malaria hotspots is an important step towards developing strategies for effective malaria control. In this study, we modelled seasonal malaria hotspots as a function of habitat suitability of Anopheles arabiensis (A. Arabiensis) as a first step towards predicting likely seasonal malaria hotspots that could provide guidance in targeted malaria control. We used Geographical information system (GIS) and spatial statistic methods to identify seasonal hotspots of malaria cases at the country level. In order to achieve this, we first determined the spatial distribution of seasonal malaria hotspots using the Getis Ord Gi* statistic based on confirmed positive malaria cases recorded at health facilities in Zimbabwe over four years (1996-1999). We then used MAXENT technique to model habitat suitability of A. arabiensis from presence data collected from 1990 to 2002 based on bioclimatic variables and altitude. Finally, we used autologistic regression to test the extent to which malaria hotspots can be predicted using A. arabiensis habitat suitability. Our results show that A. arabiensis habitat suitability consistently and significantly (p < 0.05) predicts malaria hotspots from 1996 to 1999. Overall, our results show that malaria hotspots can be predicted using A. arabiensis habitat suitability, suggesting

  5. SYMPOSIUM: Rare decays

    International Nuclear Information System (INIS)

    Anon.

    1989-01-01

    Late last year, a symposium entitled 'Rare Decays' attracted 115 participants to a hotel in Vancouver, Canada. These participants were particle physicists interested in checking conventional selection rules to look for clues of possible new behaviour outside today's accepted 'Standard Model'. For physicists, 'rare decays' include processes that have so far not been seen, explicitly forbidden by the rules of the Standard Model, or processes highly suppressed because the decay is dominated by an easier route, or includes processes resulting from multiple transitions

  6. Rare (Earth Elements [score

    Directory of Open Access Journals (Sweden)

    Camilo Méndez

    2014-12-01

    Full Text Available Rare (Earth Elements is a cycle of works for solo piano. The cycle was inspired by James Dillon’s Book of Elements (Vol. I-V. The complete cycle will consist of 14 pieces; one for each selected rare (earth element. The chosen elements are Neodymium, Erbium, Tellurium, Hafnium, Tantalum, Technetium, Indium, Dysprosium, Lanthanium, Cerium, Europium, Terbium, Yttrium and Darmstadtium. These elements were selected due to their special atomic properties that in many cases make them extremely valuable for the development of new technologies, and also because of their scarcity. To date, only 4 works have been completed Yttrium, Technetium, Indium and Tellurium.

  7. Rare muon processes: Experiment

    International Nuclear Information System (INIS)

    Walter, H.K.

    1998-01-01

    The decay properties of muons, especially their rare decays, can be used to study very accurately deviations from the Standard Model. Muons with extremely low energies and good spatial definition are preferred for the majority of such studies. With the upgrade of the 590-MeV ring accelerator, PSI possesses the most powerful cyclotron in the world. This makes it possible to operate high-intensity beams of secondary pions and muons. A short review on rare muon processes is presented, concerning μ-e conversion and muonium-antimuonium oscillations. A possible new search for μ→eγ is also mentioned

  8. An Investigation on Hot-Spot Temperature Calculation Methods of Power Transformers

    OpenAIRE

    Ahmet Y. Arabul; Ibrahim Senol; Fatma Keskin Arabul; Mustafa G. Aydeniz; Yasemin Oner; Gokhan Kalkan

    2016-01-01

    In the standards of IEC 60076-2 and IEC 60076-7, three different hot-spot temperature estimation methods are suggested. In this study, the algorithms which used in hot-spot temperature calculations are analyzed by comparing the algorithms with the results of an experimental set-up made by a Transformer Monitoring System (TMS) in use. In tested system, TMS uses only top oil temperature and load ratio for hot-spot temperature calculation. And also, it uses some constants from standards which ar...

  9. CONSERVATION. Genetic assignment of large seizures of elephant ivory reveals Africa's major poaching hotspots.

    Science.gov (United States)

    Wasser, S K; Brown, L; Mailand, C; Mondol, S; Clark, W; Laurie, C; Weir, B S

    2015-07-03

    Poaching of elephants is now occurring at rates that threaten African populations with extinction. Identifying the number and location of Africa's major poaching hotspots may assist efforts to end poaching and facilitate recovery of elephant populations. We genetically assign origin to 28 large ivory seizures (≥0.5 metric tons) made between 1996 and 2014, also testing assignment accuracy. Results suggest that the major poaching hotspots in Africa may be currently concentrated in as few as two areas. Increasing law enforcement in these two hotspots could help curtail future elephant losses across Africa and disrupt this organized transnational crime. Copyright © 2015, American Association for the Advancement of Science.

  10. Surveillance of rare cancers

    NARCIS (Netherlands)

    van der Zwan, Johannes Martinus

    2016-01-01

    The widespread incidence and effects of cancer have led to a growing development in cancer prevention in the form of screening and research programs and cancer registries. Because of the low number of patients with rare cancers this improvement is not applied to the same extent to all cancer

  11. Afganistan and rare earths

    Directory of Open Access Journals (Sweden)

    Emilian M. Dobrescu

    2013-05-01

    Full Text Available On our planet, over a quarter of new technologies for the economic production of industrial goods, are using rare earths, which are also called critical minerals and industries that rely on these precious items being worth of an estimated nearly five trillion dollars, or 5 percent of world gross domestic product. In the near future, competition will increase for the control of rare earth minerals embedded in high-tech products. Rare minerals are in the twenty-first century what oil accounted for in the twentieth century and coal in the nineteenth century: the engine of a new industrial revolution. Future energy will be produced increasingly by more sophisticated technological equipment based not just on steel and concrete, but incorporating significant quantities of metals and rare earths. Widespread application of these technologies will result in an exponential increase in demand for such minerals, and what is worrying is that minerals of this type are almost nowhere to be found in Europe and in other industrialized countries in the world, such as U.S. and Japan, but only in some Asian countries, like China and Afghanistan.

  12. Magnetic rare earth superlattices

    DEFF Research Database (Denmark)

    Majkrzak, C.F.; Kwo, J.; Hong, M.

    1991-01-01

    Advances in molecular beam epitaxy deposition techniques have recently made it possible to grow, an atomic plane at a time, single crystalline superlattices composed of alternating layers of a magnetic rare earth, such as Gd, Dy, Ho, or Er, and metallic Y, which has an identical chemical structure...

  13. Marine Caves of the Mediterranean Sea: A Sponge Biodiversity Reservoir within a Biodiversity Hotspot

    Science.gov (United States)

    Gerovasileiou, Vasilis; Voultsiadou, Eleni

    2012-01-01

    Marine caves are widely acknowledged for their unique biodiversity and constitute a typical feature of the Mediterranean coastline. Herein an attempt was made to evaluate the ecological significance of this particular ecosystem in the Mediterranean Sea, which is considered a biodiversity hotspot. This was accomplished by using Porifera, which dominate the rocky sublittoral substrata, as a reference group in a meta-analytical approach, combining primary research data from the Aegean Sea (eastern Mediterranean) with data derived from the literature. In total 311 species from all poriferan classes were recorded, representing 45.7% of the Mediterranean Porifera. Demospongiae and Homoscleromorpha are highly represented in marine caves at the family (88%), generic (70%), and species level (47.5%), the latter being the most favored group along with Dictyoceratida and Lithistida. Several rare and cave-exclusive species were reported from only one or few caves, indicating the fragmentation and peculiarity of this unique ecosystem. Species richness and phylogenetic diversity varied among Mediterranean areas; the former was positively correlated with research effort, being higher in the northern Mediterranean, while the latter was generally higher in caves than in the overall sponge assemblages of each area. Resemblance analysis among areas revealed that cavernicolous sponge assemblages followed a pattern quite similar to that of the overall Mediterranean assemblages. The same pattern was exhibited by the zoogeographic affinities of cave sponges: species with Atlanto-Mediterranean distribution and Mediterranean endemics prevailed (more than 40% each), 70% of them having warm-water affinities, since most caves were studied in shallow waters. According to our findings, Mediterranean marine caves appear to be important sponge biodiversity reservoirs of high representativeness and great scientific interest, deserving further detailed study and protection. PMID:22808070

  14. Implications of salinity pollution hotspots on agricultural production

    Science.gov (United States)

    Floerke, Martina; Fink, Julia; Malsy, Marcus; Voelker, Jeanette; Alcamo, Joseph

    2016-04-01

    , large metropolitan regions are initially loading hotspots and pollution, too, and prevention becomes important as point sources are dependent on sewer connection rates and treatment levels. In conclusion, this study provides a detailed picture of the spatial and temporal distribution of salinity pollution and identifies hotspot areas as well as the dominant sources. Furthermore, impacts of water quality degradation on agricultural production and food security are quantified, which aim for a better understanding of the risks for food security caused by water quality impairment.

  15. Implementing genomics and pharmacogenomics in the clinic: The National Human Genome Research Institute’s genomic medicine portfolio

    Science.gov (United States)

    Manolio, Teri A.

    2016-01-01

    Increasing knowledge about the influence of genetic variation on human health and growing availability of reliable, cost-effective genetic testing have spurred the implementation of genomic medicine in the clinic. As defined by the National Human Genome Research Institute (NHGRI), genomic medicine uses an individual’s genetic information in his or her clinical care, and has begun to be applied effectively in areas such as cancer genomics, pharmacogenomics, and rare and undiagnosed diseases. In 2011 NHGRI published its strategic vision for the future of genomic research, including an ambitious research agenda to facilitate and promote the implementation of genomic medicine. To realize this agenda, NHGRI is consulting and facilitating collaborations with the external research community through a series of “Genomic Medicine Meetings,” under the guidance and leadership of the National Advisory Council on Human Genome Research. These meetings have identified and begun to address significant obstacles to implementation, such as lack of evidence of efficacy, limited availability of genomics expertise and testing, lack of standards, and diffficulties in integrating genomic results into electronic medical records. The six research and dissemination initiatives comprising NHGRI’s genomic research portfolio are designed to speed the evaluation and incorporation, where appropriate, of genomic technologies and findings into routine clinical care. Actual adoption of successful approaches in clinical care will depend upon the willingness, interest, and energy of professional societies, practitioners, patients, and payers to promote their responsible use and share their experiences in doing so. PMID:27612677

  16. Rare kidney tumor provides insight on metabolic changes

    Science.gov (United States)

    Researchers in The Cancer Genome Atlas (TCGA) Network have uncovered a number of new findings about the biology and development of a rare form of kidney cancer. They found that the disease – chromophobe renal cell carcinoma – stems in part from alteratio

  17. Identification of Hotspots of Genetic Risk for Type 2 Diabetes Using GIS Methods

    Science.gov (United States)

    BACKGROUND: Having the ability to scan the entire country for potential "hotspots" with increased risk of developing chronic diseases due to various environmental, demographic, and genetic susceptibility factors may inform risk management decisions and enable better env...

  18. Imaging the Iceland Hotspot Track Beneath Greenland with Seismic Noise Correlations

    Science.gov (United States)

    Mordret, A.

    2017-12-01

    During the past 65 million years, the Greenland craton drifted over the Iceland hotspot; however, uncertainties in geodynamic modeling and a lack of geophysical evidence prevent an accurate reconstruction of the hotspot track. I image the Greenland lithosphere down to 300 km depth with seismic noise tomography. The hotspot track is observed as a linear high-velocity anomaly in the middle crust associated with magmatic intrusions. In the upper mantle, the remnant thermal signature of the hotspot manifests as low velocity and low viscosity bodies. This new detailed picture of the Greenland lithosphere will drive more accurate geodynamic reconstructions of tectonic plate motions and prediction of Greenland heat flow, which in turn will enable more precise estimations of the Greenland ice-sheet mass balance.

  19. Rational identification of aggregation hotspots based on secondary structure and amino acid hydrophobicity.

    Science.gov (United States)

    Matsui, Daisuke; Nakano, Shogo; Dadashipour, Mohammad; Asano, Yasuhisa

    2017-08-25

    Insolubility of proteins expressed in the Escherichia coli expression system hinders the progress of both basic and applied research. Insoluble proteins contain residues that decrease their solubility (aggregation hotspots). Mutating these hotspots to optimal amino acids is expected to improve protein solubility. To date, however, the identification of these hotspots has proven difficult. In this study, using a combination of approaches involving directed evolution and primary sequence analysis, we found two rules to help inductively identify hotspots: the α-helix rule, which focuses on the hydrophobicity of amino acids in the α-helix structure, and the hydropathy contradiction rule, which focuses on the difference in hydrophobicity relative to the corresponding amino acid in the consensus protein. By properly applying these two rules, we succeeded in improving the probability that expressed proteins would be soluble. Our methods should facilitate research on various insoluble proteins that were previously difficult to study due to their low solubility.

  20. ICF implosion hotspot ion temperature diagnostic techniques based on neutron time-of-flight method

    International Nuclear Information System (INIS)

    Tang Qi; Song Zifeng; Chen Jiabin; Zhan Xiayu

    2013-01-01

    Ion temperature of implosion hotspot is a very important parameter for inertial confinement fusion. It reflects the energy level of the hotspot, and it is very sensitive to implosion symmetry and implosion speed. ICF implosion hotspot ion temperature diagnostic techniques based on neutron time-of-flight method were described. A neutron TOF spectrometer was developed using a ultrafast plastic scintillator as the neutron detector. Time response of the spectrometer has 1.1 ns FWHM and 0.5 ns rising time. TOF spectrum resolving method based on deconvolution and low pass filter was illuminated. Implosion hotspot ion temperature in low neutron yield and low ion temperature condition at Shenguang-Ⅲ facility was acquired using the diagnostic techniques. (authors)

  1. Shock-induced hotspot formation and chemical reaction initiation in PETN containing a spherical void

    International Nuclear Information System (INIS)

    Shan, Tzu-Ray; Thompson, Aidan P

    2014-01-01

    We present results of reactive molecular dynamics simulations of hotspot formation and chemical reaction initiation in shock-induced compression of pentaerythritol tetranitrate (PETN) with the ReaxFF reactive force field. A supported shockwave is driven through a PETN crystal containing a 20 nm spherical void at a sub-threshold impact velocity of 2 km/s. Formation of a hotspot due to shock-induced void collapse is observed. During void collapse, NO 2 is the dominant species ejected from the upstream void surface. Once the ejecta collide with the downstream void surface and the hotspot develops, formation of final products such as N 2 and H 2 O is observed. The simulation provides a detailed picture of how void collapse and hotspot formation leads to initiation at sub-threshold impact velocities.

  2. A simple model for the pressure field from a distribution of hotspots

    International Nuclear Information System (INIS)

    Lambourn, B D; Lacy, H J; Handley, C A; James, H R

    2014-01-01

    At the APS SCCM in 2009, Hill, Zimmermann and Nichols showed that assuming burn fronts propagate at constant speed from individual point hotspots distributed randomly in a volume, the reaction rate history could be determined. In this paper a simple analytic approximation is found for the time history of the pressure in the volume. Using acoustic theory, the time history of the pressure field for burning from a single spherical, isolated hotspot of finite radius is developed. Then at any point in the volume, the overall pressure history is determined from the sum of the pressure fields from all the individual hotspots. The results are shown to be in qualitative agreement with 1D mesoscale hydrocode calculations of the reaction and burning from a finite size spherical hotspot.

  3. Application of PCARES in locating the soil erosion Hotspots in the Manupali River Watershed

    OpenAIRE

    Paningbatan, E.

    2004-01-01

    In this presentation the author covers: GIS mapping of land attributes, dynamic modeling of soil erosion at watershed scale using PCARES (Predicting Catchment Runoff and Soil Erosion for Sustainability), identifying soil erosion "hotspots" in the Manupali River watershed

  4. Hot-spot measurements on the U.S.-LCT coils in the IFSMTF

    International Nuclear Information System (INIS)

    Lue, J.W.; Dresner, L.; Fehling, D.T.; Lubell, M.S.; Luton, J.N.; McManamy, T.J.; Shen, S.S.; Wilson, C.T.; Wintenberg, R.E.

    1987-01-01

    Hot-spot temperature during a quench is a major concern for superconducting coil protection. If the allowable temperature can be increased, then the dump time constant can be made longer and the dump voltage correspondingly reduced. Thus, the insulation requirement can be less stringent and the dump operation can be safer. The U.S.-made Large Coil Task (LCT) coils are all instrumented with heaters, resistive or inductive. The hot-spot temperatures of these coils were found by repeatedly driving the conductor normal with the heaters at increasing coil currents until the normal zone propagated. The resulting hot-spot temperature was measured by the resistance of the conductor over a fixed length. The effect of dump time delay on the hot-spot temperature was also investigated. The results are compared with calculations based on various assumptions

  5. Hot-spot measurements on the US-LCT coils in the IFSMTF

    International Nuclear Information System (INIS)

    Lue, J.W.; Dresner, L.; Fehling, D.T.; Lubell, M.S.; Luton, J.N.; McManamy, T.J.; Shen, S.S.; Wilson, C.T.; Wintenberg, R.E.

    1987-01-01

    Hot-spot temperature during a quench is a major concern for superconducting coil protection. If the allowable temperature can be increased, then the dump time constant can be made longer and the dump voltage correspondingly reduced. Thus, the insulation requirement can be less stringent and the dump operation can be safer. The US-made Large Coil Task (LCT) coils are all instrumented with heaters, resistive or inductive. The hot-spot temperatures of these coils were found by repeatedly driving the conductor normal with the heaters at increasing coil currents until the normal zone propagated. The resulting hot-spot temperature was measured by the resistance of the conductor over a fixed length. The effect of dump time delay on the hot-spot temperature was also investigated. The results are compared with calculations based on various assumptions. 4 refs., 7 figs

  6. Determination of hot-spot susceptibility of multistring photovoltaic modules in a central-station application

    Science.gov (United States)

    Gonzalez, C. C.; Weaver, R. W.; Ross, R. G., Jr.; Spencer, R.; Arnett, J. C.

    1984-01-01

    Part of the effort of the Jet Propulsion Laboratory (JPL) Flat-Plate Solar Array Project (FSA) includes a program to improve module and array reliability. A collaborative activity with industry dealing with the problem of hot-spot heating due to the shadowing of photovoltaic cells in modules and arrays containing several paralleled cell strings is described. The use of multiparallel strings in large central-station arrays introduces the likelihood of unequal current sharing and increased heating levels. Test results that relate power dissipated, current imbalance, cross-strapping frequency, and shadow configuration to hot-spot heating levels are presented. Recommendations for circuit design configurations appropriate to central-station applications that reduce the risk of hot-spot problems are offered. Guidelines are provided for developing hot-spot tests for arrays when current imbalance is a threat.

  7. Distribution of enzyme activity hotspots induced by earthworms in top- and subsoil

    Science.gov (United States)

    Hoang, D. T. T.

    2016-12-01

    Earthworms (Lumbricus terrestris L.) not only affect soil physics, but they also boost microbial activities and consequently create important hotspots of microbial mediated carbon and nutrient turnover through their burrowing activity. However, it is still unknown to which extend earthworms change the enzyme distribution and activity inside their burrows in top- and subsoil horizons. We hypothesized that earthworm burrows, which are enriched in available substrates, have higher percentage of enzyme activity hotspots than soil without earthworms, and that enzyme activities decreased with increasing depth because of the increasing recalcitrance of organic matter in subsoil. We visualized enzyme distribution inside and outside of worm burrows (biopores) by in situ soil zymography and measured enzyme kinetics of 6 enzymes - β-glucosidase (GLU), cellobiohydrolase (CBH), xylanase (XYL), chitinase (NAG), leucine aminopeptidase (LAP) and acid phosphatase (APT) - in pore and bulk soil material up to 105 cm. Zymography showed a heterogeneous distribution of hotspots in worm burrows. The hotspot areas was 2.4 to 14 times larger in the burrows than in soil without earthworms. However, the dispersion index of hotspot distribution showed more aggregated hotspots in soil without earthworms than in soil with earthworms and burrow wall. Enzyme activities decreased with depth, by a factor of 2 to 8 due to fresh C input from the soil surface. Compared to bulk soil, enzyme activities in topsoil biopores were up to 11 times higher for all enzymes, but in the subsoil activities of XYL, NAG and APT were lower in earthworm biopores than bulk soil. In conclusion, hotspots were twice as concentrated close to earthworm burrows as in surrounding soil. Earthworms exerted stronger effects on enzyme activities in biopores in the topsoil than in subsoil. Keywords: Earthworms, hotspots, enzyme activities, enzyme distribution, subsoil

  8. Analysis of microstructure-dependent shock dissipation and hot-spot formation in granular metalized explosive

    Science.gov (United States)

    Chakravarthy, Sunada; Gonthier, Keith A.

    2016-07-01

    Variations in the microstructure of granular explosives (i.e., particle packing density, size, shape, and composition) can affect their shock sensitivity by altering thermomechanical fields at the particle-scale during pore collapse within shocks. If the deformation rate is fast, hot-spots can form, ignite, and interact, resulting in burn at the macro-scale. In this study, a two-dimensional finite and discrete element technique is used to simulate and examine shock-induced dissipation and hot-spot formation within low density explosives (68%-84% theoretical maximum density (TMD)) consisting of large ensembles of HMX (C4H8N8O8) and aluminum (Al) particles (size ˜ 60 -360 μm). Emphasis is placed on identifying how the inclusion of Al influences effective shock dissipation and hot-spot fields relative to equivalent ensembles of neat/pure HMX for shocks that are sufficiently strong to eliminate porosity. Spatially distributed hot-spot fields are characterized by their number density and area fraction enabling their dynamics to be described in terms of nucleation, growth, and agglomeration-dominated phases with increasing shock strength. For fixed shock particle speed, predictions indicate that decreasing packing density enhances shock dissipation and hot-spot formation, and that the inclusion of Al increases dissipation relative to neat HMX by pressure enhanced compaction resulting in fewer but larger HMX hot-spots. Ensembles having bimodal particle sizes are shown to significantly affect hot-spot dynamics by altering the spatial distribution of hot-spots behind shocks.

  9. Application of SVM on satellite images to detect hotspots in Jharia coal field region of India

    Energy Technology Data Exchange (ETDEWEB)

    Gautam, R.S.; Singh, D.; Mittal, A.; Sajin, P. [Indian Institute for Technology, Roorkee (India)

    2008-07-01

    The present paper deals with the application of Support Vector Machine (SVM) and image analysis techniques on NOAA/AVHRR satellite image to detect hotspots on the Jharia coal field region of India. One of the major advantages of using these satellite data is that the data are free with very good temporal resolution; while, one drawback is that these have low spatial resolution (i.e., approximately 1.1 km at nadir). Therefore, it is important to do research by applying some efficient optimization techniques along with the image analysis techniques to rectify these drawbacks and use satellite images for efficient hotspot detection and monitoring. For this purpose, SVM and multi-threshold techniques are explored for hotspot detection. The multi-threshold algorithm is developed to remove the cloud coverage from the land coverage. This algorithm also highlights the hotspots or fire spots in the suspected regions. SVM has the advantage over multi-thresholding technique that it can learn patterns from the examples and therefore is used to optimize the performance by removing the false points which are highlighted in the threshold technique. Both approaches can be used separately or in combination depending on the size of the image. The RBF (Radial Basis Function) kernel is used in training of three sets of inputs: brightness temperature of channel 3, Normalized Difference Vegetation Index (NDVI) and Global Environment Monitoring Index (GEMI), respectively. This makes a classified image in the output that highlights the hotspot and non-hotspot pixels. The performance of the SVM is also compared with the performance obtained from the neural networks and SVM appears to detect hotspots more accurately (greater than 91% classification accuracy) with lesser false alarm rate. The results obtained are found to be in good agreement with the ground based observations of the hotspots.

  10. CKD hotspots around the world: where, why and what the lessons are. A CKJ review series.

    Science.gov (United States)

    Martín-Cleary, Catalina; Ortiz, Alberto

    2014-12-01

    Chronic kidney disease (CKD) is one of the three causes of death that has had the highest increase in the last 20 years. The increasing CKD burden occurs in the context of lack of access of most of the world population to adequate healthcare and an incomplete understanding of the pathogenesis of CKD. However, CKD is not homogeneously distributed. CKD hotspots are defined as countries, region, communities or ethnicities with higher than average incidence of CKD. Analysis of CKD hotspots has the potential to provide valuable insights into the pathogenesis of kidney disease and to improve the life expectancy of the affected communities. Examples include ethnicities such as African Americans in the USA or Aboriginals in Australia, regions such as certain Balkan valleys or Central America and even groups of people sharing common activities or interests such as young women trying to lose weight in Belgium. The study of these CKD hotspots has identified underlying genetic factors, such as ApoL1 gene variants, environmental toxins, such as aristolochic acid and socioeconomic factors leading to nutritional deprivation and inflammation/infection. The CKD hotspots series of CKJ reviews will explore the epidemiology and causes in CKD hotspots, beginning with Australian Aboriginals in this issue. An online map of CKD hotspots around the world will feature the reviewed hotspots, highlighting known or suspected causes as well as ongoing projects to unravel the cause and providing a directory of public health officials, physicians and basic scientists involved in these efforts. Since the high prevalence of CKD in a particular region or population may only be known to local physicians, we encourage readers to propose further CKD hotspots to be reviewed.

  11. An example of capturing a hotspot of man-made radioactive 152Eu

    International Nuclear Information System (INIS)

    Hu Mingkao; Fang Jiangqi; Gu Renkang

    2002-01-01

    The author presents an example of successfully capturing a hotspot of man-made radioactive 152 Eu in Dayuan when the authors carried out airborne survey for radioactivity levels in north China. The hotspot was on the front of the gate of a concrete pipe factory in Dayuan. The activity of the source was estimated roughly 4.25 x 10 8 -7.53 x 10 8 Bq. The longitudinal positioning error was less than 15 m

  12. Re-evaluating the NO 2 hotspot over the South African Highveld

    Directory of Open Access Journals (Sweden)

    Alexandra S.M. Lourens

    2012-10-01

    Full Text Available Globally, numerous pollution hotspots have been identified using satellite-based instruments. One of these hotspots is the prominent NO2hotspot over the South African Highveld. The tropospheric NO2column density of this area is comparable to that observed for central and northern Europe, eastern North America and south-east Asia. The most well-known pollution source in this area is a large array of coal-fired power stations. Upon closer inspection, long-term means of satellite observations also show a smaller area, approximately 100 km west of the Highveld hotspot, with a seemingly less substantial NO2column density. This area correlates with the geographical location of the Johannesburg–Pretoria conurbation or megacity, one of the 40 largest metropolitan areas in the world. Ground-based measurements indicate that NO2concentrations in the megacity have diurnal peaks in the early morning and late afternoon, which coincide with peak traffic hours and domestic combustion. During these times, NO2concentrations in the megacity are higher than those in the Highveld hotspot. These diurnal NO2 peaks in the megacity have generally been overlooked by satellite observations because the satellites have fixed local overpass times that do not coincide with these peak periods. Consequently, the importance of NO2 over the megacity has been underestimated. We examined the diurnal cycles of NO2 ground-based measurements for the two areas – the megacity and the Highveld hotspot – and compared them with the satellite-based NO2 observations. Results show that the Highveld hotspot is accompanied by a second hotspot over the megacity, which is of significance for the more than 10 million people living in this megacity.

  13. Environmental and Microbial Features Affecting Denitrification and Anammox Hotspots in an Estuarine Ecosystem

    Science.gov (United States)

    Lisa, J.; Song, B.; Lefcheck, J. S.; Tobias, C. R.

    2016-02-01

    Biogeochemical hotspots are characterized as a few sites that exhibit extremely high reaction rates relative to surrounding area, and often account for a high percentage of the overall reaction rates in an ecosystem. Criteria for quantitatively identifying these sites have not been well established. Further, the underlying mechanisms of hotspots have been described in terms of environmental conditions, with little attention paid to the microbial community. The objectives of this study were to establish quantitative criteria to identify denitrification and anammox hotspots, and determine the underlying microbial and environmental factors responsible for elevated N2 production. We used 15N isotope pairing incubation experiments to measure denitrification and anammox rates in the New River Estuary, NC. Quantitative PCR assays of nitrous oxide reductase (nosZ Clades I and II) and hydrazine oxidoreductase (hzo) genes were conducted to estimate denitrifier and anammox abundance. Structural Equation Modeling (SEM) was used to elucidate complex causal relationships between environmental and biological variables. Denitrification hotspots, quantitatively defined as statistical outliers, accounted for 35.6% total denitrification while comprising only 7.3% of the sites. Anammox hotspots,10.6% of the sites, accounted for 60.9% of total anammox. SEM revealed increased sediment organics at lower salinities supported higher functional gene abundance, which in turn resulted in higher N2 production. Surprisingly, denitrification rates were significantly and positively correlated with nosZ Clade II gene abundance, after accounting for the non-significant contributions of the naturally more abundant nosZ Clade I, and other environmental covariates. This is the first time that a quantitative definition of biogeochemical hotspots was put forth and used to determine the importance of anammox and denitrification hotspots in estuarine nitrogen removal capacity. Despite the low area

  14. Genomic individuality and its biological implications.

    Science.gov (United States)

    Zhao, J

    1996-06-01

    It is a widely accepted fundamental concept that all somatic genomes of a human individual are identical to each other. The theoretical basis of this concept is that all of these somatic genomes are the descendants of the genome of a single fertilized cell as well as the simple replicated products of asexual reproduction, thus not forming any new recombined genomes. The question here is whether such a concept might only represent one side of somatic genome biology and, even worse, whether it has perhaps already led to a very prevalent misconception that within the organism body, there exists no variability among individual somatic genomes. A hypothesis, called genomic individuality, is proposed, simply saying that every individual somatic genome, perhaps with rare exceptions, has its own unique or individual 'genetic identity' or 'fingerprint', which is characterized by its distinctive sequences or patterns of deoxyribonucleic acid molecules, or both. Thus, no two somatic genomes can be identical to each other in every or all aspects, and consequently, there must be a great deal of genomic variation present within the body of any multicellular organism. The concept or hypothesis of genomic individuality would not only provide a more complete understanding of genome biology, but also suggest a new insight into the studies of the biology of cells and organisms.

  15. Genome Imprinting

    Indian Academy of Sciences (India)

    the cell nucleus (mitochondrial and chloroplast genomes), and. (3) traits governed ... tively good embryonic development but very poor development of membranes and ... Human homologies for the type of situation described above are naturally ..... imprint; (b) New modifications of the paternal genome in germ cells of each ...

  16. Baculovirus Genomics

    NARCIS (Netherlands)

    Oers, van M.M.; Vlak, J.M.

    2007-01-01

    Baculovirus genomes are covalently closed circles of double stranded-DNA varying in size between 80 and 180 kilobase-pair. The genomes of more than fourty-one baculoviruses have been sequenced to date. The majority of these (37) are pathogenic to lepidopteran hosts; three infect sawflies

  17. Genomic Testing

    Science.gov (United States)

    ... this database. Top of Page Evaluation of Genomic Applications in Practice and Prevention (EGAPP™) In 2004, the Centers for Disease Control and Prevention launched the EGAPP initiative to establish and test a ... and other applications of genomic technology that are in transition from ...

  18. Ancient genomes

    OpenAIRE

    Hoelzel, A Rus

    2005-01-01

    Ever since its invention, the polymerase chain reaction has been the method of choice for work with ancient DNA. In an application of modern genomic methods to material from the Pleistocene, a recent study has instead undertaken to clone and sequence a portion of the ancient genome of the cave bear.

  19. Sharing Rare Attitudes Attracts.

    Science.gov (United States)

    Alves, Hans

    2018-04-01

    People like others who share their attitudes. Online dating platforms as well as other social media platforms regularly rely on the social bonding power of their users' shared attitudes. However, little is known about moderating variables. In the present work, I argue that sharing rare compared with sharing common attitudes should evoke stronger interpersonal attraction among people. In five studies, I tested this prediction for the case of shared interests from different domains. I found converging evidence that people's rare compared with their common interests are especially potent to elicit interpersonal attraction. I discuss the current framework's theoretical implications for impression formation and impression management as well as its practical implications for improving online dating services.

  20. Correlation of Meiotic DSB Formation and Transcription Initiation Around Fission Yeast Recombination Hotspots.

    Science.gov (United States)

    Yamada, Shintaro; Okamura, Mika; Oda, Arisa; Murakami, Hiroshi; Ohta, Kunihiro; Yamada, Takatomi

    2017-06-01

    Meiotic homologous recombination, a critical event for ensuring faithful chromosome segregation and creating genetic diversity, is initiated by programmed DNA double-strand breaks (DSBs) formed at recombination hotspots. Meiotic DSB formation is likely to be influenced by other DNA-templated processes including transcription, but how DSB formation and transcription interact with each other has not been understood well. In this study, we used fission yeast to investigate a possible interplay of these two events. A group of hotspots in fission yeast are associated with sequences similar to the cyclic AMP response element and activated by the ATF/CREB family transcription factor dimer Atf1-Pcr1. We first focused on one of those hotspots, ade6-3049 , and Atf1. Our results showed that multiple transcripts, shorter than the ade6 full-length messenger RNA, emanate from a region surrounding the ade6-3049 hotspot. Interestingly, we found that the previously known recombination-activation region of Atf1 is also a transactivation domain, whose deletion affected DSB formation and short transcript production at ade6-3049 These results point to a possibility that the two events may be related to each other at ade6-3049 In fact, comparison of published maps of meiotic transcripts and hotspots suggested that hotspots are very often located close to meiotically transcribed regions. These observations therefore propose that meiotic DSB formation in fission yeast may be connected to transcription of surrounding regions. Copyright © 2017 by the Genetics Society of America.

  1. Double hotspots and flow redirection in the lobes of powerful extragalactic radio sources

    International Nuclear Information System (INIS)

    Lonsdale, C.J.; Barthel, P.D.; Owens Valley Radio Observatory, Pasadena, CA)

    1986-01-01

    Detailed observations of two powerful extragalactic radio sources that contain a prominent double hotspot in one of their two outer lobes are presented. These double hotspots display similar characteristics in both sources, suggesting a common mechanism for their formation. Several other examples of double hotspots are found in the literature that also display many of the characteristics of those in the present sources. These characteristics cannot easily be explained by beam-jitter models, in which secondary hotspots are interpreted as previous impact sites of a beam, which has moved on to form the primary in a new location. Instead, it is proposed that these double hotspots are caused by a flow of material from the more compact to the less compact of the two. It is found that the most probable cause of the outflow is a collision of a beam from the nucleus with a massive (100-million solar mass), dense (greater than 0.1/cm) cloud in intergalactic space. The details of the deflection process itself are unclear, but a possibility is that the beam inflates a bubble of very hot plasma inside the cloud, which then escapes through a weak point in the wall of the cloud. The existence of such intergalactic clouds is considered to be a strong possibility, based on the recent literature, as well as the present hotspot outflow arguments, despite the apparently extreme values postulated for their mass and density. 45 references

  2. Understanding the Functionality of Human Activity Hotspots from Their Scaling Pattern Using Trajectory Data

    Directory of Open Access Journals (Sweden)

    Tao Jia

    2017-11-01

    Full Text Available Human activity hotspots are the clusters of activity locations in space and time, and a better understanding of their functionality would be useful for urban land use planning and transportation. In this article, using trajectory data, we aim to infer the functionality of human activity hotspots from their scaling pattern in a reliable way. Specifically, a large number of stopping locations are extracted from trajectory data, which are then aggregated into activity hotspots. Activity hotspots are found to display scaling patterns in terms of the sublinear scaling relationships between the number of stopping locations and the number of points of interest (POIs, which indicates economies of scale of human interactions with urban land use. Importantly, this scaling pattern remains stable over time. This finding inspires us to devise an allometric ruler to identify the activity hotspots, whose functionality could be reliably estimated using the stopping locations. Thereafter, a novel Bayesian inference model is proposed to infer their urban functionality, which examines the spatial and temporal information of stopping locations covering 75 days. Experimental results suggest that the functionality of identified activity hotspots are reliably inferred by stopping locations, such as the railway station.

  3. Global hotspots of river erosion under global warming

    Science.gov (United States)

    Plink-Bjorklund, P.; Reichler, T.

    2017-12-01

    Extreme precipitation plays a significant role for river hydrology, flood hazards and landscape response. For example, the September 2013 rainstorm in the Colorado Front Range evacuated the equivalent of hundreds to thousands of years of hillslope weathering products. Although promoted by steep topography, the Colorado event is clearly linked to rainfall intensity, since most of the 1100 debris flows occurred within the highest rainfall contour. Additional evidence for a strong link between extreme precipitation and river erosion comes from the sedimentary record, and especially from that of past greenhouse climates. The existence of such a link suggests that information about global rainfall patterns can be used to define regions of increased erosion potential. However, the question arises what rainfall criteria to use and how well the method works. A related question is how ongoing climate change and the corresponding shifts in rainfall might impact the results. Here, we use atmospheric reanalysis and output from a climate model to identify regions that are particularly susceptible to landscape change in response to extreme precipitation. In order to define the regions, we combine several hydroclimatological and geomorphological criteria into a single index of erosion potential. We show that for current climate, our criteria applied to atmospheric reanalysis or to climate model data successfully localize known areas of increased erosion potential, such as the Colorado region. We then apply our criteria to climate model data for future climate to document how the location, extent, and intensity of erosion hotspots are likely to change under global warming.

  4. Pervasive Defaunation of Forest Remnants in a Tropical Biodiversity Hotspot

    Science.gov (United States)

    Canale, Gustavo R.; Peres, Carlos A.; Guidorizzi, Carlos E.; Gatto, Cassiano A. Ferreira; Kierulff, Maria Cecília M.

    2012-01-01

    Tropical deforestation and forest fragmentation are among the most important biodiversity conservation issues worldwide, yet local extinctions of millions of animal and plant populations stranded in unprotected forest remnants remain poorly explained. Here, we report unprecedented rates of local extinctions of medium to large-bodied mammals in one of the world's most important tropical biodiversity hotspots. We scrutinized 8,846 person-years of local knowledge to derive patch occupancy data for 18 mammal species within 196 forest patches across a 252,669-km2 study region of the Brazilian Atlantic Forest. We uncovered a staggering rate of local extinctions in the mammal fauna, with only 767 from a possible 3,528 populations still persisting. On average, forest patches retained 3.9 out of 18 potential species occupancies, and geographic ranges had contracted to 0–14.4% of their former distributions, including five large-bodied species that had been extirpated at a regional scale. Forest fragments were highly accessible to hunters and exposed to edge effects and fires, thereby severely diminishing the predictive power of species-area relationships, with the power model explaining only ∼9% of the variation in species richness per patch. Hence, conventional species-area curves provided over-optimistic estimates of species persistence in that most forest fragments had lost species at a much faster rate than predicted by habitat loss alone. PMID:22905103

  5. Pervasive defaunation of forest remnants in a tropical biodiversity hotspot.

    Directory of Open Access Journals (Sweden)

    Gustavo R Canale

    Full Text Available Tropical deforestation and forest fragmentation are among the most important biodiversity conservation issues worldwide, yet local extinctions of millions of animal and plant populations stranded in unprotected forest remnants remain poorly explained. Here, we report unprecedented rates of local extinctions of medium to large-bodied mammals in one of the world's most important tropical biodiversity hotspots. We scrutinized 8,846 person-years of local knowledge to derive patch occupancy data for 18 mammal species within 196 forest patches across a 252,669-km(2 study region of the Brazilian Atlantic Forest. We uncovered a staggering rate of local extinctions in the mammal fauna, with only 767 from a possible 3,528 populations still persisting. On average, forest patches retained 3.9 out of 18 potential species occupancies, and geographic ranges had contracted to 0-14.4% of their former distributions, including five large-bodied species that had been extirpated at a regional scale. Forest fragments were highly accessible to hunters and exposed to edge effects and fires, thereby severely diminishing the predictive power of species-area relationships, with the power model explaining only ~9% of the variation in species richness per patch. Hence, conventional species-area curves provided over-optimistic estimates of species persistence in that most forest fragments had lost species at a much faster rate than predicted by habitat loss alone.

  6. Incorporating evolutionary history into conservation planning in biodiversity hotspots.

    Science.gov (United States)

    Buerki, Sven; Callmander, Martin W; Bachman, Steven; Moat, Justin; Labat, Jean-Noël; Forest, Félix

    2015-02-19

    There is increased evidence that incorporating evolutionary history directly in conservation actions is beneficial, particularly given the likelihood that extinction is not random and that phylogenetic diversity (PD) is lost at higher rates than species diversity. This evidence is even more compelling in biodiversity hotspots, such as Madagascar, where less than 10% of the original vegetation remains. Here, we use the Leguminosae, an ecologically and economically important plant family, and a combination of phylogenetics and species distribution modelling, to assess biodiversity patterns and identify regions, coevolutionary processes and ecological factors that are important in shaping this diversity, especially during the Quaternary. We show evidence that species distribution and community PD are predicted by watershed boundaries, which enable the identification of a network of refugia and dispersal corridors that were perhaps important for maintaining community integrity during past climate change. Phylogenetically clustered communities are found in the southwest of the island at low elevation and share a suite of morphological characters (especially fruit morphology) indicative of coevolution with their main dispersers, the extinct and extant lemurs. Phylogenetically over-dispersed communities are found along the eastern coast at sea level and may have resulted from many independent dispersal events from the drier and more seasonal regions of Madagascar. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

  7. Urban rivers as hotspots of regional nitrogen pollution

    International Nuclear Information System (INIS)

    Zhang, Xiaohong; Wu, Yiyun; Gu, Baojing

    2015-01-01

    Excess nitrogen inputs to terrestrial ecosystems via human activities have deteriorated water qualities on regional scales. Urban areas as settlements of over half global population, however, were usually not considered in the analysis of regional water pollution. Here, we used a 72-month monitoring data of water qualities in Hangzhou, China to test the role of urban rives in regional nitrogen pollution and how they response to the changes of human activities. Concentrations of ammonium nitrogen in urban rivers were 3–5 times higher than that in regional rivers. Urban rivers have become pools of reactive nitrogen and hotspots of regional pollution. Moreover, this river pollution is not being measured by current surface water monitoring networks that are designed to measure broader regional patterns, resulting in an underestimation of regional pollution. This is crucial to urban environment not only in China, but also in other countries, where urban rivers are seriously polluted. - Highlights: • Nitrogen concentrations in urban rivers are much higher than that in regional rivers. • Domestic wastewater is the main source of urban river pollution in Hangzhou. • Pollutant collecting and water diversion can sharply reduce the urban river pollution. - Urban river pollution is not being measured by the current monitoring networks that are designed to measure regional patterns causing an underestimation

  8. Hotspots of human nutrition: Micronutrient supply, demand, and pollinator dependence

    Science.gov (United States)

    Dombeck, E.; Chaplin-Kramer, R.; Mueller, M.; Mueller, N. D.; Foley, J. A.

    2012-12-01

    While our caloric needs can mostly be met by wind-pollinated crops such as cereals, a recent analysis of USDA data shows that animal-pollinated crops contain the vast majority of many essential nutrients, including vitamins A and C, calcium, fluoride, and folic acid. In this work we combined global crop yield data with data on nutritional content in each crop to map nutrient production around the world, and to illustrate the value of pollination services to human nutrition. Spatially explicit crop yields (at 5 min resolution) were multiplied by crop nutrient content and by crop dependence on pollination to map where reductions in total nutrient production would occur if pollination services were removed. Nutrient demand maps (human nutrient requirements multiplied by population density) were generated to identify regions where local reduction in pollination services could threaten nutritional security. Nutrient deficiency maps (nutrient supply minus nutrient demand) were also created to identify hotspots where local crop production is not adequate to meet local nutritional needs.

  9. Lead Polluted Hotspot: Environmental Implication of Unplanned Industrial Development

    Directory of Open Access Journals (Sweden)

    Rikta Sharmin Yousuf

    2016-06-01

    Full Text Available In Rayer Bazaar, different industries like tannery, plastic, textile, battery recycling industry etc. are increasing rapidly without considering the environmental issues and deterioration. Since chromium (Cr pollution of this area has been widely investigated due to the presence of tannery industries, this study was focused on examining other environmental factors. Field visits and analytical results of semi-quantitative and quantitative analysis as well as three dimensional excitation emission matrix spectroscopy (3DEEM of water, soil and vegetative tissues indicated that, the area is highly polluted in term of different environmental parameters and metal content. The extremely high lead (Pb content of the soil (1171.7 mg/kg in summer, 2157.1 mg/kg in winter and blackish materials of vegetative tissues (6585.6 mg/kg in summer, 1974.1 mg/kg in winter indicates excessive lead deposition of this area that makes it a lead polluted hotspot. One of the possible sources of the extremely high lead concentration is adjacent battery recycling industry and/or other industries surrounding this area. So it is urgent to take necessary steps to find out immediate options for possible mitigation.

  10. Reservoirs as hotspots of fluvial carbon cycling in peatland catchments.

    Science.gov (United States)

    Stimson, A G; Allott, T E H; Boult, S; Evans, M G

    2017-02-15

    Inland water bodies are recognised as dynamic sites of carbon processing, and lakes and reservoirs draining peatland soils are particularly important, due to the potential for high carbon inputs combined with long water residence times. A carbon budget is presented here for a water supply reservoir (catchment area~9km 2 ) draining an area of heavily eroded upland peat in the South Pennines, UK. It encompasses a two year dataset and quantifies reservoir dissolved organic carbon (DOC), particulate organic carbon (POC) and aqueous carbon dioxide (CO 2 (aq)) inputs and outputs. The budget shows the reservoir to be a hotspot of fluvial carbon cycling, as with high levels of POC influx it acts as a net sink of fluvial carbon and has the potential for significant gaseous carbon export. The reservoir alternates between acting as a producer and consumer of DOC (a pattern linked to rainfall and temperature) which provides evidence for transformations between different carbon species. In particular, the budget data accompanied by 14 C (radiocarbon) analyses provide evidence that POC-DOC transformations are a key process, occurring at rates which could represent at least ~10% of the fluvial carbon sink. To enable informed catchment management further research is needed to produce carbon cycle models more applicable to these environments, and on the implications of high POC levels for DOC composition. Copyright © 2016 Elsevier B.V. All rights reserved.

  11. Isotopic identification of nitrogen hotspots across natural terrestrial ecosystems

    Directory of Open Access Journals (Sweden)

    E. Bai

    2012-08-01

    Full Text Available Nitrogen (N influences local biological processes, ecosystem productivity, the composition of the atmospheric-climate system, and the human endeavour as a whole. Here we use natural variations in N isotopes, coupled with two models, to trace global pathways of N loss from the land to the water and atmosphere. We show that denitrification accounts for approximately 35 % of total N losses from the natural soil, with NO, N2O, and N2 fluxes equal to 15.7 ± 4.7 Tg N yr−1, 10.2 ± 3.0 Tg N yr−1, and 21.0 ± 6.1 Tg N yr−1, respectively. Our analysis points to tropical regions as the major "hotspot" of nitrogen export from the terrestrial biosphere, accounting for 71 % of global N losses from the natural land surface. The poorly studied Congo Basin is further identified as one of the major natural sources of atmospheric N2O. Extra-tropical areas, by contrast, lose a greater fraction of N via leaching pathways (~77 % of total N losses than do tropical biomes, likely contributing to N limitations of CO2 uptake at higher latitudes. Our results provide an independent constraint on global models of the N cycle among different regions of the unfertilized biosphere.

  12. NIMS: hotspots on Io during G2 (continued)

    Science.gov (United States)

    1997-01-01

    This is another Near Infrared Mapping Spectrometer (NIMS) image of Io, taken during the G2 encounter in September 1996. This is a dayside image of Io (on the right) against the clouds of Jupiter (the blue background). On the left is a Voyager mosaic of Io with the same viewing geometry for comparison purposes. This NIMS data set has been processed to highlight the positions of hot spots on the surface of Io. At least 11 can be seen. Two of the hotspots are newly discovered by the NIMS instrument. Others correspond to sites of plume eruptions and volcanic calderas and volcanic flows. This image can be compared with the SSI image P-47971 released on October 23, 1996, which was taken almost exactly the same position.The Jet Propulsion Laboratory, Pasadena, CA manages the mission for NASA's Office of Space Science, Washington, DC.The Jet Propulsion Laboratory, Pasadena, CA manages the mission for NASA's Office of Space Science, Washington, DC.This image and other images and data received from Galileo are posted on the World Wide Web, on the Galileo mission home page at URL http://galileo.jpl.nasa.gov.

  13. Automatic Hotspot and Sun Glint Detection in UAV Multispectral Images.

    Science.gov (United States)

    Ortega-Terol, Damian; Hernandez-Lopez, David; Ballesteros, Rocio; Gonzalez-Aguilera, Diego

    2017-10-15

    Last advances in sensors, photogrammetry and computer vision have led to high-automation levels of 3D reconstruction processes for generating dense models and multispectral orthoimages from Unmanned Aerial Vehicle (UAV) images. However, these cartographic products are sometimes blurred and degraded due to sun reflection effects which reduce the image contrast and colour fidelity in photogrammetry and the quality of radiometric values in remote sensing applications. This paper proposes an automatic approach for detecting sun reflections problems (hotspot and sun glint) in multispectral images acquired with an Unmanned Aerial Vehicle (UAV), based on a photogrammetric strategy included in a flight planning and control software developed by the authors. In particular, two main consequences are derived from the approach developed: (i) different areas of the images can be excluded since they contain sun reflection problems; (ii) the cartographic products obtained (e.g., digital terrain model, orthoimages) and the agronomical parameters computed (e.g., normalized vegetation index-NVDI) are improved since radiometric defects in pixels are not considered. Finally, an accuracy assessment was performed in order to analyse the error in the detection process, getting errors around 10 pixels for a ground sample distance (GSD) of 5 cm which is perfectly valid for agricultural applications. This error confirms that the precision in the detection of sun reflections can be guaranteed using this approach and the current low-cost UAV technology.

  14. Restoring Wood-Rich Hotspots in Mountain Stream Networks

    Science.gov (United States)

    Wohl, E.; Scott, D.

    2016-12-01

    Mountain streams commonly include substantial longitudinal variability in valley and channel geometry, alternating repeatedly between steep, narrow and relatively wide, low gradient segments. Segments that are wider and lower gradient than neighboring steeper sections are hotspots with respect to: retention of large wood (LW) and finer sediment and organic matter; uptake of nutrients; and biomass and biodiversity of aquatic and riparian organisms. These segments are also more likely to be transport-limited with respect to floodplain and instream LW. Management designed to protect and restore riverine LW and the physical and ecological processes facilitated by the presence of LW is likely to be most effective if focused on relatively low-gradient stream segments. These segments can be identified using a simple, reach-scale gradient analysis based on high-resolution DEMs, with field visits to identify factors that potentially limit or facilitate LW recruitment and retention, such as forest disturbance history or land use. Drawing on field data from the western US, this presentation outlines a procedure for mapping relatively low-gradient segments in a stream network and for identifying those segments where LW reintroduction or retention is most likely to balance maximizing environmental benefits derived from the presence of LW while minimizing hazards associated with LW.

  15. Conservation businesses and conservation planning in a biological diversity hotspot.

    Science.gov (United States)

    Di Minin, Enrico; Macmillan, Douglas Craig; Goodman, Peter Styan; Escott, Boyd; Slotow, Rob; Moilanen, Atte

    2013-08-01

    The allocation of land to biological diversity conservation competes with other land uses and the needs of society for development, food, and extraction of natural resources. Trade-offs between biological diversity conservation and alternative land uses are unavoidable, given the realities of limited conservation resources and the competing demands of society. We developed a conservation-planning assessment for the South African province of KwaZulu-Natal, which forms the central component of the Maputaland-Pondoland-Albany biological diversity hotspot. Our objective was to enhance biological diversity protection while promoting sustainable development and providing spatial guidance in the resolution of potential policy conflicts over priority areas for conservation at risk of transformation. The conservation-planning assessment combined spatial-distribution models for 646 conservation features, spatial economic-return models for 28 alternative land uses, and spatial maps for 4 threats. Nature-based tourism businesses were competitive with other land uses and could provide revenues of >US$60 million/year to local stakeholders and simultaneously help meeting conservation goals for almost half the conservation features in the planning region. Accounting for opportunity costs substantially decreased conflicts between biological diversity, agricultural use, commercial forestry, and mining. Accounting for economic benefits arising from conservation and reducing potential policy conflicts with alternative plans for development can provide opportunities for successful strategies that combine conservation and sustainable development and facilitate conservation action. © 2013 Society for Conservation Biology.

  16. Atmospheric gravity waves in the Red Sea: a new hotspot

    KAUST Repository

    Magalhaes, J. M.

    2011-02-03

    The region of the Middle East around the Red Sea (between 32° E and 44° E longitude and 12° N and 28° N latitude) is a currently undocumented hotspot for atmospheric gravity waves (AGWs). Satellite imagery shows evidence that this region is prone to relatively high occurrence of AGWs compared to other areas in the world, and reveals the spatial characteristics of these waves. The favorable conditions for wave propagation in this region are illustrated with three typical cases of AGWs propagating in the lower troposphere over the sea. Using weakly nonlinear long wave theory and the observed characteristic wavelengths we obtain phase speeds which are consistent with those observed and typical for AGWs, with the Korteweg-de Vries theory performing slightly better than Benjamin-Davis-Acrivos-Ono theory as far as phase speeds are concerned. ERS-SAR and Envisat-ASAR satellite data analysis between 1993 and 2008 reveals signatures consistent with horizontally propagating large-scale internal waves. These signatures cover the entire Red Sea and are more frequently observed between April and September, although they also occur during the rest of the year. The region\\'s (seasonal) propagation conditions for AGWs, based upon average vertical atmospheric stratification profiles suggest that many of the signatures identified in the satellite images are atmospheric internal waves. © Author(s) 2011.

  17. Hotspot-mediated non-dissipative and ultrafast plasmon passage

    Science.gov (United States)

    Roller, Eva-Maria; Besteiro, Lucas V.; Pupp, Claudia; Khorashad, Larousse Khosravi; Govorov, Alexander O.; Liedl, Tim

    2017-08-01

    Plasmonic nanoparticles hold great promise as photon handling elements and as channels for coherent transfer of energy and information in future all-optical computing devices. Coherent energy oscillations between two spatially separated plasmonic entities via a virtual middle state exemplify electron-based population transfer, but their realization requires precise nanoscale positioning of heterogeneous particles. Here, we show the assembly and optical analysis of a triple-particle system consisting of two gold nanoparticles with an inter-spaced silver island. We observe strong plasmonic coupling between the spatially separated gold particles, mediated by the connecting silver particle, with almost no dissipation of energy. As the excitation energy of the silver island exceeds that of the gold particles, only quasi-occupation of the silver transfer channel is possible. We describe this effect both with exact classical electrodynamic modelling and qualitative quantum-mechanical calculations. We identify the formation of strong hotspots between all particles as the main mechanism for the lossless coupling and thus coherent ultrafast energy transfer between the remote partners. Our findings could prove useful for quantum gate operations, as well as for classical charge and information transfer processes.

  18. New law puts Bolivian biodiversity hotspot on road to deforestation.

    Science.gov (United States)

    Fernández-Llamazares, Álvaro; Helle, Joose; Eklund, Johanna; Balmford, Andrew; Mónica Moraes, R; Reyes-García, Victoria; Cabeza, Mar

    2018-01-08

    In August 2017, the Bolivian government passed a contentious law downgrading the legal protection of the Isiboro-Sécure National Park and Indigenous Territory (TIPNIS, for its Spanish acronym), the ancestral homeland of four lowland indigenous groups and one of Bolivia's most iconic protected areas. Due to its strategic position straddling the Andes and Amazonia, TIPNIS represents not only a key biodiversity hotspot in Bolivia, but one of the most biodiverse regions on Earth, harboring exceptional levels of endemism and globally important populations of megafauna, as well as protecting substantial topographic complexity likely to support both wildlife migration and species range shifts in response to climate change [1]. The new law, set to authorize the construction of a deeply-contested road through the core of the park, has reopened one of the highest profile socio-environmental conflicts in Latin America. Roads in tropical forests often lead to habitat conversion, and indeed within TIPNIS more than 58% of deforestation is concentrated 5 km or less away from existing roads. It, therefore, seems very likely that the planned road will magnify the current scale and pace of deforestation in TIPNIS, underscoring the urgent need for revisiting the road plans. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. Dynamic fracture and hot-spot modeling in energetic composites

    Science.gov (United States)

    Grilli, Nicolò; Duarte, Camilo A.; Koslowski, Marisol

    2018-02-01

    Defects such as cracks, pores, and particle-matrix interface debonding affect the sensitivity of energetic materials by reducing the time-to-ignition and the threshold pressure to initiate an explosion. Frictional sliding of preexisting cracks is considered to be one of the most important causes of localized heating. Therefore, understanding the dynamic fracture of crystalline energetic materials is of extreme importance to assess the reliability and safety of polymer-bonded explosives. Phase field damage model simulations, based on the regularization of the crack surface as a diffuse delta function, are used to describe crack propagation in cyclotetramethylene-tetranitramine crystals embedded in a Sylgard matrix. A thermal transport model that includes heat generation by friction at crack interfaces is coupled to the solution of crack propagation. 2D and 3D dynamic compression simulations are performed with different boundary velocities and initial distributions of cracks and interface defects to understand their effect on crack propagation and heat generation. It is found that, at an impact velocity of 400 m/s, localized damage at the particle-binder interface is of key importance and that the sample reaches temperatures high enough to create a hot-spot that will lead to ignition. At an impact velocity of 10 m/s, preexisting cracks advanced inside the particle, but the increase of temperature will not cause ignition.

  20. Near-island biological hotspots in barren ocean basins.

    Science.gov (United States)

    Gove, Jamison M; McManus, Margaret A; Neuheimer, Anna B; Polovina, Jeffrey J; Drazen, Jeffrey C; Smith, Craig R; Merrifield, Mark A; Friedlander, Alan M; Ehses, Julia S; Young, Charles W; Dillon, Amanda K; Williams, Gareth J

    2016-02-16

    Phytoplankton production drives marine ecosystem trophic-structure and global fisheries yields. Phytoplankton biomass is particularly influential near coral reef islands and atolls that span the oligotrophic tropical oceans. The paradoxical enhancement in phytoplankton near an island-reef ecosystem--Island Mass Effect (IME)--was first documented 60 years ago, yet much remains unknown about the prevalence and drivers of this ecologically important phenomenon. Here we provide the first basin-scale investigation of IME. We show that IME is a near-ubiquitous feature among a majority (91%) of coral reef ecosystems surveyed, creating near-island 'hotspots' of phytoplankton biomass throughout the upper water column. Variations in IME strength are governed by geomorphic type (atoll vs island), bathymetric slope, reef area and local human impacts (for example, human-derived nutrient input). These ocean oases increase nearshore phytoplankton biomass by up to 86% over oceanic conditions, providing basal energetic resources to higher trophic levels that support subsistence-based human populations.

  1. Drugs for rare disorders.

    Science.gov (United States)

    Cremers, Serge; Aronson, Jeffrey K

    2017-08-01

    Estimates of the frequencies of rare disorders vary from country to country; the global average defined prevalence is 40 per 100 000 (0.04%). Some occur in only one or a few patients. However, collectively rare disorders are fairly common, affecting 6-8% of the US population, or about 30 million people, and a similar number in the European Union. Most of them affect children and most are genetically determined. Diagnosis can be difficult, partly because of variable presentations and partly because few clinicians have experience of individual rare disorders, although they may be assisted by searching databases. Relatively few rare disorders have specific pharmacological treatments (so-called orphan drugs), partly because of difficulties in designing trials large enough to determine benefits and harms alike. Incentives have been introduced to encourage the development of orphan drugs, including tax credits and research aids, simplification of marketing authorization procedures and exemption from fees, and extended market exclusivity. Consequently, the number of applications for orphan drugs has grown, as have the costs of using them, so much so that treatments may not be cost-effective. It has therefore been suggested that not-for-profit organizations that are socially motivated to reduce those costs should be tasked with producing them. A growing role for patient organizations, improved clinical and translational infrastructures, and developments in genetics have also contributed to successful drug development. The translational discipline of clinical pharmacology is an essential component in drug development, including orphan drugs. Clinical pharmacologists, skilled in basic pharmacology and its links to clinical medicine, can be involved at all stages. They can contribute to the delineation of genetic factors that determine clinical outcomes of pharmacological interventions, develop biomarkers, design and perform clinical trials, assist regulatory decision

  2. RARE BRANCHIAL ARCH ANOMALIES

    Directory of Open Access Journals (Sweden)

    Jayanta Kumar

    2016-03-01

    Full Text Available AIM Amongst the branchial arch anomalies third arch anomaly occurs rarely and more so the fourth arch anomalies. We present our experience with cases of rare branchial arch anomalies. PATIENTS AND METHODS From June 2006 to January 2016, cases having their external opening in the lower third of sternocleidomastoid muscle with the tract going through thyroid gland and directing to pyriform sinus (PFS or cysts with internal opening in the PFS were studied. RESULTS No fourth arch anomaly was encountered. One cyst with internal opening which later on formed a fistula, three fistulae from beginning and two sinuses were encountered. The main stay of diagnosis was the fistula in the PFS and the tract lying posterior to the internal carotid artery. Simple excision technique with a small incision around the external opening was done. There was no recurrence. CONCLUSION Third arch fistula is not very rare as it was thought. Internal fistula is found in most of the cases. Though radiological investigations are helpful, fistulae can be diagnosed clinically and during operation. Extensive operation of the neck, mediastinum and pharynx is not required.

  3. Complete genomes of Hairstreak butterflies, their speciation, and nucleo-mitochondrial incongruence.

    Science.gov (United States)

    Cong, Qian; Shen, Jinhui; Borek, Dominika; Robbins, Robert K; Otwinowski, Zbyszek; Grishin, Nick V

    2016-04-28

    Comparison of complete genomes of closely related species enables research on speciation and how phenotype is determined by genotype. Lepidoptera, an insect order of 150,000 species with diverse phenotypes, is well-suited for such comparative genomics studies if new genomes, which cover additional Lepidoptera families are acquired. We report a 729 Mbp genome assembly of the Calycopis cecrops, the first genome from the family Lycaenidae and the largest available Lepidoptera genome. As detritivore, Calycopis shows expansion in detoxification and digestion enzymes. We further obtained complete genomes of 8 Calycopis specimens: 3 C. cecrops and 5 C. isobeon, including a dry specimen stored in the museum for 30 years. The two species differ subtly in phenotype and cannot be differentiated by mitochondrial DNA. However, nuclear genomes revealed a deep split between them. Genes that can clearly separate the two species (speciation hotspots) mostly pertain to circadian clock, mating behavior, transcription regulation, development and cytoskeleton. The speciation hotspots and their function significantly overlap with those we previously found in Pterourus, suggesting common speciation mechanisms in these butterflies.

  4. Generation of mutation hotspots in ageing bacterial colonies

    DEFF Research Database (Denmark)

    Sekowska, Agnieszka; Wendel, Sofie; Nørholm, Morten

    How do ageing bacterial colonies generate adaptive mutants? Over a period of two months, we isolated on ageing colonies outgrowing mutants able to use a new carbon source, and sequenced their genomes. This allowed us to uncover exquisite details on the molecular mechanism behind their adaptation:...

  5. Evolutionary melting pots: a biodiversity hotspot shaped by ring diversifications around the Black Sea in the Eastern tree frog (Hyla orientalis).

    Science.gov (United States)

    Dufresnes, Christophe; Litvinchuk, Spartak N; Leuenberger, Julien; Ghali, Karim; Zinenko, Oleksandr; Stöck, Matthias; Perrin, Nicolas

    2016-09-01

    Hotspots of intraspecific genetic diversity, which are of primary importance for the conservation of species, have been associated with glacial refugia, that is areas where species survived the Quaternary climatic oscillations. However, the proximate mechanisms generating these hotspots remain an open issue. Hotspots may reflect the long-term persistence of large refugial populations; alternatively, they may result from allopatric differentiation between small and isolated populations, that later admixed. Here, we test these two scenarios in a widely distributed species of tree frog, Hyla orientalis, which inhabits Asia Minor and southeastern Europe. We apply a fine-scale phylogeographic survey, combining fast-evolving mitochondrial and nuclear markers, with a dense sampling throughout the range, as well as ecological niche modelling, to understand what shaped the genetic variation of this species. We documented an important diversity centre around the Black Sea, composed of multiple allopatric and/or parapatric diversifications, likely driven by a combination of Pleistocene climatic fluctuations and complex regional topography. Remarkably, this diversification forms a ring around the Black Sea, from the Caucasus through Anatolia and eastern Europe, with terminal forms coming into contact and partially admixing in Crimea. Our results support the view that glacial refugia generate rather than host genetic diversity and can also function as evolutionary melting pots of biodiversity. Moreover, we report a new case of ring diversification, triggered by a large, yet cohesive dispersal barrier, a very rare situation in nature. Finally, we emphasize the Black Sea region as an important centre of intraspecific diversity in the Palearctic with implications for conservation. © 2016 John Wiley & Sons Ltd.

  6. Predictable hotspots and foraging habitat of the endangered short-tailed albatross (Phoebastria albatrus) in the North Pacific: Implications for conservation

    Science.gov (United States)

    Piatt, John F.; Wetzel, J.; Bell, K.; DeGange, A.R.; Balogh, G.R.; Drew, G.S.; Geernaert, T.; Ladd, C.; Byrd, G.V.

    2006-01-01

    The short-tailed albatross (Phoebastria albatrus) is a rare and endangered seabird that ranges widely over the northern North Pacific. Populations are slowly recovering but birds face several threats at sea, in particular the incidental capture of birds in long-line fisheries. Conservation efforts are hampered by a lack of information about the at-sea distribution of this species, especially knowledge of where it may predictably co-occur with long-line fishing effort. During 18 years of transiting the Aleutian Islands Unit of the Alaska Maritime National Wildlife Refuge on a research vessel, we observed short-tailed albatross on 65 occasions. They were consistently observed near Ingenstrem Rocks (Buldir Pass) in the western Aleutians and near Seguam Pass in the central Aleutians. Based on the oceanographic characteristics of the locations where we saw most of the birds, we hypothesized that short-tailed albatross “hotspots” were located where tidal currents and steep bottom topography generate strong vertical mixing along the Aleutian Archipelago. As a test of this hypothesis, we analyzed a database containing 1432 opportunistic observations of 2463 short-tailed albatross at sea in the North Pacific. These data showed that short-tailed albatross were closely associated with shelf-edge habitats throughout the northern Gulf of Alaska and Bering Sea. In addition to Ingenstrem Rocks and Seguam Pass, important hotspots for short-tailed albatross in the Aleutians included Near Strait, Samalga Pass, and the shelf-edge south of Umnak/Unalaska islands. In the Bering Sea, hotspots were located along margins of Zhemchug, St. Matthews and Pervenets canyons. Because these short-tailed albatross hotspots are predictable, they are also protectable by regulation of threatening activities at local spatial scales.

  7. Genomic networks of hybrid sterility.

    Directory of Open Access Journals (Sweden)

    Leslie M Turner

    2014-02-01

    Full Text Available Hybrid dysfunction, a common feature of reproductive barriers between species, is often caused by negative epistasis between loci ("Dobzhansky-Muller incompatibilities". The nature and complexity of hybrid incompatibilities remain poorly understood because identifying interacting loci that affect complex phenotypes is difficult. With subspecies in the early stages of speciation, an array of genetic tools, and detailed knowledge of reproductive biology, house mice (Mus musculus provide a model system for dissecting hybrid incompatibilities. Male hybrids between M. musculus subspecies often show reduced fertility. Previous studies identified loci and several X chromosome-autosome interactions that contribute to sterility. To characterize the genetic basis of hybrid sterility in detail, we used a systems genetics approach, integrating mapping of gene expression traits with sterility phenotypes and QTL. We measured genome-wide testis expression in 305 male F2s from a cross between wild-derived inbred strains of M. musculus musculus and M. m. domesticus. We identified several thousand cis- and trans-acting QTL contributing to expression variation (eQTL. Many trans eQTL cluster into eleven 'hotspots,' seven of which co-localize with QTL for sterility phenotypes identified in the cross. The number and clustering of trans eQTL-but not cis eQTL-were substantially lower when mapping was restricted to a 'fertile' subset of mice, providing evidence that trans eQTL hotspots are related to sterility. Functional annotation of transcripts with eQTL provides insights into the biological processes disrupted by sterility loci and guides prioritization of candidate genes. Using a conditional mapping approach, we identified eQTL dependent on interactions between loci, revealing a complex system of epistasis. Our results illuminate established patterns, including the role of the X chromosome in hybrid sterility. The integrated mapping approach we employed is

  8. Genomic networks of hybrid sterility.

    Science.gov (United States)

    Turner, Leslie M; White, Michael A; Tautz, Diethard; Payseur, Bret A

    2014-02-01

    Hybrid dysfunction, a common feature of reproductive barriers between species, is often caused by negative epistasis between loci ("Dobzhansky-Muller incompatibilities"). The nature and complexity of hybrid incompatibilities remain poorly understood because identifying interacting loci that affect complex phenotypes is difficult. With subspecies in the early stages of speciation, an array of genetic tools, and detailed knowledge of reproductive biology, house mice (Mus musculus) provide a model system for dissecting hybrid incompatibilities. Male hybrids between M. musculus subspecies often show reduced fertility. Previous studies identified loci and several X chromosome-autosome interactions that contribute to sterility. To characterize the genetic basis of hybrid sterility in detail, we used a systems genetics approach, integrating mapping of gene expression traits with sterility phenotypes and QTL. We measured genome-wide testis expression in 305 male F2s from a cross between wild-derived inbred strains of M. musculus musculus and M. m. domesticus. We identified several thousand cis- and trans-acting QTL contributing to expression variation (eQTL). Many trans eQTL cluster into eleven 'hotspots,' seven of which co-localize with QTL for sterility phenotypes identified in the cross. The number and clustering of trans eQTL-but not cis eQTL-were substantially lower when mapping was restricted to a 'fertile' subset of mice, providing evidence that trans eQTL hotspots are related to sterility. Functional annotation of transcripts with eQTL provides insights into the biological processes disrupted by sterility loci and guides prioritization of candidate genes. Using a conditional mapping approach, we identified eQTL dependent on interactions between loci, revealing a complex system of epistasis. Our results illuminate established patterns, including the role of the X chromosome in hybrid sterility. The integrated mapping approach we employed is applicable in a broad

  9. Rare Earth Polyoxometalates.

    Science.gov (United States)

    Boskovic, Colette

    2017-09-19

    Longstanding and important applications make use of the chemical and physical properties of both rare earth metals and polyoxometalates of early transition metals. The catalytic, optical, and magnetic features of rare earth metal ions are well-known, as are the reversible multielectron redox and photoredox capabilities of polyoxomolybdates and polyoxotungstates. The combination of rare earth ions and polyoxometalates in discrete molecules and coordination polymers is of interest for the unique combination of chemical and physical properties that can arise. This Account surveys our efforts to synthesize and investigate compounds with rare earth ions and polyoxometalates (RE-POMs), sometimes with carboxylate-based organic coligands. Our general synthetic approach is "bottom-up", which affords well-defined nanoscale molecules, typically in crystalline form and amenable to single-crystal X-ray diffraction for structure determination. Our particular focus is on elucidation of the physical properties conferred by the different structural components with a view to ultimately being able to tune these properties chemically. For this purpose, we employ a variety of spectroscopic, magnetochemical, electrochemical, and scattering techniques in concert with theoretical modeling and computation. Studies of RE-POM single-molecule magnets (SMMs) have utilized magnetic susceptibility, inelastic neutron scattering, and ab initio calculations. These investigations have allowed characterization of the crystal field splitting of the rare earth(III) ions that is responsible for the SMM properties of slow magnetic relaxation and magnetization quantum tunneling. Such SMMs are promising for applications in quantum computing and molecular spintronics. Photophysical measurements of a family of hybrid RE-POMs with organic ligands have afforded insights into sensitization of Tb(III) and Eu(III) emission through both organic and polyoxometalate chromophores in the same molecule. Detailed

  10. A framework for identifying carbon hotspots and forest management drivers

    Science.gov (United States)

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

    2013-01-01

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

  11. Global Natural Disaster Risk Hotspots: Transition to a Regional Approach

    Science.gov (United States)

    Lerner-Lam, A.; Chen, R.; Dilley, M.

    2005-12-01

    The "Hotspots Project" is a collaborative study of the global distribution and occurrence of multiple natural hazards and the associated exposures of populations and their economic output. In this study we assess the global risks of two disaster-related outcomes: mortality and economic losses. We estimate risk levels by combining hazard exposure with historical vulnerability for two indicators of elements at risk-gridded population and Gross Domestic Product (GDP) per unit area - for six major natural hazards: earthquakes, volcanoes, landslides, floods, drought, and cyclones. By calculating relative risks for each grid cell rather than for countries as a whole, we are able to estimate risk levels at sub-national scales. These can then be used to estimate aggregate relative multiple hazard risk at regional and national scales. Mortality-related risks are assessed on a 2.5' x 2.5' latitude-longitude grid of global population (GPW Version 3). Economic risks are assessed at the same resolution for gridded GDP per unit area, using World Bank estimates of GDP based on purchasing power parity. Global hazard data were compiled from multiple sources. The project collaborated directly with UNDP and UNEP, the International Research Institute for Climate Prediction (IRI) at Columbia, and the Norwegian Geotechnical Institute (NGI) in the creation of data sets for several hazards for which global data sets did not previously exist. Drought, flood and volcano hazards are characterized in terms of event frequency, storms by frequency and severity, earthquakes by frequency and ground acceleration exceedance probability, and landslides by an index derived from probability of occurrence. The global analysis undertaken in this project is clearly limited by issues of scale as well as by the availability and quality of data. For some hazards, there exist only 15- to 25-year global records with relatively crude spatial information. Data on historical disaster losses, and particularly on

  12. Rainfall-induced landslides in Europe: hotspots and thresholds (Invited)

    Science.gov (United States)

    Cepeda, J.; Jaedicke, C.; Nadim, F.; Kalsnes, B.

    2010-12-01

    This contribution presents preliminary results of the European project SafeLand. SafeLand is a large-scale integrating collaborative research project on landslide risks in Europe, funded by the Seventh Framework Programme for research and technological development (FP7) of the European Commission. SafeLand was launched in May 2009 and will run for three years. The project team, which comprises 27 institutions from 12 European countries, is coordinated by the International Centre for Geohazards (ICG) in Norway. SafeLand aims to develop and implement an integrated and comprehensive approach to help and guide decision-making in connection with mitigation of landslide risks. Quantifying the effects of global change (changes in demography and climate change) on evolution of landslide risk in Europe is one of the main goals of SafeLand. The methodologies are tested in selected hazard and risk "hotspots” in Europe, in turn improving knowledge, methodologies and integration strategies for the management of landslide risk. The present contribution is focused on two components of SafeLand: (1) the identification of landslide hazard and risk hotspots and (2) the estimation and assessment of rainfall thresholds for triggering of landslides. Hotspots of landslide hazard and risk were identified by an objective GIS-based analysis. The results show clearly where landslide pose the largest hazard in Europe and the objective approach allows a ranking of the countries by exposed area and population. In absolute numbers, Italy is the country with the highest amount of area and population exposed. Relative to absolute number of inhabitants and area, small alpine countries such as Lichtenstein and Montenegro score highest where as much as 40% of the population could be exposed. It is obvious that the type and quality of the input data are decisive for the quality of the results. Especially the estimation of extreme precipitation events needs improvement. These preliminary results are

  13. Genomic instability and radiation

    Energy Technology Data Exchange (ETDEWEB)

    Little, John B [Harvard School of Public Health, Boston, MA 02115 (United States)

    2003-06-01

    Genomic instability is a hallmark of cancer cells, and is thought to be involved in the process of carcinogenesis. Indeed, a number of rare genetic disorders associated with a predisposition to cancer are characterised by genomic instability occurring in somatic cells. Of particular interest is the observation that transmissible instability can be induced in somatic cells from normal individuals by exposure to ionising radiation, leading to a persistent enhancement in the rate at which mutations and chromosomal aberrations arise in the progeny of the irradiated cells after many generations of replication. If such induced instability is involved in radiation carcinogenesis, it would imply that the initial carcinogenic event may not be a rare mutation occurring in a specific gene or set of genes. Rather, radiation may induce a process of instability in many cells in a population, enhancing the rate at which the multiple gene mutations necessary for the development of cancer may arise in a given cell lineage. Furthermore, radiation could act at any stage in the development of cancer by facilitating the accumulation of the remaining genetic events required to produce a fully malignant tumour. The experimental evidence for such induced instability is reviewed. (review)

  14. Genomic instability and radiation

    International Nuclear Information System (INIS)

    Little, John B

    2003-01-01

    Genomic instability is a hallmark of cancer cells, and is thought to be involved in the process of carcinogenesis. Indeed, a number of rare genetic disorders associated with a predisposition to cancer are characterised by genomic instability occurring in somatic cells. Of particular interest is the observation that transmissible instability can be induced in somatic cells from normal individuals by exposure to ionising radiation, leading to a persistent enhancement in the rate at which mutations and chromosomal aberrations arise in the progeny of the irradiated cells after many generations of replication. If such induced instability is involved in radiation carcinogenesis, it would imply that the initial carcinogenic event may not be a rare mutation occurring in a specific gene or set of genes. Rather, radiation may induce a process of instability in many cells in a population, enhancing the rate at which the multiple gene mutations necessary for the development of cancer may arise in a given cell lineage. Furthermore, radiation could act at any stage in the development of cancer by facilitating the accumulation of the remaining genetic events required to produce a fully malignant tumour. The experimental evidence for such induced instability is reviewed. (review)

  15. Performance and consistency of indicator groups in two biodiversity hotspots.

    Directory of Open Access Journals (Sweden)

    Joaquim Trindade-Filho

    Full Text Available In a world limited by data availability and limited funds for conservation, scientists and practitioners must use indicator groups to define spatial conservation priorities. Several studies have evaluated the effectiveness of indicator groups, but still little is known about the consistency in performance of these groups in different regions, which would allow their a priori selection.We systematically examined the effectiveness and the consistency of nine indicator groups in representing mammal species in two top-ranked Biodiversity Hotspots (BH: the Brazilian Cerrado and the Atlantic Forest. To test for group effectiveness we first found the best sets of sites able to maximize the representation of each indicator group in the BH and then calculated the average representation of different target species by the indicator groups in the BH. We considered consistent indicator groups whose representation of target species was not statistically different between BH. We called effective those groups that outperformed the target-species representation achieved by random sets of species. Effective indicator groups required the selection of less than 2% of the BH area for representing target species. Restricted-range species were the most effective indicators for the representation of all mammal diversity as well as target species. It was also the only group with high consistency.We show that several indicator groups could be applied as shortcuts for representing mammal species in the Cerrado and the Atlantic Forest to develop conservation plans, however, only restricted-range species consistently held as the most effective indicator group for such a task. This group is of particular importance in conservation planning as it captures high diversity of endemic and endangered species.

  16. Performance and consistency of indicator groups in two biodiversity hotspots.

    Science.gov (United States)

    Trindade-Filho, Joaquim; Loyola, Rafael Dias

    2011-01-01

    In a world limited by data availability and limited funds for conservation, scientists and practitioners must use indicator groups to define spatial conservation priorities. Several studies have evaluated the effectiveness of indicator groups, but still little is known about the consistency in performance of these groups in different regions, which would allow their a priori selection. We systematically examined the effectiveness and the consistency of nine indicator groups in representing mammal species in two top-ranked Biodiversity Hotspots (BH): the Brazilian Cerrado and the Atlantic Forest. To test for group effectiveness we first found the best sets of sites able to maximize the representation of each indicator group in the BH and then calculated the average representation of different target species by the indicator groups in the BH. We considered consistent indicator groups whose representation of target species was not statistically different between BH. We called effective those groups that outperformed the target-species representation achieved by random sets of species. Effective indicator groups required the selection of less than 2% of the BH area for representing target species. Restricted-range species were the most effective indicators for the representation of all mammal diversity as well as target species. It was also the only group with high consistency. We show that several indicator groups could be applied as shortcuts for representing mammal species in the Cerrado and the Atlantic Forest to develop conservation plans, however, only restricted-range species consistently held as the most effective indicator group for such a task. This group is of particular importance in conservation planning as it captures high diversity of endemic and endangered species.

  17. Orchid conservation in the biodiversity hotspot of southwestern China.

    Science.gov (United States)

    Liu, Qiang; Chen, Jin; Corlett, Richard T; Fan, XuLi; Yu, DongLi; Yang, HongPei; Gao, JiangYun

    2015-12-01

    Xishuangbanna is on the northern margins of tropical Asia in southwestern China and has the largest area of tropical forest remaining in the country. It is in the Indo-Burma hotspot and contains 16% of China's vascular flora in biodiversity. To understand the effects of land-use change and collection on orchid species diversity and determine protection priorities, we conducted systematic field surveys, observed markets, interviewed orchid collectors, and then determined the conservation status of all orchids. We identified 426 orchid species in 115 genera in Xishuangbanna: 31% of all orchid species that occur in China. Species richness was highest at 1000-1200 m elevation. Three orchid species were assessed as possibly extinct in the wild, 15 as critically endangered, 82 as endangered, 124 as vulnerable, 186 as least concern, and 16 as data deficient. Declines over 20 years in harvested species suggested over-collection was the major threat, and utility value (i.e., medicinal or ornamental value) was significantly related to endangerment. Expansion of rubber tree plantations was less of a threat to orchids than to other taxa because only 75 orchid species (17.6%) occurred below the 1000-m-elevation ceiling for rubber cultivation, and most of these (46) occurred in nature reserves. However, climate change is projected to lift this ceiling to around 1300 m by 2050, and the limited area at higher elevations reduces the potential for upslope range expansion. The Xishuangbanna Tropical Botanical Garden is committed to achieving zero plant extinctions in Xishuangbanna, and orchids are a high priority. Appropriate in and ex situ conservation strategies, including new protected areas and seed banking, have been developed for every threatened orchid species and are being implemented. © 2015 Society for Conservation Biology.

  18. Multisectoral Climate Impact Hotspots in a Warming World

    Science.gov (United States)

    Piontek, Franziska; Mueller, Christoph; Pugh, Thomas A. M.; Clark, Douglas B.; Deryng, Delphine; Elliott, Joshua; deJesusColonGonzalez, Felipe; Floerke, Martina; Folberth, Christian; Franssen, Wietse; hide

    2014-01-01

    The impacts of global climate change on different aspects of humanity's diverse life-support systems are complex and often difficult to predict. To facilitate policy decisions on mitigation and adaptation strategies, it is necessary to understand, quantify, and synthesize these climate-change impacts, taking into account their uncertainties. Crucial to these decisions is an understanding of how impacts in different sectors overlap, as overlapping impacts increase exposure, lead to interactions of impacts, and are likely to raise adaptation pressure. As a first step we develop herein a framework to study coinciding impacts and identify regional exposure hotspots. This framework can then be used as a starting point for regional case studies on vulnerability and multifaceted adaptation strategies. We consider impacts related to water, agriculture, ecosystems, and malaria at different levels of global warming. Multisectoral overlap starts to be seen robustly at a mean global warming of 3 degC above the 1980-2010 mean, with 11% of the world population subject to severe impacts in at least two of the four impact sectors at 4 degC. Despite these general conclusions, we find that uncertainty arising from the impact models is considerable, and larger than that from the climate models. In a low probability-high impact worst-case assessment, almost the whole inhabited world is at risk for multisectoral pressures. Hence, there is a pressing need for an increased research effort to develop a more comprehensive understanding of impacts, as well as for the development of policy measures under existing uncertainty.

  19. Fish ladders: safe fish passage or hotspot for predation?

    Directory of Open Access Journals (Sweden)

    Angelo Antonio Agostinho

    Full Text Available Fish ladders are a strategy for conserving biodiversity, as they can provide connectivity between fragmented habitats and reduce predation on shoals that accumulate immediately below dams. Although the impact of predation downstream of reservoirs has been investigated, especially in juvenile salmonids during their downstream movements, nothing is known about predation on Neotropical fish in the attraction and containment areas commonly found in translocation facilities. This study analysed predation in a fish passage system at the Lajeado Dam on the Tocantins River in Brazil. The abundance, distribution, and the permanence (time spent of large predatory fish along the ladder, the injuries imposed by piranhas during passage and the presence of other vertebrate predators were investigated. From December 2002 to October 2003, sampling was conducted in four regions (downstream, along the ladder, in the forebay, and upstream of the reservoir using gillnets, cast nets and counts or visual observations. The captured fish were tagged with thread and beads, and any mutilations were registered. Fish, birds and dolphins were the main predator groups observed, with a predominance of the first two groups. The entrance to the ladder, in the downstream region, was the area with the highest number of large predators and was the only region with relevant non-fish vertebrates. The main predatory fish species were Rhaphiodon vulpinus, Hydrolycus armatus, and Serrasalmus rhombeus. Tagged individuals were detected predating along the ladder for up to 90 days. Mutilations caused by Serrasalmus attacks were noted in 36% of species and 4% of individuals at the top of the ladder. Our results suggested that the high density of fish in the restricted ladder environment, which is associated with injuries suffered along the ladder course and the presence of multiple predator groups with different predation strategies, transformed the fish corridor into a hotspot for

  20. Arid urban ecosystem not a hotspot for N deposition

    Science.gov (United States)

    Grimm, N. B.; Cook, E. M.; Hall, S. J.; Wheeler, M.

    2017-12-01

    Urban areas are omitted in most long-term data collection for nitrogen deposition in the United States. Nitrogen sources in and surrounding cities are notoriously variable in space and time. In the desert Southwest, cities are distinct and isolated from one another, deposition is dominated by dryfall, and rainfall is spatially and temporally heterogeneous. These conditions present a challenge for understanding the overall rate, spatial pattern, and fate of nitrogen deposition in urbanized aridlands. We quantified long-term spatial and temporal patterns of inorganic nitrogen deposition in protected aridland ecosystems across an extensive urban-rural gradient in central Arizona, using multiple sampling methods. Furthermore, we assessed the impact of nitrogen deposition along the same gradient on winter annual plant growth and community structure, as an integrative indicator of the fate and impact of nitrogen deposition. Best estimates of nitrogen deposition, based on ion-exchange resin collectors, wet-dry bucket collectors, and inferential estimates of dryfall using passive samplers, were 7.2 ± 0.4 kg N ha-1 y-1 within city boundaries and 6.1 ± 0.3 kg N ha-1 y-1 in nearby desert lands. Although the data indicate the city may not be a hotspot of nitrogen deposition, species diversity of annual plants in urban desert remnant parks is reduced in a manner similar to diversity losses associated with experimental nitrogen fertilization. Thus, reduced species diversity is a possible consequence of locally elevated nitrogen deposition within the city. The long-term mean urban deposition rate estimated with mixed methods is substantially lower than that predicted by regional models and by estimated inorganic nitrogen fixation from automobile and other combustion sources. This discrepancy raises a question about the fate of this excess nitrogen in the larger aridland region.

  1. Norepinephrine ignites local hotspots of neuronal excitation: How arousal amplifies selectivity in perception and memory.

    Science.gov (United States)

    Mather, Mara; Clewett, David; Sakaki, Michiko; Harley, Carolyn W

    2016-01-01

    Emotional arousal enhances perception and memory of high-priority information but impairs processing of other information. Here, we propose that, under arousal, local glutamate levels signal the current strength of a representation and interact with norepinephrine (NE) to enhance high priority representations and out-compete or suppress lower priority representations. In our "glutamate amplifies noradrenergic effects" (GANE) model, high glutamate at the site of prioritized representations increases local NE release from the locus coeruleus (LC) to generate "NE hotspots." At these NE hotspots, local glutamate and NE release are mutually enhancing and amplify activation of prioritized representations. In contrast, arousal-induced LC activity inhibits less active representations via two mechanisms: 1) Where there are hotspots, lateral inhibition is amplified; 2) Where no hotspots emerge, NE levels are only high enough to activate low-threshold inhibitory adrenoreceptors. Thus, LC activation promotes a few hotspots of excitation in the context of widespread suppression, enhancing high priority representations while suppressing the rest. Hotspots also help synchronize oscillations across neural ensembles transmitting high-priority information. Furthermore, brain structures that detect stimulus priority interact with phasic NE release to preferentially route such information through large-scale functional brain networks. A surge of NE before, during, or after encoding enhances synaptic plasticity at NE hotspots, triggering local protein synthesis processes that enhance selective memory consolidation. Together, these noradrenergic mechanisms promote selective attention and memory under arousal. GANE not only reconciles apparently contradictory findings in the emotion-cognition literature but also extends previous influential theories of LC neuromodulation by proposing specific mechanisms for how LC-NE activity increases neural gain.

  2. Multifaceted diversity-area relationships reveal global hotspots of mammalian species, trait and lineage diversity.

    Science.gov (United States)

    Mazel, Florent; Guilhaumon, François; Mouquet, Nicolas; Devictor, Vincent; Gravel, Dominique; Renaud, Julien; Cianciaruso, Marcus Vinicius; Loyola, Rafael Dias; Diniz-Filho, José Alexandre Felizola; Mouillot, David; Thuiller, Wilfried

    2014-08-01

    To define biome-scale hotspots of phylogenetic and functional mammalian biodiversity (PD and FD, respectively) and compare them to 'classical' hotspots based on species richness (SR) only. Global. SR, PD & FD were computed for 782 terrestrial ecoregions using distribution ranges of 4616 mammalian species. We used a set of comprehensive diversity indices unified by a recent framework that incorporates the species relative coverage in each ecoregion. We build large-scale multifaceted diversity-area relationships to rank ecoregions according to their levels of biodiversity while accounting for the effect of area on each diversity facet. Finally we defined hotspots as the top-ranked ecoregions. While ignoring species relative coverage led to a relative good congruence between biome top ranked SR, PD and FD hotspots, ecoregions harboring a rich and abundantly represented evolutionary history and functional diversity did not match with top ranked ecoregions defined by species richness. More importantly PD and FD hotspots showed important spatial mismatches. We also found that FD and PD generally reached their maximum values faster than species richness as a function of area. The fact that PD/FD reach faster their maximal value than SR may suggest that the two former facets might be less vulnerable to habitat loss than the latter. While this point is expected, it is the first time that it is quantified at global scale and should have important consequences in conservation. Incorporating species relative coverage into the delineation of multifaceted hotspots of diversity lead to weak congruence between SR, PD and FD hotspots. This means that maximizing species number may fail at preserving those nodes (in the phylogenetic or functional tree) that are relatively abundant in the ecoregion. As a consequence it may be of prime importance to adopt a multifaceted biodiversity perspective to inform conservation strategies at global scale.

  3. Hotspots of species richness, threat and endemism for terrestrial vertebrates in SW Europe

    Science.gov (United States)

    Pascual, López-López; Luigi, Maiorano; Alessandra, Falcucci; Emilio, Barba; Luigi, Boitani

    2011-09-01

    The Mediterranean basin, and the Iberian Peninsula in particular, represent an outstanding "hotspot" of biological diversity with a long history of integration between natural ecosystems and human activities. Using deductive distribution models, and considering both Spain and Portugal, we downscaled traditional range maps for terrestrial vertebrates (amphibians, breeding birds, mammals and reptiles) to the finest possible resolution with the data at hand, and we identified hotspots based on three criteria: i) species richness; ii) vulnerability, and iii) endemism. We also provided a first evaluation of the conservation status of biodiversity hotspots based on these three criteria considering both existing and proposed protected areas (i.e., Natura 2000). For the identification of hotspots, we used a method based on the cumulative distribution functions of species richness values. We found no clear surrogacy among the different types of hotspots in the Iberian Peninsula. The most important hotspots (considering all criteria) are located in the western and southwestern portions of the study area, in the Mediterranean biogeographical region. Existing protected areas are not specifically concentrated in areas of high species richness, with only 5.2% of the hotspots of total richness being currently protected. The Natura 2000 network can potentially constitute an important baseline for protecting vertebrate diversity in the Iberian Peninsula although further improvements are needed. We suggest taking a step forward in conservation planning in the Mediterranean basin, explicitly considering the history of the region as well as its present environmental context. This would allow moving from traditional reserve networks (conservation focused on "patterns") to considerations about the "processes" that generated present biodiversity.

  4. Automated hotspot analysis with aerial image CD metrology for advanced logic devices

    Science.gov (United States)

    Buttgereit, Ute; Trautzsch, Thomas; Kim, Min-ho; Seo, Jung-Uk; Yoon, Young-Keun; Han, Hak-Seung; Chung, Dong Hoon; Jeon, Chan-Uk; Meyers, Gary

    2014-09-01

    Continuously shrinking designs by further extension of 193nm technology lead to a much higher probability of hotspots especially for the manufacturing of advanced logic devices. The CD of these potential hotspots needs to be precisely controlled and measured on the mask. On top of that, the feature complexity increases due to high OPC load in the logic mask design which is an additional challenge for CD metrology. Therefore the hotspot measurements have been performed on WLCD from ZEISS, which provides the benefit of reduced complexity by measuring the CD in the aerial image and qualifying the printing relevant CD. This is especially of advantage for complex 2D feature measurements. Additionally, the data preparation for CD measurement becomes more critical due to the larger amount of CD measurements and the increasing feature diversity. For the data preparation this means to identify these hotspots and mark them automatically with the correct marker required to make the feature specific CD measurement successful. Currently available methods can address generic pattern but cannot deal with the pattern diversity of the hotspots. The paper will explore a method how to overcome those limitations and to enhance the time-to-result in the marking process dramatically. For the marking process the Synopsys WLCD Output Module was utilized, which is an interface between the CATS mask data prep software and the WLCD metrology tool. It translates the CATS marking directly into an executable WLCD measurement job including CD analysis. The paper will describe the utilized method and flow for the hotspot measurement. Additionally, the achieved results on hotspot measurements utilizing this method will be presented.

  5. Where the wild things are: Predicting hotspots of seabird aggregations in the California Current System

    Science.gov (United States)

    Nur, N.; Jahncke, J.; Herzog, M.P.; Howar, J.; Hyrenbach, K.D.; Zamon, J.E.; Ainley, D.G.; Wiens, J.A.; Morgan, K.; Balance, L.T.; Stralberg, D.

    2011-01-01

    Marine Protected Areas (MPAs) provide an important tool for conservation of marine ecosystems. To be most effective, these areas should be strategically located in a manner that supports ecosystem function. To inform marine spatial planning and support strategic establishment of MPAs within the California Current System, we identified areas predicted to support multispecies aggregations of seabirds ("hotspot????). We developed habitat-association models for 16 species using information from at-sea observations collected over an 11-year period (1997-2008), bathymetric data, and remotely sensed oceanographic data for an area from north of Vancouver Island, Canada, to the USA/Mexico border and seaward 600 km from the coast. This approach enabled us to predict distribution and abundance of seabirds even in areas of few or no surveys. We developed single-species predictive models using a machine-learning algorithm: bagged decision trees. Single-species predictions were then combined to identify potential hotspots of seabird aggregation, using three criteria: (1) overall abundance among species, (2) importance of specific areas ("core area????) to individual species, and (3) predicted persistence of hotspots across years. Model predictions were applied to the entire California Current for four seasons (represented by February, May, July, and October) in each of 11 years. Overall, bathymetric variables were often important predictive variables, whereas oceanographic variables derived from remotely sensed data were generally less important. Predicted hotspots often aligned with currently protected areas (e.g., National Marine Sanctuaries), but we also identified potential hotspots in Northern California/Southern Oregon (from Cape Mendocino to Heceta Bank), Southern California (adjacent to the Channel Islands), and adjacent to Vancouver Island, British Columbia, that are not currently included in protected areas. Prioritization and identification of multispecies hotspots

  6. Rare B decays at LEP

    CERN Document Server

    Kluit, P M

    2001-01-01

    The results of the LEP experiments for rare B decays will be reviewed, covering hadronic final states, radiative and other rare decays and results for the inclusive charmless branching ratio. (8 refs).

  7. Herbarium genomics

    DEFF Research Database (Denmark)

    Bakker, Freek T.; Lei, Di; Yu, Jiaying

    2016-01-01

    Herbarium genomics is proving promising as next-generation sequencing approaches are well suited to deal with the usually fragmented nature of archival DNA. We show that routine assembly of partial plastome sequences from herbarium specimens is feasible, from total DNA extracts and with specimens...... up to 146 years old. We use genome skimming and an automated assembly pipeline, Iterative Organelle Genome Assembly, that assembles paired-end reads into a series of candidate assemblies, the best one of which is selected based on likelihood estimation. We used 93 specimens from 12 different...... correlation between plastome coverage and nuclear genome size (C value) in our samples, but the range of C values included is limited. Finally, we conclude that routine plastome sequencing from herbarium specimens is feasible and cost-effective (compared with Sanger sequencing or plastome...

  8. A rare sight

    CERN Multimedia

    Antonella Del Rosso and The LHCb Collaboration

    2012-01-01

    Today, at the Hadron Collider Physics Symposium in Kyoto, the LHCb collaboration has presented the evidence of a very rare B decay, the rarest ever seen. The result further shrinks the region in which scientists can still look for supersymmetry.   The graph showing evidence of the Bs0 → μ+ μ- decay. The result was presented Monday 12 November at the HCP Conference in Kyoto (photo courtesy of the LHCb Collaboration). Particle decays tell us about the inner properties and functioning of Nature’s physics processes. By studying them and their occurrence, physicists infer the rules that control them. Often, it turns out that some rare decays, which are very difficult to observe, are those in which Nature could reveal the presence of new physics. This is the case of some decays of the Bs0 particle (a particle made of a bottom anti-quark bound to a strange quark), and in particular Bs0 → μ+ μ- whose...

  9. The Recombination Landscape in Wild House Mice Inferred Using Population Genomic Data.

    Science.gov (United States)

    Booker, Tom R; Ness, Rob W; Keightley, Peter D

    2017-09-01

    Characterizing variation in the rate of recombination across the genome is important for understanding several evolutionary processes. Previous analysis of the recombination landscape in laboratory mice has revealed that the different subspecies have different suites of recombination hotspots. It is unknown, however, whether hotspots identified in laboratory strains reflect the hotspot diversity of natural populations or whether broad-scale variation in the rate of recombination is conserved between subspecies. In this study, we constructed fine-scale recombination rate maps for a natural population of the Eastern house mouse, Mus musculus castaneus We performed simulations to assess the accuracy of recombination rate inference in the presence of phase errors, and we used a novel approach to quantify phase error. The spatial distribution of recombination events is strongly positively correlated between our castaneus map, and a map constructed using inbred lines derived predominantly from M. m. domesticus Recombination hotspots in wild castaneus show little overlap, however, with the locations of double-strand breaks in wild-derived house mouse strains. Finally, we also find that genetic diversity in M. m. castaneus is positively correlated with the rate of recombination, consistent with pervasive natural selection operating in the genome. Our study suggests that recombination rate variation is conserved at broad scales between house mouse subspecies, but it is not strongly conserved at fine scales. Copyright © 2017 by the Genetics Society of America.

  10. Efficient on-chip hotspot removal combined solution of thermoelectric cooler and mini-channel heat sink

    International Nuclear Information System (INIS)

    Hao, Xiaohong; Peng, Bei; Xie, Gongnan; Chen, Yi

    2016-01-01

    Highlights: • A combined solution of thermoelectric cooler (TEC) and mini-channel heat sink to remove the hotspot of the chip has been proposed. • The TEC's mathematical model is established to assess its work performance. • A comparative study on the proposed efficient On-Chip Hotspot Removal Combined Solution. - Abstract: Hotspot will significantly degrade the reliability and performance of the electronic equipment. The efficient removal of hotspot can make the temperature distribution uniform, and ensure the reliable operation of the electronic equipment. This study proposes a combined solution of thermoelectric cooler (TEC) and mini-channel heat sink to remove the hotspot of the chip in the electronic equipment. Firstly, The TEC's mathematical model is established to assess its work performance under different boundary conditions. Then, the hotspot removal capability of the TEC is discussed for different cooling conditions, which has shown that the combined equipment has better hotspot removal capability compared with others. Finally, A TEC is employed to investigate the hotspot removal capacity of the combined solution, and the results have indicated that it can effectively remove hotspot in the diameter of 0.5 mm, the power density of 600W/cm 2 when its working current is 3A and heat transfer thermal resistance is 0 K/W.

  11. [Evolution of genomic imprinting in mammals: what a zoo!].

    Science.gov (United States)

    Proudhon, Charlotte; Bourc'his, Déborah

    2010-05-01

    Genomic imprinting imposes an obligate mode of biparental reproduction in mammals. This phenomenon results from the monoparental expression of a subset of genes. This specific gene regulation mechanism affects viviparous mammals, especially eutherians, but also marsupials to a lesser extent. Oviparous mammals, or monotremes, do not seem to demonstrate monoparental allele expression. This phylogenic confinement suggests that the evolution of the placenta imposed a selective pressure for the emergence of genomic imprinting. This physiological argument is now complemented by recent genomic evidence facilitated by the sequencing of the platypus genome, a rare modern day case of a monotreme. Analysis of the platypus genome in comparison to eutherian genomes shows a chronological and functional coincidence between the appearance of genomic imprinting and transposable element accumulation. The systematic comparative analyses of genomic sequences in different species is essential for the further understanding of genomic imprinting emergence and divergent evolution along mammalian speciation.

  12. Biosynthesis of rare hexoses using microorganisms and related enzymes

    Science.gov (United States)

    Li, Zijie; Gao, Yahui; Nakanishi, Hideki

    2013-01-01

    Summary Rare sugars, referred to as monosaccharides and their derivatives that rarely exist in nature, can be applied in many areas ranging from foodstuffs to pharmaceutical and nutrition industry, or as starting materials for various natural products and drug candidates. Unfortunately, an important factor restricting the utilization of rare sugars is their limited availability, resulting from limited synthetic methods. Nowadays, microbial and enzymatic transformations have become a very powerful tool in this field. This article reviews the biosynthesis and enzymatic production of rare ketohexoses, aldohexoses and sugar alcohols (hexitols), including D-tagatose, D-psicose, D-sorbose, L-tagatose, L-fructose, 1-deoxy-L-fructose, D-allose, L-glucose, L-talose, D-gulose, L-galactose, L-fucose, allitol, D-talitol, and L-sorbitol. New systems and robust catalysts resulting from advancements in genomics and bioengineering are also discussed. PMID:24367410

  13. Biosynthesis of rare hexoses using microorganisms and related enzymes

    Directory of Open Access Journals (Sweden)

    Zijie Li

    2013-11-01

    Full Text Available Rare sugars, referred to as monosaccharides and their derivatives that rarely exist in nature, can be applied in many areas ranging from foodstuffs to pharmaceutical and nutrition industry, or as starting materials for various natural products and drug candidates. Unfortunately, an important factor restricting the utilization of rare sugars is their limited availability, resulting from limited synthetic methods. Nowadays, microbial and enzymatic transformations have become a very powerful tool in this field. This article reviews the biosynthesis and enzymatic production of rare ketohexoses, aldohexoses and sugar alcohols (hexitols, including D-tagatose, D-psicose, D-sorbose, L-tagatose, L-fructose, 1-deoxy-L-fructose, D-allose, L-glucose, L-talose, D-gulose, L-galactose, L-fucose, allitol, D-talitol, and L-sorbitol. New systems and robust catalysts resulting from advancements in genomics and bioengineering are also discussed.

  14. Biosynthesis of rare hexoses using microorganisms and related enzymes.

    Science.gov (United States)

    Li, Zijie; Gao, Yahui; Nakanishi, Hideki; Gao, Xiaodong; Cai, Li

    2013-11-12

    Rare sugars, referred to as monosaccharides and their derivatives that rarely exist in nature, can be applied in many areas ranging from foodstuffs to pharmaceutical and nutrition industry, or as starting materials for various natural products and drug candidates. Unfortunately, an important factor restricting the utilization of rare sugars is their limited availability, resulting from limited synthetic methods. Nowadays, microbial and enzymatic transformations have become a very powerful tool in this field. This article reviews the biosynthesis and enzymatic production of rare ketohexoses, aldohexoses and sugar alcohols (hexitols), including D-tagatose, D-psicose, D-sorbose, L-tagatose, L-fructose, 1-deoxy-L-fructose, D-allose, L-glucose, L-talose, D-gulose, L-galactose, L-fucose, allitol, D-talitol, and L-sorbitol. New systems and robust catalysts resulting from advancements in genomics and bioengineering are also discussed.

  15. The Arab genome: Health and wealth.

    Science.gov (United States)

    Zayed, Hatem

    2016-11-05

    The 22 Arab nations have a unique genetic structure, which reflects both conserved and diverse gene pools due to the prevalent endogamous and consanguineous marriage culture and the long history of admixture among different ethnic subcultures descended from the Asian, European, and African continents. Human genome sequencing has enabled large-scale genomic studies of different populations and has become a powerful tool for studying disease predictions and diagnosis. Despite the importance of the Arab genome for better understanding the dynamics of the human genome, discovering rare genetic variations, and studying early human migration out of Africa, it is poorly represented in human genome databases, such as HapMap and the 1000 Genomes Project. In this review, I demonstrate the significance of sequencing the Arab genome and setting an Arab genome reference(s) for better understanding the molecular pathogenesis of genetic diseases, discovering novel/rare variants, and identifying a meaningful genotype-phenotype correlation for complex diseases. Copyright © 2016. Published by Elsevier B.V.

  16. Network Kernel Density Estimation for the Analysis of Facility POI Hotspots

    Directory of Open Access Journals (Sweden)

    YU Wenhao

    2015-12-01

    Full Text Available The distribution pattern of urban facility POIs (points of interest usually forms clusters (i.e. "hotspots" in urban geographic space. To detect such type of hotspot, the methods mostly employ spatial density estimation based on Euclidean distance, ignoring the fact that the service function and interrelation of urban feasibilities is carried out on the network path distance, neither than conventional Euclidean distance. By using these methods, it is difficult to exactly and objectively delimitate the shape and the size of hotspot. Therefore, this research adopts the kernel density estimation based on the network distance to compute the density of hotspot and proposes a simple and efficient algorithm. The algorithm extends the 2D dilation operator to the 1D morphological operator, thus computing the density of network unit. Through evaluation experiment, it is suggested that the algorithm is more efficient and scalable than the existing algorithms. Based on the case study on real POI data, the range of hotspot can highlight the spatial characteristic of urban functions along traffic routes, in order to provide valuable spatial knowledge and information services for the applications of region planning, navigation and geographic information inquiring.

  17. Identifying Genetic Hotspots by Mapping Molecular Diversity of Widespread Trees: When Commonness Matters.

    Science.gov (United States)

    Souto, Cintia P; Mathiasen, Paula; Acosta, María Cristina; Quiroga, María Paula; Vidal-Russell, Romina; Echeverría, Cristian; Premoli, Andrea C

    2015-01-01

    Conservation planning requires setting priorities at the same spatial scale at which decision-making processes are undertaken considering all levels of biodiversity, but current methods for identifying biodiversity hotspots ignore its genetic component. We developed a fine-scale approach based on the definition of genetic hotspots, which have high genetic diversity and unique variants that represent their evolutionary potential and evolutionary novelties. Our hypothesis is that wide-ranging taxa with similar ecological tolerances, yet of phylogenetically independent lineages, have been and currently are shaped by ecological and evolutionary forces that result in geographically concordant genetic patterns. We mapped previously published genetic diversity and unique variants of biparentally inherited markers and chloroplast sequences for 9 species from 188 and 275 populations, respectively, of the 4 woody dominant families of the austral temperate forest, an area considered a biodiversity hotspot. Spatial distribution patterns of genetic polymorphisms differed among taxa according to their ecological tolerances. Eight genetic hotspots were detected and we recommend conservation actions for some in the southern Coastal Range in Chile. Existing spatially explicit genetic data from multiple populations and species can help to identify biodiversity hotspots and guide conservation actions to establish science-based protected areas that will preserve the evolutionary potential of key habitats and species. © The American Genetic Association 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  18. Key role of European rabbits in the conservation of the Western Mediterranean basin hotspot.

    Science.gov (United States)

    Delibes-Mateos, Miguel; Delibes, Miguel; Ferreras, Pablo; Villafuerte, Rafael

    2008-10-01

    The Mediterranean Basin is a global hotspot of biodiversity. Hotspots are said to be experiencing a major loss of habitat, but an added risk could be the decline of some species having a special role in ecological relationships of the system. We reviewed the role of European rabbits (Oryctolagus cuniculus) as a keystone species in the Iberian Peninsula portion of the Mediterranean hotspot. Rabbits conspicuously alter plant species composition and vegetation structure through grazing and seed dispersal, which creates open areas and preserves plant species diversity. Moreover, rabbit latrines have a demonstrable effect on soil fertility and plant growth and provide new feeding resources for many invertebrate species. Rabbit burrows provide nest sites and shelter for vertebrates and invertebrates. In addition, rabbits serve as prey for a number of predators, including the critically endangered Iberian lynx (Lynx pardinus) and Spanish Imperial Eagle (Aquila adalberti). Thus, the Mediterranean ecosystem of the Iberian Peninsula should be termed "the rabbit's ecosystem." To our knowledge, this is the first empirical support for existence of a multifunctional keystone species in a global hotspot of biodiversity. Rabbit populations have declined drastically on the Iberian Peninsula, with potential cascading effects and serious ecological and economic consequences. From this perspective, rabbit recovery is one of the biggest challenges for conservation of the Mediterranean Basin hotspot.

  19. New Horizons-LEISA Observations Of Io's Hotspots During The 2007 Encounter

    Science.gov (United States)

    Tsang, Constantine; Rathbun, J. A.; Spencer, J. R.

    2012-10-01

    The New Horizons spacecraft flew past Jupiter and its satellites in February 2007. The flyby provided one of the most exquisite sets of observations of Io’s active plumes and hotspots yet taken, including many observations of a large 350 km high eruption plume at Tvashtar. Among the suite of instruments active during the flyby was the Linear Etalon Infrared Spectral Array (LEISA), a near-infrared imaging spectrometer. It covers the wavelength region between 1.25 and 2.5 µm, at a resolving power of 240, with a higher resolving power segment (R=540), covering 2.1 to 2.25 µm. Both segments share the same detector array to give on a 256 x 256 pixel spectral image at 62 µrad per pixel field-of-view. LEISA identified more than 30 individual hotspots on Io, over the seven spectral cubes taken during the flyby. We can measure the thermal emission from these volcanoes, and arrive at eruption temperatures by fitting blackbody curves to hotspot spectra. The temperatures of Tvashtar, Pele and East Girru were all derived in the Spencer et al., (2007) study. These volcanoes were consistent with basaltic volcanism with temperatures between 1287 and 1335 K. Here, we present blackbody fits of the other volcanic hotspots identified in the spectral images to complete the study of hotspot locations, eruption temperatures, emitting area and temporal variability where possible.

  20. First Results from HOTSPOT: The Snake River Plain Scientific Drilling Project, Idaho, U.S.A.

    Directory of Open Access Journals (Sweden)

    John W. Shervais

    2013-03-01

    Full Text Available HOTSPOT is an international collaborative effort to understand the volcanic history of the Snake River Plain (SRP. The SRP overlies a thermal anomaly, the Yellowstone-Snake River hotspot, that is thought to represent a deep-seated mantle plume under North America. Theprimary goal of this project is to document the volcanic and stratigraphic history of the SRP, which represents the surface expression of this hotspot, and to understand how it affected the evolution of continental crust and mantle. An additional goal is to evaluate the geothermal potential of southern Idaho.Project HOTSPOT has completed three drill holes. (1 The Kimama site is located along the central volcanic axis of the SRP; our goal here was to sample a long-term record of basaltic volcanism in the wake of the SRP hotspot. (2 The Kimberly site is located near the margin of the plain; our goal here was to sample a record of high-temperaturerhyolite volcanism associated with the underlying plume. This site was chosen to form a nominally continuous record of volcanism when paired with the Kimama site. (3 The Mountain Home site is located in the western plain; our goal here was to sample the Pliocene-Pleistocene transition in lake sediments at this site and to sample older basalts that underlie the sediments.We report here on our initial results for each site, and on some of the geophysical logging studies carried out as part of this project.

  1. Environmental niche conservatism explains the accumulation of species richness in Mediterranean-hotspot plant genera.

    Science.gov (United States)

    Skeels, Alexander; Cardillo, Marcel

    2017-03-01

    The causes of exceptionally high plant diversity in Mediterranean-climate biodiversity hotspots are not fully understood. We asked whether a mechanism similar to the tropical niche conservatism hypothesis could explain the diversity of four large genera (Protea, Moraea, Banksia, and Hakea) with distributions within and adjacent to the Greater Cape Floristic Region (South Africa) or the Southwest Floristic Region (Australia). Using phylogenetic and spatial data we estimated the environmental niche of each species, and reconstructed the mode and dynamics of niche evolution, and the geographic history, of each genus. For three genera, there were strong positive relationships between the diversity of clades within a region and their inferred length of occupation of that region. Within genera, there was evidence for strong evolutionary constraint on niche axes associated with climatic seasonality and aridity, with different niche optima for hotspot and nonhotspot clades. Evolutionary transitions away from hotspots were associated with increases in niche breadth and elevated rates of niche evolution. Our results point to a process of "hotspot niche conservatism" whereby the accumulation of plant diversity in Mediterranean-type ecosystems results from longer time for speciation, with dispersal away from hotspots limited by narrow and phylogenetically conserved environmental niches. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

  2. Forecasting hotspots in East Kutai, Kutai Kartanegara, and West Kutai as early warning information

    Science.gov (United States)

    Wahyuningsih, S.; Goejantoro, R.; Rizki, N. A.

    2018-04-01

    The aims of this research are to model hotspots and forecast hotspot 2017 in East Kutai, Kutai Kartanegara and West Kutai. The methods which used in this research were Holt exponential smoothing, Holt’s additive dump trend method, Holt-Winters’ additive method, additive decomposition method, multiplicative decomposition method, Loess decomposition method and Box-Jenkins method. For smoothing techniques, additive decomposition is better than Holt’s exponential smoothing. The hotspots model using Box-Jenkins method were Autoregressive Moving Average ARIMA(1,1,0), ARIMA(0,2,1), and ARIMA(0,1,0). Comparing the results from all methods which were used in this research, and based on Root of Mean Squared Error (RMSE), show that Loess decomposition method is the best times series model, because it has the least RMSE. Thus the Loess decomposition model used to forecast the number of hotspot. The forecasting result indicatethat hotspots pattern tend to increase at the end of 2017 in Kutai Kartanegara and West Kutai, but stationary in East Kutai.

  3. Hotspot motion caused the Hawaiian-Emperor Bend and LLSVPs are not fixed

    Science.gov (United States)

    Tarduno, J. A.; Bono, R. K.

    2017-12-01

    Paleomagnetic study of volcanic rocks remains the gold standard on which to assess hotspot motion, true polar wander and plate motion recorded by oceanic plates. There is remarkable consistency between paleomagnetic results from basaltic lavas recovered by ocean drilling of the Emperor seamounts, and independent predictions of plate circuits. Both reveal greater than 40 mm/yr of southward hotspot motion; thus the dominant reason for the distinct bend morphology the Hawaiian-Emperor track is hotspot motion rather than plate motion. These findings provide the motivation for moving beyond hotspot fixity to understand mantle processes responsible for the observed motions. Global analyses as well as comparisons between the Hawaiian-Emperor and Louisville tracks indicate only a minor (if any) role for true polar wander. Two viable, non-mutually exclusive processes to explain the observed Hawaiian plume motion are: i. plume-ridge and ii plume-LLSVP interaction. Here we further explore these issues by paleomagnetic analyses of basalts from the Cenozoic Hawaiian chain and Late Cretaceous basalts of the southernmost Pacific Plate. The latter yield paleolatitudes consistent with those from the northern Pacific, indicating that long-standing non-dipole fields cannot have been large enough to affect conclusions on hotspot drift. Data from the former suggest some relative motions between the LLSVPs on tens-of-millions of year time scales, which probably record the continual reshaping of these provinces by plume motion in the lower mantle.

  4. On the use of the HOTSPOT code for evaluating accidents involving radioactive materials

    International Nuclear Information System (INIS)

    Sattinger, D.; Sarussi, R.; Tzarfati, Y.; Levinson, S.; Tshuva, A.

    2004-01-01

    The HOTSPOT Health Physics code was created by LLNL in order to provide Health Physics personnel with a fast, field portable calculation tool for evaluating accidents involving radioactive materials. The HOTSPOT code is a first order approximation of the radiation effects associated with the atmospheric release of radioactive materials. HOTSPOT programs are reasonably accurate for a timely initial assessment. More importantly, HOTSPOT code produce a consistent output for the same input assumptions, and minimize the probability of errors associated with reading a graph incorrectly. Four general programs, Plume, Explosion, Fire, and Resuspension, calculate a downwind assessment following the release of radioactive material resulting from a continuous or puff release, explosive release, fuel or fire, or an area contamination event. Additional programs estimate the dose commitment from inhalation of any one of the radionuclides listed in the database of radionuclides, calibrate a radiation survey instrument for ground survey measurements, and screening of alpha emitters in the Lung. We believe that the HOTSPOT code is extremely valuable in providing reasonable and reliable guidance for a diversity of application. For example, we demonstrate the release of 241 Am(20Ci) to the atmosphere

  5. Properties of hotspots in plasma focus discharges operating in hydrogen-argon mixtures

    International Nuclear Information System (INIS)

    Silva, P; Favre, M

    2002-01-01

    We have investigated the properties of hotspots formed in low energy plasma focus (PF) discharges operating in hydrogen-argon mixtures, at 140 kA current level. A combination of filtered pinhole and slit-wire camera is used to measure the hotspot size and temperature. The results show that the best conditions for reproducible and localized hotspot formation are obtained by adjusting the base pressure in such a way that the mass load allows the time of first radial collapse to coincide with peak current. When the PF is operated with 20% argon content, rather uniform hotspots, of 115 μm characteristic size and 300 eV characteristic temperature, are produced with a better than 80% reproducibility in their axial localization. The electron density in the hotspots is estimated to be ∼10 20 cm -3 . Calculations performed with a CRE code indicate that a significant fraction of the radiation is emitted in the 3.2 to 3.88 keV region, corresponding to K α emission from highly ionized argon

  6. Development of a hotspot detector with an acrylic filter and dose rate survey meters

    International Nuclear Information System (INIS)

    Shirakawa, Yoshiyuki; Yamano, Toshiya; Kobayashi, Yusuke; Hara, Masaki

    2013-01-01

    Fukushima and adjacent regions still have a large number of high dose rate areas called hotspots. It is necessary to know these hotspots for efficient decontamination of radioactive substances such as 137 Cs and for relief of residents coming home. To find the hotspots rapidly, we have to specify the direction of the area where the dose rate is at least 1μSv/h higher than those of surroundings. We have developed a detector that consists of an acrylic filter and three NaI(Tl) scintillation survey meters, and the detector can be expected to indicate the direction of the hotspot in the short time. A basic performance of the detector was examined by using acrylic filters of 10, 15, 20 and 25cm diameter and a tiny sealed 137 Cs source of 3 MBq as the alternative of a hotspot. It demonstrated the possibility of identifying the direction of γ-rays emitted from the source in 90 seconds. (author)

  7. Proactive and Brief Smoking Cessation Intervention for Smokers at Outdoor Smoking "Hotspots" in Hong Kong.

    Science.gov (United States)

    Chan, Sophia Siu Chee; Cheung, Yee Tak Derek; Wan, Zoe; Wang, Man Ping; Lam, Tai-Hing

    2018-04-01

    Increased outdoor smoking is a common phenomenon after indoor smoking bans were in place. A series of observational studies were conducted to evaluate a novel, proactive, and brief smoking cessation intervention at outdoor smoking "hotspots," i.e., outdoor public areas where ashtrays were available and smokers clustered to smoke. The number of smokers at 26 selected hotspots were observed and counted for two consecutive days. Further observations of the smokers' characteristics and brief smoking cessation intervention were conducted at ten of the hotspots with the greatest number of smokers. Responses of the smokers to the brief intervention, including a leaflet and brief smoking cessation advice using AWAR protocol delivered by trained smoking cessation ambassadors, were assessed. A total of 24,034 smokers were observed within 464 h, which equals 51.8 smokers per hour. Of the 5070 pedestrians observed at the ten hotspots during the intervention sessions, 1228 (24.2 %) were smokers. In the 1228 smokers who were approached during our intervention sessions, about two thirds were willing to receive the self-help leaflet on smoking cessation whereas about half received the brief smoking cessation advice. Recruiting smokers and delivering brief smoking cessation interventions at smoking hotspots are feasible and likely effective to reach large numbers of smokers. Studies to evaluate the effectiveness of using this approach for smoking cessation are warranted.

  8. Persistence of trophic hotspots and relation to human impacts within an upwelling marine ecosystem.

    Science.gov (United States)

    Santora, Jarrod A; Sydeman, William J; Schroeder, Isaac D; Field, John C; Miller, Rebecca R; Wells, Brian K

    2017-03-01

    Human impacts (e.g., fishing, pollution, and shipping) on pelagic ecosystems are increasing, causing concerns about stresses on marine food webs. Maintaining predator-prey relationships through protection of pelagic hotspots is crucial for conservation and management of living marine resources. Biotic components of pelagic, plankton-based, ecosystems exhibit high variability in abundance in time and space (i.e., extreme patchiness), requiring investigation of persistence of abundance across trophic levels to resolve trophic hotspots. Using a 26-yr record of indicators for primary production, secondary (zooplankton and larval fish), and tertiary (seabirds) consumers, we show distributions of trophic hotspots in the southern California Current Ecosystem result from interactions between a strong upwelling center and a productive retention zone with enhanced nutrients, which concentrate prey and predators across multiple trophic levels. Trophic hotspots also overlap with human impacts, including fisheries extraction of coastal pelagic and groundfish species, as well as intense commercial shipping traffic. Spatial overlap of trophic hotspots with fisheries and shipping increases vulnerability of the ecosystem to localized depletion of forage fish, ship strikes on marine mammals, and pollution. This study represents a critical step toward resolving pelagic areas of high conservation interest for planktonic ecosystems and may serve as a model for other ocean regions where ecosystem-based management and marine spatial planning of pelagic ecosystems is warranted. © 2016 by the Ecological Society of America.

  9. Climate-induced hotspots in surface energy fluxes from 1948 to 2000

    International Nuclear Information System (INIS)

    Sheng Li; Liu Shuhua; Liu Heping

    2010-01-01

    Understanding how land surfaces respond to climate change requires knowledge of land-surface processes, which control the degree to which interannual variability and mean trends in climatic variables affect the surface energy budget. We use the latest version of the Community Land Model version 3.5 (CLM3.5), which is driven by the latest updated hybrid reanalysis-observation atmospheric forcing dataset constructed by Princeton University, to obtain global distributions of the surface energy budget from 1948 to 2000. We identify climate change hotspots and surface energy flux hotspots from 1948 to 2000. Surface energy flux hotspots, which reflect regions with strong changes in surface energy fluxes, reveal seasonal variations with strong signals in winter, spring, and autumn and weak ones in summer. Locations for surface energy flux hotspots are not, however, fully linked with those for climate change hotspots, suggesting that only in some regions are land surfaces more responsive to climate change in terms of interannual variability and mean trends.

  10. Classification Model for Forest Fire Hotspot Occurrences Prediction Using ANFIS Algorithm

    Science.gov (United States)

    Wijayanto, A. K.; Sani, O.; Kartika, N. D.; Herdiyeni, Y.

    2017-01-01

    This study proposed the application of data mining technique namely Adaptive Neuro-Fuzzy inference system (ANFIS) on forest fires hotspot data to develop classification models for hotspots occurrence in Central Kalimantan. Hotspot is a point that is indicated as the location of fires. In this study, hotspot distribution is categorized as true alarm and false alarm. ANFIS is a soft computing method in which a given inputoutput data set is expressed in a fuzzy inference system (FIS). The FIS implements a nonlinear mapping from its input space to the output space. The method of this study classified hotspots as target objects by correlating spatial attributes data using three folds in ANFIS algorithm to obtain the best model. The best result obtained from the 3rd fold provided low error for training (error = 0.0093676) and also low error testing result (error = 0.0093676). Attribute of distance to road is the most determining factor that influences the probability of true and false alarm where the level of human activities in this attribute is higher. This classification model can be used to develop early warning system of forest fire.

  11. Identification of biodiversity hotspot in national level – Importance of unpublished data

    Directory of Open Access Journals (Sweden)

    Naruemon Tantipisanuh

    2018-01-01

    Full Text Available High priority areas for conservation are typically identified based on ad hoc methods without supporting data due to a lack of scientific resources and staff. The objective of this study was to show how unpublished data in combination with citizen science can be useful for identifying biodiversity hotspot areas using Thailand as an example. Species records were aggregated from various sources both published (records permanently archived or temporarily available on the internet and unpublished data (derived from interviews. Data from 2001 to 2016 were used to identify hotspot areas. In total, 15% of the data were obtained from personal interviews. Most Thai hotspot areas were already inside government protected areas. Amphibians and reptiles were the taxa that unpublished data had the greatest influence on hotspot identification, while this influence was least for birds. Spatial coverage of species records showed a bias toward particular regions and areas probably due to a number of factors including their international reputation and previous species records. Results from this project reveal the importance of unpublished records as a source for identifying hotspot locations especially for less studied species groups and indicates the continued need for encouraging scientists as well as amateur naturalists to report their observations to archived websites and/or publish in peer-reviewed journals. Keywords: Citizen science, Amphibians, Reptiles, Birds, Mammals

  12. Rare earth superlattices

    International Nuclear Information System (INIS)

    McMorrow, D.F.

    1997-01-01

    A review is given of recent experiments on the magnetism of rare earth superlattices. Early experiments in this field were concerned mainly with systems formed by combining a magnetic and a non-magnetic element in a superlattice structure. From results gathered on a variety of systems it has been established that the propagation of magnetic order through the non-magnetic spacer can be understood mostly on the basis of an RKKY-like model, where the strength and range of the coupling depends on the details of the conduction electron susceptibility of the spacer. Recent experiments on more complex systems indicate that this model does not provide a complete description. Examples include superlattices where the constituents can either be both magnetic, adopt different crystal structures (Fermi surfaces), or where one of the constituents has a non-magnetic singlet ground state. The results from such systems are presented and discussed in the context of the currently accepted model. (au)

  13. Rare nocturnal headaches.

    Science.gov (United States)

    Cohen, Anna S; Kaube, Holger

    2004-06-01

    This review describes rare headaches that can occur at night or during sleep, with a focus on cluster headaches, paroxysmal hemicrania, short-lasting unilateral neuralgiform headache attacks with conjunctival injection and tearing, hypnic headache and exploding head syndrome. It is known that cluster headaches and hypnic headache are associated with rapid eye movement sleep, as illustrated by recent polysomnographic studies. Functional imaging studies have documented hypothalamic activation that is likely to be of relevance to circadian rhythms. These headache syndromes have been shown to respond to melatonin and lithium therapy, both of which have an indirect impact on the sleep-wake cycle. There is growing evidence that cluster headache and hypnic headache are chronobiological disorders.

  14. Rare earth (3) pivalates

    International Nuclear Information System (INIS)

    Kuz'mina, N.P.; Martynenko, L.I.; Zoan An' Tu; Ch'eu Tkhi Nguet; Troyanov, S.I.; Rykov, A.N.; Korenev, Yu.M.

    1994-01-01

    Depending on synthesis conditions rare earth pivalates can be obtained in the form of either adducts NPiv·HPiv or hydrates MPiv 3 ·mH 2 O. Adducts are the most stable form of pivalates. Heating of adducts result in formation of corresponding MPiv 3 . MPiv 3 ·nHPiv compounds are characterized by IR-spectroscopy and thermal analysis data. Behaviour of MPiv 3 was studied in the regime of vacuum sublemation. Using mass spectroscopy of NdPiv 3 it was shown that gaseous phase above MPiv 3 had complex composition and contained ligomer fragments. X-ray structure analysis of [NdPiv 3 ·3HPiv] was conducted

  15. A Rare Stapes Abnormality

    Directory of Open Access Journals (Sweden)

    Hala Kanona

    2015-01-01

    Full Text Available The aim of this study is to increase awareness of rare presentations, diagnostic difficulties alongside management of conductive hearing loss and ossicular abnormalities. We report the case of a 13-year-old female reporting progressive left-sided hearing loss and high resolution computed tomography was initially reported as normal. Exploratory tympanotomy revealed an absent stapedius tendon and lack of connection between the stapes superstructure and footplate. The footplate was fixed. Stapedotomy and stapes prosthesis insertion resulted in closure of the air-bone gap by 50 dB. A review of world literature was performed using MedLine. Middle ear ossicular discontinuity can result in significant conductive hearing loss. This can be managed effectively with surgery to help restore hearing. However, some patients may not be suitable or decline surgical intervention and can be managed safely conservatively.

  16. Rare Decays at LHCb

    CERN Document Server

    Belyaev, Ivan

    2006-01-01

    Rare loop-induced decays are sensitive to New Physics in many Standard Model extensions. In this paper we discuss the reconstruction of the radiative penguin decays $B^0_d \\to K^{*0} \\gamma, B^0_s \\to \\phi \\gamma , B^0_d \\to \\omega \\gamma, \\Lambda_b \\to \\Lambda \\gamma$, the electroweak penguin decays $B^0_d \\to K^{*0} \\mu^+ \\mu^-, B^+_u \\to K^+ \\mu^+ \\mu^-$, the gluonic penguin decays $B^0_d \\to \\phi K^0_S, B^0_s \\to \\phi \\phi$, and the decay $B^0_s \\to \\mu^+\\mu^-$ at LHCb. The selection criteria, evaluated efficiencies, expected annual yields and $B/S$ estimates are presented.

  17. Rare cancers are not so rare: The rare cancer burden in Europe

    NARCIS (Netherlands)

    Gatta, Gemma; van der Zwan, Jan Maarten; Casali, Paolo G.; Siesling, Sabine; Dei Tos, Angelo Paolo; Kunkler, Ian; Otter, Renee; Licitra, Lisa

    2011-01-01

    Purpose: Epidemiologic information on rare cancers is scarce. The project Surveillance of Rare Cancers in Europe (RARECARE) provides estimates of the incidence, prevalence and survival of rare cancers in Europe based on a new and comprehensive list of these diseases. Materials and methods: RARECARE

  18. Hotspot detection using space-time scan statistics on children under five years of age in Depok

    Science.gov (United States)

    Verdiana, Miranti; Widyaningsih, Yekti

    2017-03-01

    Some problems that affect the health level in Depok is the high malnutrition rates from year to year and the more spread infectious and non-communicable diseases in some areas. Children under five years old is a vulnerable part of population to get the malnutrition and diseases. Based on this reason, it is important to observe the location and time, where and when, malnutrition in Depok happened in high intensity. To obtain the location and time of the hotspots of malnutrition and diseases that attack children under five years old, space-time scan statistics method can be used. Space-time scan statistic is a hotspot detection method, where the area and time of information and time are taken into account simultaneously in detecting the hotspots. This method detects a hotspot with a cylindrical scanning window: the cylindrical pedestal describes the area, and the height of cylinder describe the time. Cylinders formed is a hotspot candidate that may occur, which require testing of hypotheses, whether a cylinder can be summed up as a hotspot. Hotspot detection in this study carried out by forming a combination of several variables. Some combination of variables provides hotspot detection results that tend to be the same, so as to form groups (clusters). In the case of infant health level in Depok city, Beji health care center region in 2011-2012 is a hotspot. According to the combination of the variables used in the detection of hotspots, Beji health care center is most frequently as a hotspot. Hopefully the local government can take the right policy to improve the health level of children under five in the city of Depok.

  19. Genome-wide association study of multiplex schizophrenia pedigrees

    DEFF Research Database (Denmark)

    Levinson, Douglas F; Shi, Jianxin; Wang, Kai

    2012-01-01

    The authors used a genome-wide association study (GWAS) of multiply affected families to investigate the association of schizophrenia to common single-nucleotide polymorphisms (SNPs) and rare copy number variants (CNVs).......The authors used a genome-wide association study (GWAS) of multiply affected families to investigate the association of schizophrenia to common single-nucleotide polymorphisms (SNPs) and rare copy number variants (CNVs)....

  20. Rapid Diversification and Time Explain Amphibian Richness at Different Scales in the Tropical Andes, Earth's Most Biodiverse Hotspot.

    Science.gov (United States)

    Hutter, Carl R; Lambert, Shea M; Wiens, John J

    2017-12-01

    The Tropical Andes make up Earth's most species-rich biodiversity hotspot for both animals and plants. Nevertheless, the ecological and evolutionary processes underlying this extraordinary richness remain uncertain. Here, we examine the processes that generate high richness in the Tropical Andes relative to other regions in South America and across different elevations within the Andes, using frogs as a model system. We combine distributional data, a newly generated time-calibrated phylogeny for 2,318 frog species, and phylogenetic comparative methods to test the relative importance of diversification rates and colonization times for explaining Andean diversity at different scales. At larger scales (among regions and families), we find that faster diversification rates in Andean clades most likely explain high Andean richness. In contrast, at smaller temporal and spatial scales (within family-level clades within the Andes), diversification rates rarely explain richness patterns. Instead, we show that colonization times are important for shaping elevational richness patterns within the Andes, with more species found in habitats colonized earlier. We suggest that these scale-dependent patterns might apply to many other richness gradients. Recognition of this scale dependence may help to reconcile conflicting results among studies of richness patterns across habitats, regions, and organisms.

  1. Seed plant phylogenetic diversity and species richness in conservation planning within a global biodiversity hotspot in eastern Asia.

    Science.gov (United States)

    Li, Rong; Kraft, Nathan J B; Yu, Haiying; Li, Heng

    2015-12-01

    One of the main goals of conservation biology is to understand the factors shaping variation in biodiversity across the planet. This understanding is critical for conservation planners to be able to develop effective conservation strategies. Although many studies have focused on species richness and the protection of rare and endemic species, less attention has been paid to the protection of the phylogenetic dimension of biodiversity. We explored how phylogenetic diversity, species richness, and phylogenetic community structure vary in seed plant communities along an elevational gradient in a relatively understudied high mountain region, the Dulong Valley, in southeastern Tibet, China. As expected, phylogenetic diversity was well correlated with species richness among the elevational bands and among communities. At the community level, evergreen broad-leaved forests had the highest levels of species richness and phylogenetic diversity. Using null model analyses, we found evidence of nonrandom phylogenetic structure across the region. Evergreen broad-leaved forests were phylogenetically overdispersed, whereas other vegetation types tended to be phylogenetically clustered. We suggest that communities with high species richness or overdispersed phylogenetic structure should be a focus for biodiversity conservation within the Dulong Valley because these areas may help maximize the potential of this flora to respond to future global change. In biodiversity hotspots worldwide, we suggest that the phylogenetic structure of a community may serve as a useful measure of phylogenetic diversity in the context of conservation planning. © 2015 Society for Conservation Biology.

  2. Built environment analysis for road traffic hotspot locations in Moshi, Tanzania.

    Science.gov (United States)

    Waldon, Meredith; Ibingira, Treasure Joelson; de Andrade, Luciano; Mmbaga, Blandina T; Vissoci, João Ricardo N; Mvungi, Mark; Staton, Catherine A

    2018-02-08

    Road traffic injuries (RTIs) cause significant morbidity and mortality in low- and middle-income countries. Investigation of high risk areas for RTIs is needed to guide improvements. This study provides built environmental analysis of road traffic crash hotspots within Moshi, Tanzania. Spatial analysis of police data identified 36 hotspots. Qualitative comparative analysis revealed 40% of crash sites were on local roads without night lighting and increased motorcycle density. Paved narrow roads represented 26% of hotspots and 13% were unpaved roads with uneven roadsides. Roadside unevenness was more predominate in low risk [n = 19, (90.5%)] than high risk sites [n = 7 (46.7%)]. Both low [n = 6 (28.6%)] and high risk [n = 1 (6.7%)] sites had minimal signage. All sites had informal pedestrian pathways. Little variability between risk sites suggests hazardous conditions are widespread. Findings suggest improvement in municipal infrastructure, signage and enforcement is needed to reduce RTI burden.

  3. Porous Au-Ag Nanospheres with High-Density and Highly Accessible Hotspots for SERS Analysis.

    Science.gov (United States)

    Liu, Kai; Bai, Yaocai; Zhang, Lei; Yang, Zhongbo; Fan, Qikui; Zheng, Haoquan; Yin, Yadong; Gao, Chuanbo

    2016-06-08

    Colloidal plasmonic metal nanoparticles have enabled surface-enhanced Raman scattering (SERS) for a variety of analytical applications. While great efforts have been made to create hotspots for amplifying Raman signals, it remains a great challenge to ensure their high density and accessibility for improved sensitivity of the analysis. Here we report a dealloying process for the fabrication of porous Au-Ag alloy nanoparticles containing abundant inherent hotspots, which were encased in ultrathin hollow silica shells so that the need of conventional organic capping ligands for stabilization is eliminated, producing colloidal plasmonic nanoparticles with clean surface and thus high accessibility of the hotspots. As a result, these novel nanostructures show excellent SERS activity with an enhancement factor of ∼1.3 × 10(7) on a single particle basis (off-resonant condition), promising high applicability in many SERS-based analytical and biomedical applications.

  4. Research on Hotspot Discovery in Internet Public Opinions Based on Improved -Means

    Directory of Open Access Journals (Sweden)

    Gensheng Wang

    2013-01-01

    Full Text Available How to discover hotspot in the Internet public opinions effectively is a hot research field for the researchers related which plays a key role for governments and corporations to find useful information from mass data in the Internet. An improved -means algorithm for hotspot discovery in internet public opinions is presented based on the analysis of existing defects and calculation principle of original -means algorithm. First, some new methods are designed to preprocess website texts, select and express the characteristics of website texts, and define the similarity between two website texts, respectively. Second, clustering principle and the method of initial classification centers selection are analyzed and improved in order to overcome the limitations of original -means algorithm. Finally, the experimental results verify that the improved algorithm can improve the clustering stability and classification accuracy of hotspot discovery in internet public opinions when used in practice.

  5. Counting complete? Finalising the plant inventory of a global biodiversity hotspot.

    Science.gov (United States)

    Treurnicht, Martina; Colville, Jonathan F; Joppa, Lucas N; Huyser, Onno; Manning, John

    2017-01-01

    The Cape Floristic Region-the world's smallest and third richest botanical hotspot-has benefited from sustained levels of taxonomic effort and exploration for almost three centuries, but how close is this to resulting in a near-complete plant species inventory? We analyse a core component of this flora over a 250-year period for trends in taxonomic effort and species discovery linked to ecological and conservation attributes. We show that >40% of the current total of species was described within the first 100 years of exploration, followed by a continued steady rate of description. We propose that analysis provides important real-world insights for other hotspots in the context of global strategic plans for biodiversity in informing considerations of the likely effort required in attaining set targets of comprehensive plant inventories. In a time of unprecedented biodiversity loss, we argue for a focused research agenda across disciplines to increase the rate of species descriptions in global biodiversity hotspots.

  6. Effects of Hot-Spot Geometry on Backscattering and Down-Scattering Neutron Spectra

    Science.gov (United States)

    Mohamed, Z. L.; Mannion, O. M.; Forrest, C. J.; Knauer, J. P.; Anderson, K. S.; Radha, P. B.

    2017-10-01

    The measured neutron spectrum produced by a fusion experiment plays a key role in inferring observable quantities. One important observable is the areal density of an implosion, which is inferred by measuring the scattering of neutrons. This project seeks to use particle-transport simulations to model the effects of hot-spot geometry on backscattering and down-scattering neutron spectra along different lines of sight. Implosions similar to those conducted at the Laboratory of Laser Energetics are modeled by neutron transport through a DT plasma and a DT ice shell using the particle transport codes MCNP and IRIS. Effects of hot-spot geometry are obtained by ``detecting'' scattered neutrons along different lines of sight. This process is repeated for various hot-spot geometries representing known shape distortions between the hot spot and the shell. This material is based upon work supported by the Department of Energy National Nuclear Security Administration under Award Number DE-NA0001944.

  7. Research on hotspot discovery in internet public opinions based on improved K-means.

    Science.gov (United States)

    Wang, Gensheng

    2013-01-01

    How to discover hotspot in the Internet public opinions effectively is a hot research field for the researchers related which plays a key role for governments and corporations to find useful information from mass data in the Internet. An improved K-means algorithm for hotspot discovery in internet public opinions is presented based on the analysis of existing defects and calculation principle of original K-means algorithm. First, some new methods are designed to preprocess website texts, select and express the characteristics of website texts, and define the similarity between two website texts, respectively. Second, clustering principle and the method of initial classification centers selection are analyzed and improved in order to overcome the limitations of original K-means algorithm. Finally, the experimental results verify that the improved algorithm can improve the clustering stability and classification accuracy of hotspot discovery in internet public opinions when used in practice.

  8. Hot-spot mix in ignition-scale inertial confinement fusion targets.

    Science.gov (United States)

    Regan, S P; Epstein, R; Hammel, B A; Suter, L J; Scott, H A; Barrios, M A; Bradley, D K; Callahan, D A; Cerjan, C; Collins, G W; Dixit, S N; Döppner, T; Edwards, M J; Farley, D R; Fournier, K B; Glenn, S; Glenzer, S H; Golovkin, I E; Haan, S W; Hamza, A; Hicks, D G; Izumi, N; Jones, O S; Kilkenny, J D; Kline, J L; Kyrala, G A; Landen, O L; Ma, T; MacFarlane, J J; MacKinnon, A J; Mancini, R C; McCrory, R L; Meezan, N B; Meyerhofer, D D; Nikroo, A; Park, H-S; Ralph, J; Remington, B A; Sangster, T C; Smalyuk, V A; Springer, P T; Town, R P J

    2013-07-26

    Mixing of plastic ablator material, doped with Cu and Ge dopants, deep into the hot spot of ignition-scale inertial confinement fusion implosions by hydrodynamic instabilities is diagnosed with x-ray spectroscopy on the National Ignition Facility. The amount of hot-spot mix mass is determined from the absolute brightness of the emergent Cu and Ge K-shell emission. The Cu and Ge dopants placed at different radial locations in the plastic ablator show the ablation-front hydrodynamic instability is primarily responsible for hot-spot mix. Low neutron yields and hot-spot mix mass between 34(-13,+50)  ng and 4000(-2970,+17 160)  ng are observed.

  9. Research on Hotspot Discovery in Internet Public Opinions Based on Improved K-Means

    Science.gov (United States)

    2013-01-01

    How to discover hotspot in the Internet public opinions effectively is a hot research field for the researchers related which plays a key role for governments and corporations to find useful information from mass data in the Internet. An improved K-means algorithm for hotspot discovery in internet public opinions is presented based on the analysis of existing defects and calculation principle of original K-means algorithm. First, some new methods are designed to preprocess website texts, select and express the characteristics of website texts, and define the similarity between two website texts, respectively. Second, clustering principle and the method of initial classification centers selection are analyzed and improved in order to overcome the limitations of original K-means algorithm. Finally, the experimental results verify that the improved algorithm can improve the clustering stability and classification accuracy of hotspot discovery in internet public opinions when used in practice. PMID:24106496

  10. Finding radiation hot-spots for a private residence/decontamination manual

    International Nuclear Information System (INIS)

    Nishizawa, Kunihide

    2012-01-01

    Since the Fukushima Daiichi Nuclear Power Station accident, the radio-iodine and cesium analysis group of ad hoc committee of safety measures has investigated initial screening monitor of the soils and examined contamination and experienced decontamination works. Existence of hot-spots where Cs 137 is concentrated is confirmed. The report makes a manual to find such a hot-spot in a private residence and how the decontamination should be carried out. Particularly, the report provides the definite examples of hot-spots, for instances, a roof, an eaves trough (a gutter), a side drain (a ditch), dead leaves (withered grass), surface land, a wood block, etc. and how the decontamination should be confirmed and the dusts be collected and kept. (S. Ohno)

  11. Cephalopod genomics

    DEFF Research Database (Denmark)

    Albertin, Caroline B.; Bonnaud, Laure; Brown, C. Titus

    2012-01-01

    The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, ``Paths to Cephalopod Genomics-Strategies, Choices, Organization,'' held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austria......, Australia, China, Denmark, France, Italy, Japan, Spain and the USA) met to address the pressing need for genome sequencing of cephalopod mollusks. This group, drawn from cephalopod biologists, neuroscientists, developmental and evolutionary biologists, materials scientists, bioinformaticians and researchers...... active in sequencing, assembling and annotating genomes, agreed on a set of cephalopod species of particular importance for initial sequencing and developed strategies and an organization (CephSeq Consortium) to promote this sequencing. The conclusions and recommendations of this meeting are described...

  12. Threatened Plants in China’s Sanjiang Plain: Hotspot Distributions and Gap Analysis

    Directory of Open Access Journals (Sweden)

    Baojia Du

    2018-01-01

    Full Text Available Global biodiversity is markedly decreasing in response to climate change and human disturbance. Sanjiang Plain is recognized as a biodiversity hotspot in China due to its high forest and wetland coverage, but species are being lost at an unprecedented rate, induced by anthropogenic activities. Identifying hotspot distributions and conservation gaps of threatened species is of particular significance for enhancing the conservation of biodiversity. Specifically, we integrated the principles and methods of spatial hotspot inspection, geographic information system (GIS technology and spatial autocorrelation analysis along with fieldwork to determine the spatial distribution patterns and unprotected hotspots of vulnerable and endangered plants in Sanjiang Plain. A gap analysis of the conservation status of vulnerable and endangered plants was conducted. Our results indicate that six nationally-protected plants were not observed in nature reserves or were without any protection, while the protection rates were <10% for 10 other nationally-protected plants. Protected areas (PAs cover <5% of the distribution areas for 31 threatened plant species, while only five species are covered by national nature reserves (NNRs within >50% of the distribution areas. We found 30 hotspots with vulnerable and endangered plants in the study area, but the area covered by NNRs is very limited. Most of the hotspots were located in areas with a high-high aggregation of plant species. Therefore, it is necessary to expand the area of existing nature reserves, establish miniature protection plots and create new PAs and ecological corridors to link the existing PAs. Our findings can contribute to the design of a PA network for botanical conservation.

  13. Comparative phylogeography reveals deep lineages and regional evolutionary hotspots in the Mojave and Sonoran Deserts

    Science.gov (United States)

    Wood, Dustin A.; Vandergast, Amy G.; Barr, Kelly R.; Inman, Richard D.; Esque, Todd C.; Nussear, Kenneth E.; Fisher, Robert N.

    2013-01-01

    Aim: We explored lineage diversification within desert-dwelling fauna. Our goals were (1) to determine whether phylogenetic lineages and population expansions were consistent with younger Pleistocene climate fluctuation hypotheses or much older events predicted by pre-Pleistocene vicariance hypotheses, (2) to assess concordance in spatial patterns of genetic divergence and diversity among species and (3) to identify regional evolutionary hotspots of divergence and diversity and assess their conservation status. Location: Mojave, Colorado, and Sonoran Deserts, USA. Methods: We analysed previously published gene sequence data for twelve species. We used Bayesian gene tree methods to estimate lineages and divergence times. Within each lineage, we tested for population expansion and age of expansion using coalescent approaches. We mapped interpopulation genetic divergence and intra-population genetic diversity in a GIS to identify hotspots of highest genetic divergence and diversity and to assess whether protected lands overlapped with evolutionary hotspots. Results: In seven of the 12 species, lineage divergence substantially predated the Pleistocene. Historical population expansion was found in eight species, but expansion events postdated the Last Glacial Maximum (LGM) in only four. For all species assessed, six hotspots of high genetic divergence and diversity were concentrated in the Colorado Desert, along the Colorado River and in the Mojave/Sonoran ecotone. At least some proportion of the land within each recovered hotspot was categorized as protected, yet four of the six also overlapped with major areas of human development. Main conclusions: Most of the species studied here diversified into distinct Mojave and Sonoran lineages prior to the LGM – supporting older diversification hypotheses. Several evolutionary hotspots were recovered but are not strategically paired with areas of protected land. Long-term preservation of species-level biodiversity would

  14. Climatic and topographical correlates of plant palaeo- and neoendemism in a Mediterranean biodiversity hotspot

    Science.gov (United States)

    Molina-Venegas, Rafael; Aparicio, Abelardo; Lavergne, Sébastien; Arroyo, Juan

    2017-01-01

    Background and Aims Understanding the evolutionary and ecological forces contributing to the emergence of biodiversity hotspots is of outstanding importance to elucidate how they may withstand current climate changes. Here we explored patterns of phylogenetic and non-phylogenetic plant endemism in a Mediterranean biodiversity hotspot. We hypothesized that areas with wet and equable climatic conditions would be prone to long-term persistence of endemic lineages (palaeoendemism), whilst areas of recent local speciation (neoendemism) would be more related to harsher environmental conditions and to high topographical relief promoting speciation. Methods We focused on the Baetic–Rifan biodiversity hotspot (southern Iberian Peninsula and northern Morocco) in combination with molecular phylogenetic information and relative phylogenetic endemism (RPE), a recent phylogenetic measure of endemism, allowing us to discern centres of palaeo- from those of neoendemism. Using eco-geographical regions as study units, we explored correlations between both RPE and endemic species richness with precipitation- and temperature-related variables and with elevation range. Key Results Centres of neoendemism were concentrated towards the easternmost part of the hotspot, while centres of palaeoendemism were clustered in the vicinity of the Strait of Gibraltar. The RPE index, indicating more palaeoendemism, was positively correlated with total annual precipitation, while endemic species richness showed a poor correlation. In contrast, elevation range and mean annual temperature were poor predictors of RPE, despite elevation range showing a strong correlation with endemic species richness. Conclusions The Baetic–Rifan biodiversity hotspot shows clearly differentiated centres of neo- and palaeoendemism. Topographical relief may have driven evolutionary diversification of newly evolved species, while water availability seems more critical for the long-term persistence of ancient lineages in

  15. A geostatistical approach to identify and mitigate agricultural nitrous oxide emission hotspots.

    Science.gov (United States)

    Turner, P A; Griffis, T J; Mulla, D J; Baker, J M; Venterea, R T

    2016-12-01

    Anthropogenic emissions of nitrous oxide (N 2 O), a trace gas with severe environmental costs, are greatest from agricultural soils amended with nitrogen (N) fertilizer. However, accurate N 2 O emission estimates at fine spatial scales are made difficult by their high variability, which represents a critical challenge for the management of N 2 O emissions. Here, static chamber measurements (n=60) and soil samples (n=129) were collected at approximately weekly intervals (n=6) for 42-d immediately following the application of N in a southern Minnesota cornfield (15.6-ha), typical of the systems prevalent throughout the U.S. Corn Belt. These data were integrated into a geostatistical model that resolved N 2 O emissions at a high spatial resolution (1-m). Field-scale N 2 O emissions exhibited a high degree of spatial variability, and were partitioned into three classes of emission strength: hotspots, intermediate, and coldspots. Rates of emission from hotspots were 2-fold greater than non-hotspot locations. Consequently, 36% of the field-scale emissions could be attributed to hotspots, despite representing only 21% of the total field area. Variations in elevation caused hotspots to develop in predictable locations, which were prone to nutrient and moisture accumulation caused by terrain focusing. Because these features are relatively static, our data and analyses indicate that targeted management of hotspots could efficiently reduce field-scale emissions by as much 17%, a significant benefit considering the deleterious effects of atmospheric N 2 O. Copyright © 2016 Elsevier B.V. All rights reserved.

  16. Optimal Hotspots of Dynamic Surfaced-Enhanced Raman Spectroscopy for Drugs Quantitative Detection.

    Science.gov (United States)

    Yan, Xiunan; Li, Pan; Zhou, Binbin; Tang, Xianghu; Li, Xiaoyun; Weng, Shizhuang; Yang, Liangbao; Liu, Jinhuai

    2017-05-02

    Surface-enhanced Raman spectroscopy (SERS) as a powerful qualitative analysis method has been widely applied in many fields. However, SERS for quantitative analysis still suffers from several challenges partially because of the absence of stable and credible analytical strategy. Here, we demonstrate that the optimal hotspots created from dynamic surfaced-enhanced Raman spectroscopy (D-SERS) can be used for quantitative SERS measurements. In situ small-angle X-ray scattering was carried out to in situ real-time monitor the formation of the optimal hotspots, where the optimal hotspots with the most efficient hotspots were generated during the monodisperse Au-sol evaporating process. Importantly, the natural evaporation of Au-sol avoids the nanoparticles instability of salt-induced, and formation of ordered three-dimensional hotspots allows SERS detection with excellent reproducibility. Considering SERS signal variability in the D-SERS process, 4-mercaptopyridine (4-mpy) acted as internal standard to validly correct and improve stability as well as reduce fluctuation of signals. The strongest SERS spectra at the optimal hotspots of D-SERS have been extracted to statistics analysis. By using the SERS signal of 4-mpy as a stable internal calibration standard, the relative SERS intensity of target molecules demonstrated a linear response versus the negative logarithm of concentrations at the point of strongest SERS signals, which illustrates the great potential for quantitative analysis. The public drugs 3,4-methylenedioxymethamphetamine and α-methyltryptamine hydrochloride obtained precise analysis with internal standard D-SERS strategy. As a consequence, one has reason to believe our approach is promising to challenge quantitative problems in conventional SERS analysis.

  17. SPIRE, a modular pipeline for eQTL analysis of RNA-Seq data, reveals a regulatory hotspot controlling miRNA expression in C. elegans.

    Science.gov (United States)

    Kel, Ivan; Chang, Zisong; Galluccio, Nadia; Romeo, Margherita; Beretta, Stefano; Diomede, Luisa; Mezzelani, Alessandra; Milanesi, Luciano; Dieterich, Christoph; Merelli, Ivan

    2016-10-18

    The interpretation of genome-wide association study is difficult, as it is hard to understand how polymorphisms can affect gene regulation, in particular for trans-regulatory elements located far from their controlling gene. Using RNA or protein expression data as phenotypes, it is possible to correlate their variations with specific genotypes. This technique is usually referred to as expression Quantitative Trait Loci (eQTLs) analysis and only few packages exist for the integration of genotype patterns and expression profiles. In particular, tools are needed for the analysis of next-generation sequencing (NGS) data on a genome-wide scale, which is essential to identify eQTLs able to control a large number of genes (hotspots). Here we present SPIRE (Software for Polymorphism Identification Regulating Expression), a generic, modular and functionally highly flexible pipeline for eQTL processing. SPIRE integrates different univariate and multivariate approaches for eQTL analysis, paying particular attention to the scalability of the procedure in order to support cis- as well as trans-mapping, thus allowing the identification of hotspots in NGS data. In particular, we demonstrated how SPIRE can handle big association study datasets, reproducing published results and improving the identification of trans-eQTLs. Furthermore, we employed the pipeline to analyse novel data concerning the genotypes of two different C. elegans strains (N2 and Hawaii) and related miRNA expression data, obtained using RNA-Seq. A miRNA regulatory hotspot was identified in chromosome 1, overlapping the transcription factor grh-1, known to be involved in the early phases of embryonic development of C. elegans. In a follow-up qPCR experiment we were able to verify most of the predicted eQTLs, as well as to show, for a novel miRNA, a significant difference in the sequences of the two analysed strains of C. elegans. SPIRE is publicly available as open source software at , together with some example

  18. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based on transcr......The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...

  19. Simplified expression for the minimum hotspot current in long, thin-film superconductors

    International Nuclear Information System (INIS)

    Dharmadurai, G.; Murthy, N.S.S.

    1979-01-01

    A generalization of the Skocpol--Beasley--Tinkham hotspot theory to include an approximate temperature dependence of the conductive heat transfer term of the heat flow equations clearly indicates that the role of the thermal conductivity of the material of the film is not reflected in the observed temperature dependence of the minimum current I/sub h/ required to sustain a hotspot in a long, thin-film superconductor. This observation leads to the derivation of a simplified expression for I/sub h/ valid for a wider range of bath temperatures

  20. Breaking and Moving Hotspots in a Large Grain Nb Cavity with a Laser Beam

    International Nuclear Information System (INIS)

    Ciovati, G.; Cheng, G.; Flood, R. J.; Jordan, K.; Kneisel, P.; Morrone, M. L.; Turlington, L.; Wilson, K. M.; Zhang, S.; Anlage, S. M.; Gurevich, A. V.; Nemes, G.; Baldwin, C.

    2011-01-01

    Magnetic vortices pinned near the inner surface of SRF Nb cavities are a possible source of RF hotspots, frequently observed by temperature mapping of the cavities outer surface at RF surface magnetic fields of about 100 mT. Theoretically, we expect that the thermal gradient provided by a 10 W green laser shining on the inner cavity surface at the RF hotspot locations can move pinned vortices to different pinning locations. The experimental apparatus to send the beam onto the inner surface of a photoinjector-type large-grain Nb cavity is described. Preliminary results on the changes in thermal maps observed after applying the laser heating are also reported

  1. Identifying ecosystem service hotspots for environmental management in Durban, South Africa

    Directory of Open Access Journals (Sweden)

    Rashieda Davids

    2016-12-01

    Conclusion: The results indicated that substantial portions of hotspot areas lie outside of formally regulated and managed conservation areas and remain vulnerable to human impact and habitat degradation. The study identified management areas and options that could yield maximum benefits; including the need for the development of an ecosystem services management and protection strategy, the selection of areas for co-management of ecosystem service hotspots and CBAs and the need for collaborative management.

  2. Rare psi decays

    International Nuclear Information System (INIS)

    Partridge, R.

    1986-01-01

    Slightly more than ten years have passed since the psi was discovered, yet the study of psi decays continues to be an active and fruitful area of research. One reason for such longevity is that each successive experiment has increased their sensitivity over previous experiments either by improving detection efficiency or by increasing statistics. This has allowed the observation and, in some cases, detailed studies of rare psi decays. Branching ratios of ≅10-/sup 4/ are now routinely studied, while certain decay channels are beginning to show interesting effects at the 10-/sup 5/ level. Future experiments at the Beijing Electron Positron Collider (BEPC) have the potential for increasing sensitivities by one or two orders of magnitude, thus enabling many interesting studies impossible with current data samples. The author first examines the extent to which psi decays can be used to study electroweak phenomena. The remainder of this work is devoted to the more traditional task of using the psi to study quarks, gluons, and the properties of the strong interaction. Of particular interest is the study of radioactive psi decays, where a number of new particles have been discovered. Recent results regarding two of these particles, the θ(1700) and iota(1450), are discussed, as well as a study of the quark content of the eta and eta' using decays of the psi to vector-pseudoscalar final states

  3. Predicted MHC peptide binding promiscuity explains MHC class I 'hotspots' of antigen presentation defined by mass spectrometry eluted ligand data.

    Science.gov (United States)

    Jappe, Emma Christine; Kringelum, Jens; Trolle, Thomas; Nielsen, Morten

    2018-02-15

    Peptides that bind to and are presented by MHC class I and class II molecules collectively make up the immunopeptidome. In the context of vaccine development, an understanding of the immunopeptidome is essential, and much effort has been dedicated to its accurate and cost-effective identification. Current state-of-the-art methods mainly comprise in silico tools for predicting MHC binding, which is strongly correlated with peptide immunogenicity. However, only a small proportion of the peptides that bind to MHC molecules are, in fact, immunogenic, and substantial work has been dedicated to uncovering additional determinants of peptide immunogenicity. In this context, and in light of recent advancements in mass spectrometry (MS), the existence of immunological hotspots has been given new life, inciting the hypothesis that hotspots are associated with MHC class I peptide immunogenicity. We here introduce a precise terminology for defining these hotspots and carry out a systematic analysis of MS and in silico predicted hotspots. We find that hotspots defined from MS data are largely captured by peptide binding predictions, enabling their replication in silico. This leads us to conclude that hotspots, to a great degree, are simply a result of promiscuous HLA binding, which disproves the hypothesis that the identification of hotspots provides novel information in the context of immunogenic peptide prediction. Furthermore, our analyses demonstrate that the signal of ligand processing, although present in the MS data, has very low predictive power to discriminate between MS and in silico defined hotspots. © 2018 John Wiley & Sons Ltd.

  4. 75 FR 29537 - Draft Transportation Conformity Guidance for Quantitative Hot-spot Analyses in PM2.5

    Science.gov (United States)

    2010-05-26

    ... Quantitative Hot- spot Analyses in PM 2.5 and PM 10 Nonattainment and Maintenance Areas AGENCY: Environmental... finalized, this guidance would help state and local agencies complete quantitative PM 2.5 and PM 10 hot-spot... projects. A hot-spot analysis includes an estimation of project-level emissions, air quality modeling, and...

  5. Rare B decays at LHCb

    CERN Document Server

    Puig Navarro, Albert

    2017-01-01

    Rare decays are flavour changing neutral current processes that allow sensitive searches for phenomena beyond the Standard Model (SM). In the SM, rare decays are loop-suppressed and new particles in SM extensions can give significant contributions. The very rare decay $B^0_s\\to\\mu^+\\mu^-$ in addition helicity suppressed and constitutes a powerful probe for new (pseudo) scalar particles. Of particular interest are furthermore tests of lepton universality in rare $b\\to s\\ell^+\\ell^-$ decays. The LHCb experiment is designed for the study of b-hadron decays and ideally suited for the analysis of rare decays due to its high trigger efficiency, as well as excellent tracking and particle identification performance. Recent results from the LHCb experiment in the area of rare decays are presented, including tests of lepton universality and searches for lepton flavour violation.

  6. NCCOS Assessment: Groundfish biodiversity hotspots off the Pacific Coast of Oregon from 1971-09-05 to 2010-09-20 (NCEI Accession 0156467)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set comprises maps of predicted long-term groundfish biodiversity hotspot probabilities off the Pacific Coast of Oregon. Predicted hotspot probabilities...

  7. Bayesian detection of causal rare variants under posterior consistency.

    KAUST Repository

    Liang, Faming

    2013-07-26

    Identification of causal rare variants that are associated with complex traits poses a central challenge on genome-wide association studies. However, most current research focuses only on testing the global association whether the rare variants in a given genomic region are collectively associated with the trait. Although some recent work, e.g., the Bayesian risk index method, have tried to address this problem, it is unclear whether the causal rare variants can be consistently identified by them in the small-n-large-P situation. We develop a new Bayesian method, the so-called Bayesian Rare Variant Detector (BRVD), to tackle this problem. The new method simultaneously addresses two issues: (i) (Global association test) Are there any of the variants associated with the disease, and (ii) (Causal variant detection) Which variants, if any, are driving the association. The BRVD ensures the causal rare variants to be consistently identified in the small-n-large-P situation by imposing some appropriate prior distributions on the model and model specific parameters. The numerical results indicate that the BRVD is more powerful for testing the global association than the existing methods, such as the combined multivariate and collapsing test, weighted sum statistic test, RARECOVER, sequence kernel association test, and Bayesian risk index, and also more powerful for identification of causal rare variants than the Bayesian risk index method. The BRVD has also been successfully applied to the Early-Onset Myocardial Infarction (EOMI) Exome Sequence Data. It identified a few causal rare variants that have been verified in the literature.

  8. Bayesian detection of causal rare variants under posterior consistency.

    Directory of Open Access Journals (Sweden)

    Faming Liang

    Full Text Available Identification of causal rare variants that are associated with complex traits poses a central challenge on genome-wide association studies. However, most current research focuses only on testing the global association whether the rare variants in a given genomic region are collectively associated with the trait. Although some recent work, e.g., the Bayesian risk index method, have tried to address this problem, it is unclear whether the causal rare variants can be consistently identified by them in the small-n-large-P situation. We develop a new Bayesian method, the so-called Bayesian Rare Variant Detector (BRVD, to tackle this problem. The new method simultaneously addresses two issues: (i (Global association test Are there any of the variants associated with the disease, and (ii (Causal variant detection Which variants, if any, are driving the association. The BRVD ensures the causal rare variants to be consistently identified in the small-n-large-P situation by imposing some appropriate prior distributions on the model and model specific parameters. The numerical results indicate that the BRVD is more powerful for testing the global association than the existing methods, such as the combined multivariate and collapsing test, weighted sum statistic test, RARECOVER, sequence kernel association test, and Bayesian risk index, and also more powerful for identification of causal rare variants than the Bayesian risk index method. The BRVD has also been successfully applied to the Early-Onset Myocardial Infarction (EOMI Exome Sequence Data. It identified a few causal rare variants that have been verified in the literature.

  9. Bayesian detection of causal rare variants under posterior consistency.

    KAUST Repository

    Liang, Faming; Xiong, Momiao

    2013-01-01

    Identification of causal rare variants that are associated with complex traits poses a central challenge on genome-wide association studies. However, most current research focuses only on testing the global association whether the rare variants in a given genomic region are collectively associated with the trait. Although some recent work, e.g., the Bayesian risk index method, have tried to address this problem, it is unclear whether the causal rare variants can be consistently identified by them in the small-n-large-P situation. We develop a new Bayesian method, the so-called Bayesian Rare Variant Detector (BRVD), to tackle this problem. The new method simultaneously addresses two issues: (i) (Global association test) Are there any of the variants associated with the disease, and (ii) (Causal variant detection) Which variants, if any, are driving the association. The BRVD ensures the causal rare variants to be consistently identified in the small-n-large-P situation by imposing some appropriate prior distributions on the model and model specific parameters. The numerical results indicate that the BRVD is more powerful for testing the global association than the existing methods, such as the combined multivariate and collapsing test, weighted sum statistic test, RARECOVER, sequence kernel association test, and Bayesian risk index, and also more powerful for identification of causal rare variants than the Bayesian risk index method. The BRVD has also been successfully applied to the Early-Onset Myocardial Infarction (EOMI) Exome Sequence Data. It identified a few causal rare variants that have been verified in the literature.

  10. Comparative Genomics

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 11; Issue 8. Comparative Genomics - A Powerful New Tool in Biology. Anand K Bachhawat. General Article Volume 11 Issue 8 August 2006 pp 22-40. Fulltext. Click here to view fulltext PDF. Permanent link:

  11. Role of hydrodynamic instability growth in hot-spot mass gain and fusion performance of inertial confinement fusion implosions

    International Nuclear Information System (INIS)

    Srinivasan, Bhuvana; Tang, Xian-Zhu

    2014-01-01

    In an inertial confinement fusion target, energy loss due to thermal conduction from the hot-spot will inevitably ablate fuel ice into the hot-spot, resulting in a more massive but cooler hot-spot, which negatively impacts fusion yield. Hydrodynamic mix due to Rayleigh-Taylor instability at the gas-ice interface can aggravate the problem via an increased gas-ice interfacial area across which energy transfer from the hot-spot and ice can be enhanced. Here, this mix-enhanced transport effect on hot-spot fusion-performance degradation is quantified using contrasting 1D and 2D hydrodynamic simulations, and its dependence on effective acceleration, Atwood number, and ablation speed is identified

  12. The whole-genome landscape of medulloblastoma subtypes

    DEFF Research Database (Denmark)

    Northcott, Paul A.; Buchhalter, Ivo; Morrissy, A. Sorana

    2017-01-01

    actionable targets. Driver mutations were confidently assigned to most patients belonging to Group 3 and Group 4 medulloblastoma subgroups, greatly enhancing previous knowledge. New molecular subtypes were differentially enriched for specific driver events, including hotspot in-frame insertions that target...... KBTBD4 and 'enhancer hijacking' events that activate PRDM6. Thus, the application of integrative genomics to an extensive cohort of clinical samples derived from a single childhood cancer entity revealed a series of cancer genes and biologically relevant subtype diversity that represent attractive...

  13. Rare-earth elements

    Science.gov (United States)

    Van Gosen, Bradley S.; Verplanck, Philip L.; Seal, Robert R.; Long, Keith R.; Gambogi, Joseph; Schulz, Klaus J.; DeYoung,, John H.; Seal, Robert R.; Bradley, Dwight C.

    2017-12-19

    The rare-earth elements (REEs) are 15 elements that range in atomic number from 57 (lanthanum) to 71 (lutetium); they are commonly referred to as the “lanthanides.” Yttrium (atomic number 39) is also commonly regarded as an REE because it shares chemical and physical similarities and has affinities with the lanthanides. Although REEs are not rare in terms of average crustal abundance, the concentrated deposits of REEs are limited in number.Because of their unusual physical and chemical properties, the REEs have diverse defense, energy, industrial, and military technology applications. The glass industry is the leading consumer of REE raw materials, which are used for glass polishing and as additives that provide color and special optical properties to the glass. Lanthanum-based catalysts are used in petroleum refining, and cerium-based catalysts are used in automotive catalytic converters. The use of REEs in magnets is a rapidly increasing application. Neodymium-iron-boron magnets, which are the strongest known type of magnets, are used when space and weight are restrictions. Nickel-metal hydride batteries use anodes made of a lanthanum-based alloys.China, which has led the world production of REEs for decades, accounted for more than 90 percent of global production and supply, on average, during the past decade. Citing a need to retain its limited REE resources to meet domestic requirements as well as concerns about the environmental effects of mining, China began placing restrictions on the supply of REEs in 2010 through the imposition of quotas, licenses, and taxes. As a result, the global rare-earth industry has increased its stockpiling of REEs; explored for deposits outside of China; and promoted new efforts to conserve, recycle, and substitute for REEs. New mine production began at Mount Weld in Western Australia, and numerous other exploration and development projects noted in this chapter are ongoing throughout the world.The REE-bearing minerals are

  14. The whole genome sequences and experimentally phased haplotypes of over 100 personal genomes.

    Science.gov (United States)

    Mao, Qing; Ciotlos, Serban; Zhang, Rebecca Yu; Ball, Madeleine P; Chin, Robert; Carnevali, Paolo; Barua, Nina; Nguyen, Staci; Agarwal, Misha R; Clegg, Tom; Connelly, Abram; Vandewege, Ward; Zaranek, Alexander Wait; Estep, Preston W; Church, George M; Drmanac, Radoje; Peters, Brock A

    2016-10-11

    Since the completion of the Human Genome Project in 2003, it is estimated that more than 200,000 individual whole human genomes have been sequenced. A stunning accomplishment in such a short period of time. However, most of these were sequenced without experimental haplotype data and are therefore missing an important aspect of genome biology. In addition, much of the genomic data is not available to the public and lacks phenotypic information. As part of the Personal Genome Project, blood samples from 184 participants were collected and processed using Complete Genomics' Long Fragment Read technology. Here, we present the experimental whole genome haplotyping and sequencing of these samples to an average read coverage depth of 100X. This is approximately three-fold higher than the read coverage applied to most whole human genome assemblies and ensures the highest quality results. Currently, 114 genomes from this dataset are freely available in the GigaDB repository and are associated with rich phenotypic data; the remaining 70 should be added in the near future as they are approved through the PGP data release process. For reproducibility analyses, 20 genomes were sequenced at least twice using independent LFR barcoded libraries. Seven genomes were also sequenced using Complete Genomics' standard non-barcoded library process. In addition, we report 2.6 million high-quality, rare variants not previously identified in the Single Nucleotide Polymorphisms database or the 1000 Genomes Project Phase 3 data. These genomes represent a unique source of haplotype and phenotype data for the scientific community and should help to expand our understanding of human genome evolution and function.

  15. Blowing dust and highway safety in the southwestern United States: Characteristics of dust emission "hotspots" and management implications.

    Science.gov (United States)

    Li, Junran; Kandakji, Tarek; Lee, Jeffrey A; Tatarko, John; Blackwell, John; Gill, Thomas E; Collins, Joe D

    2018-04-15

    Despite the widespread media attention of chain-reaction traffic incidents and property damage caused by windblown dust in the U.S. and elsewhere in the world, very few studies have provided in-depth analysis on this issue. Remote sensing and field observations reveal that wind erosion in the southwestern U.S. typically occurs in localized source areas, characterized as "hotspots", while most of the landscape is not eroding. In this study, we identified the spatial and temporal distribution patterns of hotspots that may contribute dust blowing onto highways in the southwestern U.S. We further classified the hotspots for the potential of blowing dust production based upon field observations and wind erosion modeling. Results of land use and land cover show that shrubland, grassland, and cropland accounted for 42%, 31%, and 21% of the overall study area, respectively. However, of the 620 total hotspots identified, 164 (26%), 141 (22%), and 234 (38%) are located on shrubland, grassland, and cropland, respectively. Barren land represented 0.9% of the land area but 8% of the dust hotspots. While a majority of these hotspots are located close to highways, we focused on 55 of them, which are located hotspot sites are dominated by sand and silt particles with threshold shear velocities ranging from 0.17-0.78m s -1 , largely depending on the land use of the hotspot sites. Dust emission modeling showed that 13 hotspot sites could produce annual emissions >3.79kg m -2 , yielding highly hazardous dust emissions to ground transportation with visibility hotspots are critical information for highway authorities to make informed and timely management decisions when wind events strike. Copyright © 2017 Elsevier B.V. All rights reserved.

  16. Evolution of the Largest Mammalian Genome.

    Science.gov (United States)

    Evans, Ben J; Upham, Nathan S; Golding, Goeffrey B; Ojeda, Ricardo A; Ojeda, Agustina A

    2017-06-01

    The genome of the red vizcacha rat (Rodentia, Octodontidae, Tympanoctomys barrerae) is the largest of all mammals, and about double the size of their close relative, the mountain vizcacha rat Octomys mimax, even though the lineages that gave rise to these species diverged from each other only about 5 Ma. The mechanism for this rapid genome expansion is controversial, and hypothesized to be a consequence of whole genome duplication or accumulation of repetitive elements. To test these alternative but nonexclusive hypotheses, we gathered and evaluated evidence from whole transcriptome and whole genome sequences of T. barrerae and O. mimax. We recovered support for genome expansion due to accumulation of a diverse assemblage of repetitive elements, which represent about one half and one fifth of the genomes of T. barrerae and O. mimax, respectively, but we found no strong signal of whole genome duplication. In both species, repetitive sequences were rare in transcribed regions as compared with the rest of the genome, and mostly had no close match to annotated repetitive sequences from other rodents. These findings raise new questions about the genomic dynamics of these repetitive elements, their connection to widespread chromosomal fissions that occurred in the T. barrerae ancestor, and their fitness effects-including during the evolution of hypersaline dietary tolerance in T. barrerae. ©The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  17. China's rare-earth industry

    Science.gov (United States)

    Tse, Pui-Kwan

    2011-01-01

    Introduction China's dominant position as the producer of over 95 percent of the world output of rare-earth minerals and rapid increases in the consumption of rare earths owing to the emergence of new clean-energy and defense-related technologies, combined with China's decisions to restrict exports of rare earths, have resulted in heightened concerns about the future availability of rare earths. As a result, industrial countries such as Japan, the United States, and countries of the European Union face tighter supplies and higher prices for rare earths. This paper briefly reviews China's rare-earth production, consumption, and reserves and the important policies and regulations regarding the production and trade of rare earths, including recently announced export quotas. The 15 lanthanide elements-lanthanum, cerium, praseodymium, neodymium, promethium, samarium, europium, gadolinium, terbium, dysprosium, holmium, erbium, thulium, ytterbium, and lutetium (atomic numbers 57-71)-were originally known as the rare earths from their occurrence in oxides mixtures. Recently, some researchers have included two other elements-scandium and yttrium-in their discussion of rare earths. Yttrium (atomic number 39), which lies above lanthanum in transition group III of the periodic table and has a similar 3+ ion with a noble gas core, has both atomic and ionic radii similar in size to those of terbium and dysprosium and is generally found in nature with lanthanides. Scandium (atomic number 21) has a smaller ionic radius than yttrium and the lanthanides, and its chemical behavior is intermediate between that of aluminum and the lanthanides. It is found in nature with the lanthanides and yttrium. Rare earths are used widely in high-technology and clean-energy products because they impart special properties of magnetism, luminescence, and strength. Rare earths are also used in weapon systems to obtain the same properties.

  18. Rare earths 1998 market update

    International Nuclear Information System (INIS)

    Tourre, J.M.

    1998-01-01

    The rare earth industry has always been a world of rapid change with the emergence of new markets, new ores and new players, as well as the disappearance of old applications. Rare earth based products are used in a great diversity of applications such as hard disk drives, CD drives, batteries, capacitors, pigments, ceramics, polishing powders, fuel cells, flints, catalyst converter, fluid cracking catalysts, etc. South East Asia holds the largest share of the known reserve of rare earth ores and is one of the major markets for rare earth compounds; in the last ten years, China has become the largest producer of rare earth intermediates as well as an important exporter of separated rare earth elements. Today, China has approximately 150 factories producing rare earth compounds, most of which are experiencing financial difficulties due to the lack of knowledge of true market needs, lack of control of their distribution channels and production over-capacity. Recently the Chinese rare earth producers have recognized the situation and efforts are underway to rationalize rare earth production. Japan has dominated many of the major application markets, and is by far the largest market for metal and alloy products. This will remain the case for the next five years; however, new countries are emerging as significant users of rare earth products such as Korea, Taiwan and Malaysia. During the last ten years rare earth producers adjusted to several radical changes that affected the raw materials, the application mix and the price structure. New producers have emerged, especially from China; some have subsequently stopped their activities while others have focused their efforts in a specific market segment

  19. Privacy preserving protocol for detecting genetic relatives using rare variants.

    Science.gov (United States)

    Hormozdiari, Farhad; Joo, Jong Wha J; Wadia, Akshay; Guan, Feng; Ostrosky, Rafail; Sahai, Amit; Eskin, Eleazar

    2014-06-15

    High-throughput sequencing technologies have impacted many areas of genetic research. One such area is the identification of relatives from genetic data. The standard approach for the identification of genetic relatives collects the genomic data of all individuals and stores it in a database. Then, each pair of individuals is compared to detect the set of genetic relatives, and the matched individuals are informed. The main drawback of this approach is the requirement of sharing your genetic data with a trusted third party to perform the relatedness test. In this work, we propose a secure protocol to detect the genetic relatives from sequencing data while not exposing any information about their genomes. We assume that individuals have access to their genome sequences but do not want to share their genomes with anyone else. Unlike previous approaches, our approach uses both common and rare variants which provide the ability to detect much more distant relationships securely. We use a simulated data generated from the 1000 genomes data and illustrate that we can easily detect up to fifth degree cousins which was not possible using the existing methods. We also show in the 1000 genomes data with cryptic relationships that our method can detect these individuals. The software is freely available for download at http://genetics.cs.ucla.edu/crypto/. © The Author 2014. Published by Oxford University Press.

  20. Using a distribution and conservation status weighted hotspot approach to identify areas in need of conservation action to benefit Idaho bird species

    Science.gov (United States)

    Haines, Aaron M.; Leu, Matthias; Svancara, Leona K.; Wilson, Gina; Scott, J. Michael

    2010-01-01

    Identification of biodiversity hotspots (hereafter, hotspots) has become a common strategy to delineate important areas for wildlife conservation. However, the use of hotspots has not often incorporated important habitat types, ecosystem services, anthropogenic activity, or consistency in identifying important conservation areas. The purpose of this study was to identify hotspots to improve avian conservation efforts for Species of Greatest Conservation Need (SGCN) in the state of Idaho, United States. We evaluated multiple approaches to define hotspots and used a unique approach based on weighting species by their distribution size and conservation status to identify hotspot areas. All hotspot approaches identified bodies of water (Bear Lake, Grays Lake, and American Falls Reservoir) as important hotspots for Idaho avian SGCN, but we found that the weighted approach produced more congruent hotspot areas when compared to other hotspot approaches. To incorporate anthropogenic activity into hotspot analysis, we grouped species based on their sensitivity to specific human threats (i.e., urban development, agriculture, fire suppression, grazing, roads, and logging) and identified ecological sections within Idaho that may require specific conservation actions to address these human threats using the weighted approach. The Snake River Basalts and Overthrust Mountains ecological sections were important areas for potential implementation of conservation actions to conserve biodiversity. Our approach to identifying hotspots may be useful as part of a larger conservation strategy to aid land managers or local governments in applying conservation actions on the ground.

  1. Detecting biodiversity hotspots by species-area relationships: a case study of Mediterranean beetles.

    Science.gov (United States)

    Fattorini, Simone

    2006-08-01

    Any method of identifying hotspots should take into account the effect of area on species richness. I examined the importance of the species-a