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5. Widespread Divergence Between Incipient Anopheles gambiae Species Revealed by Whole Genome Sequences

Author

Lawniczak, M. K. N., Emrich, S. J., Holloway, A. K., Regier, A. P., Olson, M., White, B., Redmond, S., Fulton, L., Appelbaum, E., Godfrey, J., Farmer, C., Chinwalla, A., Yang, S.-P., Minx, P., Nelson, J., Kyung, K., Walenz, B. P., Garcia-Hernandez, E., Aguiar, M., Viswanathan, L. D., Rogers, Y.-H., Strausberg, R. L., Saski, C. A., Lawson, D., Collins, F. H., Kafatos, F. C., Christophides, G. K., Clifton, S. W., Kirkness, E. F., and Besansky, N. J.

Published
2010

7. Limits to the flexible re-distribution of visual working memory resources after encoding

Author

Naseem Al-Aidroos, Rak S, Blaire Dube, Holly A. Lockhart, and Emrich S

Subjects
Distribution (number theory), Computer science, Working memory, Encoding (memory), Data mining, computer.software_genre, computer
Abstract

Attention regulates visual working memory (VWM) performance by determining how its resources are distributed among encoded information. During encoding, this process is both flexible and strategic: Resources are unequally allocated to items based on the probability that each will be probed for memory recall. Here we assessed whether VWM resources can be strategically re-distributed among encoded items during maintenance. Across three experiments, participants encoded the colours of various shapes and were given information about the probability that each remembered item would be probed for recall via a retro-cue prompting the prioritization of two (E1 and E2) or one (E3) representation(s). We observe a reliable benefit of the retro-cues in all three experiments such that cued items were recalled with greater precision than non-cued items; however, we observed no evidence that the magnitude of this benefit was affected by the probability assigned to the cues when two items were prioritized, and only marginal evidence for an effect when a single item was prioritized. We argue that, although resources can be re-distributed post-encoding, the mechanism underlying this capability lacks the flexibility of that which underlies resource distribution during encoding, highlighting an important limitation in how attention regulates VWM performance.

Published
2019

8. Addressing properties and limitations of flexible resource allocation in visual short-term memory

Author

Emrich S, MacDonald Kj, and Lockhart Ha

Subjects
PsyArXiv|Social and Behavioral Sciences, Computer science, bepress|Social and Behavioral Sciences, PsyArXiv|Social and Behavioral Sciences|Cognitive Psychology, PsyArXiv|Social and Behavioral Sciences|Cognitive Psychology|Memory, Resource allocation, Visual short-term memory, Data science, bepress|Social and Behavioral Sciences|Psychology|Cognitive Psychology
Abstract

Although recent evidence suggests that visual short-term memory is a continuous resource, little is known about how flexibly this resource can be allocated. The current study used a continuous report procedure and attentional prioritization via probabilistic spatial cues to address three unknown properties of a flexible continuous resource. The first experiment measured multiple responses from each trial to assess whether multiple items could simultaneously be prioritized. Second, since past work has shown that participants could prioritize VSTM representations according to two states of attentional priority, we examined whether participants could maintain three levels of priority. Lastly, we examined whether flexible allocation is possible when the prioritization cues are provided after initial encoding (i.e. a retro-cue). The results demonstrated that when participants had to recall multiple items on each trial, there were clear differences in response precision between cued and uncued items; however, two items of the same category were not always stored with equal precision. When three attentional priority levels were provided, participants’ precision was no different between high- and medium-priority, but significantly improved over low priority items, suggesting participants did not assign different memory weights to the two higher-priority conditions. When prioritization was performed via retro-cues, participants could re-allocate memory resources, but not when more than one item was to be prioritized, suggesting limitations in the flexible allocation of resources after initial encoding. Together, the results provide evidence of a VSTM resource that is flexibly, but variably, allocated using up to two attentionally guided priority goals, primarily during encoding.

Published
2018

9. Corrigendum: Whole genome analysis of a schistosomiasis-transmitting freshwater snail

Author

Adema, CM, Hillier, LDW, Jones, CS, Loker, ES, Knight, M, Minx, P, Oliveira, G, Raghavan, N, Shedlock, A, do Amaral, LR, Arican-Goktas, HD, Assis, JG, Baba, EH, Baron, OL, Bayne, CJ, Bickham-Wright, U, Biggar, KK, Blouin, M, Bonning, BC, Botka, C, Bridger, JM, Buckley, KM, Buddenborg, SK, Lima Caldeira, R, Carleton, J, Carvalho, OS, Castillo, MG, Chalmers, IW, Christensens, M, Clifton, S, Cosseau, C, Coustau, C, Cripps, RM, Cuesta-Astroz, Y, Cummins, SF, Di Stefano, L, Dinguirard, N, Duval, D, Emrich, S, Feschotte, C, Feyereisen, R, FitzGerald, P, Fronick, C, Fulton, L, Galinier, R, Gava, SG, Geusz, M, Geyer, KK, Giraldo-Calderón, GI, de Souza Gomes, M, Gordy, MA, Gourbal, B, Grunau, C, Hanington, PC, Hoffmann, KF, Hughes, D, Humphries, J, Jackson, DJ, Jannotti-Passos, LK, de Jesus Jeremias, W, Jobling, S, Kamel, B, Kapusta, A, Kaur, S, Koene, JM, Kohn, AB, Lawson, D, Lawton, SP, Liang, D, Limpanont, Y, Liu, S, Lockyer, AE, Lovato, TAL, Ludolf, F, Magrini, V, McManus, DP, Medina, M, Misra, M, Mitta, G, Mkoji, GM, Montague, MJ, Montelongo, C, Moroz, LL, Munoz-Torres, MC, Niazi, U, Noble, LR, Oliveira, FS, Pais, FS, Papenfuss, AT, Peace, R, Pena, JJ, Pila, EA, Quelais, T, Raney, BJ, Rast, JP, Rollinson, D, Rosse, IC, Rotgans, B, Routledge, EJ, and Ryan, KM

Abstract

This corrects the article DOI: 10.1038/ncomms15451.

Published
2017

10. Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach

Author

Meyer, P., Siwo, G., Zeevi, D., Sharon, E., Norel, R., Rider, A.K., Tan, A., Pinapati, R.S., Emrich, S., Chawla, N., Ferdig, M.T., Tung, Y.A., Chen, Y.S., Chen, M.J., Chen, C.Y., Knight, J.M., Sahraeian, S.M., Esfahani, M.S., Dreos, R., Bucher, P., Maier, E., Saeys, Y., Szczurek, E., Mysicková, A., Vingron, M., Klein, H., Kielbasa, S.M., Knisley, J., Bonnell, J., Knisley, D., Kursa, M.B., Rudnicki, W.R., Bhattacharjee, M., Sillanpää, M.J., Yeung, J., Meysman, P., Rodríguez, A.S., Engelen, K.A., Marchal, K., Huang, Y., Mordelet, F., Hartemink, A., Pinello, L., Yuan, G.C., Segal, E., and Stolovitzky, G.

Subjects
Ribosomal Proteins, Resource, Saccharomyces cerevisiae Proteins, Settore BIO/18 - GENETICA, Genes, Fungal, Mammalian promoter database, Gene regulatory network, Gene Expression, Saccharomyces cerevisiae, Biology, Gene Expression Regulation, Fungal, Gene expression, Genetics, Gene Regulatory Networks, Regulatory Elements, Transcriptional, Promoter Regions, Genetic, Gene, Genetics (clinical), Regulation of gene expression, Binding Sites, Models, Genetic, Gene Expression Profiling, Systems Biology, Promoter, DNA binding site, Gene expression profiling, Mutation, Crowdsourcing, Ribosomes, Algorithms
Abstract

The Gene Promoter Expression Prediction challenge consisted of predicting gene expression from promoter sequences in a previously unknown experimentally generated data set. The challenge was presented to the community in the framework of the sixth Dialogue for Reverse Engineering Assessments and Methods (DREAM6), a community effort to evaluate the status of systems biology modeling methodologies. Nucleotide-specific promoter activity was obtained by measuring fluorescence from promoter sequences fused upstream of a gene for yellow fluorescence protein and inserted in the same genomic site of yeast Saccharomyces cerevisiae. Twenty-one teams submitted results predicting the expression levels of 53 different promoters from yeast ribosomal protein genes. Analysis of participant predictions shows that accurate values for low-expressed and mutated promoters were difficult to obtain, although in the latter case, only when the mutation induced a large change in promoter activity compared to the wild-type sequence. As in previous DREAM challenges, we found that aggregation of participant predictions provided robust results, but did not fare better than the three best algorithms. Finally, this study not only provides a benchmark for the assessment of methods predicting activity of a specific set of promoters from their sequence, but it also shows that the top performing algorithm, which used machine-learning approaches, can be improved by the addition of biological features such as transcription factor binding sites.

Published
2013

11. Experimental evidence of genome-wide impact of ecological selection during early stages of speciation-with-gene-flow

Author

Egan, S.P., Ragland, G.J., Assour, L., Powell, T.H.Q., Hood, G.R., Emrich, S., Nosil, P., and Feder, J.L.

Abstract

Theory predicts that speciation-with-gene-flow is more likely when the consequences of selection for population divergence transitions from mainly direct effects of selection acting on individual genes to a collective property of all selected genes in the genome. Thus, understanding the direct impacts of ecologically based selection, as well as the indirect effects due to correlations among loci, is critical to understanding speciation. Here, we measure the genome-wide impacts of host-associated selection between hawthorn and apple host races of Rhagoletis pomonella (Diptera: Tephritidae), a model for contemporary speciation-with-gene-flow. Allele frequency shifts of 32 455 SNPs induced in a selection experiment based on host phenology were genome wide and highly concordant with genetic divergence between co-occurring apple and hawthorn flies in nature. This striking genome-wide similarity between experimental and natural populations of R. pomonella underscores the importance of ecological selection at early stages of divergence and calls for further integration of studies of eco-evolutionary dynamics and genome divergence.

Published
2015

12. Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes

Author

Neafsey, D. E., Waterhouse, R. M., Abai, M. R., Aganezov, S. S., Alekseyev, M. A., Allen, J. E., Amon, J., Arca, B., Arensburger, P., Artemov, G., Assour, L. A., Basseri, H., Berlin, A., Birren, B. W., Blandin, S. A., Brockman, A. I., Burkot, T. R., Burt, A., Chan, C. S., Chauve, C., Chiu, J. C., Christensen, M., Costantini, C., Davidson, V. L., Deligianni, E., Dottorini, T., Dritsou, V., Gabriel, S. B., Guelbeogo, W. M., Hall, A. B., Han, M. V., Hlaing, T., Hughes, D. S., Jenkins, A. M., Jiang, X., Jungreis, I., Kakani, E. G., Kamali, M., Kemppainen, P., Kennedy, R. C., Kirmitzoglou, I. K., Koekemoer, L. L., Laban, N., Langridge, N., Lawniczak, M. K., Lirakis, M., Lobo, N. F., Lowy, E., MacCallum, R. M., Mao, C., Maslen, G., Mbogo, C., McCarthy, J., Michel, K., Mitchell, S. N., Moore, W., Murphy, K. A., Naumenko, A. N., Nolan, T., Novoa, E. M., O'Loughlin, S., Oringanje, C., Oshaghi, M. A., Pakpour, N., Papathanos, P. A., Peery, A. N., Povelones, M., Prakash, A., Price, D. P., Rajaraman, A., Reimer, L. J., Rinker, D. C., Rokas, A., Russell, T. L., Sagnon, N., Sharakhova, M. V., Shea, T., Simao, F. A., Simard, F., Slotman, M. A., Somboon, P., Stegniy, V., Struchiner, C. J., Thomas, G. W., Tojo Castro, Marta, Topalis, P., Tubio, J. M., Unger, M. F., Vontas, J., Walton, C., Wilding, C. S., Willis, J. H., Wu, Y. C., Yan, G., Zdobnov, E. M., Zhou, X., Catteruccia, F., Christophides, G. K., Collins, F. H., Cornman, R. S., Crisanti, A., Donnelly, M. J., Emrich, S. J., Fontaine, M. C., Gelbart, W., Hahn, M. W., Hansen, I. A., Howell, P. I., Kafatos, F. C., Kellis, M., Lawson, D., Louis, C., Luckhart, S., Muskavitch, M. A., Ribeiro, J. M., Riehle, M. A., Sharakhov, I. V., Tu, Z., Zwiebel, L. J., and Besansky, N. J.

Subjects
EXPRESSION, SEX-CHROMOSOME EVOLUTION, ANTENNAL TRANSCRIPTOME PROFILES, Base Sequence, R CONSENSUS, Genome, Insect, Molecular Sequence Data, GAMBIAE, CUTICULAR PROTEIN GENES, AEDES-AEGYPTI, DROSOPHILA, ANNOTATION, FAMILY, Malari, Chromosomes, Insect, Insect Vectors, Evolution, Molecular, Anopheles, Animals, Humans, Drosophila, Sequence Alignment, Phylogeny
Abstract

Variation in vectorial capacity for human malaria among Anopheles mosquito species is determined by many factors, including behavior, immunity, and life history. To investigate the genomic basis of vectorial capacity and explore new avenues for vector control, we sequenced the genomes of 16 anopheline mosquito species from diverse locations spanning ~100 million years of evolution. Comparative analyses show faster rates of gene gain and loss, elevated gene shuffling on the X chromosome, and more intron losses, relative to Drosophila. Some determinants of vectorial capacity, such as chemosensory genes, do not show elevated turnover but instead diversify through protein-sequence changes. This dynamism of anopheline genes and genomes may contribute to their flexible capacity to take advantage of new ecological niches, including adapting to humans as primary hosts.

Published
2015

13. Genome analysis of a major urban malaria vector mosquito, Anopheles stephensi

Author

Jiang, X., Peery, A., Hall, B., Sharma, A., Chen, X.-G., Waterhouse, R. M., Komissarov, A., Riehle, M. M., Shouche, Y., Sharakhova, Maria V., Lawson, D., Pakpour, Nazzy, Arensburger, Peter, Davidson, V. L. M., Eiglmeier, K., Emrich, S., George, P., Kennedy, R. C., Mane, S. P., Maslen, G., Oringanje, C., Qi, Y., Settlage, Robert E., Tojo, M., Tubio, J. M. C., Unger, Maria F., Wang, B., Vernick, K. D., Ribeiro, J. C., James, A. A., Michel, K., Riehle, M. A., Luckhart, Shirley, Sharakhov, Igor V., Tu, Zhijian Jake, and Biological Systems Engineering

Subjects
Genetics & Heredity, Biotechnology & Applied Microbiology, PLASMODIUM-FALCIPARUM, WEB SERVER, parasitic diseases, INVERSION POLYMORPHISMS, RNA-SEQ, IN-SILICO, NUCLEAR LAMINS, AEDES-AEGYPTI, GENE, EVOLUTION, CHROMOSOMAL REARRANGEMENT
Abstract

Background: Anopheles stephensi is the key vector of malaria throughout the Indian subcontinent and Middle East and an emerging model for molecular and genetic studies of mosquito-parasite interactions. The type form of the species is responsible for the majority of urban malaria transmission across its range. Results: Here, we report the genome sequence and annotation of the Indian strain of the type form of An. stephensi. The 221 Mb genome assembly represents more than 92% of the entire genome and was produced using a combination of 454, Illumina, and PacBio sequencing. Physical mapping assigned 62% of the genome onto chromosomes, enabling chromosome-based analysis. Comparisons between An. stephensi and An. gambiae reveal that the rate of gene order reshuffling on the X chromosome was three times higher than that on the autosomes. An. stephensi has more heterochromatin in pericentric regions but less repetitive DNA in chromosome arms than An. gambiae. We also identify a number of Y-chromosome contigs and BACs. Interspersed repeats constitute 7.1% of the assembled genome while LTR retrotransposons alone comprise more than 49% of the Y contigs. RNA-seq analyses provide new insights into mosquito innate immunity, development, and sexual dimorphism. Conclusions: The genome analysis described in this manuscript provides a resource and platform for fundamental and translational research into a major urban malaria vector. Chromosome-based investigations provide unique perspectives on Anopheles chromosome evolution. RNA-seq analysis and studies of immunity genes offer new insights into mosquito biology and mosquito-parasite interactions. Published version

Published
2014

14. Breakpoint structure of the Anopheles gambiae 2Rb chromosomal inversion

Author

Lobo, N. F., Sangare, D. M., Regier, A. A., Reidenbach, K. R., Bretz, D. A., Sharakhova, M. V., Emrich, S. J., Traore, S. F., Costantini, Carlo, Besansky, N. J., and Collins, F. H.

Abstract

Background: Alternative arrangements of chromosome 2 inversions in Anopheles gambiae are important sources of population structure, and are associated with adaptation to environmental heterogeneity. The forces responsible for their origin and maintenance are incompletely understood. Molecular characterization of inversion breakpoints provides insight into how they arose, and provides the basis for development of molecular karyotyping methods useful in future studies. Methods: Sequence comparison of regions near the cytological breakpoints of 2Rb allowed the molecular delineation of breakpoint boundaries. Comparisons were made between the standard 2R+(b) arrangement in the An. gambiae PEST reference genome and the inverted 2Rb arrangements in the An. gambiae M and S genome assemblies. Sequence differences between alternative 2Rb arrangements were exploited in the design of a PCR diagnostic assay, which was evaluated against the known chromosomal banding pattern of laboratory colonies and field-collected samples from Mali and Cameroon. Results: The breakpoints of the 7.55 Mb 2Rb inversion are flanked by extensive runs of the same short 72 bp) tandemly organized sequence, which was likely responsible for chromosomal breakage and rearrangement. Application of the molecular diagnostic assay suggested that 2Rb has a single common origin in An. gambiae and its sibling species, Anopheles arabiensis, and also that the standard arrangement 2R+(b)) may have arisen twice through breakpoint reuse. The molecular diagnostic was reliable when applied to laboratory colonies, but its accuracy was lower in natural populations. Conclusions: The complex repetitive sequence flanking the 2Rb breakpoint region may be prone to structural and sequence-level instability. The 2Rb molecular diagnostic has immediate application in studies based on laboratory colonies, but its usefulness in natural populations awaits development of complementary molecular tools.

Published
2010

18. The characterization of the Phlebotomus papatasi transcriptome

Author

Abrudan, J., primary, Ramalho‐Ortigão, M., additional, O'Neil, S., additional, Stayback, G., additional, Wadsworth, M., additional, Bernard, M., additional, Shoue, D., additional, Emrich, S., additional, Lawyer, P., additional, Kamhawi, S., additional, Rowton, E. D., additional, Lehane, M. J., additional, Bates, P. A., additional, Valenzeula, J. G., additional, Tomlinson, C., additional, Appelbaum, E., additional, Moeller, D., additional, Thiesing, B., additional, Dillon, R., additional, Clifton, S., additional, Lobo, N. F., additional, Wilson, R. K., additional, Collins, F. H., additional, and McDowell, M. A., additional

Published
2013
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39. Influence of tribo-induced films on damage and friction behavior of gearwheels with particular consideration of the running-in process - experimental and analytic investigations,Einf luss triboinduzierter Schichten auf Schäden und Reibungsverhalten von Zahnrädern unter besonderer Berücksichtigung des Einlaufvorgangs -experimentelle und analytische Untersuchungen

Author

Ziegltrum, A., Emrich, S., Lohner, T., Michaelis, K., Brodyanski, A., Merz, R., Kopnarski, M., Höhn, B. -R, and Karsten Stahl

41. High-throughput 454 resequencing for allele discovery and recombination mapping in Plasmodium falciparum

Author

Tan John C, Collins Brendan, Desany Brian A, Tan Asako, Regier Allison, Samarakoon Upeka, Emrich Scott J, and Ferdig Michael T

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Knowledge of the origins, distribution, and inheritance of variation in the malaria parasite (Plasmodium falciparum) genome is crucial for understanding its evolution; however the 81% (A+T) genome poses challenges to high-throughput sequencing technologies. We explore the viability of the Roche 454 Genome Sequencer FLX (GS FLX) high throughput sequencing technology for both whole genome sequencing and fine-resolution characterization of genetic exchange in malaria parasites. Results We present a scheme to survey recombination in the haploid stage genomes of two sibling parasite clones, using whole genome pyrosequencing that includes a sliding window approach to predict recombination breakpoints. Whole genome shotgun (WGS) sequencing generated approximately 2 million reads, with an average read length of approximately 300 bp. De novo assembly using a combination of WGS and 3 kb paired end libraries resulted in contigs ≤ 34 kb. More than 8,000 of the 24,599 SNP markers identified between parents were genotyped in the progeny, resulting in a marker density of approximately 1 marker/3.3 kb and allowing for the detection of previously unrecognized crossovers (COs) and many non crossover (NCO) gene conversions throughout the genome. Conclusions By sequencing the 23 Mb genomes of two haploid progeny clones derived from a genetic cross at more than 30× coverage, we captured high resolution information on COs, NCOs and genetic variation within the progeny genomes. This study is the first to resequence progeny clones to examine fine structure of COs and NCOs in malaria parasites.

Published
2011
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42. A statistical approach to finding overlooked genetic associations

Author

Siwo Geoffrey, Rider Andrew K, Chawla Nitesh V, Ferdig Michael, and Emrich Scott J

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background Complexity and noise in expression quantitative trait loci (eQTL) studies make it difficult to distinguish potential regulatory relationships among the many interactions. The predominant method of identifying eQTLs finds associations that are significant at a genome-wide level. The vast number of statistical tests carried out on these data make false negatives very likely. Corrections for multiple testing error render genome-wide eQTL techniques unable to detect modest regulatory effects. We propose an alternative method to identify eQTLs that builds on traditional approaches. In contrast to genome-wide techniques, our method determines the significance of an association between an expression trait and a locus with respect to the set of all associations to the expression trait. The use of this specific information facilitates identification of expression traits that have an expression profile that is characterized by a single exceptional association to a locus. Our approach identifies expression traits that have exceptional associations regardless of the genome-wide significance of those associations. This property facilitates the identification of possible false negatives for genome-wide significance. Further, our approach has the property of prioritizing expression traits that are affected by few strong associations. Expression traits identified by this method may warrant additional study because their expression level may be affected by targeting genes near a single locus. Results We demonstrate our method by identifying eQTL hotspots in Plasmodium falciparum (malaria) and Saccharomyces cerevisiae (yeast). We demonstrate the prioritization of traits with few strong genetic effects through Gene Ontology (GO) analysis of Yeast. Our results are strongly consistent with results gathered using genome-wide methods and identify additional hotspots and eQTLs. Conclusions New eQTLs and hotspots found with this method may represent regions of the genome or biological processes that are controlled through few relatively strong genetic interactions. These points of interest warrant experimental investigation.

Published
2010
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43. Breakpoint structure of the Anopheles gambiae 2Rb chromosomal inversion

Author

Costantini Carlo, Traore Sekou F, Emrich Scott J, Sharakhova Maria V, Bretz David A, Reidenbach Kyanne R, Regier Allison A, Sangaré Djibril M, Lobo Neil F, Besansky Nora J, and Collins Frank H

Subjects
Arctic medicine. Tropical medicine, RC955-962, Infectious and parasitic diseases, RC109-216
Abstract

Abstract Background Alternative arrangements of chromosome 2 inversions in Anopheles gambiae are important sources of population structure, and are associated with adaptation to environmental heterogeneity. The forces responsible for their origin and maintenance are incompletely understood. Molecular characterization of inversion breakpoints provides insight into how they arose, and provides the basis for development of molecular karyotyping methods useful in future studies. Methods Sequence comparison of regions near the cytological breakpoints of 2Rb allowed the molecular delineation of breakpoint boundaries. Comparisons were made between the standard 2R+b arrangement in the An. gambiae PEST reference genome and the inverted 2Rb arrangements in the An. gambiae M and S genome assemblies. Sequence differences between alternative 2Rb arrangements were exploited in the design of a PCR diagnostic assay, which was evaluated against the known chromosomal banding pattern of laboratory colonies and field-collected samples from Mali and Cameroon. Results The breakpoints of the 7.55 Mb 2Rb inversion are flanked by extensive runs of the same short (72 bp) tandemly organized sequence, which was likely responsible for chromosomal breakage and rearrangement. Application of the molecular diagnostic assay suggested that 2Rb has a single common origin in An. gambiae and its sibling species, Anopheles arabiensis, and also that the standard arrangement (2R+b) may have arisen twice through breakpoint reuse. The molecular diagnostic was reliable when applied to laboratory colonies, but its accuracy was lower in natural populations. Conclusions The complex repetitive sequence flanking the 2Rb breakpoint region may be prone to structural and sequence-level instability. The 2Rb molecular diagnostic has immediate application in studies based on laboratory colonies, but its usefulness in natural populations awaits development of complementary molecular tools.

Published
2010
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44. Population-level transcriptome sequencing of nonmodel organisms Erynnis propertius and Papilio zelicaon

Author

Emrich Scott J, Lobo Neil F, Carmichael Rory D, Dzurisin Jason DK, O'Neil Shawn T, and Hellmann Jessica J

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Several recent studies have demonstrated the use of Roche 454 sequencing technology for de novo transcriptome analysis. Low error rates and high coverage also allow for effective SNP discovery and genetic diversity estimates. However, genetically diverse datasets, such as those sourced from natural populations, pose challenges for assembly programs and subsequent analysis. Further, estimating the effectiveness of transcript discovery using Roche 454 transcriptome data is still a difficult task. Results Using the Roche 454 FLX Titanium platform, we sequenced and assembled larval transcriptomes for two butterfly species: the Propertius duskywing, Erynnis propertius (Lepidoptera: Hesperiidae) and the Anise swallowtail, Papilio zelicaon (Lepidoptera: Papilionidae). The Expressed Sequence Tags (ESTs) generated represent a diverse sample drawn from multiple populations, developmental stages, and stress treatments. Despite this diversity, > 95% of the ESTs assembled into long (> 714 bp on average) and highly covered (> 9.6× on average) contigs. To estimate the effectiveness of transcript discovery, we compared the number of bases in the hit region of unigenes (contigs and singletons) to the length of the best match silkworm (Bombyx mori) protein--this "ortholog hit ratio" gives a close estimate on the amount of the transcript discovered relative to a model lepidopteran genome. For each species, we tested two assembly programs and two parameter sets; although CAP3 is commonly used for such data, the assemblies produced by Celera Assembler with modified parameters were chosen over those produced by CAP3 based on contig and singleton counts as well as ortholog hit ratio analysis. In the final assemblies, 1,413 E. propertius and 1,940 P. zelicaon unigenes had a ratio > 0.8; 2,866 E. propertius and 4,015 P. zelicaon unigenes had a ratio > 0.5. Conclusions Ultimately, these assemblies and SNP data will be used to generate microarrays for ecoinformatics examining climate change tolerance of different natural populations. These studies will benefit from high quality assemblies with few singletons (less than 26% of bases for each assembled transcriptome are present in unassembled singleton ESTs) and effective transcript discovery (over 6,500 of our putative orthologs cover at least 50% of the corresponding model silkworm gene).

Published
2010
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46. Enhancing the lifetime of MoS2-lubricated ball bearings.

Author

Marquart, M., Wahl, M., Emrich, S., Zhang, G., Sauer, B., Kopnarski, M., and Wetzel, B.

Subjects
*BALL bearings, *LUBRICATION & lubricants, *MOLYBDENUM sulfides, *HIGH temperatures, *SIMULATION methods & models, *CONTACT mechanics
Abstract

Abstract: Solid lubricated ball bearings can be a choice, if standard lubrication cannot be used, as for example because of surroundings like high temperature or vacuum. Law enforcements as well can be a reason for choosing such bearings. Although molybdenum disulfide (MoS2) as one kind of solid lubrication for ball bearings has been known for 60 years, a universal valid lifetime prediction has not been developed yet. This paper presents an overview of the possible approaches to get an idea of the lifetime for such systems. Options to enhance the life by redesigning the cage are shown, among others by the use of mulitbody simulation. Furthermore first results of investigating the materials, coatings and the transfer of additional lubrication from the cage to the primary contact between rolling body and raceway are presented. [Copyright &y& Elsevier]

Published
2013
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47. Global surveillance of trends in cancer survival 2000-14 (concord-3): analysis of individual records for 37 513 025 patients diagnosed with one of 18 cancers from 322 population-based registries in 71 countries

Author

Claudia Allemani, Tomohiro Matsuda, Veronica Di Carlo, Rhea Harewood, Melissa Matz, Maja Nikšić, Audrey Bonaventure, Mikhail Valkov, Christopher J Johnson, Jacques Estève, Olufemi J Ogunbiyi, Gulnar Azevedo e Silva, Wan-Qing Chen, Sultan Eser, Gerda Engholm, Charles A Stiller, Alain Monnereau, Ryan R Woods, Otto Visser, Gek Hsiang Lim, Joanne Aitken, Hannah K Weir, Michel P Coleman, S Bouzbid, M Hamdi-Chérif, Z Zaidi, K Meguenni, D Regagba, S Bayo, T Cheick Bougadari, S S Manraj, A Fabowale, O J Ogunbiyi, D Bradshaw, N I M Somdyala, I Kumcher, F Moreno, G H Calabrano, S B Espinola, B Carballo Quintero, R Fita, M C Diumenjo, W D Laspada, S G Ibañez, C A Lima, P C F De Souza, K Del Pino, C Laporte, M P Curado, J C de Oliveira, C L A Veneziano, D B Veneziano, M R D O Latorre, L F Tanaka, M S Rebelo, M O Santos, G Azevedo e Silva, J C Galaz, M Aparicio Aravena, J Sanhueza Monsalve, D A Herrmann, S Vargas, V M Herrera, C J Uribe, L E Bravo, L S Garcia, N E Arias-Ortiz, D Morantes, D M Jurado, M C Yépez Chamorro, S Delgado, M Ramirez, Y H Galán Alvarez, P Torres, F Martínez-Reyes, L Jaramillo, R Quinto, J, M Mendoza, P Cueva, J G Yépez, B Bhakkan, J Deloumeaux, C Joachim, J Macni, R Carrillo, J Shalkow Klincovstein, R Rivera Gomez, E Poquioma, G Tortolero-Luna, D Zavala, R Alonso, E Barrios, A Eckstrand, C Nikiforuk, R R Woods, G Noonan, D Turner, E Kumar, B Zhang, F R McCrate, S Ryan, M MacIntyre, N Saint-Jacques, D E Nishri, C A McClure, K A Vriends, S Kozie, H Stuart-Panko, T Freeman, J T George, J T Brockhouse, D K O'Brien, A Holt, L Almon, S Kwong, C Morris, R Rycroft, L Mueller, C E Phillips, H Brown, B Cromartie, A G Schwartz, F Vigneau, G M Levin, B Wohler, R Bayakly, K C Ward, S L Gomez, M McKinley, R Cress, M D Green, K Miyagi, C J Johnson, L P Ruppert, C F Lynch, B Huang, T C Tucker, D Deapen, L Liu, M C Hsieh, X C Wu, M Schwenn, S T Gershman, R C Knowlton, G Alverson, G E Copeland, S Bushhouse, D B Rogers, J Jackson-Thompson, D Lemons, H J Zimmerman, M Hood, J Roberts-Johnson, J R Rees, B Riddle, K S Pawlish, A Stroup, C Key, C Wiggins, A R Kahn, M J Schymura, S Radhakrishnan, C Rao, L K Giljahn, R M Slocumb, R E Espinoza, F Khan, K G Aird, T Beran, J J Rubertone, S J Slack, L Garcia, D L Rousseau, T A Janes, S M Schwartz, S W Bolick, D M Hurley, M A Whiteside, P Miller-Gianturco, M A Williams, K Herget, C Sweeney, A T Johnson, M B Keitheri Cheteri, P Migliore Santiago, S E Blankenship, S Farley, R Borchers, R Malicki, J R Espinoza, J Grandpre, H K Weir, R Wilson, B K Edwards, A Mariotto. Y Lei, N Wang, J S Chen, Y Zhou, Y T He, G H Song, X P Gu, D Mei, H J Mu, H M Ge, T H Wu, Y Y Li, D L Zhao, F Jin, J H Zhang, F D Zhu, Q Junhua, Y L Yang, C X Jiang, W Biao, J Wang, Q L Li, H Yi, X Zhou, J Dong, W Li, F X Fu, S Z Liu, J G Chen, J Zhu, Y H Li, Y Q Lu, M Fan, S Q Huang, G P Guo, H Zhaolai, K Wei, W Q Chen, H Zeng, A V Demetriou, W K Mang, K C Ngan, A C Kataki, M Krishnatreya, P A Jayalekshmi, P Sebastian, A Nandakumar, R Malekzadeh, G Roshandel, L Keinan-Boker, B G Silverman, H Ito, H Nakagawa, M Sato, F Tobori, I Nakata, N Teramoto, M Hattori, Y Kaizaki, F Moki, H Sugiyama, M Utada, M Nishimura, K Yoshida, K Kurosawa, Y Nemoto, H Narimatsu, M Sakaguchi, S Kanemura, M Naito, R Narisawa, I Miyashiro, K Nakata, S Sato, M Yoshii, I Oki, N Fukushima, A Shibata, K Iwasa, C Ono, T Matsuda, O Nimri, K W Jung, Y J Won, E Alawadhi, A Elbasmi, A Ab Manan, F Adam, E Sanjaajmats, U Tudev, C Ochir, A M Al Khater, M M El Mistiri, G H Lim, Y Y Teo, C J Chiang, W C Lee, R Buasom, S Sangrajrang, S Kamsaard, S Wiangnon, K Daoprasert, D Pongnikorn, A Leklob, S Sangkitipaiboon, S L Geater, H Sriplung, O Ceylan, I Kög, O Dirican, T Köse, T Gurbuz, F E Karaşahin, D Turhan, U Aktaş, Y Halat, S Eser, C I Yakut, M Altinisik, Y Cavusoglu, A Türkköylü, N Üçüncü, M Hackl, A A Zborovskaya, O V Aleinikova, K Henau, L Van Eycken, Z Valerianova, M R Yordanova, M Šekerija, L Dušek, M Zvolský, G Engholm, H Storm, K Innos, M Mägi, N Malila, K Seppä, J Jégu, M Velten, E Cornet, X Troussard, A M Bouvier, A V Guizard, V Bouvier, G Launoy, P Arveux, M Maynadié, M Mounier, A S Worono, M Daoulas, M Robaszkiewicz, J Clavel, S Goujon, B Lacour, I Baldi, C Pouchieu, B Amadeo, G Coureau, A Monnereau, S Orazio, P M Preux, F Rharbaoui, E Marrer, B Trétarre, M Colonna, P Delafosse, K Ligier, S Plouvier, A Cowppli-Bony, F Molinié, S Bara, O Ganry, B Lapôtre- Ledoux, P Grosclaude, N Bossard, Z Uhry, F Bray, M Piñeros, J Estève, R Stabenow, H Wilsdorf-Köhler, A Eberle, S Luttmann, I Löhden, A L Nennecke, J Kieschke, E Sirri, K Emrich, S R Zeissig, B Holleczek, N Eisemann, A Katalinic, R A Asquez, V Kumar, E Petridou, E J Ólafsdóttir, L Tryggvadóttir, K Clough-Gorr, P M Walsh, H Sundseth, G Mazzoleni, F Vittadello, E Coviello, F Cuccaro, R Galasso, G Sampietro, A Giacomin, M Magoni, A Ardizzone, A D'Argenzio, M Castaing, G Grosso, A M Lavecchia, A Sutera Sardo, G Gola, L Gatti, P Ricci, S Ferretti, D Serraino, A Zucchetto, M V Celesia, R A Filiberti, F Pannozzo, A Melcarne, F Quarta, A G Russo, G Carrozzi, C Cirilli, L Cavalieri d'Oro, M Rognoni, M Fusco, M F Vitale, M Usala, R Cusimano, W Mazzucco, M Michiara, P Sgargi, L Boschetti, E Borciani, P Seghini, M M Maule, F Merletti, R Tumino, P Mancuso, M Vicentini, T Cassetti, R Sassatelli, F Falcini, S Giorgetti, A L Caiazzo, R Cavallo, R Cesaraccio, D R Pirino, M L Contrino, F Tisano, A C Fanetti, S Maspero, S Carone, A Mincuzzi, G Candela, T Scuderi, M A Gentilini, S Pier, S Rosso, A Barchielli, A Caldarella, F Bianconi, F Stracci, P Contiero, G Tagliabue, M Rugge, M Zorzi, S Beggiato, A Brustolin, F Berrino, G Gatta, M Sant, C Buzzoni, L Mangone, R Capocaccia, R De Angelis, R Zanetti, A Maurina, S Pildava, N Lipunova, I Vincerževskienė, D Agius, N Calleja, S Siesling, O Visser, Larønningen, B Møller, A Dyzmann-Sroka, M Trojanowski, S Góźdź, R Mężyk, T Mierzwa, L Molong, J Rachtan, S Szewczyk, J Błaszczyk, K Kępska, B Kościańska, K Tarocińska, M Zwierko, K Drosik, K M Maksimowicz, E Purwin-Porowska, E Reca, J Wójcik-Tomaszewska, A Tukiendorf, M Grądalska-Lampart, A U Radziszewska, A Gos, M Talerczyk, M Wyborska, J A Didkowska, U Wojciechowska, M Bielska-Lasota, G Forjaz de Lacerda, R A Rego, J Bastos, M A Silva, L Antunes, J Laranja Pontes, A Mayer-da-Silva, A Miranda, L M Blaga, D Coza, Russia: M Y Valkov, L Gusenkova, O Lazarevich, O Prudnikova, D M Vjushkov, A G Egorova, A E Orlov, L A Kudyakov, L V Pikalova, J Adamcik, C Safaei Diba, M Primic-Žakelj, V Zadnik, N Larrañaga, A Lopez de Munain, A A Herrera, R Redondas, R Marcos-Gragera, M L Vilardell Gil, E Molina, M J Sánchez Perez, P Franch Sureda, M Ramos Montserrat, M D Chirlaque, C Navarro, E E Ardanaz, M M Guevara, R Fernández-Delgado, R Peris-Bonet, M Carulla, J Galceran, C Alberich, M Vicente-Raneda, S Khan, D Pettersson, P Dickman, I Avelina, K Staehelin, B Camey, C Bouchardy, R Schaar, H Frick, C Herrmann, J L Bulliard, M Maspoli-Conconi, C E Kuehni, S M Redmond, A Bordoni, L Ortelli, A Chiolero, I Konzelmann, K L Matthes, S Rohrmann, Broggio, J Rashbass, D Fitzpatrick, A Gavin, D I Clark, A J Deas, D W Huws, C White, C Allemani, A Bonaventure, M P Coleman, V Di Carlo, R Harewood, M Matz, L Montel, M Nikšić, B Rachet, A D Turculeț, R Stephens, C A Stiller, E Chalker, H Phung, R Walton, H You, S Guthridge, F Johnson, J Aitken, P Gordon, K D'Onise, K Priest, B C Stokes, A Venn, H Farrugia, V Thurs eld, J Dowlin, D Currow, J Hendrix, C Lewis, Tıp Fakültesi, Bordeaux population health (BPH), Université de Bordeaux (UB)-Institut de Santé Publique, d'Épidémiologie et de Développement (ISPED)-Institut National de la Santé et de la Recherche Médicale (INSERM), and Claudia Allemani, Tomohiro Matsuda, Veronica Di Carlo, Rhea Harewood, Melissa Matz, Maja Nikšić, Audrey Bonaventure, Mikhail Valkov, Christopher J Johnson, Jacques Estève, Olufemi J Ogunbiyi, Gulnar Azevedo e Silva, Wan-Qing Chen, Sultan Eser, Gerda Engholm, Charles A Stiller, Alain Monnereau, Ryan R Woods, Otto Visser, Gek Hsiang Lim, Joanne Aitken, Hannah K Weir, Michel P Coleman, S Bouzbid, M Hamdi-Chérif, Z Zaidi, K Meguenni, D Regagba, S Bayo, T Cheick Bougadari, S S Manraj, A Fabowale, O J Ogunbiyi, D Bradshaw, N I M Somdyala, I Kumcher, F Moreno, G H Calabrano, S B Espinola, B Carballo Quintero, R Fita, M C Diumenjo, W D Laspada, S G Ibañez, C A Lima, P C F De Souza, K Del Pino, C Laporte, M P Curado, J C de Oliveira, C L A Veneziano, D B Veneziano, M R D O Latorre, L F Tanaka, M S Rebelo, M O Santos, G Azevedo e Silva, J C Galaz, M Aparicio Aravena, J Sanhueza Monsalve, D A Herrmann, S Vargas, V M Herrera, C J Uribe, L E Bravo, L S Garcia, N E Arias-Ortiz, D Morantes, D M Jurado, M C Yépez Chamorro, S Delgado, M Ramirez, Y H Galán Alvarez, P Torres, F Martínez-Reyes, L Jaramillo, R Quinto, J, M Mendoza, P Cueva, J G Yépez, B Bhakkan, J Deloumeaux, C Joachim, J Macni, R Carrillo, J Shalkow Klincovstein, R Rivera Gomez, E Poquioma, G Tortolero-Luna, D Zavala, R Alonso, E Barrios, A Eckstrand, C Nikiforuk, R R Woods, G Noonan, D Turner, E Kumar, B Zhang, F R McCrate, S Ryan, M MacIntyre, N Saint-Jacques, D E Nishri, C A McClure, K A Vriends, S Kozie, H Stuart-Panko, T Freeman, J T George, J T Brockhouse, D K O'Brien, A Holt, L Almon, S Kwong, C Morris, R Rycroft, L Mueller, C E Phillips, H Brown, B Cromartie, A G Schwartz, F Vigneau, G M Levin, B Wohler, R Bayakly, K C Ward, S L Gomez, M McKinley, R Cress, M D Green, K Miyagi, C J Johnson, L P Ruppert, C F Lynch, B Huang, T C Tucker, D Deapen, L Liu, M C Hsieh, X C Wu, M Schwenn, S T Gershman, R C Knowlton, G Alverson, G E Copeland, S Bushhouse, D B Rogers, J Jackson-Thompson, D Lemons, H J Zimmerman, M Hood, J Roberts-Johnson, J R Rees, B Riddle, K S Pawlish, A Stroup, C Key, C Wiggins, A R Kahn, M J Schymura, S Radhakrishnan, C Rao, L K Giljahn, R M Slocumb, R E Espinoza, F Khan, K G Aird, T Beran, J J Rubertone, S J Slack, L Garcia, D L Rousseau, T A Janes, S M Schwartz, S W Bolick, D M Hurley, M A Whiteside, P Miller-Gianturco, M A Williams, K Herget, C Sweeney, A T Johnson, M B Keitheri Cheteri, P Migliore Santiago, S E Blankenship, S Farley, R Borchers, R Malicki, J R Espinoza, J Grandpre, H K Weir, R Wilson, B K Edwards, A Mariotto. Y Lei, N Wang, J S Chen, Y Zhou, Y T He, G H Song, X P Gu, D Mei, H J Mu, H M Ge, T H Wu, Y Y Li, D L Zhao, F Jin, J H Zhang, F D Zhu, Q Junhua, Y L Yang, C X Jiang, W Biao, J Wang, Q L Li, H Yi, X Zhou, J Dong, W Li, F X Fu, S Z Liu, J G Chen, J Zhu, Y H Li, Y Q Lu, M Fan, S Q Huang, G P Guo, H Zhaolai, K Wei, W Q Chen, H Zeng, A V Demetriou, W K Mang, K C Ngan, A C Kataki, M Krishnatreya, P A Jayalekshmi, P Sebastian, A Nandakumar, R Malekzadeh, G Roshandel, L Keinan-Boker, B G Silverman, H Ito, H Nakagawa, M Sato, F Tobori, I Nakata, N Teramoto, M Hattori, Y Kaizaki, F Moki, H Sugiyama, M Utada, M Nishimura, K Yoshida, K Kurosawa, Y Nemoto, H Narimatsu, M Sakaguchi, S Kanemura, M Naito, R Narisawa, I Miyashiro, K Nakata, S Sato, M Yoshii, I Oki, N Fukushima, A Shibata, K Iwasa, C Ono, T Matsuda, O Nimri, K W Jung, Y J Won, E Alawadhi, A Elbasmi, A Ab Manan, F Adam, E Sanjaajmats, U Tudev, C Ochir, A M Al Khater, M M El Mistiri, G H Lim, Y Y Teo, C J Chiang, W C Lee, R Buasom, S Sangrajrang, S Kamsaard, S Wiangnon, K Daoprasert, D Pongnikorn, A Leklob, S Sangkitipaiboon, S L Geater, H Sriplung, O Ceylan, I Kög, O Dirican, T Köse, T Gurbuz, F E Karaşahin, D Turhan, U Aktaş, Y Halat, S Eser, C I Yakut, M Altinisik, Y Cavusoglu, A Türkköylü, N Üçüncü, M Hackl, A A Zborovskaya, O V Aleinikova, K Henau, L Van Eycken, Z Valerianova, M R Yordanova, M Šekerija, L Dušek, M Zvolský, G Engholm, H Storm, K Innos, M Mägi, N Malila, K Seppä, J Jégu, M Velten, E Cornet, X Troussard, A M Bouvier, A V Guizard, V Bouvier, G Launoy, P Arveux, M Maynadié, M Mounier, A S Worono, M Daoulas, M Robaszkiewicz, J Clavel, S Goujon, B Lacour, I Baldi, C Pouchieu, B Amadeo, G Coureau, A Monnereau, S Orazio, P M Preux, F Rharbaoui, E Marrer, B Trétarre, M Colonna, P Delafosse, K Ligier, S Plouvier, A Cowppli-Bony, F Molinié, S Bara, O Ganry, B Lapôtre- Ledoux, P Grosclaude, N Bossard, Z Uhry, F Bray, M Piñeros, J Estève, R Stabenow, H Wilsdorf-Köhler, A Eberle, S Luttmann, I Löhden, A L Nennecke, J Kieschke, E Sirri, K Emrich, S R Zeissig, B Holleczek, N Eisemann, A Katalinic, R A Asquez, V Kumar, E Petridou, E J Ólafsdóttir, L Tryggvadóttir, K Clough-Gorr, P M Walsh, H Sundseth, G Mazzoleni, F Vittadello, E Coviello, F Cuccaro, R Galasso, G Sampietro, A Giacomin, M Magoni, A Ardizzone, A D'Argenzio, M Castaing, G Grosso, A M Lavecchia, A Sutera Sardo, G Gola, L Gatti, P Ricci, S Ferretti, D Serraino, A Zucchetto, M V Celesia, R A Filiberti, F Pannozzo, A Melcarne, F Quarta, A G Russo, G Carrozzi, C Cirilli, L Cavalieri d'Oro, M Rognoni, M Fusco, M F Vitale, M Usala, R Cusimano, W Mazzucco, M Michiara, P Sgargi, L Boschetti, E Borciani, P Seghini, M M Maule, F Merletti, R Tumino, P Mancuso, M Vicentini, T Cassetti, R Sassatelli, F Falcini, S Giorgetti, A L Caiazzo, R Cavallo, R Cesaraccio, D R Pirino, M L Contrino, F Tisano, A C Fanetti, S Maspero, S Carone, A Mincuzzi, G Candela, T Scuderi, M A Gentilini, S Pier, S Rosso, A Barchielli, A Caldarella, F Bianconi, F Stracci, P Contiero, G Tagliabue, M Rugge, M Zorzi, S Beggiato, A Brustolin, F Berrino, G Gatta, M Sant, C Buzzoni, L Mangone, R Capocaccia, R De Angelis, R Zanetti, A Maurina, S Pildava, N Lipunova, I Vincerževskienė, D Agius, N Calleja, S Siesling, O Visser, Larønningen, B Møller, A Dyzmann-Sroka, M Trojanowski, S Góźdź, R Mężyk, T Mierzwa, L Molong, J Rachtan, S Szewczyk, J Błaszczyk, K Kępska, B Kościańska, K Tarocińska, M Zwierko, K Drosik, K M Maksimowicz, E Purwin-Porowska, E Reca, J Wójcik-Tomaszewska, A Tukiendorf, M Grądalska-Lampart, A U Radziszewska, A Gos, M Talerczyk, M Wyborska, J A Didkowska, U Wojciechowska, M Bielska-Lasota, G Forjaz de Lacerda, R A Rego, J Bastos, M A Silva, L Antunes, J Laranja Pontes, A Mayer-da-Silva, A Miranda, L M Blaga, D Coza, Russia: M Y Valkov, L Gusenkova, O Lazarevich, O Prudnikova, D M Vjushkov, A G Egorova, A E Orlov, L A Kudyakov, L V Pikalova, J Adamcik, C Safaei Diba, M Primic-Žakelj, V Zadnik, N Larrañaga, A Lopez de Munain, A A Herrera, R Redondas, R Marcos-Gragera, M L Vilardell Gil, E Molina, M J Sánchez Perez, P Franch Sureda, M Ramos Montserrat, M D Chirlaque, C Navarro, E E Ardanaz, M M Guevara, R Fernández-Delgado, R Peris-Bonet, M Carulla, J Galceran, C Alberich, M Vicente-Raneda, S Khan, D Pettersson, P Dickman, I Avelina, K Staehelin, B Camey, C Bouchardy, R Schaar, H Frick, C Herrmann, J L Bulliard, M Maspoli-Conconi, C E Kuehni, S M Redmond, A Bordoni, L Ortelli, A Chiolero, I Konzelmann, K L Matthes, S Rohrmann, Broggio, J Rashbass, D Fitzpatrick, A Gavin, D I Clark, A J Deas, D W Huws, C White, C Allemani, A Bonaventure, M P Coleman, V Di Carlo, R Harewood, M Matz, L Montel, M Nikšić, B Rachet, A D Turculeț, R Stephens, C A Stiller, E Chalker, H Phung, R Walton, H You, S Guthridge, F Johnson, J Aitken, P Gordon, K D'Onise, K Priest, B C Stokes, A Venn, H Farrugia, V Thurs eld, J Dowlin, D Currow, J Hendrix, C Lewis

Subjects
0301 basic medicine, Universal Health Coverage, population-based registries, Relative Survival, Settore MED/42 - Igiene Generale E Applicata, Cancer -- Treatment, Humans, Neoplasms, Population Surveillance, Registries, Survival Rate, Medicine (all), 0302 clinical medicine, cancer survival, education.field_of_study, Relative survival, EPICENE, General Medicine, 3. Good health, trend, 030220 oncology & carcinogenesis, Public-Health, cancer surveillance, Liver cancer, survival, cancer registry, CONCORD-3, Cure, Childhood-Cancer, medicine.medical_specialty, population-based cancer registries, Womens Cancers, Population, Medicine (all),cancer survival, population-based cancer registries, Socio-culturale, United-States, Article, 03 medical and health sciences, Breast cancer, Cancer epidemiology, medicine, Nordic-Countries, Cancer -- Mortality, education, Survival rate, Cancer prevention, Alternative Approach, business.industry, Public health, Cancer, Cancer -- Patients -- Long-term care, medicine.disease, 030104 developmental biology, High-Income Countries, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, business, Demography
Abstract

Eser, Sultan (Balikesir Author), Background In 2015, the second cycle of the CONCORD programme established global surveillance of cancer survival as a metric of the effectiveness of health systems and to inform global policy on cancer control. CONCORD-3 updates the worldwide surveillance of cancer survival to 2014. Methods CONCORD-3 includes individual records for 37.5 million patients diagnosed with cancer during the 15-year period 2000-14. Data were provided by 322 population-based cancer registries in 71 countries and territories, 47 of which provided data with 100% population coverage. The study includes 18 cancers or groups of cancers: oesophagus, stomach, colon, rectum, liver, pancreas, lung, breast (women), cervix, ovary, prostate, and melanoma of the skin in adults, and brain tumours, leukaemias, and lymphomas in both adults and children. Standardised quality control procedures were applied; errors were rectified by the registry concerned. We estimated 5-year net survival. Estimates were age-standardised with the International Cancer Survival Standard weights.Findings For most cancers, 5-year net survival remains among the highest in the world in the USA and Canada, in Australia and New Zealand, and in Finland, Iceland, Norway, and Sweden. For many cancers, Denmark is closing the survival gap with the other Nordic countries. Survival trends are generally increasing, even for some of the more lethal cancers: in some countries, survival has increased by up to 5% for cancers of the liver, pancreas, and lung. For women diagnosed during 2010-14, 5-year survival for breast cancer is now 89.5% in Australia and 90.2% in the USA, but international differences remain very wide, with levels as low as 66.1% in India. For gastrointestinal cancers, the highest levels of 5-year survival are seen in southeast Asia: in South Korea for cancers of the stomach (68.9%), colon (71.8%), and rectum (71.1%); in Japan for oesophageal cancer (36.0%); and in Taiwan for liver cancer (27.9%). By contrast, in the same world region, survival is generally lower than elsewhere for melanoma of the skin (59.9% in South Korea, 52.1% in Taiwan, and 49.6% in China), and for both lymphoid malignancies (52.5%, 50.5%, and 38.3%) and myeloid malignancies (45.9%, 33.4%, and 24.8%). For children diagnosed during 2010-14, 5-year survival for acute lymphoblastic leukaemia ranged from 49.8% in Ecuador to 95.2% in Finland. 5-year survival from brain tumours in children is higher than for adults but the global range is very wide (from 28.9% in Brazil to nearly 80% in Sweden and Denmark). Interpretation The CONCORD programme enables timely comparisons of the overall effectiveness of health systems in providing care for 18 cancers that collectively represent 75% of all cancers diagnosed worldwide every year. It contributes to the evidence base for global policy on cancer control. Since 2017, the Organisation for Economic Co-operation and Development has used findings from the CONCORD programme as the official benchmark of cancer survival, among their indicators of the quality of health care in 48 countries worldwide. Governments must recognise population-based cancer registries as key policy tools that can be used to evaluate both the impact of cancer prevention strategies and the effectiveness of health systems for all patients diagnosed with cancer., American Cancer Society Centers for Disease Control and Prevention Swiss Re Swiss Cancer Research foundation Swiss Cancer League Institut National du Cancer La Ligue Contre le Cancer Rossy Family Foundation US National Cancer Institute Susan G Komen Foundation

Published
2018

48. Emergence of broad cytosolic Ca 2+ oscillations in the absence of CRAC channels: A model for CRAC-mediated negative feedback on PLC and Ca 2+ oscillations through PKC.

Author

Lee L, Yoast R, Emrich S, Trebak M, Kirk V, and Sneyd J

Subjects
Humans, Calcium Channels metabolism, Protein Kinase C, Calcium metabolism, Feedback, HEK293 Cells, Calcium Signaling physiology, Protein Isoforms metabolism, Calcium Release Activated Calcium Channels metabolism
Abstract

The role of Ca 2+ release-activated Ca 2+ (CRAC) channels mediated by ORAI isoforms in calcium signalling has been extensively investigated. It has been shown that the presence or absence of different isoforms has a significant effect on store-operated calcium entry (SOCE). Yoast et al. (2020) showed that, in addition to the reported narrow-spike oscillations (whereby cytosolic calcium decreases quickly after a sharp increase), ORAI1 knockout HEK293 cells were able to oscillate with broad-spike oscillations (whereby cytosolic calcium decreases in a prolonged manner after a sharp increase) when stimulated with a muscarinic agonist. This suggests that Ca 2+ influx through ORAI-mediated CRAC channels negatively regulates the duration of Ca 2+ oscillations. We hypothesise that, through the activation of protein kinase C (PKC), ORAI1 negatively regulates phospholipase C (PLC) activity to decrease inositol 1,4,5-trisphosphate (IP 3 ) production and limit the duration of agonist-evoked Ca 2+ oscillations. Based on this hypothesis, we construct a new mathematical model, which shows that the formation of broad-spike oscillations is highly dependent on the absence of ORAI1. Predictions of this model are consistent with the experimental results., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Published
2024
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49. The chromosome-scale genome assembly for the West Nile vector Culex quinquefasciatus uncovers patterns of genome evolution in mosquitoes.

Author

Ryazansky SS, Chen C, Potters M, Naumenko AN, Lukyanchikova V, Masri RA, Brusentsov II, Karagodin DA, Yurchenko AA, Dos Anjos VL, Haba Y, Rose NH, Hoffman J, Guo R, Menna T, Kelley M, Ferrill E, Schultz KE, Qi Y, Sharma A, Deschamps S, Llaca V, Mao C, Murphy TD, Baricheva EM, Emrich S, Fritz ML, Benoit JB, Sharakhov IV, McBride CS, Tu Z, and Sharakhova MV

Subjects
Animals, Humans, Male, Phylogeny, DNA Transposable Elements genetics, Mosquito Vectors genetics, Chromosomes, Evolution, Molecular, Culex genetics, Aedes genetics
Abstract

Background: Understanding genome organization and evolution is important for species involved in transmission of human diseases, such as mosquitoes. Anophelinae and Culicinae subfamilies of mosquitoes show striking differences in genome sizes, sex chromosome arrangements, behavior, and ability to transmit pathogens. However, the genomic basis of these differences is not fully understood., Methods: In this study, we used a combination of advanced genome technologies such as Oxford Nanopore Technology sequencing, Hi-C scaffolding, Bionano, and cytogenetic mapping to develop an improved chromosome-scale genome assembly for the West Nile vector Culex quinquefasciatus., Results: We then used this assembly to annotate odorant receptors, odorant binding proteins, and transposable elements. A genomic region containing male-specific sequences on chromosome 1 and a polymorphic inversion on chromosome 3 were identified in the Cx. quinquefasciatus genome. In addition, the genome of Cx. quinquefasciatus was compared with the genomes of other mosquitoes such as malaria vectors An. coluzzi and An. albimanus, and the vector of arboviruses Ae. aegypti. Our work confirms significant expansion of the two chemosensory gene families in Cx. quinquefasciatus, as well as a significant increase and relocation of the transposable elements in both Cx. quinquefasciatus and Ae. aegypti relative to the Anophelines. Phylogenetic analysis clarifies the divergence time between the mosquito species. Our study provides new insights into chromosomal evolution in mosquitoes and finds that the X chromosome of Anophelinae and the sex-determining chromosome 1 of Culicinae have a significantly higher rate of evolution than autosomes., Conclusion: The improved Cx. quinquefasciatus genome assembly uncovered new details of mosquito genome evolution and has the potential to speed up the development of novel vector control strategies., (© 2024. The Author(s).)

Published
2024
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50. Surgery and stereotactic radiosurgery for spinal leiomyosarcoma: a single-institution retrospective series and systematic review.

Author

Zamarud A, Marianayagam NJ, Sekar V, Testa S, Park DJ, Yener U, McCleary TL, Yoo KH, Emrich S, Tayag A, Ustrzynski L, Pollom E, Soltys S, Wang L, Charville G, Ganjoo K, Chang SD, and Meola A

Subjects
Humans, Middle Aged, Aged, Female, Adult, Retrospective Studies, Male, Aged, 80 and over, Treatment Outcome, Leiomyosarcoma surgery, Leiomyosarcoma pathology, Radiosurgery methods, Spinal Neoplasms surgery, Spinal Neoplasms radiotherapy
Abstract

Objective: Leiomyosarcoma (LMS) is a rare, aggressive soft-tissue sarcoma that seldom spreads to the bone. The spine can be either the site of LMS osseous metastases or the primary tumor site. The optimal treatment option for spinal LMS is still unclear. The authors present a cohort of patients with spinal LMS treated with either upfront surgery or upfront CyberKnife stereotactic radiosurgery (SRS)., Methods: The authors retrospectively studied the clinical and radiological outcomes of 17 patients with spinal LMS treated at their institution between 2004 and 2020. Either surgery or SRS was used as the upfront treatment. The clinical and radiological outcomes were assessed. A systematic review of the literature was also conducted., Results: Of the 17 patients (20 spinal lesions), 12 (70.6%) were female. The median patient age was 61 years (range 41-80 years). Ten patients had upfront surgery for their spinal lesions, and 7 had upfront CyberKnife radiosurgery. The median follow-up was 11 months (range 0.3-130 months). The median overall survival (OS) for the entire cohort was 13 months (range 0.3-97 months). In subgroup analysis, the median OS was lower for the surgical group (13 months, range 0.3-50 months), while the median OS for the SRS group was 15 months (range 5-97 months) (p = 0.5). Forty percent (n = 4) of those treated with surgery presented with local recurrence at a median of 6.7 months (range 0.3-36 months), while only 14% (n = 1) of those treated with CyberKnife radiosurgery had local recurrence after 5 months. Local tumor control (LTC) rates at the 6-, 12-, and 18-month follow-ups were 72%, 58%, and 43%, respectively, for the SRS group and 40%, 30%, and 20%, respectively, for the surgery group (p < 0.05). The literature review included 35 papers with 70 patients harboring spinal LMS; only 2 patients were treated with SRS. The literature review confirms the clinical and radiological outcomes of the surgical group, while data on SRS are anecdotal., Conclusions: The authors present the largest series in the literature of spinal LMS and the first on SRS for spinal LMS. This study shows that LTC is statistically significantly better in patients receiving upfront SRS instead of surgery. The OS does not appear different between the two groups.

Published
2023
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