WorldWideScience

Sample records for jumbled genomes missing

  1. Genomic Variants Revealed by Invariably Missing Genotypes in Nelore Cattle.

    Directory of Open Access Journals (Sweden)

    Joaquim Manoel da Silva

    Full Text Available High density genotyping panels have been used in a wide range of applications. From population genetics to genome-wide association studies, this technology still offers the lowest cost and the most consistent solution for generating SNP data. However, in spite of the application, part of the generated data is always discarded from final datasets based on quality control criteria used to remove unreliable markers. Some discarded data consists of markers that failed to generate genotypes, labeled as missing genotypes. A subset of missing genotypes that occur in the whole population under study may be caused by technical issues but can also be explained by the presence of genomic variations that are in the vicinity of the assayed SNP and that prevent genotyping probes from annealing. The latter case may contain relevant information because these missing genotypes might be used to identify population-specific genomic variants. In order to assess which case is more prevalent, we used Illumina HD Bovine chip genotypes from 1,709 Nelore (Bos indicus samples. We found 3,200 missing genotypes among the whole population. NGS re-sequencing data from 8 sires were used to verify the presence of genomic variations within their flanking regions in 81.56% of these missing genotypes. Furthermore, we discovered 3,300 novel SNPs/Indels, 31% of which are located in genes that may affect traits of importance for the genetic improvement of cattle production.

  2. Unscrambling jumbled sentences: An authentic task for English language assessment?

    Directory of Open Access Journals (Sweden)

    Betty Lanteigne

    2017-06-01

    Full Text Available Jumbled sentence items in language assessment have been criticized by some authors as inauthentic. However, unscrambling jumbled sentences is a common occurrence in real-world communication in English as a lingua franca. Naturalistic inquiry identified 54 instances of jumbled sentence use in daily life in Dubai/Sharjah, where English is widely used as a lingua franca. Thus it is seen that jumbled sentence test items can reflect real-world language use. To evaluate scrambled sentence test items, eight test item types developed from one jumbled sentence instance (“Want taxi Dubai you?” were analyzed in terms of interactivity and authenticity. Items ranged from being completely decontextualized, non-interactive, and inauthentic to being fully contextualized, interactive, and authentic. To determine appropriate assessment standards for English tests in schools in this region, the English language standards for schools and English language requirements for university admission in the UAE were analyzed. Schools in Dubai/Sharjah use Inner Circle English varieties of English (e.g., British or American English as the standard for evaluation, as well as non-native-English-speaker varieties (e.g., Indian English(es. Also, students applying to English-medium universities in the UAE must meet the required scores on standardized English tests including the IELTS and TOEFL. Standards for evaluation of communication in English involving tasks of jumbled sentences in classroom tests must reflect the language learning goals of the school and community. Thus standards for classroom assessment of English in Dubai/Sharjah are determined by local schools’ and universities’ policies.

  3. The missing graphical user interface for genomics.

    Science.gov (United States)

    Schatz, Michael C

    2010-01-01

    The Galaxy package empowers regular users to perform rich DNA sequence analysis through a much-needed and user-friendly graphical web interface. See research article http://genomebiology.com/2010/11/8/R86 RESEARCH HIGHLIGHT: With the advent of affordable and high-throughput DNA sequencing, sequencing is becoming an essential component in nearly every genetics lab. These data are being generated to probe sequence variations, to understand transcribed, regulated or methylated DNA elements, and to explore a host of other biological features across the tree of life and across a range of environments and conditions. Given this deluge of data, novices and experts alike are facing the daunting challenge of trying to analyze the raw sequence data computationally. With so many tools available and so many assays to analyze, how can one be expected to stay current with the state of the art? How can one be expected to learn to use each tool and construct robust end-to-end analysis pipelines, all while ensuring that input formats, command-line options, sequence databases and program libraries are set correctly? Finally, once the analysis is complete, how does one ensure the results are reproducible and transparent for others to scrutinize and study?In an article published in Genome Biology, Jeremy Goecks, Anton Nekrutenko, James Taylor and the rest of the Galaxy Team (Goecks et al. 1) make a great advance towards resolving these critical questions with the latest update to their Galaxy Project. The ambitious goal of Galaxy is to empower regular users to carry out their own computational analysis without having to be an expert in computational biology or computer science. Galaxy adds a desperately needed graphical user interface to genomics research, making data analysis universally accessible in a web browser, and freeing users from the minutiae of archaic command-line parameters, data formats and scripting languages. Data inputs and computational steps are selected from

  4. Interaction Rituals and Jumbled Emotions Among “Relative Strangers”

    Directory of Open Access Journals (Sweden)

    Alison Fixsen

    2015-07-01

    Full Text Available Learning games such as role-play (which we refer to as “simulated interaction rituals” are commonly used as social tools to develop trainee health practitioners. However, the effect of such rituals on individual and group participant emotions has not been carefully studied. Using a heuristic approach, we explore the experiences of complementary therapy practitioner trainees (and their trainers participating in a personal development course. Ten trainees and two tutors were interviewed, observational notes taken, and a secondary qualitative analysis undertaken. Participants and tutors described a medley of disparate emotional and moral responses to group rituals, conceptualized in this article as “jumbled emotions.” Such emotions required disentangling, and both trainees and staff perceived participating in unfamiliar rituals “with relative strangers” as challenging. Front of stage effects are frequently processed “backstage,” as rituals threaten social embarrassment and confusion. Concerns around emotional triggers, authenticity, and outcomes of rituals arise at the time, yet trainees can find ways to work through these issues in time.

  5. From Grapheme to Phonological Output: Performance of Adults Who Stutter on a Word Jumble Task.

    Directory of Open Access Journals (Sweden)

    Megann McGill

    Full Text Available The purpose of the present study was to extend previous research by analyzing the ability of adults who stutter to use phonological working memory in conjunction with lexical access to perform a word jumble task.Forty English words consisting of 3-, 4-, 5-, and 6-letters (n = 10 per letter length category were randomly jumbled using a web-based application. During the experimental task, 26 participants were asked to silently manipulate the scrambled letters to form a real word. Each vocal response was coded for accuracy and speech reaction time (SRT.Adults who stutter attempted to solve fewer word jumble stimuli than adults who do not stutter at the 4-letter, 5-letter, and 6-letter lengths. Additionally, adults who stutter were significantly less accurate solving word jumble tasks at the 4-letter, 5-letter, and 6-letter lengths compared to adults who do not stutter. At the longest word length (6-letter, SRT was significantly slower for the adults who stutter than the fluent controls.Results of the current study lend further support to the notion that differences in various aspects of phonological processing, including vision-to-sound conversions, sub-vocal stimulus manipulation, and/or lexical access are compromised in adults who stutter.

  6. Inference of haplotypic phase and missing genotypes in polyploid organisms and variable copy number genomic regions

    Directory of Open Access Journals (Sweden)

    Balding David J

    2008-12-01

    Full Text Available Abstract Background The power of haplotype-based methods for association studies, identification of regions under selection, and ancestral inference, is well-established for diploid organisms. For polyploids, however, the difficulty of determining phase has limited such approaches. Polyploidy is common in plants and is also observed in animals. Partial polyploidy is sometimes observed in humans (e.g. trisomy 21; Down's syndrome, and it arises more frequently in some human tissues. Local changes in ploidy, known as copy number variations (CNV, arise throughout the genome. Here we present a method, implemented in the software polyHap, for the inference of haplotype phase and missing observations from polyploid genotypes. PolyHap allows each individual to have a different ploidy, but ploidy cannot vary over the genomic region analysed. It employs a hidden Markov model (HMM and a sampling algorithm to infer haplotypes jointly in multiple individuals and to obtain a measure of uncertainty in its inferences. Results In the simulation study, we combine real haplotype data to create artificial diploid, triploid, and tetraploid genotypes, and use these to demonstrate that polyHap performs well, in terms of both switch error rate in recovering phase and imputation error rate for missing genotypes. To our knowledge, there is no comparable software for phasing a large, densely genotyped region of chromosome from triploids and tetraploids, while for diploids we found polyHap to be more accurate than fastPhase. We also compare the results of polyHap to SATlotyper on an experimentally haplotyped tetraploid dataset of 12 SNPs, and show that polyHap is more accurate. Conclusion With the availability of large SNP data in polyploids and CNV regions, we believe that polyHap, our proposed method for inferring haplotypic phase from genotype data, will be useful in enabling researchers analysing such data to exploit the power of haplotype-based analyses.

  7. Radiation-induced genomic instability: Are epigenetic mechanisms the missing link?

    Energy Technology Data Exchange (ETDEWEB)

    Aypar, Umut; Morgan, William F.; Baulch, Janet E.

    2011-02-01

    Purpose: This review examines the evidence for the hypothesis that epigenetics are involved in the initiation and perpetuation of radiation-induced genomic instability (RIGI). Conclusion: In addition to the extensively studied targeted effects of radiation, it is now apparent that non-targeted delayed effects such as RIGI are also important post-irradiation outcomes. In RIGI, unirradiated progeny cells display phenotypic changes at delayed times after radiation of the parental cell. RIGI is thought to be important in the process of carcinogenesis, however, the mechanism by which this occurs remains to be elucidated. In the genomically unstable clones developed by Morgan and colleagues, radiation-induced mutations, double-strand breaks, or changes in mRNA levels alone could not account for the initiation or perpetuation of RIGI. Since changes in the DNA sequence could not fully explain the mechanism of RIGI, inherited epigenetic changes may be involved. Epigenetics are known to play an important role in many cellular processes and epigenetic aberrations can lead to carcinogenesis. Recent studies in the field of radiation biology suggest that the changes in methylation patterns may be involved in RIGI. Together these clues have led us to hypothesize that epigenetics may be the missing link in understanding the mechanism behind RIGI.

  8. Letter position coding across modalities: braille and sighted reading of sentences with jumbled words.

    Science.gov (United States)

    Perea, Manuel; Jiménez, María; Martín-Suesta, Miguel; Gómez, Pablo

    2015-04-01

    This article explores how letter position coding is attained during braille reading and its implications for models of word recognition. When text is presented visually, the reading process easily adjusts to the jumbling of some letters (jugde-judge), with a small cost in reading speed. Two explanations have been proposed: One relies on a general mechanism of perceptual uncertainty at the visual level, and the other focuses on the activation of an abstract level of representation (i.e., bigrams) that is shared by all orthographic codes. Thus, these explanations make differential predictions about reading in a tactile modality. In the present study, congenitally blind readers read sentences presented on a braille display that tracked the finger position. The sentences either were intact or involved letter transpositions. A parallel experiment was conducted in the visual modality. Results revealed a substantially greater reading cost for the sentences with transposed-letter words in braille readers. In contrast with the findings with sighted readers, in which there is a cost of transpositions in the external (initial and final) letters, the reading cost in braille readers occurs serially, with a large cost for initial letter transpositions. Thus, these data suggest that the letter-position-related effects in visual word recognition are due to the characteristics of the visual stream.

  9. Criteria of GenCall score to edit marker data and methods to handle missing markers have an influence on accuracy of genomic predictions

    DEFF Research Database (Denmark)

    Edriss, Vahid; Guldbrandtsen, Bernt; Lund, Mogens Sandø

    2013-01-01

    The aim of this study was to investigate the effect of different strategies for handling low-quality or missing data on prediction accuracy for direct genomic values of protein yield, mastitis and fertility using a Bayesian variable model and a GBLUP model in the Danish Jersey population. The data...... contained 1071 Jersey bulls that were genotyped with the Illumina Bovine 50K chip. After preliminary editing, 39227 SNP remained in the dataset. Four methods to handle missing genotypes were: 1) BEAGLE: missing markers were imputed using Beagle 3.3 software, 2) COMMON: missing genotypes at a locus were...

  10. Finding the missing honey bee genes: Lessons learned from a genome upgrade

    KAUST Repository

    Elsik, Christine G; Worley, Kim C; Bennett, Anna K; Beye, Martin; Camara, Francisco; Childers, Christopher P; de Graaf, Dirk C; Debyser, Griet; Deng, Jixin; Devreese, Bart; Elhaik, Eran; Evans, Jay D; Foster, Leonard J; Graur, Dan; Guigo, Roderic; Hoff, Katharina Jasmin; Holder, Michael E; Hudson, Matthew E; Hunt, Greg J; Jiang, Huaiyang; Joshi, Vandita; Khetani, Radhika S; Kosarev, Peter; Kovar, Christie L; Ma, Jian; Maleszka, Ryszard; Moritz, Robin F A; Munoz-Torres, Monica C; Murphy, Terence D; Muzny, Donna M; Newsham, Irene F; Reese, Justin T; Robertson, Hugh M; Robinson, Gene E; Rueppell, Olav; Solovyev, Victor; Stanke, Mario; Stolle, Eckart; Tsuruda, Jennifer M; Vaerenbergh, Matthias Van; Waterhouse, Robert M; Weaver, Daniel B; Whitfield, Charles W; Wu, Yuanqing; Zdobnov, Evgeny M; Zhang, Lan; Zhu, Dianhui; Gibbs, Richard A; Patil, S.; Gubbala, S.; Aqrawi, P.; Arias, F.; Bess, C.; Blankenburg, K. B.; Brocchini, M.; Buhay, C.; Challis, D.; Chang, K.; Chen, D.; Coleman, P.; Drummond, J.; English, A.; Evani, U.; Francisco, L.; Fu, Q.; Goodspeed, R.; Haessly, T. H.; Hale, W.; Han, H.; Hu, Y.; Jackson, L.; Jakkamsetti, A.; Jayaseelan, J. C.; Kakkar, N.; Kalra, D.; Kandadi, H.; Lee, S.; Li, H.; Liu, Y.; Macmil, S.; Mandapat, C. M.; Mata, R.; Mathew, T.; Matskevitch, T.; Munidasa, M.; Nagaswamy, U.; Najjar, R.; Nguyen, N.; Niu, J.; Opheim, D.; Palculict, T.; Paul, S.; Pellon, M.; Perales, L.; Pham, C.; Pham, P.

    2014-01-01

    Background: The first generation of genome sequence assemblies and annotations have had a significant impact upon our understanding of the biology of the sequenced species, the phylogenetic relationships among species, the study of populations within and across species, and have informed the biology of humans. As only a few Metazoan genomes are approaching finished quality (human, mouse, fly and worm), there is room for improvement of most genome assemblies. The honey bee (Apis mellifera) genome, published in 2006, was noted for its bimodal GC content distribution that affected the quality of the assembly in some regions and for fewer genes in the initial gene set (OGSv1.0) compared to what would be expected based on other sequenced insect genomes. Results: Here, we report an improved honey bee genome assembly (Amel_4.5) with a new gene annotation set (OGSv3.2), and show that the honey bee genome contains a number of genes similar to that of other insect genomes, contrary to what was suggested in OGSv1.0. The new genome assembly is more contiguous and complete and the new gene set includes ~5000 more protein-coding genes, 50% more than previously reported. About 1/6 of the additional genes were due to improvements to the assembly, and the remaining were inferred based on new RNAseq and protein data. Conclusions: Lessons learned from this genome upgrade have important implications for future genome sequencing projects. Furthermore, the improvements significantly enhance genomic resources for the honey bee, a key model for social behavior and essential to global ecology through pollination. 2014 Elsik et al.; licensee BioMed Central Ltd.

  11. Finding the missing honey bee genes: lessons learned from a genome upgrade.

    Science.gov (United States)

    Elsik, Christine G; Worley, Kim C; Bennett, Anna K; Beye, Martin; Camara, Francisco; Childers, Christopher P; de Graaf, Dirk C; Debyser, Griet; Deng, Jixin; Devreese, Bart; Elhaik, Eran; Evans, Jay D; Foster, Leonard J; Graur, Dan; Guigo, Roderic; Hoff, Katharina Jasmin; Holder, Michael E; Hudson, Matthew E; Hunt, Greg J; Jiang, Huaiyang; Joshi, Vandita; Khetani, Radhika S; Kosarev, Peter; Kovar, Christie L; Ma, Jian; Maleszka, Ryszard; Moritz, Robin F A; Munoz-Torres, Monica C; Murphy, Terence D; Muzny, Donna M; Newsham, Irene F; Reese, Justin T; Robertson, Hugh M; Robinson, Gene E; Rueppell, Olav; Solovyev, Victor; Stanke, Mario; Stolle, Eckart; Tsuruda, Jennifer M; Vaerenbergh, Matthias Van; Waterhouse, Robert M; Weaver, Daniel B; Whitfield, Charles W; Wu, Yuanqing; Zdobnov, Evgeny M; Zhang, Lan; Zhu, Dianhui; Gibbs, Richard A

    2014-01-30

    The first generation of genome sequence assemblies and annotations have had a significant impact upon our understanding of the biology of the sequenced species, the phylogenetic relationships among species, the study of populations within and across species, and have informed the biology of humans. As only a few Metazoan genomes are approaching finished quality (human, mouse, fly and worm), there is room for improvement of most genome assemblies. The honey bee (Apis mellifera) genome, published in 2006, was noted for its bimodal GC content distribution that affected the quality of the assembly in some regions and for fewer genes in the initial gene set (OGSv1.0) compared to what would be expected based on other sequenced insect genomes. Here, we report an improved honey bee genome assembly (Amel_4.5) with a new gene annotation set (OGSv3.2), and show that the honey bee genome contains a number of genes similar to that of other insect genomes, contrary to what was suggested in OGSv1.0. The new genome assembly is more contiguous and complete and the new gene set includes ~5000 more protein-coding genes, 50% more than previously reported. About 1/6 of the additional genes were due to improvements to the assembly, and the remaining were inferred based on new RNAseq and protein data. Lessons learned from this genome upgrade have important implications for future genome sequencing projects. Furthermore, the improvements significantly enhance genomic resources for the honey bee, a key model for social behavior and essential to global ecology through pollination.

  12. Finding the missing honey bee genes: Lessons learned from a genome upgrade

    KAUST Repository

    Elsik, Christine G

    2014-01-30

    Background: The first generation of genome sequence assemblies and annotations have had a significant impact upon our understanding of the biology of the sequenced species, the phylogenetic relationships among species, the study of populations within and across species, and have informed the biology of humans. As only a few Metazoan genomes are approaching finished quality (human, mouse, fly and worm), there is room for improvement of most genome assemblies. The honey bee (Apis mellifera) genome, published in 2006, was noted for its bimodal GC content distribution that affected the quality of the assembly in some regions and for fewer genes in the initial gene set (OGSv1.0) compared to what would be expected based on other sequenced insect genomes. Results: Here, we report an improved honey bee genome assembly (Amel_4.5) with a new gene annotation set (OGSv3.2), and show that the honey bee genome contains a number of genes similar to that of other insect genomes, contrary to what was suggested in OGSv1.0. The new genome assembly is more contiguous and complete and the new gene set includes ~5000 more protein-coding genes, 50% more than previously reported. About 1/6 of the additional genes were due to improvements to the assembly, and the remaining were inferred based on new RNAseq and protein data. Conclusions: Lessons learned from this genome upgrade have important implications for future genome sequencing projects. Furthermore, the improvements significantly enhance genomic resources for the honey bee, a key model for social behavior and essential to global ecology through pollination. 2014 Elsik et al.; licensee BioMed Central Ltd.

  13. Institutional Responsibility and the Flawed Genomic Biomarkers at Duke University: A Missed Opportunity for Transparency and Accountability.

    Science.gov (United States)

    DeMets, David L; Fleming, Thomas R; Geller, Gail; Ransohoff, David F

    2017-08-01

    When there have been substantial failures by institutional leadership in their oversight responsibility to protect research integrity, the public should demand that these be recognized and addressed by the institution itself, or the funding bodies. This commentary discusses a case of research failures in developing genomic predictors for cancer risk assessment and treatment at a leading university. In its review of this case, the Office of Research Integrity, an agency within the US Department of Health and Human Services, focused their report entirely on one individual faculty member and made no comment on the institution's responsibility and its failure to provide adequate oversight and investigation. These actions missed an important opportunity to emphasize the institution's critical responsibilities in oversight of research integrity and the importance of institutional transparency and accountability.

  14. The missing indels: an estimate of indel variation in a human genome and analysis of factors that impede detection

    Science.gov (United States)

    Jiang, Yue; Turinsky, Andrei L.; Brudno, Michael

    2015-01-01

    With the development of High-Throughput Sequencing (HTS) thousands of human genomes have now been sequenced. Whenever different studies analyze the same genome they usually agree on the amount of single-nucleotide polymorphisms, but differ dramatically on the number of insertion and deletion variants (indels). Furthermore, there is evidence that indels are often severely under-reported. In this manuscript we derive the total number of indel variants in a human genome by combining data from different sequencing technologies, while assessing the indel detection accuracy. Our estimate of approximately 1 million indels in a Yoruban genome is much higher than the results reported in several recent HTS studies. We identify two key sources of difficulties in indel detection: the insufficient coverage, read length or alignment quality; and the presence of repeats, including short interspersed elements and homopolymers/dimers. We quantify the effect of these factors on indel detection. The quality of sequencing data plays a major role in improving indel detection by HTS methods. However, many indels exist in long homopolymers and repeats, where their detection is severely impeded. The true number of indel events is likely even higher than our current estimates, and new techniques and technologies will be required to detect them. PMID:26130710

  15. 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...

  16. Miss Lora juveelikauplus = Miss Lora jewellery store

    Index Scriptorium Estoniae

    2009-01-01

    Narvas Fama kaubanduskeskuses (Tallinna mnt. 19c) asuva juveelikaupluse Miss Lora sisekujundusest. Sisearhitektid Annes Arro ja Hanna Karits. Poe sisu - vitriinkapid, vaip, valgustid - on valmistatud eritellimusel. Sisearhitektide tähtsamate tööde loetelu

  17. Principled Missing Data Treatments.

    Science.gov (United States)

    Lang, Kyle M; Little, Todd D

    2018-04-01

    We review a number of issues regarding missing data treatments for intervention and prevention researchers. Many of the common missing data practices in prevention research are still, unfortunately, ill-advised (e.g., use of listwise and pairwise deletion, insufficient use of auxiliary variables). Our goal is to promote better practice in the handling of missing data. We review the current state of missing data methodology and recent missing data reporting in prevention research. We describe antiquated, ad hoc missing data treatments and discuss their limitations. We discuss two modern, principled missing data treatments: multiple imputation and full information maximum likelihood, and we offer practical tips on how to best employ these methods in prevention research. The principled missing data treatments that we discuss are couched in terms of how they improve causal and statistical inference in the prevention sciences. Our recommendations are firmly grounded in missing data theory and well-validated statistical principles for handling the missing data issues that are ubiquitous in biosocial and prevention research. We augment our broad survey of missing data analysis with references to more exhaustive resources.

  18. Netbooks The Missing Manual

    CERN Document Server

    Biersdorfer, J

    2009-01-01

    Netbooks are the hot new thing in PCs -- small, inexpensive laptops designed for web browsing, email, and working with web-based programs. But chances are you don't know how to choose a netbook, let alone use one. Not to worry: with this Missing Manual, you'll learn which netbook is right for you and how to set it up and use it for everything from spreadsheets for work to hobbies like gaming and photo sharing. Netbooks: The Missing Manual provides easy-to-follow instructions and lots of advice to help you: Learn the basics for using a Windows- or Linux-based netbookConnect speakers, printe

  19. PCs The Missing Manual

    CERN Document Server

    Karp, David

    2005-01-01

    Your vacuum comes with one. Even your blender comes with one. But your PC--something that costs a whole lot more and is likely to be used daily and for tasks of far greater importance and complexity--doesn't come with a printed manual. Thankfully, that's not a problem any longer: PCs: The Missing Manual explains everything you need to know about PCs, both inside and out, and how to keep them running smoothly and working the way you want them to work. A complete PC manual for both beginners and power users, PCs: The Missing Manual has something for everyone. PC novices will appreciate the una

  20. Mani, Miss Anna Modayil

    Indian Academy of Sciences (India)

    Home; Fellowship. Fellow Profile. Elected: 1960 Section: Earth & Planetary Sciences. Mani, Miss Anna Modayil A.I.I.Sc., FNA 1971-79; Secretary 1977-79. Date of birth: 23 August 1918. Date of death: 16 August 2001. Specialization: Atmospheric Physics and Instrumentation Last known address: c/o Mr K.T. Chandy, 14, ...

  1. Some 'Near Miss ' Experiences

    African Journals Online (AJOL)

    perienced health Workers, especially at lower level units, poor referral ... in the wards or operating theatre, and inability to access the busy health .... clinics, costs incurred and by who, who decided on hospitalisation, who .... pected pregnancy as I had missed my period the previous month. .... the patient received attention.

  2. The Missing Entrepreneurs 2014

    DEFF Research Database (Denmark)

    Halabisky, David; Potter, Jonathan; Thompson, Stuart

    OECD's LEED Programme and the European Commission's DG on Employment, Social Affairs and Inclusion recently published the second book as part of their programme of work on inclusive entrepreneurship. The Missing Entrepreneurs 2014 examines how public policies at national and local levels can...

  3. Missing School Matters

    Science.gov (United States)

    Balfanz, Robert

    2016-01-01

    Results of a survey conducted by the Office for Civil Rights show that 6 million public school students (13%) are not attending school regularly. Chronic absenteeism--defined as missing more than 10% of school for any reason--has been negatively linked to many key academic outcomes. Evidence shows that students who exit chronic absentee status can…

  4. Missed opportunities in crystallography.

    Science.gov (United States)

    Dauter, Zbigniew; Jaskolski, Mariusz

    2014-09-01

    Scrutinized from the perspective of time, the giants in the history of crystallography more than once missed a nearly obvious chance to make another great discovery, or went in the wrong direction. This review analyzes such missed opportunities focusing on macromolecular crystallographers (using Perutz, Pauling, Franklin as examples), although cases of particular historical (Kepler), methodological (Laue, Patterson) or structural (Pauling, Ramachandran) relevance are also described. Linus Pauling, in particular, is presented several times in different circumstances, as a man of vision, oversight, or even blindness. His example underscores the simple truth that also in science incessant creativity is inevitably connected with some probability of fault. Published 2014. This article is a U.S. Government work and is in the public domain in the USA.

  5. Miss World going deshi

    DEFF Research Database (Denmark)

    Wildermuth, Norbert

      In November 1996 the South Indian metropolis Bangalore hosted the annual Miss World show. The live event and its televisualisation became a prominent symbol for the India's economic liberalisation and for the immanent globalizing dimensions of this development. As such, the highly prestigious......, the pageant's contestation, which gave rise to a series of vehement protests and a broad public debate about the country's cultural alienation, marked a crucial point in time and trend towards the (re)localisation of the Indian television landscape. In consequence, the 1996 Miss World show and its...... their vision and politics of gender, nation and modernity on the larger Indian public, over the last two decades. Engaging the Indian population increasingly by way of the new electronic, c&s distributed media, competing discourses of gender and sexuality were projected, basically as a necessary, effective...

  6. The missed diagnosis

    International Nuclear Information System (INIS)

    Bundy, A.L.

    1988-01-01

    One of the questions that haunts the radiologist as he shuffles through piles of films is ''What am I missing?'' This same question takes on even more meaning when the radiologist is pressed for time, when he reluctantly checks the night work of the resident, when the patient left before more or better films could be obtained; or when the radiologist is involved in a subspecialty in which he is not properly trained. According to Dr. Berlin's survey, the missed diagnosis category accounted for the largest number of radiology malpractice cases. We all know that many diagnoses are more easily made using the ''retrospectoscope.'' But is the plaintiff attorney also adept at using this instrument? Just how knowledgeable must the radiologist be in the use of the ''prospectoscope''? A familiarity with cases that have already been tried should at least alert radiologists to the chances of their own involvement in litigation. While the missed diagnosis is by no means peculiar to the radiologist, it is one of the principal reasons that he may find himself in court

  7. Semiparametric Theory and Missing Data

    CERN Document Server

    Tsiatis, Anastasios A

    2006-01-01

    Missing data arise in almost all scientific disciplines. In many cases, missing data in an analysis is treated in a casual and ad-hoc manner, leading to invalid inferences and erroneous conclusions. This book summarizes knowledge regarding the theory of estimation for semiparametric models with missing data.

  8. Facebook The Missing Manual

    CERN Document Server

    Veer, E

    2011-01-01

    Facebook's spreading about as far and fast as the Web itself: 500 million members and counting. But there's a world of fun packed into the site that most folks miss. With this bestselling guide, learn how to unlock Facebook's talents as personal website creator, souped-up address book, and bustling community forum. It's an eye-opening, timesaving tour, guaranteed to help you get the most out of your Facebook experience. Coverage includes: Get started, get connected. Signing up is easy, but the real payoff comes when you tap into networks of coworkers, classmates, and friends. Pick and choose

  9. New or ν missing energy

    DEFF Research Database (Denmark)

    Franzosi, Diogo Buarque; Frandsen, Mads T.; Shoemaker, Ian M.

    2016-01-01

    flavor structures. Monojet data alone can be used to infer the mass of the "missing particle" from the shape of the missing energy distribution. In particular, 13 TeV LHC data will have sensitivity to DM masses greater than $\\sim$ 1 TeV. In addition to the monojet channel, NSI can be probed in multi......Missing energy signals such as monojets are a possible signature of Dark Matter (DM) at colliders. However, neutrino interactions beyond the Standard Model may also produce missing energy signals. In order to conclude that new "missing particles" are observed the hypothesis of BSM neutrino......-lepton searches which we find to yield stronger limits at heavy mediator masses. The sensitivity offered by these multi-lepton channels provide a method to reject or confirm the DM hypothesis in missing energy searches....

  10. Wikipedia the missing manual

    CERN Document Server

    Broughton, John

    2008-01-01

    Want to be part of the largest group-writing project in human history? Learn how to contribute to Wikipedia, the user-generated online reference for the 21st century. Considered more popular than eBay, Microsoft.com, and Amazon.com, Wikipedia servers respond to approximately 30,000 requests per second, or about 2.5 billion per day. It's become the first point of reference for people the world over who need a fact fast.If you want to jump on board and add to the content, Wikipedia: The Missing Manual is your first-class ticket. Wikipedia has more than 9 million entries in 250 languages, over 2

  11. Flexible Imputation of Missing Data

    CERN Document Server

    van Buuren, Stef

    2012-01-01

    Missing data form a problem in every scientific discipline, yet the techniques required to handle them are complicated and often lacking. One of the great ideas in statistical science--multiple imputation--fills gaps in the data with plausible values, the uncertainty of which is coded in the data itself. It also solves other problems, many of which are missing data problems in disguise. Flexible Imputation of Missing Data is supported by many examples using real data taken from the author's vast experience of collaborative research, and presents a practical guide for handling missing data unde

  12. Missing money and missing markets: Reliability, capacity auctions and interconnectors

    International Nuclear Information System (INIS)

    Newbery, David

    2016-01-01

    In the energy trilemma of reliability, sustainability and affordability, politicians treat reliability as over-riding. The EU assumes the energy-only Target Electricity Model will deliver reliability but the UK argues that a capacity remuneration mechanism is needed. This paper argues that capacity auctions tend to over-procure capacity, exacerbating the missing money problem they were designed to address. The bias is further exacerbated by failing to address some of the missing market problems also neglected in the debate. It examines the case for, criticisms of, and outcome of the first GB capacity auction and problems of trading between different capacity markets. - Highlights: •Energy-only markets can work if they avoid missing money and missing market problems. •Policy makers over-estimate the cost of so-called “loss of load events”. •Policy makers tend to over-procure capacity, exacerbating the missing money problem. •Rectifying missing market problems simplifies trade between different capacity markets. •Addressing missing market problems makes under-procurement cheaper than over-procurement.

  13. Conversations with Miss Jane

    Directory of Open Access Journals (Sweden)

    Geneviève Fabre

    2006-05-01

    Full Text Available Considering the wide range of conversations in the autobiography, this essay will attempt to appraise the importance of these verbal exchanges in relation to the overall narrative structure of the book and to the prevalent oral tradition in Louisiana culture, as both an individual and communal expression. The variety of circumstances, the setting and staging, the interlocutors , and the complex intersection of time and place, of stories and History, will be examined; in these conversations with Miss Jane many actors participate, from  the interviewer-narrator, to most characters; even the reader becomes involved.Speaking, hearing, listening, keeping silent is an elaborate ritual that performs many functions; besides conveying news or rumors, it imparts information on the times and on the life of a “representative” woman whose existence - spanning a whole century- is both singular and emblematic. Most importantly this essay will analyse the resonance of an eventful and often dramatic era on her sensibility and conversely show how her evolving sensibility informs that history and draws attention to aspects that might have passed unnoticed or be forever silenced. Jane’s desire for liberty and justice is often challenged as she faces the possibilities of life or death.Conversations build up a complex, often contradictory, but compelling portrait: torn between silence and vehemence, between memories and the urge to meet the future, Jane summons body and mind to find her way through the maze of a fast changing world; self-willed and obstinate she claims her right to speak, to express with wit and wisdom her firm belief in the word, in the ability to express deep seated convictions and faith and a whole array of feelings and emotions.

  14. Missed hormonal contraceptives: new recommendations.

    Science.gov (United States)

    Guilbert, Edith; Black, Amanda; Dunn, Sheila; Senikas, Vyta

    2008-11-01

    To provide evidence-based guidance for women and their health care providers on the management of missed or delayed hormonal contraceptive doses in order to prevent unintended pregnancy. Medline, PubMed, and the Cochrane Database were searched for articles published in English, from 1974 to 2007, about hormonal contraceptive methods that are available in Canada and that may be missed or delayed. Relevant publications and position papers from appropriate reproductive health and family planning organizations were also reviewed. The quality of evidence is rated using the criteria developed by the Canadian Task Force on Preventive Health Care. This committee opinion will help health care providers offer clear information to women who have not been adherent in using hormonal contraception with the purpose of preventing unintended pregnancy. The Society of Obstetricians and Gynaecologists of Canada. SUMMARY STATEMENTS: 1. Instructions for what women should do when they miss hormonal contraception have been complex and women do not understand them correctly. (I) 2. The highest risk of ovulation occurs when the hormone-free interval is prolonged for more than seven days, either by delaying the start of combined hormonal contraceptives or by missing active hormone doses during the first or third weeks of combined oral contraceptives. (II) Ovulation rarely occurs after seven consecutive days of combined oral contraceptive use. (II) RECOMMENDATIONS: 1. Health care providers should give clear, simple instructions, both written and oral, on missed hormonal contraceptive pills as part of contraceptive counselling. (III-A) 2. Health care providers should provide women with telephone/electronic resources for reference in the event of missed or delayed hormonal contraceptives. (III-A) 3. In order to avoid an increased risk of unintended pregnancy, the hormone-free interval should not exceed seven days in combined hormonal contraceptive users. (II-A) 4. Back-up contraception should

  15. Droid X The Missing Manual

    CERN Document Server

    Gralla, Preston

    2011-01-01

    Get the most from your Droid X right away with this entertaining Missing Manual. Veteran tech author Preston Gralla offers a guided tour of every feature, with lots of expert tips and tricks along the way. You'll learn how to use calling and texting features, take and share photos, enjoy streaming music and video, and much more. Packed with full-color illustrations, this engaging book covers everything from getting started to advanced features and troubleshooting. Unleash the power of Motorola's hot new device with Droid X: The Missing Manual. Get organized. Import your contacts and sync wit

  16. Motorola Xoom The Missing Manual

    CERN Document Server

    Gralla, Preston

    2011-01-01

    Motorola Xoom is the first tablet to rival the iPad, and no wonder with all of the great features packed into this device. But learning how to use everything can be tricky-and Xoom doesn't come with a printed guide. That's where this Missing Manual comes in. Gadget expert Preston Gralla helps you master your Xoom with step-by-step instructions and clear explanations. As with all Missing Manuals, this book offers refreshing, jargon-free prose and informative illustrations. Use your Xoom as an e-book reader, music player, camcorder, and phoneKeep in touch with email, video and text chat, and so

  17. Missed, Not Missing: Phylogenomic Evidence for the Existence of Avian FoxP3.

    Directory of Open Access Journals (Sweden)

    Michael P Denyer

    Full Text Available The Forkhead box transcription factor FoxP3 is pivotal to the development and function of regulatory T cells (Tregs, which make a major contribution to peripheral tolerance. FoxP3 is believed to perform a regulatory role in all the vertebrate species in which it has been detected. The prevailing view is that FoxP3 is absent in birds and that avian Tregs rely on alternative developmental and suppressive pathways. Prompted by the automated annotation of foxp3 in the ground tit (Parus humilis genome, we have questioned this assumption. Our analysis of all available avian genomes has revealed that the foxp3 locus is missing, incomplete or of poor quality in the relevant genomic assemblies for nearly all avian species. Nevertheless, in two species, the peregrine falcon (Falco peregrinus and the saker falcon (F. cherrug, there is compelling evidence for the existence of exons showing synteny with foxp3 in the ground tit. A broader phylogenomic analysis has shown that FoxP3 sequences from these three species are similar to crocodilian sequences, the closest living relatives of birds. In both birds and crocodilians, we have also identified a highly proline-enriched region at the N terminus of FoxP3, a region previously identified only in mammals.

  18. Genome instability in Lactobacillus rhamnosus GG

    NARCIS (Netherlands)

    Sybesma, W.; Molenaar, D.; IJcken, W. van; Venema, K.; Korta, R.

    2013-01-01

    We describe here a comparative genome analysis of three dairy product isolates of Lactobacillus rhamnosus GG (LGG) and the ATCC 53103 reference strain to the published genome sequence of L. rhamnosus GG. The analysis showed that in two of three isolates, major DNA segments were missing from the

  19. Did you miss the eclipse?

    CERN Multimedia

    CERN Bulletin

    2015-01-01

    Not wanting to miss a moment of the beautiful celestial dance that played out on Friday, 20 March, Jens Roder of CERN’s PH group took to the Jura mountains, where he got several shots of the event. Here are a selection of his photos, which he was kind enough to share with the Bulletin and its readers.  

  20. Missing Boxes in Central Europe

    DEFF Research Database (Denmark)

    Prockl, Günter; Weibrecht Kristensen, Kirsten

    2015-01-01

    The Chinese New Year is an event that obviously happens every year. Every year however it also causes severe problems for the companies involved in the industry in form of missing containers throughout the chain but in particular in the European Hinterland. Illustrated on the symptoms of the Chin...

  1. The Human Microbiome and the Missing Heritability Problem

    Directory of Open Access Journals (Sweden)

    Santiago Sandoval-Motta

    2017-06-01

    Full Text Available The “missing heritability” problem states that genetic variants in Genome-Wide Association Studies (GWAS cannot completely explain the heritability of complex traits. Traditionally, the heritability of a phenotype is measured through familial studies using twins, siblings and other close relatives, making assumptions on the genetic similarities between them. When this heritability is compared to the one obtained through GWAS for the same traits, a substantial gap between both measurements arise with genome wide studies reporting significantly smaller values. Several mechanisms for this “missing heritability” have been proposed, such as epigenetics, epistasis, and sequencing depth. However, none of them are able to fully account for this gap in heritability. In this paper we provide evidence that suggests that in order for the phenotypic heritability of human traits to be broadly understood and accounted for, the compositional and functional diversity of the human microbiome must be taken into account. This hypothesis is based on several observations: (A The composition of the human microbiome is associated with many important traits, including obesity, cancer, and neurological disorders. (B Our microbiome encodes a second genome with nearly a 100 times more genes than the human genome, and this second genome may act as a rich source of genetic variation and phenotypic plasticity. (C Human genotypes interact with the composition and structure of our microbiome, but cannot by themselves explain microbial variation. (D Microbial genetic composition can be strongly influenced by the host's behavior, its environment or by vertical and horizontal transmissions from other hosts. Therefore, genetic similarities assumed in familial studies may cause overestimations of heritability values. We also propose a method that allows the compositional and functional diversity of our microbiome to be incorporated to genome wide association studies.

  2. Miss Julie: A Psychoanalytic Study

    Directory of Open Access Journals (Sweden)

    Sonali Jain

    2015-10-01

    Full Text Available Sigmund Freud theorized that ‘the hero of the tragedy must suffer…to bear the burden of tragic guilt…(that lay in rebellion against some divine or human authority.’ August Strindberg, the Swedish poet, playwright, author and visual artist, like Shakespeare before him, portrayed insanity as the ultimate of tragic conflict. In this paper I seek to explore and reiterate the dynamics of human relationships that are as relevant today as they were in Strindberg’s time. I propose to examine Strindberg’s Miss Julie, a play set in nineteenth century Sweden, through a psychoanalytic lens. The play deals with bold themes of class and sexual identity politics. Notwithstanding the progress made in breaking down gender barriers, the inequalities inherent in a patriarchal system persist in modern society. Miss Julie highlights these imbalances. My analysis of the play deals with issues of culture and psyche, and draws on Freud, Melanie Klein, Lacan, Luce Irigaray and other contemporary feminists. Miss Julie is a discourse on hysteria, which is still pivotal to psychoanalysis. Prominent philosophers like Hegel and the psychoanalyst Jacques Lacan have written about the dialectic of the master and the slave – a relationship that is characterized by dependence, demand and cruelty. The history of human civilization shows beyond any doubt that there is an intimate connection between cruelty and the sexual instinct. An analysis of the text is carried out using the sado-masochistic dynamic as well the slave-master discourse. I argue that Miss Julie subverts the slave-master relationship. The struggle for dominance and power is closely linked with the theme of sexuality in the unconscious. To quote the English actor and director Alan Rickman, ‘Watching or working on the plays of Strindberg is like seeing the skin, flesh and bones of life separated from each other. Challenging and timeless.’

  3. Methods for Mediation Analysis with Missing Data

    Science.gov (United States)

    Zhang, Zhiyong; Wang, Lijuan

    2013-01-01

    Despite wide applications of both mediation models and missing data techniques, formal discussion of mediation analysis with missing data is still rare. We introduce and compare four approaches to dealing with missing data in mediation analysis including list wise deletion, pairwise deletion, multiple imputation (MI), and a two-stage maximum…

  4. The 50 million missing women.

    Science.gov (United States)

    Allahbadia, Gautam N

    2002-09-01

    The epidemic of gender selection is ravaging countries like India & China. Approximately fifty million women are "missing" in the Indian population. Generally three principle causes are given: female infanticide, better food and health care for boys and maternal death at childbirth. Prenatal sex determination and the abortion of female fetuses threatens to skew the sex ratio to new highs. Estimates of the number of female fetuses being destroyed every year in India vary from two million to five million. This review from India attempts to summarize all the currently available methods of sex selection and also highlights the current medical practice regards the subject in south-east Asia.

  5. Measurement of Missing Tranverse Energy

    CERN Document Server

    The ATLAS Collaboration

    2009-01-01

    This note discusses the overall ATLAS detector performance for the reconstruction of the missing transverse energy, ETmiss. Two reconstruction algorithms are discussed and their performance is evaluated for a variety of simulated physics processes which probe different topologies and different total transverse energy regimes. In addition, effects of fake ETmiss, resulting from instrumental effects and from false reconstructions are investigated. Finally, studies with first data, corresponding to an integrated luminosity of 100 pb-1, are suggested which can be used to assess and calibrate the ETmiss performance at the startup of data taking.

  6. Bayes reconstruction of missing teeth

    DEFF Research Database (Denmark)

    Sporring, Jon; Jensen, Katrine Hommelhoff

    2008-01-01

    contains two major parts: A statistical model of a selection of tooth shapes and a reconstruction of missing data. We use a training set consisting of 3D scans of dental cast models obtained with a laser scanner, and we have build a model of the shape variability of the teeth, their neighbors...... or equivalently noise elimination and for data analysis. However for small sets of high dimensional data, the log-likelihood estimator for the covariance matrix is often far from convergence, and therefore reliable models must be obtained by use of prior information. We propose a natural and intrinsic...

  7. Windows 7 The Missing Manual

    CERN Document Server

    Pogue, David

    2010-01-01

    In early reviews, geeks raved about Windows 7. But if you're an ordinary mortal, learning what this new system is all about will be challenging. Fear not: David Pogue's Windows 7: The Missing Manual comes to the rescue. Like its predecessors, this book illuminates its subject with reader-friendly insight, plenty of wit, and hardnosed objectivity for beginners as well as veteran PC users. Windows 7 fixes many of Vista's most painful shortcomings. It's speedier, has fewer intrusive and nagging screens, and is more compatible with peripherals. Plus, Windows 7 introduces a slew of new features,

  8. Are there missing convective currents?

    International Nuclear Information System (INIS)

    Chen, C.Y.

    1992-01-01

    It is revealed in this letter that as far as distribution functions obtained from gyrokinetic equations are concerned, the standard formulae to evaluate currents in plasmas are not applicable due to the fact that those distribution functions are given in a moving coordinate frame and the moving is essentially related to perturbed fields. With heuristic and analytic approaches, appropriate formulae are obtained to evaluate several types of currents in plasmas of which some have been missing in previous approaches. (author). 6 refs, 1 fig

  9. What We’re Missing

    OpenAIRE

    Camille R. Whitney; Jing Liu

    2017-01-01

    For schools and teachers to help students develop knowledge and skills, students need to show up to class. Yet absenteeism is prevalent, especially in secondary schools. This study uses a rich data set tracking class attendance by day for over 50,000 middle and high school students from an urban district in academic years 2007–2008 through 2012–2013. Our results extend and modify the extant findings on absenteeism that have been based almost exclusively on full-day absenteeism, missing class-...

  10. Missing mass of the Universe

    International Nuclear Information System (INIS)

    Mazure, A.

    1989-01-01

    The first evidence for missing mass or dark matter comes from the 30's. On one hand, Oort noted that in the solar neighbourhood the mass of the stars (inferred from count numbers) cannot account for their observed velocities. On the other hand, observation on the sky of various galaxy condensations like the Coma cluster let suppose that they are actual bound systems and not only statistical fluctuations. However, with such an assumption, Zwicky concluded that the velocity dispersion of galaxies in Coma required 100 times more mass than contained in galaxies. Since this period, refined observations, analyses and a reevaluation of the cosmic distance scale reduced this factor but the problem is still present. It is particularly striking for spiral galaxies where systematic observations of rotation curves lead to infer the presence of spherical massive halos. These dynamical evidences form the first missing mass problem. The second one appears with the development of Great Unified Theories for which the natural laboratory is the very early Universe. A consequence of these theories is that our Universe could be closed by exotic particles which interact only gravitationally [fr

  11. Time Series Forecasting with Missing Values

    OpenAIRE

    Shin-Fu Wu; Chia-Yung Chang; Shie-Jue Lee

    2015-01-01

    Time series prediction has become more popular in various kinds of applications such as weather prediction, control engineering, financial analysis, industrial monitoring, etc. To deal with real-world problems, we are often faced with missing values in the data due to sensor malfunctions or human errors. Traditionally, the missing values are simply omitted or replaced by means of imputation methods. However, omitting those missing values may cause temporal discontinuity. Imputation methods, o...

  12. HTML5 The Missing Manual

    CERN Document Server

    MacDonald, Matthew

    2011-01-01

    HTML5 is more than a markup language-it's a dozen independent web standards all rolled into one. Until now, all it's been missing is a manual. With this thorough, jargon-free guide, you'll learn how to build web apps that include video tools, dynamic drawings, geolocation, offline web apps, drag-and-drop, and many other features. HTML5 is the future of the Web, and with this book you'll reach it quickly. The important stuff you need to know: Structure web pages in a new way. Learn how HTML5 helps make web design tools and search engines work smarter.Add audio and video without plugins. Build

  13. Integrative missing value estimation for microarray data.

    Science.gov (United States)

    Hu, Jianjun; Li, Haifeng; Waterman, Michael S; Zhou, Xianghong Jasmine

    2006-10-12

    Missing value estimation is an important preprocessing step in microarray analysis. Although several methods have been developed to solve this problem, their performance is unsatisfactory for datasets with high rates of missing data, high measurement noise, or limited numbers of samples. In fact, more than 80% of the time-series datasets in Stanford Microarray Database contain less than eight samples. We present the integrative Missing Value Estimation method (iMISS) by incorporating information from multiple reference microarray datasets to improve missing value estimation. For each gene with missing data, we derive a consistent neighbor-gene list by taking reference data sets into consideration. To determine whether the given reference data sets are sufficiently informative for integration, we use a submatrix imputation approach. Our experiments showed that iMISS can significantly and consistently improve the accuracy of the state-of-the-art Local Least Square (LLS) imputation algorithm by up to 15% improvement in our benchmark tests. We demonstrated that the order-statistics-based integrative imputation algorithms can achieve significant improvements over the state-of-the-art missing value estimation approaches such as LLS and is especially good for imputing microarray datasets with a limited number of samples, high rates of missing data, or very noisy measurements. With the rapid accumulation of microarray datasets, the performance of our approach can be further improved by incorporating larger and more appropriate reference datasets.

  14. Integrative missing value estimation for microarray data

    Directory of Open Access Journals (Sweden)

    Zhou Xianghong

    2006-10-01

    Full Text Available Abstract Background Missing value estimation is an important preprocessing step in microarray analysis. Although several methods have been developed to solve this problem, their performance is unsatisfactory for datasets with high rates of missing data, high measurement noise, or limited numbers of samples. In fact, more than 80% of the time-series datasets in Stanford Microarray Database contain less than eight samples. Results We present the integrative Missing Value Estimation method (iMISS by incorporating information from multiple reference microarray datasets to improve missing value estimation. For each gene with missing data, we derive a consistent neighbor-gene list by taking reference data sets into consideration. To determine whether the given reference data sets are sufficiently informative for integration, we use a submatrix imputation approach. Our experiments showed that iMISS can significantly and consistently improve the accuracy of the state-of-the-art Local Least Square (LLS imputation algorithm by up to 15% improvement in our benchmark tests. Conclusion We demonstrated that the order-statistics-based integrative imputation algorithms can achieve significant improvements over the state-of-the-art missing value estimation approaches such as LLS and is especially good for imputing microarray datasets with a limited number of samples, high rates of missing data, or very noisy measurements. With the rapid accumulation of microarray datasets, the performance of our approach can be further improved by incorporating larger and more appropriate reference datasets.

  15. A Review of Methods for Missing Data.

    Science.gov (United States)

    Pigott, Therese D.

    2001-01-01

    Reviews methods for handling missing data in a research study. Model-based methods, such as maximum likelihood using the EM algorithm and multiple imputation, hold more promise than ad hoc methods. Although model-based methods require more specialized computer programs and assumptions about the nature of missing data, these methods are appropriate…

  16. Methods for Handling Missing Secondary Respondent Data

    Science.gov (United States)

    Young, Rebekah; Johnson, David

    2013-01-01

    Secondary respondent data are underutilized because researchers avoid using these data in the presence of substantial missing data. The authors reviewed, evaluated, and tested solutions to this problem. Five strategies of dealing with missing partner data were reviewed: (a) complete case analysis, (b) inverse probability weighting, (c) correction…

  17. Student versus Faculty Perceptions of Missing Class.

    Science.gov (United States)

    Sleigh, Merry J.; Ritzer, Darren R.; Casey, Michael B.

    2002-01-01

    Examines and compares student and faculty attitudes towards students missing classes and class attendance. Surveys undergraduate students (n=231) in lower and upper level psychology courses and psychology faculty. Reports that students found more reasons acceptable for missing classes and that the amount of in-class material on the examinations…

  18. Methods to Minimize Zero-Missing Phenomenon

    DEFF Research Database (Denmark)

    da Silva, Filipe Miguel Faria; Bak, Claus Leth; Gudmundsdottir, Unnur Stella

    2010-01-01

    With the increasing use of high-voltage AC cables at transmission levels, phenomena such as current zero-missing start to appear more often in transmission systems. Zero-missing phenomenon can occur when energizing cable lines with shunt reactors. This may considerably delay the opening of the ci...

  19. Missed opportunities in child healthcare

    Directory of Open Access Journals (Sweden)

    Linda Jonker

    2014-08-01

    Objectives: This article describes the experiences of mothers that utilised comprehensive child health services in the Cape Metropolitan area of South Africa. Services included treatment for diseases; preventative interventions such as immunisation; and promotive interventions, such as improvement in nutrition and promotion of breastfeeding. Method: A qualitative, descriptive phenomenological approach was applied to explore the experiences and perceptions of mothers and/or carers utilising child healthcare services. Thirty percent of the clinics were selected purposively from the total population. A convenience purposive non-probability sampling method was applied to select 17 mothers who met the criteria and gave written consent. Interviews were conducted and recorded digitally using an interview guide. The data analysis was done using Tesch’s eight step model. Results: Findings of the study indicated varied experiences. Not all mothers received information about the Road to Health book or card. According to the mothers, integrated child healthcare services were not practised. The consequences were missed opportunities in immunisation, provision of vitamin A, absence of growth monitoring, feeding assessment and provision of nutritional advice. Conclusion: There is a need for simple interventions such as oral rehydration, early recognition and treatment of diseases, immunisation, growth monitoring and appropriate nutrition advice. These services were not offered diligently. Such interventions could contribute to reducing the incidence of child morbidity and mortality.

  20. Missed opportunities in child healthcare

    Directory of Open Access Journals (Sweden)

    Linda Jonker

    2014-01-01

    Full Text Available Background: Various policies in health, such as Integrated Management of Childhood Illnesses, were introduced to enhance integrated service delivery in child healthcare. During clinical practice the researcher observed that integrated services may not be rendered.Objectives: This article describes the experiences of mothers that utilised comprehensive child health services in the Cape Metropolitan area of South Africa. Services included treatment for diseases; preventative interventions such as immunisation; and promotive interventions, such as improvement in nutrition and promotion of breastfeeding.Method: A qualitative, descriptive phenomenological approach was applied to explore the experiences and perceptions of mothers and/or carers utilising child healthcare services. Thirty percent of the clinics were selected purposively from the total population. A convenience purposive non-probability sampling method was applied to select 17 mothers who met the criteria and gave written consent. Interviews were conducted and recorded digitally using an interview guide. The data analysis was done using Tesch’s eight step model.Results: Findings of the study indicated varied experiences. Not all mothers received information about the Road to Health book or card. According to the mothers, integrated child healthcare services were not practised. The consequences were missed opportunities in immunisation, provision of vitamin A, absence of growth monitoring, feeding assessment and provision of nutritional advice.Conclusion: There is a need for simple interventions such as oral rehydration, early recognition and treatment of diseases, immunisation, growth monitoring and appropriate nutrition advice. These services were not offered diligently. Such interventions could contribute to reducing the incidence of child morbidity and mortality.

  1. Creating Web Sites The Missing Manual

    CERN Document Server

    MacDonald, Matthew

    2006-01-01

    Think you have to be a technical wizard to build a great web site? Think again. For anyone who wants to create an engaging web site--for either personal or business purposes--Creating Web Sites: The Missing Manual demystifies the process and provides tools, techniques, and expert guidance for developing a professional and reliable web presence. Like every Missing Manual, you can count on Creating Web Sites: The Missing Manual to be entertaining and insightful and complete with all the vital information, clear-headed advice, and detailed instructions you need to master the task at hand. Autho

  2. Scalable Tensor Factorizations with Missing Data

    DEFF Research Database (Denmark)

    Acar, Evrim; Dunlavy, Daniel M.; Kolda, Tamara G.

    2010-01-01

    of missing data, many important data sets will be discarded or improperly analyzed. Therefore, we need a robust and scalable approach for factorizing multi-way arrays (i.e., tensors) in the presence of missing data. We focus on one of the most well-known tensor factorizations, CANDECOMP/PARAFAC (CP...... is shown to successfully factor tensors with noise and up to 70% missing data. Moreover, our approach is significantly faster than the leading alternative and scales to larger problems. To show the real-world usefulness of CP-WOPT, we illustrate its applicability on a novel EEG (electroencephalogram...

  3. 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.

  4. The prevention and handling of the missing data

    OpenAIRE

    Kang, Hyun

    2013-01-01

    Even in a well-designed and controlled study, missing data occurs in almost all research. Missing data can reduce the statistical power of a study and can produce biased estimates, leading to invalid conclusions. This manuscript reviews the problems and types of missing data, along with the techniques for handling missing data. The mechanisms by which missing data occurs are illustrated, and the methods for handling the missing data are discussed. The paper concludes with recommendations for ...

  5. 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...

  6. Maternal death and near miss measurement

    African Journals Online (AJOL)

    ABEOLUGBENGAS

    2008-05-26

    May 26, 2008 ... Maternal health services need to be accountable more than ever ... of maternal death and near miss audit, surveillance and review is ..... (d) A fundamental principle of these ..... quality assurance in obstetrics in Nigeria - a.

  7. Clustering with Missing Values: No Imputation Required

    Science.gov (United States)

    Wagstaff, Kiri

    2004-01-01

    Clustering algorithms can identify groups in large data sets, such as star catalogs and hyperspectral images. In general, clustering methods cannot analyze items that have missing data values. Common solutions either fill in the missing values (imputation) or ignore the missing data (marginalization). Imputed values are treated as just as reliable as the truly observed data, but they are only as good as the assumptions used to create them. In contrast, we present a method for encoding partially observed features as a set of supplemental soft constraints and introduce the KSC algorithm, which incorporates constraints into the clustering process. In experiments on artificial data and data from the Sloan Digital Sky Survey, we show that soft constraints are an effective way to enable clustering with missing values.

  8. Missed medical appointment among hypertensive and diabetic ...

    African Journals Online (AJOL)

    Keywords: Missed medical appointments, Hypertensive, Diabetic outpatients, Medication adherence, ... 12 weeks, at 95 % confidence level and 5 % error margin, 300 hypertensive ... monthly income and health insurance status of respondents ...

  9. Missed Radiation Therapy and Cancer Recurrence

    Science.gov (United States)

    Patients who miss radiation therapy sessions during cancer treatment have an increased risk of their disease returning, even if they eventually complete their course of radiation treatment, according to a new study.

  10. 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...

  11. Identifying missing dictionary entries with frequency-conserving context models

    Science.gov (United States)

    Williams, Jake Ryland; Clark, Eric M.; Bagrow, James P.; Danforth, Christopher M.; Dodds, Peter Sheridan

    2015-10-01

    In an effort to better understand meaning from natural language texts, we explore methods aimed at organizing lexical objects into contexts. A number of these methods for organization fall into a family defined by word ordering. Unlike demographic or spatial partitions of data, these collocation models are of special importance for their universal applicability. While we are interested here in text and have framed our treatment appropriately, our work is potentially applicable to other areas of research (e.g., speech, genomics, and mobility patterns) where one has ordered categorical data (e.g., sounds, genes, and locations). Our approach focuses on the phrase (whether word or larger) as the primary meaning-bearing lexical unit and object of study. To do so, we employ our previously developed framework for generating word-conserving phrase-frequency data. Upon training our model with the Wiktionary, an extensive, online, collaborative, and open-source dictionary that contains over 100 000 phrasal definitions, we develop highly effective filters for the identification of meaningful, missing phrase entries. With our predictions we then engage the editorial community of the Wiktionary and propose short lists of potential missing entries for definition, developing a breakthrough, lexical extraction technique and expanding our knowledge of the defined English lexicon of phrases.

  12. Insights into Conifer Giga-Genomes1

    Science.gov (United States)

    De La Torre, Amanda R.; Birol, Inanc; Bousquet, Jean; Ingvarsson, Pär K.; Jansson, Stefan; Jones, Steven J.M.; Keeling, Christopher I.; MacKay, John; Nilsson, Ove; Ritland, Kermit; Street, Nathaniel; Yanchuk, Alvin; Zerbe, Philipp; Bohlmann, Jörg

    2014-01-01

    Insights from sequenced genomes of major land plant lineages have advanced research in almost every aspect of plant biology. Until recently, however, assembled genome sequences of gymnosperms have been missing from this picture. Conifers of the pine family (Pinaceae) are a group of gymnosperms that dominate large parts of the world’s forests. Despite their ecological and economic importance, conifers seemed long out of reach for complete genome sequencing, due in part to their enormous genome size (20–30 Gb) and the highly repetitive nature of their genomes. Technological advances in genome sequencing and assembly enabled the recent publication of three conifer genomes: white spruce (Picea glauca), Norway spruce (Picea abies), and loblolly pine (Pinus taeda). These genome sequences revealed distinctive features compared with other plant genomes and may represent a window into the past of seed plant genomes. This Update highlights recent advances, remaining challenges, and opportunities in light of the publication of the first conifer and gymnosperm genomes. PMID:25349325

  13. Bioinspired Computational Approach to Missing Value Estimation

    Directory of Open Access Journals (Sweden)

    Israel Edem Agbehadji

    2018-01-01

    Full Text Available Missing data occurs when values of variables in a dataset are not stored. Estimating these missing values is a significant step during the data cleansing phase of a big data management approach. The reason of missing data may be due to nonresponse or omitted entries. If these missing data are not handled properly, this may create inaccurate results during data analysis. Although a traditional method such as maximum likelihood method extrapolates missing values, this paper proposes a bioinspired method based on the behavior of birds, specifically the Kestrel bird. This paper describes the behavior and characteristics of the Kestrel bird, a bioinspired approach, in modeling an algorithm to estimate missing values. The proposed algorithm (KSA was compared with WSAMP, Firefly, and BAT algorithm. The results were evaluated using the mean of absolute error (MAE. A statistical test (Wilcoxon signed-rank test and Friedman test was conducted to test the performance of the algorithms. The results of Wilcoxon test indicate that time does not have a significant effect on the performance, and the quality of estimation between the paired algorithms was significant; the results of Friedman test ranked KSA as the best evolutionary algorithm.

  14. Analysis of the progression of systolic blood pressure using imputation of missing phenotype values

    OpenAIRE

    Vaitsiakhovich, Tatsiana; Drichel, Dmitriy; Angisch, Marina; Becker, Tim; Herold, Christine; Lacour, André

    2014-01-01

    We present a genome-wide association study of a quantitative trait, "progression of systolic blood pressure in time," in which 142 unrelated individuals of the Genetic Analysis Workshop 18 real genotype data were analyzed. Information on systolic blood pressure and other phenotypic covariates was missing at certain time points for a considerable part of the sample. We observed that the dropout process causing missingness is not independent of the initial systolic blood pressure; that is, the ...

  15. Integrating genomics into evolutionary medicine.

    Science.gov (United States)

    Rodríguez, Juan Antonio; Marigorta, Urko M; Navarro, Arcadi

    2014-12-01

    The application of the principles of evolutionary biology into medicine was suggested long ago and is already providing insight into the ultimate causes of disease. However, a full systematic integration of medical genomics and evolutionary medicine is still missing. Here, we briefly review some cases where the combination of the two fields has proven profitable and highlight two of the main issues hindering the development of evolutionary genomic medicine as a mature field, namely the dissociation between fitness and health and the still considerable difficulties in predicting phenotypes from genotypes. We use publicly available data to illustrate both problems and conclude that new approaches are needed for evolutionary genomic medicine to overcome these obstacles. Copyright © 2014 Elsevier Ltd. All rights reserved.

  16. Comparative Reannotation of 21 Aspergillus Genomes

    Energy Technology Data Exchange (ETDEWEB)

    Salamov, Asaf; Riley, Robert; Kuo, Alan; Grigoriev, Igor

    2013-03-08

    We used comparative gene modeling to reannotate 21 Aspergillus genomes. Initial automatic annotation of individual genomes may contain some errors of different nature, e.g. missing genes, incorrect exon-intron structures, 'chimeras', which fuse 2 or more real genes or alternatively splitting some real genes into 2 or more models. The main premise behind the comparative modeling approach is that for closely related genomes most orthologous families have the same conserved gene structure. The algorithm maps all gene models predicted in each individual Aspergillus genome to the other genomes and, for each locus, selects from potentially many competing models, the one which most closely resembles the orthologous genes from other genomes. This procedure is iterated until no further change in gene models is observed. For Aspergillus genomes we predicted in total 4503 new gene models ( ~;;2percent per genome), supported by comparative analysis, additionally correcting ~;;18percent of old gene models. This resulted in a total of 4065 more genes with annotated PFAM domains (~;;3percent increase per genome). Analysis of a few genomes with EST/transcriptomics data shows that the new annotation sets also have a higher number of EST-supported splice sites at exon-intron boundaries.

  17. Stomatal vs. genome size in angiosperms: the somatic tail wagging the genomic dog?

    NARCIS (Netherlands)

    Hodgson, J.G.; Sharafi, M.; Jalili, A.; Diaz, S.; Montserrat-Marti, G.; Palmer, C.; Cerabolini, B.; Pierce, S.; Hamzehee, B.; Asri, Y.; Jamzad, Z.; Wilson, P.; Zarrinkamar, F.; Raven, J.; Band, S.R.; Basconcelo, S.; Bogard, A.; Carter, G.; Charles, M.; Castro-Diez, P.; Cornelissen, J.H.C.; Funes, G.; Jones, M.; Khoshnevis, M.; Perez-Harguindeguy, N.; Perez-Rontome, M.C.; Shirvany, F.A.; Vendramini, F.; Yazdani, S.; Abbas-Azimi, R.; Boustani, S.; Dehghan, M.; Hynd, F.A.; Kowsary, E.; Kazemi-Saeed, F.; Siavash, B.; Villar-Salvador, P.; Cragie, R.; Naqinezhad, A.; Romo-Diez, A.; De Torres Espuny, L.; Simmons, E.

    2010-01-01

    Background and Aims Genome size is a function, and the product, of cell volume. As such it is contingent on ecological circumstance. The nature of 'this ecological circumstance' is, however, hotly debated. Here, we investigate for angiosperms whether stomatal size may be this 'missing link': the

  18. MISSE PEACE Polymers Atomic Oxygen Erosion Results

    Science.gov (United States)

    deGroh, Kim, K.; Banks, Bruce A.; McCarthy, Catherine E.; Rucker, Rochelle N.; Roberts, Lily M.; Berger, Lauren A.

    2006-01-01

    Forty-one different polymer samples, collectively called the Polymer Erosion and Contamination Experiment (PEACE) Polymers, have been exposed to the low Earth orbit (LEO) environment on the exterior of the International Space Station (ISS) for nearly 4 years as part of Materials International Space Station Experiment 2 (MISSE 2). The objective of the PEACE Polymers experiment was to determine the atomic oxygen erosion yield of a wide variety of polymeric materials after long term exposure to the space environment. The polymers range from those commonly used for spacecraft applications, such as Teflon (DuPont) FEP, to more recently developed polymers, such as high temperature polyimide PMR (polymerization of monomer reactants). Additional polymers were included to explore erosion yield dependence upon chemical composition. The MISSE PEACE Polymers experiment was flown in MISSE Passive Experiment Carrier 2 (PEC 2), tray 1, on the exterior of the ISS Quest Airlock and was exposed to atomic oxygen along with solar and charged particle radiation. MISSE 2 was successfully retrieved during a space walk on July 30, 2005, during Discovery s STS-114 Return to Flight mission. Details on the specific polymers flown, flight sample fabrication, pre-flight and post-flight characterization techniques, and atomic oxygen fluence calculations are discussed along with a summary of the atomic oxygen erosion yield results. The MISSE 2 PEACE Polymers experiment is unique because it has the widest variety of polymers flown in LEO for a long duration and provides extremely valuable erosion yield data for spacecraft design purposes.

  19. Breast carcinomas: why are they missed?

    Science.gov (United States)

    Muttarak, M; Pojchamarnwiputh, S; Chaiwun, B

    2006-10-01

    Mammography has proven to be an effective modality for the detection of early breast carcinoma. However, 4-34 percent of breast cancers may be missed at mammography. Delayed diagnosis of breast carcinoma results in an unfavourable prognosis. The objective of this study was to determine the causes and characteristics of breast carcinomas missed by mammography at our institution, with the aim of reducing the rate of missed carcinoma. We reviewed the reports of 13,191 mammograms performed over a five-year period. Breast Imaging Reporting and Data Systems (BI-RADS) were used for the mammographical assessment, and reports were cross-referenced with the histological diagnosis of breast carcinoma. Causes of missed carcinomas were classified. Of 344 patients who had breast carcinoma and had mammograms done prior to surgery, 18 (5.2 percent) failed to be diagnosed by mammography. Of these, five were caused by dense breast parenchyma obscuring the lesions, 11 were due to perception and interpretation errors, and one each from unusual lesion characteristics and poor positioning. Several factors, including dense breast parenchyma obscuring a lesion, perception error, interpretation error, unusual lesion characteristics, and poor technique or positioning, are possible causes of missed breast cancers.

  20. Substituting missing data in compositional analysis

    Energy Technology Data Exchange (ETDEWEB)

    Real, Carlos, E-mail: carlos.real@usc.es [Area de Ecologia, Departamento de Biologia Celular y Ecologia, Escuela Politecnica Superior, Universidad de Santiago de Compostela, 27002 Lugo (Spain); Angel Fernandez, J.; Aboal, Jesus R.; Carballeira, Alejo [Area de Ecologia, Departamento de Biologia Celular y Ecologia, Facultad de Biologia, Universidad de Santiago de Compostela, 15782 Santiago de Compostela (Spain)

    2011-10-15

    Multivariate analysis of environmental data sets requires the absence of missing values or their substitution by small values. However, if the data is transformed logarithmically prior to the analysis, this solution cannot be applied because the logarithm of a small value might become an outlier. Several methods for substituting the missing values can be found in the literature although none of them guarantees that no distortion of the structure of the data set is produced. We propose a method for the assessment of these distortions which can be used for deciding whether to retain or not the samples or variables containing missing values and for the investigation of the performance of different substitution techniques. The method analyzes the structure of the distances among samples using Mantel tests. We present an application of the method to PCDD/F data measured in samples of terrestrial moss as part of a biomonitoring study. - Highlights: > Missing values in multivariate data sets must be substituted prior to analysis. > The substituted values can modify the structure of the data set. > We developed a method to estimate the magnitude of the alterations. > The method is simple and based on the Mantel test. > The method allowed the identification of problematic variables in a sample data set. - A method is presented for the assessment of the possible distortions in multivariate analysis caused by the substitution of missing values.

  1. Substituting missing data in compositional analysis

    International Nuclear Information System (INIS)

    Real, Carlos; Angel Fernandez, J.; Aboal, Jesus R.; Carballeira, Alejo

    2011-01-01

    Multivariate analysis of environmental data sets requires the absence of missing values or their substitution by small values. However, if the data is transformed logarithmically prior to the analysis, this solution cannot be applied because the logarithm of a small value might become an outlier. Several methods for substituting the missing values can be found in the literature although none of them guarantees that no distortion of the structure of the data set is produced. We propose a method for the assessment of these distortions which can be used for deciding whether to retain or not the samples or variables containing missing values and for the investigation of the performance of different substitution techniques. The method analyzes the structure of the distances among samples using Mantel tests. We present an application of the method to PCDD/F data measured in samples of terrestrial moss as part of a biomonitoring study. - Highlights: → Missing values in multivariate data sets must be substituted prior to analysis. → The substituted values can modify the structure of the data set. → We developed a method to estimate the magnitude of the alterations. → The method is simple and based on the Mantel test. → The method allowed the identification of problematic variables in a sample data set. - A method is presented for the assessment of the possible distortions in multivariate analysis caused by the substitution of missing values.

  2. Getting complete genomes from complex samples using nanopore sequencing

    DEFF Research Database (Denmark)

    Kirkegaard, Rasmus Hansen; Karst, Søren Michael; Albertsen, Mads

    Short read sequencing and metagenomic binning workflows have made it possible to extract bacterial genome bins from environmental microbial samples containing hundreds to thousands of different species. However, these genome bins often do not represent complete genomes, as they are mostly...... fragmented, incomplete and often contaminated with foreign DNA and with no robust strategies to validate the quality. The value of these `draft genomes` have limited, lasting value to the scientific community, as gene synteny is broken and the uncertainty of what is missing. The genetic material most often...... missed is important multi-copy and/or conserved marker genes such as the 16S rRNA gene, as sequence micro-heterogeneity prevents assembly of these genes in the de novo assembly. We demonstrate that using nanopore long reads it is now possible to overcome these issues and make complete genomes from...

  3. Getting complete genomes from complex samples using nanopore sequencing

    DEFF Research Database (Denmark)

    Kirkegaard, Rasmus Hansen; Karst, Søren Michael; Albertsen, Mads

    Background Short read DNA sequencing and metagenomic binning workflows have made it possible to extract bacterial genome bins from environmental microbial samples containing hundreds to thousands of different species. However, these genome bins often do not represent complete genomes......, as they are mostly fragmented, incomplete and often contaminated with foreign DNA. The value of these `draft genomes` have limited, lasting value to the scientific community, as gene synteny is broken and there is some uncertainty of what is missing1. The genetic material most often missed is important multi......-copy and/or conserved marker genes such as the 16S rRNA gene, as sequence micro-heterogeneity prevents assembly of these genes in the de novo assembly. However, long read sequencing technologies are emerging promising an end to fragmented genome assemblies2. Experimental design We extracted DNA from a full...

  4. Missing data imputation: focusing on single imputation.

    Science.gov (United States)

    Zhang, Zhongheng

    2016-01-01

    Complete case analysis is widely used for handling missing data, and it is the default method in many statistical packages. However, this method may introduce bias and some useful information will be omitted from analysis. Therefore, many imputation methods are developed to make gap end. The present article focuses on single imputation. Imputations with mean, median and mode are simple but, like complete case analysis, can introduce bias on mean and deviation. Furthermore, they ignore relationship with other variables. Regression imputation can preserve relationship between missing values and other variables. There are many sophisticated methods exist to handle missing values in longitudinal data. This article focuses primarily on how to implement R code to perform single imputation, while avoiding complex mathematical calculations.

  5. Time Series Forecasting with Missing Values

    Directory of Open Access Journals (Sweden)

    Shin-Fu Wu

    2015-11-01

    Full Text Available Time series prediction has become more popular in various kinds of applications such as weather prediction, control engineering, financial analysis, industrial monitoring, etc. To deal with real-world problems, we are often faced with missing values in the data due to sensor malfunctions or human errors. Traditionally, the missing values are simply omitted or replaced by means of imputation methods. However, omitting those missing values may cause temporal discontinuity. Imputation methods, on the other hand, may alter the original time series. In this study, we propose a novel forecasting method based on least squares support vector machine (LSSVM. We employ the input patterns with the temporal information which is defined as local time index (LTI. Time series data as well as local time indexes are fed to LSSVM for doing forecasting without imputation. We compare the forecasting performance of our method with other imputation methods. Experimental results show that the proposed method is promising and is worth further investigations.

  6. Collateral missing value imputation: a new robust missing value estimation algorithm for microarray data.

    Science.gov (United States)

    Sehgal, Muhammad Shoaib B; Gondal, Iqbal; Dooley, Laurence S

    2005-05-15

    Microarray data are used in a range of application areas in biology, although often it contains considerable numbers of missing values. These missing values can significantly affect subsequent statistical analysis and machine learning algorithms so there is a strong motivation to estimate these values as accurately as possible before using these algorithms. While many imputation algorithms have been proposed, more robust techniques need to be developed so that further analysis of biological data can be accurately undertaken. In this paper, an innovative missing value imputation algorithm called collateral missing value estimation (CMVE) is presented which uses multiple covariance-based imputation matrices for the final prediction of missing values. The matrices are computed and optimized using least square regression and linear programming methods. The new CMVE algorithm has been compared with existing estimation techniques including Bayesian principal component analysis imputation (BPCA), least square impute (LSImpute) and K-nearest neighbour (KNN). All these methods were rigorously tested to estimate missing values in three separate non-time series (ovarian cancer based) and one time series (yeast sporulation) dataset. Each method was quantitatively analyzed using the normalized root mean square (NRMS) error measure, covering a wide range of randomly introduced missing value probabilities from 0.01 to 0.2. Experiments were also undertaken on the yeast dataset, which comprised 1.7% actual missing values, to test the hypothesis that CMVE performed better not only for randomly occurring but also for a real distribution of missing values. The results confirmed that CMVE consistently demonstrated superior and robust estimation capability of missing values compared with other methods for both series types of data, for the same order of computational complexity. A concise theoretical framework has also been formulated to validate the improved performance of the CMVE

  7. Revisiting the missing protein-coding gene catalog of the domestic dog

    Directory of Open Access Journals (Sweden)

    Galibert Francis

    2009-02-01

    Full Text Available Abstract Background Among mammals for which there is a high sequence coverage, the whole genome assembly of the dog is unique in that it predicts a low number of protein-coding genes, ~19,000, compared to the over 20,000 reported for other mammalian species. Of particular interest are the more than 400 of genes annotated in primates and rodent genomes, but missing in dog. Results Using over 14,000 orthologous genes between human, chimpanzee, mouse rat and dog, we built multiple pairwise synteny maps to infer short orthologous intervals that were targeted for characterizing the canine missing genes. Based on gene prediction and a functionality test using the ratio of replacement to silent nucleotide substitution rates (dN/dS, we provide compelling structural and functional evidence for the identification of 232 new protein-coding genes in the canine genome and 69 gene losses, characterized as undetected gene or pseudogenes. Gene loss phyletic pattern analysis using ten species from chicken to human allowed us to characterize 28 canine-specific gene losses that have functional orthologs continuously from chicken or marsupials through human, and 10 genes that arose specifically in the evolutionary lineage leading to rodent and primates. Conclusion This study demonstrates the central role of comparative genomics for refining gene catalogs and exploring the evolutionary history of gene repertoires, particularly as applied for the characterization of species-specific gene gains and losses.

  8. 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 ...

  9. 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

  10. 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 ...

  11. 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.

  12. Missing Strands? Dealing with Hair Loss

    Science.gov (United States)

    ... 2017 Print this issue Missing Strands? Dealing with Hair Loss En español Send us your comments Hair loss is often associated with men and aging, but ... or their treatments, and many other things cause hair loss. The most common type of hair loss is ...

  13. On testing the missing at random assumption

    DEFF Research Database (Denmark)

    Jaeger, Manfred

    2006-01-01

    Most approaches to learning from incomplete data are based on the assumption that unobserved values are missing at random (mar). While the mar assumption, as such, is not testable, it can become testable in the context of other distributional assumptions, e.g. the naive Bayes assumption...

  14. Missing mass from low-luminosity stars

    International Nuclear Information System (INIS)

    Hawkins, M.R.S.

    1986-01-01

    Results from a deep photometric survey for low-luminosity stars show a turnup to the luminosity function at faint magnitudes, and reopen the possibility that the missing mass in the solar neighbourhood is made up of stars after all. (author)

  15. Dealing with gene expression missing data.

    Science.gov (United States)

    Brás, L P; Menezes, J C

    2006-05-01

    Compared evaluation of different methods is presented for estimating missing values in microarray data: weighted K-nearest neighbours imputation (KNNimpute), regression-based methods such as local least squares imputation (LLSimpute) and partial least squares imputation (PLSimpute) and Bayesian principal component analysis (BPCA). The influence in prediction accuracy of some factors, such as methods' parameters, type of data relationships used in the estimation process (i.e. row-wise, column-wise or both), missing rate and pattern and type of experiment [time series (TS), non-time series (NTS) or mixed (MIX) experiments] is elucidated. Improvements based on the iterative use of data (iterative LLS and PLS imputation--ILLSimpute and IPLSimpute), the need to perform initial imputations (modified PLS and Helland PLS imputation--MPLSimpute and HPLSimpute) and the type of relationships employed (KNNarray, LLSarray, HPLSarray and alternating PLS--APLSimpute) are proposed. Overall, it is shown that data set properties (type of experiment, missing rate and pattern) affect the data similarity structure, therefore influencing the methods' performance. LLSimpute and ILLSimpute are preferable in the presence of data with a stronger similarity structure (TS and MIX experiments), whereas PLS-based methods (MPLSimpute, IPLSimpute and APLSimpute) are preferable when estimating NTS missing data.

  16. Missed opportunities and inappropriately given vaccines reduce ...

    African Journals Online (AJOL)

    Objectives: To quantify missed opportunities for immunisation, document reasons for their occurrence and evaluate the extent of inappropriately given vaccine doses. Design: A cross sectional study of children under two years of age attending health facilities. Setting: Six health facilities predominantly serving the slums of ...

  17. Determinants Of Missed Opportunities For Immunization Among ...

    African Journals Online (AJOL)

    Factors responsible for the missed opportunities included the attitude of the health worker, prolonged time of waiting to receive vaccine, immunization clashing with other schedules and transportation problem. Respondents' level ofknowledge on immunization and educational background were significantly associated with ...

  18. All hypertopologies are hit-and-miss

    Directory of Open Access Journals (Sweden)

    Somshekhar Naimpally

    2002-04-01

    Full Text Available We solve a long standing problem by showing that all known hypertopologies are hit-and-miss. Our solution is not merely of theoretical importance. This representation is useful in the study of comparison of the Hausdorff-Bourbaki or H-B uniform topologies and the Wijsman topologies among themselves and with others. Up to now some of these comparisons needed intricate manipulations. The H-B uniform topologies were the subject of intense activity in the 1960's in connection with the Isbell-Smith problem. We show that they are proximally locally finite topologies from which the solution to the above problem follows easily. It is known that the Wijsman topology on the hyperspace is the proximal ball (hit-and-miss topology in”nice” metric spaces including the normed linear spaces. With the introduction of a new far-miss topology we show that the Wijsman topology is hit-and-miss for all metric spaces. From this follows a natural generalization of the Wijsman topology to the hyperspace of any T1 space. Several existing results in the literature are easy consequences of our work.

  19. Flash CS4: The Missing Manual

    CERN Document Server

    Grover, Chris

    2008-01-01

    Unlock the power of Flash and bring gorgeous animations to life onscreen. Flash CS4: The Missing Manual includes a complete primer on animation, a guided tour of the program's tools and capabilities, lots of new illustrations, and more details on working with video. Beginners will learn to use the software in no time, and experienced Flash designers will improve their skills.

  20. What's Missing? Anti-Racist Sex Education!

    Science.gov (United States)

    Whitten, Amanda; Sethna, Christabelle

    2014-01-01

    Contemporary sexual health curricula in Canada include information about sexual diversity and queer identities, but what remains missing is any explicit discussion of anti-racist sex education. Although there exists federal and provincial support for multiculturalism and anti-racism in schools, contemporary Canadian sex education omits crucial…

  1. How efficient is estimation with missing data?

    DEFF Research Database (Denmark)

    Karadogan, Seliz; Marchegiani, Letizia; Hansen, Lars Kai

    2011-01-01

    percentages (MDP) using a missing completely at random (MCAR) scheme. We compare three MDTs: pairwise deletion (PW), mean imputation (MI) and a maximum likelihood method that we call complete expectation maximization (CEM). We use a synthetic dataset, the Iris dataset and the Pima Indians Diabetes dataset. We...

  2. Generalized canonical correlation analysis with missing values

    NARCIS (Netherlands)

    M. van de Velden (Michel); Y. Takane

    2009-01-01

    textabstractTwo new methods for dealing with missing values in generalized canonical correlation analysis are introduced. The first approach, which does not require iterations, is a generalization of the Test Equating method available for principal component analysis. In the second approach,

  3. Missed Distal Tracheal Foreign Body in Consecutive ...

    African Journals Online (AJOL)

    2017-05-18

    May 18, 2017 ... Since invention, bronchoscopy has become the gold standard in the diagnosis and extraction of airway FB.[4]. Foreign bodies may be missed at ... Since the discovery by Gustav Killian,[9] extraction of tracheobronchial FB has been accomplished with rigid bronchoscopy which is still considered as the gold.

  4. Missed isolated volar dislocation of the scaphoid

    DEFF Research Database (Denmark)

    Kolby, Lise; Larsen, Søren; Jørring, Stig

    2007-01-01

    A patient presented with volar dislocation of the scaphoid, the diagnosis of which had been missed for two weeks. He was treated with open reduction through a combined volar and dorsal approach with decompression of the median nerve, internal fixation, and a cast for eight weeks. One year postope...... postoperatively the functional result was good. A radiograph showed no sign of avascular necrosis....

  5. Missed opportunities for immunisation at Kasungu

    African Journals Online (AJOL)

    work. Some outreach and static clinics still concen- trate their EPI activities on infants and children and largely ignore the mothers who accompany them. Health workers ... sungu District Hospital (KDH) were surveyed. Six. Health Centres ... Table 2 Missed Dpponunities for Immunisation ofEPI Tat'get Gt'Oups at Kmungu ...

  6. 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.

  7. Missed retinal breaks in rhegmatogenous retinal detachment

    Directory of Open Access Journals (Sweden)

    Brijesh Takkar

    2016-12-01

    Full Text Available AIM: To evaluate the causes and associations of missed retinal breaks (MRBs and posterior vitreous detachment (PVD in patients with rhegmatogenous retinal detachment (RRD. METHODS: Case sheets of patients undergoing vitreo retinal surgery for RRD at a tertiary eye care centre were evaluated retrospectively. Out of the 378 records screened, 253 were included for analysis of MRBs and 191 patients were included for analysis of PVD, depending on the inclusion criteria. Features of RRD and retinal breaks noted on examination were compared to the status of MRBs and PVD detected during surgery for possible associations. RESULTS: Overall, 27% patients had MRBs. Retinal holes were commonly missed in patients with lattice degeneration while missed retinal tears were associated with presence of complete PVD. Patients operated for cataract surgery were significantly associated with MRBs (P=0.033 with the odds of missing a retinal break being 1.91 as compared to patients with natural lens. Advanced proliferative vitreo retinopathy (PVR and retinal bullae were the most common reasons for missing a retinal break during examination. PVD was present in 52% of the cases and was wrongly assessed in 16%. Retinal bullae, pseudophakia/aphakia, myopia, and horse shoe retinal tears were strongly associated with presence of PVD. Traumatic RRDs were rarely associated with PVD. CONCLUSION: Pseudophakic patients, and patients with retinal bullae or advanced PVR should be carefully screened for MRBs. Though Weiss ring is a good indicator of PVD, it may still be over diagnosed in some cases. PVD is associated with retinal bullae and pseudophakia, and inversely with traumatic RRD.

  8. Incomplete Early Childhood Immunization Series and Missing Fourth DTaP Immunizations; Missed Opportunities or Missed Visits?

    Science.gov (United States)

    Robison, Steve G

    2013-01-01

    The successful completion of early childhood immunizations is a proxy for overall quality of early care. Immunization statuses are usually assessed by up-to-date (UTD) rates covering combined series of different immunizations. However, series UTD rates often only bear on which single immunization is missing, rather than the success of all immunizations. In the US, most series UTD rates are limited by missing fourth DTaP-containing immunizations (diphtheria/tetanus/pertussis) due at 15 to 18 months of age. Missing 4th DTaP immunizations are associated either with a lack of visits at 15 to 18 months of age, or to visits without immunizations. Typical immunization data however cannot distinguish between these two reasons. This study compared immunization records from the Oregon ALERT IIS with medical encounter records for two-year olds in the Oregon Health Plan. Among those with 3 valid DTaPs by 9 months of age, 31.6% failed to receive a timely 4th DTaP; of those without a 4th DTaP, 42.1% did not have any provider visits from 15 through 18 months of age, while 57.9% had at least one provider visit. Those with a 4th DTaP averaged 2.45 encounters, while those with encounters but without 4th DTaPs averaged 2.23 encounters.

  9. 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...

  10. Congenitally missing mandibular second premolars: clinical options.

    Science.gov (United States)

    Kokich, Vincent G; Kokich, Vincent O

    2006-10-01

    Congenital absence of mandibular second premolars affects many orthodontic patients. The orthodontist must make the proper decision at the appropriate time regarding management of the edentulous space. These spaces can be closed or left open. If the space will be left open for an eventual restoration, the keys during orthodontic treatment are to create the correct amount of space and to leave the alveolar ridge in an ideal condition for a future restoration. If the space will be closed, the clinician must avoid any detrimental alterations to the occlusion and the facial profile. Some early decisions that the orthodontist makes for a patient whose mandibular second premolars are congenitally missing will affect his or her dental health for a lifetime. Therefore, the correct decision must be made at the appropriate time. In this article, we present and discuss various treatment alternatives for managing orthodontic patients with at least 1 congenitally missing mandibular second premolar.

  11. The case of the missing third.

    Science.gov (United States)

    Robertson, Robin

    2005-01-01

    How is it that form arises out of chaos? In attempting to deal with this primary question, time and again a "Missing Third" is posited that lies between extremes. The problem of the "Missing Third" can be traced through nearly the entire history of thought. The form it takes, the problems that arise from it, the solutions suggested for resolving it, are each representative of an age. This paper traces the issue from Plato and Parmenides in the 4th--5th centuries, B.C.; to Neoplatonism in the 3rd--5th centuries; to Locke and Descartes in the 17th century; on to Berkeley and Kant in the 18th century; Fechner and Wundt in the 19th century; to behaviorism and Gestalt psychology, Jung, early in the 20th century, ethology and cybernetics later in the 20th century, then culminates late in the 20th century, with chaos theory.

  12. iLife '05 The Missing Manual

    CERN Document Server

    Pogue, David

    2005-01-01

    The incomparable iLife '05 is the must-have multimedia suite for everyone who owns a Mac--and the envy of everyone who doesn't. iLife '05: The Missing Manual is the definitive iLife '05 book--and what should have come with the suite. There's no better guide to your iLife experience than the #1 bestselling Macintosh author and expert--and Missing Manual series creator--David Pogue. Totally objective and utterly in-the-know, Pogue highlights the newest features, changes, and improvements of iLife '05, covers the capabilities and limitations of each program within the suite, and delivers count

  13. Absence of missing mass in clusters

    Energy Technology Data Exchange (ETDEWEB)

    Fesenko, B.I.

    1981-01-01

    The evaluation of the radial-velocity dispersion in clusters of galaxies is considered by using order statistics to reduce the distortions introduced by foreground and background galaxies and by large errors in velocity measurement. For four nearby clusters of galaxies, including the Coma cluster, velocity dispersions are obtained which are approximately four times lower than previously reported values. It is found that more remote galaxies exhibit the same tendency to a reduction in missing mass. A detailed examination of the statistical properties of galaxies in the Virgo cluster reveals that the cluster might not actually exist, but may be just a large excess in the number density of bright galaxies, possibly the result of an increase in the visibility of objects in the appropriate directions. It is concluded that the presence of a large amount of missing mass in clusters of galaxies is yet to be proven.

  14. MOLDOVA: MISSED ADVANTAGES OF EURASIAN INTEGRATION

    Directory of Open Access Journals (Sweden)

    Ludmila Vasiljevna Fokina

    2015-01-01

    Full Text Available The article is devoted to potentially missed advantages of Eurasian integration (EAEU for Moldova. Special attention is given to the branches in which the country could get evident advantages including agriculture, power engineering, external trade ties with the EAEU countries. Possible positive effects of Eurasian integration in solution of the Transnistrian problem, in the sphere of labour migration and other fields are also shown.

  15. Photoshop Elements 6 The Missing Manual

    CERN Document Server

    Brundage, Barbara

    2009-01-01

    With Photoshop Elements 6, the most popular photo-editing program on Earth just keeps getting better. It's perfect for scrapbooking, email-ready slideshows, Web galleries, you name it. But knowing what to do and when is tricky. That's why our Missing Manual is the bestselling book on the topic. This fully revised guide explains not only how the tools and commands work, but when to use them.

  16. Missing level corrections using neutron spacings

    International Nuclear Information System (INIS)

    Mitchell, G.E.; Shriner, J.F. Jr.

    2009-11-01

    Nuclear level densities are very important for a wide variety of pure and applied neutron physics. Most of the relevant information is obtained from neutron resonance data. The key correction to the raw experimental data is for missing levels. All of the standard correction methods assume that the neutron resonances obey the predictions of the Gaussian Orthogonal Ensemble version of Random Matrix Theory (RMT) and utilize comparison with the Porter-Thomas distribution of reduced widths in order to determine the fraction of missing levels. Here we adopt an alternate approach, comparing the neutron data with the predictions of RMT for eigenvalue statistics. Since in RMT the widths and eigenvalues are independent, analysis of the eigenvalues provides an independent analysis of the same data set. We summarize recent work in this area using the nearest neighbour spacing distribution, and we also develop tests that utilize several other eigenvalue statistics to provide additional estimates of the missing fraction of levels. These additional statistics include the key test for long range order - the Dyson-Mehta Δ 3 statistic - as well as the thermodynamic energy (that arises from Dyson's Circular Orthogonal Ensemble), the linear correlation coefficient of adjacent spacings (a measure of short range anti-correlation), and a statistic related to the Q statistic defined by Dyson and Mehta in the early 1960s. Developed FORTRAN code is available at http://www-nds.iaea.org/missing-levels/. These tests are applied to the s-wave neutron resonances in n + 238 U and n + 232 Th. The results for 238 U are consistent with each other and raise some issues concerning data purity. For the 232 Th data, all of the tests are in excellent agreement. (author)

  17. iWork '09 The Missing Manual

    CERN Document Server

    Clark, Josh

    2009-01-01

    With iWork '09: The Missing Manual, you'll quickly learn everything you need to know about Apple's incredible productivity programs, including the Pages word-processor, the Numbers spreadsheet, and the Keynote presentation program that Al Gore and Steve Jobs made famous. This book gives you crystal-clear and jargon-free explanations of iWork's capabilities, advantages, and limitations to help you produce stunning documents and cinema-quality digital presentations in no time.

  18. Conserved syntenic clusters of protein coding genes are missing in birds.

    Science.gov (United States)

    Lovell, Peter V; Wirthlin, Morgan; Wilhelm, Larry; Minx, Patrick; Lazar, Nathan H; Carbone, Lucia; Warren, Wesley C; Mello, Claudio V

    2014-01-01

    Birds are one of the most highly successful and diverse groups of vertebrates, having evolved a number of distinct characteristics, including feathers and wings, a sturdy lightweight skeleton and unique respiratory and urinary/excretion systems. However, the genetic basis of these traits is poorly understood. Using comparative genomics based on extensive searches of 60 avian genomes, we have found that birds lack approximately 274 protein coding genes that are present in the genomes of most vertebrate lineages and are for the most part organized in conserved syntenic clusters in non-avian sauropsids and in humans. These genes are located in regions associated with chromosomal rearrangements, and are largely present in crocodiles, suggesting that their loss occurred subsequent to the split of dinosaurs/birds from crocodilians. Many of these genes are associated with lethality in rodents, human genetic disorders, or biological functions targeting various tissues. Functional enrichment analysis combined with orthogroup analysis and paralog searches revealed enrichments that were shared by non-avian species, present only in birds, or shared between all species. Together these results provide a clearer definition of the genetic background of extant birds, extend the findings of previous studies on missing avian genes, and provide clues about molecular events that shaped avian evolution. They also have implications for fields that largely benefit from avian studies, including development, immune system, oncogenesis, and brain function and cognition. With regards to the missing genes, birds can be considered ‘natural knockouts’ that may become invaluable model organisms for several human diseases.

  19. Uncovering missing links with cold ends

    Science.gov (United States)

    Zhu, Yu-Xiao; Lü, Linyuan; Zhang, Qian-Ming; Zhou, Tao

    2012-11-01

    To evaluate the performance of prediction of missing links, the known data are randomly divided into two parts, the training set and the probe set. We argue that this straightforward and standard method may lead to terrible bias, since in real biological and information networks, missing links are more likely to be links connecting low-degree nodes. We therefore study how to uncover missing links with low-degree nodes, namely links in the probe set are of lower degree products than a random sampling. Experimental analysis on ten local similarity indices and four disparate real networks reveals a surprising result that the Leicht-Holme-Newman index [E.A. Leicht, P. Holme, M.E.J. Newman, Vertex similarity in networks, Phys. Rev. E 73 (2006) 026120] performs the best, although it was known to be one of the worst indices if the probe set is a random sampling of all links. We further propose an parameter-dependent index, which considerably improves the prediction accuracy. Finally, we show the relevance of the proposed index to three real sampling methods: acquaintance sampling, random-walk sampling and path-based sampling.

  20. MISSE 6 Polymer Film Tensile Experiment

    Science.gov (United States)

    Miller, Sharon K. R.; Dever, Joyce A.; Banks, Bruce A.; Waters, Deborah L.; Sechkar, Edward; Kline, Sara

    2010-01-01

    The Polymer Film Tensile Experiment (PFTE) was flown as part of Materials International Space Station Experiment 6 (MISSE 6). The purpose of the experiment was to expose a variety of polymer films to the low Earth orbital environment under both relaxed and tension conditions. The polymers selected are those commonly used for spacecraft thermal control and those under consideration for use in spacecraft applications such as sunshields, solar sails, and inflatable and deployable structures. The dog-bone shaped samples of polymers that were flown were exposed on both the side of the MISSE 6 Passive Experiment Container (PEC) that was facing into the ram direction (receiving atomic oxygen, ultraviolet (UV) radiation, ionizing radiation, and thermal cycling) and the wake facing side (which was supposed to have experienced predominantly the same environmental effects except for atomic oxygen which was present due to reorientation of the International Space Station). A few of the tensile samples were coated with vapor deposited aluminum on the back and wired to determine the point in the flight when the tensile sample broke as recorded by a change in voltage that was stored on battery powered data loggers for post flight retrieval and analysis. The data returned on the data loggers was not usable. However, post retrieval observation and analysis of the samples was performed. This paper describes the preliminary analysis and observations of the polymers exposed on the MISSE 6 PFTE.

  1. Planned Missing Data Designs in Educational Psychology Research

    NARCIS (Netherlands)

    Rhemtulla, M.; Hancock, G.R.

    2016-01-01

    Although missing data are often viewed as a challenge for applied researchers, in fact missing data can be highly beneficial. Specifically, when the amount of missing data on specific variables is carefully controlled, a balance can be struck between statistical power and research costs. This

  2. Missing value imputation for epistatic MAPs

    LENUS (Irish Health Repository)

    Ryan, Colm

    2010-04-20

    Abstract Background Epistatic miniarray profiling (E-MAPs) is a high-throughput approach capable of quantifying aggravating or alleviating genetic interactions between gene pairs. The datasets resulting from E-MAP experiments typically take the form of a symmetric pairwise matrix of interaction scores. These datasets have a significant number of missing values - up to 35% - that can reduce the effectiveness of some data analysis techniques and prevent the use of others. An effective method for imputing interactions would therefore increase the types of possible analysis, as well as increase the potential to identify novel functional interactions between gene pairs. Several methods have been developed to handle missing values in microarray data, but it is unclear how applicable these methods are to E-MAP data because of their pairwise nature and the significantly larger number of missing values. Here we evaluate four alternative imputation strategies, three local (Nearest neighbor-based) and one global (PCA-based), that have been modified to work with symmetric pairwise data. Results We identify different categories for the missing data based on their underlying cause, and show that values from the largest category can be imputed effectively. We compare local and global imputation approaches across a variety of distinct E-MAP datasets, showing that both are competitive and preferable to filling in with zeros. In addition we show that these methods are effective in an E-MAP from a different species, suggesting that pairwise imputation techniques will be increasingly useful as analogous epistasis mapping techniques are developed in different species. We show that strongly alleviating interactions are significantly more difficult to predict than strongly aggravating interactions. Finally we show that imputed interactions, generated using nearest neighbor methods, are enriched for annotations in the same manner as measured interactions. Therefore our method potentially

  3. A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases

    Directory of Open Access Journals (Sweden)

    Karp Peter D

    2004-06-01

    Full Text Available Abstract Background The PathoLogic program constructs Pathway/Genome databases by using a genome's annotation to predict the set of metabolic pathways present in an organism. PathoLogic determines the set of reactions composing those pathways from the enzymes annotated in the organism's genome. Most annotation efforts fail to assign function to 40–60% of sequences. In addition, large numbers of sequences may have non-specific annotations (e.g., thiolase family protein. Pathway holes occur when a genome appears to lack the enzymes needed to catalyze reactions in a pathway. If a protein has not been assigned a specific function during the annotation process, any reaction catalyzed by that protein will appear as a missing enzyme or pathway hole in a Pathway/Genome database. Results We have developed a method that efficiently combines homology and pathway-based evidence to identify candidates for filling pathway holes in Pathway/Genome databases. Our program not only identifies potential candidate sequences for pathway holes, but combines data from multiple, heterogeneous sources to assess the likelihood that a candidate has the required function. Our algorithm emulates the manual sequence annotation process, considering not only evidence from homology searches, but also considering evidence from genomic context (i.e., is the gene part of an operon? and functional context (e.g., are there functionally-related genes nearby in the genome? to determine the posterior belief that a candidate has the required function. The method can be applied across an entire metabolic pathway network and is generally applicable to any pathway database. The program uses a set of sequences encoding the required activity in other genomes to identify candidate proteins in the genome of interest, and then evaluates each candidate by using a simple Bayes classifier to determine the probability that the candidate has the desired function. We achieved 71% precision at a

  4. 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...

  5. Using nanopore sequencing to get complete genomes from complex samples

    DEFF Research Database (Denmark)

    Kirkegaard, Rasmus Hansen; Karst, Søren Michael; Nielsen, Per Halkjær

    The advantages of “next generation sequencing” has come at the cost of genome finishing. The dominant sequencing technology provides short reads of 150-300 bp, which has made genome assembly very difficult as the reads do not span important repeat regions. Genomes have thus been added...... to the databases as fragmented assemblies and not as finished contigs that resemble the chromosomes in which the DNA is organised within the cells. This is especially troublesome for genomes derived from complex metagenome sequencing. Databases with incomplete genomes can lead to false conclusions about...... the absence of genes and functional predictions of the organisms. Furthermore, it is common that repetitive elements and marker genes such as the 16S rRNA gene are missing completely from these genome bins. Using nanopore long reads, we demonstrate that it is possible to span these regions and make complete...

  6. AUTOMATIC CLASSIFICATION OF VARIABLE STARS IN CATALOGS WITH MISSING DATA

    International Nuclear Information System (INIS)

    Pichara, Karim; Protopapas, Pavlos

    2013-01-01

    We present an automatic classification method for astronomical catalogs with missing data. We use Bayesian networks and a probabilistic graphical model that allows us to perform inference to predict missing values given observed data and dependency relationships between variables. To learn a Bayesian network from incomplete data, we use an iterative algorithm that utilizes sampling methods and expectation maximization to estimate the distributions and probabilistic dependencies of variables from data with missing values. To test our model, we use three catalogs with missing data (SAGE, Two Micron All Sky Survey, and UBVI) and one complete catalog (MACHO). We examine how classification accuracy changes when information from missing data catalogs is included, how our method compares to traditional missing data approaches, and at what computational cost. Integrating these catalogs with missing data, we find that classification of variable objects improves by a few percent and by 15% for quasar detection while keeping the computational cost the same

  7. AUTOMATIC CLASSIFICATION OF VARIABLE STARS IN CATALOGS WITH MISSING DATA

    Energy Technology Data Exchange (ETDEWEB)

    Pichara, Karim [Computer Science Department, Pontificia Universidad Católica de Chile, Santiago (Chile); Protopapas, Pavlos [Institute for Applied Computational Science, Harvard University, Cambridge, MA (United States)

    2013-11-10

    We present an automatic classification method for astronomical catalogs with missing data. We use Bayesian networks and a probabilistic graphical model that allows us to perform inference to predict missing values given observed data and dependency relationships between variables. To learn a Bayesian network from incomplete data, we use an iterative algorithm that utilizes sampling methods and expectation maximization to estimate the distributions and probabilistic dependencies of variables from data with missing values. To test our model, we use three catalogs with missing data (SAGE, Two Micron All Sky Survey, and UBVI) and one complete catalog (MACHO). We examine how classification accuracy changes when information from missing data catalogs is included, how our method compares to traditional missing data approaches, and at what computational cost. Integrating these catalogs with missing data, we find that classification of variable objects improves by a few percent and by 15% for quasar detection while keeping the computational cost the same.

  8. Missing value imputation: with application to handwriting data

    Science.gov (United States)

    Xu, Zhen; Srihari, Sargur N.

    2015-01-01

    Missing values make pattern analysis difficult, particularly with limited available data. In longitudinal research, missing values accumulate, thereby aggravating the problem. Here we consider how to deal with temporal data with missing values in handwriting analysis. In the task of studying development of individuality of handwriting, we encountered the fact that feature values are missing for several individuals at several time instances. Six algorithms, i.e., random imputation, mean imputation, most likely independent value imputation, and three methods based on Bayesian network (static Bayesian network, parameter EM, and structural EM), are compared with children's handwriting data. We evaluate the accuracy and robustness of the algorithms under different ratios of missing data and missing values, and useful conclusions are given. Specifically, static Bayesian network is used for our data which contain around 5% missing data to provide adequate accuracy and low computational cost.

  9. 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...

  10. Are We Really Missing Small Galaxies?

    Science.gov (United States)

    Kohler, Susanna

    2018-02-01

    One long-standing astrophysical puzzle is that of so-called missing dwarf galaxies: the number of small dwarf galaxies that we observe is far fewer than that predicted by theory. New simulations, however, suggest that perhaps theres no mystery after all.Missing DwarfsDark-matter cosmological simulations predict many small galaxy halos for every large halo that forms. [The Via Lactea project]Models of a lambda-cold-dark-matter (CDM) universe predict the distribution of galaxy halo sizes throughout the universe, suggesting there should be many more small galaxies than large ones. In what has become known as the missing dwarf problem, however, we find that while we observe the expected numbers of galaxies at the larger end of the scale, we dont see nearly enough small galaxies to match the predictions.Are these galaxies actually missing? Are our predictions wrong? Or are the galaxies there and were just not spotting them? A recent study led by Alyson Brooks (Rutgers University) uses new simulations to explore whatscausing the difference between theory and observation.The fraction of detectable halos as a function of velocity, according to the authors simulations. Below 35 km/s, the detectability of the galaxies drops precipitously. [Brooks et al. 2017]Simulating Galactic VelocitiesBecause we cant weigh a galaxy directly, one proxy used for galaxy mass is its circular velocity; the more massive a galaxy, the faster gas and stars rotate around its center. The discrepancy between models and observations lies in whats known as the galaxy velocity function, which describes the number density of galaxies for a given circular velocity. While theory and observations agree for galaxies with circular velocities above 100 km/s, theory predicts far more dwarfs below this velocity than we observe.To investigate this problem, Brooks and collaborators ran a series of cosmological simulations based on our understanding of a CDM universe. Instead of exploring the result using only

  11. Microbial genome analysis: the COG approach.

    Science.gov (United States)

    Galperin, Michael Y; Kristensen, David M; Makarova, Kira S; Wolf, Yuri I; Koonin, Eugene V

    2017-09-14

    For the past 20 years, the Clusters of Orthologous Genes (COG) database had been a popular tool for microbial genome annotation and comparative genomics. Initially created for the purpose of evolutionary classification of protein families, the COG have been used, apart from straightforward functional annotation of sequenced genomes, for such tasks as (i) unification of genome annotation in groups of related organisms; (ii) identification of missing and/or undetected genes in complete microbial genomes; (iii) analysis of genomic neighborhoods, in many cases allowing prediction of novel functional systems; (iv) analysis of metabolic pathways and prediction of alternative forms of enzymes; (v) comparison of organisms by COG functional categories; and (vi) prioritization of targets for structural and functional characterization. Here we review the principles of the COG approach and discuss its key advantages and drawbacks in microbial genome analysis. Published by Oxford University Press 2017. This work is written by US Government employees and is in the public domain in the US.

  12. iPod the missing manual

    CERN Document Server

    Biersdorfer, J D

    2008-01-01

    With the tiny Shuffle, the Nano, the Classic, or the Touch, Apple's gotten the world hooked on portable music, pictures, videos -- and the iPod. One thing they haven't delivered is an easy guide for getting the most from this sleek entertainment center. iPod: The Missing Manual, 7th Edition gives you a no-nonsense view of the latest iPod line, with crystal-clear explanations, easy-to-follow color graphics, and guidance on the most useful things your iPod can do.

  13. Switching to the Mac The Missing Manual

    CERN Document Server

    Pogue, David

    2010-01-01

    Is Windows giving you pause? Ready to make the leap to the Mac instead? There has never been a better time to switch from Windows to Mac, and this incomparable guide will help you make a smooth transition. New York Times columnist and Missing Manuals creator David Pogue gets you past three challenges: transferring your stuff, assembling Mac programs so you can do what you did with Windows, and learning your way around Mac OS X. Learning to use a Mac is not a piece of cake, but once you do, the rewards are oh-so-much better. No viruses, worms, or spyware. No questionable firewalls, inefficien

  14. Dreamweaver CS55 The Missing Manual

    CERN Document Server

    McFarland, David

    2011-01-01

    Dreamweaver is the tool most widely used for designing and managing professional-looking websites, but it's a complex program. That's where Dreamweaver CS5.5: The Missing Manual comes in. With its jargon-free explanations, 13 hands-on tutorials, and savvy advice from Dreamweaver expert Dave McFarland, you'll master this versatile program with ease. Get A to Z guidance. Go from building your first web page to creating interactive, database-driven sites.Build skills as you learn. Apply your knowledge through tutorials and downloadable practice files.Create a state-of-the-art website. Use powerf

  15. Handling missing data in ranked set sampling

    CERN Document Server

    Bouza-Herrera, Carlos N

    2013-01-01

    The existence of missing observations is a very important aspect to be considered in the application of survey sampling, for example. In human populations they may be caused by a refusal of some interviewees to give the true value for the variable of interest. Traditionally, simple random sampling is used to select samples. Most statistical models are supported by the use of samples selected by means of this design. In recent decades, an alternative design has started being used, which, in many cases, shows an improvement in terms of accuracy compared with traditional sampling. It is called R

  16. Flash CS5 The Missing Manual

    CERN Document Server

    Grover, Chris

    2010-01-01

    Once you know how to use Flash, you can create everything from simple animations to high-end desktop applications, but it's a complex tool that can be difficult to master on your own-unless you have this Missing Manual. This book will help you learn all you need to know about Flash CS5 to create animations that bring your ideas to life. Learn animation basics. Find everything you need to know to get started with FlashMaster the Flash tools. Learn the animation and effects toolset, with clear explanations and hands-on examplesUse 3D effects. Rotate and put objects in motion in three dimensions

  17. Droid X2 The Missing Manual

    CERN Document Server

    Gralla, Preston

    2011-01-01

    Droid X2 has more power and better graphics than its predecessor, but it still doesn't offer a printed guide to its amazing features. This Missing Manual helps you dig deep into everything Droid X2 can do. Learn how to shop, keep in touch, play with photos, listen to music, and even do some work. Unleash the power of this popular device with expert advice. The important stuff you need to know: Get organized. Sync Droid X2 with Google Calendar, Exchange, and Outlook.Go online. Navigate the Web, use email, and tap into Facebook and Twitter.Listen to tunes. Play and manage music using Droid X2'

  18. Creating a Website The Missing Manual

    CERN Document Server

    MacDonald, Matthew

    2011-01-01

    Think you need an army of skilled programmers to build a website? Think again. With nothing more than an ordinary PC, some raw ambition, and this book, you'll learn how to create and maintain a professional-looking, visitor-friendly site. This Missing Manual gives you all the tools, techniques, and expert advice you need. Plan your site. Create web pages by learning the basics of HTML and HTML5.Control page design with CSS. Format text, images, links, tables, and other elements.Attract visitors. Ensure that people can find your site through popular search engines.Build a community. Add forums

  19. Creating a web site the missing manual

    CERN Document Server

    MacDonald, Matthew

    2008-01-01

    Think you have to be a technical wizard to build a great web site? Think again. If you want to create an engaging web site, this thoroughly revised, completely updated edition of Creating a Web Site: The Missing Manual demystifies the process and provides tools, techniques, and expert guidance for developing a professional and reliable web presence. Whether you want to build a personal web site, an e-commerce site, a blog, or a web site for a specific occasion or promotion, this book gives you detailed instructions and clear-headed advice for: Everything from planning to launching. From pi

  20. Windows Vista for Starters The Missing Manual

    CERN Document Server

    Pogue, David

    2010-01-01

    Fast-paced and easy to use, this concise book teaches you the basics of Windows Vista so you can start using this operating system right away. Written by "New York Times" columnist, bestselling author, Emmy-winning CBS News correspondent and Missing Manuals creator David Pogue, the book will help you: Navigate the desktop, including the fast, powerful and fully integrated desktop search functionUse the Media Center to record TV and radio, present photos, play music, and record all of these to a DVDBreeze across the Web with the vastly improved Internet Explorer 7 tabbed browserBecome familiar

  1. 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:

  2. "Nudge" and the epidemic of missed appointments.

    Science.gov (United States)

    Aggarwal, Ajay; Davies, Joanna; Sullivan, Richard

    2016-06-20

    Purpose - Missed appointments constitute a significant problem in the UK National Health Service (NHS) and this remains an area where improvements could yield substantial efficiency savings. The purpose of this paper is to suggest that nudge policies based on behavioural theories may help target interventions to improve patient motivation to attend appointments. Design/methodology/approach - The authors propose two policies to reduce missed appointments. The first attempts to empower patients through making the appointment system more individualised to them and utilising their intrinsic feelings of social responsibility. The second policy utilises a financial commitment given by the patient at the time of booking. The different mechanisms of influencing patient behaviour are based on two different views of what motivates individuals' actions. The first policy is based on individuals being "knights". They are altruistic and have well-intentioned values. The second policy option is constructed on the premise that an individual is governed by self-interest, and they are in fact "knaves". Findings - A policy, which avoids the use of financial penalties is likely to be more culturally acceptable within the NHS. It could also prevent the phenomenon of "crowding out" whereby the desire to act dutifully gets displaced by the motivation to avoid incurring a monetary fine. Originality/value - Testing both strategies would provide insight into patient attitudes towards health care and society. This would help optimise behavioural strategies which may influence not only appointment attendances but also have wider implications for encouraging rational health care consumption.

  3. Missed lung cancer: when, where, and why?

    Science.gov (United States)

    del Ciello, Annemilia; Franchi, Paola; Contegiacomo, Andrea; Cicchetti, Giuseppe; Bonomo, Lorenzo; Larici, Anna Rita

    2017-01-01

    Missed lung cancer is a source of concern among radiologists and an important medicolegal challenge. In 90% of the cases, errors in diagnosis of lung cancer occur on chest radiographs. It may be challenging for radiologists to distinguish a lung lesion from bones, pulmonary vessels, mediastinal structures, and other complex anatomical structures on chest radiographs. Nevertheless, lung cancer can also be overlooked on computed tomography (CT) scans, regardless of the context, either if a clinical or radiologic suspect exists or for other reasons. Awareness of the possible causes of overlooking a pulmonary lesion can give radiologists a chance to reduce the occurrence of this eventuality. Various factors contribute to a misdiagnosis of lung cancer on chest radiographs and on CT, often very similar in nature to each other. Observer error is the most significant one and comprises scanning error, recognition error, decision-making error, and satisfaction of search. Tumor characteristics such as lesion size, conspicuity, and location are also crucial in this context. Even technical aspects can contribute to the probability of skipping lung cancer, including image quality and patient positioning and movement. Albeit it is hard to remove missed lung cancer completely, strategies to reduce observer error and methods to improve technique and automated detection may be valuable in reducing its likelihood. PMID:28206951

  4. Tidal Dwarf Galaxies and Missing Baryons

    Directory of Open Access Journals (Sweden)

    Frederic Bournaud

    2010-01-01

    Full Text Available Tidal dwarf galaxies form during the interaction, collision, or merger of massive spiral galaxies. They can resemble “normal” dwarf galaxies in terms of mass, size, and become dwarf satellites orbiting around their massive progenitor. They nevertheless keep some signatures from their origin, making them interesting targets for cosmological studies. In particular, they should be free from dark matter from a spheroidal halo. Flat rotation curves and high dynamical masses may then indicate the presence of an unseen component, and constrain the properties of the “missing baryons,” known to exist but not directly observed. The number of dwarf galaxies in the Universe is another cosmological problem for which it is important to ascertain if tidal dwarf galaxies formed frequently at high redshift, when the merger rate was high, and many of them survived until today. In this paper, “dark matter” is used to refer to the nonbaryonic matter, mostly located in large dark halos, that is, CDM in the standard paradigm, and “missing baryons” or “dark baryons” is used to refer to the baryons known to exist but hardly observed at redshift zero, and are a baryonic dark component that is additional to “dark matter”.

  5. Missing baryonic resonances in the Hagedorn spectrum

    Energy Technology Data Exchange (ETDEWEB)

    Man Lo, Pok [University of Wroclaw, Institute of Theoretical Physics, Wroclaw (Poland); GSI, Extreme Matter Institute EMMI, Darmstadt (Germany); Marczenko, Michal; Sasaki, Chihiro [University of Wroclaw, Institute of Theoretical Physics, Wroclaw (Poland); Redlich, Krzysztof [University of Wroclaw, Institute of Theoretical Physics, Wroclaw (Poland); GSI, Extreme Matter Institute EMMI, Darmstadt (Germany); Duke University, Department of Physics, Durham, NC (United States)

    2016-08-15

    The hadronic medium of QCD is modeled as a gas of point-like hadrons, with its composition determined by the Hagedorn mass spectrum. The spectrum consists of a discrete and a continuous part. The former is determined by the experimentally confirmed resonances tabulated by the Particle Data Group (PDG), while the latter can be extracted from the existing lattice data. This formulation of the hadron resonance gas (HRG) provides a transparent framework to relate the fluctuation of conserved charges as calculated in the lattice QCD approach to the particle content of the medium. A comparison of the two approaches shows that the equation of state is well described by the standard HRG model, which includes only a discrete spectrum of known hadrons. The corresponding description in the strange sector, however, shows clear discrepancies, thus a continuous spectrum is added to incorporate the effect of missing resonances. We propose a method to extract the strange-baryon spectrum from the lattice data. The result is consistent with the trend set by the unconfirmed strange baryons resonances listed by the PDG, suggesting that most of the missing interaction strength for the strange baryons reside in the S = 1 sector. This scenario is also supported by recent lattice calculations, and might be important in the energy region covered by the NICA accelerator in Dubna, where in the heavy-ion collisions, baryons are the dominating degrees of freedom in the final state. (orig.)

  6. Missed pills: frequency, reasons, consequences and solutions.

    Science.gov (United States)

    Chabbert-Buffet, Nathalie; Jamin, Christian; Lete, Iñaki; Lobo, Paloma; Nappi, Rossella E; Pintiaux, Axelle; Häusler, Günther; Fiala, Christian

    2017-06-01

    Oral hormonal contraception is an effective contraceptive method as long as regular daily intake is maintained. However, a daily routine is a constraint for many women and can lead to missed pills, pill discontinuation and/or unintended pregnancy. This article describes the frequency of inconsistent use, the consequences, the risk factors and the possible solutions. The article comprises a narrative review of the literature. Forgetting one to three pills per cycle is a frequent problem among 15-51% of users, generally adolescents. The reasons for this are age, inability to establish a routine, pill unavailability, side effects, loss of motivation and lack of involvement in the initial decision to use oral contraceptives. The consequences are 'escape ovulations' and, possibly, unintended pregnancy. Solutions are either to use a long-acting method or, for women who prefer to take oral contraceptives, use a continuous or long-cycle regimen to reduce the risks of follicular development and thus the likelihood of ovulation and unintended pregnancy. A progestogen with a long half-life can increase ovarian suppression. For women deciding to use oral contraceptives, a shortened or eliminated hormone-free interval and a progestogen with a long half-life may be an option to reduce the negative consequences of missed oral contraceptive pills.

  7. Investigator's Guide to Missing Child Cases. For Law-Enforcement Officers Locating Missing Children. Second Edition.

    Science.gov (United States)

    Patterson, John C.

    This booklet provides guidance to law enforcement officers investigating missing children cases, whether through parental kidnappings, abductions by strangers, runaway or "throwaway" cases, and those in which the circumstances are unknown. The guide describes, step-by-step, the investigative process required for each of the four types of missing…

  8. What's missing in missing data? Omissions in survey responses among parents of children with advanced cancer.

    Science.gov (United States)

    Rosenberg, Abby R; Dussel, Veronica; Orellana, Liliana; Kang, Tammy; Geyer, J Russel; Feudtner, Chris; Wolfe, Joanne

    2014-08-01

    Missing data is a common phenomenon with survey-based research; patterns of missing data may elucidate why participants decline to answer certain questions. To describe patterns of missing data in the Pediatric Quality of Life and Evaluation of Symptoms Technology (PediQUEST) study, and highlight challenges in asking sensitive research questions. Cross-sectional, survey-based study embedded within a randomized controlled trial. Three large children's hospitals: Dana-Farber/Boston Children's Cancer and Blood Disorders Center (DF/BCCDC); Children's Hospital of Philadelphia (CHOP); and Seattle Children's Hospital (SCH). At the time of their child's enrollment, parents completed the Survey about Caring for Children with Cancer (SCCC), including demographics, perceptions of prognosis, treatment goals, quality of life, and psychological distress. Eighty-six of 104 parents completed surveys (83% response). The proportion of missing data varied by question type. While 14 parents (16%) left demographic fields blank, over half (n=48; 56%) declined to answer at least one question about their child's prognosis, especially life expectancy. The presence of missing data was unrelated to the child's diagnosis, time from progression, time to death, or parent distress (p>0.3 for each). Written explanations in survey margins suggested that addressing a child's life expectancy is particularly challenging for parents. Parents of children with cancer commonly refrain from answering questions about their child's prognosis, however, they may be more likely to address general cure likelihood than explicit life expectancy. Understanding acceptability of sensitive questions in survey-based research will foster higher quality palliative care research.

  9. The History of Miss Jane Pittman

    Directory of Open Access Journals (Sweden)

    Christopher Mulvey

    2006-05-01

    Full Text Available This paper explores the ways in which Ernest J. Gaines uses fiction in The Autobiography of Miss Jane Pittman to write a history of the African American from 1861 to 1961. The “Introduction” sets the novel going, but its direction has already been given in the unusual dedication to his grandmother, stepfather and aunt “who did not walk a day in her life but who taught me the importance of standing” (Gaines iv. The significance for Gaines is that what happened a hundred years ago is part of his present-day lived life.The nineteenth-century novel was possessed by history, and white nineteenth-century novelists found their great subject in the war of European nations that was fought between 1799 and 1815. But that was not an American war nor was it an African American war. For Gaines, the war that makes the great turning point of a nation and a people is the American Civil War, fought from 1861 to 1865. It resulted in a moment of history after which life would not be the same. However, one of the main points that Gaines makes about that great turning point in history is that everything changed and nothing changed. And his main fictional device to establish that truth is to tell the history of the hundred years since Emancipation as the story of one woman. Her autobiography becomes an ethno-biography.The continuity forwards from 1861 is given through the life of one woman, but Gaines’s uses another device to provide a continuity backwards from 1861. The young man who wants to get Miss Jane Pittman’s story upsets her with his persistence: “What you want know about Miss Jane for?’ Mary said. ‘I teach history,’ I said. ‘I’m sure her life’s story can help me explain things to my students.’ ‘What’s wrong with them books you already got?’ Mary said. ‘Miss Jane is not in them,’ I said” (Gaines v. Ernest J. Gaines wrote at a time when historians finally began to recognize that they could get no true history of the

  10. Personal genomics services: whose genomes?

    Science.gov (United States)

    Gurwitz, David; Bregman-Eschet, Yael

    2009-07-01

    New companies offering personal whole-genome information services over the internet are dynamic and highly visible players in the personal genomics field. For fees currently ranging from US$399 to US$2500 and a vial of saliva, individuals can now purchase online access to their individual genetic information regarding susceptibility to a range of chronic diseases and phenotypic traits based on a genome-wide SNP scan. Most of the companies offering such services are based in the United States, but their clients may come from nearly anywhere in the world. Although the scientific validity, clinical utility and potential future implications of such services are being hotly debated, several ethical and regulatory questions related to direct-to-consumer (DTC) marketing strategies of genetic tests have not yet received sufficient attention. For example, how can we minimize the risk of unauthorized third parties from submitting other people's DNA for testing? Another pressing question concerns the ownership of (genotypic and phenotypic) information, as well as the unclear legal status of customers regarding their own personal information. Current legislation in the US and Europe falls short of providing clear answers to these questions. Until the regulation of personal genomics services catches up with the technology, we call upon commercial providers to self-regulate and coordinate their activities to minimize potential risks to individual privacy. We also point out some specific steps, along the trustee model, that providers of DTC personal genomics services as well as regulators and policy makers could consider for addressing some of the concerns raised below.

  11. Missing transverse energy performance of the CMS detector

    Energy Technology Data Exchange (ETDEWEB)

    Chatrchyan, Serguei [Yerevan Physics Inst. (Armenia); et al.

    2011-09-01

    During 2010 the LHC delivered pp collisions with a centre-of-mass energy of 7 TeV. In this paper, the results of comprehensive studies of missing transverse energy as measured by the CMS detector are presented. The results cover the measurements of the scale and resolution for missing transverse energy, and the effects of multiple pp interactions within the same bunch crossings on the scale and resolution. Anomalous measurements of missing transverse energy are studied, and algorithms for their identification are described. The performances of several reconstruction algorithms for calculating missing transverse energy are compared. An algorithm, called missing-transverse-energy significance, which estimates the compatibility of the reconstructed missing transverse energy with zero, is described, and its performance is demonstrated.

  12. Missing transverse energy performance of the CMS detector

    International Nuclear Information System (INIS)

    2011-01-01

    During 2010 the LHC delivered pp collisions with a centre-of-mass energy of 7 TeV. In this paper, the results of comprehensive studies of missing transverse energy as measured by the CMS detector are presented. The results cover the measurements of the scale and resolution for missing transverse energy, and the effects of multiple pp interactions within the same bunch crossings on the scale and resolution. Anomalous measurements of missing transverse energy are studied, and algorithms for their identification are described. The performance of several reconstruction algorithms for calculating missing transverse energy are compared. An algorithm, called missing-transverse-energy significance, which estimates the compatibility of the reconstructed missing transverse energy with zero, is described, and its performance is demonstrated.

  13. Reducing Competitive Cache Misses in Modern Processor Architectures

    OpenAIRE

    Prisagjanec, Milcho; Mitrevski, Pece

    2017-01-01

    The increasing number of threads inside the cores of a multicore processor, and competitive access to the shared cache memory, become the main reasons for an increased number of competitive cache misses and performance decline. Inevitably, the development of modern processor architectures leads to an increased number of cache misses. In this paper, we make an attempt to implement a technique for decreasing the number of competitive cache misses in the first level of cache memory. This tec...

  14. Impact of teamwork on missed care in four Australian hospitals.

    Science.gov (United States)

    Chapman, Rose; Rahman, Asheq; Courtney, Mary; Chalmers, Cheyne

    2017-01-01

    Investigate effects of teamwork on missed nursing care across a healthcare network in Australia. Missed care is universally used as an indicator of quality nursing care, however, little is known about mitigating effects of teamwork on these events. A descriptive exploratory study. Missed Care and Team Work surveys were completed by 334 nurses. Using Stata software, nursing staff demographic information and components of missed care and teamwork were compared across the healthcare network. Statistical tests were performed to identify predicting factors for missed care. The most commonly reported components of missed care were as follows: ambulation three times per day (43·3%), turning patient every two hours (29%) and mouth care (27·7%). The commonest reasons mentioned for missed care were as follows: inadequate labour resources (range 69·8-52·7%), followed by material resources (range 59·3-33·3%) and communication (range 39·3-27·2%). There were significant differences in missed care scores across units. Using the mean scores in regression correlation matrix, the negative relationship of missed care and teamwork was supported (r = -0·34, p teamwork alone accounted for about 9% of missed nursing care. Similar to previous international research findings, our results showed nursing teamwork significantly impacted on missed nursing care. Teamwork may be a mitigating factor to address missed care and future research is needed. These results may provide administrators, educators and clinicians with information to develop practices and policies to improve patient care internationally. © 2016 John Wiley & Sons Ltd.

  15. Visualization for genomics: the Microbial Genome Viewer.

    NARCIS (Netherlands)

    Kerkhoven, R.; Enckevort, F.H.J. van; Boekhorst, J.; Molenaar, D; Siezen, R.J.

    2004-01-01

    SUMMARY: A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a

  16. iPod The Missing Manual

    CERN Document Server

    Biersdorfer, J D

    2010-01-01

    With iPod and iTunes, Apple's gotten the world hooked on portable music, pictures, and videos. One thing they haven't delivered, though, is an easy guide for getting the most from your sleek little entertainment center. Enter iPod: The Missing Manual, 5th Edition-a book as breathtaking and satisfying as its subject. Our latest edition thoroughly covers the redesigned iPod Nanos, the video iPod, the tiny Shuffle and the overhauled iTunes 7. Each custom-designed page sports easy-to-follow color graphics, crystal-clear explanations, and guidance on the most useful things your iPod can do. Topic

  17. Bladder injuries frequently missed in polytrauma patients

    Directory of Open Access Journals (Sweden)

    Tanweer Karim

    2010-05-01

    Full Text Available Tanweer Karim, Margaret Topno, Vinod Sharma, Raymond Picardo, Ankur HastirSurgery, MGM Medical College, Kamothe, Navi Mumbai, IndiaAbstract: Bladder injuries are very common in patients who have had road traffic accidents. The method of diagnosis and management of such injuries is well established and accepted. However, trauma to the bladder can be associated with other life-threatening injuries which are frequently missed, and often diagnosed during laparotomy for other reasons. The aim of this study was to diagnose bladder injury in polytrauma patients as early as possible, taking into consideration the fact that these patients are hemodynamically unstable and require rapid evaluation and management. In order to achieve our objective, we used bedside sonography with retrograde instillation of normal saline to diagnose bladder injury in addition to use of the conventional retrograde cystogram.Keywords: bladder injury, bladder rupture, retrograde cystogram

  18. iPad The Missing Manual

    CERN Document Server

    Biersdorfer, J

    2010-01-01

    The iPad 2 is faster, lighter, and more versatile than its predecessor, but there's still no printed guide to using its amazing features. That's where this full-color Missing Manual comes in. Learn how to stream HD video, make video calls, manage your email, surf the Web, listen to music, play games, and maybe even do a little iWork. This is the book that should have been in the box. Build your media library. Fill your iPad with music, movies, TV shows, eBooks, photos, and more.Share with others. Stream music, HD movies, TV shows, and more, to and from your iPad.Create your own media. Use the

  19. iPad 2 The Missing Manual

    CERN Document Server

    Biersdorfer, JD

    2011-01-01

    With iOS 5, Apple added more than 200 new features to the iPad 2, but there's still no printed guide to using all its amazing capabilities. That's where this full-color Missing Manual comes in. You'll learn how to stuff your iPad with media, organize your personal life, wirelessly stream content to and from your tablet, stay connected to friends, and much more. The important stuff you need to know: Build your media library. Fill your iPad with music, movies, TV shows, eBooks, eMagazines, photos, and more.Go wireless. Sync content between your computer and iPad-no wires needed.Get online. Con

  20. Missing IUD Despite Threads at the Cervix

    Directory of Open Access Journals (Sweden)

    Andrew L. Atkinson

    2014-01-01

    Full Text Available Today, the intrauterine device (IUD is by far the most popular form of long term reversible contraception in the world. Side effects from the IUD are minimal and complications are rare. Uterine perforation and migration of the IUD outside the uterine cavity are the most serious complications. Physician visualization and/or the patient feeling retrieval threads at the cervical os are confirmation that the IUD has not been expelled or migrated. We present a case of a perforated, intraperitoneal IUD with threads noted at the cervical os. Office removal was not possible using gentle traction on the threads. Multiple imaging and endoscopic modalities were used to try and locate the IUD including pelvic ultrasound, diagnostic hysteroscopy, cystoscopy, and pelvic magnetic resonance imaging (MRI. The studies gave conflicting results on location of the IUD. Ultimately, the missing IUD was removed via laparoscopy.

  1. iPod The Missing Manual

    CERN Document Server

    Biersdorfer, J D

    2011-01-01

    Apple's iPod still has the world hooked on portable music, pictures, videos, movies, and more, but one thing it doesn't have is a manual that helps you can get the most out this amazing device. That's where this book comes in. Get the complete scoop on the latest line of iPods and the latest version of iTunes with the guide that outshines them all-iPod: The Missing Manual. The 10th edition is as useful, satisfying, and reliable as its subject. Teeming with high-quality color graphics, each page helps you accomplish a specific task-everything from managing your media and installing and browsi

  2. The missing mass of the universe

    International Nuclear Information System (INIS)

    Lachieze-Rey, M.

    2002-01-01

    The existence of dark matter is suggested by 2 facts: 1) the real mass of matter inside galaxies must be 10 times greater than the observed mass to explain the values of the spinning velocity of galaxies around their centers. Furthermore the value of this velocity does not depend a lot on the distance to the center of the galaxy, this implies that the missing mass is uniformly distributed inside galaxies; 2) According to general relativity, massive celestial bodies produce a curvature of space-time that generates a deviation of light beams. These deviations have been studied and it appears that they require the presence of a far more important quantity of matter than the quantity reduced to visible matter. The missing mass issue arises 3 problems, the first problem comes from the existence of a great part of ordinary (baryonic) matter that is invisible: the global mass of stars represents only 10 % of the total baryonic mass of the universe. This invisible ordinary matter might exist in condensed form in black-hole, giant planets or brown dwarfs roaming the galaxies. The second problem arose when most scientists were convinced of the existence of huge quantity of non-baryonic matter, 10 times more abundant than the baryonic matter. The supersymmetric extension of the standard model allows the existence of particles that might be candidate for carrying this non-baryonic mass. The third problem appeared recently when measurement of the curvature of the space-time has shown that the 3 forms of matter: visible matter, invisible ordinary matter and non-baryonic matter contribute together to only one third of the total energy of the universe. (A.C.)

  3. Missed Opportunities For Immunization In Children And Pregnant Women

    Directory of Open Access Journals (Sweden)

    Benjamin A I

    1990-01-01

    Full Text Available The role of immunization in reducing childhood mortality cannot be over-emphasised, yet many opportunities for immunization are missed when children and pregnant women visit a health facility. Reducing missed opportunities is the cheapest way to increase immunization coverage. The present study discusses the extent of the problem of missed opportunities for immunization in children and pregnant women and the factors contributing to the problem, in spatiality and community outreach clinics of Christian Medical College & Hospital, Ludhiana. Recommendations are made regarding ways and means of reducing missed opportunities.

  4. Social perspective: the missing element in mental health practice

    National Research Council Canada - National Science Library

    U'Ren, Richard C

    2011-01-01

    .... ________________________________________________________________ Library and Archives Canada Cataloguing in Publication U'Ren, Richard, 1939- Social perspective : the missing element in mental health practice / Richard U'Ren...

  5. Mind the gap; seven reasons to close fragmented genome assemblies.

    Science.gov (United States)

    Thomma, Bart P H J; Seidl, Michael F; Shi-Kunne, Xiaoqian; Cook, David E; Bolton, Melvin D; van Kan, Jan A L; Faino, Luigi

    2016-05-01

    Like other domains of life, research into the biology of filamentous microbes has greatly benefited from the advent of whole-genome sequencing. Next-generation sequencing (NGS) technologies have revolutionized sequencing, making genomic sciences accessible to many academic laboratories including those that study non-model organisms. Thus, hundreds of fungal genomes have been sequenced and are publically available today, although these initiatives have typically yielded considerably fragmented genome assemblies that often lack large contiguous genomic regions. Many important genomic features are contained in intergenic DNA that is often missing in current genome assemblies, and recent studies underscore the significance of non-coding regions and repetitive elements for the life style, adaptability and evolution of many organisms. The study of particular types of genetic elements, such as telomeres, centromeres, repetitive elements, effectors, and clusters of co-regulated genes, but also of phenomena such as structural rearrangements, genome compartmentalization and epigenetics, greatly benefits from having a contiguous and high-quality, preferably even complete and gapless, genome assembly. Here we discuss a number of important reasons to produce gapless, finished, genome assemblies to help answer important biological questions. Copyright © 2015 Elsevier Inc. All rights reserved.

  6. [Missed lessons, missed opportunities: a role for public health services in medical absenteeism in young people].

    Science.gov (United States)

    Vanneste, Y T M; van de Goor, L A M; Feron, F J M

    2016-01-01

    Young people who often miss school for health reasons are not only missing education, but also the daily routine of school, and social intercourse with their classmates. Medical absenteeism among students merits greater attention. For a number of years, in various regions in the Netherlands, students with extensive medical absenteeism have been invited to see a youth healthcare specialist. The MASS intervention (Medical Advice of Students reported Sick; in Dutch: Medische Advisering van de Ziekgemelde Leerling, abbreviated as M@ZL) has been developed by the West Brabant Regional Public Health Service together with secondary schools to address school absenteeism due to reporting sick. In this paper we discuss the MASS intervention and explain why attention should be paid by public health services to the problem of school absenteeism, especially absenteeism on health grounds.

  7. STUDY ON MATERNAL MORTALITY AND NEAR MISS CASE

    Directory of Open Access Journals (Sweden)

    Ritanjali Behera

    2017-12-01

    Full Text Available BACKGROUND Maternal mortality traditionally has been the indicator of maternal health. More recently the review of cases of near miss obstetric event is found to be useful to investigate maternal mortality. Cases of near miss are those, where a woman nearly died but survived a complication that occur during pregnancy or child birth. Aim and Objective 1. To analyse near miss cases and maternal deaths. 2. To determine maternal near miss indicator and to analyse the cause and contributing factors for both of them. MATERIALS AND METHODS This prospective observational study conducted in M.K.C.G. medical college, Berhampur from 1st October 2015 to 30th September 2017. All the cases of maternal deaths and near miss cases defined by WHO criteria are taken. Information regarding demographic profile and reproductive parameters are collected and results are analysed using percentage and proportion. RESULTS Out of 17977 deliveries 201 were near miss cases and 116 were maternal deaths. MMR was 681, near miss incidence 1.18, maternal death to near miss ratio was 1:1.73. Hypertensive disorder of pregnancy (37.4% was the leading cause followed by haemorrhage (17.4%. For near miss cases 101 cases fulfilled clinical criteria, 61 laboratory criteria and 131 cases management based criteria. CONCLUSION Hypertensive disorder of pregnancy and haemorrhage are the leading cause of maternal death and for near miss cases most common organ system involved was cardiovascular system. All the near miss cases should be interpreted as opportunities to improve the health care services.

  8. Handling missing values in the MDS-UPDRS.

    Science.gov (United States)

    Goetz, Christopher G; Luo, Sheng; Wang, Lu; Tilley, Barbara C; LaPelle, Nancy R; Stebbins, Glenn T

    2015-10-01

    This study was undertaken to define the number of missing values permissible to render valid total scores for each Movement Disorder Society Unified Parkinson's Disease Rating Scale (MDS-UPDRS) part. To handle missing values, imputation strategies serve as guidelines to reject an incomplete rating or create a surrogate score. We tested a rigorous, scale-specific, data-based approach to handling missing values for the MDS-UPDRS. From two large MDS-UPDRS datasets, we sequentially deleted item scores, either consistently (same items) or randomly (different items) across all subjects. Lin's Concordance Correlation Coefficient (CCC) compared scores calculated without missing values with prorated scores based on sequentially increasing missing values. The maximal number of missing values retaining a CCC greater than 0.95 determined the threshold for rendering a valid prorated score. A second confirmatory sample was selected from the MDS-UPDRS international translation program. To provide valid part scores applicable across all Hoehn and Yahr (H&Y) stages when the same items are consistently missing, one missing item from Part I, one from Part II, three from Part III, but none from Part IV can be allowed. To provide valid part scores applicable across all H&Y stages when random item entries are missing, one missing item from Part I, two from Part II, seven from Part III, but none from Part IV can be allowed. All cutoff values were confirmed in the validation sample. These analyses are useful for constructing valid surrogate part scores for MDS-UPDRS when missing items fall within the identified threshold and give scientific justification for rejecting partially completed ratings that fall below the threshold. © 2015 International Parkinson and Movement Disorder Society.

  9. An interference account of the missing-VP effect

    Directory of Open Access Journals (Sweden)

    Markus eBader

    2015-06-01

    Full Text Available Sentences with doubly center-embedded relative clauses in which a verb phrase (VP is missing are sometimes perceived as grammatical, thus giving rise to an illusion of grammaticality. In this paper, we provide a new account of why missing-VP sentences, which are both complex and ungrammatical, lead to an illusion of grammaticality, the so-called missing-VP effect. We propose that the missing-VP effect in particular, and processing difficulties with multiply center-embedded clauses more generally, are best understood as resulting from interference during cue-based retrieval. When processing a sentence with double center-embedding, a retrieval error due to interference can cause the verb of an embedded clause to be erroneously attached into a higher clause. This can lead to an illusion of grammaticality in the case of missing-VP sentences and to processing complexity in the case of complete sentences with double center-embedding. Evidence for an interference account of the missing-VP effect comes from experiments that have investigated the missing-VP effect in German using a speeded grammaticality judgments procedure. We review this evidence and then present two new experiments that show that the missing VP effect can be found in German also with less restricting procedures. One experiment was a questionnaire study which required grammaticality judgments from participants but without imposing any time constraints. The second experiment used a self-paced reading procedure and did not require any judgments. Both experiments confirm the prior findings of missing-VP effects in German and also show that the missing-VP effect is subject to a primacy effect as known from the memory literature. Based on this evidence, we argue that an account of missing-VP effects in terms of interference during cue-based retrieval is superior to accounts in terms of limited memory resources or in terms of experience with embedded structures.

  10. Ancient genomics

    DEFF Research Database (Denmark)

    Der Sarkissian, Clio; Allentoft, Morten Erik; Avila Arcos, Maria del Carmen

    2015-01-01

    throughput of next generation sequencing platforms and the ability to target short and degraded DNA molecules. Many ancient specimens previously unsuitable for DNA analyses because of extensive degradation can now successfully be used as source materials. Additionally, the analytical power obtained...... by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans...

  11. Marine genomics

    DEFF Research Database (Denmark)

    Oliveira Ribeiro, Ângela Maria; Foote, Andrew David; Kupczok, Anne

    2017-01-01

    Marine ecosystems occupy 71% of the surface of our planet, yet we know little about their diversity. Although the inventory of species is continually increasing, as registered by the Census of Marine Life program, only about 10% of the estimated two million marine species are known. This lag......-throughput sequencing approaches have been helping to improve our knowledge of marine biodiversity, from the rich microbial biota that forms the base of the tree of life to a wealth of plant and animal species. In this review, we present an overview of the applications of genomics to the study of marine life, from...

  12. The Hunt for Missing Dwarf Galaxies

    Science.gov (United States)

    Kohler, Susanna

    2015-11-01

    Theories of galaxy formation and evolution predict that there should be significantly more dwarf galaxies than have been observed. Are our theories wrong? Or are dwarf galaxies just difficult to detect? Recent results from a survey of a galaxy cluster 62 million light-years away suggest there may be lots of undiscovered dwarf galaxies hiding throughout the universe!Hiding in FaintnessThe missing dwarf problem has had hints of a resolution with the recent discovery of Ultra-Diffuse Galaxies (UDGs) in the Coma and Virgo galaxy clusters. UDGs have low masses and large radii, resulting in a very low surface brightness that makes them extremely difficult to detect. If many dwarfs are UDGs, this could well explain why weve been missing them!But the Coma and Virgo galaxy clusters are similar in that theyre both very massive. Are there UDGs in other galaxy clusters as well? To answer this question, an international team of scientists is running the Next Generation Fornax Survey (NGFS), a survey searching for faint dwarf galaxies in the central 30 square degrees of the Fornax galaxy cluster.The NGFS uses near-UV and optical observations from the Dark Energy Camera mounted on the 4m Blanco Telescope in Chile. The survey is still underway, but in a recent publication led by Roberto P. Muoz (Institute of Astrophysics at the Pontifical Catholic University of Chile), the team has released an overview of the first results from only the central 3 square degrees of the NGFS field.Surprising DetectionGalaxy radii vs. their absolute i-band magnitudes, for the dwarfs found in NGFS as well as other stellar systems in the nearby universe. The NGFS dwarfs are similar to the ultra-diffuse dwarfs found in the Virgo and Coma clusters, but are several orders of magnitude fainter. [Muoz et al. 2015]In just this small central field, the team has found an astounding 284 low-surface-brightness dwarf galaxy candidates 158 of them previously undetected. At the bright end of this sample are dwarf

  13. 9 CFR 2.128 - Inspection for missing animals.

    Science.gov (United States)

    2010-01-01

    ... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Inspection for missing animals. 2.128 Section 2.128 Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE ANIMAL WELFARE REGULATIONS Miscellaneous § 2.128 Inspection for missing animals. Each dealer...

  14. Why Patients Miss Follow-Up Appointments: A Prospective Control ...

    African Journals Online (AJOL)

    Reasons include: transport (19 responses), ill-health (6) and financial constraints (5). State transport was unavailable to almost twothirds of the responders who cited transport as a problem. Conclusions: The 17% missed appointment rate is largely due to transport constraints. The commonest time for patients to miss ...

  15. 577 Missed opportunities for inununisation in Natal health facilities

    African Journals Online (AJOL)

    Wkly Epidemwl Rec 1984; 59: 117-119. 5. Expanded Programme on Immunization. Missed immunizacion opportunities and acceptability of immunization. Wkly Epidemiol Rec. 1989;64: 181-184. . . 6. Loevinsohn BP. Missed opportunities for immunization during visits for curative care: practical reasons for their occurrence.

  16. 40 CFR 75.37 - Missing data procedures for moisture.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 16 2010-07-01 2010-07-01 false Missing data procedures for moisture... data procedures for moisture. (a) The owner or operator of a unit with a continuous moisture monitoring system shall substitute for missing moisture data using the procedures of this section. (b) Where no...

  17. 40 CFR 98.405 - Procedures for estimating missing data.

    Science.gov (United States)

    2010-07-01

    ... meter malfunctions), a substitute data value for the missing quantity measurement must be used in the... period for any reason, the reporter shall use either its delivering pipeline measurements or the default... § 98.405 Procedures for estimating missing data. (a) Whenever a quality-assured value of the quantity...

  18. Incidence and Correlates of Maternal Near Miss in Southeast Iran

    Directory of Open Access Journals (Sweden)

    Tayebeh Naderi

    2015-01-01

    Full Text Available This prospective study aimed to estimate the incidence and associated factors of severe maternal morbidity in southeast Iran. During a 9-month period in 2013, all women referring to eight hospitals for termination of pregnancy as well as women admitted during 42 days after the termination of pregnancy were enrolled into the study. Maternal near miss conditions were defined based on Say et al.’s recommendations. Five hundred and one cases of maternal near miss and 19,908 live births occurred in the study period, yielding a maternal near miss ratio of 25.2 per 1000 live births. This rate was 7.5 and 105 per 1000 in private and tertiary care settings, respectively. The rate of maternal death in near miss cases was 0.40% with a case:fatality ratio of 250 : 1. The most prevalent causes of near miss were severe preeclampsia (27.3%, ectopic pregnancy (18.4%, and abruptio placentae (16.2%. Higher age, higher education, and being primiparous were associated with a higher risk of near miss. Considering the high rate of maternal near miss in referral hospitals, maternal near miss surveillance system should be set up in these hospitals to identify cases of severe maternal morbidity as soon as possible.

  19. 78 FR 37598 - Missing Participants in Individual Account Plans

    Science.gov (United States)

    2013-06-21

    ... information from the public to assist it in making decisions about implementing a new program to deal with... allocated to such participant's account.'' Before making decisions about implementing a missing participants... PENSION BENEFIT GUARANTY CORPORATION Missing Participants in Individual Account Plans AGENCY...

  20. Handling of incidents, near-misses

    International Nuclear Information System (INIS)

    Renborg, Bo; Jonsson, Klas; Broqvist, Kristoffer; Keski-Seppaelae, Sven

    2006-12-01

    This work has primarily been done as a study of available literature about reporting systems. The following items have also been considered: the participants' experience of safety work in general and reporting systems in particular, as well as correspondence with researchers and organisations that have experience from reporting systems in safety-critical applications. A number of definitions of the English term 'near-miss' have been found in the documentation about safety-critical systems. An important conclusion is that creating a precise definition in itself is not critical. The main objective is to persuade the individuals to report perceived risks as well as actual events or conditions. In this report, we have chosen to use the following definition of what should be reported: A condition or an incident with potential for more serious consequences. The reporting systems that have been evaluated have all data in the same system; they do not divide data into separate systems for incidents or 'near-misses'. The term incident in the literature is not used consistently, especially if both Swedish and English texts are considered. In a large portion of the documentation where the reporting system is mentioned, the focus lies more on analysis than on the problem with the willingness to report. Even when the focus is on reporting it is often dealing with the design of the actual report in order to enable the subsequent treatment of data. In some cases this has led to unnecessary complicated report forms. The cornerstone of a high willingness to report is the creation of a 'no-blame' culture. Based on experience it can be concluded that the question whether a report could lead to personal reprisals is crucial. Even a system that explicitly gives the reporter immunity is still brittle. The bare suspicion (that immunity may vanish) in the mind of the one reporting reduces the willingness to report dramatically. Meaning that the purpose of the analysis of reports must be to

  1. Missed opportunities for HPV immunization among young adult women

    Science.gov (United States)

    Oliveira, Carlos R.; Rock, Robert M.; Shapiro, Eugene D.; Xu, Xiao; Lundsberg, Lisbet; Zhang, Liye B.; Gariepy, Aileen; Illuzzi, Jessica L.; Sheth, Sangini S.

    2018-01-01

    BACKGROUND Despite the availability of a safe and efficacious vaccine against human papillomavirus, uptake of the vaccine in the United States is low. Missed clinical opportunities to recommend and to administer human papillomavirus vaccine are considered one of the most important reasons for its low uptake in adolescents; however, little is known about the frequency or characteristics of missed opportunities in the young adult (18–26 years of age) population. OBJECTIVE The objective of the study was to assess both the rates of and the factors associated with missed opportunities for human papillomavirus immunization among young adult women who attended an urban obstetrics and gynecology clinic. STUDY DESIGN In this cross-sectional study, medical records were reviewed for all women 18–26 years of age who were underimmunized (<3 doses) and who sought care from Feb. 1, 2013, to January 31, 2014, at an urban, hospital-based obstetrics and gynecology clinic. A missed opportunity for human papillomavirus immunization was defined as a clinic visit at which the patient was eligible to receive the vaccine and a dose was due but not administered. Multivariable logistic regression was used to test associations between sociodemographic variables and missed opportunities. RESULTS There were 1670 vaccine-eligible visits by 1241 underimmunized women, with a mean of 1.3 missed opportunities/person. During the study period, 833 of the vaccine eligible women (67.1%) had at least 1 missed opportunity. Overall, the most common types of visits during which a missed opportunity occurred were postpartum visits (17%) or visits for either sexually transmitted disease screening (21%) or contraception (33%). Of the patients with a missed opportunity, 26.5% had a visit at which an injectable medication or a different vaccine was administered. Women who identified their race as black had higher adjusted odds of having a missed opportunity compared with white women (adjusted odds ratio, 1

  2. Missing transverse momentum in ATLAS: current and future performance

    CERN Document Server

    Schramm, S; The ATLAS collaboration

    2014-01-01

    During the Run-I data taking period, ATLAS has developed and refined several approaches for measuring missing transverse momentum in proton-proton collisions. Standard calorimeter-based $\\mathrm{E}_\\mathrm{T}^\\mathrm{miss}$ reconstruction techniques have been improved to obtain new levels of precision, while new track-based $\\mathrm{p}_\\mathrm{T}^\\mathrm{miss}$ methods provide for a way to have a second independent measurement of the momentum lost due to particles which do not leave tracks in the inner detectors. While both procedures are individually useful, preliminary studies have shown that combining information from both techniques leads to an improved understanding of missing transverse momentum. Data taking conditions during Run-I varied extensively, especially with respect to the amount of pileup activity present in each event, which provides unique challenges to calorimeter-based $\\mathrm{E}_\\mathrm{T}^\\mathrm{miss}$. Multiple solutions have been demonstrated, including methods which exploit both cal...

  3. MISSE in the Materials and Processes Technical Information System (MAPTIS )

    Science.gov (United States)

    Burns, DeWitt; Finckenor, Miria; Henrie, Ben

    2013-01-01

    Materials International Space Station Experiment (MISSE) data is now being collected and distributed through the Materials and Processes Technical Information System (MAPTIS) at Marshall Space Flight Center in Huntsville, Alabama. MISSE data has been instrumental in many programs and continues to be an important source of data for the space community. To facilitate great access to the MISSE data the International Space Station (ISS) program office and MAPTIS are working to gather this data into a central location. The MISSE database contains information about materials, samples, and flights along with pictures, pdfs, excel files, word documents, and other files types. Major capabilities of the system are: access control, browsing, searching, reports, and record comparison. The search capabilities will search within any searchable files so even if the desired meta-data has not been associated data can still be retrieved. Other functionality will continue to be added to the MISSE database as the Athena Platform is expanded

  4. Maternal Near-Miss: A Multicenter Surveillance in Kathmandu Valley

    Directory of Open Access Journals (Sweden)

    Ashma Rana

    2013-06-01

    Full Text Available Introduction: Multicenter surveillance has been carried out on maternal near-miss in the hospitals with sentinel units. Near-miss is recognized as the predictor of level of care and maternal death. Reducing maternal mortality ratio is one of the challenges to achieve Millennium Development Goal. Objective was to determine the frequency and the nature of near-miss (severe acute maternal morbidity events and analysis of near-miss morbidities among pregnant women. Methods: Prospective surveillance was done for a year in 2012 in nine hospitals in Kathmandu valley. Cases eligible by definition recorded as a census based on WHO near-miss guideline. Similar questionnaire and dummy tables were used to present the result by non-inferential statistics. Results: Out of 157 cases identified with near-miss rate of 3.8, severe complications were PPH (40% and preeclampsia-eclampsia (17%. Blood transfusion (65%, ICU admission (54% and surgery (32% were the common critical intervention. Oxytocin was the main uterotonic used both prophylactically (86% and therapeutically (76%, and 19% arrived health facility after delivery or abortion. MgSO4 was used in all cases of eclampsia. All of the laparotomies were performed within 3 hours of arrival. Near-miss to mortality ratio was 6:1 and MMR 62. Conclusions: Study result yields similar pattern amongst developing countries and same near-miss conditions as the causes of maternal death reported by national statistics. Process indicators qualify the recommended standard of care. The near-miss event can be used as a surrogate marker of maternal death and a window for system level intervention. Keywords: abortion, eclampsia, hemorrhage, near-miss, surveillance

  5. The Mystery of the Missing Antimatter

    CERN Document Server

    Quinn, Helen R

    2008-01-01

    In the first fractions of a second after the Big Bang lingers a question at the heart of our very existence: why does the universe contain matter but almost no antimatter? The laws of physics tell us that equal amounts of matter and antimatter were produced in the early universe--but then, something odd happened. Matter won out over antimatter; had it not, the universe today would be dark and barren. But how and when did this occur? Helen Quinn and Yossi Nir guide readers into the very heart of this mystery--and along the way offer an exhilarating grand tour of cutting-edge physics. They explain both the history of antimatter and recent advances in particle physics and cosmology. And they discuss the enormous, high-precision experiments that particle physicists are undertaking to test the laws of physics at their most fundamental levels--and how their results reveal tantalizing new possibilities for solving this puzzle at the heart of the cosmos. The Mystery of the Missing Antimatter is at once a history of i...

  6. Why is microcalcification missed on mammography?

    International Nuclear Information System (INIS)

    Peters, Gudrun; Jones, Catherine M.; Daniels, Katie

    2013-01-01

    Ductal carcinoma in situ (DCIS) is often only mammographically evident as microcalcification. Although the overall percentage of screening cases with histologically proven DCIS microcalcification is small, the clinical relevance of missing this finding is significant. The current guidelines in Australia for breast screening departments are for double reading of mammograms to reduce both perceptive and interpretative error. This retrospective study identified patients from a state screening program with histologically proven DCIS whose mammograms showed microcalcification. The initial double reader results were documented according to the 5-point grading scale of BreastScreen Tasmania, and discrepancies between readers were noted. Mammographic factors such as breast density, lesion location, morphology, distribution, size and presence on previous imaging were assessed for significant influence on inter-reader discrepancy. Histological evidence of invasion and grade of malignancy were also analysed. Of 65 identified cases, 29 (45%) showed that one of the two readers had not flagged the microcalcification on the report. Analyses revealed no significant difference in reader discrepancy with any of the analysed factors including breast density, size of microcalcification or presence on previous imaging. Twenty-five of 29 (86%) cases of discrepancy were perceptive. Breast screening reading for microcalcification is poorly correlated to mammographic or histological features. The majority of errors were perceptive rather than interpretative. Double reading is advocated as standard practice to reduce perceptive error.

  7. Search for missing baryons through scintillation

    International Nuclear Information System (INIS)

    Habibi, F.

    2011-06-01

    Cool molecular hydrogen H 2 may be the ultimate possible constituent to the Milky-Way missing baryon. We describe a new way to search for such transparent matter in the Galactic disc and halo, through the diffractive and refractive effects on the light of background stars. By simulating the phase delay induced by a turbulent medium, we computed the corresponding illumination pattern on the earth for an extended source and a given passband. We show that in favorable cases, the light of a background star can be subjected to stochastic fluctuations of the order of a few percent at a characteristic time scale of a few minutes. We have searched for scintillation induced by molecular gas in visible dark nebulae as well as by hypothetical halo clumpuscules of cool molecular hydrogen (H 2 -He) during two nights, using the NTT telescope and the IR SOFI detector. Amongst a few thousands of monitored stars, we found one light-curve that is compatible with a strong scintillation effect through a turbulent structure in the B68 nebula. Because no candidate were found toward the SMC (Small Magellan Cloud), we are able to establish upper limits on the contribution of gas clumpuscules to the Galactic halo mass. We show that the short time-scale monitoring of a few 10 6 star*hour in the visible band with a >4 m telescope and a fast readout camera should allow one to interestingly quantify or constrain the contribution of turbulent molecular gas to the Galactic halo. (author)

  8. Paediatrics and psychoanalysis--Miss Anna Freud.

    Science.gov (United States)

    1983-01-01

    Miss Anna Freud died during the winter at the age of 86. She had been a pioneer in the understanding of children through psychoanalysis and a great champion of the rights of children. Her life began in Vienna as the youngest child of Sigmund Freud, and her early work with children was in Austria. In 1938, because of the Nazi régime and even though she was nursing her father during his terminal illness, she had to escape with him to London. Her work with homeless children and with those in residential nurseries in London during the second world war is well known, as is her work on child development and psychopathology in the postwar years. But one less well known aspect of her life that was of immense importance to a few fortunate British paediatricians was the 'paediatric group' that she ran for over a quarter of a century and which Dr Christine Cooper recalled at the memorial meeting in London earlier this year. PMID:6344806

  9. Reduction of artefacts due to missing projections using OSEM

    International Nuclear Information System (INIS)

    Hutton, B.F.; Kyme, A.; Choong, K.

    2002-01-01

    Full text: It is well recognised that missing or corrupted projections can result in artefacts. This occasionally occurs due to errors in data transfer from acquisition memory to disk. A possible approach for reducing these artefacts was investigated, Using ordered subsets expectation maximization (OSEM) the iterative reconstruction proceeds by progressively including additional projections until a single iteration is complete. Clinically useful results can be obtained using a small subset size in a single iteration. Stopping prior to the complete iteration so as to avoid inclusion of missing or corrupted data should provide a 'partial' reconstruction with minimal artefacts. To test this hypothesis projections were selectively removed from a complete data set (2, 4, 8, 12 adjacent projections) and reconstructions were performed using both filtered back projection (FBP) and OSEM. To maintain a constant number of sub-iterations in OSEM an equal number of duplicate projections were substituted for the missing projections. Both 180 and 360 degrees reconstructions with missing data were compared with reconstruction for the complete data using sum of absolute differences. Results indicate that missing data causes artefacts for both FBP and OSEM however the severity of artefacts is significantly reduced using OSEM. The effect of missing data is generally greater for 180 degrees acquisition. OSEM is recommended for minimising reconstruction artefacts due to missing projections. Copyright (2002) The Australian and New Zealand Society of Nuclear Medicine Inc

  10. Recurrent Neural Networks for Multivariate Time Series with Missing Values.

    Science.gov (United States)

    Che, Zhengping; Purushotham, Sanjay; Cho, Kyunghyun; Sontag, David; Liu, Yan

    2018-04-17

    Multivariate time series data in practical applications, such as health care, geoscience, and biology, are characterized by a variety of missing values. In time series prediction and other related tasks, it has been noted that missing values and their missing patterns are often correlated with the target labels, a.k.a., informative missingness. There is very limited work on exploiting the missing patterns for effective imputation and improving prediction performance. In this paper, we develop novel deep learning models, namely GRU-D, as one of the early attempts. GRU-D is based on Gated Recurrent Unit (GRU), a state-of-the-art recurrent neural network. It takes two representations of missing patterns, i.e., masking and time interval, and effectively incorporates them into a deep model architecture so that it not only captures the long-term temporal dependencies in time series, but also utilizes the missing patterns to achieve better prediction results. Experiments of time series classification tasks on real-world clinical datasets (MIMIC-III, PhysioNet) and synthetic datasets demonstrate that our models achieve state-of-the-art performance and provide useful insights for better understanding and utilization of missing values in time series analysis.

  11. Ensembl Genomes 2016: more genomes, more complexity.

    Science.gov (United States)

    Kersey, Paul Julian; Allen, James E; Armean, Irina; Boddu, Sanjay; Bolt, Bruce J; Carvalho-Silva, Denise; Christensen, Mikkel; Davis, Paul; Falin, Lee J; Grabmueller, Christoph; Humphrey, Jay; Kerhornou, Arnaud; Khobova, Julia; Aranganathan, Naveen K; Langridge, Nicholas; Lowy, Ernesto; McDowall, Mark D; Maheswari, Uma; Nuhn, Michael; Ong, Chuang Kee; Overduin, Bert; Paulini, Michael; Pedro, Helder; Perry, Emily; Spudich, Giulietta; Tapanari, Electra; Walts, Brandon; Williams, Gareth; Tello-Ruiz, Marcela; Stein, Joshua; Wei, Sharon; Ware, Doreen; Bolser, Daniel M; Howe, Kevin L; Kulesha, Eugene; Lawson, Daniel; Maslen, Gareth; Staines, Daniel M

    2016-01-04

    Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial genomes, 400 fungal genomes and 100 protist genomes, in addition to 55 genomes from invertebrate metazoa and 39 genomes from plants. This dramatic increase in the number of included genomes is one part of a broader effort to automate the integration of archival data (genome sequence, but also associated RNA sequence data and variant calls) within the context of reference genomes and make it available through the Ensembl user interfaces. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  12. Rodent malaria parasites : genome organization & comparative genomics

    NARCIS (Netherlands)

    Kooij, Taco W.A.

    2006-01-01

    The aim of the studies described in this thesis was to investigate the genome organization of rodent malaria parasites (RMPs) and compare the organization and gene content of the genomes of RMPs and the human malaria parasite P. falciparum. The release of the complete genome sequence of P.

  13. Geochemical modelling: what phenomena are missing

    International Nuclear Information System (INIS)

    Jacquier, P.

    1989-12-01

    In the framework of safety assessment of radioactive waste disposal, retention phenomena are usually taken into account by the Kd concept. It is well recognized that this concept is not enough for safety assessment models, because of the several and strong assumptions which are involved in this kind of representation. One way to have a better representation of the retention phenomena, is to substitute for this Kd concept an explicit description of geochemical phenomena and then couple transport codes with geochemical codes in a fully or a two-step procedure. We use currently such codes, but the scope of this paper is to display the limits today of the geochemical modelling in connection with sites analysis for deep disposal. In this paper, we intend to give an overview of phenomena which are missing in the geochemical models, or which are not completely introduced in the models. We can distinguish, on one hand phenomena for which modelling concepts exist such as adsorption/desorption and, on the other hand, phenomena for which modelling concepts do not exist for the moment such as colloids, and complexation by polyelectrolyte solutions (organics). Moreover we have to take care of very low concentrations of radionuclides, which can be expected from the leaching processes in the repository. Under those conditions, some reactions may not occur. After a critical review of the involved phenomena, we intend to stress the main directions of the wishful evolution of the geochemical modelling. This evolution should improve substantially the quality of the above-mentioned site assessments

  14. China's "missing girls": prospects and policy.

    Science.gov (United States)

    Riley, N E

    1996-02-01

    Women's conditions in China are viewed as deteriorating. The reduction in government control over urban factories and other places of employment has resulted in fewer women being hired. This leaves women in positions with low wages, poor working conditions, and discrimination based on sex, age, and marital status. The shift from rural state-controlled agricultural collectives to patriarchal family controls resulted in land distribution that gave men preference. The rapid growth in the economy and higher standards of living placed women at risk. Although the pressures to kill girl babies have relaxed, there is growing interest in making money from abducting and selling women for prostitution, marriage, and slavery. Women gained in recent decades greater participation in the labor force and higher educational levels. Women's access to health care is better. Female life expectancy is 72 years compared to 69 years for men. Maternal mortality is 95 deaths per 100,000 live births. Yet women hold subordinate positions to men in their jobs, and women are segregated in the textile and service industries. Women in rural areas have primarily access to agricultural jobs, which can be combined with child care. Women are less likely to be promoted and are retired 5 years earlier than men. Women carry a double burden of domestic labor and paid or unpaid labor. Women still have higher illiteracy rates than men, and the gender gap in higher education has remained stable since the 1970s. The imbalanced sex ratio is increasing. In some provinces it is 114 males for every 100 females, when the normal ratio is 105-106 males per 100 females. An estimated 12% of females are unaccounted for each year. The reasons for the missing children are identified as sex-selective abortion, infanticide, or underreporting. The next five-year plan holds the hope for improvement in women's status and an end to abuses against women and children.

  15. The Mysterious Case of the Missing Filaments

    Science.gov (United States)

    Alden, C. R.

    2016-12-01

    Coronal Mass Ejections, or CMEs, are large solar eruptions that can have major debilitating impacts on society. Typically, these eruptions have the three following key structures: the leading edge, the empty chamber known as the cavity, and the filament which often is the brightest part of the CME. When we can see all three structures clearly with a coronagraph, it is called a classic three-part CME, also referred to as a 'lightbulb' CME. According to current knowledge, when a CME erupts, a filament should also erupt or lift off the Sun in order to have the bright center within the CME. However, we do not always see a filament erupt at the surface, and yet we still get a 'filament' within the coronagraph CME. To better understand what might be occurring with these missing filaments, we looked at three-part CMEs using the SOHO LASCO CME Catalog and filaments from the SDO AIA Filament Catalog in order to create a list of 50 CMEs without a listed filament erupting at the surface. For those CMEs without filaments in the list we closely inspected the AIA images for evidence of filament eruption. To ensure that there were no filaments past the limb of the Sun, we used data from the STEREO-A and STEREO-B spacecraft's to look at the Sun from other angles. We have found numerous events where no filament erupts from the surface, but we still see the classic three-part CME. We believe this may be due to an optical illusion occurring from the twisting of the flux rope.

  16. Maternal near-miss: a multicenter surveillance in Kathmandu Valley.

    Science.gov (United States)

    Rana, Ashma; Baral, Gehanath; Dangal, Ganesh

    2013-01-01

    Multicenter surveillance has been carried out on maternal near-miss in the hospitals with sentinel units. Near-miss is recognized as the predictor of level of care and maternal death. Reducing Maternal Mortality Ratio is one of the challenges to achieve Millennium Development Goal. The objective was to determine the frequency and the nature of near-miss events and to analyze the near-miss morbidities among pregnant women. A prospective surveillance was done for a year in 2012 at nine hospitals in Kathmandu valley. Cases eligible by definition were recorded as a census based on WHO near-miss guideline. Similar questionnaires and dummy tables were used to present the results by non-inferential statistics. Out of 157 cases identified with near-miss rate of 3.8 per 1000 live births, severe complications were postpartum hemorrhage 62 (40%) and preeclampsia-eclampsia 25 (17%). Blood transfusion 102 (65%), ICU admission 85 (54%) and surgery 53 (32%) were common critical interventions. Oxytocin was main uterotonic used both prophylactically and therapeutically at health facilities. Total of 30 (19%) cases arrived at health facility after delivery or abortion. MgSO4 was used in all cases of eclampsia. All laparotomies were performed within three hours of arrival. Near-miss to maternal death ratio was 6:1 and MMR was 62. Study result yielded similar pattern amongst developing countries and same near-miss conditions as the causes of maternal death reported by national statistics. Process indicators qualified the recommended standard of care. The near-miss event could be used as a surrogate marker of maternal death and a window for system level intervention.

  17. Missing and Spurious Level Corrections for Nuclear Resonances

    International Nuclear Information System (INIS)

    Mitchell, G E; Agvaanluvsan, U; Pato, M P; Shriner, J F

    2005-01-01

    Neutron and proton resonances provide detailed level density information. However, due to experimental limitations, some levels are missed and some are assigned incorrect quantum numbers. The standard method to correct for missing levels uses the experimental widths and the Porter-Thomas distribution. Analysis of the spacing distribution provides an independent determination of the fraction of missing levels. We have derived a general expression for such an imperfect spacing distribution using the maximum entropy principle and applied it to a variety of nuclear resonance data. The problem of spurious levels has not been extensively addressed

  18. Topology-Based Estimation of Missing Smart Meter Readings

    Directory of Open Access Journals (Sweden)

    Daisuke Kodaira

    2018-01-01

    Full Text Available Smart meters often fail to measure or transmit the data they record when measuring energy consumption, known as meter readings, owing to faulty measuring equipment or unreliable communication modules. Existing studies do not address successive and non-periodical missing meter readings. This paper proposes a method whereby missing readings observed at a node are estimated by using circuit theory principles that leverage the voltage and current data from adjacent nodes. A case study is used to demonstrate the ability of the proposed method to successfully estimate the missing readings over an entire day during which outages and unpredictable perturbations occurred.

  19. Funding Opportunity: Genomic Data Centers

    Science.gov (United States)

    Funding Opportunity CCG, Funding Opportunity Center for Cancer Genomics, CCG, Center for Cancer Genomics, CCG RFA, Center for cancer genomics rfa, genomic data analysis network, genomic data analysis network centers,

  20. ErythropoieSIS stimulating agent (ESA use is increased following missed dialysis sessions

    Directory of Open Access Journals (Sweden)

    T. Christopher Bond

    2012-06-01

    Missed session episodes result in significant increases in ESA utilization in the post-miss period, and also in total monthly ESA use. Such increases should be considered in any assessment of impact of missed sessions: both clinical and economic.

  1. Reducing Misses and Near Misses Related to Multitasking on the Electronic Health Record: Observational Study and Qualitative Analysis.

    Science.gov (United States)

    Ratanawongsa, Neda; Matta, George Y; Bohsali, Fuad B; Chisolm, Margaret S

    2018-02-06

    Clinicians' use of electronic health record (EHR) systems while multitasking may increase the risk of making errors, but silent EHR system use may lower patient satisfaction. Delaying EHR system use until after patient visits may increase clinicians' EHR workload, stress, and burnout. We aimed to describe the perspectives of clinicians, educators, administrators, and researchers about misses and near misses that they felt were related to clinician multitasking while using EHR systems. This observational study was a thematic analysis of perspectives elicited from 63 continuing medical education (CME) participants during 2 workshops and 1 interactive lecture about challenges and strategies for relationship-centered communication during clinician EHR system use. The workshop elicited reflection about memorable times when multitasking EHR use was associated with "misses" (errors that were not caught at the time) or "near misses" (mistakes that were caught before leading to errors). We conducted qualitative analysis using an editing analysis style to identify codes and then select representative themes and quotes. All workshop participants shared stories of misses or near misses in EHR system ordering and documentation or patient-clinician communication, wondering about "misses we don't even know about." Risk factors included the computer's position, EHR system usability, note content and style, information overload, problematic workflows, systems issues, and provider and patient communication behaviors and expectations. Strategies to reduce multitasking EHR system misses included clinician transparency when needing silent EHR system use (eg, for prescribing), narrating EHR system use, patient activation during EHR system use, adapting visit organization and workflow, improving EHR system design, and improving team support and systems. CME participants shared numerous stories of errors and near misses in EHR tasks and communication that they felt related to EHR

  2. Partitioning of genomic variance using prior biological information

    DEFF Research Database (Denmark)

    Edwards, Stefan McKinnon; Janss, Luc; Madsen, Per

    2013-01-01

    variants influence complex diseases. Despite the successes, the variants identified as being statistically significant have generally explained only a small fraction of the heritable component of the trait, the so-called problem of missing heritability. Insufficient modelling of the underlying genetic...... architecture may in part explain this missing heritability. Evidence collected across genome-wide association studies in human provides insight into the genetic architecture of complex traits. Although many genetic variants with small or moderate effects contribute to the overall genetic variation, it appears...... that the associated genetic variants are enriched for genes that are connected in biol ogical pathways or for likely functional effects on genes. These biological findings provide valuable insight for developing better genomic models. These are statistical models for predicting complex trait phenotypes on the basis...

  3. Genomic evaluations with many more genotypes

    Directory of Open Access Journals (Sweden)

    Wiggans George R

    2011-03-01

    Full Text Available Abstract Background Genomic evaluations in Holstein dairy cattle have quickly become more reliable over the last two years in many countries as more animals have been genotyped for 50,000 markers. Evaluations can also include animals genotyped with more or fewer markers using new tools such as the 777,000 or 2,900 marker chips recently introduced for cattle. Gains from more markers can be predicted using simulation, whereas strategies to use fewer markers have been compared using subsets of actual genotypes. The overall cost of selection is reduced by genotyping most animals at less than the highest density and imputing their missing genotypes using haplotypes. Algorithms to combine different densities need to be efficient because numbers of genotyped animals and markers may continue to grow quickly. Methods Genotypes for 500,000 markers were simulated for the 33,414 Holsteins that had 50,000 marker genotypes in the North American database. Another 86,465 non-genotyped ancestors were included in the pedigree file, and linkage disequilibrium was generated directly in the base population. Mixed density datasets were created by keeping 50,000 (every tenth of the markers for most animals. Missing genotypes were imputed using a combination of population haplotyping and pedigree haplotyping. Reliabilities of genomic evaluations using linear and nonlinear methods were compared. Results Differing marker sets for a large population were combined with just a few hours of computation. About 95% of paternal alleles were determined correctly, and > 95% of missing genotypes were called correctly. Reliability of breeding values was already high (84.4% with 50,000 simulated markers. The gain in reliability from increasing the number of markers to 500,000 was only 1.6%, but more than half of that gain resulted from genotyping just 1,406 young bulls at higher density. Linear genomic evaluations had reliabilities 1.5% lower than the nonlinear evaluations with 50

  4. DWARF GALAXY CLUSTERING AND MISSING SATELLITES

    International Nuclear Information System (INIS)

    Carlberg, R. G.; Sullivan, M.; Le Borgne, D.

    2009-01-01

    At redshifts around 0.1 the Canada-France-Hawaii Telescope Legacy Survey Deep fields contain some 6 x 10 4 galaxies spanning the mass range from 10 5 to 10 12 M sun . We measure the stellar mass dependence of the two-point correlation using angular measurements to largely bypass the errors, approximately 0.02 in the median, of the photometric redshifts. Inverting the power-law fits with Limber's equation we find that the autocorrelation length increases from a very low 0.4 h -1 Mpc at 10 5.5 M sun to the conventional 4.5 h -1 Mpc at 10 10.5 M sun . The power-law fit to the correlation function has a slope which increases from γ ≅ 1.6 at high mass to γ ≅ 2.3 at low mass. The spatial cross-correlation of dwarf galaxies with more massive galaxies shows fairly similar trends, with a steeper radial dependence at low mass than predicted in numerical simulations of subhalos within galaxy halos. To examine the issue of 'missing satellites' we combine the cross-correlation measurements with our estimates of the low-mass galaxy number density. We find on the average there are 60 ± 20 dwarfs in subhalos with M(total)>10 7 M sun for a typical Local Group M(total)/M(stars) = 30, corresponding to M/L V ≅ 100 for a galaxy with no recent star formation. The number of dwarfs per galaxy is about a factor of 2 larger than currently found for the Milky Way. Nevertheless, the average dwarf counts are about a factor of 30 below lambda cold dark matter (LCDM) simulation results. The divergence from LCDM predictions is one of the slope of the relation, approximately dN/dln M ≅ -0.5 rather than the predicted -0.9, not sudden onset at some characteristic scale. The dwarf galaxy star formation rates span the range from passive to bursting, which suggests that there are few completely dark halos.

  5. Exploring Other Genomes: Bacteria.

    Science.gov (United States)

    Flannery, Maura C.

    2001-01-01

    Points out the importance of genomes other than the human genome project and provides information on the identified bacterial genomes Pseudomonas aeuroginosa, Leprosy, Cholera, Meningitis, Tuberculosis, Bubonic Plague, and plant pathogens. Considers the computer's use in genome studies. (Contains 14 references.) (YDS)

  6. Near-miss maternal morbidity from severe haemorrhage at ...

    African Journals Online (AJOL)

    ... at caesarean section: A process and structure audit of system deficiencies in South Africa. ... The Donabedian model assumes that clinical outcomes are influenced by ... Dominant risk factors for near misses were previous caesarean section ...

  7. The role of proxy information in missing data analysis.

    Science.gov (United States)

    Huang, Rong; Liang, Yuanyuan; Carrière, K C

    2005-10-01

    This article investigates the role of proxy data in dealing with the common problem of missing data in clinical trials using repeated measures designs. In an effort to avoid the missing data situation, some proxy information can be gathered. The question is how to treat proxy information, that is, is it always better to utilize proxy information when there are missing data? A model for repeated measures data with missing values is considered and a strategy for utilizing proxy information is developed. Then, simulations are used to compare the power of a test using proxy to simply utilizing all available data. It is concluded that using proxy information can be a useful alternative when such information is available. The implications for various clinical designs are also considered and a data collection strategy for efficiently estimating parameters is suggested.

  8. ATLAS event featuring two charm jets and missing energy

    CERN Multimedia

    ATLAS Collaboration

    2012-01-01

    Proton collision event in the ATLAS detector featuring two tagged charm jets and missing transverse energy. The zoomed view in the bottom right panel shows a displaced vertex of one of the c-tagged jets (marked in blue).

  9. Missing Links: Gender Equity in Science and Technology for ...

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

    Missing Links: Gender Equity in Science and Technology for Development. Book cover ... Gender Working Group of the United Nations Commission on Science and Technology for Development. Publisher(s): ... Knowledge. Innovation.

  10. 40 CFR 98.55 - Procedures for estimating missing data.

    Science.gov (United States)

    2010-07-01

    ... accounting purposes (such as sales records). (b) For missing values related to the performance test, including emission factors, production rate, and N2O concentration, you must conduct a new performance test...

  11. 40 CFR 98.225 - Procedures for estimating missing data.

    Science.gov (United States)

    2010-07-01

    ... accounting purposes (such as sales records). (b) For missing values related to the performance test, including emission factors, production rate, and N2O concentration, you must conduct a new performance test...

  12. Prevalence and Correlates of Missed First Appointments among ...

    African Journals Online (AJOL)

    quality of care, results in poor treatment outcomes and drains financial resources. In Nigeria, where mental .... and physical aggression. Each subscale has four .... missed first appointments observed in this study falls within the range of 17 and ...

  13. Missed injury – decreasing morbidity and mortality: A literature review

    African Journals Online (AJOL)

    Advanced Trauma Life Support®), although they may also be inju- ries identified after a defined .... highly recommended for practice quality assurance. ... when injuries are missed, continuous audit is essential in prevent- ing repeated errors!

  14. Estimating range of influence in case of missing spatial data

    DEFF Research Database (Denmark)

    Bihrmann, Kristine; Ersbøll, Annette Kjær

    2015-01-01

    BACKGROUND: The range of influence refers to the average distance between locations at which the observed outcome is no longer correlated. In many studies, missing data occur and a popular tool for handling missing data is multiple imputation. The objective of this study was to investigate how...... the estimated range of influence is affected when 1) the outcome is only observed at some of a given set of locations, and 2) multiple imputation is used to impute the outcome at the non-observed locations. METHODS: The study was based on the simulation of missing outcomes in a complete data set. The range...... of influence was estimated from a logistic regression model with a spatially structured random effect, modelled by a Gaussian field. Results were evaluated by comparing estimates obtained from complete, missing, and imputed data. RESULTS: In most simulation scenarios, the range estimates were consistent...

  15. Computerized Analysis and Detection of Missed Cancer in Screening Mammogram

    National Research Council Canada - National Science Library

    Li, Lihua

    2005-01-01

    This project is to explore an innovative CAD strategy for improving early detection of breast cancer in screening mammograms by focusing on computerized analysis and detection of cancers missed by radiologists...

  16. Computerized Analysis and Detection of Missed Cancer in Screening Mammogram

    National Research Council Canada - National Science Library

    Li, Lihua

    2004-01-01

    This project is to explore an innovative CAD strategy for improving early detection of breast cancer in screening mammograms by focusing on computerized analysis and detection of cancers missed by radiologists...

  17. Prevalence and Correlates of Missed First Appointments among ...

    African Journals Online (AJOL)

    In Nigeria, where mental health services are poorly organized, missed appointments and its resultant consequences may be burdensome. Aim: This ... However, having received previous treatment for a psychiatric illness (P = 0.02) and having ...

  18. missed opportunities for the diagnosis of pulmonary tuberculosis

    African Journals Online (AJOL)

    User

    MISSED OPPORTUNITIES FOR THE DIAGNOSIS OF. PULMONARY .... Data analysis. Data were pooled across all sites for analysis. .... tecting 70% of new smear positive cases by. 2005 (case ... False negative is one big factor with smear ...

  19. High-throughput metabolic state analysis: The missing link in integrated functional genomics of yeasts

    DEFF Research Database (Denmark)

    Villas-Bôas, Silas Granato; Moxley, Joel. F; Åkesson, Mats Fredrik

    2005-01-01

    that achieve comparable throughput, effort and cost compared with DNA arrays. Our sample workup method enables simultaneous metabolite measurements throughout central carbon metabolism and amino acid biosynthesis, using a standard GC-MS platform that was optimized for this Purpose. As an implementation proof......-of-concept, we assayed metabolite levels in two yeast strains and two different environmental conditions in the context of metabolic pathway reconstruction. We demonstrate that these differential metabolite level data distinguish among sample types, such as typical metabolic fingerprinting or footprinting. More...

  20. Maternal near-miss in a rural hospital in Sudan

    Directory of Open Access Journals (Sweden)

    Adam Gamal K

    2011-06-01

    Full Text Available Abstract Background Investigation of maternal near-miss is a useful complement to the investigation of maternal mortality with the aim of meeting the United Nations' fifth Millennium Development Goal. The present study was conducted to investigate the frequency of near-miss events, to calculate the mortality index for each event and to compare the socio-demographic and obstetrical data (age, parity, gestational age, education and antenatal care of the near-miss cases with maternal deaths. Methods Near-miss cases and events (hemorrhage, infection, hypertensive disorders, anemia and dystocia, maternal deaths and their causes were retrospectively reviewed and the mortality index for each event was calculated in Kassala Hospital, eastern Sudan over a 2-year period, from January 2008 to December 2010. Disease-specific criteria were applied for these events. Results There were 9578 deliveries, 205 near-miss cases, 228 near-miss events and 40 maternal deaths. Maternal near-miss and maternal mortality ratio were 22.1/1000 live births and 432/100 000 live births, respectively. Hemorrhage accounted for the most common event (40.8%, followed by infection (21.5%, hypertensive disorders (18.0%, anemia (11.8% and dystocia (7.9%. The mortality index were 22.2%, 10.0%, 10.0%, 8.8% and 2.4% for infection, dystocia, anemia, hemorrhage and hypertensive disorders, respectively. Conclusion There is a high frequency of maternal morbidity and mortality at the level of this facility. Therefore maternal health policy needs to be concerned not only with averting the loss of life, but also with preventing or ameliorating maternal-near miss events (hemorrhage, infections, hypertension and anemia at all care levels including primary level.

  1. Diabetes or hypertension as risk indicators for missing teeth ...

    African Journals Online (AJOL)

    A negative binomial regression (NBR) model was generated. Results: Mean age was 50.7 ± 16.2 and 50.0% were women. Mean number of missing teeth was 4.98 ± 4.17. In the multivariate NBR model, we observed that individuals with T2DM had higher risk of more missing teeth (incidence rate ratios [IRRs] = 3.13; 95% ...

  2. Exoatmospheric intercepts using zero effort miss steering for midcourse guidance

    Science.gov (United States)

    Newman, Brett

    The suitability of proportional navigation, or an equivalent zero effort miss formulation, for exatmospheric intercepts during midcourse guidance, followed by a ballistic coast to the endgame, is addressed. The problem is formulated in terms of relative motion in a general, three dimensional framework. The proposed guidance law for the commanded thrust vector orientation consists of the sum of two terms: (1) along the line of sight unit direction and (2) along the zero effort miss component perpendicular to the line of sight and proportional to the miss itself and a guidance gain. If the guidance law is to be suitable for longer range targeting applications with significant ballistic coasting after burnout, determination of the zero effort miss must account for the different gravitational accelerations experienced by each vehicle. The proposed miss determination techniques employ approximations for the true differential gravity effect and thus, are less accurate than a direct numerical propagation of the governing equations, but more accurate than a baseline determination, which assumes equal accelerations for both vehicles. Approximations considered are constant, linear, quadratic, and linearized inverse square models. Theoretical results are applied to a numerical engagement scenario and the resulting performance is evaluated in terms of the miss distances determined from nonlinear simulation.

  3. Spacecraft intercept guidance using zero effort miss steering

    Science.gov (United States)

    Newman, Brett

    The suitability of proportional navigation, or an equivalent zero effort miss formulation, for spacecraft intercepts during midcourse guidance, followed by a ballistic coast to the endgame, is addressed. The problem is formulated in terms of relative motion in a general 3D framework. The proposed guidance law for the commanded thrust vector orientation consists of the sum of two terms: (1) along the line of sight unit direction and (2) along the zero effort miss component perpendicular to the line of sight and proportional to the miss itself and a guidance gain. If the guidance law is to be suitable for longer range targeting applications with significant ballistic coasting after burnout, determination of the zero effort miss must account for the different gravitational accelerations experienced by each vehicle. The proposed miss determination techniques employ approximations for the true differential gravity effect. Theoretical results are applied to a numerical engagement scenario and the resulting performance is evaluated in terms of the miss distances determined from nonlinear simulation.

  4. Bayesian Sensitivity Analysis of Statistical Models with Missing Data.

    Science.gov (United States)

    Zhu, Hongtu; Ibrahim, Joseph G; Tang, Niansheng

    2014-04-01

    Methods for handling missing data depend strongly on the mechanism that generated the missing values, such as missing completely at random (MCAR) or missing at random (MAR), as well as other distributional and modeling assumptions at various stages. It is well known that the resulting estimates and tests may be sensitive to these assumptions as well as to outlying observations. In this paper, we introduce various perturbations to modeling assumptions and individual observations, and then develop a formal sensitivity analysis to assess these perturbations in the Bayesian analysis of statistical models with missing data. We develop a geometric framework, called the Bayesian perturbation manifold, to characterize the intrinsic structure of these perturbations. We propose several intrinsic influence measures to perform sensitivity analysis and quantify the effect of various perturbations to statistical models. We use the proposed sensitivity analysis procedure to systematically investigate the tenability of the non-ignorable missing at random (NMAR) assumption. Simulation studies are conducted to evaluate our methods, and a dataset is analyzed to illustrate the use of our diagnostic measures.

  5. Software for handling and replacement of missing data

    Directory of Open Access Journals (Sweden)

    Mayer, Benjamin

    2009-10-01

    Full Text Available In medical research missing values often arise in the course of a data analysis. This fact constitutes a problem for different reasons, so e.g. standard methods for analyzing data lead to biased estimates and a loss of statistical power due to missing values, since those methods require complete data sets and therefore omit incomplete cases for the analyses. Furthermore missing values imply a certain loss of information for what reason the validity of results of a study with missing values has to be rated less than in a case where all data had been available. For years there are methods for replacement of missing values (Rubin, Schafer to tackle these problems and solve them in parts. Hence in this article we want to present the existing software to handle and replace missing values on the one hand and give an outline about the available options to get information on the other hand. The methodological aspects of the replacement strategies are delineated just briefly in this article.

  6. Posttraumatic stress disorder in women with war missing family members.

    Science.gov (United States)

    Baraković, Devla; Avdibegović, Esmina; Sinanović, Osman

    2014-12-01

    Research in crisis areas indicate that survivors' responses to the forced disappearance of family members are similar to reactions to other traumatic events. The aim of this study was to determine the presence of symptoms of posttraumatic stress disorder (PTSD) in women with war missing family members in Bosnia and Herzegovina 18 years after the war in this region (1992-1995). The study included 160 women aged 47.1±14.0 from three regions of Bosnia and Herzegovina. It was carried out in the period from April 2010 to May 2011. Of the 160 participants, 120 women had a war missing family member and 40 women had no war missing family members. The Harvard Trauma Questionnaire (HTQ), the Beck Depression Inventory (BDI) and the Hamilton Anxiety Rating Scale (HAMA) were used for data collection. Basic socio-demographic data and data concerning the missing family members were also collected. Women with war missing family members experienced significantly more traumatic war experiences (18.43±5.27 vs 6.57±4.34, pfamily members. Women with war missing family members showed significantly more severe PTSD symptoms. Based on the results of this study, it was determined that the forced disappearance of a family member is an ambiguous situation that can be characterized as a traumatic experience.

  7. Dentistry to the rescue of missing children: A review

    Science.gov (United States)

    Vij, Nitika; Kochhar, Gulsheen Kaur; Chachra, Sanjay; Kaur, Taranjot

    2016-01-01

    Today's society is becoming increasingly unsafe for children: we frequently hear about new incidents of missing children, which lead to emotional trauma for the loved ones and expose systemic failures of law and order. Parents can take extra precautions to ensure the safety of their children by educating them about ways to protect themselves and keep important records of the child such as updated color photographs, fingerprints, deoxyribonucleic acid (DNA) samples, etc., handy. However, in spite of all efforts, the problem of missing children still remains. Developments in the field of dentistry have empowered dentists with various tools and techniques to play a pivotal role in tracing a missing child. One such tool is Toothprints, a patented arch-shaped thermoplastic dental impression wafer developed by Dr. David Tesini, a paediatric dentist from Massachusetts. Toothprints enables a unique identification of the missing children not only through the bite impression but also through salivary DNA. Besides the use of Toothprints, a dentist can assist investigating agencies in identifying the missing children in multiple ways, including postmortem dental profiling, labeled dental fixtures, DNA extraction from teeth, and serial number engraving on the children's teeth. More importantly, all these tools cause minimal inconvenience to the individual, making a dentist's role in tracking a missing child even more significant. Thus, the simple discipline of maintaining timely dental records with the help of their dentists can save potential hassles for the parents in the future. PMID:27051216

  8. Imputation of missing data in time series for air pollutants

    Science.gov (United States)

    Junger, W. L.; Ponce de Leon, A.

    2015-02-01

    Missing data are major concerns in epidemiological studies of the health effects of environmental air pollutants. This article presents an imputation-based method that is suitable for multivariate time series data, which uses the EM algorithm under the assumption of normal distribution. Different approaches are considered for filtering the temporal component. A simulation study was performed to assess validity and performance of proposed method in comparison with some frequently used methods. Simulations showed that when the amount of missing data was as low as 5%, the complete data analysis yielded satisfactory results regardless of the generating mechanism of the missing data, whereas the validity began to degenerate when the proportion of missing values exceeded 10%. The proposed imputation method exhibited good accuracy and precision in different settings with respect to the patterns of missing observations. Most of the imputations obtained valid results, even under missing not at random. The methods proposed in this study are implemented as a package called mtsdi for the statistical software system R.

  9. Dentistry to the rescue of missing children: A review.

    Science.gov (United States)

    Vij, Nitika; Kochhar, Gulsheen Kaur; Chachra, Sanjay; Kaur, Taranjot

    2016-01-01

    Today's society is becoming increasingly unsafe for children: we frequently hear about new incidents of missing children, which lead to emotional trauma for the loved ones and expose systemic failures of law and order. Parents can take extra precautions to ensure the safety of their children by educating them about ways to protect themselves and keep important records of the child such as updated color photographs, fingerprints, deoxyribonucleic acid (DNA) samples, etc., handy. However, in spite of all efforts, the problem of missing children still remains. Developments in the field of dentistry have empowered dentists with various tools and techniques to play a pivotal role in tracing a missing child. One such tool is Toothprints, a patented arch-shaped thermoplastic dental impression wafer developed by Dr. David Tesini, a paediatric dentist from Massachusetts. Toothprints enables a unique identification of the missing children not only through the bite impression but also through salivary DNA. Besides the use of Toothprints, a dentist can assist investigating agencies in identifying the missing children in multiple ways, including postmortem dental profiling, labeled dental fixtures, DNA extraction from teeth, and serial number engraving on the children's teeth. More importantly, all these tools cause minimal inconvenience to the individual, making a dentist's role in tracking a missing child even more significant. Thus, the simple discipline of maintaining timely dental records with the help of their dentists can save potential hassles for the parents in the future.

  10. Genomics With Cloud Computing

    OpenAIRE

    Sukhamrit Kaur; Sandeep Kaur

    2015-01-01

    Abstract Genomics is study of genome which provides large amount of data for which large storage and computation power is needed. These issues are solved by cloud computing that provides various cloud platforms for genomics. These platforms provides many services to user like easy access to data easy sharing and transfer providing storage in hundreds of terabytes more computational power. Some cloud platforms are Google genomics DNAnexus and Globus genomics. Various features of cloud computin...

  11. Genome Maps, a new generation genome browser.

    Science.gov (United States)

    Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

    2013-07-01

    Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org.

  12. Governance or Governing – the Missing Link?

    Directory of Open Access Journals (Sweden)

    Luminiţa Maria Crăciun

    2010-07-01

    , of giving a sense of responsibility to the public and private sectors, of imposing, observing and materializing a real commitment for preventing and fighting corruption, the risk of which may be a threat to national security. Human governance creates a favorable environment for human development and elimination of poverty. If the preoccupations of the governance institutions are centered on the interests, needs, and fundamental rights of the population, progress may be achieved in the fight against poverty. If a country tries to apply economic policies in order to promote a beneficial increase to the poor ones, along with programs meant to help reach the targeted goals, the effects may be attenuated or annulled, when the governance institutions are ineffective or passive. The conclusion is that the governance is the missing link between the efforts of struggle against poverty and reaching the objective of poverty reduction.

  13. Missing data in trauma registries: A systematic review.

    Science.gov (United States)

    Shivasabesan, Gowri; Mitra, Biswadev; O'Reilly, Gerard M

    2018-03-30

    Trauma registries play an integral role in trauma systems but their valid use hinges on data quality. The aim of this study was to determine, among contemporary publications using trauma registry data, the level of reporting of data completeness and the methods used to deal with missing data. A systematic review was conducted of all trauma registry-based manuscripts published from 01 January 2015 to current date (17 March 2017). Studies were identified by searching MEDLINE, EMBASE, and CINAHL using relevant subject headings and keywords. Included manuscripts were evaluated based on previously published recommendations regarding the reporting and discussion of missing data. Manuscripts were graded on their degree of characterization of such observations. In addition, the methods used to manage missing data were examined. There were 539 manuscripts that met inclusion criteria. Among these, 208 (38.6%) manuscripts did not mention data completeness and 88 (16.3%) mentioned missing data but did not quantify the extent. Only a handful (n = 26; 4.8%) quantified the 'missingness' of all variables. Most articles (n = 477; 88.5%) contained no details such as a comparison between patient characteristics in cohorts with and without missing data. Of the 331 articles which made at least some mention of data completeness, the method of managing missing data was unknown in 34 (10.3%). When method(s) to handle missing data were identified, 234 (78.8%) manuscripts used complete case analysis only, 18 (6.1%) used multiple imputation only and 34 (11.4%) used a combination of these. Most manuscripts using trauma registry data did not quantify the extent of missing data for any variables and contained minimal discussion regarding missingness. Out of the studies which identified a method of managing missing data, most used complete case analysis, a method that may bias results. The lack of standardization in the reporting and management of missing data questions the validity of

  14. Genomic and Genetic Diversity within the Pseudomonas fluorescens Complex.

    Directory of Open Access Journals (Sweden)

    Daniel Garrido-Sanz

    Full Text Available The Pseudomonas fluorescens complex includes Pseudomonas strains that have been taxonomically assigned to more than fifty different species, many of which have been described as plant growth-promoting rhizobacteria (PGPR with potential applications in biocontrol and biofertilization. So far the phylogeny of this complex has been analyzed according to phenotypic traits, 16S rDNA, MLSA and inferred by whole-genome analysis. However, since most of the type strains have not been fully sequenced and new species are frequently described, correlation between taxonomy and phylogenomic analysis is missing. In recent years, the genomes of a large number of strains have been sequenced, showing important genomic heterogeneity and providing information suitable for genomic studies that are important to understand the genomic and genetic diversity shown by strains of this complex. Based on MLSA and several whole-genome sequence-based analyses of 93 sequenced strains, we have divided the P. fluorescens complex into eight phylogenomic groups that agree with previous works based on type strains. Digital DDH (dDDH identified 69 species and 75 subspecies within the 93 genomes. The eight groups corresponded to clustering with a threshold of 31.8% dDDH, in full agreement with our MLSA. The Average Nucleotide Identity (ANI approach showed inconsistencies regarding the assignment to species and to the eight groups. The small core genome of 1,334 CDSs and the large pan-genome of 30,848 CDSs, show the large diversity and genetic heterogeneity of the P. fluorescens complex. However, a low number of strains were enough to explain most of the CDSs diversity at core and strain-specific genomic fractions. Finally, the identification and analysis of group-specific genome and the screening for distinctive characters revealed a phylogenomic distribution of traits among the groups that provided insights into biocontrol and bioremediation applications as well as their role as

  15. JGI Fungal Genomics Program

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor V.

    2011-03-14

    Genomes of energy and environment fungi are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 50 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such 'parts' suggested by comparative genomics and functional analysis in these areas are presented here

  16. Genomic Encyclopedia of Fungi

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor

    2012-08-10

    Genomes of fungi relevant to energy and environment are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 150 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such parts suggested by comparative genomics and functional analysis in these areas are presented here.

  17. Between the Cup and the Lip: Missed Dental Appointments.

    Science.gov (United States)

    Tandon, Sandeep; Duhan, Reena; Sharma, Meenakshi; Vasudeva, Suraj

    2016-05-01

    Missed appointments are an issue which have been very commonly noticed but overlooked in Indian dental society. Almost every dentist, general or specialized, private or public, has faced this problem in routine practice but very less research has been conducted on this issue in Asian countries. The aim of this study was to determine the frequency and distribution of missed dental appointments among children and the reasons behind the non-attendance in department of paediatric and preventive dentistry. Patients under 15 years of age who reported during the period March through August 2014 were included in this study. Attendance data and demographical data for patients was obtained from patient records and the hospital database. The type of treatment patients were to receive was gathered from the appointment diaries of staff, postgraduate students and undergraduates. A structured questionnaire regarding the most frequent reasons given by patients for not attending the scheduled appointment was also prepared. The data were analysed using descriptive analysis. Of the total 2294 patients 886 patients failed to come on their scheduled appointment. Percentage of patients who missed their appointments was 38.6%. A 38.2% of them required primary teeth pulp therapy. No significant differences was found between genders regarding the prevalence of missed dental appointments. Only 40% dentist witnessed that the most common reason for their patients to miss dental appointment was "no leave from school". Illness was the second frequent excuse heard by dentists (5/20= 25%) from their patients and attendants. Missed dental appointment was found to be a common issue in paediatric age group. Counseling and motivation is required to be done at first dental visit to reduce the chances of missed appointment.

  18. Genomics With Cloud Computing

    Directory of Open Access Journals (Sweden)

    Sukhamrit Kaur

    2015-04-01

    Full Text Available Abstract Genomics is study of genome which provides large amount of data for which large storage and computation power is needed. These issues are solved by cloud computing that provides various cloud platforms for genomics. These platforms provides many services to user like easy access to data easy sharing and transfer providing storage in hundreds of terabytes more computational power. Some cloud platforms are Google genomics DNAnexus and Globus genomics. Various features of cloud computing to genomics are like easy access and sharing of data security of data less cost to pay for resources but still there are some demerits like large time needed to transfer data less network bandwidth.

  19. Comparative genomics of a plant-parasitic nematode endosymbiont suggest a role in nutritional symbiosis

    Science.gov (United States)

    Bacterial mutualists can increase the biochemical capacity of animals. Highly co-evolved nutritional mutualists do this by synthesizing nutrients missing from the host's diet. Genomics tools have recently advanced the study of these partnerships. Here we examined the endosymbiont Xiphinematobacter (...

  20. A nonparametric multiple imputation approach for missing categorical data

    Directory of Open Access Journals (Sweden)

    Muhan Zhou

    2017-06-01

    Full Text Available Abstract Background Incomplete categorical variables with more than two categories are common in public health data. However, most of the existing missing-data methods do not use the information from nonresponse (missingness probabilities. Methods We propose a nearest-neighbour multiple imputation approach to impute a missing at random categorical outcome and to estimate the proportion of each category. The donor set for imputation is formed by measuring distances between each missing value with other non-missing values. The distance function is calculated based on a predictive score, which is derived from two working models: one fits a multinomial logistic regression for predicting the missing categorical outcome (the outcome model and the other fits a logistic regression for predicting missingness probabilities (the missingness model. A weighting scheme is used to accommodate contributions from two working models when generating the predictive score. A missing value is imputed by randomly selecting one of the non-missing values with the smallest distances. We conduct a simulation to evaluate the performance of the proposed method and compare it with several alternative methods. A real-data application is also presented. Results The simulation study suggests that the proposed method performs well when missingness probabilities are not extreme under some misspecifications of the working models. However, the calibration estimator, which is also based on two working models, can be highly unstable when missingness probabilities for some observations are extremely high. In this scenario, the proposed method produces more stable and better estimates. In addition, proper weights need to be chosen to balance the contributions from the two working models and achieve optimal results for the proposed method. Conclusions We conclude that the proposed multiple imputation method is a reasonable approach to dealing with missing categorical outcome data with

  1. A novel statistic for genome-wide interaction analysis.

    Directory of Open Access Journals (Sweden)

    Xuesen Wu

    2010-09-01

    Full Text Available Although great progress in genome-wide association studies (GWAS has been made, the significant SNP associations identified by GWAS account for only a few percent of the genetic variance, leading many to question where and how we can find the missing heritability. There is increasing interest in genome-wide interaction analysis as a possible source of finding heritability unexplained by current GWAS. However, the existing statistics for testing interaction have low power for genome-wide interaction analysis. To meet challenges raised by genome-wide interactional analysis, we have developed a novel statistic for testing interaction between two loci (either linked or unlinked. The null distribution and the type I error rates of the new statistic for testing interaction are validated using simulations. Extensive power studies show that the developed statistic has much higher power to detect interaction than classical logistic regression. The results identified 44 and 211 pairs of SNPs showing significant evidence of interactions with FDR<0.001 and 0.001genome-wide interaction analysis is a valuable tool for finding remaining missing heritability unexplained by the current GWAS, and the developed novel statistic is able to search significant interaction between SNPs across the genome. Real data analysis showed that the results of genome-wide interaction analysis can be replicated in two independent studies.

  2. Patterns and Outcome of Missed Injuries in Egyptians Polytrauma Patients

    Directory of Open Access Journals (Sweden)

    Adel Hamed Elbaih

    2018-01-01

    Full Text Available Introduction: “polytrauma” patients are higher risk of complications and death than the summation of expected mortality and morbidity of their individual injuries. The ideal goal in trauma resuscitation care is to identify and treat all injuries. With clinical and technological advanced imaging available for diagnosis and treatment of traumatic patients, missed injuries still significant affect modern trauma services and its outcome. Aim: to improve outcome and determine the incidence and nature of missed injuries in polytrauma patients. Methods: the study is a cross-sectional, prospective study included 600 polytraumatized patients admitted in Suez Canal University Hospital. Firstly assessed and treated accordingly to Advanced Trauma Life Support (ATLS guidelines and treat the life threading conditions if present with follow-up short outcome for 28 days. Results: The most common precipitate factor for missed injuries in my study was clinical evaluation error due to Inadequate diagnostic workup in 42.9%. And the second risk factor was Deficiency in Physical Examination in 35.7%. Lastly Incomplete assessment due to patient instability in 10.7% and incorrect interpretation of imaging10.7%.low rates of missed injuries (40.8% in patients arriving during the day compared with (59.2% of night arrivals. Conclusion: the incidence of missed injuries in the study is 9.0 % which is still high compared to many trauma centers. And mostly increase the period of stay in the hospital and affect the outcome of polytrauma patients.

  3. Moderation analysis with missing data in the predictors.

    Science.gov (United States)

    Zhang, Qian; Wang, Lijuan

    2017-12-01

    The most widely used statistical model for conducting moderation analysis is the moderated multiple regression (MMR) model. In MMR modeling, missing data could pose a challenge, mainly because the interaction term is a product of two or more variables and thus is a nonlinear function of the involved variables. In this study, we consider a simple MMR model, where the effect of the focal predictor X on the outcome Y is moderated by a moderator U. The primary interest is to find ways of estimating and testing the moderation effect with the existence of missing data in X. We mainly focus on cases when X is missing completely at random (MCAR) and missing at random (MAR). Three methods are compared: (a) Normal-distribution-based maximum likelihood estimation (NML); (b) Normal-distribution-based multiple imputation (NMI); and (c) Bayesian estimation (BE). Via simulations, we found that NML and NMI could lead to biased estimates of moderation effects under MAR missingness mechanism. The BE method outperformed NMI and NML for MMR modeling with missing data in the focal predictor, missingness depending on the moderator and/or auxiliary variables, and correctly specified distributions for the focal predictor. In addition, more robust BE methods are needed in terms of the distribution mis-specification problem of the focal predictor. An empirical example was used to illustrate the applications of the methods with a simple sensitivity analysis. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

  4. The handling of missing binary data in language research

    Directory of Open Access Journals (Sweden)

    François Pichette

    2015-01-01

    Full Text Available Researchers are frequently confronted with unanswered questions or items on their questionnaires and tests, due to factors such as item difficulty, lack of testing time, or participant distraction. This paper first presents results from a poll confirming previous claims (Rietveld & van Hout, 2006; Schafer & Gra- ham, 2002 that data replacement and deletion methods are common in research. Language researchers declared that when faced with missing answers of the yes/no type (that translate into zero or one in data tables, the three most common solutions they adopt are to exclude the participant’s data from the analyses, to leave the square empty, or to fill in with zero, as for an incorrect answer. This study then examines the impact on Cronbach’s α of five types of data insertion, using simulated and actual data with various numbers of participants and missing percentages. Our analyses indicate that the three most common methods we identified among language researchers are the ones with the greatest impact  n Cronbach's α coefficients; in other words, they are the least desirable solutions to the missing data problem. On the basis of our results, we make recommendations for language researchers concerning the best way to deal with missing data. Given that none of the most common simple methods works properly, we suggest that the missing data be replaced either by the item’s mean or by the participants’ overall mean to provide a better, more accurate image of the instrument’s internal consistency.

  5. Ultrasonographic findings of Myoma, H-mole and Missed abortion

    International Nuclear Information System (INIS)

    Huh, Nam Yoon; You, H. S.; Seong, K. J.; Park, C. Y.

    1982-01-01

    Ultrasonography is very important in the diagnosis of various kinds of diseases in Obsterics and Gynecology. It has high diagnostic accuracy in the diagnosis of pelvic masses and widely used for the detection of normal orpathologic pregnancy. But still it is difficult to differentiate degenerated myoma, H-mole and missed abortion by ultrasonography. So the authors analyzed the ultrasonographic findings of 81 patients with myoma(29 cases), H-mole(23 cases), and missed abortion(29 cases) and the results are as follows; 1. Diagnostic accuracy was 8.6% in myoma, 87% in H-mole and 89% in missed abortion. 2. The most typical ultrasonographic finding of myoma was obulated mass contour with nonhomogenous internal echo. 3. The most characteristic finding of H-mole was fine vesicular pattern internal echo with globular enlargement of uterus. 4. The most frequent finding of missed abortion was deformed gestational sac with or without remained fetal echo. 5. Clinical correlation was very important for accurate diagnosis, especially when differential diagnosis was very difficult between myoma with marked cystic degeneration, missed abortion with large distorted gestational sac and H-mole with severe degeneration

  6. Principal Component Analysis of Process Datasets with Missing Values

    Directory of Open Access Journals (Sweden)

    Kristen A. Severson

    2017-07-01

    Full Text Available Datasets with missing values arising from causes such as sensor failure, inconsistent sampling rates, and merging data from different systems are common in the process industry. Methods for handling missing data typically operate during data pre-processing, but can also occur during model building. This article considers missing data within the context of principal component analysis (PCA, which is a method originally developed for complete data that has widespread industrial application in multivariate statistical process control. Due to the prevalence of missing data and the success of PCA for handling complete data, several PCA algorithms that can act on incomplete data have been proposed. Here, algorithms for applying PCA to datasets with missing values are reviewed. A case study is presented to demonstrate the performance of the algorithms and suggestions are made with respect to choosing which algorithm is most appropriate for particular settings. An alternating algorithm based on the singular value decomposition achieved the best results in the majority of test cases involving process datasets.

  7. Comparative Genome Analysis and Genome Evolution

    NARCIS (Netherlands)

    Snel, Berend

    2002-01-01

    This thesis described a collection of bioinformatic analyses on complete genome sequence data. We have studied the evolution of gene content and find that vertical inheritance dominates over horizontal gene trasnfer, even to the extent that we can use the gene content to make genome phylogenies.

  8. Correcting Inconsistencies and Errors in Bacterial Genome Metadata Using an Automated Curation Tool in Excel (AutoCurE).

    Science.gov (United States)

    Schmedes, Sarah E; King, Jonathan L; Budowle, Bruce

    2015-01-01

    Whole-genome data are invaluable for large-scale comparative genomic studies. Current sequencing technologies have made it feasible to sequence entire bacterial genomes with relative ease and time with a substantially reduced cost per nucleotide, hence cost per genome. More than 3,000 bacterial genomes have been sequenced and are available at the finished status. Publically available genomes can be readily downloaded; however, there are challenges to verify the specific supporting data contained within the download and to identify errors and inconsistencies that may be present within the organizational data content and metadata. AutoCurE, an automated tool for bacterial genome database curation in Excel, was developed to facilitate local database curation of supporting data that accompany downloaded genomes from the National Center for Biotechnology Information. AutoCurE provides an automated approach to curate local genomic databases by flagging inconsistencies or errors by comparing the downloaded supporting data to the genome reports to verify genome name, RefSeq accession numbers, the presence of archaea, BioProject/UIDs, and sequence file descriptions. Flags are generated for nine metadata fields if there are inconsistencies between the downloaded genomes and genomes reports and if erroneous or missing data are evident. AutoCurE is an easy-to-use tool for local database curation for large-scale genome data prior to downstream analyses.

  9. Genomic Data Commons launches

    Science.gov (United States)

    The Genomic Data Commons (GDC), a unified data system that promotes sharing of genomic and clinical data between researchers, launched today with a visit from Vice President Joe Biden to the operations center at the University of Chicago.

  10. Rat Genome Database (RGD)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Rat Genome Database (RGD) is a collaborative effort between leading research institutions involved in rat genetic and genomic research to collect, consolidate,...

  11. Visualization for genomics: the Microbial Genome Viewer.

    Science.gov (United States)

    Kerkhoven, Robert; van Enckevort, Frank H J; Boekhorst, Jos; Molenaar, Douwe; Siezen, Roland J

    2004-07-22

    A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a MySQL database. The generated images are in scalable vector graphics (SVG) format, which is suitable for creating high-quality scalable images and dynamic Web representations. Gene-related data such as transcriptome and time-course microarray experiments can be superimposed on the maps for visual inspection. The Microbial Genome Viewer 1.0 is freely available at http://www.cmbi.kun.nl/MGV

  12. Prediction of Missing Streamflow Data using Principle of Information Entropy

    Directory of Open Access Journals (Sweden)

    Santosa, B.

    2014-01-01

    Full Text Available Incomplete (missing of streamflow data often occurs. This can be caused by a not continous data recording or poor storage. In this study, missing consecutive streamflow data are predicted using the principle of information entropy. Predictions are performed ​​using the complete monthly streamflow information from the nearby river. Data on average monthly streamflow used as a simulation sample are taken from observation stations Katulampa, Batubeulah, and Genteng, which are the Ciliwung Cisadane river areas upstream. The simulated prediction of missing streamflow data in 2002 and 2003 at Katulampa Station are based on information from Genteng Station, and Batubeulah Station. The mean absolute error (MAE average obtained was 0,20 and 0,21 in 2002 and the MAE average in 2003 was 0,12 and 0,16. Based on the value of the error and pattern of filled gaps, this method has the potential to be developed further.

  13. Genomic prediction using subsampling

    OpenAIRE

    Xavier, Alencar; Xu, Shizhong; Muir, William; Rainey, Katy Martin

    2017-01-01

    Background Genome-wide assisted selection is a critical tool for the?genetic improvement of plants and animals. Whole-genome regression models in Bayesian framework represent the main family of prediction methods. Fitting such models with a large number of observations involves a prohibitive computational burden. We propose the use of subsampling bootstrap Markov chain in genomic prediction. Such method consists of fitting whole-genome regression models by subsampling observations in each rou...

  14. Analyzing time-ordered event data with missed observations.

    Science.gov (United States)

    Dokter, Adriaan M; van Loon, E Emiel; Fokkema, Wimke; Lameris, Thomas K; Nolet, Bart A; van der Jeugd, Henk P

    2017-09-01

    A common problem with observational datasets is that not all events of interest may be detected. For example, observing animals in the wild can difficult when animals move, hide, or cannot be closely approached. We consider time series of events recorded in conditions where events are occasionally missed by observers or observational devices. These time series are not restricted to behavioral protocols, but can be any cyclic or recurring process where discrete outcomes are observed. Undetected events cause biased inferences on the process of interest, and statistical analyses are needed that can identify and correct the compromised detection processes. Missed observations in time series lead to observed time intervals between events at multiples of the true inter-event time, which conveys information on their detection probability. We derive the theoretical probability density function for observed intervals between events that includes a probability of missed detection. Methodology and software tools are provided for analysis of event data with potential observation bias and its removal. The methodology was applied to simulation data and a case study of defecation rate estimation in geese, which is commonly used to estimate their digestive throughput and energetic uptake, or to calculate goose usage of a feeding site from dropping density. Simulations indicate that at a moderate chance to miss arrival events ( p  = 0.3), uncorrected arrival intervals were biased upward by up to a factor 3, while parameter values corrected for missed observations were within 1% of their true simulated value. A field case study shows that not accounting for missed observations leads to substantial underestimates of the true defecation rate in geese, and spurious rate differences between sites, which are introduced by differences in observational conditions. These results show that the derived methodology can be used to effectively remove observational biases in time-ordered event

  15. Ultrasonographic findings of hydatidiform mole and missed abortion

    International Nuclear Information System (INIS)

    Yun, Kwang Myeong; Lee, Yeong Hwan; Chung, Hye Kyeong; Chung, Duck Soo; Kim, Ok Dong

    1990-01-01

    To establish the sonographic characteristics of the hydatidiform mole and the missed abortion with placental degeneration, we have retrospectively analyzed 12 cases of complete mole, 10 cases of partial mole, and 10 cases of missed abortion with placental hydropic degeneration, collected at Taegu Catholic General Hospital, from January 1986 to December 1989. The results were as follows : 1. Of 12 cases of complete mole, all demonstrated diffuse intrauterine vesicular pattern of internal echo without a gestational sac. Two cases were recurred after D and E. 2. The partial mole was characterized by focal (70%) or diffuse (20%) distribution of hydatidiform placental change and a gestational sac (100%) with or without a macerated fetus. But the striking hydatidiform placental change was not present in one cases of partial mole. 3. The uterus was larger for dates in 9 cases (90%) of complete mole, but smaller for dates in 7 cases (70%) of partial mole. 4. The missed abortion with placental hydropic degeneration was indistinguished from a partial mole due to their similar sonographic appearance : focal or diffuse cystic change of a placenta, a distorted gestational sac with or without a fetus, and a smaller uterus for dates. On conclusion, the complete mole could be easily distinguished from a partial mole or a missed abortion by sonography : a gestational sac or an area of noncystic placenta was not identified in a complete mole. The partial mole was indistinguished from a missed abortion, but if there is the suspicion of trophoblastic proliferation, such as a convex placental surface or a larger uterus for dates, then the diagnosis is probably a partial mole rather than a missed abortion

  16. VIGAN: Missing View Imputation with Generative Adversarial Networks.

    Science.gov (United States)

    Shang, Chao; Palmer, Aaron; Sun, Jiangwen; Chen, Ko-Shin; Lu, Jin; Bi, Jinbo

    2017-01-01

    In an era when big data are becoming the norm, there is less concern with the quantity but more with the quality and completeness of the data. In many disciplines, data are collected from heterogeneous sources, resulting in multi-view or multi-modal datasets. The missing data problem has been challenging to address in multi-view data analysis. Especially, when certain samples miss an entire view of data, it creates the missing view problem. Classic multiple imputations or matrix completion methods are hardly effective here when no information can be based on in the specific view to impute data for such samples. The commonly-used simple method of removing samples with a missing view can dramatically reduce sample size, thus diminishing the statistical power of a subsequent analysis. In this paper, we propose a novel approach for view imputation via generative adversarial networks (GANs), which we name by VIGAN. This approach first treats each view as a separate domain and identifies domain-to-domain mappings via a GAN using randomly-sampled data from each view, and then employs a multi-modal denoising autoencoder (DAE) to reconstruct the missing view from the GAN outputs based on paired data across the views. Then, by optimizing the GAN and DAE jointly, our model enables the knowledge integration for domain mappings and view correspondences to effectively recover the missing view. Empirical results on benchmark datasets validate the VIGAN approach by comparing against the state of the art. The evaluation of VIGAN in a genetic study of substance use disorders further proves the effectiveness and usability of this approach in life science.

  17. Empirical Likelihood in Nonignorable Covariate-Missing Data Problems.

    Science.gov (United States)

    Xie, Yanmei; Zhang, Biao

    2017-04-20

    Missing covariate data occurs often in regression analysis, which frequently arises in the health and social sciences as well as in survey sampling. We study methods for the analysis of a nonignorable covariate-missing data problem in an assumed conditional mean function when some covariates are completely observed but other covariates are missing for some subjects. We adopt the semiparametric perspective of Bartlett et al. (Improving upon the efficiency of complete case analysis when covariates are MNAR. Biostatistics 2014;15:719-30) on regression analyses with nonignorable missing covariates, in which they have introduced the use of two working models, the working probability model of missingness and the working conditional score model. In this paper, we study an empirical likelihood approach to nonignorable covariate-missing data problems with the objective of effectively utilizing the two working models in the analysis of covariate-missing data. We propose a unified approach to constructing a system of unbiased estimating equations, where there are more equations than unknown parameters of interest. One useful feature of these unbiased estimating equations is that they naturally incorporate the incomplete data into the data analysis, making it possible to seek efficient estimation of the parameter of interest even when the working regression function is not specified to be the optimal regression function. We apply the general methodology of empirical likelihood to optimally combine these unbiased estimating equations. We propose three maximum empirical likelihood estimators of the underlying regression parameters and compare their efficiencies with other existing competitors. We present a simulation study to compare the finite-sample performance of various methods with respect to bias, efficiency, and robustness to model misspecification. The proposed empirical likelihood method is also illustrated by an analysis of a data set from the US National Health and

  18. Ebolavirus comparative genomics

    DEFF Research Database (Denmark)

    Jun, Se-Ran; Leuze, Michael R.; Nookaew, Intawat

    2015-01-01

    The 2014 Ebola outbreak in West Africa is the largest documented for this virus. To examine the dynamics of this genome, we compare more than 100 currently available ebolavirus genomes to each other and to other viral genomes. Based on oligomer frequency analysis, the family Filoviridae forms...

  19. The mystery of Japan's missing centenarians explained

    Directory of Open Access Journals (Sweden)

    Yasuhiko Saito

    2012-03-01

    Full Text Available This report elucidates the issue of Japan's missing centenarians, which was uncovered in 2010. We provide the latest figures from verification efforts, discuss sources of centenarian information in Japan, examine possible causes, and evaluate the effect of the missing centenarians on official statistics. In Japan 234,354 people registered before 1910 remained on the family registers in 2010, without being crossed out. They would have been 100 years old at least and represent 0.5Š of the births recorded between 1872 and 1910. The impact of this group on life expectancy statistics, however, is effectively nil.

  20. Genome sequencing elucidates Sardinian genetic architecture and augments association analyses for lipid and blood inflammatory markers

    Science.gov (United States)

    Zoledziewska, Magdalena; Mulas, Antonella; Pistis, Giorgio; Steri, Maristella; Danjou, Fabrice; Kwong, Alan; Ortega del Vecchyo, Vicente Diego; Chiang, Charleston W. K.; Bragg-Gresham, Jennifer; Pitzalis, Maristella; Nagaraja, Ramaiah; Tarrier, Brendan; Brennan, Christine; Uzzau, Sergio; Fuchsberger, Christian; Atzeni, Rossano; Reinier, Frederic; Berutti, Riccardo; Huang, Jie; Timpson, Nicholas J; Toniolo, Daniela; Gasparini, Paolo; Malerba, Giovanni; Dedoussis, George; Zeggini, Eleftheria; Soranzo, Nicole; Jones, Chris; Lyons, Robert; Angius, Andrea; Kang, Hyun M.; Novembre, John; Sanna, Serena; Schlessinger, David; Cucca, Francesco; Abecasis, Gonçalo R

    2015-01-01

    We report ~17.6M genetic variants from whole-genome sequencing of 2,120 Sardinians; 22% are absent from prior sequencing-based compilations and enriched for predicted functional consequence. Furthermore, ~76K variants common in our sample (frequency >5%) are rare elsewhere (Genomes Project). We assessed the impact of these variants on circulating lipid levels and five inflammatory biomarkers. Fourteen signals, including two major new loci, were observed for lipid levels, and 19, including two novel loci, for inflammatory markers. New associations would be missed in analyses based on 1000 Genomes data, underlining the advantages of large-scale sequencing in this founder population. PMID:26366554

  1. The Sequenced Angiosperm Genomes and Genome Databases.

    Science.gov (United States)

    Chen, Fei; Dong, Wei; Zhang, Jiawei; Guo, Xinyue; Chen, Junhao; Wang, Zhengjia; Lin, Zhenguo; Tang, Haibao; Zhang, Liangsheng

    2018-01-01

    Angiosperms, the flowering plants, provide the essential resources for human life, such as food, energy, oxygen, and materials. They also promoted the evolution of human, animals, and the planet earth. Despite the numerous advances in genome reports or sequencing technologies, no review covers all the released angiosperm genomes and the genome databases for data sharing. Based on the rapid advances and innovations in the database reconstruction in the last few years, here we provide a comprehensive review for three major types of angiosperm genome databases, including databases for a single species, for a specific angiosperm clade, and for multiple angiosperm species. The scope, tools, and data of each type of databases and their features are concisely discussed. The genome databases for a single species or a clade of species are especially popular for specific group of researchers, while a timely-updated comprehensive database is more powerful for address of major scientific mysteries at the genome scale. Considering the low coverage of flowering plants in any available database, we propose construction of a comprehensive database to facilitate large-scale comparative studies of angiosperm genomes and to promote the collaborative studies of important questions in plant biology.

  2. Moving, sensing intersectionality: a case study of Miss China Europe

    NARCIS (Netherlands)

    Chow, Y.F.

    2011-01-01

    Every year, Miss China Europe, a transnational beauty pageant organized for the Chinese diaspora, is held in the Netherlands. The hypervisuality of Chinese diasporic women at the event stands in painful contrast to their everyday invisibility, whether in the Netherlands, China, or elsewhere in the

  3. The Politics and Paradoxes of Censorship: "Miss Lonelyhearts" in Hollywood.

    Science.gov (United States)

    Veitch, Jonathan

    1997-01-01

    Examines how Nathanael West's darkly critical text in his novel "Miss Lonelyhearts" was censored, through a series of demurrals and evasions, displacements and substitutions, even repression, to make it acceptable for the screen. Suggests that the resulting script illuminates the momentous cultural struggles underway in 1930s America--in…

  4. Exploratory Factor Analysis With Small Samples and Missing Data.

    Science.gov (United States)

    McNeish, Daniel

    2017-01-01

    Exploratory factor analysis (EFA) is an extremely popular method for determining the underlying factor structure for a set of variables. Due to its exploratory nature, EFA is notorious for being conducted with small sample sizes, and recent reviews of psychological research have reported that between 40% and 60% of applied studies have 200 or fewer observations. Recent methodological studies have addressed small size requirements for EFA models; however, these models have only considered complete data, which are the exception rather than the rule in psychology. Furthermore, the extant literature on missing data techniques with small samples is scant, and nearly all existing studies focus on topics that are not of primary interest to EFA models. Therefore, this article presents a simulation to assess the performance of various missing data techniques for EFA models with both small samples and missing data. Results show that deletion methods do not extract the proper number of factors and estimate the factor loadings with severe bias, even when data are missing completely at random. Predictive mean matching is the best method overall when considering extracting the correct number of factors and estimating factor loadings without bias, although 2-stage estimation was a close second.

  5. Proposed Interventions to Decrease the Frequency of Missed Test Results

    Science.gov (United States)

    Wahls, Terry L.; Cram, Peter

    2009-01-01

    Numerous studies have identified that delays in diagnosis related to the mishandling of abnormal test results are an import contributor to diagnostic errors. Factors contributing to missed results included organizational factors, provider factors and patient-related factors. At the diagnosis error conference continuing medical education conference…

  6. Introducing CSR - The Missing Ingredient in the Land Reform Recipe?

    African Journals Online (AJOL)

    This article identifies corporate social responsibility (CSR) as one of the missing ingredients in the recipe for a successful land reform programme. The article introduces CSR and discusses the business case for CSR; identifies its benefits; considers its possible limitations; and examines the major drivers behind the notion.

  7. 40 CFR 98.415 - Procedures for estimating missing data.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 20 2010-07-01 2010-07-01 false Procedures for estimating missing data. 98.415 Section 98.415 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) MANDATORY GREENHOUSE GAS REPORTING Suppliers of Industrial Greenhouse Gases § 98.415...

  8. On Stories and Theories: In Appreciation of Miss Freud

    Science.gov (United States)

    Cottle, Thomas J.

    2007-01-01

    In this article, the author reflects on Bert Cohler's essay "Desire, Teaching and Learning" and relates it to his teacher, Miss Anna Freud's story. The author asks whether it is possible that what one sees and hears, and encounters as teacher is only partially what is really out there in one's classroom and in the heads of one's students and…

  9. Hepatitis B and the Case of the Missing Women

    Science.gov (United States)

    Oster, Emily

    2005-01-01

    In many Asian countries the ratio of male to female population is higher than in the West: as high as 1.07 in China and India, and even higher in Pakistan. A number of authors (most notably Amartya Sen) have suggested that this imbalance reflects excess female mortality and have argued that as many as 100 million women are "missing."…

  10. Knowledge of Consequences of missing teeth in patients attending ...

    African Journals Online (AJOL)

    There was no significant difference between the knowledge of the consequences of missing teeth and sex or on level of education (p 0.05). Dentists constituted the largest source of information to these patients (25.6%) while the media constituted the least (0.5%). Conclusion: The result of this study showed poor knowledge ...

  11. Missed vaccination opportunities at a secondary health facility in ...

    African Journals Online (AJOL)

    The study aimed to identify missed vaccination visits and the associated factors in children presenting at the general out-patient clinic of a secondary health facility in Ilorin, Nigeria. Method: Through a descriptive cross-sectional study, the vaccination data of all children seen at the out-patient clinic were critically reviewed ...

  12. The Dutch Are Missing in the American Curriculum

    Science.gov (United States)

    Claunch, Ann

    2009-01-01

    The Dutch are missing in any U.S. history textbook, in the content standards, and in the nationally endorsed curriculum. Outside of New York State history classes, there is almost no mention of the Dutch influence in early 17th-century America. Fleeting references to the Netherlands as a staging area for the Pilgrims' famous "Mayflower"…

  13. Near miss reporting in the chemical process industry: an overview

    NARCIS (Netherlands)

    Schaaf, van der T.W.

    1995-01-01

    The research programme described in this paper focuses on the human component of system failure in general, and more specifically on the design and implementation of information systems for registration and analysis of so called near misses (or: near accidents) in the chemical process industry. Its

  14. Vesical Calculus 10 Years Post Missing Intrauterine Contraceptive ...

    African Journals Online (AJOL)

    Vesical Calculus 10 Years Post Missing Intrauterine. Contraceptive Device. Abdullahi Abdulwahab-Ahmed, Oluwagbemiga Olabisi Ogunleye. INTRODUCTION. Intrauterine contraceptive devices (IUCD) are acceptable means of contraception world over.[1-4] There have been reports of its migration to other adjourning sites ...

  15. Vesical Calculus 10 Years Post Missing Intrauterine Contraceptive ...

    African Journals Online (AJOL)

    Intravesical migration of intrauterine contraceptive device (IUCD) is rare. Early diagnosis of this rare entity is difficult because of its non‑specific manifestations and very low index of suspicion. We present this case of bladder stone following intravesical migration of IUCD found to have been missing since insertion 10 years ...

  16. Sample-Based Extreme Learning Machine with Missing Data

    Directory of Open Access Journals (Sweden)

    Hang Gao

    2015-01-01

    Full Text Available Extreme learning machine (ELM has been extensively studied in machine learning community during the last few decades due to its high efficiency and the unification of classification, regression, and so forth. Though bearing such merits, existing ELM algorithms cannot efficiently handle the issue of missing data, which is relatively common in practical applications. The problem of missing data is commonly handled by imputation (i.e., replacing missing values with substituted values according to available information. However, imputation methods are not always effective. In this paper, we propose a sample-based learning framework to address this issue. Based on this framework, we develop two sample-based ELM algorithms for classification and regression, respectively. Comprehensive experiments have been conducted in synthetic data sets, UCI benchmark data sets, and a real world fingerprint image data set. As indicated, without introducing extra computational complexity, the proposed algorithms do more accurate and stable learning than other state-of-the-art ones, especially in the case of higher missing ratio.

  17. Missed Opportunities for Health Education on Pap Smears in Peru

    Science.gov (United States)

    Bayer, Angela M.; Nussbaum, Lauren; Cabrera, Lilia; Paz-Soldan, Valerie A.

    2011-01-01

    Despite cervical cancer being one of the leading causes of cancer-related deaths among women in Peru, cervical Pap smear coverage is low. This article uses findings from 185 direct clinician observations in four cities of Peru (representing the capital and each of the three main geographic regions of the country) to assess missed opportunities for…

  18. Altering the "Near-Miss" Effect in Slot Machine Gamblers

    Science.gov (United States)

    Dixon, Mark R.; Nastally, Becky L.; Jackson, James E.; Habib, Reza

    2009-01-01

    This study investigated the potential for recreational gamblers to respond as if certain types of losing slot machine outcomes were actually closer to a win than others (termed the "near-miss effect"). Exposure to conditional discrimination training and testing disrupted this effect for 10 of the 16 participants. These 10 participants demonstrated…

  19. Missing Mass Searches in Dimuon Events with CT-PPS

    CERN Document Server

    Mironova, Maria

    2017-01-01

    In this summer student project the feasibility of missing mass searches with the CMS TOTEM Precision Proton Spectrometer was studied. Using a combination of CMS and CT-PPS data and Monte Carlo simulations, cuts to reduce the Drell Yan background were made and the expected signal was estimated.

  20. Optimal simultaneous superpositioning of multiple structures with missing data.

    Science.gov (United States)

    Theobald, Douglas L; Steindel, Phillip A

    2012-08-01

    Superpositioning is an essential technique in structural biology that facilitates the comparison and analysis of conformational differences among topologically similar structures. Performing a superposition requires a one-to-one correspondence, or alignment, of the point sets in the different structures. However, in practice, some points are usually 'missing' from several structures, for example, when the alignment contains gaps. Current superposition methods deal with missing data simply by superpositioning a subset of points that are shared among all the structures. This practice is inefficient, as it ignores important data, and it fails to satisfy the common least-squares criterion. In the extreme, disregarding missing positions prohibits the calculation of a superposition altogether. Here, we present a general solution for determining an optimal superposition when some of the data are missing. We use the expectation-maximization algorithm, a classic statistical technique for dealing with incomplete data, to find both maximum-likelihood solutions and the optimal least-squares solution as a special case. The methods presented here are implemented in THESEUS 2.0, a program for superpositioning macromolecular structures. ANSI C source code and selected compiled binaries for various computing platforms are freely available under the GNU open source license from http://www.theseus3d.org. dtheobald@brandeis.edu Supplementary data are available at Bioinformatics online.

  1. Explaining Tevatron leptons photons missing- T events with ...

    Indian Academy of Sciences (India)

    Abstract. The CDF experiment reported a lepton photon missing transverse energy. (/ET) signal 3σ in excess of the standard model prediction in Tevatron Run I data. The excess can be explained by the resonant production of a smuon, which subsequently decays to a muon, a photon and a gravitino. Here, we perform ...

  2. Gingival Recession in a Child‑Patient; Easily Missed Etiologies ...

    African Journals Online (AJOL)

    with age-appropriate complement of teeth except for a missing tooth 42. ... frenal attachment is more important in gingival recession in the child‑patient. A healthy child‑ ... spared rules out a possible role of brushing-induced gingival abrasion.

  3. Missing Chapters II: West Virginia Women in History.

    Science.gov (United States)

    Hensley, Frances S., Ed.

    This collection of essays chronicles the contributions of 14 West Virginia women active in individual and group endeavors from 1824 to the present. Because the achievements of these women are absent from previous histories of West Virginia, their stories constitute missing chapters in the state's history. Some of these women made contributions in…

  4. Stomatal vs. genome size in angiosperms: the somatic tail wagging the genomic dog?

    Science.gov (United States)

    Hodgson, J G; Sharafi, M; Jalili, A; Díaz, S; Montserrat-Martí, G; Palmer, C; Cerabolini, B; Pierce, S; Hamzehee, B; Asri, Y; Jamzad, Z; Wilson, P; Raven, J A; Band, S R; Basconcelo, S; Bogard, A; Carter, G; Charles, M; Castro-Díez, P; Cornelissen, J H C; Funes, G; Jones, G; Khoshnevis, M; Pérez-Harguindeguy, N; Pérez-Rontomé, M C; Shirvany, F A; Vendramini, F; Yazdani, S; Abbas-Azimi, R; Boustani, S; Dehghan, M; Guerrero-Campo, J; Hynd, A; Kowsary, E; Kazemi-Saeed, F; Siavash, B; Villar-Salvador, P; Craigie, R; Naqinezhad, A; Romo-Díez, A; de Torres Espuny, L; Simmons, E

    2010-04-01

    Genome size is a function, and the product, of cell volume. As such it is contingent on ecological circumstance. The nature of 'this ecological circumstance' is, however, hotly debated. Here, we investigate for angiosperms whether stomatal size may be this 'missing link': the primary determinant of genome size. Stomata are crucial for photosynthesis and their size affects functional efficiency. Stomatal and leaf characteristics were measured for 1442 species from Argentina, Iran, Spain and the UK and, using PCA, some emergent ecological and taxonomic patterns identified. Subsequently, an assessment of the relationship between genome-size values obtained from the Plant DNA C-values database and measurements of stomatal size was carried out. Stomatal size is an ecologically important attribute. It varies with life-history (woody species < herbaceous species < vernal geophytes) and contributes to ecologically and physiologically important axes of leaf specialization. Moreover, it is positively correlated with genome size across a wide range of major taxa. Stomatal size predicts genome size within angiosperms. Correlation is not, however, proof of causality and here our interpretation is hampered by unexpected deficiencies in the scientific literature. Firstly, there are discrepancies between our own observations and established ideas about the ecological significance of stomatal size; very large stomata, theoretically facilitating photosynthesis in deep shade, were, in this study (and in other studies), primarily associated with vernal geophytes of unshaded habitats. Secondly, the lower size limit at which stomata can function efficiently, and the ecological circumstances under which these minute stomata might occur, have not been satisfactorally resolved. Thus, our hypothesis, that the optimization of stomatal size for functional efficiency is a major ecological determinant of genome size, remains unproven.

  5. Diagnostic Laparoscopy for Trauma: How Not to Miss Injuries.

    Science.gov (United States)

    Koto, Modise Z; Matsevych, Oleh Y; Aldous, Colleen

    2018-05-01

    Diagnostic laparoscopy (DL) is a well-accepted approach for penetrating abdominal trauma (PAT). However, the steps of procedure and the systematic laparoscopic examination are not clearly defined in the literature. The aim of this study was to clarify the definition of DL in trauma surgery by auditing DL performed for PAT at our institution, and to describe the strategies on how to avoid missed injuries. The data of patients managed with laparoscopy for PAT from January 2012 to December 2015 were retrospectively analyzed. The details of operative technique and strategies on how to avoid missed injuries were discussed. Out of 250 patients managed with laparoscopy for PAT, 113 (45%) patients underwent DL. Stab wounds sustained 94 (83%) patients. The penetration of the peritoneal cavity or retroperitoneum was documented in 67 (59%) of patients. Organ evisceration was present in 21 (19%) patients. Multiple injuries were present in 22% of cases. The chest was the most common associated injury. Two (1.8%) iatrogenic injuries were recorded. The conversion rate was 1.7% (2/115). The mean length of hospital stay was 4 days. There were no missed injuries. In the therapeutic laparoscopy (TL) group, DL was performed as the initial part and identified all injuries. There were no missed injuries in the TL group. The predetermined sequential steps of DL and the standard systematic examination of intraabdominal organs were described. DL is a feasible and safe procedure. It accurately identifies intraabdominal injuries. The selected use of preoperative imaging, adherence to the predetermined steps of procedure and the standard systematic laparoscopic examination will minimize the rate of missed injuries.

  6. Missed injuries in the era of the trauma scan.

    Science.gov (United States)

    Lawson, Christy M; Daley, Brian J; Ormsby, Christine B; Enderson, Blaine

    2011-02-01

    A rapid computed tomography technique or "trauma scan" (TS) provides high-resolution studies of the head, cervical spine, chest, abdomen, and pelvis. We sought to determine whether TS has decreased missed injuries. A previous study of TS found a 3% missed rate. After institutional review board approval, trauma patients from January 2001 through December 2008 were reviewed for delayed diagnosis (DD) of injury to the head, cervical spine, chest, abdomen, or pelvis. Missed extremity injuries were excluded. Injury Severity Score, length of stay, type of injury, outcomes, and days to detection were captured. Of 26,264 patients reviewed, 90 patients had DD, with an incidence of 0.34%. DD most commonly presented on day 2. Injuries included 16 bowel/mesentery, 12 spine, 11 pelvic, 8 spleen, 6 diaphragm, 5 clavicle, 4 scapula, 4 cervical spine, 4 intracranial, 4 sternum, 3 maxillofacial, 3 liver, 2 heart/aorta, 2 vascular, 2 urethra/bladder, 2 pneumothorax, and 2 pancreas/common bile duct. DD resulted in 1 death, 6 prolonged intensive care unit stays, 19 operative interventions, and 38 additional interventions. TS is an effective way of evaluating trauma patients for intracranial, cervical spine, chest, abdomen, and pelvic injuries that have the potential to impact morbidity and mortality. The incidence of injuries missed in these crucial areas has been reduced at our institution by the use of this radiographic modality. The most common missed injury remains bowel, and so a high index of suspicion and the tertiary survey must remain a mainstay of therapy.

  7. Detection and analysis of ancient segmental duplications in mammalian genomes.

    Science.gov (United States)

    Pu, Lianrong; Lin, Yu; Pevzner, Pavel A

    2018-05-07

    Although segmental duplications (SDs) represent hotbeds for genomic rearrangements and emergence of new genes, there are still no easy-to-use tools for identifying SDs. Moreover, while most previous studies focused on recently emerged SDs, detection of ancient SDs remains an open problem. We developed an SDquest algorithm for SD finding and applied it to analyzing SDs in human, gorilla, and mouse genomes. Our results demonstrate that previous studies missed many SDs in these genomes and show that SDs account for at least 6.05% of the human genome (version hg19), a 17% increase as compared to the previous estimate. Moreover, SDquest classified 6.42% of the latest GRCh38 version of the human genome as SDs, a large increase as compared to previous studies. We thus propose to re-evaluate evolution of SDs based on their accurate representation across multiple genomes. Toward this goal, we analyzed the complex mosaic structure of SDs and decomposed mosaic SDs into elementary SDs, a prerequisite for follow-up evolutionary analysis. We also introduced the concept of the breakpoint graph of mosaic SDs that revealed SD hotspots and suggested that some SDs may have originated from circular extrachromosomal DNA (ecDNA), not unlike ecDNA that contributes to accelerated evolution in cancer. © 2018 Pu et al.; Published by Cold Spring Harbor Laboratory Press.

  8. RADseq dataset with 90% missing data fully resolves recent radiation of Petalidium (Acanthaceae) in the ultra-arid deserts of Namibia.

    Science.gov (United States)

    Tripp, Erin A; Tsai, Yi-Hsin Erica; Zhuang, Yongbin; Dexter, Kyle G

    2017-10-01

    Deserts, even those at tropical latitudes, often have strikingly low levels of plant diversity, particularly within genera. One remarkable exception to this pattern is the genus Petalidium (Acanthaceae), in which 37 of 40 named species occupy one of the driest environments on Earth, the Namib Desert of Namibia and neighboring Angola. To contribute to understanding this enigmatic diversity, we generated RADseq data for 47 accessions of Petalidium representing 22 species. We explored the impacts of 18 different combinations of assembly parameters in de novo assembly of the data across nine levels of missing data plus a best practice assembly using a reference Acanthaceae genome for a total of 171 sequence datasets assembled. RADseq data assembled at several thresholds of missing data, including 90% missing data, yielded phylogenetic hypotheses of Petalidium that were confidently and nearly fully resolved, which is notable given that divergence time analyses suggest a crown age for African species of 3.6-1.4 Ma. De novo assembly of our data yielded the most strongly supported and well-resolved topologies; in contrast, reference-based assembly performed poorly, perhaps due in part to moderate phylogenetic divergence between the reference genome, Ruellia speciosa , and the ingroup. Overall, we found that Petalidium , despite the harshness of the environment in which species occur, shows a net diversification rate (0.8-2.1 species per my) on par with those of diverse genera in tropical, Mediterranean, and alpine environments.

  9. High-density rhesus macaque oligonucleotide microarray design using early-stage rhesus genome sequence information and human genome annotations

    Directory of Open Access Journals (Sweden)

    Magness Charles L

    2007-01-01

    a closely related species. Conclusion The number of different genes represented on microarrays for unfinished genomes can be greatly increased by matching known gene transcript annotations from a closely related species with sequence data from the unfinished genome. Signal intensity on both EST- and genome-derived arrays was highly correlated with probe distance from the 3' UTR, information often missing from ESTs yet present in early-stage genome projects.

  10. Comparative genomics analysis of rice and pineapple contributes to understand the chromosome number reduction and genomic changes in grasses

    Directory of Open Access Journals (Sweden)

    Jinpeng Wang

    2016-10-01

    Full Text Available Rice is one of the most researched model plant, and has a genome structure most resembling that of the grass common ancestor after a grass common tetraploidization ~100 million years ago. There has been a standing controversy whether there had been 5 or 7 basic chromosomes, before the tetraploidization, which were tackled but could not be well solved for the lacking of a sequenced and assembled outgroup plant to have a conservative genome structure. Recently, the availability of pineapple genome, which has not been subjected to the grass-common tetraploidization, provides a precious opportunity to solve the above controversy and to research into genome changes of rice and other grasses. Here, we performed a comparative genomics analysis of pineapple and rice, and found solid evidence that grass-common ancestor had 2n =2x =14 basic chromosomes before the tetraploidization and duplicated to 2n = 4x = 28 after the event. Moreover, we proposed that enormous gene missing from duplicated regions in rice should be explained by an allotetraploid produced by prominently divergent parental lines, rather than gene losses after their divergence. This means that genome fractionation might have occurred before the formation of the allotetraploid grass ancestor.

  11. A family of selfish minicircular chromosomes with jumbled chloroplast gene fragments from a dinoflagellate.

    Science.gov (United States)

    Zhang, Z; Cavalier-Smith, T; Green, B R

    2001-08-01

    Chloroplast genes of several dinoflagellate species are located on unigenic DNA minicircular chromosomes. We have now completely sequenced five aberrant minicircular chromosomes from the dinoflagellate Heterocapsa triquetra. These probably nonfunctional DNA circles lack complete genes, with each being composed of several short fragments of two or three different chloroplast genes and a common conserved region with a tripartite 9G-9A-9G core like the putative replicon origin of functional single-gene circular chloroplast chromosomes. Their sequences imply that all five circles evolved by differential deletions and duplications from common ancestral circles bearing fragments of four genes: psbA, psbC, 16S rRNA, and 23S rRNA. It appears that recombination between separate unigenic chromosomes initially gave intermediate heterodimers, which were subsequently stabilized by deletions that included part or all of one putative replicon origin. We suggest that homologous recombination at the 9G-9A-9G core regions produced a psbA/psbC heterodimer which generated two distinct chimeric circles by differential deletions and duplications. A 23S/16S rRNA heterodimer more likely formed by illegitimate recombination between 16S and 23S rRNA genes. Homologous recombination between the 9G-9A-9G core regions of both heterodimers and additional differential deletions and duplications could then have yielded the other three circles. Near identity of the gene fragments and 9G-9A-9G cores, despite diverging adjacent regions, may be maintained by gene conversion. The conserved organization of the 9G-9A-9G cores alone favors the idea that they are replicon origins and suggests that they may enable the aberrant minicircles to parasitize the chloroplast's replication machinery as selfish circles.

  12. Genome-Based Comparison of Clostridioides difficile: Average Amino Acid Identity Analysis of Core Genomes.

    Science.gov (United States)

    Cabal, Adriana; Jun, Se-Ran; Jenjaroenpun, Piroon; Wanchai, Visanu; Nookaew, Intawat; Wongsurawat, Thidathip; Burgess, Mary J; Kothari, Atul; Wassenaar, Trudy M; Ussery, David W

    2018-02-14

    Infections due to Clostridioides difficile (previously known as Clostridium difficile) are a major problem in hospitals, where cases can be caused by community-acquired strains as well as by nosocomial spread. Whole genome sequences from clinical samples contain a lot of information but that needs to be analyzed and compared in such a way that the outcome is useful for clinicians or epidemiologists. Here, we compare 663 public available complete genome sequences of C. difficile using average amino acid identity (AAI) scores. This analysis revealed that most of these genomes (640, 96.5%) clearly belong to the same species, while the remaining 23 genomes produce four distinct clusters within the Clostridioides genus. The main C. difficile cluster can be further divided into sub-clusters, depending on the chosen cutoff. We demonstrate that MLST, either based on partial or full gene-length, results in biased estimates of genetic differences and does not capture the true degree of similarity or differences of complete genomes. Presence of genes coding for C. difficile toxins A and B (ToxA/B), as well as the binary C. difficile toxin (CDT), was deduced from their unique PfamA domain architectures. Out of the 663 C. difficile genomes, 535 (80.7%) contained at least one copy of ToxA or ToxB, while these genes were missing from 128 genomes. Although some clusters were enriched for toxin presence, these genes are variably present in a given genetic background. The CDT genes were found in 191 genomes, which were restricted to a few clusters only, and only one cluster lacked the toxin A/B genes consistently. A total of 310 genomes contained ToxA/B without CDT (47%). Further, published metagenomic data from stools were used to assess the presence of C. difficile sequences in blinded cases of C. difficile infection (CDI) and controls, to test if metagenomic analysis is sensitive enough to detect the pathogen, and to establish strain relationships between cases from the same

  13. Bioinformatics decoding the genome

    CERN Multimedia

    CERN. Geneva; Deutsch, Sam; Michielin, Olivier; Thomas, Arthur; Descombes, Patrick

    2006-01-01

    Extracting the fundamental genomic sequence from the DNA From Genome to Sequence : Biology in the early 21st century has been radically transformed by the availability of the full genome sequences of an ever increasing number of life forms, from bacteria to major crop plants and to humans. The lecture will concentrate on the computational challenges associated with the production, storage and analysis of genome sequence data, with an emphasis on mammalian genomes. The quality and usability of genome sequences is increasingly conditioned by the careful integration of strategies for data collection and computational analysis, from the construction of maps and libraries to the assembly of raw data into sequence contigs and chromosome-sized scaffolds. Once the sequence is assembled, a major challenge is the mapping of biologically relevant information onto this sequence: promoters, introns and exons of protein-encoding genes, regulatory elements, functional RNAs, pseudogenes, transposons, etc. The methodological ...

  14. Genomic research in Eucalyptus.

    Science.gov (United States)

    Poke, Fiona S; Vaillancourt, René E; Potts, Brad M; Reid, James B

    2005-09-01

    Eucalyptus L'Hérit. is a genus comprised of more than 700 species that is of vital importance ecologically to Australia and to the forestry industry world-wide, being grown in plantations for the production of solid wood products as well as pulp for paper. With the sequencing of the genomes of Arabidopsis thaliana and Oryza sativa and the recent completion of the first tree genome sequence, Populus trichocarpa, attention has turned to the current status of genomic research in Eucalyptus. For several eucalypt species, large segregating families have been established, high-resolution genetic maps constructed and large EST databases generated. Collaborative efforts have been initiated for the integration of diverse genomic projects and will provide the framework for future research including exploiting the sequence of the entire eucalypt genome which is currently being sequenced. This review summarises the current position of genomic research in Eucalyptus and discusses the direction of future research.

  15. KONVERGENSI ESTIMATOR DALAM MODEL MIXTURE BERBASIS MISSING DATA

    Directory of Open Access Journals (Sweden)

    N Dwidayati

    2014-06-01

    Full Text Available Abstrak __________________________________________________________________________________________ Model mixture dapat mengestimasi proporsi pasien yang sembuh (cured dan fungsi survival pasien tak sembuh (uncured. Pada kajian ini, model mixture dikembangkan untuk  analisis cure rate berbasis missing data. Ada beberapa metode yang dapat digunakan untuk analisis missing data. Salah satu metode yang dapat digunakan adalah Algoritma EM, Metode ini didasarkan pada 2 (dua langkah, yaitu: (1 Expectation Step dan (2 Maximization Step. Algoritma EM merupakan pendekatan iterasi untuk mempelajari model dari data dengan nilai hilang melalui 4 (empat langkah, yaitu(1 pilih himpunan inisial dari parameter untuk sebuah model, (2 tentukan nilai ekspektasi untuk data hilang, (3 buat induksi parameter model baru dari gabungan nilai ekspekstasi dan data asli, dan (4 jika parameter tidak converged, ulangi langkah 2 menggunakan model baru. Berdasar kajian yang dilakukan dapat ditunjukkan bahwa pada algoritma EM, log-likelihood untuk missing data mengalami kenaikan setelah dilakukan setiap iterasi dari algoritmanya. Dengan demikian berdasar algoritma EM, barisan likelihood konvergen jika likelihood terbatas ke bawah.   Abstract __________________________________________________________________________________________ Model mixture can estimate proportion of recovering patient  and function of patient survival do not recover. At this study, model mixture developed to analyse cure rate bases on missing data. There are some method which applicable to analyse missing data. One of method which can be applied is Algoritma EM, This method based on 2 ( two step, that is: ( 1 Expectation Step and ( 2 Maximization Step. EM Algorithm is approach of iteration to study model from data with value loses through 4 ( four step, yaitu(1 select;chooses initial gathering from parameter for a model, ( 2 determines expectation value for data to lose, ( 3 induce newfangled parameter

  16. Genome packaging in viruses

    OpenAIRE

    Sun, Siyang; Rao, Venigalla B.; Rossmann, Michael G.

    2010-01-01

    Genome packaging is a fundamental process in a viral life cycle. Many viruses assemble preformed capsids into which the genomic material is subsequently packaged. These viruses use a packaging motor protein that is driven by the hydrolysis of ATP to condense the nucleic acids into a confined space. How these motor proteins package viral genomes had been poorly understood until recently, when a few X-ray crystal structures and cryo-electron microscopy structures became available. Here we discu...

  17. Comparative analyses identified species-specific functional roles in oral microbial genomes

    Science.gov (United States)

    Chen, Tsute; Gajare, Prasad; Olsen, Ingar; Dewhirst, Floyd E.

    2017-01-01

    ABSTRACT The advent of next generation sequencing is producing more genomic sequences for various strains of many human oral microbial species and allows for insightful functional comparisons at both intra- and inter-species levels. This study performed in-silico functional comparisons for currently available genomic sequences of major species associated with periodontitis including Aggregatibacter actinomycetemcomitans (AA), Porphyromonas gingivalis (PG), Treponema denticola (TD), and Tannerella forsythia (TF), as well as several cariogenic and commensal streptococcal species. Complete or draft sequences were annotated with the RAST to infer structured functional subsystems for each genome. The subsystems profiles were clustered to groups of functions with similar patterns. Functional enrichment and depletion were evaluated based on hypergeometric distribution to identify subsystems that are unique or missing between two groups of genomes. Unique or missing metabolic pathways and biological functions were identified in different species. For example, components involved in flagellar motility were found only in the motile species TD, as expected, with few exceptions scattered in several streptococcal species, likely associated with chemotaxis. Transposable elements were only found in the two Bacteroidales species PG and TF, and half of the AA genomes. Genes involved in CRISPR were prevalent in most oral species. Furthermore, prophage related subsystems were also commonly found in most species except for PG and Streptococcus mutans, in which very few genomes contain prophage components. Comparisons between pathogenic (P) and nonpathogenic (NP) genomes also identified genes potentially important for virulence. Two such comparisons were performed between AA (P) and several A. aphrophilus (NP) strains, and between S. mutans + S. sobrinus (P) and other oral streptococcal species (NP). This comparative genomics approach can be readily used to identify functions unique to

  18. Saturated linkage map construction in Rubus idaeus using genotyping by sequencing and genome-independent imputation

    Directory of Open Access Journals (Sweden)

    Ward Judson A

    2013-01-01

    Full Text Available Abstract Background Rapid development of highly saturated genetic maps aids molecular breeding, which can accelerate gain per breeding cycle in woody perennial plants such as Rubus idaeus (red raspberry. Recently, robust genotyping methods based on high-throughput sequencing were developed, which provide high marker density, but result in some genotype errors and a large number of missing genotype values. Imputation can reduce the number of missing values and can correct genotyping errors, but current methods of imputation require a reference genome and thus are not an option for most species. Results Genotyping by Sequencing (GBS was used to produce highly saturated maps for a R. idaeus pseudo-testcross progeny. While low coverage and high variance in sequencing resulted in a large number of missing values for some individuals, a novel method of imputation based on maximum likelihood marker ordering from initial marker segregation overcame the challenge of missing values, and made map construction computationally tractable. The two resulting parental maps contained 4521 and 2391 molecular markers spanning 462.7 and 376.6 cM respectively over seven linkage groups. Detection of precise genomic regions with segregation distortion was possible because of map saturation. Microsatellites (SSRs linked these results to published maps for cross-validation and map comparison. Conclusions GBS together with genome-independent imputation provides a rapid method for genetic map construction in any pseudo-testcross progeny. Our method of imputation estimates the correct genotype call of missing values and corrects genotyping errors that lead to inflated map size and reduced precision in marker placement. Comparison of SSRs to published R. idaeus maps showed that the linkage maps constructed with GBS and our method of imputation were robust, and marker positioning reliable. The high marker density allowed identification of genomic regions with segregation

  19. Between Two Fern Genomes

    Science.gov (United States)

    2014-01-01

    Ferns are the only major lineage of vascular plants not represented by a sequenced nuclear genome. This lack of genome sequence information significantly impedes our ability to understand and reconstruct genome evolution not only in ferns, but across all land plants. Azolla and Ceratopteris are ideal and complementary candidates to be the first ferns to have their nuclear genomes sequenced. They differ dramatically in genome size, life history, and habit, and thus represent the immense diversity of extant ferns. Together, this pair of genomes will facilitate myriad large-scale comparative analyses across ferns and all land plants. Here we review the unique biological characteristics of ferns and describe a number of outstanding questions in plant biology that will benefit from the addition of ferns to the set of taxa with sequenced nuclear genomes. We explain why the fern clade is pivotal for understanding genome evolution across land plants, and we provide a rationale for how knowledge of fern genomes will enable progress in research beyond the ferns themselves. PMID:25324969

  20. Causes of genome instability

    DEFF Research Database (Denmark)

    Langie, Sabine A S; Koppen, Gudrun; Desaulniers, Daniel

    2015-01-01

    function, chromosome segregation, telomere length). The purpose of this review is to describe the crucial aspects of genome instability, to outline the ways in which environmental chemicals can affect this cancer hallmark and to identify candidate chemicals for further study. The overall aim is to make......Genome instability is a prerequisite for the development of cancer. It occurs when genome maintenance systems fail to safeguard the genome's integrity, whether as a consequence of inherited defects or induced via exposure to environmental agents (chemicals, biological agents and radiation). Thus...

  1. Fungal Genomics Program

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor

    2012-03-12

    The JGI Fungal Genomics Program aims to scale up sequencing and analysis of fungal genomes to explore the diversity of fungi important for energy and the environment, and to promote functional studies on a system level. Combining new sequencing technologies and comparative genomics tools, JGI is now leading the world in fungal genome sequencing and analysis. Over 120 sequenced fungal genomes with analytical tools are available via MycoCosm (www.jgi.doe.gov/fungi), a web-portal for fungal biologists. Our model of interacting with user communities, unique among other sequencing centers, helps organize these communities, improves genome annotation and analysis work, and facilitates new larger-scale genomic projects. This resulted in 20 high-profile papers published in 2011 alone and contributing to the Genomics Encyclopedia of Fungi, which targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts). Our next grand challenges include larger scale exploration of fungal diversity (1000 fungal genomes), developing molecular tools for DOE-relevant model organisms, and analysis of complex systems and metagenomes.

  2. MIPS plant genome information resources.

    Science.gov (United States)

    Spannagl, Manuel; Haberer, Georg; Ernst, Rebecca; Schoof, Heiko; Mayer, Klaus F X

    2007-01-01

    The Munich Institute for Protein Sequences (MIPS) has been involved in maintaining plant genome databases since the Arabidopsis thaliana genome project. Genome databases and analysis resources have focused on individual genomes and aim to provide flexible and maintainable data sets for model plant genomes as a backbone against which experimental data, for example from high-throughput functional genomics, can be organized and evaluated. In addition, model genomes also form a scaffold for comparative genomics, and much can be learned from genome-wide evolutionary studies.

  3. A dynamic programming approach to missing data estimation using neural networks

    CSIR Research Space (South Africa)

    Nelwamondo, FV

    2013-01-01

    Full Text Available method where dynamic programming is not used. This paper also suggests a different way of formulating a missing data problem such that the dynamic programming is applicable to estimate the missing data....

  4. The use of the bootstrap in the analysis of case-control studies with missing data

    DEFF Research Database (Denmark)

    Siersma, Volkert Dirk; Johansen, Christoffer

    2004-01-01

    nonparametric bootstrap, bootstrap confidence intervals, missing values, multiple imputation, matched case-control study......nonparametric bootstrap, bootstrap confidence intervals, missing values, multiple imputation, matched case-control study...

  5. Amplification of DNA mixtures--Missing data approach

    DEFF Research Database (Denmark)

    Tvedebrink, Torben; Eriksen, Poul Svante; Mogensen, Helle Smidt

    2008-01-01

    This paper presents a model for the interpretation of results of STR typing of DNA mixtures based on a multivariate normal distribution of peak areas. From previous analyses of controlled experiments with mixed DNA samples, we exploit the linear relationship between peak heights and peak areas...... DNA samples, it is only possible to observe the cumulative peak heights and areas. Complying with this latent structure, we use the EM-algorithm to impute the missing variables based on a compound symmetry model. That is the measurements are subject to intra- and inter-loci correlations not depending...... on the actual alleles of the DNA profiles. Due to factorization of the likelihood, properties of the normal distribution and use of auxiliary variables, an ordinary implementation of the EM-algorithm solves the missing data problem. We estimate the parameters in the model based on a training data set. In order...

  6. Mac OS X : Tiger edition the missing manual

    CERN Document Server

    Pogue, David

    2005-01-01

    You can set your watch to it: As soon as Apple comes out with another version of Mac OS X, David Pogue hits the streets with another meticulous Missing Manual to cover it with a wealth of detail. The new Mac OS X 10.4, better known as Tiger, is faster than its predecessors, but nothing's too fast for Pogue and Mac OS X: The Missing Manual. There are many reasons why this is the most popular computer book of all time. With its hallmark objectivity, the Tiger Edition thoroughly explores the latest features to grace the Mac OS. Which ones work well and which do not? What should you look for? Th

  7. Leptophobic Boson Signals with Leptons, Jets and Missing Energy

    Energy Technology Data Exchange (ETDEWEB)

    Dobrescu, Bogdan A.

    2015-06-14

    Color-singlet gauge bosons with renormalizable couplings to quarks but not to leptons must interact with additional fermions (''anomalons'') required to cancel the gauge anomalies. Analyzing the decays of such leptophobic bosons into anomalons, I show that they produce final states involving leptons at the LHC. Resonant production of a flavor-universal leptophobic Z' boson leads to cascade decays via anomalons, whose signatures include a leptonically decaying Z, missing energy and several jets. A Z' boson that couples to the right-handed quarks of the first and second generations undergoes cascade decays that violate lepton universality and include signals with two leptons and jets, or with a Higgs boson, a lepton, a W and missing energy.

  8. Accounting for Missing Correlation Coefficients in Fixed-Effects MASEM.

    Science.gov (United States)

    Jak, Suzanne; Cheung, Mike W-L

    2018-01-01

    Meta-analytic structural equation modeling (MASEM) is increasingly applied to advance theories by synthesizing existing findings. MASEM essentially consists of two stages. In Stage 1, a pooled correlation matrix is estimated based on the reported correlation coefficients in the individual studies. In Stage 2, a structural model (such as a path model) is fitted to explain the pooled correlations. Frequently, the individual studies do not provide all the correlation coefficients between the research variables. In this study, we modify the currently optimal MASEM-method to deal with missing correlation coefficients, and compare its performance with existing methods. This study is the first to evaluate the performance of fixed-effects MASEM methods under different levels of missing correlation coefficients. We found that the often used univariate methods performed very poorly, while the multivariate methods performed well overall.

  9. Managing missing scores on the Roland Morris Disability Questionnaire

    DEFF Research Database (Denmark)

    Lauridsen, Henrik Hein

    2009-01-01

    systematically dropped from each person’s raw scores and the standardized score was proportionally recalculated. This process was repeated until 6 questions had been dropped from each person’s questionnaire. ·         The error (absolute and percentage) introduced by each level of dropped question was calculated......MANAGING MISSING SCORES ON THE ROLAND MORRIS DISABILITY QUESTIONNAIRE  Peter Kenta and Henrik Hein Lauridsenb  aBack Research Centre and bInstitute of Sports Science and Clinical Biomechanics, University of Southern Denmark Background There is no standard method to calculate Roland Morris...... Disability Questionnaire (RMDQ) sum scores when one or more questions have not been answered. However, missing data are common on the RMDQ and the current options are: calculate a sum score regardless of unanswered questions, reject all data containing unanswered questions, or to impute scores. Other...

  10. Closed central slip injuries--a missed diagnosis?

    LENUS (Irish Health Repository)

    Nugent, N

    2011-09-01

    The extensor apparatus of the finger is a complex structure and injury can lead to significant digital dysfunction. Closed central slip injuries may be missed or diagnosis delayed because of lack of an open wound and often no radiographic abnormality, and can result in boutonniere deformities if untreated. This study aimed to quantify the number of patients attending with closed central slip injuries and to ascertain if the initial diagnosis was correct. The number of patients presenting to us over a 6 month period was recorded. The original diagnosis, time to diagnosis of central slip injury and the presence\\/absence of a boutonniere deformity were recorded. Ten patients were included in the study. Seven (70%) injuries were due to sport. Eight (80%) had a delayed diagnosis of central slip injury. Six (60%) had previously presented to general practitioners or emergency departments. Seven (70%) had boutonniere deformities. Closed central slip injuries can be missed. Simple clinical tests can diagnose central slip disruption.

  11. Mathematics Intensive Summer Session (MISS). Final technical report

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1998-11-01

    This final technical report appears in two parts: the report for the 1995 summer MISS program and the report for the 1996 summer MISS program. Copies of the US Department of Energy Pre-Freshman Enrichment Program 1995 Entry Form and 1996 Entry Form completed by all participants were sent to the Oak Ridge Institute for Science and Education in the fall of 1995 and 1996 respectively. Those forms are on file should they be needed. Attached also is a copy of the Summary of ideas for panel discussions, problem-solving sessions, or small group discussions presented at the Department of Energy Oak Ridge Institute for Science and Education Pre-Freshman Enrichment Program Project Directors Meeting held in San Antonio, TX, November 12--14, 1995.

  12. Characteristics of Missing Physical Activity Data in Children and Youth

    Science.gov (United States)

    Zhuang, Jie; Chen, Peijie; Wang, Chao; Huang, Liang; Zhu, Zheng; Zhang, Wenjie; Fan, Xiang

    2013-01-01

    Purpose: The purpose of this study was to investigate the characteristics of missing physical activity (PA) data of children and youth. Method: PA data from the Chinese City Children and Youth Physical Activity Study ("N" = 2,758; 1,438 boys and 1,320 girls; aged 9-17 years old) were used for the study. After the data were sorted by the…

  13. Missing Peroxy Radical Sources Within a Rural Forest Canopy

    Science.gov (United States)

    Wolfe, G. M.; Cantrell, C.; Kim, S.; Mauldin, R. L., III; Karl, T.; Harley, P.; Turnipseed, A.; Zheng, W.; Flocke, F.; Apel, E. C.; hide

    2013-01-01

    Organic peroxy (RO2) and hydroperoxy (HO2) radicals are key intermediates in the photochemical processes that generate ozone, secondary organic aerosol and reactive nitrogen reservoirs throughout the troposphere. In regions with ample biogenic hydrocarbons, the richness and complexity of peroxy radical chemistry presents a significant challenge to current-generation models, especially given the scarcity of measurements in such environments. We present peroxy radical observations acquired within a Ponderosa pine forest during the summer 2010 Bio-hydro-atmosphere interactions of Energy, Aerosols, Carbon, H2O, Organics and Nitrogen - Rocky Mountain Organic Carbon Study (BEACHON-ROCS). Total peroxy radical mixing ratios reach as high as 180 pptv and are among the highest yet recorded. Using the comprehensive measurement suite to constrain a near-explicit 0-D box model, we investigate the sources, sinks and distribution of peroxy radicals below the forest canopy. The base chemical mechanism underestimates total peroxy radicals by as much as a factor of 3. Since primary reaction partners for peroxy radicals are either measured (NO) or under-predicted (HO2 and RO2, i.e. self-reaction), missing sources are the most likely explanation for this result. A close comparison of model output with observations reveals at least two distinct source signatures. The first missing source, characterized by a sharp midday maximum and a strong dependence on solar radiation, is consistent with photolytic production of HO2. The diel profile of the second missing source peaks in the afternoon and suggests a process that generates RO2 independently of sun-driven photochemistry, such as ozonolysis of reactive hydrocarbons. The maximum magnitudes of these missing sources (approximately 120 and 50 pptv min-1, respectively) are consistent with previous observations alluding to unexpectedly intense oxidation within forests. We conclude that a similar mechanism may underlie many such observations.

  14. MMAPS: Missing-Mass A-Prime Search

    OpenAIRE

    Alexander Jim

    2017-01-01

    An experiment is proposed to search for dark photons via electron-positron annihilation into photon plus dark photon. The dark photon would be reconstructed in a missing-mass technique, thus ensuring complete model independent. The Cornell University synchrotron can provide a positron beam suitable to probe the interesting mass range for dark photons. A detector based on CsI calorimetry is proposed, and the potential experimental reach in coupling constant and dark photon mass is shown.

  15. Diagnostic miss rate for colorectal cancer: an audit.

    Science.gov (United States)

    Than, Mary; Witherspoon, Jolene; Shami, Javed; Patil, Prachi; Saklani, Avanish

    2015-01-01

    Colorectal cancer (CRC) is a common cancer worldwide. While screening improves survival, avoiding delayed diagnosis in symptomatic patients is crucial. Computed tomographic colonography (CTC) or colonoscopy is recommended as first-line investigation and most societies recommend counseling patients undergoing colonoscopy about a miss rate of 5%. This audit evaluates "miss rate" of colorectal investigations, which have led to diagnostic delay in symptomatic cases in a district general hospital in the United Kingdom. This is a retrospective review of 150 consecutive CRC cases presenting between August 2010 and July 2011. Evidence of bowel investigations done in the 3 years prior to diagnosis was obtained from computerized health records. Data regarding previous bowel investigations such as colonoscopy, CTC, double contrast barium enema (DCBE), and CT abdomen/pelvis were collected. 6.7% cases were identified via screening pathway while 93% were identified through symptomatic pathway. 17% (26/150) of newly diagnosed CRC had been investigated in the preceding 3 years. Of these, 8% (12/150) had false negative results. The false negative rate for CRC diagnosis was 3.5% for colonoscopy (3/85), 6.7% for CTC (1/17), 9.4% for CT (5/53), and 26.7% for DCBE (4/15). Some patients had a missed diagnosis despite more than one diagnostic test. Time delay to diagnosis ranged from 21-456 days. 17% of patients diagnosed with CRC had been investigated in the previous 3 years. Higher miss rate of barium enema should preclude its use as a first-line modality to investigate CRC.

  16. The missing link: leadership, identity, and the social brain.

    Science.gov (United States)

    van Vugt, Mark

    2012-05-01

    How the cohesion of a social network is being maintained in spite of having different layers of social interaction is an important question. I argue that the evolution of both (political) hierarchy and social identity play a crucial role in scaling up and bonding social networks. Together they are missing links in the social brain hypothesis, and further research is needed to understand the functions of leadership and social identity. ©2011 The British Psychological Society.

  17. Estimation of Poisson-Dirichlet Parameters with Monotone Missing Data

    Directory of Open Access Journals (Sweden)

    Xueqin Zhou

    2017-01-01

    Full Text Available This article considers the estimation of the unknown numerical parameters and the density of the base measure in a Poisson-Dirichlet process prior with grouped monotone missing data. The numerical parameters are estimated by the method of maximum likelihood estimates and the density function is estimated by kernel method. A set of simulations was conducted, which shows that the estimates perform well.

  18. The Missing Response to Selection in the Wild

    OpenAIRE

    Pujol, Benoit; Blanchet, Simon; Charmantier, Anne; Danchin, Etienne; Facon, Benoit; Marrot, Pascal; Roux, Fabrice; Scotti, Ivan; Teplitsky, Céline; Thomson, Caroline E.; Winney, Isabel

    2018-01-01

    Although there are many examples of contemporary directional selection, evidence for responses to selection that match predictions are often missing in quantitative genetic studies of wild populations. This is despite the presence of genetic variation and selection pressures – theoretical prerequisites for the response to selection. This conundrum can be explained by statistical issues with accurate parameter estimation, and by biological mechanisms that interfere with the response to selecti...

  19. Baseline Predictors of Missed Visits in the Look AHEAD Study

    Science.gov (United States)

    Fitzpatrick, Stephanie L.; Jeffery, Robert; Johnson, Karen C.; Roche, Cathy C.; Van Dorsten, Brent; Gee, Molly; Johnson, Ruby Ann; Charleston, Jeanne; Dotson, Kathy; Walkup, Michael P.; Hill-Briggs, Felicia; Brancati, Frederick L.

    2013-01-01

    Objective To identify baseline attributes associated with consecutively missed data collection visits during the first 48 months of Look AHEAD—a randomized, controlled trial in 5145 overweight/obese adults with type 2 diabetes designed to determine the long-term health benefits of weight loss achieved by lifestyle change. Design and Methods The analyzed sample consisted of 5016 participants who were alive at month 48 and enrolled at Look AHEAD sites. Demographic, baseline behavior, psychosocial factors, and treatment randomization were included as predictors of missed consecutive visits in proportional hazard models. Results In multivariate Cox proportional hazard models, baseline attributes of participants who missed consecutive visits (n=222) included: younger age ( Hazard Ratio [HR] 1.18 per 5 years younger; 95% Confidence Interval 1.05, 1.30), higher depression score (HR 1.04; 1.01, 1.06), non-married status (HR 1.37; 1.04, 1.82), never self-weighing prior to enrollment (HR 2.01; 1.25, 3.23), and randomization to minimal vs. intensive lifestyle intervention (HR 1.46; 1.11, 1.91). Conclusions Younger age, symptoms of depression, non-married status, never self-weighing, and randomization to minimal intervention were associated with a higher likelihood of missing consecutive data collection visits, even in a high-retention trial like Look AHEAD. Whether modifications to screening or retention efforts targeted to these attributes might enhance long-term retention in behavioral trials requires further investigation. PMID:23996977

  20. Something Missing. Czech Society and Transcarpathia after 1989

    Czech Academy of Sciences Publication Activity Database

    Zahradníček, Tomáš

    2017-01-01

    Roč. 5, č. 1 (2017), s. 72-80 ISSN 2336-3312 Institutional support: RVO:68378114 Keywords : Transcarpathia * borders * Czechoslovakia Subject RIV: AB - History OBOR OECD: History (history of science and technology to be 6.3, history of specific sciences to be under the respective headings) http://www.slu.cz/fvp/cz/web-cep/archiv-casopisu/2017-vol-5-no.1/zahradnicek_something-missing

  1. Predicting appointment misses in hospitals using data analytics

    Science.gov (United States)

    Karpagam, Sylvia; Ma, Nang Laik

    2017-01-01

    Background There is growing attention over the last few years about non-attendance in hospitals and its clinical and economic consequences. There have been several studies documenting the various aspects of non-attendance in hospitals. Project Predicting Appoint Misses (PAM) was started with the intention of being able to predict the type of patients that would not come for appointments after making bookings. Methods Historic hospital appointment data merged with “distance from hospital” variable was used to run Logistic Regression, Support Vector Machine and Recursive Partitioning to decide the contributing variables to missed appointments. Results Variables that are “class”, “time”, “demographics” related have an effect on the target variable, however, prediction models may not perform effectively due to very subtle influence on the target variable. Previously assumed major contributors like “age”, “distance” did not have a major effect on the target variable. Conclusions With the given data it will be very difficult to make any moderate/strong prediction of the Appointment misses. That being said with the help of the cut off we are able to capture all of the “appointment misses” in addition to also capturing the actualized appointments. PMID:28567409

  2. Missing Data Bias on a Selective Hedging Strategy

    Directory of Open Access Journals (Sweden)

    Kiss Gábor Dávid

    2017-03-01

    Full Text Available Foreign exchange rates affect corporate profitability both on the macro and cash-flow level. The current study analyses the bias of missing data on a selective hedging strategy, where currency options are applied in case of Value at Risk (1% signs. However, there can be special occasions when one or some data is missing due to lack of a trading activity. This paper focuses on the impact of different missing data handling methods on GARCH and Value at Risk model parameters, because of selective hedging and option pricing based on them. The main added value of the current paper is the comparison of the impact of different methods, such as listwise deletion, mean substitution, and maximum likelihood based Expectation Maximization, on risk management because this subject has insufficient literature. The current study tested daily closing data of floating currencies from Kenya (KES, Ghana (GHS, South Africa (ZAR, Tanzania (TZS, Uganda (UGX, Gambia (GMD, Madagascar (MGA and Mozambique (MZN in USD denomination against EUR/USD rate between March 8, 2000 and March 6, 2015 acquired from the Bloomberg database. Our results suggested the biases of missingness on Value at Risk and volatility models, presenting significant differences among the number of extreme fluctuations or model parameters. A selective hedging strategy can have different expenditures due to the choice of method. This paper suggests the usage of mean substitution or listwise deletion for daily financial time series due to their tendency to have a close to zero first momentum

  3. Ambivalence and Ambiguity in The Autobiography of Miss Jane Pittman

    Directory of Open Access Journals (Sweden)

    Monica Michlin

    2006-05-01

    Full Text Available This close reading of the text highlights how Miss Jane, in her double role as protagonist and narrator, shows considerable ambivalence towards friend and foe alike, with the result that the apparently transparent ideological meaning of entire episodes is blurred by what some critics have merely put down to “conservatism.” I examine Miss Jane’s almost constant suppression of emotion, and frequent displays of ambivalence towards other black people; her ambiguous relationship to oppressive, but familiar whites like Albert Cluveau or Robert Samson; and her conflicted relation to black heroes and heroics. Is the leading character a variation on the “mammy” who has internalized racist figures of speech, and uses contradictory images that undermine black heroics and validate white oppression? Or is Gaines’s point to undo the “retrick” of heroics and of alienation alike, and, against of backdrop of constant, ordinary destruction of black lives, to cast the adult Miss Jane as a Brer Rabbit-like figure, for whom survival and resistance are both dialectically connected and opposed? Is there a contradiction between her “progress” towards resistance shown in the last section, and her metadiscursive comments in the present, and does her literally walking out of her own story give a conclusive meaning to her narrative, or does it point to the author’s not having been able to resolve the ambivalence and ambiguities within the text?

  4. Reconstruction of missing daily streamflow data using dynamic regression models

    Science.gov (United States)

    Tencaliec, Patricia; Favre, Anne-Catherine; Prieur, Clémentine; Mathevet, Thibault

    2015-12-01

    River discharge is one of the most important quantities in hydrology. It provides fundamental records for water resources management and climate change monitoring. Even very short data-gaps in this information can cause extremely different analysis outputs. Therefore, reconstructing missing data of incomplete data sets is an important step regarding the performance of the environmental models, engineering, and research applications, thus it presents a great challenge. The objective of this paper is to introduce an effective technique for reconstructing missing daily discharge data when one has access to only daily streamflow data. The proposed procedure uses a combination of regression and autoregressive integrated moving average models (ARIMA) called dynamic regression model. This model uses the linear relationship between neighbor and correlated stations and then adjusts the residual term by fitting an ARIMA structure. Application of the model to eight daily streamflow data for the Durance river watershed showed that the model yields reliable estimates for the missing data in the time series. Simulation studies were also conducted to evaluate the performance of the procedure.

  5. MISSE 6 Stressed Polymers Experiment Atomic Oxygen Erosion Data

    Science.gov (United States)

    deGroh, Kim K.; Banks, Bruce A.; Mitchell, Gianna G.; Yi, Grace T.; Guo, Aobo; Ashmeade, Claire C.; Roberts, Lily M.; McCarthy, Catherine E.; Sechkar, Edward A.

    2013-01-01

    Polymers and other oxidizable materials used on the exterior of spacecraft in the low Earth orbit (LEO) space environment can be eroded away by reaction with atomic oxygen (AO). For spacecraft design, it is important to know the LEO AO erosion yield, Ey (volume loss per incident oxygen atom), of materials susceptible to AO erosion. The Stressed Polymers Experiment was developed and flown as part of the Materials International Space Station Experiment 6 (MISSE 6) to compare the AO erosion yields of stressed and non-stressed polymers to determine if erosion is dependent upon stress while in LEO. The experiment contained 36 thin film polymer samples that were exposed to ram AO for 1.45 years. This paper provides an overview of the Stressed Polymers Experiment with details on the polymers flown, the characterization techniques used, the AO fluence, and the erosion yield results. The MISSE 6 data are compared to data for similar samples flown on previous MISSE missions to determine fluence or solar radiation effects on erosion yield.

  6. Estimating Potential Evapotranspiration by Missing Temperature Data Reconstruction

    Directory of Open Access Journals (Sweden)

    Eladio Delgadillo-Ruiz

    2015-01-01

    Full Text Available This work studies the statistical characteristics of potential evapotranspiration calculations and their relevance within the water balance used to determine water availability in hydrological basins. The purpose of this study was as follows: first, to apply a missing data reconstruction scheme in weather stations of the Rio Queretaro basin; second, to reduce the generated uncertainty of temperature data: mean, minimum, and maximum values in the evapotranspiration calculation which has a paramount importance in the manner of obtaining the water balance at any hydrological basin. The reconstruction of missing data was carried out in three steps: (1 application of a 4-parameter sinusoidal type regression to temperature data, (2 linear regression to residuals to obtain a regional behavior, and (3 estimation of missing temperature values for a certain year and during a certain season within the basin under study; estimated and observed temperature values were compared. Finally, using the obtained temperature values, the methods of Hamon, Papadakis, Blaney and Criddle, Thornthwaite, and Hargreaves were employed to calculate potential evapotranspiration that was compared to the real observed values in weather stations. With the results obtained from the application of this procedure, the surface water balance was corrected for the case study.

  7. Social Media Use and the Fear of Missing out (FoMO) While Studying Abroad

    Science.gov (United States)

    Hetz, Patricia R.; Dawson, Christi L.; Cullen, Theresa A.

    2015-01-01

    Fear of Missing Out (FoMO) is a social construct that examines whether students are concerned that they are missing out on experiences that others are having, and we examined this relation to their concerns over missing activities in their home culture. This mixed-methods pilot study sought to determine how social media affects the study abroad…

  8. 78 FR 2256 - Extension of the Extended Missing Parts Pilot Program

    Science.gov (United States)

    2013-01-10

    ...] Extension of the Extended Missing Parts Pilot Program AGENCY: United States Patent and Trademark Office... pilot program (Extended Missing Parts Pilot Program) in which an applicant, under certain conditions... nonprovisional application. The Extended Missing Parts Pilot Program benefits applicants by permitting additional...

  9. Statistical analysis of longitudinal quality of life data with missing measurements

    NARCIS (Netherlands)

    Zwinderman, A. H.

    1992-01-01

    The statistical analysis of longitudinal quality of life data in the presence of missing data is discussed. In cancer trials missing data are generated due to the fact that patients die, drop out, or are censored. These missing data are problematic in the monitoring of the quality of life during the

  10. Prevalence and Correlates of Missing Meals Among High School Students-United States, 2010.

    Science.gov (United States)

    Demissie, Zewditu; Eaton, Danice K; Lowry, Richard; Nihiser, Allison J; Foltz, Jennifer L

    2018-01-01

    To determine the prevalence and correlates of missing meals among adolescents. The 2010 National Youth Physical Activity and Nutrition Study, a cross-sectional study. School based. A nationally representative sample of 11 429 high school students. Breakfast, lunch, and dinner consumption; demographics; measured and perceived weight status; physical activity and sedentary behaviors; and fruit, vegetable, milk, sugar-sweetened beverage, and fast-food intake. Prevalence estimates for missing breakfast, lunch, or dinner on ≥1 day during the past 7 days were calculated. Associations between demographics and missing meals were tested. Associations of lifestyle and dietary behaviors with missing meals were examined using logistic regression controlling for sex, race/ethnicity, and grade. In 2010, 63.1% of students missed breakfast, 38.2% missed lunch, and 23.3% missed dinner; the prevalence was highest among female and non-Hispanic black students. Being overweight/obese, perceiving oneself to be overweight, and video game/computer use were associated with increased risk of missing meals. Physical activity behaviors were associated with reduced risk of missing meals. Students who missed breakfast were less likely to eat fruits and vegetables and more likely to consume sugar-sweetened beverages and fast food. Breakfast was the most frequently missed meal, and missing breakfast was associated with the greatest number of less healthy dietary practices. Intervention and education efforts might prioritize breakfast consumption.

  11. Computational genomics of hyperthermophiles

    NARCIS (Netherlands)

    Werken, van de H.J.G.

    2008-01-01

    With the ever increasing number of completely sequenced prokaryotic genomes and the subsequent use of functional genomics tools, e.g. DNA microarray and proteomics, computational data analysis and the integration of microbial and molecular data is inevitable. This thesis describes the computational

  12. Safeguarding genome integrity

    DEFF Research Database (Denmark)

    Sørensen, Claus Storgaard; Syljuåsen, Randi G

    2012-01-01

    Mechanisms that preserve genome integrity are highly important during the normal life cycle of human cells. Loss of genome protective mechanisms can lead to the development of diseases such as cancer. Checkpoint kinases function in the cellular surveillance pathways that help cells to cope with D...

  13. Human genome I

    International Nuclear Information System (INIS)

    Anon.

    1989-01-01

    An international conference, Human Genome I, was held Oct. 2-4, 1989 in San Diego, Calif. Selected speakers discussed: Current Status of the Genome Project; Technique Innovations; Interesting regions; Applications; and Organization - Different Views of Current and Future Science and Procedures. Posters, consisting of 119 presentations, were displayed during the sessions. 119 were indexed for inclusion to the Energy Data Base

  14. Effect of genomics-related literacy on non-communicable diseases.

    Science.gov (United States)

    Nakamura, Sho; Narimatsu, Hiroto; Katayama, Kayoko; Sho, Ri; Yoshioka, Takashi; Fukao, Akira; Kayama, Takamasa

    2017-09-01

    Recent progress in genomic research has raised expectations for the development of personalized preventive medicine, although genomics-related literacy of patients will be essential. Thus, enhancing genomics-related literacy is crucial, particularly for individuals with low genomics-related literacy because they might otherwise miss the opportunity to receive personalized preventive care. This should be especially emphasized when a lack of genomics-related literacy is associated with elevated disease risk, because patients could therefore be deprived of the added benefits of preventive interventions; however, whether such an association exists is unclear. Association between genomics-related literacy, calculated as the genomics literacy score (GLS), and the prevalence of non-communicable diseases was assessed using propensity score matching on 4646 participants (males: 1891; 40.7%). Notably, the low-GLS group (score below median) presented a higher risk of hypertension (relative risk (RR) 1.09, 95% confidence interval (CI) 1.03-1.16) and obesity (RR 1.11, 95% CI 1.01-1.22) than the high-GLS group. Our results suggest that a low level of genomics-related literacy could represent a risk factor for hypertension and obesity. Evaluating genomics-related literacy could be used to identify a more appropriate population for health and educational interventions.

  15. Statistical analysis with missing exposure data measured by proxy respondents: a misclassification problem within a missing-data problem.

    Science.gov (United States)

    Shardell, Michelle; Hicks, Gregory E

    2014-11-10

    In studies of older adults, researchers often recruit proxy respondents, such as relatives or caregivers, when study participants cannot provide self-reports (e.g., because of illness). Proxies are usually only sought to report on behalf of participants with missing self-reports; thus, either a participant self-report or proxy report, but not both, is available for each participant. Furthermore, the missing-data mechanism for participant self-reports is not identifiable and may be nonignorable. When exposures are binary and participant self-reports are conceptualized as the gold standard, substituting error-prone proxy reports for missing participant self-reports may produce biased estimates of outcome means. Researchers can handle this data structure by treating the problem as one of misclassification within the stratum of participants with missing self-reports. Most methods for addressing exposure misclassification require validation data, replicate data, or an assumption of nondifferential misclassification; other methods may result in an exposure misclassification model that is incompatible with the analysis model. We propose a model that makes none of the aforementioned requirements and still preserves model compatibility. Two user-specified tuning parameters encode the exposure misclassification model. Two proposed approaches estimate outcome means standardized for (potentially) high-dimensional covariates using multiple imputation followed by propensity score methods. The first method is parametric and uses maximum likelihood to estimate the exposure misclassification model (i.e., the imputation model) and the propensity score model (i.e., the analysis model); the second method is nonparametric and uses boosted classification and regression trees to estimate both models. We apply both methods to a study of elderly hip fracture patients. Copyright © 2014 John Wiley & Sons, Ltd.

  16. Missed losses loom larger than missed gains: Electrodermal reactivity to decision choices and outcomes in a gambling task.

    Science.gov (United States)

    Wu, Yin; Van Dijk, Eric; Aitken, Mike; Clark, Luke

    2016-04-01

    Loss aversion is a defining characteristic of prospect theory, whereby responses are stronger to losses than to equivalently sized gains (Kahneman & Tversky Econometrica, 47, 263-291, 1979). By monitoring electrodermal activity (EDA) during a gambling task, in this study we examined physiological activity during risky decisions, as well as to both obtained (e.g., gains and losses) and counterfactual (e.g., narrowly missed gains and losses) outcomes. During the bet selection phase, EDA increased linearly with bet size, highlighting the role of somatic signals in decision-making under uncertainty in a task without any learning requirement. Outcome-related EDA scaled with the magnitudes of monetary wins and losses, and losses had a stronger impact on EDA than did equivalently sized wins. Narrowly missed wins (i.e., near-wins) and narrowly missed losses (i.e., near-losses) also evoked EDA responses, and the change of EDA as a function of the size of the missed outcome was modestly greater for near-losses than for near-wins, suggesting that near-losses have more impact on subjective value than do near-wins. Across individuals, the slope for choice-related EDA (as a function of bet size) correlated with the slope for outcome-related EDA as a function of both the obtained and counterfactual outcome magnitudes, and these correlations were stronger for loss and near-loss conditions than for win and near-win conditions. Taken together, these asymmetrical EDA patterns to objective wins and losses, as well as to near-wins and near-losses, provide a psychophysiological instantiation of the value function curve in prospect theory, which is steeper in the negative than in the positive domain.

  17. Rumen microbial genomics

    International Nuclear Information System (INIS)

    Morrison, M.; Nelson, K.E.

    2005-01-01

    Improving microbial degradation of plant cell wall polysaccharides remains one of the highest priority goals for all livestock enterprises, including the cattle herds and draught animals of developing countries. The North American Consortium for Genomics of Fibrolytic Ruminal Bacteria was created to promote the sequencing and comparative analysis of rumen microbial genomes, offering the potential to fully assess the genetic potential in a functional and comparative fashion. It has been found that the Fibrobacter succinogenes genome encodes many more endoglucanases and cellodextrinases than previously isolated, and several new processive endoglucanases have been identified by genome and proteomic analysis of Ruminococcus albus, in addition to a variety of strategies for its adhesion to fibre. The ramifications of acquiring genome sequence data for rumen microorganisms are profound, including the potential to elucidate and overcome the biochemical, ecological or physiological processes that are rate limiting for ruminal fibre degradation. (author)

  18. Microbial Genomes Multiply

    Science.gov (United States)

    Doolittle, Russell F.

    2002-01-01

    The publication of the first complete sequence of a bacterial genome in 1995 was a signal event, underscored by the fact that the article has been cited more than 2,100 times during the intervening seven years. It was a marvelous technical achievement, made possible by automatic DNA-sequencing machines. The feat is the more impressive in that complete genome sequencing has now been adopted in many different laboratories around the world. Four years ago in these columns I examined the situation after a dozen microbial genomes had been completed. Now, with upwards of 60 microbial genome sequences determined and twice that many in progress, it seems reasonable to assess just what is being learned. Are new concepts emerging about how cells work? Have there been practical benefits in the fields of medicine and agriculture? Is it feasible to determine the genomic sequence of every bacterial species on Earth? The answers to these questions maybe Yes, Perhaps, and No, respectively.

  19. Musa sebagai Model Genom

    Directory of Open Access Journals (Sweden)

    RITA MEGIA

    2005-12-01

    Full Text Available During the meeting in Arlington, USA in 2001, the scientists grouped in PROMUSA agreed with the launching of the Global Musa Genomics Consortium. The Consortium aims to apply genomics technologies to the improvement of this important crop. These genome projects put banana as the third model species after Arabidopsis and rice that will be analyzed and sequenced. Comparing to Arabidopsis and rice, banana genome provides a unique and powerful insight into structural and in functional genomics that could not be found in those two species. This paper discussed these subjects-including the importance of banana as the fourth main food in the world, the evolution and biodiversity of this genetic resource and its parasite.

  20. The genome editing revolution

    DEFF Research Database (Denmark)

    Stella, Stefano; Montoya, Guillermo

    2016-01-01

    -Cas system has become the main tool for genome editing in many laboratories. Currently the targeted genome editing technology has been used in many fields and may be a possible approach for human gene therapy. Furthermore, it can also be used to modifying the genomes of model organisms for studying human......In the last 10 years, we have witnessed a blooming of targeted genome editing systems and applications. The area was revolutionized by the discovery and characterization of the transcription activator-like effector proteins, which are easier to engineer to target new DNA sequences than...... sequence). This ribonucleoprotein complex protects bacteria from invading DNAs, and it was adapted to be used in genome editing. The CRISPR ribonucleic acid (RNA) molecule guides to the specific DNA site the Cas9 nuclease to cleave the DNA target. Two years and more than 1000 publications later, the CRISPR...

  1. The African Genome Variation Project shapes medical genetics in Africa.

    Science.gov (United States)

    Gurdasani, Deepti; Carstensen, Tommy; Tekola-Ayele, Fasil; Pagani, Luca; Tachmazidou, Ioanna; Hatzikotoulas, Konstantinos; Karthikeyan, Savita; Iles, Louise; Pollard, Martin O; Choudhury, Ananyo; Ritchie, Graham R S; Xue, Yali; Asimit, Jennifer; Nsubuga, Rebecca N; Young, Elizabeth H; Pomilla, Cristina; Kivinen, Katja; Rockett, Kirk; Kamali, Anatoli; Doumatey, Ayo P; Asiki, Gershim; Seeley, Janet; Sisay-Joof, Fatoumatta; Jallow, Muminatou; Tollman, Stephen; Mekonnen, Ephrem; Ekong, Rosemary; Oljira, Tamiru; Bradman, Neil; Bojang, Kalifa; Ramsay, Michele; Adeyemo, Adebowale; Bekele, Endashaw; Motala, Ayesha; Norris, Shane A; Pirie, Fraser; Kaleebu, Pontiano; Kwiatkowski, Dominic; Tyler-Smith, Chris; Rotimi, Charles; Zeggini, Eleftheria; Sandhu, Manjinder S

    2015-01-15

    Given the importance of Africa to studies of human origins and disease susceptibility, detailed characterization of African genetic diversity is needed. The African Genome Variation Project provides a resource with which to design, implement and interpret genomic studies in sub-Saharan Africa and worldwide. The African Genome Variation Project represents dense genotypes from 1,481 individuals and whole-genome sequences from 320 individuals across sub-Saharan Africa. Using this resource, we find novel evidence of complex, regionally distinct hunter-gatherer and Eurasian admixture across sub-Saharan Africa. We identify new loci under selection, including loci related to malaria susceptibility and hypertension. We show that modern imputation panels (sets of reference genotypes from which unobserved or missing genotypes in study sets can be inferred) can identify association signals at highly differentiated loci across populations in sub-Saharan Africa. Using whole-genome sequencing, we demonstrate further improvements in imputation accuracy, strengthening the case for large-scale sequencing efforts of diverse African haplotypes. Finally, we present an efficient genotype array design capturing common genetic variation in Africa.

  2. The African Genome Variation Project shapes medical genetics in Africa

    Science.gov (United States)

    Gurdasani, Deepti; Carstensen, Tommy; Tekola-Ayele, Fasil; Pagani, Luca; Tachmazidou, Ioanna; Hatzikotoulas, Konstantinos; Karthikeyan, Savita; Iles, Louise; Pollard, Martin O.; Choudhury, Ananyo; Ritchie, Graham R. S.; Xue, Yali; Asimit, Jennifer; Nsubuga, Rebecca N.; Young, Elizabeth H.; Pomilla, Cristina; Kivinen, Katja; Rockett, Kirk; Kamali, Anatoli; Doumatey, Ayo P.; Asiki, Gershim; Seeley, Janet; Sisay-Joof, Fatoumatta; Jallow, Muminatou; Tollman, Stephen; Mekonnen, Ephrem; Ekong, Rosemary; Oljira, Tamiru; Bradman, Neil; Bojang, Kalifa; Ramsay, Michele; Adeyemo, Adebowale; Bekele, Endashaw; Motala, Ayesha; Norris, Shane A.; Pirie, Fraser; Kaleebu, Pontiano; Kwiatkowski, Dominic; Tyler-Smith, Chris; Rotimi, Charles; Zeggini, Eleftheria; Sandhu, Manjinder S.

    2015-01-01

    Given the importance of Africa to studies of human origins and disease susceptibility, detailed characterization of African genetic diversity is needed. The African Genome Variation Project provides a resource with which to design, implement and interpret genomic studies in sub-Saharan Africa and worldwide. The African Genome Variation Project represents dense genotypes from 1,481 individuals and whole-genome sequences from 320 individuals across sub-Saharan Africa. Using this resource, we find novel evidence of complex, regionally distinct hunter-gatherer and Eurasian admixture across sub-Saharan Africa. We identify new loci under selection, including loci related to malaria susceptibility and hypertension. We show that modern imputation panels (sets of reference genotypes from which unobserved or missing genotypes in study sets can be inferred) can identify association signals at highly differentiated loci across populations in sub-Saharan Africa. Using whole-genome sequencing, we demonstrate further improvements in imputation accuracy, strengthening the case for large-scale sequencing efforts of diverse African haplotypes. Finally, we present an efficient genotype array design capturing common genetic variation in Africa.

  3. Characterizing and annotating the genome using RNA-seq data.

    Science.gov (United States)

    Chen, Geng; Shi, Tieliu; Shi, Leming

    2017-02-01

    Bioinformatics methods for various RNA-seq data analyses are in fast evolution with the improvement of sequencing technologies. However, many challenges still exist in how to efficiently process the RNA-seq data to obtain accurate and comprehensive results. Here we reviewed the strategies for improving diverse transcriptomic studies and the annotation of genetic variants based on RNA-seq data. Mapping RNA-seq reads to the genome and transcriptome represent two distinct methods for quantifying the expression of genes/transcripts. Besides the known genes annotated in current databases, many novel genes/transcripts (especially those long noncoding RNAs) still can be identified on the reference genome using RNA-seq. Moreover, owing to the incompleteness of current reference genomes, some novel genes are missing from them. Genome- guided and de novo transcriptome reconstruction are two effective and complementary strategies for identifying those novel genes/transcripts on or beyond the reference genome. In addition, integrating the genes of distinct databases to conduct transcriptomics and genetics studies can improve the results of corresponding analyses.

  4. Personomics: The Missing Link in the Evolution from Precision Medicine to Personalized Medicine

    Directory of Open Access Journals (Sweden)

    Roy C. Ziegelstein

    2017-10-01

    Full Text Available Clinical practice guidelines have been developed for many common conditions based on data from randomized controlled trials. When medicine is informed solely by clinical practice guidelines, however, the patient is not treated as an individual, but rather a member of a group. Precision medicine, as defined herein, characterizes unique biological characteristics of the individual or of specimens obtained from an individual to tailor diagnostics and therapeutics to a specific patient. These unique biological characteristics are defined by the tools of precision medicine: genomics, proteomics, metabolomics, epigenomics, pharmacogenomics, and other “-omics.” Personalized medicine, as defined herein, uses additional information about the individual derived from knowing the patient as a person. These unique personal characteristics are defined by tools known as personomics which takes into account an individual’s personality, preferences, values, goals, health beliefs, social support network, financial resources, and unique life circumstances that affect how and when a given health condition will manifest in that person and how that condition will respond to treatment. In this paradigm, precision medicine may be considered a necessary step in the evolution of medical care to personalized medicine, with personomics as the missing link.

  5. Living long and ageing well: is epigenomics the missing link between nature and nurture?

    Science.gov (United States)

    Rea, Irene Maeve; Dellet, Margaret; Mills, Ken I

    2016-02-01

    Human longevity is a complex trait and increasingly we understand that both genes and lifestyle interact in the longevity phenotype. Non-genetic factors, including diet, physical activity, health habits, and psychosocial factors contribute approximately 50% of the variability in human lifespan with another 25% explained by genetic differences. Family clusters of nonagenarian and centenarian siblings, who show both exceptional age-span and health-span, are likely to have inherited facilitatory gene groups, but also have nine decades of life experiences and behaviours which have interacted with their genetic profiles. Identification of their shared genes is just one small step in the link from genes to their physical and psychological profiles. Behavioural genomics is beginning to demonstrate links to biological mechanisms through regulation of gene expression, which directs the proteome and influences the personal phenotype. Epigenetics has been considered the missing link between nature and nurture. Although there is much that remains to be discovered, this article will discuss some of genetic and environmental factors which appear important in good quality longevity and link known epigenetic mechanisms to themes identified by nonagenarians themselves related to their longevity. Here we suggest that exceptional 90-year old siblings have adopted a range of behaviours and life-styles which have contributed to their ageing-well-phenotype and which link with important public health messages.

  6. Missed nursing care and its relationship with confidence in delegation among hospital nurses.

    Science.gov (United States)

    Saqer, Tahani J; AbuAlRub, Raeda F

    2018-04-06

    To (i) identify the types and reasons for missed nursing care among Jordanian hospital nurses; (ii) identify predictors of missed nursing care based on study variables; and (iii) examine the relationship between nurses' confidence in delegation and missed nursing care. Missed nursing care is a global concern for nurses and nurse administrators. Investigating the relation between the confidence in delegation and missed nursing care might help in designing strategies that enable nurses to minimise missed care and enhance quality of services. A correlational research design was used for this study. A convenience sample of 362 hospital nurses completed the missed nursing care survey, and confidence and intent to delegate scale. The results of the study revealed that ambulating and feeding patients on time, doing mouth care and attending interdisciplinary care conferences were the most frequent types of missed care. The mean score for missed nursing care was (2.78) on a scale from 1-5. The most prevalent reasons for missed care were "labour resources, followed by material resources, and then communication". Around 45% of the variation in the perceived level of "missed nursing care" was explained by background variables and perceived reasons for missed nursing. However, the relationship between confidence in delegation and missed care was insignificant. The results of this study add to the body of international literature on most prevalent types and reasons for missed nursing care in a different cultural context. Highlighting most prevalent reasons for missed nursing care could help nurse administrators in designing responsive strategies to eliminate or reduces such reasons. © 2018 John Wiley & Sons Ltd.

  7. Phytozome Comparative Plant Genomics Portal

    Energy Technology Data Exchange (ETDEWEB)

    Goodstein, David; Batra, Sajeev; Carlson, Joseph; Hayes, Richard; Phillips, Jeremy; Shu, Shengqiang; Schmutz, Jeremy; Rokhsar, Daniel

    2014-09-09

    The Dept. of Energy Joint Genome Institute is a genomics user facility supporting DOE mission science in the areas of Bioenergy, Carbon Cycling, and Biogeochemistry. The Plant Program at the JGI applies genomic, analytical, computational and informatics platforms and methods to: 1. Understand and accelerate the improvement (domestication) of bioenergy crops 2. Characterize and moderate plant response to climate change 3. Use comparative genomics to identify constrained elements and infer gene function 4. Build high quality genomic resource platforms of JGI Plant Flagship genomes for functional and experimental work 5. Expand functional genomic resources for Plant Flagship genomes

  8. Dalla «più difforme congerie di oggetti» ad un «perfetto ambiente spirituale» per l’opera d’arte. L’allestimento del Museo Nazionale di Palermo alla fine degli anni Venti del Novecento / From the “più difforme congerie di oggetti” (most dissimilar jumble of objects to a “perfetto ambiente spirituale” (perfect spiritual environment for the work of art. The display of Palermo National Museum at the end of the 1920s

    Directory of Open Access Journals (Sweden)

    Ivana Bruno

    2016-12-01

    prepared a “makeover” which she published in the «Bollettino d’Arte del Ministero dell’Educazione Nazionale». In many ways, it corresponded with the museographical trends expressed in those years by the Offi ce International des Musées (IOM and object of considerable debate in Europe. Maria Accascina’s work changed the face of Palermo’s Museo Nazionale – until then the rooms and corridors were fi lled with «a rather disorderly jumble of objects» – and anticipated museological trends that would find  more concrete and tangible expression after WWII with Carlo Scarpa’s more famous work at Palazzo Abatellis. This paper seeks to analyze the exhibition strategies applied in the late twenties at he Museo Nazionale di Palermo whose innovative nature has recently been recognized in light of both the rich documentary and photographic evidence which remains largely unpublished. It will consider this material through the lens of contemporary critics and through the museum classifi cation systems which were being codifi ed in the interwar period.

  9. Genome-derived vaccines.

    Science.gov (United States)

    De Groot, Anne S; Rappuoli, Rino

    2004-02-01

    Vaccine research entered a new era when the complete genome of a pathogenic bacterium was published in 1995. Since then, more than 97 bacterial pathogens have been sequenced and at least 110 additional projects are now in progress. Genome sequencing has also dramatically accelerated: high-throughput facilities can draft the sequence of an entire microbe (two to four megabases) in 1 to 2 days. Vaccine developers are using microarrays, immunoinformatics, proteomics and high-throughput immunology assays to reduce the truly unmanageable volume of information available in genome databases to a manageable size. Vaccines composed by novel antigens discovered from genome mining are already in clinical trials. Within 5 years we can expect to see a novel class of vaccines composed by genome-predicted, assembled and engineered T- and Bcell epitopes. This article addresses the convergence of three forces--microbial genome sequencing, computational immunology and new vaccine technologies--that are shifting genome mining for vaccines onto the forefront of immunology research.

  10. The Banana Genome Hub

    Science.gov (United States)

    Droc, Gaëtan; Larivière, Delphine; Guignon, Valentin; Yahiaoui, Nabila; This, Dominique; Garsmeur, Olivier; Dereeper, Alexis; Hamelin, Chantal; Argout, Xavier; Dufayard, Jean-François; Lengelle, Juliette; Baurens, Franc-Christophe; Cenci, Alberto; Pitollat, Bertrand; D’Hont, Angélique; Ruiz, Manuel; Rouard, Mathieu; Bocs, Stéphanie

    2013-01-01

    Banana is one of the world’s favorite fruits and one of the most important crops for developing countries. The banana reference genome sequence (Musa acuminata) was recently released. Given the taxonomic position of Musa, the completed genomic sequence has particular comparative value to provide fresh insights about the evolution of the monocotyledons. The study of the banana genome has been enhanced by a number of tools and resources that allows harnessing its sequence. First, we set up essential tools such as a Community Annotation System, phylogenomics resources and metabolic pathways. Then, to support post-genomic efforts, we improved banana existing systems (e.g. web front end, query builder), we integrated available Musa data into generic systems (e.g. markers and genetic maps, synteny blocks), we have made interoperable with the banana hub, other existing systems containing Musa data (e.g. transcriptomics, rice reference genome, workflow manager) and finally, we generated new results from sequence analyses (e.g. SNP and polymorphism analysis). Several uses cases illustrate how the Banana Genome Hub can be used to study gene families. Overall, with this collaborative effort, we discuss the importance of the interoperability toward data integration between existing information systems. Database URL: http://banana-genome.cirad.fr/ PMID:23707967

  11. Genomic instability following irradiation

    International Nuclear Information System (INIS)

    Hacker-Klom, U.B.; Goehde, W.

    2001-01-01

    Ionising irradiation may induce genomic instability. The broad spectrum of stress reactions in eukaryontic cells to irradiation complicates the discovery of cellular targets and pathways inducing genomic instability. Irradiation may initiate genomic instability by deletion of genes controlling stability, by induction of genes stimulating instability and/or by activating endogeneous cellular viruses. Alternatively or additionally it is discussed that the initiation of genomic instability may be a consequence of radiation or other agents independently of DNA damage implying non nuclear targets, e.g. signal cascades. As a further mechanism possibly involved our own results may suggest radiation-induced changes in chromatin structure. Once initiated the process of genomic instability probably is perpetuated by endogeneous processes necessary for proliferation. Genomic instability may be a cause or a consequence of the neoplastic phenotype. As a conclusion from the data available up to now a new interpretation of low level radiation effects for radiation protection and in radiotherapy appears useful. The detection of the molecular mechanisms of genomic instability will be important in this context and may contribute to a better understanding of phenomenons occurring at low doses <10 cSv which are not well understood up to now. (orig.)

  12. Association of the Nurse Work Environment, Collective Efficacy, and Missed Care.

    Science.gov (United States)

    Smith, Jessica G; Morin, Karen H; Wallace, Leigh E; Lake, Eileen T

    2018-06-01

    Missed nursing care is a significant threat to quality patient care. Promoting collective efficacy within nurse work environments could decrease missed care. The purpose was to understand how missed care is associated with nurse work environments and collective efficacy of hospital staff nurses. A cross-sectional, convenience sample was obtained through online surveys from registered nurses working at five southwestern U.S. hospitals. Descriptive, correlational, regression, and path analyses were conducted ( N = 233). The percentage of nurses who reported that at least one care activity was missed frequently or always was 94%. Mouth care (36.0% of nurses) and ambulation (35.3%) were missed frequently or always. Nurse work environments and collective efficacy were moderately, positively correlated. Nurse work environments and collective efficacy were associated with less missed care (χ 2 = 10.714, p = .0054). Fostering collective efficacy in the nurse work environment could reduce missed care and improve patient outcomes.

  13. Missed breast carcinoma; why and how to avoid?

    International Nuclear Information System (INIS)

    Kamal, R.; Abdel Razek, N.M.; Hassan, M.A.; Shaalan, M.A.

    2007-01-01

    Despite the advances in mammography techniques, it still has a number of limitations. It is estimated that about 10 to 25% of lesions are overlooked in mammograms out of which about two thirds are detected retrospectively by radiologists and oncologists. Causes of missed breast cancer on mammography can be secondary to many factors including those related to the patient (whether inherent or acquired), the nature of the malignant mass itself, poor mammographic techniques, provider factors or interpretive skills of radiologists and oncologists (including perception and interpretation errors). Aim of Work: The aim of this study is to investigate the aforementioned factors hindering early breast cancer detection and in turn lowering mammographic sensitivity and to outline the major guidelines to overcome these factors aiming to an optimum mammographic examination and interpretation by radiologists and oncologists. Subject and Methods: We conducted this multicenter study over a two-year interval. We included 152 histo-pathological proven breast carcinomas that were initially missed on mammography. The cases were subjected to mammography, complementary US, MRI and digital mammography in some cases and all cases were histo-pathologically proven either by FNAB, CNB or open biopsy. Results: Revision of the pathological specimens of these 152 cases revealed 121 infiltrating ductal carcinomas, 2 lobular, 4 mucinous, 14 inflammatory carcinomas, 6 carcinomas in situ (3 of which were intracystic), 2 intraductal papillary carcinomas and 3 cases with Paget's disease of the nipple. In analyzing the causes responsible for misdiagnosis of these carcinomas we classified them into 4 causative factors; patient, tumor, technical or provider factors. Tumor factors were the most commonly encountered, accounting for 44. I %, while provider factors were the least commonly encountered in 14.5%. Carcino- mas were detected using several individual or combined complementary techniques. These

  14. Measuring adequacy of prenatal care: does missing visit information matter?

    Science.gov (United States)

    Kurtzman, Jordan H; Wasserman, Erin B; Suter, Barbara J; Glantz, J Christopher; Dozier, Ann M

    2014-09-01

    Kotelchuck's Adequacy of Prenatal Care Utilization (APNCU) Index is frequently used to classify levels of prenatal care. In the Finger Lakes Region (FLR) of upstate New York, prenatal care visit information late in pregnancy is often not documented on the birth certificate. We studied the extent of this missing information and its impact on the validity of regional APNCU scores. We calculated the "weeks between" a mother's last prenatal care visit and her infant's date of birth. We adjusted the APNCU algorithm creating the Last Visit Adequacy of Prenatal Care (LV-APNC) Index using the last recorded prenatal care visit date as the end point of care and the expected number of visits at that time. We compared maternal characteristics by care level with each index, examining rates of reclassification and number of "weeks between" by birth hospital. Stuart-Maxwell, McNemar, chi-square, and t-tests were used to determine statistical significance. Based on 58,462 births, the mean "weeks between" was 2.8 weeks. Compared with their APNCU Index score, 42.4 percent of mothers were reclassified using the LV-APNC Index. Major movement occurred from Intermediate (APNCU) to Adequate or Adequate Plus (LV-APNC) leaving the Intermediate Care group a more at-risk group of mothers. Those with Adequate or Adequate Plus Care (LV-APNC) increased by 31.6 percent, surpassing the Healthy People 2020 objective. In the FLR, missing visit information at the end of pregnancy results in an underestimation of mothers' prenatal care. Future research is needed to determine the extent of this missing visit information on the national level. © 2014 Wiley Periodicals, Inc.

  15. The impact of missing sensor information on surgical workflow management.

    Science.gov (United States)

    Liebmann, Philipp; Meixensberger, Jürgen; Wiedemann, Peter; Neumuth, Thomas

    2013-09-01

    Sensor systems in the operating room may encounter intermittent data losses that reduce the performance of surgical workflow management systems (SWFMS). Sensor data loss could impact SWFMS-based decision support, device parameterization, and information presentation. The purpose of this study was to understand the robustness of surgical process models when sensor information is partially missing. SWFMS changes caused by wrong or no data from the sensor system which tracks the progress of a surgical intervention were tested. The individual surgical process models (iSPMs) from 100 different cataract procedures of 3 ophthalmologic surgeons were used to select a randomized subset and create a generalized surgical process model (gSPM). A disjoint subset was selected from the iSPMs and used to simulate the surgical process against the gSPM. The loss of sensor data was simulated by removing some information from one task in the iSPM. The effect of missing sensor data was measured using several metrics: (a) successful relocation of the path in the gSPM, (b) the number of steps to find the converging point, and (c) the perspective with the highest occurrence of unsuccessful path findings. A gSPM built using 30% of the iSPMs successfully found the correct path in 90% of the cases. The most critical sensor data were the information regarding the instrument used by the surgeon. We found that use of a gSPM to provide input data for a SWFMS is robust and can be accurate despite missing sensor data. A surgical workflow management system can provide the surgeon with workflow guidance in the OR for most cases. Sensor systems for surgical process tracking can be evaluated based on the stability and accuracy of functional and spatial operative results.

  16. Traditional medicine and genomics

    Directory of Open Access Journals (Sweden)

    Kalpana Joshi

    2010-01-01

    Full Text Available ′Omics′ developments in the form of genomics, proteomics and metabolomics have increased the impetus of traditional medicine research. Studies exploring the genomic, proteomic and metabolomic basis of human constitutional types based on Ayurveda and other systems of oriental medicine are becoming popular. Such studies remain important to developing better understanding of human variations and individual differences. Countries like India, Korea, China and Japan are investing in research on evidence-based traditional medicines and scientific validation of fundamental principles. This review provides an account of studies addressing relationships between traditional medicine and genomics.

  17. Traditional medicine and genomics.

    Science.gov (United States)

    Joshi, Kalpana; Ghodke, Yogita; Shintre, Pooja

    2010-01-01

    'Omics' developments in the form of genomics, proteomics and metabolomics have increased the impetus of traditional medicine research. Studies exploring the genomic, proteomic and metabolomic basis of human constitutional types based on Ayurveda and other systems of oriental medicine are becoming popular. Such studies remain important to developing better understanding of human variations and individual differences. Countries like India, Korea, China and Japan are investing in research on evidence-based traditional medicines and scientific validation of fundamental principles. This review provides an account of studies addressing relationships between traditional medicine and genomics.

  18. Bacillus subtilis genome diversity.

    Science.gov (United States)

    Earl, Ashlee M; Losick, Richard; Kolter, Roberto

    2007-02-01

    Microarray-based comparative genomic hybridization (M-CGH) is a powerful method for rapidly identifying regions of genome diversity among closely related organisms. We used M-CGH to examine the genome diversity of 17 strains belonging to the nonpathogenic species Bacillus subtilis. Our M-CGH results indicate that there is considerable genetic heterogeneity among members of this species; nearly one-third of Bsu168-specific genes exhibited variability, as measured by the microarray hybridization intensities. The variable loci include those encoding proteins involved in antibiotic production, cell wall synthesis, sporulation, and germination. The diversity in these genes may reflect this organism's ability to survive in diverse natural settings.

  19. Genomic taxonomy of vibrios

    Directory of Open Access Journals (Sweden)

    Iida Tetsuya

    2009-10-01

    Full Text Available Abstract Background Vibrio taxonomy has been based on a polyphasic approach. In this study, we retrieve useful taxonomic information (i.e. data that can be used to distinguish different taxonomic levels, such as species and genera from 32 genome sequences of different vibrio species. We use a variety of tools to explore the taxonomic relationship between the sequenced genomes, including Multilocus Sequence Analysis (MLSA, supertrees, Average Amino Acid Identity (AAI, genomic signatures, and Genome BLAST atlases. Our aim is to analyse the usefulness of these tools for species identification in vibrios. Results We have generated four new genome sequences of three Vibrio species, i.e., V. alginolyticus 40B, V. harveyi-like 1DA3, and V. mimicus strains VM573 and VM603, and present a broad analyses of these genomes along with other sequenced Vibrio species. The genome atlas and pangenome plots provide a tantalizing image of the genomic differences that occur between closely related sister species, e.g. V. cholerae and V. mimicus. The vibrio pangenome contains around 26504 genes. The V. cholerae core genome and pangenome consist of 1520 and 6923 genes, respectively. Pangenomes might allow different strains of V. cholerae to occupy different niches. MLSA and supertree analyses resulted in a similar phylogenetic picture, with a clear distinction of four groups (Vibrio core group, V. cholerae-V. mimicus, Aliivibrio spp., and Photobacterium spp.. A Vibrio species is defined as a group of strains that share > 95% DNA identity in MLSA and supertree analysis, > 96% AAI, ≤ 10 genome signature dissimilarity, and > 61% proteome identity. Strains of the same species and species of the same genus will form monophyletic groups on the basis of MLSA and supertree. Conclusion The combination of different analytical and bioinformatics tools will enable the most accurate species identification through genomic computational analysis. This endeavour will culminate in

  20. Human Genome Project

    Energy Technology Data Exchange (ETDEWEB)

    Block, S. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Cornwall, J. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Dally, W. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Dyson, F. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Fortson, N. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Joyce, G. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Kimble, H. J. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Lewis, N. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Max, C. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Prince, T. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Schwitters, R. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Weinberger, P. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Woodin, W. H. [The MITRE Corporation, McLean, VA (US). JASON Program Office

    1998-01-04

    The study reviews Department of Energy supported aspects of the United States Human Genome Project, the joint National Institutes of Health/Department of Energy program to characterize all human genetic material, to discover the set of human genes, and to render them accessible for further biological study. The study concentrates on issues of technology, quality assurance/control, and informatics relevant to current effort on the genome project and needs beyond it. Recommendations are presented on areas of the genome program that are of particular interest to and supported by the Department of Energy.

  1. Human Genome Program

    Energy Technology Data Exchange (ETDEWEB)

    1993-01-01

    The DOE Human Genome program has grown tremendously, as shown by the marked increase in the number of genome-funded projects since the last workshop held in 1991. The abstracts in this book describe the genome research of DOE-funded grantees and contractors and invited guests, and all projects are represented at the workshop by posters. The 3-day meeting includes plenary sessions on ethical, legal, and social issues pertaining to the availability of genetic data; sequencing techniques, informatics support; and chromosome and cDNA mapping and sequencing.

  2. Genomic signal processing

    CERN Document Server

    Shmulevich, Ilya

    2007-01-01

    Genomic signal processing (GSP) can be defined as the analysis, processing, and use of genomic signals to gain biological knowledge, and the translation of that knowledge into systems-based applications that can be used to diagnose and treat genetic diseases. Situated at the crossroads of engineering, biology, mathematics, statistics, and computer science, GSP requires the development of both nonlinear dynamical models that adequately represent genomic regulation, and diagnostic and therapeutic tools based on these models. This book facilitates these developments by providing rigorous mathema

  3. Health insurance theory: the case of the missing welfare gain.

    Science.gov (United States)

    Nyman, John A

    2008-11-01

    An important source of value is missing from the conventional welfare analysis of moral hazard, namely, the effect of income transfers (from those who purchase insurance and remain healthy to those who become ill) on purchases of medical care. Income transfers are contained within the price reduction that is associated with standard health insurance. However, in contrast to the income effects contained within an exogenous price decrease, these income transfers act to shift out the demand for medical care. As a result, the consumer's willingness to pay for medical care increases and the resulting additional consumption is welfare increasing.

  4. Multiple sclerosis pathogenesis: missing pieces of an old puzzle.

    Science.gov (United States)

    Rahmanzadeh, Reza; Brück, Wolfgang; Minagar, Alireza; Sahraian, Mohammad Ali

    2018-06-08

    Traditionally, multiple sclerosis (MS) was considered to be a CD4 T cell-mediated CNS autoimmunity, compatible with experimental autoimmune encephalitis model, which can be characterized by focal lesions in the white matter. However, studies of recent decades revealed several missing pieces of MS puzzle and showed that MS pathogenesis is more complex than the traditional view and may include the following: a primary degenerative process (e.g. oligodendroglial pathology), generalized abnormality of normal-appearing brain tissue, pronounced gray matter pathology, involvement of innate immunity, and CD8 T cells and B cells. Here, we review these findings and discuss their implications in MS pathogenesis.

  5. FileMaker Pro 11 The Missing Manual

    CERN Document Server

    Prosser, Susan

    2010-01-01

    This hands-on, friendly guide shows you how to harness FileMaker's power to make your information work for you. With a few mouse clicks, the FileMaker Pro 11 database helps you create and print corporate reports, manage a mailing list, or run your entire business. FileMaker Pro 11: The Missing Manual helps you get started, build your database, and produce results, whether you're running a business, pursuing a hobby, or planning your retirement. It's a thorough, accessible guide for new, non-technical users, as well as those with more experience. Start up: Get your first database up and runnin

  6. Managing missing scores on the Roland Morris Disability Questionnaire

    DEFF Research Database (Denmark)

    Kent, Peter; Lauridsen, Henrik Hein

    2011-01-01

    Study Design: Analysis of Roland Morris Disability Questionnaire (RMDQ) and Oswestry Disability Index (Oswestry) responses.Objectives: To determine the prevalence of unanswered questions on the RMDQ23 (23-item RMDQ version) and Oswestry questionnaires. To determine if managing RMDQ23 missing data...... fully completed RMDQ23 and matching Oswestry questionnaire sets. Raw sum scores were calculated, and questions systematically dropped. At each stage, sum scores were converted to a score on a 0-100 scale and the error calculated. Wilcoxon Tests were used to compare the magnitude of the error scores...

  7. Missed cases of multiple forms of child abuse and neglect.

    Science.gov (United States)

    Koc, Feyza; Oral, Resmiye; Butteris, Regina

    2014-01-01

    Child abuse and neglect is a public health problem and usually associated with family dysfunction due to multiple psychosocial, individual, and environmental factors. The diagnosis of child abuse may be difficult and require a high index of suspicion on the part of the practitioners encountering the child and the family. System-related factors may also enable abuse or prevent the early recognition of abuse. Child abuse and neglect that goes undiagnosed may give rise to chronic abuse and increased morbidity-mortality. In this report, we present two siblings who missed early diagnosis and we emphasize the importance of systems issues to allow early recognition of child abuse and neglect.

  8. Flash CS5.5 The Missing Manual

    CERN Document Server

    Grover, Chris

    2011-01-01

    You can build everything from simple animations to full-fledged iOS and Android apps with Flash CS5.5, but learning this complex program can be difficult-unless you have this fully updated, bestselling guide. Learn how to create gorgeous Flash effects even if you have no programming experience. With Flash CS5.5: The Missing Manual, you'll move from the basics to power-user tools with ease. Learn animation basics. Discover how to turn simple ideas into stunning animations.Master Flash's tools. Learn the animation and effects tools with clear explanations and hands-on examples.Use 3D effects. R

  9. Combination of Multiple Spectral Libraries Improves the Current Search Methods Used to Identify Missing Proteins in the Chromosome-Centric Human Proteome Project.

    Science.gov (United States)

    Cho, Jin-Young; Lee, Hyoung-Joo; Jeong, Seul-Ki; Kim, Kwang-Youl; Kwon, Kyung-Hoon; Yoo, Jong Shin; Omenn, Gilbert S; Baker, Mark S; Hancock, William S; Paik, Young-Ki

    2015-12-04

    Approximately 2.9 billion long base-pair human reference genome sequences are known to encode some 20 000 representative proteins. However, 3000 proteins, that is, ~15% of all proteins, have no or very weak proteomic evidence and are still missing. Missing proteins may be present in rare samples in very low abundance or be only temporarily expressed, causing problems in their detection and protein profiling. In particular, some technical limitations cause missing proteins to remain unassigned. For example, current mass spectrometry techniques have high limits and error rates for the detection of complex biological samples. An insufficient proteome coverage in a reference sequence database and spectral library also raises major issues. Thus, the development of a better strategy that results in greater sensitivity and accuracy in the search for missing proteins is necessary. To this end, we used a new strategy, which combines a reference spectral library search and a simulated spectral library search, to identify missing proteins. We built the human iRefSPL, which contains the original human reference spectral library and additional peptide sequence-spectrum match entries from other species. We also constructed the human simSPL, which contains the simulated spectra of 173 907 human tryptic peptides determined by MassAnalyzer (version 2.3.1). To prove the enhanced analytical performance of the combination of the human iRefSPL and simSPL methods for the identification of missing proteins, we attempted to reanalyze the placental tissue data set (PXD000754). The data from each experiment were analyzed using PeptideProphet, and the results were combined using iProphet. For the quality control, we applied the class-specific false-discovery rate filtering method. All of the results were filtered at a false-discovery rate of libraries, iRefSPL and simSPL, were designed to ensure no overlap of the proteome coverage. They were shown to be complementary to spectral library

  10. Evolution of pathogenicity and sexual reproduction in eight Candida genomes

    Science.gov (United States)

    Butler, Geraldine; Rasmussen, Matthew D.; Lin, Michael F.; Santos, Manuel A.S.; Sakthikumar, Sharadha; Munro, Carol A.; Rheinbay, Esther; Grabherr, Manfred; Forche, Anja; Reedy, Jennifer L.; Agrafioti, Ino; Arnaud, Martha B.; Bates, Steven; Brown, Alistair J.P.; Brunke, Sascha; Costanzo, Maria C.; Fitzpatrick, David A.; de Groot, Piet W. J.; Harris, David; Hoyer, Lois L.; Hube, Bernhard; Klis, Frans M.; Kodira, Chinnappa; Lennard, Nicola; Logue, Mary E.; Martin, Ronny; Neiman, Aaron M.; Nikolaou, Elissavet; Quail, Michael A.; Quinn, Janet; Santos, Maria C.; Schmitzberger, Florian F.; Sherlock, Gavin; Shah, Prachi; Silverstein, Kevin; Skrzypek, Marek S.; Soll, David; Staggs, Rodney; Stansfield, Ian; Stumpf, Michael P H; Sudbery, Peter E.; Thyagarajan, Srikantha; Zeng, Qiandong; Berman, Judith; Berriman, Matthew; Heitman, Joseph; Gow, Neil A. R.; Lorenz, Michael C.; Birren, Bruce W.; Kellis, Manolis; Cuomo, Christina A.

    2009-01-01

    Candida species are the most common cause of opportunistic fungal infection worldwide. We report the genome sequences of six Candida species and compare these and related pathogens and nonpathogens. There are significant expansions of cell wall, secreted, and transporter gene families in pathogenic species, suggesting adaptations associated with virulence. Large genomic tracts are homozygous in three diploid species, possibly resulting from recent recombination events. Surprisingly, key components of the mating and meiosis pathways are missing from several species. These include major differences at the Mating-type loci (MTL); Lodderomyces elongisporus lacks MTL, and components of the a1/alpha2 cell identity determinant were lost in other species, raising questions about how mating and cell types are controlled. Analysis of the CUG leucine to serine genetic code change reveals that 99% of ancestral CUG codons were erased and new ones arose elsewhere. Lastly, we revise the C. albicans gene catalog, identifying many new genes. PMID:19465905

  11. Complete mitochondrial genome of sublittoral macroalga Rhodymenia pseudopalmata (Rhodymeniales, Rhodophyta).

    Science.gov (United States)

    Kim, Kyeong Mi; Yang, Eun Chan; Yi, Gangman; Yoon, Hwan Su

    2014-08-01

    We sequenced and characterized the first complete mitochondrial genome of the sublittoral red alga Rhodymenia pseudopalmata (Rhodymeniales, Rhodophyta). The mitogenome is 26,166 bp in length with 29.5% GC content. The circular mitogenome contains 47 genes, including 24 protein-coding, 2 rRNA and 21 tRNA genes including two copies of trnG, trnL, trnM and trnS. There are two cases of gene-overlapping, found between sdhD and nad4, and between secY and rps12. The R. pseudopalmata mitochondria genome differs from that of Gracilariopsis lemaneiformis by three missing genes (orf60, rpl20 and trnH).

  12. Increasing Genome Sampling and Improving SNP Genotyping for Genotyping-by-Sequencing with New Combinations of Restriction Enzymes.

    Science.gov (United States)

    Fu, Yong-Bi; Peterson, Gregory W; Dong, Yibo

    2016-04-07

    Genotyping-by-sequencing (GBS) has emerged as a useful genomic approach for exploring genome-wide genetic variation. However, GBS commonly samples a genome unevenly and can generate a substantial amount of missing data. These technical features would limit the power of various GBS-based genetic and genomic analyses. Here we present software called IgCoverage for in silico evaluation of genomic coverage through GBS with an individual or pair of restriction enzymes on one sequenced genome, and report a new set of 21 restriction enzyme combinations that can be applied to enhance GBS applications. These enzyme combinations were developed through an application of IgCoverage on 22 plant, animal, and fungus species with sequenced genomes, and some of them were empirically evaluated with different runs of Illumina MiSeq sequencing in 12 plant species. The in silico analysis of 22 organisms revealed up to eight times more genome coverage for the new combinations consisted of pairing four- or five-cutter restriction enzymes than the commonly used enzyme combination PstI + MspI. The empirical evaluation of the new enzyme combination (HinfI + HpyCH4IV) in 12 plant species showed 1.7-6 times more genome coverage than PstI + MspI, and 2.3 times more genome coverage in dicots than monocots. Also, the SNP genotyping in 12 Arabidopsis and 12 rice plants revealed that HinfI + HpyCH4IV generated 7 and 1.3 times more SNPs (with 0-16.7% missing observations) than PstI + MspI, respectively. These findings demonstrate that these novel enzyme combinations can be utilized to increase genome sampling and improve SNP genotyping in various GBS applications. Copyright © 2016 Fu et al.

  13. Genomics and fish adaptation

    Directory of Open Access Journals (Sweden)

    Agostinho Antunes

    2015-12-01

    Full Text Available The completion of the human genome sequencing in 2003 opened a new perspective into the importance of whole genome sequencing projects, and currently multiple species are having their genomes completed sequenced, from simple organisms, such as bacteria, to more complex taxa, such as mammals. This voluminous sequencing data generated across multiple organisms provides also the framework to better understand the genetic makeup of such species and related ones, allowing to explore the genetic changes underlining the evolution of diverse phenotypic traits. Here, recent results from our group retrieved from comparative evolutionary genomic analyses of varied fish species will be considered to exemplify how gene novelty and gene enhancement by positive selection might have been determinant in the success of adaptive radiations into diverse habitats and lifestyles.

  14. Lophotrochozoan mitochondrial genomes

    Energy Technology Data Exchange (ETDEWEB)

    Valles, Yvonne; Boore, Jeffrey L.

    2005-10-01

    Progress in both molecular techniques and phylogeneticmethods has challenged many of the interpretations of traditionaltaxonomy. One example is in the recognition of the animal superphylumLophotrochozoa (annelids, mollusks, echiurans, platyhelminthes,brachiopods, and other phyla), although the relationships within thisgroup and the inclusion of some phyla remain uncertain. While much ofthis progress in phylogenetic reconstruction has been based on comparingsingle gene sequences, we are beginning to see the potential of comparinglarge-scale features of genomes, such as the relative order of genes.Even though tremendous progress is being made on the sequencedetermination of whole nuclear genomes, the dataset of choice forgenome-level characters for many animals across a broad taxonomic rangeremains mitochondrial genomes. We review here what is known aboutmitochondrial genomes of the lophotrochozoans and discuss the promisethat this dataset will enable insight into theirrelationships.

  15. Mouse Genome Informatics (MGI)

    Data.gov (United States)

    U.S. Department of Health & Human Services — MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human...

  16. Genomic definition of species

    Energy Technology Data Exchange (ETDEWEB)

    Crkvenjakov, R.; Drmanac, R.

    1991-07-01

    The subject of this paper is the definition of species based on the assumption that genome is the fundamental level for the origin and maintenance of biological diversity. For this view to be logically consistent it is necessary to assume the existence and operation of the new law which we call genome law. For this reason the genome law is included in the explanation of species phenomenon presented here even if its precise formulation and elaboration are left for the future. The intellectual underpinnings of this definition can be traced to Goldschmidt. We wish to explore some philosophical aspects of the definition of species in terms of the genome. The point of proposing the definition on these grounds is that any real advance in evolutionary theory has to be correct in both its philosophy and its science.

  17. Structural genomics in endocrinology

    NARCIS (Netherlands)

    Smit, J. W.; Romijn, J. A.

    2001-01-01

    Traditionally, endocrine research evolved from the phenotypical characterisation of endocrine disorders to the identification of underlying molecular pathophysiology. This approach has been, and still is, extremely successful. The introduction of genomics and proteomics has resulted in a reversal of

  18. Epidemiology & Genomics Research Program

    Science.gov (United States)

    The Epidemiology and Genomics Research Program, in the National Cancer Institute's Division of Cancer Control and Population Sciences, funds research in human populations to understand the determinants of cancer occurrence and outcomes.

  19. Annotating individual human genomes.

    Science.gov (United States)

    Torkamani, Ali; Scott-Van Zeeland, Ashley A; Topol, Eric J; Schork, Nicholas J

    2011-10-01

    Advances in DNA sequencing technologies have made it possible to rapidly, accurately and affordably sequence entire individual human genomes. As impressive as this ability seems, however, it will not likely amount to much if one cannot extract meaningful information from individual sequence data. Annotating variations within individual genomes and providing information about their biological or phenotypic impact will thus be crucially important in moving individual sequencing projects forward, especially in the context of the clinical use of sequence information. In this paper we consider the various ways in which one might annotate individual sequence variations and point out limitations in the available methods for doing so. It is arguable that, in the foreseeable future, DNA sequencing of individual genomes will become routine for clinical, research, forensic, and personal purposes. We therefore also consider directions and areas for further research in annotating genomic variants. Copyright © 2011 Elsevier Inc. All rights reserved.

  20. ANNOTATING INDIVIDUAL HUMAN GENOMES*

    Science.gov (United States)

    Torkamani, Ali; Scott-Van Zeeland, Ashley A.; Topol, Eric J.; Schork, Nicholas J.

    2014-01-01

    Advances in DNA sequencing technologies have made it possible to rapidly, accurately and affordably sequence entire individual human genomes. As impressive as this ability seems, however, it will not likely to amount to much if one cannot extract meaningful information from individual sequence data. Annotating variations within individual genomes and providing information about their biological or phenotypic impact will thus be crucially important in moving individual sequencing projects forward, especially in the context of the clinical use of sequence information. In this paper we consider the various ways in which one might annotate individual sequence variations and point out limitations in the available methods for doing so. It is arguable that, in the foreseeable future, DNA sequencing of individual genomes will become routine for clinical, research, forensic, and personal purposes. We therefore also consider directions and areas for further research in annotating genomic variants. PMID:21839162

  1. Yeast genome sequencing:

    DEFF Research Database (Denmark)

    Piskur, Jure; Langkjær, Rikke Breinhold

    2004-01-01

    For decades, unicellular yeasts have been general models to help understand the eukaryotic cell and also our own biology. Recently, over a dozen yeast genomes have been sequenced, providing the basis to resolve several complex biological questions. Analysis of the novel sequence data has shown...... of closely related species helps in gene annotation and to answer how many genes there really are within the genomes. Analysis of non-coding regions among closely related species has provided an example of how to determine novel gene regulatory sequences, which were previously difficult to analyse because...... they are short and degenerate and occupy different positions. Comparative genomics helps to understand the origin of yeasts and points out crucial molecular events in yeast evolutionary history, such as whole-genome duplication and horizontal gene transfer(s). In addition, the accumulating sequence data provide...

  2. Lynch Syndrome: Genomics Update and Imaging Review.

    Science.gov (United States)

    Cox, Veronica L; Saeed Bamashmos, Anas A; Foo, Wai Chin; Gupta, Shiva; Yedururi, Sireesha; Garg, Naveen; Kang, Hyunseon Christine

    2018-01-01

    Lynch syndrome is the most common hereditary cancer syndrome, the most common cause of heritable colorectal cancer, and the only known heritable cause of endometrial cancer. Other cancers associated with Lynch syndrome include cancers of the ovary, stomach, urothelial tract, and small bowel, and less frequently, cancers of the brain, biliary tract, pancreas, and prostate. The oncogenic tendency of Lynch syndrome stems from a set of genomic alterations of mismatch repair proteins. Defunct mismatch repair proteins cause unusually high instability of regions of the genome called microsatellites. Over time, the accumulation of mutations in microsatellites and elsewhere in the genome can affect the production of important cellular proteins, spurring tumorigenesis. Universal testing of colorectal tumors for microsatellite instability (MSI) is now recommended to (a) prevent cases of Lynch syndrome being missed owing to the use of clinical criteria alone, (b) reduce morbidity and mortality among the relatives of affected individuals, and (c) guide management decisions. Organ-specific cancer risks and associated screening paradigms vary according to the sex of the affected individual and the type of germline DNA alteration causing the MSI. Furthermore, Lynch syndrome-associated cancers have different pathologic, radiologic, and clinical features compared with their sporadic counterparts. Most notably, Lynch syndrome-associated tumors tend to be more indolent than non-Lynch syndrome-associated neoplasms and thus may respond differently to traditional chemotherapy regimens. The high MSI in cases of colorectal cancer reflects a difference in the biologic features of the tumor, possibly with a unique susceptibility to immunotherapy. © RSNA, 2018.

  3. Genetical Genomics for Evolutionary Studies

    NARCIS (Netherlands)

    Prins, J.C.P.; Smant, G.; Jansen, R.C.

    2012-01-01

    Genetical genomics combines acquired high-throughput genomic data with genetic analysis. In this chapter, we discuss the application of genetical genomics for evolutionary studies, where new high-throughput molecular technologies are combined with mapping quantitative trait loci (QTL) on the genome

  4. A systematic review of missed opportunities for improving tuberculosis and HIV/AIDS control in Sub-saharan Africa: what is still missed by health experts?

    Science.gov (United States)

    Keugoung, Basile; Fouelifack, Florent Ymele; Fotsing, Richard; Macq, Jean; Meli, Jean; Criel, Bart

    2014-01-01

    In sub-Saharan Africa, HIV/AIDS and tuberculosis are major public health problems. In 2010, 64% of the 34 million of people infected with HIV were reported to be living in sub-Saharan Africa. Only 41% of eligible HIV-positive people had access to antiretroviral therapy (ART). Regarding tuberculosis, in 2010, the region had 12% of the world's population but reported 26% of the 8.8 million incident cases and 254000 tuberculosis-related deaths. This paper aims to review missed opportunities for improving HIV/AIDS and tuberculosis prevention and care. We conducted a systematic review in PubMed using the terms 'missed'(Title) AND 'opportunities'(Title). We included systematic review and original research articles done in sub-Saharan Africa on missed opportunities in HIV/AIDS and/or tuberculosis care. Missed opportunities for improving HIV/AIDS and/or tuberculosis care can be classified into five categories: i) patient and community; ii) health professional; iii) health facility; iv) local health system; and v) vertical programme (HIV/AIDS and/or tuberculosis control programmes). None of the reviewed studies identified any missed opportunities related to health system strengthening. Opportunities that are missed hamper tuberculosis and/or HIV/AIDS care in sub-Saharan Africa where health systems remain weak. What is still missing in the analysis of health experts is the acknowledgement that opportunities that are missed to strengthen health systems also undermine tuberculosis and HIV/AIDS prevention and care. Studying why these opportunities are missed will help to understand the rationales behind the missed opportunities, and customize adequate strategies to seize them and for effective diseases control.

  5. The human genome project

    International Nuclear Information System (INIS)

    Worton, R.

    1996-01-01

    The Human Genome Project is a massive international research project, costing 3 to 5 billion dollars and expected to take 15 years, which will identify the all the genes in the human genome - i.e. the complete sequence of bases in human DNA. The prize will be the ability to identify genes causing or predisposing to disease, and in some cases the development of gene therapy, but this new knowledge will raise important ethical issues

  6. Decoding the human genome

    CERN Multimedia

    CERN. Geneva. Audiovisual Unit; Antonerakis, S E

    2002-01-01

    Decoding the Human genome is a very up-to-date topic, raising several questions besides purely scientific, in view of the two competing teams (public and private), the ethics of using the results, and the fact that the project went apparently faster and easier than expected. The lecture series will address the following chapters: Scientific basis and challenges. Ethical and social aspects of genomics.

  7. Molluscan Evolutionary Genomics

    Energy Technology Data Exchange (ETDEWEB)

    Simison, W. Brian; Boore, Jeffrey L.

    2005-12-01

    In the last 20 years there have been dramatic advances in techniques of high-throughput DNA sequencing, most recently accelerated by the Human Genome Project, a program that has determined the three billion base pair code on which we are based. Now this tremendous capability is being directed at other genome targets that are being sampled across the broad range of life. This opens up opportunities as never before for evolutionary and organismal biologists to address questions of both processes and patterns of organismal change. We stand at the dawn of a new 'modern synthesis' period, paralleling that of the early 20th century when the fledgling field of genetics first identified the underlying basis for Darwin's theory. We must now unite the efforts of systematists, paleontologists, mathematicians, computer programmers, molecular biologists, developmental biologists, and others in the pursuit of discovering what genomics can teach us about the diversity of life. Genome-level sampling for mollusks to date has mostly been limited to mitochondrial genomes and it is likely that these will continue to provide the best targets for broad phylogenetic sampling in the near future. However, we are just beginning to see an inroad into complete nuclear genome sequencing, with several mollusks and other eutrochozoans having been selected for work about to begin. Here, we provide an overview of the state of molluscan mitochondrial genomics, highlight a few of the discoveries from this research, outline the promise of broadening this dataset, describe upcoming projects to sequence whole mollusk nuclear genomes, and challenge the community to prepare for making the best use of these data.

  8. Human Germline Genome Editing

    OpenAIRE

    Ormond, Kelly E.; Mortlock, Douglas P.; Scholes, Derek T.; Bombard, Yvonne; Brody, Lawrence C.; Faucett, W. Andrew; Garrison, Nanibaa’ A.; Hercher, Laura; Isasi, Rosario; Middleton, Anna; Musunuru, Kiran; Shriner, Daniel; Virani, Alice; Young, Caroline E.

    2017-01-01

    With CRISPR/Cas9 and other genome-editing technologies, successful somatic and germline genome editing are becoming feasible. To respond, an American Society of Human Genetics (ASHG) workgroup developed this position statement, which was approved by the ASHG Board in March 2017. The workgroup included representatives from the UK Association of Genetic Nurses and Counsellors, Canadian Association of Genetic Counsellors, International Genetic Epidemiology Society, and US National Society of Gen...

  9. Patient understanding of oral contraceptive pill instructions related to missed pills: a systematic review.

    Science.gov (United States)

    Zapata, Lauren B; Steenland, Maria W; Brahmi, Dalia; Marchbanks, Polly A; Curtis, Kathryn M

    2013-05-01

    Instructions on what to do after pills are missed are critical to reducing unintended pregnancies resulting from patient non-adherence to oral contraceptive (OC) regimens. Missed pill instructions have previously been criticized for being too complex, lacking a definition of what is meant by "missed pills," and for being confusing to women who may not know the estrogen content of their formulation. To help inform the development of missed pill guidance to be included in the forthcoming US Selected Practice Recommendations, the objective of this systematic review was to evaluate the evidence on patient understanding of missed pill instructions. We searched the PubMed database for peer-reviewed articles that examined patient understanding of OC pill instructions that were published in any language from inception of the database through March 2012. We included studies that examined women's knowledge and understanding of missed pill instructions after exposure to some written material (e.g., patient package insert, brochure), as well as studies that compared different types of missed pill instructions on women's comprehension. We used standard abstract forms and grading systems to summarize and assess the quality of the evidence. From 1620 articles, nine studies met our inclusion criteria. Evidence from one randomized controlled trial (RCT) and two descriptive studies found that more women knew what to do after missing 1 pill than after missing 2 or 3 pills (Level I, good, to Level II-3, poor), and two descriptive studies found that more women knew what to do after missing 2 pills than after missing 3 pills (Level II-3, fair). Data from two descriptive studies documented the difficulty women have understanding missed pill instructions contained in patient package inserts (Level II-3, poor), and evidence from two RCTs found that providing written brochures with information on missed pill instructions in addition to contraceptive counseling significantly improved

  10. The effect of tertiary surveys on missed injuries in trauma: a systematic review

    Directory of Open Access Journals (Sweden)

    Keijzers Gerben B

    2012-11-01

    Full Text Available Abstract Background Trauma tertiary surveys (TTS are advocated to reduce the rate of missed injuries in hospitalized trauma patients. Moreover, the missed injury rate can be a quality indicator of trauma care performance. Current variation of the definition of missed injury restricts interpretation of the effect of the TTS and limits the use of missed injury for benchmarking. Only a few studies have specifically assessed the effect of the TTS on missed injury. We aimed to systematically appraise these studies using outcomes of two common definitions of missed injury rates and long-term health outcomes. Methods A systematic review was performed. An electronic search (without language or publication restrictions of the Cochrane Library, Medline and Ovid was used to identify studies assessing TTS with short-term measures of missed injuries and long-term health outcomes. ‘Missed injury’ was defined as either: Type I any injury missed at primary and secondary survey and detected by the TTS; or Type II any injury missed at primary and secondary survey and missed by the TTS, detected during hospital stay. Two authors independently selected studies. Risk of bias for observational studies was assessed using the Newcastle-Ottawa scale. Results Ten observational studies met our inclusion criteria. None was randomized and none reported long-term health outcomes. Their risk of bias varied considerably. Nine studies assessed Type I missed injury and found an overall rate of 4.3%. A single study reported Type II missed injury with a rate of 1.5%. Three studies reported outcome data on missed injuries for both control and intervention cohorts, with two reporting an increase in Type I missed injuries (3% vs. 7%, PP=0.01. Conclusions Overall Type I and Type II missed injury rates were 4.3% and 1.5%. Routine TTS performance increased Type I and reduced Type II missed injuries. However, evidence is sub-optimal: few observational studies, non-uniform outcome

  11. Search for missing schizophrenia genes will require a new ...

    Indian Academy of Sciences (India)

    Even the most powerful experimental designs in search of genetic causes of schizophrenia have not met the desired goal. It is imperative to review the reasons for such an outcome and to formulate novel strategies for the future direction of this research in the new era of individual genomes. Here, we will review aspects of ...

  12. "Asia's missing women" as a problem in applied evolutionary psychology?

    Science.gov (United States)

    Brooks, Robert

    2012-12-20

    In many parts of Asia, the Middle East and North Africa, women and children are so undervalued, neglected, abused, and so often killed, that sex ratios are now strongly male biased. In recent decades, sex-biased abortion has exacerbated the problem. In this article I highlight several important insights from evolutionary biology into both the origin and the severe societal consequences of "Asia's missing women", paying particular attention to interactions between evolution, economics and culture. Son preferences and associated cultural practices like patrilineal inheritance, patrilocality and the Indian Hindu dowry system arise among the wealthy and powerful elites for reasons consistent with models of sex-biased parental investment. Those practices then spread via imitation as technology gets cheaper and economic development allows the middle class to grow rapidly. I will consider evidence from India, China and elsewhere that grossly male-biased sex ratios lead to increased crime, violence, local warfare, political instability, drug abuse, prostitution and trafficking of women. The problem of Asia's missing women presents a challenge for applied evolutionary psychology to help us understand and ameliorate sex ratio biases and their most severe consequences.

  13. Sensitivity analysis for missing data in regulatory submissions.

    Science.gov (United States)

    Permutt, Thomas

    2016-07-30

    The National Research Council Panel on Handling Missing Data in Clinical Trials recommended that sensitivity analyses have to be part of the primary reporting of findings from clinical trials. Their specific recommendations, however, seem not to have been taken up rapidly by sponsors of regulatory submissions. The NRC report's detailed suggestions are along rather different lines than what has been called sensitivity analysis in the regulatory setting up to now. Furthermore, the role of sensitivity analysis in regulatory decision-making, although discussed briefly in the NRC report, remains unclear. This paper will examine previous ideas of sensitivity analysis with a view to explaining how the NRC panel's recommendations are different and possibly better suited to coping with present problems of missing data in the regulatory setting. It will also discuss, in more detail than the NRC report, the relevance of sensitivity analysis to decision-making, both for applicants and for regulators. Published 2015. This article is a U.S. Government work and is in the public domain in the USA. Published 2015. This article is a U.S. Government work and is in the public domain in the USA.

  14. Critical thinking, delegation, and missed care in nursing practice.

    Science.gov (United States)

    Bittner, Nancy Phoenix; Gravlin, Gayle

    2009-03-01

    The aim of this study was to understand how nurses use critical thinking to delegate nursing care. Nurses must synthesize large amounts of information and think through complex and often emergent clinical situations when making critical decisions about patient care, including delegation. A qualitative, descriptive study was used in this article. Before delegating, nurses reported considering patient condition, competency, experience, and workload of unlicensed assistive personnel (UAP). Nurses expected UAP to report significant findings and have higher level knowledge, including assessment and prioritizing skills. Successful delegation was dependent on the relationship between the RN and the UAP, communication, system support, and nursing leadership. Nurses reported frequent instances of missed or omitted routine care. Findings from this project provide insight into factors that influence delegation effectiveness. These can guide CNOs and frontline nurse leaders to focus on implementing strategies to mitigate the consequence of missed care. Ineffective delegation of basic nursing care can result in poor patient outcomes, potentially impacting quality measures, satisfaction, and reimbursement for the institution.

  15. The Missing Curriculum in Physics Problem-Solving Education

    Science.gov (United States)

    Williams, Mobolaji

    2018-05-01

    Physics is often seen as an excellent introduction to science because it allows students to learn not only the laws governing the world around them, but also, through the problems students solve, a way of thinking which is conducive to solving problems outside of physics and even outside of science. In this article, we contest this latter idea and argue that in physics classes, students do not learn widely applicable problem-solving skills because physics education almost exclusively requires students to solve well-defined problems rather than the less-defined problems which better model problem solving outside of a formal class. Using personal, constructed, and the historical accounts of Schrödinger's development of the wave equation and Feynman's development of path integrals, we argue that what is missing in problem-solving education is practice in identifying gaps in knowledge and in framing these knowledge gaps as questions of the kind answerable using techniques students have learned. We discuss why these elements are typically not taught as part of the problem-solving curriculum and end with suggestions on how to incorporate these missing elements into physics classes.

  16. A Dialectical Reading of Strindberg’s Miss Julie

    Directory of Open Access Journals (Sweden)

    Hossein Davari

    2017-11-01

    Full Text Available A dialectical reading of Miss Julie offers an explicit depiction of history’s change and progress; it shows how society changes by the growing needs of the subjects and how void relations are negated into new ones. In this play, the transition of feudalist and patriarchal relations have been depicted through a new type of woman who does not believe in the supremacy of her father and husband as owners of the family; the subjects’ desire to escape from restrictive relations, breaking the hierarchal relation, and the decline of nobility as well as loyalty. In Miss Julie, Strindberg shows that the subjects cannot be liberated under the class relation of the coming capitalist mode and profit-oriented relation of the subjects ends only in destruction. He represents the problem of women becoming worse under capitalism and the new bourgeois ideology of bourgeois feminism not only fails to liberate women but also provokes a battle of the sexes as well as chaos.

  17. Statistical inference for imperfect maintenance models with missing data

    International Nuclear Information System (INIS)

    Dijoux, Yann; Fouladirad, Mitra; Nguyen, Dinh Tuan

    2016-01-01

    The paper considers complex industrial systems with incomplete maintenance history. A corrective maintenance is performed after the occurrence of a failure and its efficiency is assumed to be imperfect. In maintenance analysis, the databases are not necessarily complete. Specifically, the observations are assumed to be window-censored. This situation arises relatively frequently after the purchase of a second-hand unit or in the absence of maintenance record during the burn-in phase. The joint assessment of the wear-out of the system and the maintenance efficiency is investigated under missing data. A review along with extensions of statistical inference procedures from an observation window are proposed in the case of perfect and minimal repair using the renewal and Poisson theories, respectively. Virtual age models are employed to model imperfect repair. In this framework, new estimation procedures are developed. In particular, maximum likelihood estimation methods are derived for the most classical virtual age models. The benefits of the new estimation procedures are highlighted by numerical simulations and an application to a real data set. - Highlights: • New estimation procedures for window-censored observations and imperfect repair. • Extensions of inference methods for perfect and minimal repair with missing data. • Overview of maximum likelihood method with complete and incomplete observations. • Benefits of the new procedures highlighted by simulation studies and real application.

  18. RadGenomics project

    Energy Technology Data Exchange (ETDEWEB)

    Iwakawa, Mayumi; Imai, Takashi; Harada, Yoshinobu [National Inst. of Radiological Sciences, Chiba (Japan). Frontier Research Center] [and others

    2002-06-01

    Human health is determined by a complex interplay of factors, predominantly between genetic susceptibility, environmental conditions and aging. The ultimate aim of the RadGenomics (Radiation Genomics) project is to understand the implications of heterogeneity in responses to ionizing radiation arising from genetic variation between individuals in the human population. The rapid progression of the human genome sequencing and the recent development of new technologies in molecular genetics are providing us with new opportunities to understand the genetic basis of individual differences in susceptibility to natural and/or artificial environmental factors, including radiation exposure. The RadGenomics project will inevitably lead to improved protocols for personalized radiotherapy and reductions in the potential side effects of such treatment. The project will contribute to future research into the molecular mechanisms of radiation sensitivity in humans and will stimulate the development of new high-throughput technologies for a broader application of biological and medical sciences. The staff members are specialists in a variety of fields, including genome science, radiation biology, medical science, molecular biology, and informatics, and have joined the RadGenomics project from various universities, companies, and research institutes. The project started in April 2001. (author)

  19. Comparative Genome Viewer

    International Nuclear Information System (INIS)

    Molineris, I.; Sales, G.

    2009-01-01

    The amount of information about genomes, both in the form of complete sequences and annotations, has been exponentially increasing in the last few years. As a result there is the need for tools providing a graphical representation of such information that should be comprehensive and intuitive. Visual representation is especially important in the comparative genomics field since it should provide a combined view of data belonging to different genomes. We believe that existing tools are limited in this respect as they focus on a single genome at a time (conservation histograms) or compress alignment representation to a single dimension. We have therefore developed a web-based tool called Comparative Genome Viewer (Cgv): it integrates a bidimensional representation of alignments between two regions, both at small and big scales, with the richness of annotations present in other genome browsers. We give access to our system through a web-based interface that provides the user with an interactive representation that can be updated in real time using the mouse to move from region to region and to zoom in on interesting details.

  20. Human social genomics.

    Directory of Open Access Journals (Sweden)

    Steven W Cole

    2014-08-01

    Full Text Available A growing literature in human social genomics has begun to analyze how everyday life circumstances influence human gene expression. Social-environmental conditions such as urbanity, low socioeconomic status, social isolation, social threat, and low or unstable social status have been found to associate with differential expression of hundreds of gene transcripts in leukocytes and diseased tissues such as metastatic cancers. In leukocytes, diverse types of social adversity evoke a common conserved transcriptional response to adversity (CTRA characterized by increased expression of proinflammatory genes and decreased expression of genes involved in innate antiviral responses and antibody synthesis. Mechanistic analyses have mapped the neural "social signal transduction" pathways that stimulate CTRA gene expression in response to social threat and may contribute to social gradients in health. Research has also begun to analyze the functional genomics of optimal health and thriving. Two emerging opportunities now stand to revolutionize our understanding of the everyday life of the human genome: network genomics analyses examining how systems-level capabilities emerge from groups of individual socially sensitive genomes and near-real-time transcriptional biofeedback to empirically optimize individual well-being in the context of the unique genetic, geographic, historical, developmental, and social contexts that jointly shape the transcriptional realization of our innate human genomic potential for thriving.

  1. RadGenomics project

    International Nuclear Information System (INIS)

    Iwakawa, Mayumi; Imai, Takashi; Harada, Yoshinobu

    2002-01-01

    Human health is determined by a complex interplay of factors, predominantly between genetic susceptibility, environmental conditions and aging. The ultimate aim of the RadGenomics (Radiation Genomics) project is to understand the implications of heterogeneity in responses to ionizing radiation arising from genetic variation between individuals in the human population. The rapid progression of the human genome sequencing and the recent development of new technologies in molecular genetics are providing us with new opportunities to understand the genetic basis of individual differences in susceptibility to natural and/or artificial environmental factors, including radiation exposure. The RadGenomics project will inevitably lead to improved protocols for personalized radiotherapy and reductions in the potential side effects of such treatment. The project will contribute to future research into the molecular mechanisms of radiation sensitivity in humans and will stimulate the development of new high-throughput technologies for a broader application of biological and medical sciences. The staff members are specialists in a variety of fields, including genome science, radiation biology, medical science, molecular biology, and informatics, and have joined the RadGenomics project from various universities, companies, and research institutes. The project started in April 2001. (author)

  2. Establishing a threshold for the number of missing days using 7 d pedometer data.

    Science.gov (United States)

    Kang, Minsoo; Hart, Peter D; Kim, Youngdeok

    2012-11-01

    The purpose of this study was to examine the threshold of the number of missing days of recovery using the individual information (II)-centered approach. Data for this study came from 86 participants, aged from 17 to 79 years old, who had 7 consecutive days of complete pedometer (Yamax SW 200) wear. Missing datasets (1 d through 5 d missing) were created by a SAS random process 10,000 times each. All missing values were replaced using the II-centered approach. A 7 d average was calculated for each dataset, including the complete dataset. Repeated measure ANOVA was used to determine the differences between 1 d through 5 d missing datasets and the complete dataset. Mean absolute percentage error (MAPE) was also computed. Mean (SD) daily step count for the complete 7 d dataset was 7979 (3084). Mean (SD) values for the 1 d through 5 d missing datasets were 8072 (3218), 8066 (3109), 7968 (3273), 7741 (3050) and 8314 (3529), respectively (p > 0.05). The lower MAPEs were estimated for 1 d missing (5.2%, 95% confidence interval (CI) 4.4-6.0) and 2 d missing (8.4%, 95% CI 7.0-9.8), while all others were greater than 10%. The results of this study show that the 1 d through 5 d missing datasets, with replaced values, were not significantly different from the complete dataset. Based on the MAPE results, it is not recommended to replace more than two days of missing step counts.

  3. Ultrafast comparison of personal genomes

    OpenAIRE

    Mauldin, Denise; Hood, Leroy; Robinson, Max; Glusman, Gustavo

    2017-01-01

    We present an ultra-fast method for comparing personal genomes. We transform the standard genome representation (lists of variants relative to a reference) into 'genome fingerprints' that can be readily compared across sequencing technologies and reference versions. Because of their reduced size, computation on the genome fingerprints is fast and requires little memory. This enables scaling up a variety of important genome analyses, including quantifying relatedness, recognizing duplicative s...

  4. Results of Database Studies in Spine Surgery Can Be Influenced by Missing Data.

    Science.gov (United States)

    Basques, Bryce A; McLynn, Ryan P; Fice, Michael P; Samuel, Andre M; Lukasiewicz, Adam M; Bohl, Daniel D; Ahn, Junyoung; Singh, Kern; Grauer, Jonathan N

    2017-12-01

    National databases are increasingly being used for research in spine surgery; however, one limitation of such databases that has received sparse mention is the frequency of missing data. Studies using these databases often do not emphasize the percentage of missing data for each variable used and do not specify how patients with missing data are incorporated into analyses. This study uses the American College of Surgeons National Surgical Quality Improvement Program (ACS-NSQIP) database to examine whether different treatments of missing data can influence the results of spine studies. (1) What is the frequency of missing data fields for demographics, medical comorbidities, preoperative laboratory values, operating room times, and length of stay recorded in ACS-NSQIP? (2) Using three common approaches to handling missing data, how frequently do those approaches agree in terms of finding particular variables to be associated with adverse events? (3) Do different approaches to handling missing data influence the outcomes and effect sizes of an analysis testing for an association with these variables with occurrence of adverse events? Patients who underwent spine surgery between 2005 and 2013 were identified from the ACS-NSQIP database. A total of 88,471 patients undergoing spine surgery were identified. The most common procedures were anterior cervical discectomy and fusion, lumbar decompression, and lumbar fusion. Demographics, comorbidities, and perioperative laboratory values were tabulated for each patient, and the percent of missing data was noted for each variable. These variables were tested for an association with "any adverse event" using three separate multivariate regressions that used the most common treatments for missing data. In the first regression, patients with any missing data were excluded. In the second regression, missing data were treated as a negative or "reference" value; for continuous variables, the mean of each variable's reference range

  5. Effect of imputing markers from a low-density chip on the reliability of genomic breeding values in Holstein populations

    DEFF Research Database (Denmark)

    Dassonneville, R; Brøndum, Rasmus Froberg; Druet, T

    2011-01-01

    The purpose of this study was to investigate the imputation error and loss of reliability of direct genomic values (DGV) or genomically enhanced breeding values (GEBV) when using genotypes imputed from a 3,000-marker single nucleotide polymorphism (SNP) panel to a 50,000-marker SNP panel. Data...... of missing markers and prediction of breeding values were performed using 2 different reference populations in each country: either a national reference population or a combined EuroGenomics reference population. Validation for accuracy of imputation and genomic prediction was done based on national test...... with a national reference data set gave an absolute loss of 0.05 in mean reliability of GEBV in the French study, whereas a loss of 0.03 was obtained for reliability of DGV in the Nordic study. When genotypes were imputed using the EuroGenomics reference, a loss of 0.02 in mean reliability of GEBV was detected...

  6. Composition and genomic organization of arthropod Hox clusters.

    Science.gov (United States)

    Pace, Ryan M; Grbić, Miodrag; Nagy, Lisa M

    2016-01-01

    The ancestral arthropod is believed to have had a clustered arrangement of ten Hox genes. Within arthropods, Hox gene mutations result in transformation of segment identities. Despite the fact that variation in segment number/character was common in the diversification of arthropods, few examples of Hox gene gains/losses have been correlated with morphological evolution. Furthermore, a full appreciation of the variation in the genomic arrangement of Hox genes in extant arthropods has not been recognized, as genome sequences from each major arthropod clade have not been reported until recently. Initial genomic analysis of the chelicerate Tetranychus urticae suggested that loss of Hox genes and Hox gene clustering might be more common than previously assumed. To further characterize the genomic evolution of arthropod Hox genes, we compared the genomic arrangement and general characteristics of Hox genes from representative taxa from each arthropod subphylum. In agreement with others, we find arthropods generally contain ten Hox genes arranged in a common orientation in the genome, with an increasing number of sampled species missing either Hox3 or abdominal-A orthologs. The genomic clustering of Hox genes in species we surveyed varies significantly, ranging from 0.3 to 13.6 Mb. In all species sampled, arthropod Hox genes are dispersed in the genome relative to the vertebrate Mus musculus. Differences in Hox cluster size arise from variation in the number of intervening genes, intergenic spacing, and the size of introns and UTRs. In the arthropods surveyed, Hox gene duplications are rare and four microRNAs are, in general, conserved in similar genomic positions relative to the Hox genes. The tightly clustered Hox complexes found in the vertebrates are not evident within arthropods, and differential patterns of Hox gene dispersion are found throughout the arthropods. The comparative genomic data continue to support an ancestral arthropod Hox cluster of ten genes with

  7. Genomics using the Assembly of the Mink Genome

    DEFF Research Database (Denmark)

    Guldbrandtsen, Bernt; Cai, Zexi; Sahana, Goutam

    2018-01-01

    The American Mink’s (Neovison vison) genome has recently been sequenced. This opens numerous avenues of research both for studying the basic genetics and physiology of the mink as well as genetic improvement in mink. Using genotyping-by-sequencing (GBS) generated marker data for 2,352 Danish farm...... mink runs of homozygosity (ROH) were detect in mink genomes. Detectable ROH made up on average 1.7% of the genome indicating the presence of at most a moderate level of genomic inbreeding. The fraction of genome regions found in ROH varied. Ten percent of the included regions were never found in ROH....... The ability to detect ROH in the mink genome also demonstrates the general reliability of the new mink genome assembly. Keywords: american mink, run of homozygosity, genome, selection, genomic inbreeding...

  8. Retrotransposon silencing by DNA methylation can drive mammalian genomic imprinting.

    Directory of Open Access Journals (Sweden)

    Shunsuke Suzuki

    2007-04-01

    Full Text Available Among mammals, only eutherians and marsupials are viviparous and have genomic imprinting that leads to parent-of-origin-specific differential gene expression. We used comparative analysis to investigate the origin of genomic imprinting in mammals. PEG10 (paternally expressed 10 is a retrotransposon-derived imprinted gene that has an essential role for the formation of the placenta of the mouse. Here, we show that an orthologue of PEG10 exists in another therian mammal, the marsupial tammar wallaby (Macropus eugenii, but not in a prototherian mammal, the egg-laying platypus (Ornithorhynchus anatinus, suggesting its close relationship to the origin of placentation in therian mammals. We have discovered a hitherto missing link of the imprinting mechanism between eutherians and marsupials because tammar PEG10 is the first example of a differentially methylated region (DMR associated with genomic imprinting in marsupials. Surprisingly, the marsupial DMR was strictly limited to the 5' region of PEG10, unlike the eutherian DMR, which covers the promoter regions of both PEG10 and the adjacent imprinted gene SGCE. These results not only demonstrate a common origin of the DMR-associated imprinting mechanism in therian mammals but provide the first demonstration that DMR-associated genomic imprinting in eutherians can originate from the repression of exogenous DNA sequences and/or retrotransposons by DNA methylation.

  9. Genome size analyses of Pucciniales reveal the largest fungal genomes.

    Science.gov (United States)

    Tavares, Sílvia; Ramos, Ana Paula; Pires, Ana Sofia; Azinheira, Helena G; Caldeirinha, Patrícia; Link, Tobias; Abranches, Rita; Silva, Maria do Céu; Voegele, Ralf T; Loureiro, João; Talhinhas, Pedro

    2014-01-01

    Rust fungi (Basidiomycota, Pucciniales) are biotrophic plant pathogens which exhibit diverse complexities in their life cycles and host ranges. The completion of genome sequencing of a few rust fungi has revealed the occurrence of large genomes. Sequencing efforts for other rust fungi have been hampered by uncertainty concerning their genome sizes. Flow cytometry was recently applied to estimate the genome size of a few rust fungi, and confirmed the occurrence of large genomes in this order (averaging 225.3 Mbp, while the average for Basidiomycota was 49.9 Mbp and was 37.7 Mbp for all fungi). In this work, we have used an innovative and simple approach to simultaneously isolate nuclei from the rust and its host plant in order to estimate the genome size of 30 rust species by flow cytometry. Genome sizes varied over 10-fold, from 70 to 893 Mbp, with an average genome size value of 380.2 Mbp. Compared to the genome sizes of over 1800 fungi, Gymnosporangium confusum possesses the largest fungal genome ever reported (893.2 Mbp). Moreover, even the smallest rust genome determined in this study is larger than the vast majority of fungal genomes (94%). The average genome size of the Pucciniales is now of 305.5 Mbp, while the average Basidiomycota genome size has shifted to 70.4 Mbp and the average for all fungi reached 44.2 Mbp. Despite the fact that no correlation could be drawn between the genome sizes, the phylogenomics or the life cycle of rust fungi, it is interesting to note that rusts with Fabaceae hosts present genomes clearly larger than those with Poaceae hosts. Although this study comprises only a small fraction of the more than 7000 rust species described, it seems already evident that the Pucciniales represent a group where genome size expansion could be a common characteristic. This is in sharp contrast to sister taxa, placing this order in a relevant position in fungal genomics research.

  10. Lessons Learned from Missing Flooding Barriers Operating Experience

    International Nuclear Information System (INIS)

    Simic, Z.; Veira, M. P.

    2016-01-01

    Flooding hazard is highly significant for nuclear power plant safety because of its potential for common cause impact on safety related systems, and because operating experience reviews regularly identify flooding as a cause of concern. Source of the flooding could be external (location) or internal (plant design). The amount of flooding water could vary but even small amount might suffice to affect redundant trains of safety related systems for power supply and cooling. The protection from the flooding is related to the design-basis flood level (DBFL) and it consists of three elements: structural, organizational and accessibility. Determination of the DBFL is critical, as Fukushima Daiichi accident terribly proved. However, as the topic of flooding is very broad, the scope of this paper is focused only on the issues related to the missing flood barriers. Structural measures are physically preventing flooding water to reach or damage safety related system, and they could be permanent or temporary. For temporary measures it is important to have necessary material, equipment and organizational capacity for the timely implementation. Maintenance is important for permanent protection and periodical review is important for assuring readiness and feasibility of temporary flooding protection. Final flooding protection element is assured accessibility to safety related systems during the flooding. Appropriate flooding protection is based on the right implementation of design requirements, proper maintenance and periodic reviews. Operating experience is constantly proving how numerous water sources and systems interactions make flooding protection challenging. This paper is presenting recent related operating experience feedback involving equipment, procedures and analysis. Most frequent deficiencies are: inadequate, degraded or missing seals that would allow floodwaters into safety related spaces. Procedures are inadequate typically because they underestimate necessary

  11. Tensor Completion for Estimating Missing Values in Visual Data

    KAUST Repository

    Liu, Ji

    2012-01-25

    In this paper, we propose an algorithm to estimate missing values in tensors of visual data. The values can be missing due to problems in the acquisition process or because the user manually identified unwanted outliers. Our algorithm works even with a small amount of samples and it can propagate structure to fill larger missing regions. Our methodology is built on recent studies about matrix completion using the matrix trace norm. The contribution of our paper is to extend the matrix case to the tensor case by proposing the first definition of the trace norm for tensors and then by building a working algorithm. First, we propose a definition for the tensor trace norm that generalizes the established definition of the matrix trace norm. Second, similarly to matrix completion, the tensor completion is formulated as a convex optimization problem. Unfortunately, the straightforward problem extension is significantly harder to solve than the matrix case because of the dependency among multiple constraints. To tackle this problem, we developed three algorithms: simple low rank tensor completion (SiLRTC), fast low rank tensor completion (FaLRTC), and high accuracy low rank tensor completion (HaLRTC). The SiLRTC algorithm is simple to implement and employs a relaxation technique to separate the dependant relationships and uses the block coordinate descent (BCD) method to achieve a globally optimal solution; the FaLRTC algorithm utilizes a smoothing scheme to transform the original nonsmooth problem into a smooth one and can be used to solve a general tensor trace norm minimization problem; the HaLRTC algorithm applies the alternating direction method of multipliers (ADMMs) to our problem. Our experiments show potential applications of our algorithms and the quantitative evaluation indicates that our methods are more accurate and robust than heuristic approaches. The efficiency comparison indicates that FaLTRC and HaLRTC are more efficient than SiLRTC and between Fa

  12. Tensor Completion for Estimating Missing Values in Visual Data

    KAUST Repository

    Liu, Ji; Musialski, Przemyslaw; Wonka, Peter; Ye, Jieping

    2012-01-01

    In this paper, we propose an algorithm to estimate missing values in tensors of visual data. The values can be missing due to problems in the acquisition process or because the user manually identified unwanted outliers. Our algorithm works even with a small amount of samples and it can propagate structure to fill larger missing regions. Our methodology is built on recent studies about matrix completion using the matrix trace norm. The contribution of our paper is to extend the matrix case to the tensor case by proposing the first definition of the trace norm for tensors and then by building a working algorithm. First, we propose a definition for the tensor trace norm that generalizes the established definition of the matrix trace norm. Second, similarly to matrix completion, the tensor completion is formulated as a convex optimization problem. Unfortunately, the straightforward problem extension is significantly harder to solve than the matrix case because of the dependency among multiple constraints. To tackle this problem, we developed three algorithms: simple low rank tensor completion (SiLRTC), fast low rank tensor completion (FaLRTC), and high accuracy low rank tensor completion (HaLRTC). The SiLRTC algorithm is simple to implement and employs a relaxation technique to separate the dependant relationships and uses the block coordinate descent (BCD) method to achieve a globally optimal solution; the FaLRTC algorithm utilizes a smoothing scheme to transform the original nonsmooth problem into a smooth one and can be used to solve a general tensor trace norm minimization problem; the HaLRTC algorithm applies the alternating direction method of multipliers (ADMMs) to our problem. Our experiments show potential applications of our algorithms and the quantitative evaluation indicates that our methods are more accurate and robust than heuristic approaches. The efficiency comparison indicates that FaLTRC and HaLRTC are more efficient than SiLRTC and between Fa

  13. Comparison of Three Prehospital Cervical Spine Protocols for Missed Injuries

    Directory of Open Access Journals (Sweden)

    Rick Hong

    2014-07-01

    Full Text Available Introduction: We wanted to compare 3 existing emergency medical services (EMS immobilization protocols: the Prehospital Trauma Life Support (PHTLS, mechanism-based; the Domeier protocol (parallels the National Emergency X-Radiography Utilization Study [NEXUS] criteria; and the Hankins’ criteria (immobilization for patients 65 years, those with altered consciousness, focal neurologic deficit, distracting injury, or midline or paraspinal tenderness.To determine the proportion of patients who would require cervical immobilization per protocol and the number of missed cervical spine injuries, had each protocol been followed with 100% compliance. Methods: This was a cross-sectional study of patients ≥18 years transported by EMS post-traumatic mechanism to an inner city emergency department. Demographic and clinical/historical data obtained by physicians were recorded prior to radiologic imaging. Medical record review ascertained cervical spine injuries. Both physicians and EMS were blinded to the objective of the study. Results: Of 498 participants, 58% were male and mean age was 48 years. The following participants would have required cervical spine immobilization based on the respective protocol: PHTLS, 95.4% (95% CI: 93.1-96.9%; Domeier, 68.7% (95% CI: 64.5-72.6%; Hankins, 81.5% (95% CI: 77.9-84.7%. There were 18 cervical spine injuries: 12 vertebral fractures, 2 subluxations/dislocations and 4 spinal cord injuries. Compliance with each of the 3 protocols would have led to appropriate cervical spine immobilization of all injured patients. In practice, 2 injuries were missed when the PHTLS criteria were mis-applied. Conclusion: Although physician-determined presence of cervical spine immobilization criteria cannot be generalized to the findings obtained by EMS personnel, our findings suggest that the mechanism-based PHTLS criteria may result in unnecessary cervical spine immobilization without apparent benefit to injured patients. PHTLS

  14. Tensor completion for estimating missing values in visual data.

    Science.gov (United States)

    Liu, Ji; Musialski, Przemyslaw; Wonka, Peter; Ye, Jieping

    2013-01-01

    In this paper, we propose an algorithm to estimate missing values in tensors of visual data. The values can be missing due to problems in the acquisition process or because the user manually identified unwanted outliers. Our algorithm works even with a small amount of samples and it can propagate structure to fill larger missing regions. Our methodology is built on recent studies about matrix completion using the matrix trace norm. The contribution of our paper is to extend the matrix case to the tensor case by proposing the first definition of the trace norm for tensors and then by building a working algorithm. First, we propose a definition for the tensor trace norm that generalizes the established definition of the matrix trace norm. Second, similarly to matrix completion, the tensor completion is formulated as a convex optimization problem. Unfortunately, the straightforward problem extension is significantly harder to solve than the matrix case because of the dependency among multiple constraints. To tackle this problem, we developed three algorithms: simple low rank tensor completion (SiLRTC), fast low rank tensor completion (FaLRTC), and high accuracy low rank tensor completion (HaLRTC). The SiLRTC algorithm is simple to implement and employs a relaxation technique to separate the dependent relationships and uses the block coordinate descent (BCD) method to achieve a globally optimal solution; the FaLRTC algorithm utilizes a smoothing scheme to transform the original nonsmooth problem into a smooth one and can be used to solve a general tensor trace norm minimization problem; the HaLRTC algorithm applies the alternating direction method of multipliers (ADMMs) to our problem. Our experiments show potential applications of our algorithms and the quantitative evaluation indicates that our methods are more accurate and robust than heuristic approaches. The efficiency comparison indicates that FaLTRC and HaLRTC are more efficient than SiLRTC and between FaLRTC an

  15. The Strengths and Limitations of South Africa's Search for Apartheid-Era Missing Persons.

    Science.gov (United States)

    Aronson, Jay D

    2011-07-01

    This article examines efforts to account for missing persons from the apartheid era in South Africa by family members, civil society organizations and the current government's Missing Persons Task Team, which emerged out of the Truth and Reconciliation Commission process. It focuses on how missing persons have been officially defined in the South African context and the extent to which the South African government is able to address the current needs and desires of relatives of the missing. I make two main arguments: that family members ought to have an active role in shaping the initiatives and institutions that seek to resolve the fate of missing people, and that the South African government ought to take a more holistic 'grave-to-grave' approach to the process of identifying, returning and reburying the remains of the missing.

  16. Autoregressive-model-based missing value estimation for DNA microarray time series data.

    Science.gov (United States)

    Choong, Miew Keen; Charbit, Maurice; Yan, Hong

    2009-01-01

    Missing value estimation is important in DNA microarray data analysis. A number of algorithms have been developed to solve this problem, but they have several limitations. Most existing algorithms are not able to deal with the situation where a particular time point (column) of the data is missing entirely. In this paper, we present an autoregressive-model-based missing value estimation method (ARLSimpute) that takes into account the dynamic property of microarray temporal data and the local similarity structures in the data. ARLSimpute is especially effective for the situation where a particular time point contains many missing values or where the entire time point is missing. Experiment results suggest that our proposed algorithm is an accurate missing value estimator in comparison with other imputation methods on simulated as well as real microarray time series datasets.

  17. Medical surgical nurses describe missed nursing care tasks-Evaluating our work environment.

    Science.gov (United States)

    Winsett, Rebecca P; Rottet, Kendra; Schmitt, Abby; Wathen, Ellen; Wilson, Debra

    2016-11-01

    The purpose of the study was to explore the nurse work environment by evaluating the self-report of missed nursing care and the reasons for the missed care. A convenience sample of medical surgical nurses from four hospitals was invited to complete the survey for this descriptive study. The sample included 168 nurses. The MISSCARE survey assessed the frequency and reason of 24 routine nursing care elements. The most frequently reported missed care was ambulation as ordered, medications given within a 30 minute window, and mouth care. Moderate or significant reasons reported for the missed care were: unexpected rise in volume/acuity, heavy admissions/discharges, inadequate assistants, inadequate staff, meds not available when needed, and urgent situations. Identifying missed nursing care and reasons for missed care provides an opportunity for exploring strategies to reduce interruptions, develop unit cohesiveness, improve the nurse work environment, and ultimately leading to improved patient outcomes. Copyright © 2016 Elsevier Inc. All rights reserved.

  18. The genomic signature of human rhinoviruses A, B and C.

    Directory of Open Access Journals (Sweden)

    Spyridon Megremis

    Full Text Available Human rhinoviruses are single stranded positive sense RNA viruses that are presented in more than 50% of acute upper respiratory tract infections. Despite extensive studies on the genetic diversity of the virus, little is known about the forces driving it. In order to explain this diversity, many research groups have focused on protein sequence requirements for viable, functional and transmissible virus but have missed out an important aspect of viral evolution such as the genomic ontology of the virus. This study presents for the first time the genomic signature of 111 fully sequenced HRV strains from all three groups HRV-A, HRV-B and HRV-C. We observed an HRV genome tendency to eliminate CpG and UpA dinucleotides, coupling with over-representation of UpG and CpA. We propose a specific mechanism which describes how rapid changes in the HRV genomic sequence can take place under the strict control of conservation of the polypeptide backbone. Moreover, the distribution of the observed under- and over-represented dinucleotides along the HRV genome is presented. Distance matrice tables based on CpG and UpA odds ratios were constructed and viewed as heatmaps and distance trees. None of the suppressions can be attributed to codon usage or in RNA secondary structure requirements. Since viral recognition is dependent on RNA motifs rich in CpG and UpA, it is possible that the overall described genome evolution mechanism acts in order to protect the virus from host recognition.

  19. Functional genomics in renal transplantation and chronic kidney disease

    International Nuclear Information System (INIS)

    Wilflingseder, J.

    2010-01-01

    For the past decade, the development of genomic technology has revolutionized modern biological research. Functional genomic analyses enable biologists to study genetic events on a genome wide scale. Examples of applications are gene discovery, biomarker determination, disease classification, and drug target identification. Global expression profiles performed with microarrays enable a better understanding of molecular signature of human disease, including acute and chronic kidney disease. About 10 % of the population in western industrialized nations suffers from chronic kidney disease (CKD). Treatment of end stage renal disease, the final stage of CKD is performed by either hemo- or peritoneal dialysis or renal transplantation. The preferred treatment is renal transplantation, because of the higher quality of life. But the pathophysiology of the disease on a molecular level is not well enough understood and early biomarkers for acute and chronic kidney disease are missing. In my studies I focused on genomics of allograft biopsies, prevention of delayed graft function after renal transplantation, anemia after renal transplantation, biocompatibility of hemodialysis membranes and peritoneal dialysis fluids and cardiovascular diseases and bone disorders in CKD patients. Gene expression profiles, pathway analysis and protein-protein interaction networks were used to elucidate the underlying pathophysiological mechanism of the disease or phenomena, identifying early biomarkers or predictors of disease state and potentially drug targets. In summery my PhD thesis represents the application of functional genomic analyses in chronic kidney disease and renal transplantation. The results provide a deeper view into the molecular and cellular mechanisms of kidney disease. Nevertheless, future multicenter collaborative studies, meta-analyses of existing data, incorporation of functional genomics into large-scale prospective clinical trials are needed and will give biomedical

  20. Genomes to Proteomes

    Energy Technology Data Exchange (ETDEWEB)

    Panisko, Ellen A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Grigoriev, Igor [USDOE Joint Genome Inst., Walnut Creek, CA (United States); Daly, Don S. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Webb-Robertson, Bobbie-Jo [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Baker, Scott E. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2009-03-01

    Biologists are awash with genomic sequence data. In large part, this is due to the rapid acceleration in the generation of DNA sequence that occurred as public and private research institutes raced to sequence the human genome. In parallel with the large human genome effort, mostly smaller genomes of other important model organisms were sequenced. Projects following on these initial efforts have made use of technological advances and the DNA sequencing infrastructure that was built for the human and other organism genome projects. As a result, the genome sequences of many organisms are available in high quality draft form. While in many ways this is good news, there are limitations to the biological insights that can be gleaned from DNA sequences alone; genome sequences offer only a bird's eye view of the biological processes endemic to an organism or community. Fortunately, the genome sequences now being produced at such a high rate can serve as the foundation for other global experimental platforms such as proteomics. Proteomic methods offer a snapshot of the proteins present at a point in time for a given biological sample. Current global proteomics methods combine enzymatic digestion, separations, mass spectrometry and database searching for peptide identification. One key aspect of proteomics is the prediction of peptide sequences from mass spectrometry data. Global proteomic analysis uses computational matching of experimental mass spectra with predicted spectra based on databases of gene models that are often generated computationally. Thus, the quality of gene models predicted from a genome sequence is crucial in the generation of high quality peptide identifications. Once peptides are identified they can be assigned to their parent protein. Proteins identified as expressed in a given experiment are most useful when compared to other expressed proteins in a larger biological context or biochemical pathway. In this chapter we will discuss the automatic

  1. Experimental Induction of Genome Chaos.

    Science.gov (United States)

    Ye, Christine J; Liu, Guo; Heng, Henry H

    2018-01-01

    Genome chaos, or karyotype chaos, represents a powerful survival strategy for somatic cells under high levels of stress/selection. Since the genome context, not the gene content, encodes the genomic blueprint of the cell, stress-induced rapid and massive reorganization of genome topology functions as a very important mechanism for genome (karyotype) evolution. In recent years, the phenomenon of genome chaos has been confirmed by various sequencing efforts, and many different terms have been coined to describe different subtypes of the chaotic genome including "chromothripsis," "chromoplexy," and "structural mutations." To advance this exciting field, we need an effective experimental system to induce and characterize the karyotype reorganization process. In this chapter, an experimental protocol to induce chaotic genomes is described, following a brief discussion of the mechanism and implication of genome chaos in cancer evolution.

  2. Use of a Pre-Insertion Resistor to Minimize Zero-Missing Phenomenon and Switching Overvoltages

    DEFF Research Database (Denmark)

    Bak, Claus Leth; da Silva, Filipe Miguel Faria; Gudmundsdottir, Unnur Stella

    2009-01-01

    With the increasing use of High-Voltage Cables, which have different electric characteristics from Overhead Lines, phenomenon like current zero-missing start to appear more often on the transmission systems. Methods to prevent zero-missing phenomenon are still being studied and compared to see wh...... an optimal value of the resistance of the pre-insertion resistor that results in minimizing both the zero-missing phenomenon and switching overvoltages simultaneously....

  3. Genome Sequences of Oryza Species

    KAUST Repository

    Kumagai, Masahiko; Tanaka, Tsuyoshi; Ohyanagi, Hajime; Hsing, Yue-Ie C.; Itoh, Takeshi

    2018-01-01

    This chapter summarizes recent data obtained from genome sequencing, annotation projects, and studies on the genome diversity of Oryza sativa and related Oryza species. O. sativa, commonly known as Asian rice, is the first monocot species whose complete genome sequence was deciphered based on physical mapping by an international collaborative effort. This genome, along with its accurate and comprehensive annotation, has become an indispensable foundation for crop genomics and breeding. With the development of innovative sequencing technologies, genomic studies of O. sativa have dramatically increased; in particular, a large number of cultivars and wild accessions have been sequenced and compared with the reference rice genome. Since de novo genome sequencing has become cost-effective, the genome of African cultivated rice, O. glaberrima, has also been determined. Comparative genomic studies have highlighted the independent domestication processes of different rice species, but it also turned out that Asian and African rice share a common gene set that has experienced similar artificial selection. An international project aimed at constructing reference genomes and examining the genome diversity of wild Oryza species is currently underway, and the genomes of some species are publicly available. This project provides a platform for investigations such as the evolution, development, polyploidization, and improvement of crops. Studies on the genomic diversity of Oryza species, including wild species, should provide new insights to solve the problem of growing food demands in the face of rapid climatic changes.

  4. Genome Sequences of Oryza Species

    KAUST Repository

    Kumagai, Masahiko

    2018-02-14

    This chapter summarizes recent data obtained from genome sequencing, annotation projects, and studies on the genome diversity of Oryza sativa and related Oryza species. O. sativa, commonly known as Asian rice, is the first monocot species whose complete genome sequence was deciphered based on physical mapping by an international collaborative effort. This genome, along with its accurate and comprehensive annotation, has become an indispensable foundation for crop genomics and breeding. With the development of innovative sequencing technologies, genomic studies of O. sativa have dramatically increased; in particular, a large number of cultivars and wild accessions have been sequenced and compared with the reference rice genome. Since de novo genome sequencing has become cost-effective, the genome of African cultivated rice, O. glaberrima, has also been determined. Comparative genomic studies have highlighted the independent domestication processes of different rice species, but it also turned out that Asian and African rice share a common gene set that has experienced similar artificial selection. An international project aimed at constructing reference genomes and examining the genome diversity of wild Oryza species is currently underway, and the genomes of some species are publicly available. This project provides a platform for investigations such as the evolution, development, polyploidization, and improvement of crops. Studies on the genomic diversity of Oryza species, including wild species, should provide new insights to solve the problem of growing food demands in the face of rapid climatic changes.

  5. Genome position specific priors for genomic prediction

    DEFF Research Database (Denmark)

    Brøndum, Rasmus Froberg; Su, Guosheng; Lund, Mogens Sandø

    2012-01-01

    casual mutation is different between the populations but affects the same gene. Proportions of a four-distribution mixture for SNP effects in segments of fixed size along the genome are derived from one population and set as location specific prior proportions of distributions of SNP effects...... for the target population. The model was tested using dairy cattle populations of different breeds: 540 Australian Jersey bulls, 2297 Australian Holstein bulls and 5214 Nordic Holstein bulls. The traits studied were protein-, fat- and milk yield. Genotypic data was Illumina 777K SNPs, real or imputed Results...

  6. Missed deadline notification in best-effort schedulers

    Science.gov (United States)

    Banachowski, Scott A.; Wu, Joel; Brandt, Scott A.

    2003-12-01

    It is common to run multimedia and other periodic, soft real-time applications on general-purpose computer systems. These systems use best-effort scheduling algorithms that cannot guarantee applications will receive responsive scheduling to meet deadline or timing requirements. We present a simple mechanism called Missed Deadline Notification (MDN) that allows applications to notify the system when they do not receive their desired level of responsiveness. Consisting of a single system call with no arguments, this simple interface allows the operating system to provide better support for soft real-time applications without any a priori information about their timing or resource needs. We implemented MDN in three different schedulers: Linux, BEST, and BeRate. We describe these implementations and their performance when running real-time applications and discuss policies to prevent applications from abusing MDN to gain extra resources.

  7. Adult hypopituitarism: Are we missing or is it clinical lethargy?

    Directory of Open Access Journals (Sweden)

    K S Brar

    2011-01-01

    Full Text Available Hypopituitarism, a disease of varied etiologies, is a serious endocrine illness that requires early recognition and prompt treatment to avoid its severe deleterious effects. In adults it is often missed due to non-specific symptoms of growth hormone deficiency and hypogonadism or mild deficiencies of other pituitary hormones. In some it may present with acute onset of symptoms suggestive of acute adrenal (corticotropin insufficiency or symptoms due to mass lesion in/or around pituitary. High index of suspicion is required to seek hypopituitarism in patients with non-specific symptoms such as fatigue and malaise. Treatment of isolated hormone deficiency, partial or panhypopituitarism, has gratifying results although they require lifelong treatment and follow-up.

  8. Search for dark sectors in missing energy events

    CERN Multimedia

    Enik, T; Rubbia, A; Depero, E; Krasnikov, N; Petukhov, O; Kuleshov, S; Volkov, P; Trifonov, A; Radics, B; Toropin, A; Dermenev, A; Ahmed, N; Peshekhonov, D; Peshekhonov, V; Kekelidze, G; Dusaev, R; Vasilishin, B; Crivelli, P; Tlisov, D; Karjavine, V; Donskov, S; Lyubovitsky, V; Zhukov, K; Kirsanov, M; Karneyeu, A; Matveev, V; Lysan, V; Samoylenko, V

    The NA64 experiment (known as P348 at the proposal stage) is a fixed-target experiment at the CERN SPS combining the active beam dump and missing energy techniques to search for rare events. The experiment will build and operate a fully hermetic detector placed on the H4 beam line with the primary goal to search for light dark bosons (Z') from dark sector that are coupled to photons, e.g. dark photons (A'), or sub-GeV Z' coupled only to quarks. In some cases the Z' is coupled only to µ or tau, so we call the Z′ the dark leptonic gauge boson. The experiment is also capable to search for K_L -> invisible decay, which is complementary to K+ -> π+ + ν ν, and invisible decays of π0, η, η′, K_S mesons.

  9. Orexin: a Missing Link Between Sleep Disorders and Heart Failure?

    Science.gov (United States)

    Pan, Stephen; Cabral, Carolina S; Ashley, Euan A; Perez, Marco V

    2017-04-01

    Sleep disorders represent a significant comorbidity in the heart failure population, and there is mounting evidence that treatment of sleep disorders such as obstructive sleep apnea can significantly improve cardiac function. However, the link between these two disorders is still not entirely clear. Recently, a novel neurohormonal pathway has been elucidated involving signaling molecules now collectively known as the orexins, which have been implicated in regulating autonomic function during sleep/wake cycles. Further evidence has mounted that orexin signaling is deeply perturbed in the setting of sleep disorders, and furthermore that abnormal orexin signaling may be implicated in the pathology of heart failure. The orexin signaling pathway represents an enticing novel target for both the treatment of sleep disorders as well as heart failure, and may represent one facet of the "missing link" between these two prevalent and often comorbid diseases.

  10. Understanding conflict as a (missed) opportunity for social development

    DEFF Research Database (Denmark)

    Ravn, Ib

    and the parties may learn and grow, or it may be missed--lost in suppression, projections, fear, etc. Conflict is thus seen, not as an outcome of regrettably incompatible goals or activities, but as an active potential for learning and development. Some implications for conflict resolution practice are outlined.......In the literature on conflict management, conflict is usually defined in terms of incompatible goals and activities. In contrast, Thomas (1992), making no reference to such incompatibilities, defines conflict as a process that begins when one party feels negatively affected by another. This paper...... modifies and extends Thomas’ definition thus: One party is in conflict with another when he or she 1. experiences psychological or physical pain, 2. holds the other party to be responsible for this pain, and 3. does not accept this situation. This definition is nested in a theoretical perspective that sees...

  11. How not to miss autoinflammatory diseases masquerading as urticaria

    DEFF Research Database (Denmark)

    Krause, K; Grattan, C E; Bindslev-Jensen, C

    2012-01-01

    Urticarial skin reactions are one of the most frequent problems seen by allergists and clinical immunologists in daily practice. The most common reason for recurrent wheals is spontaneous urticaria. There are, however, several less common diseases that present with urticarial rash...... symptoms including recurrent fever attacks, arthralgia or arthritis and fatigue. Autoinflammatory diseases are often associated with a diagnostic delay of many years and do not respond to antihistamines and other treatments of urticaria. Also, the chronic inflammation may lead to long-term complications...... such as amyloidosis. It is therefore important not to miss these diseases when diagnosing and treating patients with chronic recurrent urticarial rash. Here, we present clinical clues and tips that can help to identify autoinflammatory disorders in patients presenting with chronic urticarial rash and discuss...

  12. An MVA Approach to Missing $E_T$

    CERN Document Server

    Herwig, Theodor Christian

    2013-01-01

    We present an overview of an analysis of the missing transverse energy (MET) resolution in the CMS detector studying $Z\\to\\mu\\mu$ decay events as a part of the University of Michigan Summer REU Program. We make use of boosted decision trees and specialized recoil variables in an attempt to isolate separate effects contributing to the detector resolution such as pileup, the underlying event, and detector inefficiencies. A metric is developed to study the body of high-MET events in the distribution. Emphasis is placed on constructing a multivariate analysis that effectively models and corrects these `tail' regions, resulting in an overall improvement in our MET resolution. In Monte-Carlo simulation, we see an improvement from a mean value of MET = 18.12 GeV to MET= 8.14 GeV with full MVA corrections.

  13. Conflicts and missed signals in psychoanalysis, behaviorism, and Gestalt psychology.

    Science.gov (United States)

    Murray, David J; Kilgour, Andrea R; Wasylkiw, Louise

    2000-04-01

    At the turn of the 20th century, European psychologists found themselves in conflict situations with respect to the role that private mental states should play in a scientific psychology. Out of this conflict arose 3 of the best-known schools of the 20th century: psychoanalysis, behaviorism, and Gestalt psychology. Each of these schools is discussed with respect to two characteristics. First, the authors discuss the attitude of each school on the meaning of the word unconscious as it was understood around 1900. Second, the authors discuss the influence of each school on the reception accorded to books written around 1900 espousing viewpoints that did not cohere with the school's beliefs. Such books may be considered "missed signals" in the history of psychology. "Hits" associated with each school are also highlighted.

  14. Polynomials, Riemann surfaces, and reconstructing missing-energy events

    CERN Document Server

    Gripaios, Ben; Webber, Bryan

    2011-01-01

    We consider the problem of reconstructing energies, momenta, and masses in collider events with missing energy, along with the complications introduced by combinatorial ambiguities and measurement errors. Typically, one reconstructs more than one value and we show how the wrong values may be correlated with the right ones. The problem has a natural formulation in terms of the theory of Riemann surfaces. We discuss examples including top quark decays in the Standard Model (relevant for top quark mass measurements and tests of spin correlation), cascade decays in models of new physics containing dark matter candidates, decays of third-generation leptoquarks in composite models of electroweak symmetry breaking, and Higgs boson decay into two tau leptons.

  15. The Missing Response to Selection in the Wild.

    Science.gov (United States)

    Pujol, Benoit; Blanchet, Simon; Charmantier, Anne; Danchin, Etienne; Facon, Benoit; Marrot, Pascal; Roux, Fabrice; Scotti, Ivan; Teplitsky, Céline; Thomson, Caroline E; Winney, Isabel

    2018-05-01

    Although there are many examples of contemporary directional selection, evidence for responses to selection that match predictions are often missing in quantitative genetic studies of wild populations. This is despite the presence of genetic variation and selection pressures - theoretical prerequisites for the response to selection. This conundrum can be explained by statistical issues with accurate parameter estimation, and by biological mechanisms that interfere with the response to selection. These biological mechanisms can accelerate or constrain this response. These mechanisms are generally studied independently but might act simultaneously. We therefore integrated these mechanisms to explore their potential combined effect. This has implications for explaining the apparent evolutionary stasis of wild populations and the conservation of wildlife. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

  16. Moving, sensing intersectionality: a case study of Miss China Europe.

    Science.gov (United States)

    Chow, Yiu Fai

    2011-01-01

    Every year, Miss China Europe, a transnational beauty pageant organized for the Chinese diaspora, is held in the Netherlands. The hypervisuality of Chinese diasporic women at the event stands in painful contrast to their everyday invisibility, whether in the Netherlands, China, or elsewhere in the world. Informed by intersectional and transnational feminist scholarship, this empirical study zooms in on one group of women, ethnic Chinese born and/or growing up in the Netherlands, to identify and recuperate their neglected lived experience in a particular historical-cultural context. It takes their own voices as central, hopefully to contribute to their visibility. It aims to provide an understanding of diasporic Chinese women as living in the dynamics not only of their multiple subordinations but also of their subjective consciousness, experienced autonomy, and agency. Drawing insights from the subjective accounts of both contestants and audiences of Miss China Europe, I suggest that one way to foreground marginalized women's agency is to understand their intersectionality in terms of movements and sensory experiences. On the one hand, while the contestants articulated a readiness to perform their modern and yet Chinese selves, they were making movements along two intersecting axes of inequality and power relations - Chineseness and Dutchness - precisely to negotiate their sense of inequality and power relations. On the other hand, among the audiences, two major topics - the blood issue (or whether Chineseness should be defined by ancestry) and the language problem (or whether Chineseness should be defined by the ability to speak Chinese) - were raised regularly, underscoring a complex viewing experience of seeing and hearing, of the tension between visual and audio identifications.

  17. Semiparametric approach for non-monotone missing covariates in a parametric regression model

    KAUST Repository

    Sinha, Samiran

    2014-02-26

    Missing covariate data often arise in biomedical studies, and analysis of such data that ignores subjects with incomplete information may lead to inefficient and possibly biased estimates. A great deal of attention has been paid to handling a single missing covariate or a monotone pattern of missing data when the missingness mechanism is missing at random. In this article, we propose a semiparametric method for handling non-monotone patterns of missing data. The proposed method relies on the assumption that the missingness mechanism of a variable does not depend on the missing variable itself but may depend on the other missing variables. This mechanism is somewhat less general than the completely non-ignorable mechanism but is sometimes more flexible than the missing at random mechanism where the missingness mechansim is allowed to depend only on the completely observed variables. The proposed approach is robust to misspecification of the distribution of the missing covariates, and the proposed mechanism helps to nullify (or reduce) the problems due to non-identifiability that result from the non-ignorable missingness mechanism. The asymptotic properties of the proposed estimator are derived. Finite sample performance is assessed through simulation studies. Finally, for the purpose of illustration we analyze an endometrial cancer dataset and a hip fracture dataset.

  18. Protannotator: a semiautomated pipeline for chromosome-wise functional annotation of the "missing" human proteome.

    Science.gov (United States)

    Islam, Mohammad T; Garg, Gagan; Hancock, William S; Risk, Brian A; Baker, Mark S; Ranganathan, Shoba

    2014-01-03

    The chromosome-centric human proteome project (C-HPP) aims to define the complete set of proteins encoded in each human chromosome. The neXtProt database (September 2013) lists 20,128 proteins for the human proteome, of which 3831 human proteins (∼19%) are considered "missing" according to the standard metrics table (released September 27, 2013). In support of the C-HPP initiative, we have extended the annotation strategy developed for human chromosome 7 "missing" proteins into a semiautomated pipeline to functionally annotate the "missing" human proteome. This pipeline integrates a suite of bioinformatics analysis and annotation software tools to identify homologues and map putative functional signatures, gene ontology, and biochemical pathways. From sequential BLAST searches, we have primarily identified homologues from reviewed nonhuman mammalian proteins with protein evidence for 1271 (33.2%) "missing" proteins, followed by 703 (18.4%) homologues from reviewed nonhuman mammalian proteins and subsequently 564 (14.7%) homologues from reviewed human proteins. Functional annotations for 1945 (50.8%) "missing" proteins were also determined. To accelerate the identification of "missing" proteins from proteomics studies, we generated proteotypic peptides in silico. Matching these proteotypic peptides to ENCODE proteogenomic data resulted in proteomic evidence for 107 (2.8%) of the 3831 "missing proteins, while evidence from a recent membrane proteomic study supported the existence for another 15 "missing" proteins. The chromosome-wise functional annotation of all "missing" proteins is freely available to the scientific community through our web server (http://biolinfo.org/protannotator).

  19. Application of pattern mixture models to address missing data in longitudinal data analysis using SPSS.

    Science.gov (United States)

    Son, Heesook; Friedmann, Erika; Thomas, Sue A

    2012-01-01

    Longitudinal studies are used in nursing research to examine changes over time in health indicators. Traditional approaches to longitudinal analysis of means, such as analysis of variance with repeated measures, are limited to analyzing complete cases. This limitation can lead to biased results due to withdrawal or data omission bias or to imputation of missing data, which can lead to bias toward the null if data are not missing completely at random. Pattern mixture models are useful to evaluate the informativeness of missing data and to adjust linear mixed model (LMM) analyses if missing data are informative. The aim of this study was to provide an example of statistical procedures for applying a pattern mixture model to evaluate the informativeness of missing data and conduct analyses of data with informative missingness in longitudinal studies using SPSS. The data set from the Patients' and Families' Psychological Response to Home Automated External Defibrillator Trial was used as an example to examine informativeness of missing data with pattern mixture models and to use a missing data pattern in analysis of longitudinal data. Prevention of withdrawal bias, omitted data bias, and bias toward the null in longitudinal LMMs requires the assessment of the informativeness of the occurrence of missing data. Missing data patterns can be incorporated as fixed effects into LMMs to evaluate the contribution of the presence of informative missingness to and control for the effects of missingness on outcomes. Pattern mixture models are a useful method to address the presence and effect of informative missingness in longitudinal studies.

  20. Holding on to hope: A review of the literature exploring missing persons, hope and ambiguous loss.

    Science.gov (United States)

    Wayland, Sarah; Maple, Myfanwy; McKay, Kathy; Glassock, Geoffrey

    2016-01-01

    When a person goes missing, those left behind mourn an ambiguous loss where grief can be disenfranchised. Different to bereavement following death, hope figures into this experience as a missing person has the potential to return. This review explores hope for families of missing people. Lived experience of ambiguous loss was deconstructed to reveal responses punctuated by hope, which had practical and psychological implications for those learning to live with an unresolved absence. Future lines of enquiry must address the dearth of research exploring the role of hope, unresolved grief, and its clinical implications when a person is missing.

  1. Learning from near misses: from quick fixes to closing off the Swiss-cheese holes.

    Science.gov (United States)

    Jeffs, Lianne; Berta, Whitney; Lingard, Lorelei; Baker, G Ross

    2012-04-01

    The extent to which individuals in healthcare use near misses as learning opportunities remains poorly understood. Thus, an exploratory study was conducted to gain insight into the nature of, and contributing factors to, organisational learning from near misses in clinical practice. A constructivist grounded theory approach was employed which included semi-structured interviews with 24 participants (16 clinicians and 8 administrators) from a large teaching hospital in Canada. This study revealed three scenarios for the responses to near misses, the most common involved 'doing a quick fix' where clinicians recognised and corrected an error with no further action. The second scenario consisted of reporting near misses but not hearing back from management, which some participants characterised as 'going into a black hole'. The third scenario was 'closing off the Swiss-cheese holes', in which a reported near miss generated corrective action at an organisational level. Explanations for 'doing a quick fix' included the pervasiveness of near misses that cause no harm and fear associated with reporting the near miss. 'Going into a black hole' reflected managers' focus on operational duties and events that harmed patients. 'Closing off the Swiss-cheese holes' occurred when managers perceived substantial potential for harm and preventability. Where learning was perceived to occur, leaders played a pivotal role in encouraging near-miss reporting. To optimise learning, organisations will need to determine which near misses are appropriate to be responded to as 'quick fixes' and which ones require further action at the unit and corporate levels.

  2. Known and missing left ventricular ejection fraction and survival in patients with heart failure

    DEFF Research Database (Denmark)

    Poppe, Katrina K; Squire, Iain B; Whalley, Gillian A

    2013-01-01

    Treatment of patients with heart failure (HF) relies on measurement of LVEF. However, the extent to which EF is recorded varies markedly. We sought to characterize the patient group that is missing a measure of EF, and to explore the association between missing EF and outcome.......Treatment of patients with heart failure (HF) relies on measurement of LVEF. However, the extent to which EF is recorded varies markedly. We sought to characterize the patient group that is missing a measure of EF, and to explore the association between missing EF and outcome....

  3. Factors influencing the missed nursing care in patients from a private hospital

    Directory of Open Access Journals (Sweden)

    Raúl Hernández-Cruz

    Full Text Available ABSTRACT Objective: to determine the factors that influence the missed nursing care in hospitalized patients. Methods: descriptive correlational study developed at a private hospital in Mexico. To identify the missed nursing care and related factors, the MISSCARE survey was used, which measures the care missed and associated factors. The care missed and the factors were grouped in global and dimension rates. For the analysis, descriptive statistics, Spearman’s correlation and simple linear regression were used. Approval for the study was obtained from the ethics committee. Results: the participants were 71 nurses from emergency, intensive care and inpatient services. The global missed care index corresponded to M=7.45 (SD=10.74; the highest missed care index was found in the dimension basic care interventions (M=13.02, SD=17.60. The main factor contributing to the care missed was human resources (M=56.13, SD=21.38. The factors related to the care missed were human resources (rs=0.408, p<0.001 and communication (rs=0.418, p<0.001. Conclusions: the nursing care missed is mainly due to the human resource factor; these study findings will permit the strengthening of nursing care continuity.

  4. Missing Value Imputation Based on Gaussian Mixture Model for the Internet of Things

    Directory of Open Access Journals (Sweden)

    Xiaobo Yan

    2015-01-01

    Full Text Available This paper addresses missing value imputation for the Internet of Things (IoT. Nowadays, the IoT has been used widely and commonly by a variety of domains, such as transportation and logistics domain and healthcare domain. However, missing values are very common in the IoT for a variety of reasons, which results in the fact that the experimental data are incomplete. As a result of this, some work, which is related to the data of the IoT, can’t be carried out normally. And it leads to the reduction in the accuracy and reliability of the data analysis results. This paper, for the characteristics of the data itself and the features of missing data in IoT, divides the missing data into three types and defines three corresponding missing value imputation problems. Then, we propose three new models to solve the corresponding problems, and they are model of missing value imputation based on context and linear mean (MCL, model of missing value imputation based on binary search (MBS, and model of missing value imputation based on Gaussian mixture model (MGI. Experimental results showed that the three models can improve the accuracy, reliability, and stability of missing value imputation greatly and effectively.

  5. Accuracy of genomic selection for alfalfa biomass yield in different reference populations.

    Science.gov (United States)

    Annicchiarico, Paolo; Nazzicari, Nelson; Li, Xuehui; Wei, Yanling; Pecetti, Luciano; Brummer, E Charles

    2015-12-01

    Genomic selection based on genotyping-by-sequencing (GBS) data could accelerate alfalfa yield gains, if it displayed moderate ability to predict parent breeding values. Its interest would be enhanced by predicting ability also for germplasm/reference populations other than those for which it was defined. Predicting accuracy may be influenced by statistical models, SNP calling procedures and missing data imputation strategies. Landrace and variety material from two genetically-contrasting reference populations, i.e., 124 elite genotypes adapted to the Po Valley (sub-continental climate; PV population) and 154 genotypes adapted to Mediterranean-climate environments (Me population), were genotyped by GBS and phenotyped in separate environments for dry matter yield of their dense-planted half-sib progenies. Both populations showed no sub-population genetic structure. Predictive accuracy was higher by joint rather than separate SNP calling for the two data sets, and using random forest imputation of missing data. Highest accuracy was obtained using Support Vector Regression (SVR) for PV, and Ridge Regression BLUP and SVR for Me germplasm. Bayesian methods (Bayes A, Bayes B and Bayesian Lasso) tended to be less accurate. Random Forest Regression was the least accurate model. Accuracy attained about 0.35 for Me in the range of 0.30-0.50 missing data, and 0.32 for PV at 0.50 missing data, using at least 10,000 SNP markers. Cross-population predictions based on a smaller subset of common SNPs implied a relative loss of accuracy of about 25% for Me and 30% for PV. Genome-wide association analyses based on large subsets of M. truncatula-aligned markers revealed many SNPs with modest association with yield, and some genome areas hosting putative QTLs. A comparison of genomic vs. conventional selection for parent breeding value assuming 1-year vs. 5-year selection cycles, respectively, indicated over three-fold greater predicted yield gain per unit time for genomic selection

  6. Genomics of Volvocine Algae

    Science.gov (United States)

    Umen, James G.; Olson, Bradley J.S.C.

    2015-01-01

    Volvocine algae are a group of chlorophytes that together comprise a unique model for evolutionary and developmental biology. The species Chlamydomonas reinhardtii and Volvox carteri represent extremes in morphological diversity within the Volvocine clade. Chlamydomonas is unicellular and reflects the ancestral state of the group, while Volvox is multicellular and has evolved numerous innovations including germ-soma differentiation, sexual dimorphism, and complex morphogenetic patterning. The Chlamydomonas genome sequence has shed light on several areas of eukaryotic cell biology, metabolism and evolution, while the Volvox genome sequence has enabled a comparison with Chlamydomonas that reveals some of the underlying changes that enabled its transition to multicellularity, but also underscores the subtlety of this transition. Many of the tools and resources are in place to further develop Volvocine algae as a model for evolutionary genomics. PMID:25883411

  7. Genomics of Preterm Birth

    Science.gov (United States)

    Swaggart, Kayleigh A.; Pavlicev, Mihaela; Muglia, Louis J.

    2015-01-01

    The molecular mechanisms controlling human birth timing at term, or resulting in preterm birth, have been the focus of considerable investigation, but limited insights have been gained over the past 50 years. In part, these processes have remained elusive because of divergence in reproductive strategies and physiology shown by model organisms, making extrapolation to humans uncertain. Here, we summarize the evolution of progesterone signaling and variation in pregnancy maintenance and termination. We use this comparative physiology to support the hypothesis that selective pressure on genomic loci involved in the timing of parturition have shaped human birth timing, and that these loci can be identified with comparative genomic strategies. Previous limitations imposed by divergence of mechanisms provide an important new opportunity to elucidate fundamental pathways of parturition control through increasing availability of sequenced genomes and associated reproductive physiology characteristics across diverse organisms. PMID:25646385

  8. Genomics of Salmonella Species

    Science.gov (United States)

    Canals, Rocio; McClelland, Michael; Santiviago, Carlos A.; Andrews-Polymenis, Helene

    Progress in the study of Salmonella survival, colonization, and virulence has increased rapidly with the advent of complete genome sequencing and higher capacity assays for transcriptomic and proteomic analysis. Although many of these techniques have yet to be used to directly assay Salmonella growth on foods, these assays are currently in use to determine Salmonella factors necessary for growth in animal models including livestock animals and in in vitro conditions that mimic many different environments. As sequencing of the Salmonella genome and microarray analysis have revolutionized genomics and transcriptomics of salmonellae over the last decade, so are new high-throughput sequencing technologies currently accelerating the pace of our studies and allowing us to approach complex problems that were not previously experimentally tractable.

  9. Ebolavirus comparative genomics

    Science.gov (United States)

    Jun, Se-Ran; Leuze, Michael R.; Nookaew, Intawat; Uberbacher, Edward C.; Land, Miriam; Zhang, Qian; Wanchai, Visanu; Chai, Juanjuan; Nielsen, Morten; Trolle, Thomas; Lund, Ole; Buzard, Gregory S.; Pedersen, Thomas D.; Wassenaar, Trudy M.; Ussery, David W.

    2015-01-01

    The 2014 Ebola outbreak in West Africa is the largest documented for this virus. To examine the dynamics of this genome, we compare more than 100 currently available ebolavirus genomes to each other and to other viral genomes. Based on oligomer frequency analysis, the family Filoviridae forms a distinct group from all other sequenced viral genomes. All filovirus genomes sequenced to date encode proteins with similar functions and gene order, although there is considerable divergence in sequences between the three genera Ebolavirus, Cuevavirus and Marburgvirus within the family Filoviridae. Whereas all ebolavirus genomes are quite similar (multiple sequences of the same strain are often identical), variation is most common in the intergenic regions and within specific areas of the genes encoding the glycoprotein (GP), nucleoprotein (NP) and polymerase (L). We predict regions that could contain epitope-binding sites, which might be good vaccine targets. This information, combined with glycosylation sites and experimentally determined epitopes, can identify the most promising regions for the development of therapeutic strategies. This manuscript has been authored by UT-Battelle, LLC under Contract No. DE-AC05-00OR22725 with the U.S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes. The Department of Energy will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan (http://energy.gov/downloads/doe-public-access-plan). PMID:26175035

  10. The Contribution of Health Technology Assessment, Health Needs Assessment, and Health Impact Assessment to the Assessment and Translation of Technologies in the Field of Public Health Genomics

    NARCIS (Netherlands)

    Rosenköttera, N.; Vondeling, Hindrik; Blancquaert, I.; Mekel, O.C.L.; Kristensen, F.B.; Brand, A.

    2011-01-01

    The European Union has named genomics as one of the promising research fields for the development of new health technologies. Major concerns with regard to these fields are, on the one hand, the rather slow and limited translation of new knowledge and, on the other hand, missing insights into the

  11. Brief Guide to Genomics: DNA, Genes and Genomes

    Science.gov (United States)

    ... clinic. Most new drugs based on genome-based research are estimated to be at least 10 to 15 years away, though recent genome-driven efforts in lipid-lowering therapy have considerably shortened that interval. According ...

  12. Genomic Prediction in Barley

    DEFF Research Database (Denmark)

    Edriss, Vahid; Cericola, Fabio; Jensen, Jens D

    2015-01-01

    to next generation. The main goal of this study was to see the potential of using genomic prediction in a commercial Barley breeding program. The data used in this study was from Nordic Seed company which is located in Denmark. Around 350 advanced lines were genotyped with 9K Barely chip from Illumina....... Traits used in this study were grain yield, plant height and heading date. Heading date is number days it takes after 1st June for plant to head. Heritabilities were 0.33, 0.44 and 0.48 for yield, height and heading, respectively for the average of nine plots. The GBLUP model was used for genomic...

  13. Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium.

    Science.gov (United States)

    Machado, Henrique; Gram, Lone

    2017-01-01

    Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationships using several analyses (16S rRNA, MLSA, fur , amino-acid usage, ANI), which allowed us to identify two misidentified strains. Genome analyses also revealed occurrence of higher and lower GC content clades, correlating with phylogenetic clusters. Pan- and core-genome analysis revealed the conservation of 25% of the genome throughout the genus, with a large and open pan-genome. The major source of genomic diversity could be traced to the smaller chromosome and plasmids. Several of the physiological traits studied in the genus did not correlate with phylogenetic data. Since horizontal gene transfer (HGT) is often suggested as a source of genetic diversity and a potential driver of genomic evolution in bacterial species, we looked into evidence of such in Photobacterium genomes. Genomic islands were the source of genomic differences between strains of the same species. Also, we found transposase genes and CRISPR arrays that suggest multiple encounters with foreign DNA. Presence of genomic exchange traits was widespread and abundant in the genus, suggesting a role in genomic evolution. The high genetic variability and indications of genetic exchange make it difficult to elucidate genome evolutionary paths and raise the awareness of the roles of foreign DNA in the genomic evolution of environmental organisms.

  14. phiGENOME: an integrative navigation throughout bacteriophage genomes.

    Science.gov (United States)

    Stano, Matej; Klucar, Lubos

    2011-11-01

    phiGENOME is a web-based genome browser generating dynamic and interactive graphical representation of phage genomes stored in the phiSITE, database of gene regulation in bacteriophages. phiGENOME is an integral part of the phiSITE web portal (http://www.phisite.org/phigenome) and it was optimised for visualisation of phage genomes with the emphasis on the gene regulatory elements. phiGENOME consists of three components: (i) genome map viewer built using Adobe Flash technology, providing dynamic and interactive graphical display of phage genomes; (ii) sequence browser based on precisely formatted HTML tags, providing detailed exploration of genome features on the sequence level and (iii) regulation illustrator, based on Scalable Vector Graphics (SVG) and designed for graphical representation of gene regulations. Bringing 542 complete genome sequences accompanied with their rich annotations and references, makes phiGENOME a unique information resource in the field of phage genomics. Copyright © 2011 Elsevier Inc. All rights reserved.

  15. "Near-miss" obstetric events and maternal deaths in Sagamu, Nigeria: a retrospective study

    Directory of Open Access Journals (Sweden)

    Daniel Olusoji J

    2005-11-01

    Full Text Available Abstract Aim To determine the frequency of near-miss (severe acute maternal morbidity and the nature of near-miss events, and comparatively analysed near-miss morbidities and maternal deaths among pregnant women managed over a 3-year period in a Nigerian tertiary centre. Methods Retrospective facility-based review of cases of near-miss and maternal death which occurred between 1 January 2002 and 31 December 2004. Near-miss case definition was based on validated disease-specific criteria, comprising of five diagnostic categories: haemorrhage, hypertensive disorders in pregnancy, dystocia, infection and anaemia. The near-miss morbidities were compared with maternal deaths with respect to demographic features and disease profiles. Mortality indices were determined for various disease processes to appreciate the standard of care provided for life-threatening obstetric conditions. The maternal death to near-miss ratios for the three years were compared to assess the trend in the quality of obstetric care. Results There were 1501 deliveries, 211 near-miss cases and 44 maternal deaths. The total near-miss events were 242 with a decreasing trend from 2002 to 2004. Demographic features of cases of near-miss and maternal death were comparable. Besides infectious morbidity, the categories of complications responsible for near-misses and maternal deaths followed the same order of decreasing frequency. Hypertensive disorders in pregnancy and haemorrhage were responsible for 61.1% of near-miss cases and 50.0% of maternal deaths. More women died after developing severe morbidity due to uterine rupture and infection, with mortality indices of 37.5% and 28.6%, respectively. Early pregnancy complications and antepartum haemorrhage had the lowest mortality indices. Majority of the cases of near-miss (82.5% and maternal death (88.6% were unbooked for antenatal care and delivery in this hospital. Maternal mortality ratio for the period was 2931.4 per 100

  16. The impact of 'missed care' on the professional socialisation of nursing students: A qualitative research study.

    Science.gov (United States)

    Gibbon, Bernard; Crane, Julie

    2018-04-07

    Missed care is a recently described concept that is subject to an increasing amount of international nursing research. The impact of missed care is associated with poorer patient outcomes (mortality and morbidity) and poorer levels of patient satisfaction with the services provided by the hospital. Missed care has also been linked to decreased staff satisfaction and increased intention to leave. Overall disaffection amongst registered nurses has also been reported. Professional socialisation refers to the acquisition of behaviours within cultural norms, and it has been suggested that students enter a period of professional socialisation during their programme. Whilst it has been proposed that students may absorb the characteristics of those around them, to date, no empirical studies have reported the impact of missed care on student nurses. The aim of this project is to explore the impact of missed care on the professional socialisation of student nurses. A qualitative study was undertaken in one higher education institute in UK with final year pre-registration nursing degree (adult field) students. Focus group interviews, utilizing a broad topic guide, were used to collect data which was analysed using thematic analysis. Student nurses were aware that some planned care is missed and these findings resonated with those identified in the literature. In addition to illuminating aspects of professional socialisation, analysis yielded five themes with regards to missed care: awareness, rationale, impact, strategies to avoid and influence of missed care on career aspiration. Student nurses exposed to missed care appear to accept this as part of their professional socialisation. With regards to professional socialisation, student nurses developed a pragmatic acceptance that care would be missed and that this could happen in any environment. As such they did not see missed care as influencing their career aspirations. Copyright © 2018 Elsevier Ltd. All rights reserved.

  17. Illuminating the Druggable Genome (IDG)

    Data.gov (United States)

    Federal Laboratory Consortium — Results from the Human Genome Project revealed that the human genome contains 20,000 to 25,000 genes. A gene contains (encodes) the information that each cell uses...

  18. National Human Genome Research Institute

    Science.gov (United States)

    ... Care Genomic Medicine Working Group New Horizons and Research Patient Management Policy and Ethics Issues Quick Links for Patient Care Education All About the Human Genome Project Fact Sheets Genetic Education Resources for ...

  19. Missed doses of oral antihyperglycemic medications in US adults with type 2 diabetes mellitus: prevalence and self-reported reasons.

    Science.gov (United States)

    Vietri, Jeffrey T; Wlodarczyk, Catherine S; Lorenzo, Rose; Rajpathak, Swapnil

    2016-09-01

    Adherence to antihyperglycemic medication is thought to be suboptimal, but the proportion of patients missing doses, the number of doses missed, and reasons for missing are not well described. This survey was conducted to estimate the prevalence of and reasons for missed doses of oral antihyperglycemic medications among US adults with type 2 diabetes mellitus, and to explore associations between missed doses and health outcomes. The study was a cross-sectional patient survey. Respondents were contacted via a commercial survey panel and completed an on-line questionnaire via the Internet. Respondents provided information about their use of oral antihyperglycemic medications including doses missed in the prior 4 weeks, personal characteristics, and health outcomes. Weights were calculated to project the prevalence to the US adult population with type 2 diabetes mellitus. Outcomes were compared according to number of doses missed in the past 4 weeks using bivariate statistics and generalized linear models. Approximately 30% of adult patients with type 2 diabetes mellitus reported missing or reducing ≥1 dose of oral antihyperglycemic medication in the prior 4 weeks. Accidental missing was more commonly reported than purposeful skipping, with forgetting the most commonly reported reason. The timing of missed doses suggested respondents had also forgotten about doses missed, so the prevalence of missed doses is likely higher than reported. Outcomes were poorer among those who reported missing three or more doses in the prior 4 weeks. A substantial number of US adults with type 2 diabetes mellitus miss doses of their oral antihyperglycemic medications.

  20. Genomic prediction using subsampling.

    Science.gov (United States)

    Xavier, Alencar; Xu, Shizhong; Muir, William; Rainey, Katy Martin

    2017-03-24

    Genome-wide assisted selection is a critical tool for the genetic improvement of plants and animals. Whole-genome regression models in Bayesian framework represent the main family of prediction methods. Fitting such models with a large number of observations involves a prohibitive computational burden. We propose the use of subsampling bootstrap Markov chain in genomic prediction. Such method consists of fitting whole-genome regression models by subsampling observations in each round of a Markov Chain Monte Carlo. We evaluated the effect of subsampling bootstrap on prediction and computational parameters. Across datasets, we observed an optimal subsampling proportion of observations around 50% with replacement, and around 33% without replacement. Subsampling provided a substantial decrease in computation time, reducing the time to fit the model by half. On average, losses on predictive properties imposed by subsampling were negligible, usually below 1%. For each dataset, an optimal subsampling point that improves prediction properties was observed, but the improvements were also negligible. Combining subsampling with Gibbs sampling is an interesting ensemble algorithm. The investigation indicates that the subsampling bootstrap Markov chain algorithm substantially reduces computational burden associated with model fitting, and it may slightly enhance prediction properties.

  1. The Lotus japonicus genome

    DEFF Research Database (Denmark)

    Fabaceae, groundbreaking genetic and genomic research has established a significant body of knowledge on Lotus japonicus, which was adopted as a model species more than 20 years ago. The diverse nature of legumes means that such research has a wide potential and agricultural impact, for example...

  2. Genomic taxonomy of vibrios

    DEFF Research Database (Denmark)

    Thompson, Cristiane C.; Vicente, Ana Carolina P.; Souza, Rangel C.

    2009-01-01

    BACKGROUND: Vibrio taxonomy has been based on a polyphasic approach. In this study, we retrieve useful taxonomic information (i.e. data that can be used to distinguish different taxonomic levels, such as species and genera) from 32 genome sequences of different vibrio species. We use a variety of...

  3. The Genome Atlas Resource

    DEFF Research Database (Denmark)

    Azam Qureshi, Matloob; Rotenberg, Eva; Stærfeldt, Hans Henrik

    2010-01-01

    with scripts and algorithms developed in a variety of programming languages at the Centre for Biological Sequence Analysis in order to create a three-tier software application for genome analysis. The results are made available via a web interface developed in Java, PHP and Perl CGI. User...

  4. Genomic Signatures of Reinforcement

    Directory of Open Access Journals (Sweden)

    Austin G. Garner

    2018-04-01

    Full Text Available Reinforcement is the process by which selection against hybridization increases reproductive isolation between taxa. Much research has focused on demonstrating the existence of reinforcement, yet relatively little is known about the genetic basis of reinforcement or the evolutionary conditions under which reinforcement can occur. Inspired by reinforcement’s characteristic phenotypic pattern of reproductive trait divergence in sympatry but not in allopatry, we discuss whether reinforcement also leaves a distinct genomic pattern. First, we describe three patterns of genetic variation we expect as a consequence of reinforcement. Then, we discuss a set of alternative processes and complicating factors that may make the identification of reinforcement at the genomic level difficult. Finally, we consider how genomic analyses can be leveraged to inform if and to what extent reinforcement evolved in the face of gene flow between sympatric lineages and between allopatric and sympatric populations of the same lineage. Our major goals are to understand if genome scans for particular patterns of genetic variation could identify reinforcement, isolate the genetic basis of reinforcement, or infer the conditions under which reinforcement evolved.

  5. Better chocolate through genomics

    Science.gov (United States)

    Theobroma cacao, the cacao or chocolate tree, is a tropical understory tree whose seeds are used to make chocolate. And like any important crop, cacao is the subject of much research. On September 15, 2010, scientists publicly released a preliminary sequence of the cacao genome--which contains all o...

  6. Functional genomics of tomato

    Indian Academy of Sciences (India)

    2014-10-20

    Oct 20, 2014 ... 1Repository of Tomato Genomics Resources, Department of Plant Sciences, School .... Due to its position at the crossroads of Sanger's sequencing .... replacement for the microarray-based expression profiling. .... during RNA fragmentation step prior to library construction, ...... tomato pollen as a test case.

  7. Genomic Signatures of Reinforcement

    Science.gov (United States)

    Goulet, Benjamin E.

    2018-01-01

    Reinforcement is the process by which selection against hybridization increases reproductive isolation between taxa. Much research has focused on demonstrating the existence of reinforcement, yet relatively little is known about the genetic basis of reinforcement or the evolutionary conditions under which reinforcement can occur. Inspired by reinforcement’s characteristic phenotypic pattern of reproductive trait divergence in sympatry but not in allopatry, we discuss whether reinforcement also leaves a distinct genomic pattern. First, we describe three patterns of genetic variation we expect as a consequence of reinforcement. Then, we discuss a set of alternative processes and complicating factors that may make the identification of reinforcement at the genomic level difficult. Finally, we consider how genomic analyses can be leveraged to inform if and to what extent reinforcement evolved in the face of gene flow between sympatric lineages and between allopatric and sympatric populations of the same lineage. Our major goals are to understand if genome scans for particular patterns of genetic variation could identify reinforcement, isolate the genetic basis of reinforcement, or infer the conditions under which reinforcement evolved. PMID:29614048

  8. The Nostoc punctiforme Genome

    Energy Technology Data Exchange (ETDEWEB)

    John C. Meeks

    2001-12-31

    Nostoc punctiforme is a filamentous cyanobacterium with extensive phenotypic characteristics and a relatively large genome, approaching 10 Mb. The phenotypic characteristics include a photoautotrophic, diazotrophic mode of growth, but N. punctiforme is also facultatively heterotrophic; its vegetative cells have multiple development alternatives, including terminal differentiation into nitrogen-fixing heterocysts and transient differentiation into spore-like akinetes or motile filaments called hormogonia; and N. punctiforme has broad symbiotic competence with fungi and terrestrial plants, including bryophytes, gymnosperms and an angiosperm. The shotgun-sequencing phase of the N. punctiforme strain ATCC 29133 genome has been completed by the Joint Genome Institute. Annotation of an 8.9 Mb database yielded 7432 open reading frames, 45% of which encode proteins with known or probable known function and 29% of which are unique to N. punctiforme. Comparative analysis of the sequence indicates a genome that is highly plastic and in a state of flux, with numerous insertion sequences and multilocus repeats, as well as genes encoding transposases and DNA modification enzymes. The sequence also reveals the presence of genes encoding putative proteins that collectively define almost all characteristics of cyanobacteria as a group. N. punctiforme has an extensive potential to sense and respond to environmental signals as reflected by the presence of more than 400 genes encoding sensor protein kinases, response regulators and other transcriptional factors. The signal transduction systems and any of the large number of unique genes may play essential roles in the cell differentiation and symbiotic interaction properties of N. punctiforme.

  9. Comparative Genomics of Eukaryotes.

    NARCIS (Netherlands)

    Noort, V. van

    2007-01-01

    This thesis focuses on developing comparative genomics methods in eukaryotes, with an emphasis on applications for gene function prediction and regulatory element detection. In the past, methods have been developed to predict functional associations between gene pairs in prokaryotes. The challenge

  10. Searching for genomic constraints

    Energy Technology Data Exchange (ETDEWEB)

    Lio` , P [Cambridge, Univ. (United Kingdom). Genetics Dept.; Ruffo, S [Florence, Univ. (Italy). Fac. di Ingegneria. Dipt. di Energetica ` S. Stecco`

    1998-01-01

    The authors have analyzed general properties of very long DNA sequences belonging to simple and complex organisms, by using different correlation methods. They have distinguished those base compositional rules that concern the entire genome which they call `genomic constraints` from the rules that depend on the `external natural selection` acting on single genes, i. e. protein-centered constraints. They show that G + C content, purine / pyrimidine distributions and biological complexity of the organism are the most important factors which determine base compositional rules and genome complexity. Three main facts are here reported: bacteria with high G + C content have more restrictions on base composition than those with low G + C content; at constant G + C content more complex organisms, ranging from prokaryotes to higher eukaryotes (e.g. human) display an increase of repeats 10-20 nucleotides long, which are also partly responsible for long-range correlations; work selection of length 3 to 10 is stronger in human and in bacteria for two distinct reasons. With respect to previous studies, they have also compared the genomic sequence of the archeon Methanococcus jannaschii with those of bacteria and eukaryotes: it shows sometimes an intermediate statistical behaviour.

  11. Searching for genomic constraints

    International Nuclear Information System (INIS)

    Lio', P.; Ruffo, S.

    1998-01-01

    The authors have analyzed general properties of very long DNA sequences belonging to simple and complex organisms, by using different correlation methods. They have distinguished those base compositional rules that concern the entire genome which they call 'genomic constraints' from the rules that depend on the 'external natural selection' acting on single genes, i. e. protein-centered constraints. They show that G + C content, purine / pyrimidine distributions and biological complexity of the organism are the most important factors which determine base compositional rules and genome complexity. Three main facts are here reported: bacteria with high G + C content have more restrictions on base composition than those with low G + C content; at constant G + C content more complex organisms, ranging from prokaryotes to higher eukaryotes (e.g. human) display an increase of repeats 10-20 nucleotides long, which are also partly responsible for long-range correlations; work selection of length 3 to 10 is stronger in human and in bacteria for two distinct reasons. With respect to previous studies, they have also compared the genomic sequence of the archeon Methanococcus jannaschii with those of bacteria and eukaryotes: it shows sometimes an intermediate statistical behaviour

  12. Genomic sequencing in clinical trials

    OpenAIRE

    Mestan, Karen K; Ilkhanoff, Leonard; Mouli, Samdeep; Lin, Simon

    2011-01-01

    Abstract Human genome sequencing is the process by which the exact order of nucleic acid base pairs in the 24 human chromosomes is determined. Since the completion of the Human Genome Project in 2003, genomic sequencing is rapidly becoming a major part of our translational research efforts to understand and improve human health and disease. This article reviews the current and future directions of clinical research with respect to genomic sequencing, a technology that is just beginning to fin...

  13. Statistical Methods in Integrative Genomics

    Science.gov (United States)

    Richardson, Sylvia; Tseng, George C.; Sun, Wei

    2016-01-01

    Statistical methods in integrative genomics aim to answer important biology questions by jointly analyzing multiple types of genomic data (vertical integration) or aggregating the same type of data across multiple studies (horizontal integration). In this article, we introduce different types of genomic data and data resources, and then review statistical methods of integrative genomics, with emphasis on the motivation and rationale of these methods. We conclude with some summary points and future research directions. PMID:27482531

  14. From plant genomes to phenotypes

    OpenAIRE

    Bolger, Marie; Gundlach, Heidrun; Scholz, Uwe; Mayer, Klaus; Usadel, Björn; Schwacke, Rainer; Schmutzer, Thomas; Chen, Jinbo; Arend, Daniel; Oppermann, Markus; Weise, Stephan; Lange, Matthias; Fiorani, Fabio; Spannagl, Manuel

    2017-01-01

    Recent advances in sequencing technologies have greatly accelerated the rate of plant genome and applied breeding research. Despite this advancing trend, plant genomes continue to present numerous difficulties to the standard tools and pipelines not only for genome assembly but also gene annotation and downstream analysis.Here we give a perspective on tools, resources and services necessary to assemble and analyze plant genomes and link them to plant phenotypes.

  15. Genome analysis of Diploscapter coronatus: insights into molecular peculiarities of a nematode with parthenogenetic reproduction.

    Science.gov (United States)

    Hiraki, Hideaki; Kagoshima, Hiroshi; Kraus, Christopher; Schiffer, Philipp H; Ueta, Yumiko; Kroiher, Michael; Schierenberg, Einhard; Kohara, Yuji

    2017-06-24

    Sexual reproduction involving the fusion of egg and sperm is prevailing among eukaryotes. In contrast, the nematode Diploscapter coronatus, a close relative of the model Caenorhabditis elegans, reproduces parthenogenetically. Neither males nor sperm have been observed and some steps of meiosis are apparently skipped in this species. To uncover the genomic changes associated with the evolution of parthenogenesis in this nematode, we carried out a genome analysis. We obtained a 170 Mbp draft genome in only 511 scaffolds with a N 50 length of 1 Mbp. Nearly 90% of these scaffolds constitute homologous pairs with a 5.7% heterozygosity on average and inversions and translocations, meaning that the 170 Mbp sequences correspond to the diploid genome. Fluorescent staining shows that the D. coronatus genome consists of two chromosomes (2n = 2). In our genome annotation, we found orthologs of 59% of the C. elegans genes. However, a number of genes were missing or very divergent. These include genes involved in sex determination (e.g. xol-1, tra-2) and meiosis (e.g. the kleisins rec-8 and coh-3/4) giving a possible explanation for the absence of males and the second meiotic division. The high degree of heterozygosity allowed us to analyze the expression level of individual alleles. Most of the homologous pairs show very similar expression levels but others exhibit a 2-5-fold difference. Our high-quality draft genome of D. coronatus reveals the peculiarities of the genome of parthenogenesis and provides some clues to the genetic basis for parthenogenetic reproduction. This draft genome should be the basis to elucidate fundamental questions related to parthenogenesis such as its origin and mechanisms through comparative analyses with other nematodes. Furthermore, being the closest outgroup to the genus Caenorhabditis, the draft genome will help to disclose many idiosyncrasies of the model C. elegans and its congeners in future studies.

  16. Genome sequencing of bacteria: sequencing, de novo assembly and rapid analysis using open source tools.

    Science.gov (United States)

    Kisand, Veljo; Lettieri, Teresa

    2013-04-01

    De novo genome sequencing of previously uncharacterized microorganisms has the potential to open up new frontiers in microbial genomics by providing insight into both functional capabilities and biodiversity. Until recently, Roche 454 pyrosequencing was the NGS method of choice for de novo assembly because it generates hundreds of thousands of long reads (tools for processing NGS data are increasingly free and open source and are often adopted for both their high quality and role in promoting academic freedom. The error rate of pyrosequencing the Alcanivorax borkumensis genome was such that thousands of insertions and deletions were artificially introduced into the finished genome. Despite a high coverage (~30 fold), it did not allow the reference genome to be fully mapped. Reads from regions with errors had low quality, low coverage, or were missing. The main defect of the reference mapping was the introduction of artificial indels into contigs through lower than 100% consensus and distracting gene calling due to artificial stop codons. No assembler was able to perform de novo assembly comparable to reference mapping. Automated annotation tools performed similarly on reference mapped and de novo draft genomes, and annotated most CDSs in the de novo assembled draft genomes. Free and open source software (FOSS) tools for assembly and annotation of NGS data are being developed rapidly to provide accurate results with less computational effort. Usability is not high priority and these tools currently do not allow the data to be processed without manual intervention. Despite this, genome assemblers now readily assemble medium short reads into long contigs (>97-98% genome coverage). A notable gap in pyrosequencing technology is the quality of base pair calling and conflicting base pairs between single reads at the same nucleotide position. Regardless, using draft whole genomes that are not finished and remain fragmented into tens of contigs allows one to characterize

  17. Will Big Data Close the Missing Heritability Gap?

    Science.gov (United States)

    Kim, Hwasoon; Grueneberg, Alexander; Vazquez, Ana I; Hsu, Stephen; de Los Campos, Gustavo

    2017-11-01

    Despite the important discoveries reported by genome-wide association (GWA) studies, for most traits and diseases the prediction R-squared (R-sq.) achieved with genetic scores remains considerably lower than the trait heritability. Modern biobanks will soon deliver unprecedentedly large biomedical data sets: Will the advent of big data close the gap between the trait heritability and the proportion of variance that can be explained by a genomic predictor? We addressed this question using Bayesian methods and a data analysis approach that produces a surface response relating prediction R-sq. with sample size and model complexity ( e.g. , number of SNPs). We applied the methodology to data from the interim release of the UK Biobank. Focusing on human height as a model trait and using 80,000 records for model training, we achieved a prediction R-sq. in testing ( n = 22,221) of 0.24 (95% C.I.: 0.23-0.25). Our estimates show that prediction R-sq. increases with sample size, reaching an estimated plateau at values that ranged from 0.1 to 0.37 for models using 500 and 50,000 (GWA-selected) SNPs, respectively. Soon much larger data sets will become available. Using the estimated surface response, we forecast that larger sample sizes will lead to further improvements in prediction R-sq. We conclude that big data will lead to a substantial reduction of the gap between trait heritability and the proportion of interindividual differences that can be explained with a genomic predictor. However, even with the power of big data, for complex traits we anticipate that the gap between prediction R-sq. and trait heritability will not be fully closed. Copyright © 2017 by the Genetics Society of America.

  18. A simple method for analyzing data from a randomized trial with a missing binary outcome

    Directory of Open Access Journals (Sweden)

    Freedman Laurence S

    2003-05-01

    Full Text Available Abstract Background Many randomized trials involve missing binary outcomes. Although many previous adjustments for missing binary outcomes have been proposed, none of these makes explicit use of randomization to bound the bias when the data are not missing at random. Methods We propose a novel approach that uses the randomization distribution to compute the anticipated maximum bias when missing at random does not hold due to an unobserved binary covariate (implying that missingness depends on outcome and treatment group. The anticipated maximum bias equals the product of two factors: (a the anticipated maximum bias if there were complete confounding of the unobserved covariate with treatment group among subjects with an observed outcome and (b an upper bound factor that depends only on the fraction missing in each randomization group. If less than 15% of subjects are missing in each group, the upper bound factor is less than .18. Results We illustrated the methodology using data from the Polyp Prevention Trial. We anticipated a maximum bias under complete confounding of .25. With only 7% and 9% missing in each arm, the upper bound factor, after adjusting for age and sex, was .10. The anticipated maximum bias of .25 × .10 =.025 would not have affected the conclusion of no treatment effect. Conclusion This approach is easy to implement and is particularly informative when less than 15% of subjects are missing in each arm.

  19. Restoring method for missing data of spatial structural stress monitoring based on correlation

    Science.gov (United States)

    Zhang, Zeyu; Luo, Yaozhi

    2017-07-01

    Long-term monitoring of spatial structures is of great importance for the full understanding of their performance and safety. The missing part of the monitoring data link will affect the data analysis and safety assessment of the structure. Based on the long-term monitoring data of the steel structure of the Hangzhou Olympic Center Stadium, the correlation between the stress change of the measuring points is studied, and an interpolation method of the missing stress data is proposed. Stress data of correlated measuring points are selected in the 3 months of the season when missing data is required for fitting correlation. Data of daytime and nighttime are fitted separately for interpolation. For a simple linear regression when single point's correlation coefficient is 0.9 or more, the average error of interpolation is about 5%. For multiple linear regression, the interpolation accuracy is not significantly increased after the number of correlated points is more than 6. Stress baseline value of construction step should be calculated before interpolating missing data in the construction stage, and the average error is within 10%. The interpolation error of continuous missing data is slightly larger than that of the discrete missing data. The data missing rate of this method should better not exceed 30%. Finally, a measuring point's missing monitoring data is restored to verify the validity of the method.

  20. A Comparison of Missing-Data Procedures for Arima Time-Series Analysis

    Science.gov (United States)

    Velicer, Wayne F.; Colby, Suzanne M.

    2005-01-01

    Missing data are a common practical problem for longitudinal designs. Time-series analysis is a longitudinal method that involves a large number of observations on a single unit. Four different missing-data methods (deletion, mean substitution, mean of adjacent observations, and maximum likelihood estimation) were evaluated. Computer-generated…

  1. Missing data in trial-based cost-effectiveness analysis: An incomplete journey.

    Science.gov (United States)

    Leurent, Baptiste; Gomes, Manuel; Carpenter, James R

    2018-06-01

    Cost-effectiveness analyses (CEA) conducted alongside randomised trials provide key evidence for informing healthcare decision making, but missing data pose substantive challenges. Recently, there have been a number of developments in methods and guidelines addressing missing data in trials. However, it is unclear whether these developments have permeated CEA practice. This paper critically reviews the extent of and methods used to address missing data in recently published trial-based CEA. Issues of the Health Technology Assessment journal from 2013 to 2015 were searched. Fifty-two eligible studies were identified. Missing data were very common; the median proportion of trial participants with complete cost-effectiveness data was 63% (interquartile range: 47%-81%). The most common approach for the primary analysis was to restrict analysis to those with complete data (43%), followed by multiple imputation (30%). Half of the studies conducted some sort of sensitivity analyses, but only 2 (4%) considered possible departures from the missing-at-random assumption. Further improvements are needed to address missing data in cost-effectiveness analyses conducted alongside randomised trials. These should focus on limiting the extent of missing data, choosing an appropriate method for the primary analysis that is valid under contextually plausible assumptions, and conducting sensitivity analyses to departures from the missing-at-random assumption. © 2018 The Authors Health Economics published by John Wiley & Sons Ltd.

  2. 33 CFR 110.194a - Mobile Bay, Ala., and Mississippi Sound, Miss.

    Science.gov (United States)

    2010-07-01

    ... Sound, Miss. 110.194a Section 110.194a Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF... Mississippi Sound, Miss. (a) The anchorage grounds. (1) The waters of lower Mobile Bay, near Cedar Point... south by latitude 30°20′00″, and on the west by longitude 88°06′00″. (2) The waters of Mississippi Sound...

  3. The Effectiveness of Supermarket Posters in Helping to Find Missing Children

    Science.gov (United States)

    Lampinen, James Michael; Arnal, Jack; Hicks, Jason L.

    2009-01-01

    One approach used to help find missing children is to place posters of them at the exits of supermarkets. The present research addresses the question of how effective that approach is likely to be. Posters of 8 missing children were displayed on a bulletin board at a cooperating grocery store. Customers leaving the store completed a survey and…

  4. 20 CFR 364.4 - Placement of missing children posters in Board field offices.

    Science.gov (United States)

    2010-04-01

    ... 20 Employees' Benefits 1 2010-04-01 2010-04-01 false Placement of missing children posters in... CHILDREN § 364.4 Placement of missing children posters in Board field offices. (a) Poster content. The... information about that child, which may include a photograph of the child, that will appear on the poster. The...

  5. Missed posterior dislocation of the hip in a head-injured patient with ...

    African Journals Online (AJOL)

    Background: Head injury increases the risk of missed diagnosis by making patient-derived history impossible. The risk of missing a posterior dislocation of the hip in a head-injured patient is aggravated when an ipsilateral femoral shaft fracture co-exists. Adequate radiological evaluation of bone and joints is therefore of ...

  6. Orthodontic Management of Congenitally Missing Maxillary Lateral Incisors: A Case Report

    OpenAIRE

    Paduano, Sergio; Cioffi, Iacopo; Rongo, Roberto; Cupo, Antonello; Bucci, Rosaria; Valletta, Rosa

    2014-01-01

    This case report describes the orthodontic treatment of a woman, aged 15 years, with permanent dentition, brachyfacial typology, with congenitally missing maxillary lateral incisors. Multibracket straightwire fixed appliance was used to open the space for dental implant placement, and treat the impaired occlusion. The missing lateral incisors were substituted with oral implants.

  7. Assessment of Working Memory Capacity in Preschool Children Using the Missing Scan Task

    Science.gov (United States)

    Roman, Adrienne S.; Pisoni, David B.; Kronenberger, William G.

    2014-01-01

    The purpose of this study was to investigate the feasibility and validity of a modified version of Buschke's missing scan methodology, the Missing Scan Task (MST), to assess working memory capacity (WMC) and cognitive control processes in preschool children 3-6?years in age. Forty typically developing monolingual English-speaking children between…

  8. Maternal Near-Miss Due to Unsafe Abortion and Associated Short ...

    African Journals Online (AJOL)

    Abstract. Little is known about maternal near-miss (MNM) due to unsafe abortion in Nigeria. We used the WHO criteria to identify near-miss events and the proportion due to unsafe abortion among women of childbearing age in eight large secondary and tertiary hospitals across the six geo-political zones. We also explored ...

  9. Generalized canonical correlation analysis of matrices with missing rows : A simulation study

    NARCIS (Netherlands)

    van de Velden, Michel; Bijmolt, Tammo H. A.

    A method is presented for generalized canonical correlation analysis of two or more matrices with missing rows. The method is a combination of Carroll's (1968) method and the missing data approach of the OVERALS technique (Van der Burg, 1988). In a simulation study we assess the performance of the

  10. Handling Missing Data in Structural Equation Models in R: A Replication Study for Applied Researchers

    Science.gov (United States)

    Wolgast, Anett; Schwinger, Malte; Hahnel, Carolin; Stiensmeier-Pelster, Joachim

    2017-01-01

    Introduction: Multiple imputation (MI) is one of the most highly recommended methods for replacing missing values in research data. The scope of this paper is to demonstrate missing data handling in SEM by analyzing two modified data examples from educational psychology, and to give practical recommendations for applied researchers. Method: We…

  11. Modelling non-ignorable missing data mechanisms with item response theory models

    NARCIS (Netherlands)

    Holman, Rebecca; Glas, Cornelis A.W.

    2005-01-01

    A model-based procedure for assessing the extent to which missing data can be ignored and handling non-ignorable missing data is presented. The procedure is based on item response theory modelling. As an example, the approach is worked out in detail in conjunction with item response data modelled

  12. Modelling non-ignorable missing-data mechanisms with item response theory models

    NARCIS (Netherlands)

    Holman, Rebecca; Glas, Cees A. W.

    2005-01-01

    A model-based procedure for assessing the extent to which missing data can be ignored and handling non-ignorable missing data is presented. The procedure is based on item response theory modelling. As an example, the approach is worked out in detail in conjunction with item response data modelled

  13. Effects of Missing Data Methods in SEM under Conditions of Incomplete and Nonnormal Data

    Science.gov (United States)

    Li, Jian; Lomax, Richard G.

    2017-01-01

    Using Monte Carlo simulations, this research examined the performance of four missing data methods in SEM under different multivariate distributional conditions. The effects of four independent variables (sample size, missing proportion, distribution shape, and factor loading magnitude) were investigated on six outcome variables: convergence rate,…

  14. Strategies for Handling Missing Data with Maximum Likelihood Estimation in Career and Technical Education Research

    Science.gov (United States)

    Lee, In Heok

    2012-01-01

    Researchers in career and technical education often ignore more effective ways of reporting and treating missing data and instead implement traditional, but ineffective, missing data methods (Gemici, Rojewski, & Lee, 2012). The recent methodological, and even the non-methodological, literature has increasingly emphasized the importance of…

  15. Eesti Miss teeb videofilmi / Evelyn Mikomägi ; interv. Valdo Jahilo

    Index Scriptorium Estoniae

    Mikomägi, Evelyn

    2001-01-01

    Eesti Miss Estonia 2000 Evelyn Mikomägi tegi koos sõbra, Sven-Olof Svenne Englundiga dokfilmi Küprosel peetud maailma suurimast iludusvõistlusest Miss Universe 2000. Neile kuulub ühisfirma "Living Frames" Rootsis, mille peategevus on suunatud 16mm ja 35mm filmide tootmisele

  16. Barriers to obstetric care among maternal near-misses | Soma-Pillay ...

    African Journals Online (AJOL)

    One hundred maternal near-misses were prospectively identified using the World Health Organization criteria. ... The above causes were also the most important factors causing delays for the leading causes of maternal near-misses – obstetric haemorrhage, hypertension/pre-eclampsia, and medical and surgical conditions.

  17. Orthodontic Management of Congenitally Missing Maxillary Lateral Incisors: A Case Report

    Directory of Open Access Journals (Sweden)

    Sergio Paduano

    2014-01-01

    Full Text Available This case report describes the orthodontic treatment of a woman, aged 15 years, with permanent dentition, brachyfacial typology, with congenitally missing maxillary lateral incisors. Multibracket straightwire fixed appliance was used to open the space for dental implant placement, and treat the impaired occlusion. The missing lateral incisors were substituted with oral implants.

  18. The Impact of the Nursing Practice Environment on Missed Nursing Care.

    Science.gov (United States)

    Hessels, Amanda J; Flynn, Linda; Cimiotti, Jeannie P; Cadmus, Edna; Gershon, Robyn R M

    2015-12-01

    Missed nursing care is an emerging problem negatively impacting patient outcomes. There are gaps in our knowledge of factors associated with missed nursing care. The aim of this study was to determine the relationship between the nursing practice environment and missed nursing care in acute care hospitals. This is a secondary analysis of cross sectional data from a survey of over 7.000 nurses from 70 hospitals on workplace and process of care. Ordinary least squares and multiple regression models were constructed to examine the relationship between the nursing practice environment and missed nursing care while controlling for characteristics of nurses and hospitals. Nurses missed delivering a significant amount of necessary patient care (10-27%). Inadequate staffing and inadequate resources were the practice environment factors most strongly associated with missed nursing care events. This multi-site study examined the risk and risk factors associated with missed nursing care. Improvements targeting modifiable risk factors may reduce the risk of missed nursing care.

  19. Nurses' personal and ward accountability and missed nursing care: A cross-sectional study.

    Science.gov (United States)

    Srulovici, Einav; Drach-Zahavy, Anat

    2017-10-01

    Missed nursing care is considered an act of omission with potentially detrimental consequences for patients, nurses, and organizations. Although the theoretical conceptualization of missed nursing care specifies nurses' values, attitudes, and perceptions of their work environment as its core antecedents, empirical studies have mainly focused on nurses' socio-demographic and professional attributes. Furthermore, assessment of missed nursing care has been mainly based on same-source methods. This study aimed to test the joint effects of personal and ward accountability on missed nursing care, by using both focal (the nurse whose missed nursing care is examined) and incoming (the nurse responsible for the same patients at the subsequent shift) nurses' assessments of missed nursing care. A cross-sectional design, where nurses were nested in wards. A total of 172 focal and 123 incoming nurses from 32 nursing wards in eight hospitals. Missed nursing care was assessed with the 22-item MISSCARE survey using two sources: focal and incoming nurses. Personal and ward accountability were assessed by the focal nurse with two 19-item scales. Nurses' socio-demographics and ward and shift characteristics were also collected. Mixed linear models were used as the analysis strategy. Focal and incoming nurses reported occasional missed nursing care of the focal nurse (Mean=1.87, SD=0.71 and Mean=2.09, SD=0.84, respectively; r=0.55, ppersonal socio-demographic characteristics, higher personal accountability was significantly associated with decreased missed care (β=-0.29, p0.05). The interaction effect was significant (β=-0.31, ppersonal accountability and missed nursing care. Similar patterns were obtained for the incoming nurses' assessment of focal nurse's missed care. Use of focal and incoming nurses' missed nursing care assessments limited the common source bias and strengthened our findings. Personal and ward accountability are significant values, which are associated with

  20. A Thousand Fly Genomes: An Expanded Drosophila Genome Nexus.

    Science.gov (United States)

    Lack, Justin B; Lange, Jeremy D; Tang, Alison D; Corbett-Detig, Russell B; Pool, John E

    2016-12-01

    The Drosophila Genome Nexus is a population genomic resource that provides D. melanogaster genomes from multiple sources. To facilitate comparisons across data sets, genomes are aligned using a common reference alignment pipeline which involves two rounds of mapping. Regions of residual heterozygosity, identity-by-descent, and recent population admixture are annotated to enable data filtering based on the user's needs. Here, we present a significant expansion of the Drosophila Genome Nexus, which brings the current data object to a total of 1,121 wild-derived genomes. New additions include 305 previously unpublished genomes from inbred lines representing six population samples in Egypt, Ethiopia, France, and South Africa, along with another 193 genomes added from recently-published data sets. We also provide an aligned D. simulans genome to facilitate divergence comparisons. This improved resource will broaden the range of population genomic questions that can addressed from multi-population allele frequencies and haplotypes in this model species. The larger set of genomes will also enhance the discovery of functionally relevant natural variation that exists within and between populations. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.