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.

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.

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...

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.

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

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.

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

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.

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.

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.

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.

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

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

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

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

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....

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...

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 ...

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.

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.

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

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.

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.

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

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.

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.

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 (...

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.

Genomics, Endoscopy, and Control of Gastroesophageal Cancers: A PerspectiveSummary

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Brian J. Reid

2017-05-01

Full Text Available In The Cancer Genome Atlas the goals were to define how to treat advanced cancers with targeted therapy. However, the challenges facing cancer interception for early detection and prevention include length bias in which current screening and surveillance approaches frequently miss rapidly progressing cancers that then present at advanced stages in the clinic with symptoms (underdiagnosis. In contrast, many early detection strategies detect benign conditions that may never progress to cancer during a lifetime, and the patient dies of unrelated causes (overdiagnosis. This challenge to cancer interception is believed to be due to the speed at which the neoplasm evolves, called length bias sampling; rapidly progressing cancers are missed by current early detection strategies. In contrast, slowly or non-progressing cancers or their precursors are selectively detected. This has led to the concept of cancer interception, which can be defined as active interception of a biological process that drives cancer development before the patient presents in the clinic with an advanced, symptomatic cancer. The solutions needed to advance strategies for cancer interception require assessing the rate at which the cancer evolves over time and space. This is an essential challenge that needs to be addressed by robust study designs including normal and non-progressing controls when known to be appropriate. Keywords: Barrett's Esophagus, Biomarkers, Chromosome Aberrations, Esophageal Neoplasms, Gastroesophageal Reflux, Genomic Instability, Genomics, Stomach

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.

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.

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

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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

Differential genomic arrangements in Caryophyllales through deep transcriptome sequencing of A. hypochondriacus.

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Meeta Sunil

Full Text Available Genome duplication event in edible dicots under the orders Rosid and Asterid, common during the oligocene period, is missing for species under the order Caryophyllales. Despite this, grain amaranths not only survived this period but display many desirable traits missing in species under rosids and asterids. For example, grain amaranths display traits like C4 photosynthesis, high-lysine seeds, high-yield, drought resistance, tolerance to infection and resilience to stress. It is, therefore, of interest to look for minor genome rearrangements with potential functional implications that are unique to grain amaranths. Here, by deep sequencing and assembly of 16 transcriptomes (86.8 billion bases we have interrogated differential genome rearrangement unique to Amaranthus hypochondriacus with potential links to these phenotypes. We have predicted 125,581 non-redundant transcripts including 44,529 protein coding transcripts identified based on homology to known proteins and 13,529 predicted as novel/amaranth specific coding transcripts. Of the protein coding de novo assembled transcripts, we have identified 1810 chimeric transcripts. More than 30% and 19% of the gene pairs within the chimeric transcripts are found within the same loci in the genomes of A. hypochondriacus and Beta vulgaris respectively and are considered real positives. Interestingly, one of the chimeric transcripts comprises two important genes, namely DHDPS1, a key enzyme implicated in the biosynthesis of lysine, and alpha-glucosidase, an enzyme involved in sucrose catabolism, in close proximity to each other separated by a distance of 612 bases in the genome of A. hypochondriacus in a convergent configuration. We have experimentally validated that transcripts of these two genes are also overlapping in the 3' UTR with their expression negatively correlated from bud to mature seed, suggesting a potential link between the high seed lysine trait and unique genome organization.

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.

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

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 ...

Integrative missing value estimation for microarray data.

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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.

Efficient genome-wide genotyping strategies and data integration in crop plants.

Science.gov (United States)

Torkamaneh, Davoud; Boyle, Brian; Belzile, François

2018-03-01

Next-generation sequencing (NGS) has revolutionized plant and animal research by providing powerful genotyping methods. This review describes and discusses the advantages, challenges and, most importantly, solutions to facilitate data processing, the handling of missing data, and cross-platform data integration. Next-generation sequencing technologies provide powerful and flexible genotyping methods to plant breeders and researchers. These methods offer a wide range of applications from genome-wide analysis to routine screening with a high level of accuracy and reproducibility. Furthermore, they provide a straightforward workflow to identify, validate, and screen genetic variants in a short time with a low cost. NGS-based genotyping methods include whole-genome re-sequencing, SNP arrays, and reduced representation sequencing, which are widely applied in crops. The main challenges facing breeders and geneticists today is how to choose an appropriate genotyping method and how to integrate genotyping data sets obtained from various sources. Here, we review and discuss the advantages and challenges of several NGS methods for genome-wide genetic marker development and genotyping in crop plants. We also discuss how imputation methods can be used to both fill in missing data in genotypic data sets and to integrate data sets obtained using different genotyping tools. It is our hope that this synthetic view of genotyping methods will help geneticists and breeders to integrate these NGS-based methods in crop plant breeding and research.

The African Genome Variation Project shapes medical genetics in Africa

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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.

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.

Integrative missing value estimation for microarray data

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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.

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).

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

Assembly and diploid architecture of an individual human genome via single-molecule technologies.

Science.gov (United States)

Pendleton, Matthew; Sebra, Robert; Pang, Andy Wing Chun; Ummat, Ajay; Franzen, Oscar; Rausch, Tobias; Stütz, Adrian M; Stedman, William; Anantharaman, Thomas; Hastie, Alex; Dai, Heng; Fritz, Markus Hsi-Yang; Cao, Han; Cohain, Ariella; Deikus, Gintaras; Durrett, Russell E; Blanchard, Scott C; Altman, Roger; Chin, Chen-Shan; Guo, Yan; Paxinos, Ellen E; Korbel, Jan O; Darnell, Robert B; McCombie, W Richard; Kwok, Pui-Yan; Mason, Christopher E; Schadt, Eric E; Bashir, Ali

2015-08-01

We present the first comprehensive analysis of a diploid human genome that combines single-molecule sequencing with single-molecule genome maps. Our hybrid assembly markedly improves upon the contiguity observed from traditional shotgun sequencing approaches, with scaffold N50 values approaching 30 Mb, and we identified complex structural variants (SVs) missed by other high-throughput approaches. Furthermore, by combining Illumina short-read data with long reads, we phased both single-nucleotide variants and SVs, generating haplotypes with over 99% consistency with previous trio-based studies. Our work shows that it is now possible to integrate single-molecule and high-throughput sequence data to generate de novo assembled genomes that approach reference quality.

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.

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...

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.

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.

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…

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

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.

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.

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

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.

Multiple-Trait Genomic Selection Methods Increase Genetic Value Prediction Accuracy

Science.gov (United States)

Jia, Yi; Jannink, Jean-Luc

2012-01-01

Genetic correlations between quantitative traits measured in many breeding programs are pervasive. These correlations indicate that measurements of one trait carry information on other traits. Current single-trait (univariate) genomic selection does not take advantage of this information. Multivariate genomic selection on multiple traits could accomplish this but has been little explored and tested in practical breeding programs. In this study, three multivariate linear models (i.e., GBLUP, BayesA, and BayesCπ) were presented and compared to univariate models using simulated and real quantitative traits controlled by different genetic architectures. We also extended BayesA with fixed hyperparameters to a full hierarchical model that estimated hyperparameters and BayesCπ to impute missing phenotypes. We found that optimal marker-effect variance priors depended on the genetic architecture of the trait so that estimating them was beneficial. We showed that the prediction accuracy for a low-heritability trait could be significantly increased by multivariate genomic selection when a correlated high-heritability trait was available. Further, multiple-trait genomic selection had higher prediction accuracy than single-trait genomic selection when phenotypes are not available on all individuals and traits. Additional factors affecting the performance of multiple-trait genomic selection were explored. PMID:23086217

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

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.

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.

Diversity in non-repetitive human sequences not found in the reference genome.

Science.gov (United States)

Kehr, Birte; Helgadottir, Anna; Melsted, Pall; Jonsson, Hakon; Helgason, Hannes; Jonasdottir, Adalbjörg; Jonasdottir, Aslaug; Sigurdsson, Asgeir; Gylfason, Arnaldur; Halldorsson, Gisli H; Kristmundsdottir, Snaedis; Thorgeirsson, Gudmundur; Olafsson, Isleifur; Holm, Hilma; Thorsteinsdottir, Unnur; Sulem, Patrick; Helgason, Agnar; Gudbjartsson, Daniel F; Halldorsson, Bjarni V; Stefansson, Kari

2017-04-01

Genomes usually contain some non-repetitive sequences that are missing from the reference genome and occur only in a population subset. Such non-repetitive, non-reference (NRNR) sequences have remained largely unexplored in terms of their characterization and downstream analyses. Here we describe 3,791 breakpoint-resolved NRNR sequence variants called using PopIns from whole-genome sequence data of 15,219 Icelanders. We found that over 95% of the 244 NRNR sequences that are 200 bp or longer are present in chimpanzees, indicating that they are ancestral. Furthermore, 149 variant loci are in linkage disequilibrium (r 2 > 0.8) with a genome-wide association study (GWAS) catalog marker, suggesting disease relevance. Additionally, we report an association (P = 3.8 × 10 -8 , odds ratio (OR) = 0.92) with myocardial infarction (23,360 cases, 300,771 controls) for a 766-bp NRNR sequence variant. Our results underline the importance of including variation of all complexity levels when searching for variants that associate with disease.

Assembly of the Lactuca sativa, L. cv. Tizian draft genome sequence reveals differences within major resistance complex 1 as compared to the cv. Salinas reference genome.

Science.gov (United States)

Verwaaijen, Bart; Wibberg, Daniel; Nelkner, Johanna; Gordin, Miriam; Rupp, Oliver; Winkler, Anika; Bremges, Andreas; Blom, Jochen; Grosch, Rita; Pühler, Alfred; Schlüter, Andreas

2018-02-10

Lettuce (Lactuca sativa, L.) is an important annual plant of the family Asteraceae (Compositae). The commercial lettuce cultivar Tizian has been used in various scientific studies investigating the interaction of the plant with phytopathogens or biological control agents. Here, we present the de novo draft genome sequencing and gene prediction for this specific cultivar derived from transcriptome sequence data. The assembled scaffolds amount to a size of 2.22 Gb. Based on RNAseq data, 31,112 transcript isoforms were identified. Functional predictions for these transcripts were determined within the GenDBE annotation platform. Comparison with the cv. Salinas reference genome revealed a high degree of sequence similarity on genome and transcriptome levels, with an average amino acid identity of 99%. Furthermore, it was observed that two large regions are either missing or are highly divergent within the cv. Tizian genome compared to cv. Salinas. One of these regions covers the major resistance complex 1 region of cv. Salinas. The cv. Tizian draft genome sequence provides a valuable resource for future functional and transcriptome analyses focused on this lettuce cultivar. Copyright © 2017 Elsevier B.V. All rights reserved.

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

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

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

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...

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.

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...

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.

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.

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

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.

Embryo genome profiling by single-cell sequencing for preimplantation genetic diagnosis in a β-thalassemia family

DEFF Research Database (Denmark)

Xu, Yanwen; Chen, Shengpei; Yin, Xuyang

2015-01-01

for a β-thalassemia-carrier couple to have a healthy second baby. We carried out sequencing for single blastomere cells and the family trio and further developed the analysis pipeline, including recovery of the missing alleles, removal of the majority of errors, and phasing of the embryonic genome...... leukocyte antigen matching tests. CONCLUSIONS: This retrospective study in a β-thalassemia family demonstrates a method for embryo genome recovery through single-cell sequencing, which permits detection of genetic variations in preimplantation genetic diagnosis. It shows the potential of single...

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.

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.

Comparative Genomic Analysis of Globally Dominant ST131 Clone with Other Epidemiologically Successful Extraintestinal Pathogenic Escherichia coli (ExPEC Lineages

Directory of Open Access Journals (Sweden)

Sabiha Shaik

2017-10-01

Full Text Available Escherichia coli sequence type 131 (ST131, a pandemic clone responsible for the high incidence of extraintestinal pathogenic E. coli (ExPEC infections, has been known widely for its contribution to the worldwide dissemination of multidrug resistance. Although other ExPEC-associated and extended-spectrum-β-lactamase (ESBL-producing E. coli clones, such as ST38, ST405, and ST648 have been studied widely, no comparative genomic data with respect to other genotypes exist for ST131. In this study, comparative genomic analysis was performed for 99 ST131 E. coli strains with 40 genomes from three other STs, including ST38 (n = 12, ST405 (n = 10, and ST648 (n = 18, and functional studies were performed on five in-house strains corresponding to the four STs. Phylogenomic analysis results from this study corroborated with the sequence type-specific clonality. Results from the genome-wide resistance profiling confirmed that all strains were inherently multidrug resistant. ST131 genomes showed unique virulence profiles, and analysis of mobile genetic elements and their associated methyltransferases (MTases has revealed that several of them were missing from the majority of the non-ST131 strains. Despite the fact that non-ST131 strains lacked few essential genes belonging to the serum resistome, the in-house strains representing all four STs demonstrated similar resistance levels to serum antibactericidal activity. Core genome analysis data revealed that non-ST131 strains usually lacked several ST131-defined genomic coordinates, and a significant number of genes were missing from the core of the ST131 genomes. Data from this study reinforce adaptive diversification of E. coli strains belonging to the ST131 lineage and provide new insights into the molecular mechanisms underlying clonal diversification of the ST131 lineage.

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.

Defining and Evaluating a Core Genome Multilocus Sequence Typing Scheme for Genome-Wide Typing of Clostridium difficile.

Science.gov (United States)

Bletz, Stefan; Janezic, Sandra; Harmsen, Dag; Rupnik, Maja; Mellmann, Alexander

2018-06-01

Clostridium difficile , recently renamed Clostridioides difficile , is the most common cause of antibiotic-associated nosocomial gastrointestinal infections worldwide. To differentiate endogenous infections and transmission events, highly discriminatory subtyping is necessary. Today, methods based on whole-genome sequencing data are increasingly used to subtype bacterial pathogens; however, frequently a standardized methodology and typing nomenclature are missing. Here we report a core genome multilocus sequence typing (cgMLST) approach developed for C. difficile Initially, we determined the breadth of the C. difficile population based on all available MLST sequence types with Bayesian inference (BAPS). The resulting BAPS partitions were used in combination with C. difficile clade information to select representative isolates that were subsequently used to define cgMLST target genes. Finally, we evaluated the novel cgMLST scheme with genomes from 3,025 isolates. BAPS grouping ( n = 6 groups) together with the clade information led to a total of 11 representative isolates that were included for cgMLST definition and resulted in 2,270 cgMLST genes that were present in all isolates. Overall, 2,184 to 2,268 cgMLST targets were detected in the genome sequences of 70 outbreak-associated and reference strains, and on average 99.3% cgMLST targets (1,116 to 2,270 targets) were present in 2,954 genomes downloaded from the NCBI database, underlining the representativeness of the cgMLST scheme. Moreover, reanalyzing different cluster scenarios with cgMLST were concordant to published single nucleotide variant analyses. In conclusion, the novel cgMLST is representative for the whole C. difficile population, is highly discriminatory in outbreak situations, and provides a unique nomenclature facilitating interlaboratory exchange. Copyright © 2018 American Society for Microbiology.

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

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

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

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.

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.

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

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.

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.

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.

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.

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

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.

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.

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…

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...

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.

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.

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…

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

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.

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...

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.

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.

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

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…

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

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

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.

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...

A nonparametric multiple imputation approach for missing categorical data

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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

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

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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.

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

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.

The chloroplast genome sequence of the green alga Leptosira terrestris: multiple losses of the inverted repeat and extensive genome rearrangements within the Trebouxiophyceae

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Turmel Monique

2007-07-01

Full Text Available Abstract Background In the Chlorophyta – the green algal phylum comprising the classes Prasinophyceae, Ulvophyceae, Trebouxiophyceae and Chlorophyceae – the chloroplast genome displays a highly variable architecture. While chlorophycean chloroplast DNAs (cpDNAs deviate considerably from the ancestral pattern described for the prasinophyte Nephroselmis olivacea, the degree of remodelling sustained by the two ulvophyte cpDNAs completely sequenced to date is intermediate relative to those observed for chlorophycean and trebouxiophyte cpDNAs. Chlorella vulgaris (Chlorellales is currently the only photosynthetic trebouxiophyte whose complete cpDNA sequence has been reported. To gain insights into the evolutionary trends of the chloroplast genome in the Trebouxiophyceae, we sequenced cpDNA from the filamentous alga Leptosira terrestris (Ctenocladales. Results The 195,081-bp Leptosira chloroplast genome resembles the 150,613-bp Chlorella genome in lacking a large inverted repeat (IR but differs greatly in gene order. Six of the conserved genes present in Chlorella cpDNA are missing from the Leptosira gene repertoire. The 106 conserved genes, four introns and 11 free standing open reading frames (ORFs account for 48.3% of the genome sequence. This is the lowest gene density yet observed among chlorophyte cpDNAs. Contrary to the situation in Chlorella but similar to that in the chlorophycean Scenedesmus obliquus, the gene distribution is highly biased over the two DNA strands in Leptosira. Nine genes, compared to only three in Chlorella, have significantly expanded coding regions relative to their homologues in ancestral-type green algal cpDNAs. As observed in chlorophycean genomes, the rpoB gene is fragmented into two ORFs. Short repeats account for 5.1% of the Leptosira genome sequence and are present mainly in intergenic regions. Conclusion Our results highlight the great plasticity of the chloroplast genome in the Trebouxiophyceae and indicate

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.

Protein Interaction-Based Genome-Wide Analysis of Incident Coronary Heart Disease

DEFF Research Database (Denmark)

Jensen, Majken Karoline; Pers, Tune Hannes; Dworzynski, Piotr

2011-01-01

in genes associated with risk of coronary heart disease (CHD). Methods and Results-Genome-wide association analyses of approximately approximate to 700 000 single-nucleotide polymorphisms in 899 incident CHD cases and 1823 age-and sex-matched controls within the Nurses' Health and the Health Professionals...... complex. Conclusions-The integration of a GWA study with PPI data successfully identifies a set of candidate susceptibility genes for incident CHD that would have been missed in single-marker GWA analysis. (Circ Cardiovasc Genet. 2011; 4:549-556.)...

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.

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

Whole-Genome Analysis of a Novel Fish Reovirus (MsReV Discloses Aquareovirus Genomic Structure Relationship with Host in Saline Environments

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Zhong-Yuan Chen

2015-08-01

Full Text Available Aquareoviruses are serious pathogens of aquatic animals. Here, genome characterization and functional gene analysis of a novel aquareovirus, largemouth bass Micropterus salmoides reovirus (MsReV, was described. It comprises 11 dsRNA segments (S1–S11 covering 24,024 bp, and encodes 12 putative proteins including the inclusion forming-related protein NS87 and the fusion-associated small transmembrane (FAST protein NS22. The function of NS22 was confirmed by expression in fish cells. Subsequently, MsReV was compared with two representative aquareoviruses, saltwater fish turbot Scophthalmus maximus reovirus (SMReV and freshwater fish grass carp reovirus strain 109 (GCReV-109. MsReV NS87 and NS22 genes have the same structure and function with those of SMReV, whereas GCReV-109 is either missing the coiled-coil region in NS79 or the gene-encoding NS22. Significant similarities are also revealed among equivalent genome segments between MsReV and SMReV, but a difference is found between MsReV and GCReV-109. Furthermore, phylogenetic analysis showed that 13 aquareoviruses could be divided into freshwater and saline environments subgroups, and MsReV was closely related to SMReV in saline environments. Consequently, these viruses from hosts in saline environments have more genomic structural similarities than the viruses from hosts in freshwater. This is the first study of the relationships between aquareovirus genomic structure and their host environments.

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.

Genome Stability Maintenance in Naked Mole-Rat.

Science.gov (United States)

Petruseva, I O; Evdokimov, A N; Lavrik, O I

2017-01-01

The naked mole-rat ( Heterocephalus glaber ) is one of the most promising models used to study genome maintenance systems, including the effective repair of damage to DNA. The naked mole-rat is the longest lived rodent species, which is extraordinarily resistant to cancer and has a number of other unique phenotypic traits. For at least 80% of its lifespan, this animal shows no signs of aging or any increased likelihood of death and retains the ability to reproduce. The naked mole-rat draws the heightened attention of researchers who study the molecular basis of lengthy lifespan and cancer resistance. Despite the fact that the naked mole-rat lives under genotoxic stress conditions (oxidative, etc.), the main characteristics of its genome and proteome are a high stability and effective functioning. Replicative senescence in the somatic cells of naked mole-rats is missing, while an additional p53/pRb-dependent mechanism of early contact inhibition has been revealed in its fibroblasts, which controls cell proliferation and its mechanism of arf- dependent aging. The unique traits of phenotypic and molecular adaptations found in the naked mole-rat speak to a high stability and effective functioning of the molecular machinery that counteract damage accumulation in its genome. This review analyzes existing results in the study of the molecular basis of longevity and high cancer resistance in naked mole-rats.

Time Series Forecasting with Missing Values

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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.

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…

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...

"Tandem duplication-random loss" is not a real feature of oyster mitochondrial genomes

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Zhang Guofan

2009-02-01

Full Text Available Abstract Duplications and rearrangements of coding genes are major themes in the evolution of mitochondrial genomes, bearing important consequences in the function of mitochondria and the fitness of organisms. Yu et al. (BMC Genomics 2008, 9:477 reported the complete mt genome sequence of the oyster Crassostrea hongkongensis (16,475 bp and found that a DNA segment containing four tRNA genes (trnK1, trnC, trnQ1 and trnN, a duplicated (rrnS and a split rRNA gene (rrnL5' was absent compared with that of two other Crassostrea species. It was suggested that the absence was a novel case of "tandem duplication-random loss" with evolutionary significance. We independently sequenced the complete mt genome of three C. hongkongensis individuals, all of which were 18,622 bp and contained the segment that was missing in Yu et al.'s sequence. Further, we designed primers, verified sequences and demonstrated that the sequence loss in Yu et al.'s study was an artifact caused by placing primers in a duplicated region. The duplication and split of ribosomal RNA genes are unique for Crassostrea oysters and not lost in C. hongkongensis. Our study highlights the need for caution when amplifying and sequencing through duplicated regions of the genome.

Topology-Based Estimation of Missing Smart Meter Readings

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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.

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.

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.

Missed retinal breaks in rhegmatogenous retinal detachment

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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.

Miss Julie: A Psychoanalytic Study

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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.’

Sample-Based Extreme Learning Machine with Missing Data

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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.

Conservation and losses of non-coding RNAs in avian genomes.

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Paul P Gardner

Full Text Available Here we present the results of a large-scale bioinformatics annotation of non-coding RNA loci in 48 avian genomes. Our approach uses probabilistic models of hand-curated families from the Rfam database to infer conserved RNA families within each avian genome. We supplement these annotations with predictions from the tRNA annotation tool, tRNAscan-SE and microRNAs from miRBase. We identify 34 lncRNA-associated loci that are conserved between birds and mammals and validate 12 of these in chicken. We report several intriguing cases where a reported mammalian lncRNA, but not its function, is conserved. We also demonstrate extensive conservation of classical ncRNAs (e.g., tRNAs and more recently discovered ncRNAs (e.g., snoRNAs and miRNAs in birds. Furthermore, we describe numerous "losses" of several RNA families, and attribute these to either genuine loss, divergence or missing data. In particular, we show that many of these losses are due to the challenges associated with assembling avian microchromosomes. These combined results illustrate the utility of applying homology-based methods for annotating novel vertebrate genomes.

Genomic Prediction and Association Mapping of Curd-Related Traits in Gene Bank Accessions of Cauliflower.

Science.gov (United States)

Thorwarth, Patrick; Yousef, Eltohamy A A; Schmid, Karl J

2018-02-02

Genetic resources are an important source of genetic variation for plant breeding. Genome-wide association studies (GWAS) and genomic prediction greatly facilitate the analysis and utilization of useful genetic diversity for improving complex phenotypic traits in crop plants. We explored the potential of GWAS and genomic prediction for improving curd-related traits in cauliflower ( Brassica oleracea var. botrytis ) by combining 174 randomly selected cauliflower gene bank accessions from two different gene banks. The collection was genotyped with genotyping-by-sequencing (GBS) and phenotyped for six curd-related traits at two locations and three growing seasons. A GWAS analysis based on 120,693 single-nucleotide polymorphisms identified a total of 24 significant associations for curd-related traits. The potential for genomic prediction was assessed with a genomic best linear unbiased prediction model and BayesB. Prediction abilities ranged from 0.10 to 0.66 for different traits and did not differ between prediction methods. Imputation of missing genotypes only slightly improved prediction ability. Our results demonstrate that GWAS and genomic prediction in combination with GBS and phenotyping of highly heritable traits can be used to identify useful quantitative trait loci and genotypes among genetically diverse gene bank material for subsequent utilization as genetic resources in cauliflower breeding. Copyright © 2018 Thorwarth et al.

Genomic Prediction and Association Mapping of Curd-Related Traits in Gene Bank Accessions of Cauliflower

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Patrick Thorwarth

2018-02-01

Full Text Available Genetic resources are an important source of genetic variation for plant breeding. Genome-wide association studies (GWAS and genomic prediction greatly facilitate the analysis and utilization of useful genetic diversity for improving complex phenotypic traits in crop plants. We explored the potential of GWAS and genomic prediction for improving curd-related traits in cauliflower (Brassica oleracea var. botrytis by combining 174 randomly selected cauliflower gene bank accessions from two different gene banks. The collection was genotyped with genotyping-by-sequencing (GBS and phenotyped for six curd-related traits at two locations and three growing seasons. A GWAS analysis based on 120,693 single-nucleotide polymorphisms identified a total of 24 significant associations for curd-related traits. The potential for genomic prediction was assessed with a genomic best linear unbiased prediction model and BayesB. Prediction abilities ranged from 0.10 to 0.66 for different traits and did not differ between prediction methods. Imputation of missing genotypes only slightly improved prediction ability. Our results demonstrate that GWAS and genomic prediction in combination with GBS and phenotyping of highly heritable traits can be used to identify useful quantitative trait loci and genotypes among genetically diverse gene bank material for subsequent utilization as genetic resources in cauliflower breeding.

Principal Component Analysis of Process Datasets with Missing Values

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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.

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...

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...

VIGAN: Missing View Imputation with Generative Adversarial Networks.

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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.

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

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

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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.

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.

Expressed Peptide Tags: An additional layer of data for genome annotation

Energy Technology Data Exchange (ETDEWEB)

Savidor, Alon [ORNL; Donahoo, Ryan S [ORNL; Hurtado-Gonzales, Oscar [University of Tennessee, Knoxville (UTK); Verberkmoes, Nathan C [ORNL; Shah, Manesh B [ORNL; Lamour, Kurt H [ORNL; McDonald, W Hayes [ORNL

2006-01-01

While genome sequencing is becoming ever more routine, genome annotation remains a challenging process. Identification of the coding sequences within the genomic milieu presents a tremendous challenge, especially for eukaryotes with their complex gene architectures. Here we present a method to assist the annotation process through the use of proteomic data and bioinformatics. Mass spectra of digested protein preparations of the organism of interest were acquired and searched against a protein database created by a six frame translation of the genome. The identified peptides were mapped back to the genome, compared to the current annotation, and then categorized as supporting or extending the current genome annotation. We named the classified peptides Expressed Peptide Tags (EPTs). The well annotated bacterium Rhodopseudomonas palustris was used as a control for the method and showed high degree of correlation between EPT mapping and the current annotation, with 86% of the EPTs confirming existing gene calls and less than 1% of the EPTs expanding on the current annotation. The eukaryotic plant pathogens Phytophthora ramorum and Phytophthora sojae, whose genomes have been recently sequenced and are much less well annotated, were also subjected to this method. A series of algorithmic steps were taken to increase the confidence of EPT identification for these organisms, including generation of smaller sub-databases to be searched against, and definition of EPT criteria that accommodates the more complex eukaryotic gene architecture. As expected, the analysis of the Phytophthora species showed less correlation between EPT mapping and their current annotation. While ~77% of Phytophthora EPTs supported the current annotation, a portion of them (7.2% and 12.6% for P. ramorum and P. sojae, respectively) suggested modification to current gene calls or identified novel genes that were missed by the current genome annotation of these organisms.

Repetitive elements may comprise over two-thirds of the human genome.

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A P Jason de Koning

2011-12-01

Full Text Available Transposable elements (TEs are conventionally identified in eukaryotic genomes by alignment to consensus element sequences. Using this approach, about half of the human genome has been previously identified as TEs and low-complexity repeats. We recently developed a highly sensitive alternative de novo strategy, P-clouds, that instead searches for clusters of high-abundance oligonucleotides that are related in sequence space (oligo "clouds". We show here that P-clouds predicts >840 Mbp of additional repetitive sequences in the human genome, thus suggesting that 66%-69% of the human genome is repetitive or repeat-derived. To investigate this remarkable difference, we conducted detailed analyses of the ability of both P-clouds and a commonly used conventional approach, RepeatMasker (RM, to detect different sized fragments of the highly abundant human Alu and MIR SINEs. RM can have surprisingly low sensitivity for even moderately long fragments, in contrast to P-clouds, which has good sensitivity down to small fragment sizes (∼25 bp. Although short fragments have a high intrinsic probability of being false positives, we performed a probabilistic annotation that reflects this fact. We further developed "element-specific" P-clouds (ESPs to identify novel Alu and MIR SINE elements, and using it we identified ∼100 Mb of previously unannotated human elements. ESP estimates of new MIR sequences are in good agreement with RM-based predictions of the amount that RM missed. These results highlight the need for combined, probabilistic genome annotation approaches and suggest that the human genome consists of substantially more repetitive sequence than previously believed.

Alignment of 1000 Genomes Project reads to reference assembly GRCh38.

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Zheng-Bradley, Xiangqun; Streeter, Ian; Fairley, Susan; Richardson, David; Clarke, Laura; Flicek, Paul

2017-07-01

The 1000 Genomes Project produced more than 100 trillion basepairs of short read sequence from more than 2600 samples in 26 populations over a period of five years. In its final phase, the project released over 85 million genotyped and phased variants on human reference genome assembly GRCh37. An updated reference assembly, GRCh38, was released in late 2013, but there was insufficient time for the final phase of the project analysis to change to the new assembly. Although it is possible to lift the coordinates of the 1000 Genomes Project variants to the new assembly, this is a potentially error-prone process as coordinate remapping is most appropriate only for non-repetitive regions of the genome and those that did not see significant change between the two assemblies. It will also miss variants in any region that was newly added to GRCh38. Thus, to produce the highest quality variants and genotypes on GRCh38, the best strategy is to realign the reads and recall the variants based on the new alignment. As the first step of variant calling for the 1000 Genomes Project data, we have finished remapping all of the 1000 Genomes sequence reads to GRCh38 with alternative scaffold-aware BWA-MEM. The resulting alignments are available as CRAM, a reference-based sequence compression format. The data have been released on our FTP site and are also available from European Nucleotide Archive to facilitate researchers discovering variants on the primary sequences and alternative contigs of GRCh38. © The Authors 2017. Published by Oxford University Press.

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

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

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

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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.

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...

Missed Opportunities for Hepatitis A Vaccination, National Immunization Survey-Child, 2013.

Science.gov (United States)

Casillas, Shannon M; Bednarczyk, Robert A

2017-08-01

To quantify the number of missed opportunities for vaccination with hepatitis A vaccine in children and assess the association of missed opportunities for hepatitis A vaccination with covariates of interest. Weighted data from the 2013 National Immunization Survey of US children aged 19-35 months were used. Analysis was restricted to children with provider-verified vaccination history (n = 13 460). Missed opportunities for vaccination were quantified by determining the number of medical visits a child made when another vaccine was administered during eligibility for hepatitis A vaccine, but hepatitis A vaccine was not administered. Cross-sectional bivariate and multivariate polytomous logistic regression were used to assess the association of missed opportunities for vaccination with child and maternal demographic, socioeconomic, and geographic covariates. In 2013, 85% of children in our study population had initiated the hepatitis A vaccine series, and 60% received 2 or more doses. Children who received zero doses of hepatitis A vaccine had an average of 1.77 missed opportunities for vaccination compared with 0.43 missed opportunities for vaccination in those receiving 2 doses. Children with 2 or more missed opportunities for vaccination initiated the vaccine series 6 months later than children without missed opportunities. In the fully adjusted multivariate model, children who were younger, had ever received WIC benefits, or lived in a state with childcare entry mandates were at a reduced odds for 2 or more missed opportunities for vaccination; children living in the Northeast census region were at an increased odds. Missed opportunities for vaccination likely contribute to the poor coverage for hepatitis A vaccination in children; it is important to understand why children are not receiving the vaccine when eligible. Copyright © 2017 Elsevier Inc. All rights reserved.

The draft genome of the carcinogenic human liver fluke Clonorchis sinensis

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2011-01-01

Background Clonorchis sinensis is a carcinogenic human liver fluke that is widespread in Asian countries. Increasing infection rates of this neglected tropical disease are leading to negative economic and public health consequences in affected regions. Experimental and epidemiological studies have shown a strong association between the incidence of cholangiocarcinoma and the infection rate of C. sinensis. To aid research into this organism, we have sequenced its genome. Results We combined de novo sequencing with computational techniques to provide new information about the biology of this liver fluke. The assembled genome has a total size of 516 Mb with a scaffold N50 length of 42 kb. Approximately 16,000 reliable protein-coding gene models were predicted. Genes for the complete pathways for glycolysis, the Krebs cycle and fatty acid metabolism were found, but key genes involved in fatty acid biosynthesis are missing from the genome, reflecting the parasitic lifestyle of a liver fluke that receives lipids from the bile of its host. We also identified pathogenic molecules that may contribute to liver fluke-induced hepatobiliary diseases. Large proteins such as multifunctional secreted proteases and tegumental proteins were identified as potential targets for the development of drugs and vaccines. Conclusions This study provides valuable genomic information about the human liver fluke C. sinensis and adds to our knowledge on the biology of the parasite. The draft genome will serve as a platform to develop new strategies for parasite control. PMID:22023798

Missing data in trial-based cost-effectiveness analysis: An incomplete journey.

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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.

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.

Analyzing time-ordered event data with missed observations.

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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

Empirical Likelihood in Nonignorable Covariate-Missing Data Problems.

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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

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

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.

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

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.

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

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

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.

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.

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

The complete mitochondrial genome of the invasive Africanized Honey Bee, Apis mellifera scutellata (Insecta: Hymenoptera: Apidae).

Science.gov (United States)

Gibson, Joshua D; Hunt, Greg J

2016-01-01

The complete mitochondrial genome from an Africanized honey bee population (AHB, derived from Apis mellifera scutellata) was assembled and analyzed. The mitogenome is 16,411 bp long and contains the same gene repertoire and gene order as the European honey bee (13 protein coding genes, 22 tRNA genes and 2 rRNA genes). ND4 appears to use an alternate start codon and the long rRNA gene is 48 bp shorter in AHB due to a deletion in a terminal AT dinucleotide repeat. The dihydrouracil arm is missing from tRNA-Ser (AGN) and tRNA-Glu is missing the TV loop. The A + T content is comparable to the European honey bee (84.7%), which increases to 95% for the 3rd position in the protein coding genes.

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).

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

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.

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.

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...

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.

Outlier Removal in Model-Based Missing Value Imputation for Medical Datasets

Directory of Open Access Journals (Sweden)

Min-Wei Huang

2018-01-01

Full Text Available Many real-world medical datasets contain some proportion of missing (attribute values. In general, missing value imputation can be performed to solve this problem, which is to provide estimations for the missing values by a reasoning process based on the (complete observed data. However, if the observed data contain some noisy information or outliers, the estimations of the missing values may not be reliable or may even be quite different from the real values. The aim of this paper is to examine whether a combination of instance selection from the observed data and missing value imputation offers better performance than performing missing value imputation alone. In particular, three instance selection algorithms, DROP3, GA, and IB3, and three imputation algorithms, KNNI, MLP, and SVM, are used in order to find out the best combination. The experimental results show that that performing instance selection can have a positive impact on missing value imputation over the numerical data type of medical datasets, and specific combinations of instance selection and imputation methods can improve the imputation results over the mixed data type of medical datasets. However, instance selection does not have a definitely positive impact on the imputation result for categorical medical datasets.

Cyclists’ Anger As Determinant of Near Misses Involving Different Road Users

Directory of Open Access Journals (Sweden)

Víctor Marín Puchades

2017-12-01

Full Text Available Road anger constitutes one of the determinant factors related to safety outcomes (e.g., accidents, near misses. Although cyclists are considered vulnerable road users due to their relatively high rate of fatalities in traffic, previous research has solely focused on car drivers, and no study has yet investigated the effect of anger on cyclists’ safety outcomes. The present research aims to investigate, for the first time, the effects of cycling anger toward different types of road users on near misses involving such road users and near misses in general. Using a daily diary web-based questionnaire, we collected data about daily trips, bicycle use, near misses experienced, cyclist’s anger and demographic information from 254 Spanish cyclists. Poisson regression was used to assess the association of cycling anger with near misses, which is a count variable. No relationship was found between general cycling anger and near misses occurrence. Anger toward specific road users had different effects on the probability of near misses with different road users. Anger toward the interaction with car drivers increased the probability of near misses involving cyclists and pedestrians. Anger toward interaction with pedestrians was associated with higher probability of near misses with pedestrians. Anger toward cyclists exerted no effect on the probability of near misses with any road user (i.e., car drivers, cyclists or pedestrians, whereas anger toward the interactions with the police had a diminishing effect on the occurrence of near misses’ involving all types of road users. The present study demonstrated that the effect of road anger on safety outcomes among cyclists is different from that of motorists. Moreover, the target of anger played an important role on safety both for the cyclist and the specific road users. Possible explanations for these differences are based on the difference in status and power with motorists, as well as on the potential

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

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

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

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.

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, ...

Assembly and comparative analysis of complete mitochondrial genome sequence of an economic plant Salix suchowensis

Directory of Open Access Journals (Sweden)

Ning Ye

2017-03-01

Full Text Available Willow is a widely used dioecious woody plant of Salicaceae family in China. Due to their high biomass yields, willows are promising sources for bioenergy crops. In this study, we assembled the complete mitochondrial (mt genome sequence of S. suchowensis with the length of 644,437 bp using Roche-454 GS FLX Titanium sequencing technologies. Base composition of the S. suchowensis mt genome is A (27.43%, T (27.59%, C (22.34%, and G (22.64%, which shows a prevalent GC content with that of other angiosperms. This long circular mt genome encodes 58 unique genes (32 protein-coding genes, 23 tRNA genes and 3 rRNA genes, and 9 of the 32 protein-coding genes contain 17 introns. Through the phylogenetic analysis of 35 species based on 23 protein-coding genes, it is supported that Salix as a sister to Populus. With the detailed phylogenetic information and the identification of phylogenetic position, some ribosomal protein genes and succinate dehydrogenase genes are found usually lost during evolution. As a native shrub willow species, this worthwhile research of S. suchowensis mt genome will provide more desirable information for better understanding the genomic breeding and missing pieces of sex determination evolution in the future.

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.

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

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.

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 ...

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...

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

Screening of whole genome sequences identified high-impact variants for stallion fertility.

Science.gov (United States)

Schrimpf, Rahel; Gottschalk, Maren; Metzger, Julia; Martinsson, Gunilla; Sieme, Harald; Distl, Ottmar

2016-04-14

Stallion fertility is an economically important trait due to the increase of artificial insemination in horses. The availability of whole genome sequence data facilitates identification of rare high-impact variants contributing to stallion fertility. The aim of our study was to genotype rare high-impact variants retrieved from next-generation sequencing (NGS)-data of 11 horses in order to unravel harmful genetic variants in large samples of stallions. Gene ontology (GO) terms and search results from public databases were used to obtain a comprehensive list of human und mice genes predicted to participate in the regulation of male reproduction. The corresponding equine orthologous genes were searched in whole genome sequence data of seven stallions and four mares and filtered for high-impact genetic variants using SnpEFF, SIFT and Polyphen 2 software. All genetic variants with the missing homozygous mutant genotype were genotyped on 337 fertile stallions of 19 breeds using KASP genotyping assays or PCR-RFLP. Mixed linear model analysis was employed for an association analysis with de-regressed estimated breeding values of the paternal component of the pregnancy rate per estrus (EBV-PAT). We screened next generation sequenced data of whole genomes from 11 horses for equine genetic variants in 1194 human and mice genes involved in male fertility and linked through common gene ontology (GO) with male reproductive processes. Variants were filtered for high-impact on protein structure and validated through SIFT and Polyphen 2. Only those genetic variants were followed up when the homozygote mutant genotype was missing in the detection sample comprising 11 horses. After this filtering process, 17 single nucleotide polymorphism (SNPs) were left. These SNPs were genotyped in 337 fertile stallions of 19 breeds using KASP genotyping assays or PCR-RFLP. An association analysis in 216 Hanoverian stallions revealed a significant association of the splice-site disruption variant

Missing data and the accuracy of magnetic-observatory hour means

Directory of Open Access Journals (Sweden)

J. J. Love

2009-09-01

Full Text Available Analysis is made of the accuracy of magnetic-observatory hourly means constructed from definitive minute data having missing values (gaps. Bootstrap sampling from different data-gap distributions is used to estimate average errors on hourly means as a function of the number of missing data. Absolute and relative error results are calculated for horizontal-intensity, declination, and vertical-component data collected at high, medium, and low magnetic latitudes. For 90% complete coverage (10% missing data, average (RMS absolute errors on hourly means are generally less than errors permitted by Intermagnet for minute data. As a rule of thumb, the average relative error for hourly means with 10% missing minute data is approximately equal to 10% of the hourly standard deviation of the source minute data.

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.

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

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)

A clone-free, single molecule map of the domestic cow (Bos taurus) genome.

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Zhou, Shiguo; Goldstein, Steve; Place, Michael; Bechner, Michael; Patino, Diego; Potamousis, Konstantinos; Ravindran, Prabu; Pape, Louise; Rincon, Gonzalo; Hernandez-Ortiz, Juan; Medrano, Juan F; Schwartz, David C

2015-08-28

The cattle (Bos taurus) genome was originally selected for sequencing due to its economic importance and unique biology as a model organism for understanding other ruminants, or mammals. Currently, there are two cattle genome sequence assemblies (UMD3.1 and Btau4.6) from groups using dissimilar assembly algorithms, which were complemented by genetic and physical map resources. However, past comparisons between these assemblies revealed substantial differences. Consequently, such discordances have engendered ambiguities when using reference sequence data, impacting genomic studies in cattle and motivating construction of a new optical map resource--BtOM1.0--to guide comparisons and improvements to the current sequence builds. Accordingly, our comprehensive comparisons of BtOM1.0 against the UMD3.1 and Btau4.6 sequence builds tabulate large-to-immediate scale discordances requiring mediation. The optical map, BtOM1.0, spanning the B. taurus genome (Hereford breed, L1 Dominette 01449) was assembled from an optical map dataset consisting of 2,973,315 (439 X; raw dataset size before assembly) single molecule optical maps (Rmaps; 1 Rmap = 1 restriction mapped DNA molecule) generated by the Optical Mapping System. The BamHI map spans 2,575.30 Mb and comprises 78 optical contigs assembled by a combination of iterative (using the reference sequence: UMD3.1) and de novo assembly techniques. BtOM1.0 is a high-resolution physical map featuring an average restriction fragment size of 8.91 Kb. Comparisons of BtOM1.0 vs. UMD3.1, or Btau4.6, revealed that Btau4.6 presented far more discordances (7,463) vs. UMD3.1 (4,754). Overall, we found that Btau4.6 presented almost double the number of discordances than UMD3.1 across most of the 6 categories of sequence vs. map discrepancies, which are: COMPLEX (misassembly), DELs (extraneous sequences), INSs (missing sequences), ITs (Inverted/Translocated sequences), ECs (extra restriction cuts) and MCs (missing restriction cuts

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...

Multiple imputation by chained equations for systematically and sporadically missing multilevel data.

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Resche-Rigon, Matthieu; White, Ian R

2018-06-01

In multilevel settings such as individual participant data meta-analysis, a variable is 'systematically missing' if it is wholly missing in some clusters and 'sporadically missing' if it is partly missing in some clusters. Previously proposed methods to impute incomplete multilevel data handle either systematically or sporadically missing data, but frequently both patterns are observed. We describe a new multiple imputation by chained equations (MICE) algorithm for multilevel data with arbitrary patterns of systematically and sporadically missing variables. The algorithm is described for multilevel normal data but can easily be extended for other variable types. We first propose two methods for imputing a single incomplete variable: an extension of an existing method and a new two-stage method which conveniently allows for heteroscedastic data. We then discuss the difficulties of imputing missing values in several variables in multilevel data using MICE, and show that even the simplest joint multilevel model implies conditional models which involve cluster means and heteroscedasticity. However, a simulation study finds that the proposed methods can be successfully combined in a multilevel MICE procedure, even when cluster means are not included in the imputation models.

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

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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.

A regressive methodology for estimating missing data in rainfall daily time series

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Barca, E.; Passarella, G.

2009-04-01

The "presence" of gaps in environmental data time series represents a very common, but extremely critical problem, since it can produce biased results (Rubin, 1976). Missing data plagues almost all surveys. The problem is how to deal with missing data once it has been deemed impossible to recover the actual missing values. Apart from the amount of missing data, another issue which plays an important role in the choice of any recovery approach is the evaluation of "missingness" mechanisms. When data missing is conditioned by some other variable observed in the data set (Schafer, 1997) the mechanism is called MAR (Missing at Random). Otherwise, when the missingness mechanism depends on the actual value of the missing data, it is called NCAR (Not Missing at Random). This last is the most difficult condition to model. In the last decade interest arose in the estimation of missing data by using regression (single imputation). More recently multiple imputation has become also available, which returns a distribution of estimated values (Scheffer, 2002). In this paper an automatic methodology for estimating missing data is presented. In practice, given a gauging station affected by missing data (target station), the methodology checks the randomness of the missing data and classifies the "similarity" between the target station and the other gauging stations spread over the study area. Among different methods useful for defining the similarity degree, whose effectiveness strongly depends on the data distribution, the Spearman correlation coefficient was chosen. Once defined the similarity matrix, a suitable, nonparametric, univariate, and regressive method was applied in order to estimate missing data in the target station: the Theil method (Theil, 1950). Even though the methodology revealed to be rather reliable an improvement of the missing data estimation can be achieved by a generalization. A first possible improvement consists in extending the univariate technique to

Evaluating Phylogenetic Congruence in the Post-Genomic Era

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Leigh, Jessica W.; Lapointe, François-Joseph; Lopez, Philippe; Bapteste, Eric

2011-01-01

Congruence is a broadly applied notion in evolutionary biology used to justify multigene phylogeny or phylogenomics, as well as in studies of coevolution, lateral gene transfer, and as evidence for common descent. Existing methods for identifying incongruence or heterogeneity using character data were designed for data sets that are both small and expected to be rarely incongruent. At the same time, methods that assess incongruence using comparison of trees test a null hypothesis of uncorrelated tree structures, which may be inappropriate for phylogenomic studies. As such, they are ill-suited for the growing number of available genome sequences, most of which are from prokaryotes and viruses, either for phylogenomic analysis or for studies of the evolutionary forces and events that have shaped these genomes. Specifically, many existing methods scale poorly with large numbers of genes, cannot accommodate high levels of incongruence, and do not adequately model patterns of missing taxa for different markers. We propose the development of novel incongruence assessment methods suitable for the analysis of the molecular evolution of the vast majority of life and support the investigation of homogeneity of evolutionary process in cases where markers do not share identical tree structures. PMID:21712432

Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote.

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Jonathan A Eisen

2006-09-01

Full Text Available The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct nuclei within a single cell. The germline-like micronucleus (MIC has its genome held in reserve for sexual reproduction. The soma-like macronucleus (MAC, which possesses a genome processed from that of the MIC, is the center of gene expression and does not directly contribute DNA to sexual progeny. We report here the shotgun sequencing, assembly, and analysis of the MAC genome of T. thermophila, which is approximately 104 Mb in length and composed of approximately 225 chromosomes. Overall, the gene set is robust, with more than 27,000 predicted protein-coding genes, 15,000 of which have strong matches to genes in other organisms. The functional diversity encoded by these genes is substantial and reflects the complexity of processes required for a free-living, predatory, single-celled organism. This is highlighted by the abundance of lineage-specific duplications of genes with predicted roles in sensing and responding to environmental conditions (e.g., kinases, using diverse resources (e.g., proteases and transporters, and generating structural complexity (e.g., kinesins and dyneins. In contrast to the other lineages of alveolates (apicomplexans and dinoflagellates, no compelling evidence could be found for plastid-derived genes in the genome. UGA, the only T. thermophila stop codon, is used in some genes to encode selenocysteine, thus making this organism the first known with the potential to translate all 64 codons in nuclear genes into amino acids. We present genomic evidence supporting the hypothesis that the excision of DNA from the MIC to generate the MAC specifically targets foreign DNA as a form of genome self-defense. The combination of the genome sequence, the functional diversity encoded therein, and the presence of some pathways missing from

Estimation of Missing Observations in Two-Level Split-Plot Designs

DEFF Research Database (Denmark)

Almimi, Ashraf A.; Kulahci, Murat; Montgomery, Douglas C.

2008-01-01

Inserting estimates for the missing observations from split-plot designs restores their balanced or orthogonal structure and alleviates the difficulties in the statistical analysis. In this article, we extend a method due to Draper and Stoneman to estimate the missing observations from unreplicated...... two-level factorial and fractional factorial split-plot (FSP and FFSP) designs. The missing observations, which can either be from the same whole plot, from different whole plots, or comprise entire whole plots, are estimated by equating to zero a number of specific contrast columns equal...... to the number of the missing observations. These estimates are inserted into the design table and the estimates for the remaining effects (or alias chains of effects as the case with FFSP designs) are plotted on two half-normal plots: one for the whole-plot effects and the other for the subplot effects...

Genome analysis of Diploscapter coronatus: insights into molecular peculiarities of a nematode with parthenogenetic reproduction.

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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.

Genome sequencing of bacteria: sequencing, de novo assembly and rapid analysis using open source tools.

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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

The effect of maternal near miss on adverse infant nutritional outcomes

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Dulce M. Zanardi

Full Text Available OBJECTIVES: To evaluate the association between self-reported maternal near miss and adverse nutritional status in children under one year of age. METHODS: This study is a secondary analysis of a study in which women who took their children under one year of age to the national vaccine campaign were interviewed. The self-reported condition of maternal near miss used the criteria of Intensive Care Unit admission; eclampsia; blood transfusion and hysterectomy; and their potential associations with any type of nutritional disorder in children, including deficits in weight-for-age, deficits in height-for-age, obesity and breastfeeding. The rates of near miss for the country, regions and states were initially estimated. The relative risks of infant adverse nutritional status according to near miss and maternal/childbirth characteristics were estimated with their 95% CIs using bivariate and multiple analyses. RESULTS: The overall prevalence of near miss was 2.9% and was slightly higher for the Legal Amazon than for other regions. No significant associations were found with nutritional disorders in children. Only a 12% decrease in overall maternal breastfeeding was associated with near miss. Living in the countryside and child over 6 months of age increased the risk of altered nutritional status by approximately 15%, while female child gender decreased this risk by 30%. Maternal near miss was not associated with an increased risk of any alteration in infant nutritional status. CONCLUSIONS: There was no association between maternal near miss and altered nutritional status in children up to one year of age. The risk of infant adverse nutritional status was greater in women living in the countryside, for children over 6 months of age and for male gender.

Lynch Syndrome: Genomics Update and Imaging Review.

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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.

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

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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

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

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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.

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

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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.

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

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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.

Recombination and its impact on the genome of the haplodiploid parasitoid wasp Nasonia.

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Oliver Niehuis

2010-01-01

Full Text Available Homologous meiotic recombination occurs in most sexually reproducing organisms, yet its evolutionary advantages are elusive. Previous research explored recombination in the honeybee, a eusocial hymenopteran with an exceptionally high genome-wide recombination rate. A comparable study in a non-social member of the Hymenoptera that would disentangle the impact of sociality from Hymenoptera-specific features such as haplodiploidy on the evolution of the high genome-wide recombination rate in social Hymenoptera is missing. Utilizing single-nucleotide polymorphisms (SNPs between two Nasonia parasitoid wasp genomes, we developed a SNP genotyping microarray to infer a high-density linkage map for Nasonia. The map comprises 1,255 markers with an average distance of 0.3 cM. The mapped markers enabled us to arrange 265 scaffolds of the Nasonia genome assembly 1.0 on the linkage map, representing 63.6% of the assembled N. vitripennis genome. We estimated a genome-wide recombination rate of 1.4-1.5 cM/Mb for Nasonia, which is less than one tenth of the rate reported for the honeybee. The local recombination rate in Nasonia is positively correlated with the distance to the center of the linkage groups, GC content, and the proportion of simple repeats. In contrast to the honeybee genome, gene density in the parasitoid wasp genome is positively associated with the recombination rate; regions of low recombination are characterized by fewer genes with larger introns and by a greater distance between genes. Finally, we found that genes in regions of the genome with a low recombination frequency tend to have a higher ratio of non-synonymous to synonymous substitutions, likely due to the accumulation of slightly deleterious non-synonymous substitutions. These findings are consistent with the hypothesis that recombination reduces interference between linked sites and thereby facilitates adaptive evolution and the purging of deleterious mutations. Our results imply

Comparative genomic analysis of Brucella abortus vaccine strain 104M reveals a set of candidate genes associated with its virulence attenuation.

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Yu, Dong; Hui, Yiming; Zai, Xiaodong; Xu, Junjie; Liang, Long; Wang, Bingxiang; Yue, Junjie; Li, Shanhu

2015-01-01

The Brucella abortus strain 104M, a spontaneously attenuated strain, has been used as a vaccine strain in humans against brucellosis for 6 decades in China. Despite many studies, the molecular mechanisms that cause the attenuation are still unclear. Here, we determined the whole-genome sequence of 104M and conducted a comprehensive comparative analysis against the whole genome sequences of the virulent strain, A13334, and other reference strains. This analysis revealed a highly similar genome structure between 104M and A13334. The further comparative genomic analysis between 104M and A13334 revealed a set of genes missing in 104M. Some of these genes were identified to be directly or indirectly associated with virulence. Similarly, a set of mutations in the virulence-related genes was also identified, which may be related to virulence alteration. This study provides a set of candidate genes associated with virulence attenuation in B.abortus vaccine strain 104M.

The SGC beyond structural genomics: redefining the role of 3D structures by coupling genomic stratification with fragment-based discovery.

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Bradley, Anthony R; Echalier, Aude; Fairhead, Michael; Strain-Damerell, Claire; Brennan, Paul; Bullock, Alex N; Burgess-Brown, Nicola A; Carpenter, Elisabeth P; Gileadi, Opher; Marsden, Brian D; Lee, Wen Hwa; Yue, Wyatt; Bountra, Chas; von Delft, Frank

2017-11-08

The ongoing explosion in genomics data has long since outpaced the capacity of conventional biochemical methodology to verify the large number of hypotheses that emerge from the analysis of such data. In contrast, it is still a gold-standard for early phenotypic validation towards small-molecule drug discovery to use probe molecules (or tool compounds), notwithstanding the difficulty and cost of generating them. Rational structure-based approaches to ligand discovery have long promised the efficiencies needed to close this divergence; in practice, however, this promise remains largely unfulfilled, for a host of well-rehearsed reasons and despite the huge technical advances spearheaded by the structural genomics initiatives of the noughties. Therefore the current, fourth funding phase of the Structural Genomics Consortium (SGC), building on its extensive experience in structural biology of novel targets and design of protein inhibitors, seeks to redefine what it means to do structural biology for drug discovery. We developed the concept of a Target Enabling Package (TEP) that provides, through reagents, assays and data, the missing link between genetic disease linkage and the development of usefully potent compounds. There are multiple prongs to the ambition: rigorously assessing targets' genetic disease linkages through crowdsourcing to a network of collaborating experts; establishing a systematic approach to generate the protocols and data that comprise each target's TEP; developing new, X-ray-based fragment technologies for generating high quality chemical matter quickly and cheaply; and exploiting a stringently open access model to build multidisciplinary partnerships throughout academia and industry. By learning how to scale these approaches, the SGC aims to make structures finally serve genomics, as originally intended, and demonstrate how 3D structures systematically allow new modes of druggability to be discovered for whole classes of targets. © 2017 The

The detection of large deletions or duplications in genomic DNA.

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Armour, J A L; Barton, D E; Cockburn, D J; Taylor, G R

2002-11-01

While methods for the detection of point mutations and small insertions or deletions in genomic DNA are well established, the detection of larger (>100 bp) genomic duplications or deletions can be more difficult. Most mutation scanning methods use PCR as a first step, but the subsequent analyses are usually qualitative rather than quantitative. Gene dosage methods based on PCR need to be quantitative (i.e., they should report molar quantities of starting material) or semi-quantitative (i.e., they should report gene dosage relative to an internal standard). Without some sort of quantitation, heterozygous deletions and duplications may be overlooked and therefore be under-ascertained. Gene dosage methods provide the additional benefit of reporting allele drop-out in the PCR. This could impact on SNP surveys, where large-scale genotyping may miss null alleles. Here we review recent developments in techniques for the detection of this type of mutation and compare their relative strengths and weaknesses. We emphasize that comprehensive mutation analysis should include scanning for large insertions and deletions and duplications. Copyright 2002 Wiley-Liss, Inc.

IRB PERSPECTIVES ON THE RETURN OF INDIVIDUAL RESULTS FROM GENOMIC RESEARCH

Science.gov (United States)

Dressler, Lynn G.; Smolek, Sondra; Ponsaran, Roselle; Markey, Janell M.; Starks, Helene; Gerson, Nancy; Lewis, Susan; Press, Nancy; Juengst, Eric; Wiesner, Georgia L.

2012-01-01

Purpose Return of individual research results from genomic studies is a hotly debated ethical issue in genomic research. However, the perspective of key stakeholders—Institutional Review Board (IRB) reviewers—has been missing from this dialogue. This study explores the positions and experiences of IRB members and staff regarding this issue. Methods In depth interviews with 31 IRB professionals at six sites across the United States. Results IRB professionals agreed that research results should be returned to research participants when results are medically actionable but only if the participants wanted to know the result. Many respondents expected researchers to address the issue of return of results (ROR) in the IRB application and informed-consent document. Many respondents were not comfortable with their expertise in genomics research, and only a few described actual experiences in addressing ROR. Although participants agreed that guidelines would be helpful, most were reticent to develop them in isolation. Even where IRB guidance exists (e.g., CLIA lab certification required for return), in practice, the guidance has been overruled to allow return (e.g., no CLIA lab performs the assay). Conclusion An IRB-researcher partnership is needed to help inform responsible and feasible institutional approaches to returning research results. PMID:22241094

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...

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.

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.

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.

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% ...

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

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...

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.

Insights into the genome structure and copy-number variation of Eimeria tenella

Directory of Open Access Journals (Sweden)

Lim Lik-Sin

2012-08-01

method to improve the assembly of the genome of E. tenella from shotgun data, and to help reveal its overall structure. A preliminary assessment of copy-number variation (extra or missing copies of genomic segments between strains of E. tenella was also carried out. The emerging picture is of a very unusual genome architecture displaying inter-strain copy-number variation. We suggest that these features may be related to the known ability of this parasite to rapidly develop drug resistance.

Implicit Valuation of the Near-Miss is Dependent on Outcome Context.

Science.gov (United States)

Banks, Parker J; Tata, Matthew S; Bennett, Patrick J; Sekuler, Allison B; Gruber, Aaron J

2018-03-01

Gambling studies have described a "near-miss effect" wherein the experience of almost winning increases gambling persistence. The near-miss has been proposed to inflate the value of preceding actions through its perceptual similarity to wins. We demonstrate here, however, that it acts as a conditioned stimulus to positively or negatively influence valuation, dependent on reward expectation and cognitive engagement. When subjects are asked to choose between two simulated slot machines, near-misses increase valuation of machines with a low payout rate, whereas they decrease valuation of high payout machines. This contextual effect impairs decisions and persists regardless of manipulations to outcome feedback or financial incentive provided for good performance. It is consistent with proposals that near-misses cause frustration when wins are expected, and we propose that it increases choice stochasticity and overrides avoidance of low-valued options. Intriguingly, the near-miss effect disappears when subjects are required to explicitly value machines by placing bets, rather than choosing between them. We propose that this task increases cognitive engagement and recruits participation of brain regions involved in cognitive processing, causing inhibition of otherwise dominant systems of decision-making. Our results reveal that only implicit, rather than explicit strategies of decision-making are affected by near-misses, and that the brain can fluidly shift between these strategies according to task demands.

Airline Safety Improvement Through Experience with Near-Misses: A Cautionary Tale.

Science.gov (United States)

Madsen, Peter; Dillon, Robin L; Tinsley, Catherine H

2016-05-01

In recent years, the U.S. commercial airline industry has achieved unprecedented levels of safety, with the statistical risk associated with U.S. commercial aviation falling to 0.003 fatalities per 100 million passengers. But decades of research on organizational learning show that success often breeds complacency and failure inspires improvement. With accidents as rare events, can the airline industry continue safety advancements? This question is complicated by the complex system in which the industry operates where chance combinations of multiple factors contribute to what are largely probabilistic (rather than deterministic) outcomes. Thus, some apparent successes are realized because of good fortune rather than good processes, and this research intends to bring attention to these events, the near-misses. The processes that create these near-misses could pose a threat if multiple contributing factors combine in adverse ways without the intervention of good fortune. Yet, near-misses (if recognized as such) can, theoretically, offer a mechanism for continuing safety improvements, above and beyond learning gleaned from observable failure. We test whether or not this learning is apparent in the airline industry. Using data from 1990 to 2007, fixed effects Poisson regressions show that airlines learn from accidents (their own and others), and from one category of near-misses-those where the possible dangers are salient. Unfortunately, airlines do not improve following near-miss incidents when the focal event has no clear warnings of significant danger. Therefore, while airlines need to and can learn from certain near-misses, we conclude with recommendations for improving airline learning from all near-misses. © 2015 Society for Risk Analysis.

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.

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.

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.

The other side of comparative genomics: genes with no orthologs between the cow and other mammalian species

Directory of Open Access Journals (Sweden)

Ajmone-Marsan Paolo

2009-12-01

Full Text Available Abstract Background With the rapid growth in the availability of genome sequence data, the automated identification of orthologous genes between species (orthologs is of fundamental importance to facilitate functional annotation and studies on comparative and evolutionary genomics. Genes with no apparent orthologs between the bovine and human genome may be responsible for major differences between the species, however, such genes are often neglected in functional genomics studies. Results A BLAST-based method was exploited to explore the current annotation and orthology predictions in Ensembl. Genes with no orthologs between the two genomes were classified into groups based on alignments, ontology, manual curation and publicly available information. Starting from a high quality and specific set of orthology predictions, as provided by Ensembl, hidden relationship between genes and genomes of different mammalian species were unveiled using a highly sensitive approach, based on sequence similarity and genomic comparison. Conclusions The analysis identified 3,801 bovine genes with no orthologs in human and 1010 human genes with no orthologs in cow, among which 411 and 43 genes, respectively, had no match at all in the other species. Most of the apparently non-orthologous genes may potentially have orthologs which were missed in the annotation process, despite having a high percentage of identity, because of differences in gene length and structure. The comparative analysis reported here identified gene variants, new genes and species-specific features and gave an overview of the other side of orthology which may help to improve the annotation of the bovine genome and the knowledge of structural differences between species.

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…

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....

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.

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.

Patterns of genomic variation in the poplar rust fungus Melampsora larici-populina identify pathogenesis-related factors

Directory of Open Access Journals (Sweden)

Antoine ePersoons

2014-09-01

Full Text Available Melampsora larici-populina is a fungal pathogen responsible for foliar rust disease on poplar trees, which causes damage to forest plantations worldwide, particularly in Northern Europe. The reference genome of the isolate 98AG31 was previously sequenced using a whole genome shotgun strategy, revealing a large genome of 101 megabases containing 16,399 predicted genes, which included secreted protein genes representing poplar rust candidate effectors. In the present study, the genomes of 15 isolates collected over the past 20 years throughout the French territory, representing distinct virulence profiles, were characterized by massively parallel sequencing to assess genetic variation in the poplar rust fungus. Comparison to the reference genome revealed striking structural variations. Analysis of coverage and sequencing depth identified large missing regions between isolates related to the mating type loci. More than 611,824 single-nucleotide polymorphism (SNP positions were uncovered overall, indicating a remarkable level of polymorphism. Based on the accumulation of non-synonymous substitutions in coding sequences and the relative frequencies of synonymous and non-synonymous polymorphisms (i.e. PN/PS, we identify candidate genes that may be involved in fungal pathogenesis. Correlation between non-synonymous SNPs in genes encoding secreted proteins and pathotypes of the studied isolates revealed candidate genes potentially related to virulences 1, 6 and 8 of the poplar rust fungus.

Interpolation of Missing Precipitation Data Using Kernel Estimations for Hydrologic Modeling

Directory of Open Access Journals (Sweden)

Hyojin Lee

2015-01-01

Full Text Available Precipitation is the main factor that drives hydrologic modeling; therefore, missing precipitation data can cause malfunctions in hydrologic modeling. Although interpolation of missing precipitation data is recognized as an important research topic, only a few methods follow a regression approach. In this study, daily precipitation data were interpolated using five different kernel functions, namely, Epanechnikov, Quartic, Triweight, Tricube, and Cosine, to estimate missing precipitation data. This study also presents an assessment that compares estimation of missing precipitation data through Kth nearest neighborhood (KNN regression to the five different kernel estimations and their performance in simulating streamflow using the Soil Water Assessment Tool (SWAT hydrologic model. The results show that the kernel approaches provide higher quality interpolation of precipitation data compared with the KNN regression approach, in terms of both statistical data assessment and hydrologic modeling performance.

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.

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.

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.

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 ...

A New Missing Values Estimation Algorithm in Wireless Sensor Networks Based on Convolution

Directory of Open Access Journals (Sweden)

Feng Liu

2013-04-01

Full Text Available Nowadays, with the rapid development of Internet of Things (IoT applications, data missing phenomenon becomes very common in wireless sensor networks. This problem can greatly and directly threaten the stability and usability of the Internet of things applications which are constructed based on wireless sensor networks. How to estimate the missing value has attracted wide interest, and some solutions have been proposed. Different with the previous works, in this paper, we proposed a new convolution based missing value estimation algorithm. The convolution theory, which is usually used in the area of signal and image processing, can also be a practical and efficient way to estimate the missing sensor data. The results show that the proposed algorithm in this paper is practical and effective, and can estimate the missing value accurately.

Fatty acid synthesis in Xylella fastidiosa: correlations between genome studies, 13C NMR data, and molecular models

International Nuclear Information System (INIS)

Osiro, Denise; Muniz, Joao Renato C.; Coleta Filho, Helvecio Della; Alves de Sousa, Alessandra; Machado, Marcos Antonio; Garratt, Richard C.; Colnago, Luiz Alberto

2004-01-01

Xylella fastidiosa was the first plant pathogen to have its complete genome sequence elucidated. Routine database analyses suggested that two enzymes essential for fatty acid synthesis were missing, one of these is the holo-acyl-carrier-protein synthase. However, here we demonstrate, using 13 C NMR spectroscopy, that X. fastidiosa is indeed able to synthesize fatty acids from acetate via an apparently conventional metabolic pathway. We further identify a gene product HetI, an alternative phosphopantetheinyl transferase, which we propose to fill the missing link. Homology modeling of HetI shows conservation of the Coenzyme A binding site suggesting it to be an active enzyme and reveals several interesting structural features when compared with the surfactin synthase-activating enzyme, on which the model was built. These include a simplified topology due to N- and C-terminal deletions and the observation of a novel serine ladder

Predictors of missed appointments in patients referred for congenital or pediatric cardiac magnetic resonance

Energy Technology Data Exchange (ETDEWEB)

Lu, Jimmy C.; Dorfman, Adam L. [C.S. Mott Children' s Hospital, Department of Pediatrics and Communicable Diseases, Division of Pediatric Cardiology, University of Michigan Health System, University of Michigan Congenital Heart Center, Ann Arbor, MI (United States); C.S. Mott Children' s Hospital, Department of Radiology, University of Michigan Health System, Section of Pediatric Radiology, Ann Arbor, MI (United States); Lowery, Ray; Yu, Sunkyung [C.S. Mott Children' s Hospital, Department of Pediatrics and Communicable Diseases, Division of Pediatric Cardiology, University of Michigan Health System, University of Michigan Congenital Heart Center, Ann Arbor, MI (United States); Ghadimi Mahani, Maryam [C.S. Mott Children' s Hospital, Department of Radiology, University of Michigan Health System, Section of Pediatric Radiology, Ann Arbor, MI (United States); Agarwal, Prachi P. [University of Michigan Health System, Department of Radiology, Division of Cardiothoracic Radiology, Ann Arbor, MI (United States)

2017-07-15

Congenital cardiac magnetic resonance is a limited resource because of scanner and physician availability. Missed appointments decrease scheduling efficiency, have financial implications and represent missed care opportunities. To characterize the rate of missed appointments and identify modifiable predictors. This single-center retrospective study included all patients with outpatient congenital or pediatric cardiac MR appointments from Jan. 1, 2014, through Dec. 31, 2015. We identified missed appointments (no-shows or same-day cancellations) from the electronic medical record. We obtained demographic and clinical factors from the medical record and assessed socioeconomic factors by U.S. Census block data by patient ZIP code. Statistically significant variables (P<0.05) were included into a multivariable analysis. Of 795 outpatients (median age 18.5 years, interquartile range 13.4-27.1 years) referred for congenital cardiac MR, a total of 91 patients (11.4%) missed appointments; 28 (3.5%) missed multiple appointments. Reason for missed appointment could be identified in only 38 patients (42%), but of these, 28 (74%) were preventable or could have been identified prior to the appointment. In multivariable analysis, independent predictors of missed appointments were referral by a non-cardiologist (adjusted odds ratio [AOR] 5.8, P=0.0002), referral for research (AOR 3.6, P=0.01), having public insurance (AOR 2.1, P=0.004), and having scheduled cardiac MR from November to April (AOR 1.8, P=0.01). Demographic factors can identify patients at higher risk for missing appointments. These data may inform initiatives to limit missed appointments, such as targeted education of referring providers and patients. Further data are needed to evaluate the efficacy of potential interventions. (orig.)

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).

Bone scan as a screening test for missed fractures in severely injured patients.

Science.gov (United States)

Lee, K-J; Jung, K; Kim, J; Kwon, J

2014-12-01

In many cases, patients with severe blunt trauma have multiple fractures throughout the body. These fractures are not often detectable by history or physical examination, and their diagnosis can be delayed or even missed. Thus, screening test fractures of the whole body is required after initial management. We performed this study to evaluate the reliability of bone scans for detecting missed fractures in patients with multiple severe traumas and we analyzed the causes of missed fractures by using bone scan. A bone scan is useful as a screening test for fractures of the entire body of severe trauma patients who are passed the acute phase. We reviewed the electronic medical records of severe trauma patients who underwent a bone scan from September 2009 to December 2010. Demographic and medical data were compared and statistically analyzed to determine whether missed fractures were detected after bone scan in the two groups. A total of 382 patients who had an injury severity score [ISS] greater than 16 points with multiple traumas visited the emergency room. One hundred and thirty-one patients underwent bone scan and 81 patients were identified with missed fractures by bone scan. The most frequent location for missed fractures was the rib area (55 cases, 41.98%), followed by the extremities (42 cases, 32.06%). The missed fractures that required surgery or splint were most common in extremities (11 cases). In univariate analysis, higher ISS scores and mechanism of injury were related with the probability that missed fractures would be found with a bone scan. The ISS score was statistically significant in multivariate analysis. Bone scan is an effective method of detecting missed fractures among patients with multiple severe traumas. Level IV, retrospective study. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

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)

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.  

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.

Past and future implications of near-misses and their emotional consequences.

Science.gov (United States)

Zhang, Qiyuan; Covey, Judith

2014-01-01

The Reflection and Evaluation Model (REM) of comparative thinking predicts that temporal perspective could moderate people's emotional reactions to close counterfactuals following near-misses (Markman & McMullen, 2003). The experiments reported in this paper tested predictions derived from this theory by examining how people's emotional reactions to a near-miss at goal during a football match (Experiment 1) or a close score in a TV game show (Experiment 2) depended on the level of perceived future possibility. In support of the theory it was found that the presence of future possibility enhanced affective assimilation (e.g., if the near-miss occurred at the beginning of the game the players who had nearly scored were hopeful of future success) whereas the absence of future possibility enhanced affective contrast (e.g., if the near-miss occurred at the end of the game the players who had nearly scored were disappointed about missing an opportunity). Furthermore the experiments built upon our theoretical understanding by exploring the mechanisms which produce assimilation and contrast effects. In Experiment 1 we examined the incidence of present-oriented or future-oriented thinking, and in Experiment 2 we examined the mediating role of counterfactual thinking in the observed effect of proximity on emotions by testing whether stronger counterfactuals (measured using counterfactual probability estimates) produce bigger contrast and assimilation effects. While the results of these investigations generally support the REM, they also highlight the necessity to consider other psychological mechanisms (e.g., social comparison), in addition to counterfactual thinking, that might contribute to the emotional consequences of near-miss outcomes.

Genome-wide search for gene-gene interactions in colorectal cancer.

Directory of Open Access Journals (Sweden)

Shuo Jiao

Full Text Available Genome-wide association studies (GWAS have successfully identified a number of single-nucleotide polymorphisms (SNPs associated with colorectal cancer (CRC risk. However, these susceptibility loci known today explain only a small fraction of the genetic risk. Gene-gene interaction (GxG is considered to be one source of the missing heritability. To address this, we performed a genome-wide search for pair-wise GxG associated with CRC risk using 8,380 cases and 10,558 controls in the discovery phase and 2,527 cases and 2,658 controls in the replication phase. We developed a simple, but powerful method for testing interaction, which we term the Average Risk Due to Interaction (ARDI. With this method, we conducted a genome-wide search to identify SNPs showing evidence for GxG with previously identified CRC susceptibility loci from 14 independent regions. We also conducted a genome-wide search for GxG using the marginal association screening and examining interaction among SNPs that pass the screening threshold (p<10(-4. For the known locus rs10795668 (10p14, we found an interacting SNP rs367615 (5q21 with replication p = 0.01 and combined p = 4.19×10(-8. Among the top marginal SNPs after LD pruning (n = 163, we identified an interaction between rs1571218 (20p12.3 and rs10879357 (12q21.1 (nominal combined p = 2.51×10(-6; Bonferroni adjusted p = 0.03. Our study represents the first comprehensive search for GxG in CRC, and our results may provide new insight into the genetic etiology of CRC.

Comparison of methods for genomic localization of gene trap sequences

Directory of Open Access Journals (Sweden)

Ferrin Thomas E

2006-09-01

Full Text Available Abstract Background Gene knockouts in a model organism such as mouse provide a valuable resource for the study of basic biology and human disease. Determining which gene has been inactivated by an untargeted gene trapping event poses a challenging annotation problem because gene trap sequence tags, which represent sequence near the vector insertion site of a trapped gene, are typically short and often contain unresolved residues. To understand better the localization of these sequences on the mouse genome, we compared stand-alone versions of the alignment programs BLAT, SSAHA, and MegaBLAST. A set of 3,369 sequence tags was aligned to build 34 of the mouse genome using default parameters for each algorithm. Known genome coordinates for the cognate set of full-length genes (1,659 sequences were used to evaluate localization results. Results In general, all three programs performed well in terms of localizing sequences to a general region of the genome, with only relatively subtle errors identified for a small proportion of the sequence tags. However, large differences in performance were noted with regard to correctly identifying exon boundaries. BLAT correctly identified the vast majority of exon boundaries, while SSAHA and MegaBLAST missed the majority of exon boundaries. SSAHA consistently reported the fewest false positives and is the fastest algorithm. MegaBLAST was comparable to BLAT in speed, but was the most susceptible to localizing sequence tags incorrectly to pseudogenes. Conclusion The differences in performance for sequence tags and full-length reference sequences were surprisingly small. Characteristic variations in localization results for each program were noted that affect the localization of sequence at exon boundaries, in particular.

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.

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

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.

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.

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 ...

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.

Bacillus anthracis genome organization in light of whole transcriptome sequencing

Energy Technology Data Exchange (ETDEWEB)

Martin, Jeffrey; Zhu, Wenhan; Passalacqua, Karla D.; Bergman, Nicholas; Borodovsky, Mark

2010-03-22

Emerging knowledge of whole prokaryotic transcriptomes could validate a number of theoretical concepts introduced in the early days of genomics. What are the rules connecting gene expression levels with sequence determinants such as quantitative scores of promoters and terminators? Are translation efficiency measures, e.g. codon adaptation index and RBS score related to gene expression? We used the whole transcriptome shotgun sequencing of a bacterial pathogen Bacillus anthracis to assess correlation of gene expression level with promoter, terminator and RBS scores, codon adaptation index, as well as with a new measure of gene translational efficiency, average translation speed. We compared computational predictions of operon topologies with the transcript borders inferred from RNA-Seq reads. Transcriptome mapping may also improve existing gene annotation. Upon assessment of accuracy of current annotation of protein-coding genes in the B. anthracis genome we have shown that the transcriptome data indicate existence of more than a hundred genes missing in the annotation though predicted by an ab initio gene finder. Interestingly, we observed that many pseudogenes possess not only a sequence with detectable coding potential but also promoters that maintain transcriptional activity.

Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs).

Science.gov (United States)

Natale, D A; Shankavaram, U T; Galperin, M Y; Wolf, Y I; Aravind, L; Koonin, E V

2000-01-01

Standard archival sequence databases have not been designed as tools for genome annotation and are far from being optimal for this purpose. We used the database of Clusters of Orthologous Groups of proteins (COGs) to reannotate the genomes of two archaea, Aeropyrum pernix, the first member of the Crenarchaea to be sequenced, and Pyrococcus abyssi. A. pernix and P. abyssi proteins were assigned to COGs using the COGNITOR program; the results were verified on a case-by-case basis and augmented by additional database searches using the PSI-BLAST and TBLASTN programs. Functions were predicted for over 300 proteins from A. pernix, which could not be assigned a function using conventional methods with a conservative sequence similarity threshold, an approximately 50% increase compared to the original annotation. A. pernix shares most of the conserved core of proteins that were previously identified in the Euryarchaeota. Cluster analysis or distance matrix tree construction based on the co-occurrence of genomes in COGs showed that A. pernix forms a distinct group within the archaea, although grouping with the two species of Pyrococci, indicative of similar repertoires of conserved genes, was observed. No indication of a specific relationship between Crenarchaeota and eukaryotes was obtained in these analyses. Several proteins that are conserved in Euryarchaeota and most bacteria are unexpectedly missing in A. pernix, including the entire set of de novo purine biosynthesis enzymes, the GTPase FtsZ (a key component of the bacterial and euryarchaeal cell-division machinery), and the tRNA-specific pseudouridine synthase, previously considered universal. A. pernix is represented in 48 COGs that do not contain any euryarchaeal members. Many of these proteins are TCA cycle and electron transport chain enzymes, reflecting the aerobic lifestyle of A. pernix. Special-purpose databases organized on the basis of phylogenetic analysis and carefully curated with respect to known and

Applying modern error theory to the problem of missed injuries in trauma.

Science.gov (United States)

Clarke, D L; Gouveia, J; Thomson, S R; Muckart, D J J

2008-06-01

Modern theory of human error has helped reduce the incidence of adverse events in commercial aviation. It remains unclear whether these lessons are applicable to adverse events in trauma surgery. Missed injuries in a large metropolitan surgical service were prospectively audited and analyzed using a modern error taxonomy to define its applicability to trauma. A prospective database of all patients who experienced a missed injury during a 6-month period in a busy surgical service was maintained from July 2006. A missed injury was defined as one that escaped detection from primary assessment to operative exploration. Each missed injury was recorded and categorized. The clinical significance of the error and the level of physician responsible was documented. Errors were divided into planning or execution errors, acts of omission or commission, or violations, slips, and lapses. A total of 1,024 trauma patients were treated by the surgical services over the 6-month period from July to December 2006 in Pietermaritzburg. Thirty-four patients (2.5%) with missed injuries were identified during this period. There were 29 men and 5 women with an average age of 29 years (range: 21-67 years). In 14 patients, errors were related to inadequate clinical assessment. In 11 patients errors involved the misinterpretation of, or failure to respond to radiological imaging. There were 9 cases in which an injury was missed during surgical exploration. Overall mortality was 27% (9 patients). In 5 cases death was directly attributable to the missed injury. The level of the physicians making the error was consultant surgeon (4 cases), resident in training (15 cases), career medical officer (2 cases), referring doctor (6 cases). Missed injuries are uncommon and are made by all grades of staff. They are associated with increased morbidity and mortality. Understanding the pattern of these errors may help develop error-reduction strategies. Current taxonomies help in understanding the error

FORESEE: Fully Outsourced secuRe gEnome Study basEd on homomorphic Encryption.

Science.gov (United States)

Zhang, Yuchen; Dai, Wenrui; Jiang, Xiaoqian; Xiong, Hongkai; Wang, Shuang

2015-01-01

The increasing availability of genome data motivates massive research studies in personalized treatment and precision medicine. Public cloud services provide a flexible way to mitigate the storage and computation burden in conducting genome-wide association studies (GWAS). However, data privacy has been widely concerned when sharing the sensitive information in a cloud environment. We presented a novel framework (FORESEE: Fully Outsourced secuRe gEnome Study basEd on homomorphic Encryption) to fully outsource GWAS (i.e., chi-square statistic computation) using homomorphic encryption. The proposed framework enables secure divisions over encrypted data. We introduced two division protocols (i.e., secure errorless division and secure approximation division) with a trade-off between complexity and accuracy in computing chi-square statistics. The proposed framework was evaluated for the task of chi-square statistic computation with two case-control datasets from the 2015 iDASH genome privacy protection challenge. Experimental results show that the performance of FORESEE can be significantly improved through algorithmic optimization and parallel computation. Remarkably, the secure approximation division provides significant performance gain, but without missing any significance SNPs in the chi-square association test using the aforementioned datasets. Unlike many existing HME based studies, in which final results need to be computed by the data owner due to the lack of the secure division operation, the proposed FORESEE framework support complete outsourcing to the cloud and output the final encrypted chi-square statistics.

A genomic background based method for association analysis in related individuals.

Directory of Open Access Journals (Sweden)

Najaf Amin

Full Text Available BACKGROUND: Feasibility of genotyping of hundreds and thousands of single nucleotide polymorphisms (SNPs in thousands of study subjects have triggered the need for fast, powerful, and reliable methods for genome-wide association analysis. Here we consider a situation when study participants are genetically related (e.g. due to systematic sampling of families or because a study was performed in a genetically isolated population. Of the available methods that account for relatedness, the Measured Genotype (MG approach is considered the 'gold standard'. However, MG is not efficient with respect to time taken for the analysis of genome-wide data. In this context we proposed a fast two-step method called Genome-wide Association using Mixed Model and Regression (GRAMMAR for the analysis of pedigree-based quantitative traits. This method certainly overcomes the drawback of time limitation of the measured genotype (MG approach, but pays in power. One of the major drawbacks of both MG and GRAMMAR, is that they crucially depend on the availability of complete and correct pedigree data, which is rarely available. METHODOLOGY: In this study we first explore type 1 error and relative power of MG, GRAMMAR, and Genomic Control (GC approaches for genetic association analysis. Secondly, we propose an extension to GRAMMAR i.e. GRAMMAR-GC. Finally, we propose application of GRAMMAR-GC using the kinship matrix estimated through genomic marker data, instead of (possibly missing and/or incorrect genealogy. CONCLUSION: Through simulations we show that MG approach maintains high power across a range of heritabilities and possible pedigree structures, and always outperforms other contemporary methods. We also show that the power of our proposed GRAMMAR-GC approaches to that of the 'gold standard' MG for all models and pedigrees studied. We show that this method is both feasible and powerful and has correct type 1 error in the context of genome-wide association analysis

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

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

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…

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.

The Network Completion Problem: Inferring Missing Nodes and Edges in Networks

Energy Technology Data Exchange (ETDEWEB)

Kim, M; Leskovec, J

2011-11-14

Network structures, such as social networks, web graphs and networks from systems biology, play important roles in many areas of science and our everyday lives. In order to study the networks one needs to first collect reliable large scale network data. While the social and information networks have become ubiquitous, the challenge of collecting complete network data still persists. Many times the collected network data is incomplete with nodes and edges missing. Commonly, only a part of the network can be observed and we would like to infer the unobserved part of the network. We address this issue by studying the Network Completion Problem: Given a network with missing nodes and edges, can we complete the missing part? We cast the problem in the Expectation Maximization (EM) framework where we use the observed part of the network to fit a model of network structure, and then we estimate the missing part of the network using the model, re-estimate the parameters and so on. We combine the EM with the Kronecker graphs model and design a scalable Metropolized Gibbs sampling approach that allows for the estimation of the model parameters as well as the inference about missing nodes and edges of the network. Experiments on synthetic and several real-world networks show that our approach can effectively recover the network even when about half of the nodes in the network are missing. Our algorithm outperforms not only classical link-prediction approaches but also the state of the art Stochastic block modeling approach. Furthermore, our algorithm easily scales to networks with tens of thousands of nodes.

On the Counterfactual Nature of Gambling Near‐misses: An Experimental Study

Science.gov (United States)

van Dijk, Eric; Li, Hong; Aitken, Michael; Clark, Luke

2017-01-01

Abstract Research on gambling near‐misses has shown that objectively equivalent outcomes can yield divergent emotional and motivational responses. The subjective processing of gambling outcomes is affected substantially by close but non‐obtained outcomes (i.e. counterfactuals). In the current paper, we investigate how different types of near‐misses influence self‐perceived luck and subsequent betting behavior in a wheel‐of‐fortune task. We investigate the counterfactual mechanism of these effects by testing the relationship with a second task measuring regret/relief processing. Across two experiments (Experiment 1, n = 51; Experiment 2, n = 104), we demonstrate that near‐wins (neutral outcomes that are close to a jackpot) decreased self‐perceived luck, whereas near‐losses (neutral outcomes that are close to a major penalty) increased luck ratings. The effects of near‐misses varied by near‐miss position (i.e. whether the spinner stopped just short of, or passed through, the counterfactual outcome), consistent with established distinctions between upward versus downward, and additive versus subtractive, counterfactual thinking. In Experiment 1, individuals who showed stronger counterfactual processing on the regret/relief task were more responsive to near‐wins and near‐losses on the wheel‐of‐fortune task. The effect of near‐miss position was attenuated when the anticipatory phase (i.e. the spin and deceleration) was removed in Experiment 2. Further differences were observed within the objective gains and losses, between “clear” and “narrow” outcomes. Taken together, these results help substantiate the counterfactual mechanism of near‐misses. © 2017 The Authors Journal of Behavioral Decision Making Published by John Wiley & Sons Ltd. PMID:29081596

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-...

Cognitive distortions and gambling near-misses in Internet Gaming Disorder: A preliminary study.

Directory of Open Access Journals (Sweden)

Yin Wu

Full Text Available Increased cognitive distortions (i.e. biased processing of chance, probability and skill are a key psychopathological process in disordered gambling. The present study investigated state and trait aspects of cognitive distortions in 22 individuals with Internet Gaming Disorder (IGD and 22 healthy controls. Participants completed the Gambling Related Cognitions Scale as a trait measure of cognitive distortions, and played a slot machine task delivering wins, near-misses and full-misses. Ratings of pleasure ("liking" and motivation to play ("wanting" were taken following the different outcomes, and gambling persistence was measured after a mandatory phase. IGD was associated with elevated trait cognitive distortions, in particular skill-oriented cognitions. On the slot machine task, the IGD group showed increased "wanting" ratings compared with control participants, while the two groups did not differ regarding their "liking" of the game. The IGD group displayed increased persistence on the slot machine task. Near-miss outcomes did not elicit stronger motivation to play compared to full-miss outcomes overall, and there was no group difference on this measure. However, a near-miss position effect was observed, such that near-misses stopping before the payline were rated as more motivating than near-misses that stopped after the payline, and this differentiation was attenuated in the IGD group, suggesting possible counterfactual thinking deficits in this group. These data provide preliminary evidence for increased incentive motivation and cognitive distortions in IGD, at least in the context of a chance-based gambling environment.

Cognitive distortions and gambling near-misses in Internet Gaming Disorder: A preliminary study.

Science.gov (United States)

Wu, Yin; Sescousse, Guillaume; Yu, Hongbo; Clark, Luke; Li, Hong

2018-01-01

Increased cognitive distortions (i.e. biased processing of chance, probability and skill) are a key psychopathological process in disordered gambling. The present study investigated state and trait aspects of cognitive distortions in 22 individuals with Internet Gaming Disorder (IGD) and 22 healthy controls. Participants completed the Gambling Related Cognitions Scale as a trait measure of cognitive distortions, and played a slot machine task delivering wins, near-misses and full-misses. Ratings of pleasure ("liking") and motivation to play ("wanting") were taken following the different outcomes, and gambling persistence was measured after a mandatory phase. IGD was associated with elevated trait cognitive distortions, in particular skill-oriented cognitions. On the slot machine task, the IGD group showed increased "wanting" ratings compared with control participants, while the two groups did not differ regarding their "liking" of the game. The IGD group displayed increased persistence on the slot machine task. Near-miss outcomes did not elicit stronger motivation to play compared to full-miss outcomes overall, and there was no group difference on this measure. However, a near-miss position effect was observed, such that near-misses stopping before the payline were rated as more motivating than near-misses that stopped after the payline, and this differentiation was attenuated in the IGD group, suggesting possible counterfactual thinking deficits in this group. These data provide preliminary evidence for increased incentive motivation and cognitive distortions in IGD, at least in the context of a chance-based gambling environment.

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…

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 ...

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.

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.

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

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....

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

Comparative genome analysis of non-toxigenic non-O1 versus toxigenic O1 Vibrio cholerae

Science.gov (United States)

Mukherjee, Munmun; Kakarla, Prathusha; Kumar, Sanath; Gonzalez, Esmeralda; Floyd, Jared T.; Inupakutika, Madhuri; Devireddy, Amith Reddy; Tirrell, Selena R.; Bruns, Merissa; He, Guixin; Lindquist, Ingrid E.; Sundararajan, Anitha; Schilkey, Faye D.; Mudge, Joann; Varela, Manuel F.

2015-01-01

Pathogenic strains of Vibrio cholerae are responsible for endemic and pandemic outbreaks of the disease cholera. The complete toxigenic mechanisms underlying virulence in Vibrio strains are poorly understood. The hypothesis of this work was that virulent versus non-virulent strains of V. cholerae harbor distinctive genomic elements that encode virulence. The purpose of this study was to elucidate genomic differences between the O1 serotypes and non-O1 V. cholerae PS15, a non-toxigenic strain, in order to identify novel genes potentially responsible for virulence. In this study, we compared the whole genome of the non-O1 PS15 strain to the whole genomes of toxigenic serotypes at the phylogenetic level, and found that the PS15 genome was distantly related to those of toxigenic V. cholerae. Thus we focused on a detailed gene comparison between PS15 and the distantly related O1 V. cholerae N16961. Based on sequence alignment we tentatively assigned chromosome numbers 1 and 2 to elements within the genome of non-O1 V. cholerae PS15. Further, we found that PS15 and O1 V. cholerae N16961 shared 98% identity and 766 genes, but of the genes present in N16961 that were missing in the non-O1 V. cholerae PS15 genome, 56 were predicted to encode not only for virulence–related genes (colonization, antimicrobial resistance, and regulation of persister cells) but also genes involved in the metabolic biosynthesis of lipids, nucleosides and sulfur compounds. Additionally, we found 113 genes unique to PS15 that were predicted to encode other properties related to virulence, disease, defense, membrane transport, and DNA metabolism. Here, we identified distinctive and novel genomic elements between O1 and non-O1 V. cholerae genomes as potential virulence factors and, thus, targets for future therapeutics. Modulation of such novel targets may eventually enhance eradication efforts of endemic and pandemic disease cholera in afflicted nations. PMID:25722857

Including α s1 casein gene information in genomic evaluations of French dairy goats.

Science.gov (United States)

Carillier-Jacquin, Céline; Larroque, Hélène; Robert-Granié, Christèle

2016-08-04

Genomic best linear unbiased prediction methods assume that all markers explain the same fraction of the genetic variance and do not account effectively for genes with major effects such as the α s1 casein polymorphism in dairy goats. In this study, we investigated methods to include the available α s1 casein genotype effect in genomic evaluations of French dairy goats. First, the α s1 casein genotype was included as a fixed effect in genomic evaluation models based only on bucks that were genotyped at the α s1 casein locus. Less than 1 % of the females with phenotypes were genotyped at the α s1 casein gene. Thus, to incorporate these female phenotypes in the genomic evaluation, two methods that allowed for this large number of missing α s1 casein genotypes were investigated. Probabilities for each possible α s1 casein genotype were first estimated for each female of unknown genotype based on iterative peeling equations. The second method is based on a multiallelic gene content approach. For each model tested, we used three datasets each divided into a training and a validation set: (1) two-breed population (Alpine + Saanen), (2) Alpine population, and (3) Saanen population. The α s1 casein genotype had a significant effect on milk yield, fat content and protein content. Including an α s1 casein effect in genetic and genomic evaluations based only on male known α s1 casein genotypes improved accuracies (from 6 to 27 %). In genomic evaluations based on all female phenotypes, the gene content approach performed better than the other tested methods but the improvement in accuracy was only slightly better (from 1 to 14 %) than that of a genomic model without the α s1 casein effect. Including the α s1 casein effect in a genomic evaluation model for French dairy goats is possible and useful to improve accuracy. Difficulties in predicting the genotypes for ungenotyped animals limited the improvement in accuracy of the obtained estimated breeding values.

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.

Satisfaction in motion: Subsequent search misses are more likely in moving search displays.

Science.gov (United States)

Stothart, Cary; Clement, Andrew; Brockmole, James R

2018-02-01

People often conduct visual searches in which multiple targets are possible (e.g., medical X-rays can contain multiple abnormalities). In this type of search, observers are more likely to miss a second target after having found a first one (a subsequent search miss). Recent evidence has suggested that this effect may be due to a depletion of cognitive resources from tracking the identities and locations of found targets. Given that tracking moving objects is resource-demanding, would finding a moving target further increase the chances of missing a subsequent one? To address this question, we had participants search for one or more targets hidden among distractors. Subsequent search misses were more likely when the targets and distractors moved throughout the display than when they remained stationary. However, when the found targets were highlighted in a unique color, subsequent search misses were no more likely in moving displays. Together, these results suggest that the effect of movement is likely due to the increased cognitive demands of tracking moving targets. Overall, our findings reveal that activities that involve searching for moving targets (e.g., driving) are more susceptible to subsequent search misses than are those that involve searching for stationary targets (e.g., baggage screening).

Conservation and divergence of ADAM family proteins in the Xenopus genome

Directory of Open Access Journals (Sweden)

Shah Anoop

2010-07-01

Full Text Available Abstract Background Members of the disintegrin metalloproteinase (ADAM family play important roles in cellular and developmental processes through their functions as proteases and/or binding partners for other proteins. The amphibian Xenopus has long been used as a model for early vertebrate development, but genome-wide analyses for large gene families were not possible until the recent completion of the X. tropicalis genome sequence and the availability of large scale expression sequence tag (EST databases. In this study we carried out a systematic analysis of the X. tropicalis genome and uncovered several interesting features of ADAM genes in this species. Results Based on the X. tropicalis genome sequence and EST databases, we identified Xenopus orthologues of mammalian ADAMs and obtained full-length cDNA clones for these genes. The deduced protein sequences, synteny and exon-intron boundaries are conserved between most human and X. tropicalis orthologues. The alternative splicing patterns of certain Xenopus ADAM genes, such as adams 22 and 28, are similar to those of their mammalian orthologues. However, we were unable to identify an orthologue for ADAM7 or 8. The Xenopus orthologue of ADAM15, an active metalloproteinase in mammals, does not contain the conserved zinc-binding motif and is hence considered proteolytically inactive. We also found evidence for gain of ADAM genes in Xenopus as compared to other species. There is a homologue of ADAM10 in Xenopus that is missing in most mammals. Furthermore, a single scaffold of X. tropicalis genome contains four genes encoding ADAM28 homologues, suggesting genome duplication in this region. Conclusions Our genome-wide analysis of ADAM genes in X. tropicalis revealed both conservation and evolutionary divergence of these genes in this amphibian species. On the one hand, all ADAMs implicated in normal development and health in other species are conserved in X. tropicalis. On the other hand, some

Professional experience and traffic accidents/near-miss accidents among truck drivers.

Science.gov (United States)

Girotto, Edmarlon; Andrade, Selma Maffei de; González, Alberto Durán; Mesas, Arthur Eumann

2016-10-01

To investigate the relationship between the time working as a truck driver and the report of involvement in traffic accidents or near-miss accidents. A cross-sectional study was performed with truck drivers transporting products from the Brazilian grain harvest to the Port of Paranaguá, Paraná, Brazil. The drivers were interviewed regarding sociodemographic characteristics, working conditions, behavior in traffic and involvement in accidents or near-miss accidents in the previous 12 months. Subsequently, the participants answered a self-applied questionnaire on substance use. The time of professional experience as drivers was categorized in tertiles. Statistical analyses were performed through the construction of models adjusted by multinomial regression to assess the relationship between the length of experience as a truck driver and the involvement in accidents or near-miss accidents. This study included 665 male drivers with an average age of 42.2 (±11.1) years. Among them, 7.2% and 41.7% of the drivers reported involvement in accidents and near-miss accidents, respectively. In fully adjusted analysis, the 3rd tertile of professional experience (>22years) was shown to be inversely associated with involvement in accidents (odds ratio [OR] 0.29; 95% confidence interval [CI] 0.16-0.52) and near-miss accidents (OR 0.17; 95% CI 0.05-0.53). The 2nd tertile of professional experience (11-22 years) was inversely associated with involvement in accidents (OR 0.63; 95% CI 0.40-0.98). An evident relationship was observed between longer professional experience and a reduction in reporting involvement in accidents and near-miss accidents, regardless of age, substance use, working conditions and behavior in traffic. Copyright © 2016 Elsevier Ltd. All rights reserved.

Ma_MISS on ExoMars: Mineralogical Characterization of the Martian Subsurface

Science.gov (United States)

De Sanctis, Maria Cristina; Altieri, Francesca; Ammannito, Eleonora; Biondi, David; De Angelis, Simone; Meini, Marco; Mondello, Giuseppe; Novi, Samuele; Paolinetti, Riccardo; Soldani, Massimo; Mugnuolo, Raffaele; Pirrotta, Simone; Vago, Jorge L.; Ma_MISS Team

2017-07-01

The Ma_MISS (Mars Multispectral Imager for Subsurface Studies) experiment is the visible and near infrared (VNIR) miniaturized spectrometer hosted by the drill system of the ExoMars 2020 rover. Ma_MISS will perform IR spectral reflectance investigations in the 0.4-2.2 μm range to characterize the mineralogy of excavated borehole walls at different depths (between 0 and 2 m). The spectral sampling is about 20 nm, whereas the spatial resolution over the target is 120 μm. Making use of the drill's movement, the instrument slit can scan a ring and build up hyperspectral images of a borehole. The main goal of the Ma_MISS instrument is to study the martian subsurface environment. Access to the martian subsurface is crucial to our ability to constrain the nature, timing, and duration of alteration and sedimentation processes on Mars, as well as habitability conditions. Subsurface deposits likely host and preserve H2O ice and hydrated materials that will contribute to our understanding of the H2O geochemical environment (both in the liquid and in the solid state) at the ExoMars 2020 landing site. The Ma_MISS spectral range and sampling capabilities have been carefully selected to allow the study of minerals and ices in situ before the collection of samples. Ma_MISS will be implemented to accomplish the following scientific objectives: (1) determine the composition of subsurface materials, (2) map the distribution of subsurface H2O and volatiles, (3) characterize important optical and physical properties of materials (e.g., grain size), and (4) produce a stratigraphic column that will inform with regard to subsurface geological processes. The Ma_MISS findings will help to refine essential criteria that will aid in our selection of the most interesting subsurface formations from which to collect samples.

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.

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…

Dealing with missing data in a multi-question depression scale: a comparison of imputation methods

Directory of Open Access Journals (Sweden)

Stuart Heather

2006-12-01

Full Text Available Abstract Background Missing data present a challenge to many research projects. The problem is often pronounced in studies utilizing self-report scales, and literature addressing different strategies for dealing with missing data in such circumstances is scarce. The objective of this study was to compare six different imputation techniques for dealing with missing data in the Zung Self-reported Depression scale (SDS. Methods 1580 participants from a surgical outcomes study completed the SDS. The SDS is a 20 question scale that respondents complete by circling a value of 1 to 4 for each question. The sum of the responses is calculated and respondents are classified as exhibiting depressive symptoms when their total score is over 40. Missing values were simulated by randomly selecting questions whose values were then deleted (a missing completely at random simulation. Additionally, a missing at random and missing not at random simulation were completed. Six imputation methods were then considered; 1 multiple imputation, 2 single regression, 3 individual mean, 4 overall mean, 5 participant's preceding response, and 6 random selection of a value from 1 to 4. For each method, the imputed mean SDS score and standard deviation were compared to the population statistics. The Spearman correlation coefficient, percent misclassified and the Kappa statistic were also calculated. Results When 10% of values are missing, all the imputation methods except random selection produce Kappa statistics greater than 0.80 indicating 'near perfect' agreement. MI produces the most valid imputed values with a high Kappa statistic (0.89, although both single regression and individual mean imputation also produced favorable results. As the percent of missing information increased to 30%, or when unbalanced missing data were introduced, MI maintained a high Kappa statistic. The individual mean and single regression method produced Kappas in the 'substantial agreement' range

Causal inference with missing exposure information: Methods and applications to an obstetric study.

Science.gov (United States)

Zhang, Zhiwei; Liu, Wei; Zhang, Bo; Tang, Li; Zhang, Jun

2016-10-01

Causal inference in observational studies is frequently challenged by the occurrence of missing data, in addition to confounding. Motivated by the Consortium on Safe Labor, a large observational study of obstetric labor practice and birth outcomes, this article focuses on the problem of missing exposure information in a causal analysis of observational data. This problem can be approached from different angles (i.e. missing covariates and causal inference), and useful methods can be obtained by drawing upon the available techniques and insights in both areas. In this article, we describe and compare a collection of methods based on different modeling assumptions, under standard assumptions for missing data (i.e. missing-at-random and positivity) and for causal inference with complete data (i.e. no unmeasured confounding and another positivity assumption). These methods involve three models: one for treatment assignment, one for the dependence of outcome on treatment and covariates, and one for the missing data mechanism. In general, consistent estimation of causal quantities requires correct specification of at least two of the three models, although there may be some flexibility as to which two models need to be correct. Such flexibility is afforded by doubly robust estimators adapted from the missing covariates literature and the literature on causal inference with complete data, and by a newly developed triply robust estimator that is consistent if any two of the three models are correct. The methods are applied to the Consortium on Safe Labor data and compared in a simulation study mimicking the Consortium on Safe Labor. © The Author(s) 2013.

Missing value imputation in DNA microarrays based on conjugate gradient method.

Science.gov (United States)

Dorri, Fatemeh; Azmi, Paeiz; Dorri, Faezeh

2012-02-01

Analysis of gene expression profiles needs a complete matrix of gene array values; consequently, imputation methods have been suggested. In this paper, an algorithm that is based on conjugate gradient (CG) method is proposed to estimate missing values. k-nearest neighbors of the missed entry are first selected based on absolute values of their Pearson correlation coefficient. Then a subset of genes among the k-nearest neighbors is labeled as the best similar ones. CG algorithm with this subset as its input is then used to estimate the missing values. Our proposed CG based algorithm (CGimpute) is evaluated on different data sets. The results are compared with sequential local least squares (SLLSimpute), Bayesian principle component analysis (BPCAimpute), local least squares imputation (LLSimpute), iterated local least squares imputation (ILLSimpute) and adaptive k-nearest neighbors imputation (KNNKimpute) methods. The average of normalized root mean squares error (NRMSE) and relative NRMSE in different data sets with various missing rates shows CGimpute outperforms other methods. Copyright © 2011 Elsevier Ltd. All rights reserved.

The features of endometrium receptor apparatus in women with missed abortion

Directory of Open Access Journals (Sweden)

Александра Николаевна Тищенко

2015-05-01

Full Text Available A new complex of modern methods of investigation, both the endometrium and immune system changes in local and hormonal status is developed in this article, rehabilitation of reproductive function in patients with the missed abortion is proposed.Methods. The study involved 124 women, including 64 women with diagnosed missed abortion. The comparison group included 30 women with physiological pregnancy who were performed artificial abortion. 30 healthy women in pregravidae period were examined. The clinical and anamnestic, histological and immunological features of the endometrium and its functional activity were investigated.Results. Pathogenetic mechanisms of menstrual dysfunction were defined in women with the missed abortion. The changes in the secretory transformation of the endometrium, a sharp decrease in its receptor and functional activity, confirming the lack of development of the luteal phase are observed. Based on the research, an algorithm for the restoration of menstrual function in women in the postgravidae period is developed and implemented in practice.Conclusions. The data confirmed the feasibility of implementing the proposed examination and treatment of women with the missed abortion

Obstetric near-miss and maternal mortality in maternity university hospital, Damascus, Syria: a retrospective study

Directory of Open Access Journals (Sweden)

Al Chamat Ahmad

2010-10-01

Full Text Available Abstract Background Investigating severe maternal morbidity (near-miss is a newly recognised tool that identifies women at highest risk of maternal death and helps allocate resources especially in low income countries. This study aims to i. document the frequency and nature of maternal near-miss at hospital level in Damascus, Capital of Syria, ii. evaluate the level of care at maternal life-saving emergency services by comparatively analysing near-misses and maternal mortalities. Methods Retrospective facility-based review of cases of near-miss and maternal mortality that took place in the years 2006-2007 at Damascus Maternity University Hospital, Syria. Near-miss cases were defined based on disease-specific criteria (Filippi 2005 including: haemorrhage, hypertensive disorders in pregnancy, dystocia, infection and anaemia. Main outcomes included maternal mortality ratio (MMR, maternal near miss ratio (MNMR, mortality indices and proportion of near-miss cases and mortality cases to hospital admissions. Results There were 28 025 deliveries, 15 maternal deaths and 901 near-miss cases. The study showed a MNMR of 32.9/1000 live births, a MMR of 54.8/100 000 live births and a relatively low mortality index of 1.7%. Hypertensive disorders (52% and haemorrhage (34% were the top causes of near-misses. Late pregnancy haemorrhage was the leading cause of maternal mortality (60% while sepsis had the highest mortality index (7.4%. Most cases (93% were referred in critical conditions from other facilities; namely traditional birth attendants homes (67%, primary (5% and secondary (10% healthcare unites and private practices (11%. 26% of near-miss cases were admitted to Intensive Care Unit (ICU. Conclusion Near-miss analyses provide valuable information on obstetric care. The study highlights the need to improve antenatal care which would help early identification of high risk pregnancies. It also emphasises the importance of both: developing protocols to

Obstetric near-miss and maternal mortality in maternity university hospital, Damascus, Syria: a retrospective study.

Science.gov (United States)

Almerie, Yara; Almerie, Muhammad Q; Matar, Hosam E; Shahrour, Yasser; Al Chamat, Ahmad Abo; Abdulsalam, Asmaa

2010-10-19

Investigating severe maternal morbidity (near-miss) is a newly recognised tool that identifies women at highest risk of maternal death and helps allocate resources especially in low income countries. This study aims to i. document the frequency and nature of maternal near-miss at hospital level in Damascus, Capital of Syria, ii. evaluate the level of care at maternal life-saving emergency services by comparatively analysing near-misses and maternal mortalities. Retrospective facility-based review of cases of near-miss and maternal mortality that took place in the years 2006-2007 at Damascus Maternity University Hospital, Syria. Near-miss cases were defined based on disease-specific criteria (Filippi 2005) including: haemorrhage, hypertensive disorders in pregnancy, dystocia, infection and anaemia. Main outcomes included maternal mortality ratio (MMR), maternal near miss ratio (MNMR), mortality indices and proportion of near-miss cases and mortality cases to hospital admissions. There were 28,025 deliveries, 15 maternal deaths and 901 near-miss cases. The study showed a MNMR of 32.9/1000 live births, a MMR of 54.8/100,000 live births and a relatively low mortality index of 1.7%. Hypertensive disorders (52%) and haemorrhage (34%) were the top causes of near-misses. Late pregnancy haemorrhage was the leading cause of maternal mortality (60%) while sepsis had the highest mortality index (7.4%). Most cases (93%) were referred in critical conditions from other facilities; namely traditional birth attendants homes (67%), primary (5%) and secondary (10%) healthcare unites and private practices (11%). 26% of near-miss cases were admitted to Intensive Care Unit (ICU). Near-miss analyses provide valuable information on obstetric care. The study highlights the need to improve antenatal care which would help early identification of high risk pregnancies. It also emphasises the importance of both: developing protocols to prevent/manage post-partum haemorrhage and training health

Imputation of variants from the 1000 Genomes Project modestly improves known associations and can identify low-frequency variant-phenotype associations undetected by HapMap based imputation.

Science.gov (United States)

Wood, Andrew R; Perry, John R B; Tanaka, Toshiko; Hernandez, Dena G; Zheng, Hou-Feng; Melzer, David; Gibbs, J Raphael; Nalls, Michael A; Weedon, Michael N; Spector, Tim D; Richards, J Brent; Bandinelli, Stefania; Ferrucci, Luigi; Singleton, Andrew B; Frayling, Timothy M

2013-01-01

Genome-wide association (GWA) studies have been limited by the reliance on common variants present on microarrays or imputable from the HapMap Project data. More recently, the completion of the 1000 Genomes Project has provided variant and haplotype information for several million variants derived from sequencing over 1,000 individuals. To help understand the extent to which more variants (including low frequency (1% ≤ MAF 1000 Genomes imputation, respectively, and 9 and 11 that reached a stricter, likely conservative, threshold of P1000 Genomes genotype data modestly improved the strength of known associations. Of 20 associations detected at P1000 Genomes imputed data and one was nominally more strongly associated in HapMap imputed data. We also detected an association between a low frequency variant and phenotype that was previously missed by HapMap based imputation approaches. An association between rs112635299 and alpha-1 globulin near the SERPINA gene represented the known association between rs28929474 (MAF = 0.007) and alpha1-antitrypsin that predisposes to emphysema (P = 2.5×10(-12)). Our data provide important proof of principle that 1000 Genomes imputation will detect novel, low frequency-large effect associations.

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...

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 ...

Facebook intrusion, fear of missing out, narcissism, and life satisfaction: A cross-sectional study.

Science.gov (United States)

Błachnio, Agata; Przepiórka, Aneta

2018-01-01

Facebook is one of the most popular social networking sites. The present paper examines the relations between fear of missing out, narcissism, Facebook intrusion, and life satisfaction. We hypothesized that the fear of missing out and narcissism would play a significant role in Facebook intrusion. The participants in the study were 360 Polish users of Facebook. We administered the Facebook Intrusion Scale, the Fear of Missing Out Scale, the Narcissistic Personality Inventory, and the Satisfaction with Life Scale. The results showed that a high level of fear of missing out and high narcissism are predictors of Facebook intrusion, while a low level of fear of missing out and high narcissism are related to satisfaction with life. Our findings provide a more comprehensive picture of the predictors of Facebook intrusion and reveal interesting patterns. Copyright © 2017 Elsevier B.V. All rights reserved.

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

On detection and assessment of statistical significance of Genomic Islands

Directory of Open Access Journals (Sweden)

Chaudhuri Probal

2008-04-01

Full Text Available Abstract Background Many of the available methods for detecting Genomic Islands (GIs in prokaryotic genomes use markers such as transposons, proximal tRNAs, flanking repeats etc., or they use other supervised techniques requiring training datasets. Most of these methods are primarily based on the biases in GC content or codon and amino acid usage of the islands. However, these methods either do not use any formal statistical test of significance or use statistical tests for which the critical values and the P-values are not adequately justified. We propose a method, which is unsupervised in nature and uses Monte-Carlo statistical tests based on randomly selected segments of a chromosome. Such tests are supported by precise statistical distribution theory, and consequently, the resulting P-values are quite reliable for making the decision. Results Our algorithm (named Design-Island, an acronym for Detection of Statistically Significant Genomic Island runs in two phases. Some 'putative GIs' are identified in the first phase, and those are refined into smaller segments containing horizontally acquired genes in the refinement phase. This method is applied to Salmonella typhi CT18 genome leading to the discovery of several new pathogenicity, antibiotic resistance and metabolic islands that were missed by earlier methods. Many of these islands contain mobile genetic elements like phage-mediated genes, transposons, integrase and IS elements confirming their horizontal acquirement. Conclusion The proposed method is based on statistical tests supported by precise distribution theory and reliable P-values along with a technique for visualizing statistically significant islands. The performance of our method is better than many other well known methods in terms of their sensitivity and accuracy, and in terms of specificity, it is comparable to other methods.

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.

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…

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

Conflicting Evolutionary Histories of the Mitochondrial and Nuclear Genomes in New World Myotis Bats.

Science.gov (United States)

Platt, Roy N; Faircloth, Brant C; Sullivan, Kevin A M; Kieran, Troy J; Glenn, Travis C; Vandewege, Michael W; Lee, Thomas E; Baker, Robert J; Stevens, Richard D; Ray, David A

2018-03-01

The rapid diversification of Myotis bats into more than 100 species is one of the most extensive mammalian radiations available for study. Efforts to understand relationships within Myotis have primarily utilized mitochondrial markers and trees inferred from nuclear markers lacked resolution. Our current understanding of relationships within Myotis is therefore biased towards a set of phylogenetic markers that may not reflect the history of the nuclear genome. To resolve this, we sequenced the full mitochondrial genomes of 37 representative Myotis, primarily from the New World, in conjunction with targeted sequencing of 3648 ultraconserved elements (UCEs). We inferred the phylogeny and explored the effects of concatenation and summary phylogenetic methods, as well as combinations of markers based on informativeness or levels of missing data, on our results. Of the 294 phylogenies generated from the nuclear UCE data, all are significantly different from phylogenies inferred using mitochondrial genomes. Even within the nuclear data, quartet frequencies indicate that around half of all UCE loci conflict with the estimated species tree. Several factors can drive such conflict, including incomplete lineage sorting, introgressive hybridization, or even phylogenetic error. Despite the degree of discordance between nuclear UCE loci and the mitochondrial genome and among UCE loci themselves, the most common nuclear topology is recovered in one quarter of all analyses with strong nodal support. Based on these results, we re-examine the evolutionary history of Myotis to better understand the phenomena driving their unique nuclear, mitochondrial, and biogeographic histories.

Rhabdovirus-like endogenous viral elements in the genome of Spodoptera frugiperda insect cells are actively transcribed: Implications for adventitious virus detection.

Science.gov (United States)

Geisler, Christoph; Jarvis, Donald L

2016-07-01

Spodoptera frugiperda (Sf) cell lines are used to produce several biologicals for human and veterinary use. Recently, it was discovered that all tested Sf cell lines are persistently infected with Sf-rhabdovirus, a novel rhabdovirus. As part of an effort to search for other adventitious viruses, we searched the Sf cell genome and transcriptome for sequences related to Sf-rhabdovirus. To our surprise, we found intact Sf-rhabdovirus N- and P-like ORFs, and partial Sf-rhabdovirus G- and L-like ORFs. The transcribed and genomic sequences matched, indicating the transcripts were derived from the genomic sequences. These appear to be endogenous viral elements (EVEs), which result from the integration of partial viral genetic material into the host cell genome. It is theoretically impossible for the Sf-rhabdovirus-like EVEs to produce infectious virus particles as 1) they are disseminated across 4 genomic loci, 2) the G and L ORFs are incomplete, and 3) the M ORF is missing. Our finding of transcribed virus-like sequences in Sf cells underscores that MPS-based searches for adventitious viruses in cell substrates used to manufacture biologics should take into account both genomic and transcribed sequences to facilitate the identification of transcribed EVE's, and to avoid false positive detection of replication-competent adventitious viruses. Copyright © 2016 International Alliance for Biological Standardization. Published by Elsevier Ltd. All rights reserved.

Genome-wide analysis of poly(A) site selection in Schizosaccharomyces pombe

KAUST Repository

Schlackow, M.

2013-10-23

Polyadenylation of pre-mRNAs, a critical step in eukaryotic gene expression, is mediated by cis elements collectively called the polyadenylation signal. Genome-wide analysis of such polyadenylation signals was missing in fission yeast, even though it is an important model organism. We demonstrate that the canonical AATAAA motif is the most frequent and functional polyadenylation signal in Schizosaccharomyces pombe. Using analysis of RNA-Seq data sets from cells grown under various physiological conditions, we identify 3\\' UTRs for nearly 90% of the yeast genes. Heterogeneity of cleavage sites is common, as is alternative polyadenylation within and between conditions. We validated the computationally identified sequence elements likely to promote polyadenylation by functional assays, including qRT-PCR and 3\\'RACE analysis. The biological importance of the AATAAA motif is underlined by functional analysis of the genes containing it. Furthermore, it has been shown that convergent genes require trans elements, like cohesin for efficient transcription termination. Here we show that convergent genes lacking cohesin (on chromosome 2) are generally associated with longer overlapping mRNA transcripts. Our bioinformatic and experimental genome-wide results are summarized and can be accessed and customized in a user-friendly database Pomb(A).

Genome-wide analysis of poly(A) site selection in Schizosaccharomyces pombe

KAUST Repository

Schlackow, M.; Marguerat, S.; Proudfoot, N. J.; Bahler, J.; Erban, R.; Gullerova, M.

2013-01-01

Polyadenylation of pre-mRNAs, a critical step in eukaryotic gene expression, is mediated by cis elements collectively called the polyadenylation signal. Genome-wide analysis of such polyadenylation signals was missing in fission yeast, even though it is an important model organism. We demonstrate that the canonical AATAAA motif is the most frequent and functional polyadenylation signal in Schizosaccharomyces pombe. Using analysis of RNA-Seq data sets from cells grown under various physiological conditions, we identify 3' UTRs for nearly 90% of the yeast genes. Heterogeneity of cleavage sites is common, as is alternative polyadenylation within and between conditions. We validated the computationally identified sequence elements likely to promote polyadenylation by functional assays, including qRT-PCR and 3'RACE analysis. The biological importance of the AATAAA motif is underlined by functional analysis of the genes containing it. Furthermore, it has been shown that convergent genes require trans elements, like cohesin for efficient transcription termination. Here we show that convergent genes lacking cohesin (on chromosome 2) are generally associated with longer overlapping mRNA transcripts. Our bioinformatic and experimental genome-wide results are summarized and can be accessed and customized in a user-friendly database Pomb(A).

Replacement of missing tooth in esthetic zone with implant-supported fixed prosthesis

Directory of Open Access Journals (Sweden)

Sunil Kumar Mishra

2017-01-01

Full Text Available In the anterior region, the common reason for tooth loss is due to traumatic injury or congenital anomaly. Loss of a single tooth may cause functional and esthetic deficits to the patient. There are different treatment options available for replacing a missing incisor. Implant dentistry should be considered as first treatment alternative for replace a missing tooth. This case report presents the replacement of a missing maxillary left central incisor in a compromised site with dental implants along with bone graft followed by frenectomy to obtain a good clinical result and for better function and esthetics of the patient.

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

Learning-Based Adaptive Imputation Methodwith kNN Algorithm for Missing Power Data

Directory of Open Access Journals (Sweden)

Minkyung Kim

2017-10-01

Full Text Available This paper proposes a learning-based adaptive imputation method (LAI for imputing missing power data in an energy system. This method estimates the missing power data by using the pattern that appears in the collected data. Here, in order to capture the patterns from past power data, we newly model a feature vector by using past data and its variations. The proposed LAI then learns the optimal length of the feature vector and the optimal historical length, which are significant hyper parameters of the proposed method, by utilizing intentional missing data. Based on a weighted distance between feature vectors representing a missing situation and past situation, missing power data are estimated by referring to the k most similar past situations in the optimal historical length. We further extend the proposed LAI to alleviate the effect of unexpected variation in power data and refer to this new approach as the extended LAI method (eLAI. The eLAI selects a method between linear interpolation (LI and the proposed LAI to improve accuracy under unexpected variations. Finally, from a simulation under various energy consumption profiles, we verify that the proposed eLAI achieves about a 74% reduction of the average imputation error in an energy system, compared to the existing imputation methods.

The fast changing landscape of sequencing technologies and their impact on microbial genome assemblies and annotation.

Science.gov (United States)

Mavromatis, Konstantinos; Land, Miriam L; Brettin, Thomas S; Quest, Daniel J; Copeland, Alex; Clum, Alicia; Goodwin, Lynne; Woyke, Tanja; Lapidus, Alla; Klenk, Hans Peter; Cottingham, Robert W; Kyrpides, Nikos C

2012-01-01

The emergence of next generation sequencing (NGS) has provided the means for rapid and high throughput sequencing and data generation at low cost, while concomitantly creating a new set of challenges. The number of available assembled microbial genomes continues to grow rapidly and their quality reflects the quality of the sequencing technology used, but also of the analysis software employed for assembly and annotation. In this work, we have explored the quality of the microbial draft genomes across various sequencing technologies. We have compared the draft and finished assemblies of 133 microbial genomes sequenced at the Department of Energy-Joint Genome Institute and finished at the Los Alamos National Laboratory using a variety of combinations of sequencing technologies, reflecting the transition of the institute from Sanger-based sequencing platforms to NGS platforms. The quality of the public assemblies and of the associated gene annotations was evaluated using various metrics. Results obtained with the different sequencing technologies, as well as their effects on downstream processes, were analyzed. Our results demonstrate that the Illumina HiSeq 2000 sequencing system, the primary sequencing technology currently used for de novo genome sequencing and assembly at JGI, has various advantages in terms of total sequence throughput and cost, but it also introduces challenges for the downstream analyses. In all cases assembly results although on average are of high quality, need to be viewed critically and consider sources of errors in them prior to analysis. These data follow the evolution of microbial sequencing and downstream processing at the JGI from draft genome sequences with large gaps corresponding to missing genes of significant biological role to assemblies with multiple small gaps (Illumina) and finally to assemblies that generate almost complete genomes (Illumina+PacBio).

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.

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.

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.

AN OBSERVATIONAL STUDY OF MATERNAL NEAR MISS CASES IN A TERTIARY CARE CENTRE

Directory of Open Access Journals (Sweden)

Elizabeth Joseph

2016-12-01

Full Text Available BACKGROUND DM WIMS is the only tertiary care referral hospital in the hilly tribal district of Wayanad. This is an observational study of 20 maternal near miss cases that presented in our hospital over a period of 4 months. MATERIALS AND METHODS This study was conducted by collecting data over a period of 4 months. Total number of live births in this period was 373. There were 20 cases of maternal near miss cases. Maternal near miss cases were chosen based on the inclusion criteria provided by WHO near miss approach for maternal health. RESULTS There were 373 live births in the 4-month observational period. In these 4 months, there were 20 cases of maternal near miss cases in our hospital. That is, maternal near miss ratio was 53.6/1000 live births. The majority were referred cases with MNM ratio of intrahospital cases being 13.4/1000 live births. The potentially life-threatening complications were obstetric haemorrhage and hypertensive disorders, which coexisted in majority of the women. The obstetric haemorrhage was mainly due to abruptio placenta, which can be attributed to the hypertensive complications. Preexisting anaemia was present in 35% of the MNM cases increasing their morbidity. CONCLUSION The maternal near miss ratio was 53.6/1000 live births, which is high. This can be attributed to the fact that our hospital is the only tertiary referral hospital in the hilly tribal district of Wayanad. Despite the MNM ratio being high, there were no cases of maternal death in this period. Low maternal mortality indicates the good first line of management given at the periphery hospital.

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.

The History of Miss Jane Pittman

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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

The perennial ryegrass GenomeZipper: targeted use of genome resources for comparative grass genomics.

Science.gov (United States)

Pfeifer, Matthias; Martis, Mihaela; Asp, Torben; Mayer, Klaus F X; Lübberstedt, Thomas; Byrne, Stephen; Frei, Ursula; Studer, Bruno

2013-02-01

Whole-genome sequences established for model and major crop species constitute a key resource for advanced genomic research. For outbreeding forage and turf grass species like ryegrasses (Lolium spp.), such resources have yet to be developed. Here, we present a model of the perennial ryegrass (Lolium perenne) genome on the basis of conserved synteny to barley (Hordeum vulgare) and the model grass genome Brachypodium (Brachypodium distachyon) as well as rice (Oryza sativa) and sorghum (Sorghum bicolor). A transcriptome-based genetic linkage map of perennial ryegrass served as a scaffold to establish the chromosomal arrangement of syntenic genes from model grass species. This scaffold revealed a high degree of synteny and macrocollinearity and was then utilized to anchor a collection of perennial ryegrass genes in silico to their predicted genome positions. This resulted in the unambiguous assignment of 3,315 out of 8,876 previously unmapped genes to the respective chromosomes. In total, the GenomeZipper incorporates 4,035 conserved grass gene loci, which were used for the first genome-wide sequence divergence analysis between perennial ryegrass, barley, Brachypodium, rice, and sorghum. The perennial ryegrass GenomeZipper is an ordered, information-rich genome scaffold, facilitating map-based cloning and genome assembly in perennial ryegrass and closely related Poaceae species. It also represents a milestone in describing synteny between perennial ryegrass and fully sequenced model grass genomes, thereby increasing our understanding of genome organization and evolution in the most important temperate forage and turf grass species.

Low Multilinear Rank Approximation of Tensors and Application in Missing Traffic Data

Directory of Open Access Journals (Sweden)

Huachun Tan

2014-02-01

Full Text Available The problem of missing data in multiway arrays (i.e., tensors is common in many fields such as bibliographic data analysis, image processing, and computer vision. We consider the problems of approximating a tensor by another tensor with low multilinear rank in the presence of missing data and possibly reconstructing it (i.e., tensor completion. In this paper, we propose a weighted Tucker model which models only the known elements for capturing the latent structure of the data and reconstructing the missing elements. To treat the nonuniqueness of the proposed weighted Tucker model, a novel gradient descent algorithm based on a Grassmann manifold, which is termed Tucker weighted optimization (Tucker-Wopt, is proposed for guaranteeing the global convergence to a local minimum of the problem. Based on extensive experiments, Tucker-Wopt is shown to successfully reconstruct tensors with noise and up to 95% missing data. Furthermore, the experiments on traffic flow volume data demonstrate the usefulness of our algorithm on real-world application.

Primates, Lice and Bacteria: Speciation and Genome Evolution in the Symbionts of Hominid Lice.

Science.gov (United States)

Boyd, Bret M; Allen, Julie M; Nguyen, Nam-Phuong; Vachaspati, Pranjal; Quicksall, Zachary S; Warnow, Tandy; Mugisha, Lawrence; Johnson, Kevin P; Reed, David L

2017-07-01

Insects with restricted diets rely on symbiotic bacteria to provide essential metabolites missing in their diet. The blood-sucking lice are obligate, host-specific parasites of mammals and are themselves host to symbiotic bacteria. In human lice, these bacterial symbionts supply the lice with B-vitamins. Here, we sequenced the genomes of symbiotic and heritable bacterial of human, chimpanzee, gorilla, and monkey lice and used phylogenomics to investigate their evolutionary relationships. We find that these symbionts have a phylogenetic history reflecting the louse phylogeny, a finding contrary to previous reports of symbiont replacement. Examination of the highly reduced symbiont genomes (0.53-0.57 Mb) reveals much of the genomes are dedicated to vitamin synthesis. This is unchanged in the smallest symbiont genome and one that appears to have been reorganized. Specifically, symbionts from human lice, chimpanzee lice, and gorilla lice carry a small plasmid that encodes synthesis of vitamin B5, a vitamin critical to the bacteria-louse symbiosis. This plasmid is absent in an old world monkey louse symbiont, where this pathway is on its primary chromosome. This suggests the unique genomic configuration brought about by the plasmid is not essential for symbiosis, but once obtained, it has persisted for up to 25 My. We also find evidence that human, chimpanzee, and gorilla louse endosymbionts have lost a pathway for synthesis of vitamin B1, whereas the monkey louse symbiont has retained this pathway. It is unclear whether these changes are adaptive, but they may point to evolutionary responses of louse symbionts to shifts in primate biology. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

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 ...

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,

Family genome browser: visualizing genomes with pedigree information.

Science.gov (United States)

Juan, Liran; Liu, Yongzhuang; Wang, Yongtian; Teng, Mingxiang; Zang, Tianyi; Wang, Yadong

2015-07-15

Families with inherited diseases are widely used in Mendelian/complex disease studies. Owing to the advances in high-throughput sequencing technologies, family genome sequencing becomes more and more prevalent. Visualizing family genomes can greatly facilitate human genetics studies and personalized medicine. However, due to the complex genetic relationships and high similarities among genomes of consanguineous family members, family genomes are difficult to be visualized in traditional genome visualization framework. How to visualize the family genome variants and their functions with integrated pedigree information remains a critical challenge. We developed the Family Genome Browser (FGB) to provide comprehensive analysis and visualization for family genomes. The FGB can visualize family genomes in both individual level and variant level effectively, through integrating genome data with pedigree information. Family genome analysis, including determination of parental origin of the variants, detection of de novo mutations, identification of potential recombination events and identical-by-decent segments, etc., can be performed flexibly. Diverse annotations for the family genome variants, such as dbSNP memberships, linkage disequilibriums, genes, variant effects, potential phenotypes, etc., are illustrated as well. Moreover, the FGB can automatically search de novo mutations and compound heterozygous variants for a selected individual, and guide investigators to find high-risk genes with flexible navigation options. These features enable users to investigate and understand family genomes intuitively and systematically. The FGB is available at http://mlg.hit.edu.cn/FGB/. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

A simple method for analyzing data from a randomized trial with a missing binary outcome

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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.

An Improved Fuzzy Based Missing Value Estimation in DNA Microarray Validated by Gene Ranking

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Sujay Saha

2016-01-01

Full Text Available Most of the gene expression data analysis algorithms require the entire gene expression matrix without any missing values. Hence, it is necessary to devise methods which would impute missing data values accurately. There exist a number of imputation algorithms to estimate those missing values. This work starts with a microarray dataset containing multiple missing values. We first apply the modified version of the fuzzy theory based existing method LRFDVImpute to impute multiple missing values of time series gene expression data and then validate the result of imputation by genetic algorithm (GA based gene ranking methodology along with some regular statistical validation techniques, like RMSE method. Gene ranking, as far as our knowledge, has not been used yet to validate the result of missing value estimation. Firstly, the proposed method has been tested on the very popular Spellman dataset and results show that error margins have been drastically reduced compared to some previous works, which indirectly validates the statistical significance of the proposed method. Then it has been applied on four other 2-class benchmark datasets, like Colorectal Cancer tumours dataset (GDS4382, Breast Cancer dataset (GSE349-350, Prostate Cancer dataset, and DLBCL-FL (Leukaemia for both missing value estimation and ranking the genes, and the results show that the proposed method can reach 100% classification accuracy with very few dominant genes, which indirectly validates the biological significance of the proposed method.

Materials International Space Station Experiment (MISSE): Overview, Accomplishments and Future Needs

Science.gov (United States)

deGroh, Kim K.; Jaworske, Donald A.; Pippin, Gary; Jenkins, Philip P.; Walters, Robert J.; Thibeault, Sheila A.; Palusinski, Iwona; Lorentzen, Justin R.

2014-01-01

Materials and devices used on the exterior of spacecraft in low Earth orbit (LEO) are subjected to environmental threats that can cause degradation in material properties, possibly threatening spacecraft mission success. These threats include: atomic oxygen (AO), ultraviolet and x-ray radiation, charged particle radiation, temperature extremes and thermal cycling, micrometeoroid and debris impacts, and contamination. Space environmental threats vary greatly based on spacecraft materials, thicknesses and stress levels, and the mission environment and duration. For more than a decade the Materials International Space Station Experiment (MISSE) has enabled the study of the long duration environmental durability of spacecraft materials in the LEO environment. The overall objective of MISSE is to test the stability and durability of materials and devices in the space environment in order to gain valuable knowledge on the performance of materials in space, as well as to enable lifetime predictions of new materials that may be used in future space flight. MISSE is a series of materials flight experiments, which are attached to the exterior of the International Space Station (ISS). Individual experiments were loaded onto suitcase-like trays, called Passive Experiment Containers (PECs). The PECs were transported to the ISS in the Space Shuttle cargo bay and attached to, and removed from, the ISS during extravehicular activities (EVAs). The PECs were retrieved after one or more years of space exposure and returned to Earth enabling post-flight experiment evaluation. MISSE is a multi-organization project with participants from the National Aeronautics and Space Administration (NASA), the Department of Defense (DoD), industry and academia. MISSE has provided a platform for environmental durability studies for thousands of samples and numerous devices, and it has produced many tangible impacts. Ten PECs (and one smaller tray) have been flown, representing MISSE 1 through MISSE

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

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.

High-Affinity Methanotrophy Informed by Genome-Wide Analysis of Upland Soil Cluster Alpha (USCα) from Axel Heiberg Island, Canadian High Arctic

Science.gov (United States)

Rusley, C.; Onstott, T. C.; Lau, M.

2017-12-01

Methane (CH4) is a potent greenhouse gas whose proper budgeting is vital to climate predictions. Recent studies have identified upland Arctic mineral cryosols as consistent CH4 sinks, drawing CH4 from both the atmosphere and underlying anaerobic soil layers. Global atmospheric CH4 uptake is proposed to be mediated by high-affinity methanotrophs based on the detection of the marker gene pmoA (particulate methane monooxygenase beta subunit). However, a lack of pure cultures and scarcity of genomic information have hindered our understanding of their metabolic capabilities and versatility. Together with the missing genetic linkage between its pmoA and 16S ribosomal RNA (rRNA) gene, the factors that control the distribution and magnitude of high-affinity methanotrophy in the Arctic permafrost-affected region have remained elusive. Using 21 metagenomic datasets of surface soils obtained from long-term core incubation experiments,1 this bioinformatics study aimed to reconstruct the draft genome of the Upland Soil Cluster α-proteobacteria (USCα), the high-affinity methanotroph previously detected in the samples,2 and to determine its phylogeny and metabolic requirements. We obtained a genome bin containing the high-affinity form of the USCα-like pmoA gene. The 3.03 Mbp assembly is 91.6% complete with a unique set of single-copy marker genes. The 16S rRNA gene fragment of USCα belongs to the α-proteobacterial family Beijerinckiaceae. Genome annotation indicates possible formaldehyde oxidation via tetrahydromethanopterin-linked C1 transfer pathways, acetate utilization, carbon fixation via the Calvin-Benson-Bassham cycle, and glycogen production. Notably, the key enzymes for formaldehyde assimilation via the serine and ribulose monophosphate pathways are missing. The presence of genes encoding nitrate reductase and hemoglobin suggests adaptation to low O2 under water-logged conditions. Since USCα has versatile carbon metabolisms, it may not be an obligate methanotroph

eGenomics: Cataloguing Our Complete Genome Collection III

Directory of Open Access Journals (Sweden)

Dawn Field

2007-01-01

Full Text Available This meeting report summarizes the proceedings of the “eGenomics: Cataloguing our Complete Genome Collection III” workshop held September 11–13, 2006, at the National Institute for Environmental eScience (NIEeS, Cambridge, United Kingdom. This 3rd workshop of the Genomic Standards Consortium was divided into two parts. The first half of the three-day workshop was dedicated to reviewing the genomic diversity of our current and future genome and metagenome collection, and exploring linkages to a series of existing projects through formal presentations. The second half was dedicated to strategic discussions. Outcomes of the workshop include a revised “Minimum Information about a Genome Sequence” (MIGS specification (v1.1, consensus on a variety of features to be added to the Genome Catalogue (GCat, agreement by several researchers to adopt MIGS for imminent genome publications, and an agreement by the EBI and NCBI to input their genome collections into GCat for the purpose of quantifying the amount of optional data already available (e.g., for geographic location coordinates and working towards a single, global list of all public genomes and metagenomes.

Genomic Prediction from Whole Genome Sequence in Livestock: The 1000 Bull Genomes Project

DEFF Research Database (Denmark)

Hayes, Benjamin J; MacLeod, Iona M; Daetwyler, Hans D

Advantages of using whole genome sequence data to predict genomic estimated breeding values (GEBV) include better persistence of accuracy of GEBV across generations and more accurate GEBV across breeds. The 1000 Bull Genomes Project provides a database of whole genome sequenced key ancestor bulls....... In a dairy data set, predictions using BayesRC and imputed sequence data from 1000 Bull Genomes were 2% more accurate than with 800k data. We could demonstrate the method identified causal mutations in some cases. Further improvements will come from more accurate imputation of sequence variant genotypes...

Near-misses are an opportunity to improve patient safety: adapting strategies of high reliability organizations to healthcare.

Science.gov (United States)

Van Spall, Harriette; Kassam, Alisha; Tollefson, Travis T

2015-08-01

Near-miss investigations in high reliability organizations (HROs) aim to mitigate risk and improve system safety. Healthcare settings have a higher rate of near-misses and subsequent adverse events than most high-risk industries, but near-misses are not systematically reported or analyzed. In this review, we will describe the strategies for near-miss analysis that have facilitated a culture of safety and continuous quality improvement in HROs. Near-miss analysis is routine and systematic in HROs such as aviation. Strategies implemented in aviation include the Commercial Aviation Safety Team, which undertakes systematic analyses of near-misses, so that findings can be incorporated into Standard Operating Procedures (SOPs). Other strategies resulting from incident analyses include Crew Resource Management (CRM) for enhanced communication, situational awareness training, adoption of checklists during operations, and built-in redundancy within systems. Health care organizations should consider near-misses as opportunities for quality improvement. The systematic reporting and analysis of near-misses, commonplace in HROs, can be adapted to health care settings to prevent adverse events and improve clinical outcomes.

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....

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

Science.gov (United States)

Hernández-Cruz, Raúl; Moreno-Monsiváis, María Guadalupe; Cheverría-Rivera, Sofía; Díaz-Oviedo, Aracely

2017-07-10

to determine the factors that influence the missed nursing care in hospitalized patients. 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. 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, precursos humanos (M=56,13, DE=21,38). Os fatores relacionados ao cuidado omitido foram os recursos humanos (rs=0,408, precursos humanos; com base nos resultados deste estudo pode-se fortalecer a continuidade do cuidado de enfermagem. determinar los factores que influyen en el cuidado de enfermería perdido en pacientes hospitalizados. estudio descriptivo correlacional, se realizó en un hospital privado de México. Para identificar el cuidado perdido y factores relacionados se utilizó el instrumento MISSCARE que mide el cuidado perdido y los factores asociados. El cuidado perdido y los factores se agruparon en índices globales y por dimensiones. Para el análisis se utilizó estadística descriptiva, correlación de Spearman y regresión lineal simple. El estudio fue aprobado por el comité de ética. participaron 71 enfermeras de los servicios de urgencias, terapia intensiva y hospitalización. El índice global de cuidado perdido mostró una M=7,45 (DE=10,74); el índice con mayor cuidado perdido correspondió a

Assessing genetic diversity among Brettanomyces yeasts by DNA fingerprinting and whole-genome sequencing.

Science.gov (United States)

Crauwels, Sam; Zhu, Bo; Steensels, Jan; Busschaert, Pieter; De Samblanx, Gorik; Marchal, Kathleen; Willems, Kris A; Verstrepen, Kevin J; Lievens, Bart

2014-07-01

Brettanomyces yeasts, with the species Brettanomyces (Dekkera) bruxellensis being the most important one, are generally reported to be spoilage yeasts in the beer and wine industry due to the production of phenolic off flavors. However, B. bruxellensis is also known to be a beneficial contributor in certain fermentation processes, such as the production of certain specialty beers. Nevertheless, despite its economic importance, Brettanomyces yeasts remain poorly understood at the genetic and genomic levels. In this study, the genetic relationship between more than 50 Brettanomyces strains from all presently known species and from several sources was studied using a combination of DNA fingerprinting techniques. This revealed an intriguing correlation between the B. bruxellensis fingerprints and the respective isolation source. To further explore this relationship, we sequenced a (beneficial) beer isolate of B. bruxellensis (VIB X9085; ST05.12/22) and compared its genome sequence with the genome sequences of two wine spoilage strains (AWRI 1499 and CBS 2499). ST05.12/22 was found to be substantially different from both wine strains, especially at the level of single nucleotide polymorphisms (SNPs). In addition, there were major differences in the genome structures between the strains investigated, including the presence of large duplications and deletions. Gene content analysis revealed the presence of 20 genes which were present in both wine strains but absent in the beer strain, including many genes involved in carbon and nitrogen metabolism, and vice versa, no genes that were missing in both AWRI 1499 and CBS 2499 were found in ST05.12/22. Together, this study provides tools to discriminate Brettanomyces strains and provides a first glimpse at the genetic diversity and genome plasticity of B. bruxellensis. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

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 ...

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...

Maternal near-misses at a provincial hospital in Papua New Guinea: A prospective observational study.

Science.gov (United States)

Bolnga, John W; Morris, Marilyn; Totona, Catherine; Laman, Moses

2017-12-01

Maternal near-miss indices are World Health Organisation (WHO) recognised indicators that may improve our understanding of factors associated with maternal morbidity and mortality. In Papua New Guinea (PNG) where maternal mortality is among the highest in the world, only one study has documented near-miss indices in a tertiary-level hospital, but none from provincial hospitals where the majority of under-privileged women access healthcare services. To determine the near-miss ratio, maternal mortality index (MMI), and associated maternal indices for Modilon Hospital in Madang Province of PNG. All women attending Modilon Hospital who met the WHO maternal near-miss definition and/or a WHO-modified (PNG-specific) near-miss definition, were prospectively enrolled. There were 6019 live births during the audit period; 163 women presented with life-threatening conditions (153 near-misses and 10 maternal deaths). The maternal near-miss ratio was 25.4/1000 live births and the maternal mortality ratio (MMR) was 166/100 000 live births, with a maternal death to near-miss ratio of 1:15.3. The severe maternal outcome ratio was 27.1/1000 live births and the total mortality index was 6.8%. Higher proportions of near-miss women were aged ≥30 years, nulliparous, illiterate, from rural communities, lacked formal employment, referred from peripheral health facilities, unbooked, had history of still births and were anaemic. Sociodemographic factors such as women's rights, education level and status in society, in addition to appropriate health reforms with greater financial and political support are urgently needed to ensure underprivileged women in rural PNG have access to family planning, supervised deliveries and skilled emergency obstetric care. © 2017 The Royal Australian and New Zealand College of Obstetricians and Gynaecologists.

Intention-to-treat analyses and missing data approaches in pharmacotherapy trials for alcohol use disorders.

Science.gov (United States)

Del Re, A C; Maisel, Natalya C; Blodgett, Janet C; Finney, John W

2013-11-12

Intention to treat (ITT) is an analytic strategy for reducing potential bias in treatment effects arising from missing data in randomised controlled trials (RCTs). Currently, no universally accepted definition of ITT exists, although many researchers consider it to require either no attrition or a strategy to handle missing data. Using the reports of a large pool of RCTs, we examined discrepancies between the types of analyses that alcohol pharmacotherapy researchers stated they used versus those they actually used. We also examined the linkage between analytic strategy (ie, ITT or not) and how missing data on outcomes were handled (if at all), and whether data analytic and missing data strategies have changed over time. Descriptive statistics were generated for reported and actual data analytic strategy and for missing data strategy. In addition, generalised linear models determined changes over time in the use of ITT analyses and missing data strategies. 165 RCTs of pharmacotherapy for alcohol use disorders. Of the 165 studies, 74 reported using an ITT strategy. However, less than 40% of the studies actually conducted ITT according to the rigorous definition above. Whereas no change in the use of ITT analyses over time was found, censored (last follow-up completed) and imputed missing data strategies have increased over time, while analyses of data only for the sample actually followed have decreased. Discrepancies in reporting versus actually conducting ITT analyses were found in this body of RCTs. Lack of clarity regarding the missing data strategy used was common. Consensus on a definition of ITT is important for an adequate understanding of research findings. Clearer reporting standards for analyses and the handling of missing data in pharmacotherapy trials and other intervention studies are needed.

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.

Sparse subspace clustering for data with missing entries and high-rank matrix completion.

Science.gov (United States)

Fan, Jicong; Chow, Tommy W S

2017-09-01

Many methods have recently been proposed for subspace clustering, but they are often unable to handle incomplete data because of missing entries. Using matrix completion methods to recover missing entries is a common way to solve the problem. Conventional matrix completion methods require that the matrix should be of low-rank intrinsically, but most matrices are of high-rank or even full-rank in practice, especially when the number of subspaces is large. In this paper, a new method called Sparse Representation with Missing Entries and Matrix Completion is proposed to solve the problems of incomplete-data subspace clustering and high-rank matrix completion. The proposed algorithm alternately computes the matrix of sparse representation coefficients and recovers the missing entries of a data matrix. The proposed algorithm recovers missing entries through minimizing the representation coefficients, representation errors, and matrix rank. Thorough experimental study and comparative analysis based on synthetic data and natural images were conducted. The presented results demonstrate that the proposed algorithm is more effective in subspace clustering and matrix completion compared with other existing methods. Copyright © 2017 Elsevier Ltd. All rights reserved.

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.

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.

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

Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products.

Science.gov (United States)

Almeida, Mathieu; Hébert, Agnès; Abraham, Anne-Laure; Rasmussen, Simon; Monnet, Christophe; Pons, Nicolas; Delbès, Céline; Loux, Valentin; Batto, Jean-Michel; Leonard, Pierre; Kennedy, Sean; Ehrlich, Stanislas Dusko; Pop, Mihai; Montel, Marie-Christine; Irlinger, Françoise; Renault, Pierre

2014-12-13

Microbial communities of traditional cheeses are complex and insufficiently characterized. The origin, safety and functional role in cheese making of these microbial communities are still not well understood. Metagenomic analysis of these communities by high throughput shotgun sequencing is a promising approach to characterize their genomic and functional profiles. Such analyses, however, critically depend on the availability of appropriate reference genome databases against which the sequencing reads can be aligned. We built a reference genome catalog suitable for short read metagenomic analysis using a low-cost sequencing strategy. We selected 142 bacteria isolated from dairy products belonging to 137 different species and 67 genera, and succeeded to reconstruct the draft genome of 117 of them at a standard or high quality level, including isolates from the genera Kluyvera, Luteococcus and Marinilactibacillus, still missing from public database. To demonstrate the potential of this catalog, we analysed the microbial composition of the surface of two smear cheeses and one blue-veined cheese, and showed that a significant part of the microbiota of these traditional cheeses was composed of microorganisms newly sequenced in our study. Our study provides data, which combined with publicly available genome references, represents the most expansive catalog to date of cheese-associated bacteria. Using this extended dairy catalog, we revealed the presence in traditional cheese of dominant microorganisms not deliberately inoculated, mainly Gram-negative genera such as Pseudoalteromonas haloplanktis or Psychrobacter immobilis, that may contribute to the characteristics of cheese produced through traditional methods.

A patient with protrusion and multiple missing teeth treated with autotransplantation and space closure.

Science.gov (United States)

Ko, Jeong-Min; Paik, Cheol-Ho; Choi, Simon; Baek, Seung-Hak

2014-05-01

To present a patient treated with submerging autotransplantation (SA) of an immature premolar and subsequent orthodontic space closure (OSC) and to report a 10-year follow-up result. A 10-year-old boy had multiple missing premolars with an asymmetric pattern (maxillary right first and second premolars, teeth 14 and 15; maxillary left second premolar, tooth 25; and mandibular right second premolar, tooth 45). After considering several treatment options, tooth 35 with immature root development underwent SA into the missing site of tooth 15 at a depth 5 mm below the occlusal plane and was stabilized with sutures to create a symmetric missing condition of the premolars in the four quadrants. Three months after autotransplantation, spontaneous eruption of the transplanted tooth was observed. Nine months after autotransplantation, presence of the lamina dura of the transplanted tooth was confirmed with a periapical radiograph. Active orthodontic treatment was initiated to reduce lip protrusion by closing the missing spaces of teeth 14, 25, 35, and 45 and to correct dental midline deviation. After 33 months of active orthodontic treatment, Class I canine and molar relationships were obtained. During the 10-year follow-up, the pulp vitality of the transplanted tooth was maintained without any pathologic findings, including root resorption or pulp canal obliteration. In a patient with lip protrusion and multiple congenitally missing premolars with an asymmetric pattern, SA of one premolar from the normal quadrant into the quadrant missing two premolars with subsequent OSC of the missing sites of the other premolars can be an effective treatment modality.

Review of guidelines and literature for handling missing data in longitudinal clinical trials with a case study.

Science.gov (United States)

Liu, M; Wei, L; Zhang, J

2006-01-01

Missing data in clinical trials are inevitable. We highlight the ICH guidelines and CPMP points to consider on missing data. Specifically, we outline how we should consider missing data issues when designing, planning and conducting studies to minimize missing data impact. We also go beyond the coverage of the above two documents, provide a more detailed review of the basic concepts of missing data and frequently used terminologies, and examples of the typical missing data mechanism, and discuss technical details and literature for several frequently used statistical methods and associated software. Finally, we provide a case study where the principles outlined in this paper are applied to one clinical program at protocol design, data analysis plan and other stages of a clinical trial.

The impact of near-miss events on betting behavior: An examination of casino rapid roulette play

Directory of Open Access Journals (Sweden)

James A. Sundali

2012-11-01

Full Text Available We examine how almost winning in roulette affects subsequent betting behavior. Our main finding is heterogeneity in gambler behavior with some gamblers less likely to bet on numbers that were near misses on the prior spin and other gamblers more likely to bet on near miss numbers. Using a unique data set from the game rapid roulette, we model the likelihood of a gambler betting on a near miss number while controlling for the favorite number bias and the likelihood of a number being a near miss. We also find no evidence that near misses in roulette leads to gamblers extending the time spent gambling or to the placing of more bets.

Complete genome sequencing of Agrobacterium sp. H13-3, the former Rhizobium lupini H13-3, reveals a tripartite genome consisting of a circular and a linear chromosome and an accessory plasmid but lacking a tumor-inducing Ti-plasmid.

Science.gov (United States)

Wibberg, Daniel; Blom, Jochen; Jaenicke, Sebastian; Kollin, Florian; Rupp, Oliver; Scharf, Birgit; Schneiker-Bekel, Susanne; Sczcepanowski, Rafael; Goesmann, Alexander; Setubal, Joao Carlos; Schmitt, Rüdiger; Pühler, Alfred; Schlüter, Andreas

2011-08-20

Agrobacterium sp. H13-3, formerly known as Rhizobium lupini H13-3, is a soil bacterium that was isolated from the rhizosphere of Lupinus luteus. The isolate has been established as a model system for studying novel features of flagellum structure, motility and chemotaxis within the family Rhizobiaceae. The complete genome sequence of Agrobacterium sp. H13-3 has been established and the genome structure and phylogenetic assignment of the organism was analysed. For de novo sequencing of the Agrobacterium sp. H13-3 genome, a combined strategy comprising 454-pyrosequencing on the Genome Sequencer FLX platform and PCR-based amplicon sequencing for gap closure was applied. The finished genome consists of three replicons and comprises 5,573,770 bases. Based on phylogenetic analyses, the isolate could be assigned to the genus Agrobacterium biovar I and represents a genomic species G1 strain within this biovariety. The highly conserved circular chromosome (2.82 Mb) of Agrobacterium sp. H13-3 mainly encodes housekeeping functions characteristic for an aerobic, heterotrophic bacterium. Agrobacterium sp. H13-3 is a motile bacterium driven by the rotation of several complex flagella. Its behaviour towards external stimuli is regulated by a large chemotaxis regulon and a total of 17 chemoreceptors. Comparable to the genome of Agrobacterium tumefaciens C58, Agrobacterium sp. H13-3 possesses a linear chromosome (2.15 Mb) that is related to its reference replicon and features chromosomal and plasmid-like properties. The accessory plasmid pAspH13-3a (0.6 Mb) is only distantly related to the plasmid pAtC58 of A. tumefaciens C58 and shows a mosaic structure. A tumor-inducing Ti-plasmid is missing in the sequenced strain H13-3 indicating that it is a non-virulent isolate. Copyright © 2011 Elsevier B.V. All rights reserved.

Construction and Analysis of Two Genome-Scale Deletion Libraries for Bacillus subtilis.

Science.gov (United States)

Koo, Byoung-Mo; Kritikos, George; Farelli, Jeremiah D; Todor, Horia; Tong, Kenneth; Kimsey, Harvey; Wapinski, Ilan; Galardini, Marco; Cabal, Angelo; Peters, Jason M; Hachmann, Anna-Barbara; Rudner, David Z; Allen, Karen N; Typas, Athanasios; Gross, Carol A

2017-03-22

A systems-level understanding of Gram-positive bacteria is important from both an environmental and health perspective and is most easily obtained when high-quality, validated genomic resources are available. To this end, we constructed two ordered, barcoded, erythromycin-resistance- and kanamycin-resistance-marked single-gene deletion libraries of the Gram-positive model organism, Bacillus subtilis. The libraries comprise 3,968 and 3,970 genes, respectively, and overlap in all but four genes. Using these libraries, we update the set of essential genes known for this organism, provide a comprehensive compendium of B. subtilis auxotrophic genes, and identify genes required for utilizing specific carbon and nitrogen sources, as well as those required for growth at low temperature. We report the identification of enzymes catalyzing several missing steps in amino acid biosynthesis. Finally, we describe a suite of high-throughput phenotyping methodologies and apply them to provide a genome-wide analysis of competence and sporulation. Altogether, we provide versatile resources for studying gene function and pathway and network architecture in Gram-positive bacteria. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Genome U-Plot: a whole genome visualization.

Science.gov (United States)

Gaitatzes, Athanasios; Johnson, Sarah H; Smadbeck, James B; Vasmatzis, George

2018-05-15

The ability to produce and analyze whole genome sequencing (WGS) data from samples with structural variations (SV) generated the need to visualize such abnormalities in simplified plots. Conventional two-dimensional representations of WGS data frequently use either circular or linear layouts. There are several diverse advantages regarding both these representations, but their major disadvantage is that they do not use the two-dimensional space very efficiently. We propose a layout, termed the Genome U-Plot, which spreads the chromosomes on a two-dimensional surface and essentially quadruples the spatial resolution. We present the Genome U-Plot for producing clear and intuitive graphs that allows researchers to generate novel insights and hypotheses by visualizing SVs such as deletions, amplifications, and chromoanagenesis events. The main features of the Genome U-Plot are its layered layout, its high spatial resolution and its improved aesthetic qualities. We compare conventional visualization schemas with the Genome U-Plot using visualization metrics such as number of line crossings and crossing angle resolution measures. Based on our metrics, we improve the readability of the resulting graph by at least 2-fold, making apparent important features and making it easy to identify important genomic changes. A whole genome visualization tool with high spatial resolution and improved aesthetic qualities. An implementation and documentation of the Genome U-Plot is publicly available at https://github.com/gaitat/GenomeUPlot. vasmatzis.george@mayo.edu. Supplementary data are available at Bioinformatics online.

Perinatal outcome and near-miss morbidity between placenta previa versus abruptio placentae

International Nuclear Information System (INIS)

Siddique, S.A.; Tariq, G.; Sheikh, A.; Hussain, F.S.U.; Memon, K.A.

2010-01-01

To compare perinatal outcome and near-miss morbidities between placenta previa versus abruptio placentae in patients of antepartum haemorrhage (APH). Patients with APH diagnosed as placenta previa and abruptio placentae who delivered after 24 weeks of regnancy were selected from labour room. Outcome measures were birth weight, neonatal intensive care admission, stillbirth, perinatal mortality rates, near-miss, surgical intensive care admission, postpartum haemorrhage, hysterectomy, massive transfusion, renal failure, coagulopathy and maternal death. Stillbirth was defined as a fetus weighing greater or equal to 500 gm showing no sign of life after birth. Near-miss was defined as severe organ dysfunction which if not treated appropriately, could result in death. Descriptive statistics were calculated and chi-square was applied with significance level < 0.05. Stillbirths and perinatal mortality rates were significantly higher in abruptio placentae, 52.97% versus 18.18% and 534/1000 versus 230/1000 (p < 0.01). Near-miss cases were also significantly higher in abruptio placentae, 22.27%. Verus 11.18% (p < 0.01). Hypovolemic shock and coagulation failure were also significantly higher in abruptio placentae (p < 0.05). (author)

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.

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.

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

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...

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 ...

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...

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

Near miss and minor occupational injury: Does it share a common causal pathway with major injury?

Science.gov (United States)

Alamgir, Hasanat; Yu, Shicheng; Gorman, Erin; Ngan, Karen; Guzman, Jaime

2009-01-01

An essential assumption of injury prevention programs is the common cause hypothesis that the causal pathways of near misses and minor injuries are similar to those of major injuries. The rates of near miss, minor injury and major injury of all reported incidents and musculoskeletal incidents (MSIs) were calculated for three health regions using information from a surveillance database and productive hours from payroll data. The relative distribution of individual causes and activities involved in near miss, minor injury and major injury were then compared. For all reported incidents, there were significant differences in the relative distribution of causes for near miss, minor, and major injury. However, the relative distribution of causes and activities involved in minor and major MSIs were similar. The top causes and activities involved were the same across near miss, minor, and major injury. Finding from this study support the use of near miss and minor injury data as potential outcome measures for injury prevention programs. (c) 2008 Wiley-Liss, Inc.

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...

Effects of Negative Emotions and Life Events on Women's Missed Miscarriage.

Science.gov (United States)

Xing, Huilin; Luo, Yaping; Wang, Shouying

2018-02-01

To investigate the effects of negative emotions and life events on women's missed miscarriage. Overall, 214 women diagnosed with a missed miscarriage by prenatal examination from 2016-2017 in Xiamen Maternal and Child Health Care Hospital, Xiamen, China were selected as the observation group compared to 214 women as control group. The general data of the patients were investigated by self-programmed questionnaires. Zung Self-Rating Anxiety Scale, Center Epidemiological Studies Depression Scale; Life Events Scale for Pregnant Women were used conduct the study. General data, anxiety, depression and life events were compared between the two groups of patients, and statistically different factors were included in the multivariate Logistic regression analysis. There were statistically significant differences in the educational level, pre-pregnancy health status, planned pregnancy, pre-pregnancy or gestational gynecological inflammation and the initiative to obtain knowledge of prenatal and postnatal care between the two groups of pregnant women ( P life events, score of anxiety and score of depression between them ( P life events, anxiety and depression were independent risk factors for it. Negative emotions and life events increase the risk of women's missed miscarriage, and the high educational level, good health status before pregnancy and the initiative to obtain the knowledge of prenatal and postnatal care reduce the risk of women's missed miscarriage.

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.

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.

GACT: a Genome build and Allele definition Conversion Tool for SNP imputation and meta-analysis in genetic association studies.

Science.gov (United States)

Sulovari, Arvis; Li, Dawei

2014-07-19

Genome-wide association studies (GWAS) have successfully identified genes associated with complex human diseases. Although much of the heritability remains unexplained, combining single nucleotide polymorphism (SNP) genotypes from multiple studies for meta-analysis will increase the statistical power to identify new disease-associated variants. Meta-analysis requires same allele definition (nomenclature) and genome build among individual studies. Similarly, imputation, commonly-used prior to meta-analysis, requires the same consistency. However, the genotypes from various GWAS are generated using different genotyping platforms, arrays or SNP-calling approaches, resulting in use of different genome builds and allele definitions. Incorrect assumptions of identical allele definition among combined GWAS lead to a large portion of discarded genotypes or incorrect association findings. There is no published tool that predicts and converts among all major allele definitions. In this study, we have developed a tool, GACT, which stands for Genome build and Allele definition Conversion Tool, that predicts and inter-converts between any of the common SNP allele definitions and between the major genome builds. In addition, we assessed several factors that may affect imputation quality, and our results indicated that inclusion of singletons in the reference had detrimental effects while ambiguous SNPs had no measurable effect. Unexpectedly, exclusion of genotypes with missing rate > 0.001 (40% of study SNPs) showed no significant decrease of imputation quality (even significantly higher when compared to the imputation with singletons in the reference), especially for rare SNPs. GACT is a new, powerful, and user-friendly tool with both command-line and interactive online versions that can accurately predict, and convert between any of the common allele definitions and between genome builds for genome-wide meta-analysis and imputation of genotypes from SNP-arrays or deep

Low missing mass, single- and double diffraction dissociation at the LHC

CERN Document Server

Jenkovszky, Laszlo; Orava, Risto; Salii, Andrii

2014-01-01

Low missing mass, single- and double diffraction dissociation is calculated for the LHC energies from a dual-Regge model, dominated by a Pomeron Regge pole exchange. The model reproduces the rich resonance structure in the low missing mass Mx region. The diffractionly excited states lie on the nucleon trajectory, appended by the isolated Roper resonance. Detailed predictions for the squared momentum transfer and missing mass dependence of the differential and integrated single- and double diffraction dissociation in the kinematical range of present and future LHC measurements are given. The model predicts a possible turn-down of the cross section towards, t -> 0 in a region probably accessible in future experiments in the nearly forward direction. The present work is a continuation and extension (e.g. with double diffraction) of a previous work using the dual Regge approach.

C-Section Recovery: What to Expect

Science.gov (United States)

... Mood changes. Childbirth triggers a jumble of powerful emotions. Many new moms experience a period of feeling ... labor-and-delivery/in-depth/c-section-recovery/art-20047310 . Mayo Clinic Footer Legal Conditions and Terms ...

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 ...

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 ...

Genomic analysis for managing small and endangered populations: A case study in Tyrol Grey cattle

Directory of Open Access Journals (Sweden)

Gábor eMészáros

2015-05-01

Full Text Available Analysis of genomic data is increasingly becoming part of the livestock industry. Therefore the routine collection of genomic information would be an invaluable resource for management of breeding programs in small, endangered populations. The objectives of this project were to analyse 1. linkage disequlibrium decay and the effective population size; 2. Inbreeding level and effective population size (NeROH based on runs of homozygosity (ROH; 3. Prediction of genomic breeding values (GEBV within and across breeds. In addition, the use of genomic information for breed management is discussed. The study was based on all available genotypes of Tyrol Grey AI bulls. ROHs were derived based on regions covering at least 4 Mb, 8 Mb and 16 Mb regions, with the corresponding mean inbreeding coefficients 4.0%, 2.9% and 1.6%, respectively. The NeROH was 125 (NeROH>16Mb, 186 (NeROH>8Mb and 370 (NeROH>4Mb, indicating strict avoidance of close inbreeding in the population.The genomic selection was developed for and is working well in large breeds. Contrary to the expectations, the accuracy of GEBVs with very small within breed reference populations were very high, between 0.13-0.91 and 0.12-0.63, when EBVs and dEBVs were used as pseudo-phenotypes, respectively. Subsequent analyses confirmed the high accuracies being heavily influenced by parent averages. Multi-breed and across breed reference sets gave inconsistent and lower accuracies. Genomic information may have a crucial role in management of small breeds. It allows to assess relatedness between individuals, trends in inbreeding and to take decisions accordingly. These decisions would be based on the real genome architecture, rather than conventional pedigree information, which can be missing or incomplete. We strongly suggest the routine genotyping of all individuals that belong to a small breed in order to facilitate the effective management of endangered livestock populations.

Impact of marker ascertainment bias on genomic selection accuracy and estimates of genetic diversity.

Directory of Open Access Journals (Sweden)

Nicolas Heslot

Full Text Available Genome-wide molecular markers are often being used to evaluate genetic diversity in germplasm collections and for making genomic selections in breeding programs. To accurately predict phenotypes and assay genetic diversity, molecular markers should assay a representative sample of the polymorphisms in the population under study. Ascertainment bias arises when marker data is not obtained from a random sample of the polymorphisms in the population of interest. Genotyping-by-sequencing (GBS is rapidly emerging as a low-cost genotyping platform, even for the large, complex, and polyploid wheat (Triticum aestivum L. genome. With GBS, marker discovery and genotyping occur simultaneously, resulting in minimal ascertainment bias. The previous platform of choice for whole-genome genotyping in many species such as wheat was DArT (Diversity Array Technology and has formed the basis of most of our knowledge about cereals genetic diversity. This study compared GBS and DArT marker platforms for measuring genetic diversity and genomic selection (GS accuracy in elite U.S. soft winter wheat. From a set of 365 breeding lines, 38,412 single nucleotide polymorphism GBS markers were discovered and genotyped. The GBS SNPs gave a higher GS accuracy than 1,544 DArT markers on the same lines, despite 43.9% missing data. Using a bootstrap approach, we observed significantly more clustering of markers and ascertainment bias with DArT relative to GBS. The minor allele frequency distribution of GBS markers had a deficit of rare variants compared to DArT markers. Despite the ascertainment bias of the DArT markers, GS accuracy for three traits out of four was not significantly different when an equal number of markers were used for each platform. This suggests that the gain in accuracy observed using GBS compared to DArT markers was mainly due to a large increase in the number of markers available for the analysis.

Impact of Marker Ascertainment Bias on Genomic Selection Accuracy and Estimates of Genetic Diversity

Science.gov (United States)

Heslot, Nicolas; Rutkoski, Jessica; Poland, Jesse; Jannink, Jean-Luc; Sorrells, Mark E.

2013-01-01

Genome-wide molecular markers are often being used to evaluate genetic diversity in germplasm collections and for making genomic selections in breeding programs. To accurately predict phenotypes and assay genetic diversity, molecular markers should assay a representative sample of the polymorphisms in the population under study. Ascertainment bias arises when marker data is not obtained from a random sample of the polymorphisms in the population of interest. Genotyping-by-sequencing (GBS) is rapidly emerging as a low-cost genotyping platform, even for the large, complex, and polyploid wheat (Triticum aestivum L.) genome. With GBS, marker discovery and genotyping occur simultaneously, resulting in minimal ascertainment bias. The previous platform of choice for whole-genome genotyping in many species such as wheat was DArT (Diversity Array Technology) and has formed the basis of most of our knowledge about cereals genetic diversity. This study compared GBS and DArT marker platforms for measuring genetic diversity and genomic selection (GS) accuracy in elite U.S. soft winter wheat. From a set of 365 breeding lines, 38,412 single nucleotide polymorphism GBS markers were discovered and genotyped. The GBS SNPs gave a higher GS accuracy than 1,544 DArT markers on the same lines, despite 43.9% missing data. Using a bootstrap approach, we observed significantly more clustering of markers and ascertainment bias with DArT relative to GBS. The minor allele frequency distribution of GBS markers had a deficit of rare variants compared to DArT markers. Despite the ascertainment bias of the DArT markers, GS accuracy for three traits out of four was not significantly different when an equal number of markers were used for each platform. This suggests that the gain in accuracy observed using GBS compared to DArT markers was mainly due to a large increase in the number of markers available for the analysis. PMID:24040295

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.

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 ...

A study of using smartphone to detect and identify construction workers' near-miss falls based on ANN

Science.gov (United States)

Zhang, Mingyuan; Cao, Tianzhuo; Zhao, Xuefeng

2018-03-01

As an effective fall accident preventive method, insight into near-miss falls provides an efficient solution to find out the causes of fall accidents, classify the type of near-miss falls and control the potential hazards. In this context, the paper proposes a method to detect and identify near-miss falls that occur when a worker walks in a workplace based on artificial neural network (ANN). The energy variation generated by workers who meet with near-miss falls is measured by sensors embedded in smart phone. Two experiments were designed to train the algorithm to identify various types of near-miss falls and test the recognition accuracy, respectively. At last, a test was conducted by workers wearing smart phones as they walked around a simulated construction workplace. The motion data was collected, processed and inputted to the trained ANN to detect and identify near-miss falls. Thresholds were obtained to measure the relationship between near-miss falls and fall accidents in a quantitate way. This approach, which integrates smart phone and ANN, will help detect near-miss fall events, identify hazardous elements and vulnerable workers, providing opportunities to eliminate dangerous conditions in a construction site or to alert possible victims that need to change their behavior before the occurrence of a fall accident.

Multilevel Weighted Support Vector Machine for Classification on Healthcare Data with Missing Values.

Directory of Open Access Journals (Sweden)

Talayeh Razzaghi

Full Text Available This work is motivated by the needs of predictive analytics on healthcare data as represented by Electronic Medical Records. Such data is invariably problematic: noisy, with missing entries, with imbalance in classes of interests, leading to serious bias in predictive modeling. Since standard data mining methods often produce poor performance measures, we argue for development of specialized techniques of data-preprocessing and classification. In this paper, we propose a new method to simultaneously classify large datasets and reduce the effects of missing values. It is based on a multilevel framework of the cost-sensitive SVM and the expected maximization imputation method for missing values, which relies on iterated regression analyses. We compare classification results of multilevel SVM-based algorithms on public benchmark datasets with imbalanced classes and missing values as well as real data in health applications, and show that our multilevel SVM-based method produces fast, and more accurate and robust classification results.

Imputation methods for filling missing data in urban air pollution data for Malaysia

Directory of Open Access Journals (Sweden)

Nur Afiqah Zakaria

2018-06-01

Full Text Available The air quality measurement data obtained from the continuous ambient air quality monitoring (CAAQM station usually contained missing data. The missing observations of the data usually occurred due to machine failure, routine maintenance and human error. In this study, the hourly monitoring data of CO, O3, PM10, SO2, NOx, NO2, ambient temperature and humidity were used to evaluate four imputation methods (Mean Top Bottom, Linear Regression, Multiple Imputation and Nearest Neighbour. The air pollutants observations were simulated into four percentages of simulated missing data i.e. 5%, 10%, 15% and 20%. Performance measures namely the Mean Absolute Error, Root Mean Squared Error, Coefficient of Determination and Index of Agreement were used to describe the goodness of fit of the imputation methods. From the results of the performance measures, Mean Top Bottom method was selected as the most appropriate imputation method for filling in the missing values in air pollutants data.

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.

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.

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.;

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...

GenColors-based comparative genome databases for small eukaryotic genomes.

Science.gov (United States)

Felder, Marius; Romualdi, Alessandro; Petzold, Andreas; Platzer, Matthias; Sühnel, Jürgen; Glöckner, Gernot

2013-01-01

Many sequence data repositories can give a quick and easily accessible overview on genomes and their annotations. Less widespread is the possibility to compare related genomes with each other in a common database environment. We have previously described the GenColors database system (http://gencolors.fli-leibniz.de) and its applications to a number of bacterial genomes such as Borrelia, Legionella, Leptospira and Treponema. This system has an emphasis on genome comparison. It combines data from related genomes and provides the user with an extensive set of visualization and analysis tools. Eukaryote genomes are normally larger than prokaryote genomes and thus pose additional challenges for such a system. We have, therefore, adapted GenColors to also handle larger datasets of small eukaryotic genomes and to display eukaryotic gene structures. Further recent developments include whole genome views, genome list options and, for bacterial genome browsers, the display of horizontal gene transfer predictions. Two new GenColors-based databases for two fungal species (http://fgb.fli-leibniz.de) and for four social amoebas (http://sacgb.fli-leibniz.de) were set up. Both new resources open up a single entry point for related genomes for the amoebozoa and fungal research communities and other interested users. Comparative genomics approaches are greatly facilitated by these resources.

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

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

Science.gov (United States)

Manolio, Teri A

2016-10-01

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

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.

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.

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.

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.

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...

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.

Use of missing data methods in longitudinal studies: the persistence of bad practices in developmental psychology.

Science.gov (United States)

Jelicić, Helena; Phelps, Erin; Lerner, Richard M

2009-07-01

Developmental science rests on describing, explaining, and optimizing intraindividual changes and, hence, empirically requires longitudinal research. Problems of missing data arise in most longitudinal studies, thus creating challenges for interpreting the substance and structure of intraindividual change. Using a sample of reports of longitudinal studies obtained from three flagship developmental journals-Child Development, Developmental Psychology, and Journal of Research on Adolescence-we examined the number of longitudinal studies reporting missing data and the missing data techniques used. Of the 100 longitudinal studies sampled, 57 either reported having missing data or had discrepancies in sample sizes reported for different analyses. The majority of these studies (82%) used missing data techniques that are statistically problematic (either listwise deletion or pairwise deletion) and not among the methods recommended by statisticians (i.e., the direct maximum likelihood method and the multiple imputation method). Implications of these results for developmental theory and application, and the need for understanding the consequences of using statistically inappropriate missing data techniques with actual longitudinal data sets, are discussed.

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 ...

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.

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

The complete chloroplast genome sequence of an endemic monotypic genus Hagenia (Rosaceae: structural comparative analysis, gene content and microsatellite detection

Directory of Open Access Journals (Sweden)

Andrew W. Gichira

2017-01-01

Full Text Available Hagenia is an endangered monotypic genus endemic to the topical mountains of Africa. The only species, Hagenia abyssinica (Bruce J.F. Gmel, is an important medicinal plant producing bioactive compounds that have been traditionally used by African communities as a remedy for gastrointestinal ailments in both humans and animals. Complete chloroplast genomes have been applied in resolving phylogenetic relationships within plant families. We employed high-throughput sequencing technologies to determine the complete chloroplast genome sequence of H. abyssinica. The genome is a circular molecule of 154,961 base pairs (bp, with a pair of Inverted Repeats (IR 25,971 bp each, separated by two single copies; a large (LSC, 84,320 bp and a small single copy (SSC, 18,696. H. abyssinica’s chloroplast genome has a 37.1% GC content and encodes 112 unique genes, 78 of which code for proteins, 30 are tRNA genes and four are rRNA genes. A comparative analysis with twenty other species, sequenced to-date from the family Rosaceae, revealed similarities in structural organization, gene content and arrangement. The observed size differences are attributed to the contraction/expansion of the inverted repeats. The translational initiation factor gene (infA which had been previously reported in other chloroplast genomes was conspicuously missing in H. abyssinica. A total of 172 microsatellites and 49 large repeat sequences were detected in the chloroplast genome. A Maximum Likelihood analyses of 71 protein-coding genes placed Hagenia in Rosoideae. The availability of a complete chloroplast genome, the first in the Sanguisorbeae tribe, is beneficial for further molecular studies on taxonomic and phylogenomic resolution within the Rosaceae family.

The complete chloroplast genome sequence of an endemic monotypic genus Hagenia (Rosaceae): structural comparative analysis, gene content and microsatellite detection.

Science.gov (United States)

Gichira, Andrew W; Li, Zhizhong; Saina, Josphat K; Long, Zhicheng; Hu, Guangwan; Gituru, Robert W; Wang, Qingfeng; Chen, Jinming

2017-01-01

Hagenia is an endangered monotypic genus endemic to the topical mountains of Africa. The only species, Hagenia abyssinica (Bruce) J.F. Gmel, is an important medicinal plant producing bioactive compounds that have been traditionally used by African communities as a remedy for gastrointestinal ailments in both humans and animals. Complete chloroplast genomes have been applied in resolving phylogenetic relationships within plant families. We employed high-throughput sequencing technologies to determine the complete chloroplast genome sequence of H. abyssinica. The genome is a circular molecule of 154,961 base pairs (bp), with a pair of Inverted Repeats (IR) 25,971 bp each, separated by two single copies; a large (LSC, 84,320 bp) and a small single copy (SSC, 18,696). H. abyssinica 's chloroplast genome has a 37.1% GC content and encodes 112 unique genes, 78 of which code for proteins, 30 are tRNA genes and four are rRNA genes. A comparative analysis with twenty other species, sequenced to-date from the family Rosaceae, revealed similarities in structural organization, gene content and arrangement. The observed size differences are attributed to the contraction/expansion of the inverted repeats. The translational initiation factor gene ( infA ) which had been previously reported in other chloroplast genomes was conspicuously missing in H. abyssinica . A total of 172 microsatellites and 49 large repeat sequences were detected in the chloroplast genome. A Maximum Likelihood analyses of 71 protein-coding genes placed Hagenia in Rosoideae. The availability of a complete chloroplast genome, the first in the Sanguisorbeae tribe, is beneficial for further molecular studies on taxonomic and phylogenomic resolution within the Rosaceae family.

Comparison of methods for dealing with missing values in the EPV-R.

Science.gov (United States)

Paniagua, David; Amor, Pedro J; Echeburúa, Enrique; Abad, Francisco J

2017-08-01

The development of an effective instrument to assess the risk of partner violence is a topic of great social relevance. This study evaluates the scale of “Predicción del Riesgo de Violencia Grave Contra la Pareja” –Revisada– (EPV-R - Severe Intimate Partner Violence Risk Prediction Scale-Revised), a tool developed in Spain, which is facing the problem of how to treat the high rate of missing values, as is usual in this type of scale. First, responses to the EPV-R in a sample of 1215 male abusers who were reported to the police were used to analyze the patterns of occurrence of missing values, as well as the factor structure. Second, we analyzed the performance of various imputation methods using simulated data that emulates the missing data mechanism found in the empirical database. The imputation procedure originally proposed by the authors of the scale provides acceptable results, although the application of a method based on the Item Response Theory could provide greater accuracy and offers some additional advantages. Item Response Theory appears to be a useful tool for imputing missing data in this type of questionnaire.

ML-MG: Multi-label Learning with Missing Labels Using a Mixed Graph

KAUST Repository

Wu, Baoyuan

2015-12-07

This work focuses on the problem of multi-label learning with missing labels (MLML), which aims to label each test instance with multiple class labels given training instances that have an incomplete/partial set of these labels (i.e. some of their labels are missing). To handle missing labels, we propose a unified model of label dependencies by constructing a mixed graph, which jointly incorporates (i) instance-level similarity and class co-occurrence as undirected edges and (ii) semantic label hierarchy as directed edges. Unlike most MLML methods, We formulate this learning problem transductively as a convex quadratic matrix optimization problem that encourages training label consistency and encodes both types of label dependencies (i.e. undirected and directed edges) using quadratic terms and hard linear constraints. The alternating direction method of multipliers (ADMM) can be used to exactly and efficiently solve this problem. To evaluate our proposed method, we consider two popular applications (image and video annotation), where the label hierarchy can be derived from Wordnet. Experimental results show that our method achieves a significant improvement over state-of-the-art methods in performance and robustness to missing labels.

An adaptive functional regression-based prognostic model for applications with missing data

International Nuclear Information System (INIS)

Fang, Xiaolei; Zhou, Rensheng; Gebraeel, Nagi

2015-01-01

Most prognostic degradation models rely on a relatively accurate and comprehensive database of historical degradation signals. Typically, these signals are used to identify suitable degradation trends that are useful for predicting lifetime. In many real-world applications, these degradation signals are usually incomplete, i.e., contain missing observations. Often the amount of missing data compromises the ability to identify a suitable parametric degradation model. This paper addresses this problem by developing a semi-parametric approach that can be used to predict the remaining lifetime of partially degraded systems. First, key signal features are identified by applying Functional Principal Components Analysis (FPCA) to the available historical data. Next, an adaptive functional regression model is used to model the extracted signal features and the corresponding times-to-failure. The model is then used to predict remaining lifetimes and to update these predictions using real-time signals observed from fielded components. Results show that the proposed approach is relatively robust to significant levels of missing data. The performance of the model is evaluated and shown to provide significantly accurate predictions of residual lifetime using two case studies. - Highlights: • We model degradation signals with missing data with the goal of predicting remaining lifetime. • We examine two types of signal characteristics, fragmented and sparse. • We provide framework that updates remaining life predictions by incorporating real-time signal observations. • For the missing data, we show that the proposed model outperforms other benchmark models. • For the complete data, we show that the proposed model performs at least as good as a benchmark model

Missing value imputation for microarray gene expression data using histone acetylation information

Directory of Open Access Journals (Sweden)

Feng Jihua

2008-05-01

Full Text Available Abstract Background It is an important pre-processing step to accurately estimate missing values in microarray data, because complete datasets are required in numerous expression profile analysis in bioinformatics. Although several methods have been suggested, their performances are not satisfactory for datasets with high missing percentages. Results The paper explores the feasibility of doing missing value imputation with the help of gene regulatory mechanism. An imputation framework called histone acetylation information aided imputation method (HAIimpute method is presented. It incorporates the histone acetylation information into the conventional KNN(k-nearest neighbor and LLS(local least square imputation algorithms for final prediction of the missing values. The experimental results indicated that the use of acetylation information can provide significant improvements in microarray imputation accuracy. The HAIimpute methods consistently improve the widely used methods such as KNN and LLS in terms of normalized root mean squared error (NRMSE. Meanwhile, the genes imputed by HAIimpute methods are more correlated with the original complete genes in terms of Pearson correlation coefficients. Furthermore, the proposed methods also outperform GOimpute, which is one of the existing related methods that use the functional similarity as the external information. Conclusion We demonstrated that the using of histone acetylation information could greatly improve the performance of the imputation especially at high missing percentages. This idea can be generalized to various imputation methods to facilitate the performance. Moreover, with more knowledge accumulated on gene regulatory mechanism in addition to histone acetylation, the performance of our approach can be further improved and verified.

Sister Dehalobacter Genomes Reveal Specialization in Organohalide Respiration and Recent Strain Differentiation Likely Driven by Chlorinated Substrates

Directory of Open Access Journals (Sweden)

Shuiquan eTang

2016-02-01

Full Text Available The genomes of two closely related Dehalobacter strains (strain CF and strain DCA were assembled from the metagenome of an anaerobic enrichment culture that reductively dechlorinates chloroform (CF, 1,1,1-trichloroethane (1,1,1-TCA and 1,1-dichloroethane (1,1-DCA. The 3.1 Mbp genomes of strain CF (that dechlorinates CF and 1,1,1-TCA and strain DCA (that dechlorinates 1,1-DCA each contain 17 putative reductive dehalogenase homologous (rdh genes. These two genomes were systematically compared to three other available organohalide-respiring Dehalobacter genomes (Dehalobacter restrictus strain PER-K23, Dehalobacter sp. strain E1 and Dehalobacter sp. strain UNSWDHB, and to the genomes of Dehalococcoides mccartyi strain 195 and Desulfitobacterium hafniense strain Y51. This analysis compared 42 different metabolic and physiological categories. The genomes of strains CF and DCA share 90% overall average nucleotide identity and greater than 99.8% identity over a 2.9 Mbp alignment that excludes large insertions, indicating that these genomes differentiated from a close common ancestor. This differentiation was likely driven by selection pressures around two orthologous reductive dehalogenase genes, cfrA and dcrA, that code for the enzymes that reduce CF or 1,1,1-TCA and 1,1-DCA. The many reductive dehalogenase genes found in the five Dehalobacter genomes cluster into two small conserved regions and were often associated with Crp/Fnr transcriptional regulators. Specialization is on-going on a strain-specific basis, as some strains but not others have lost essential genes in the Wood-Ljungdahl (strain E1 and corrinoid biosynthesis pathways (strains E1 and PER-K23. The gene encoding phosphoserine phosphatase, which catalyzes the last step of serine biosynthesis, is missing from all five Dehalobacter genomes, yet D. restrictus can grow without serine, suggesting an alternative or unrecognized biosynthesis route exists. In contrast to Dehalococcoides mccartyi

Retroelements (LINEs and SINEs) in vole genomes: differential distribution in the constitutive heterochromatin.

Science.gov (United States)

Acosta, M J; Marchal, J A; Fernández-Espartero, C H; Bullejos, M; Sánchez, A

2008-01-01

The chromosomal distribution of mobile genetic elements is scarcely known in Arvicolinae species, but could be of relevance to understand the origin and complex evolution of the sex chromosome heterochromatin. In this work we cloned two retrotransposon sequences, L1 and SINE-B1, from the genome of Chionomys nivalis and investigated their chromosomal distribution on several arvicoline species. Our results demonstrate first that both retroelements are the most abundant repeated DNA sequences in the genome of these species. L1 elements, in most species, are highly accumulated in the sex chromosomes compared to the autosomes. This favoured L1 insertion could have played an important role in the origin of the enlarged heterochromatic blocks existing in the sex chromosomes of some Microtus species. Also, we propose that L1 accumulation on the X heterochromatin could have been the consequence of different, independent and rapid amplification processes acting in each species. SINE elements, however, were completely lacking from the constitutive heterochromatin, either in autosomes or in the heterochromatic blocks of sex chromosomes. These data could indicate that some SINE elements are incompatible with the formation of heterochromatic complexes and hence are necessarily missing from the constitutive heterochromatin.

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.

Randomly and Non-Randomly Missing Renal Function Data in the Strong Heart Study: A Comparison of Imputation Methods.

Directory of Open Access Journals (Sweden)

Nawar Shara

Full Text Available Kidney and cardiovascular disease are widespread among populations with high prevalence of diabetes, such as American Indians participating in the Strong Heart Study (SHS. Studying these conditions simultaneously in longitudinal studies is challenging, because the morbidity and mortality associated with these diseases result in missing data, and these data are likely not missing at random. When such data are merely excluded, study findings may be compromised. In this article, a subset of 2264 participants with complete renal function data from Strong Heart Exams 1 (1989-1991, 2 (1993-1995, and 3 (1998-1999 was used to examine the performance of five methods used to impute missing data: listwise deletion, mean of serial measures, adjacent value, multiple imputation, and pattern-mixture. Three missing at random models and one non-missing at random model were used to compare the performance of the imputation techniques on randomly and non-randomly missing data. The pattern-mixture method was found to perform best for imputing renal function data that were not missing at random. Determining whether data are missing at random or not can help in choosing the imputation method that will provide the most accurate results.

Pragmatic criteria of the definition of neonatal near miss: a comparative study.

Science.gov (United States)

Kale, Pauline Lorena; Jorge, Maria Helena Prado de Mello; Laurenti, Ruy; Fonseca, Sandra Costa; Silva, Kátia Silveira da

2017-12-04

The objective of this study was to test the validity of the pragmatic criteria of the definitions of neonatal near miss, extending them throughout the infant period, and to estimate the indicators of perinatal care in public maternity hospitals. A cohort of live births from six maternity hospitals in the municipalities of São Paulo, Niterói, and Rio de Janeiro, Brazil, was carried out in 2011. We carried out interviews and checked prenatal cards and medical records. We compared the pragmatic criteria (birth weight, gestational age, and 5' Apgar score) of the definitions of near miss of Pileggi et al., Pileggi-Castro et al., Souza et al., and Silva et al. We calculated sensitivity, specificity (gold standard: infant mortality), percentage of deaths among newborns with life-threatening conditions, and rates of near miss, mortality, and severe outcomes per 1,000 live births. A total 7,315 newborns were analyzed (completeness of information > 99%). The sensitivity of the definition of Pileggi-Castro et al. was higher, resulting in a higher number of cases of near miss, Souza et al. presented lower value, and Pileggi et al. and de Silva et al. presented intermediate values. There is an increase in sensitivity when the period goes from 0-6 to 0-27 days, and there is a decrease when it goes to 0-364 days. Specificities were high (≥ 97%) and above sensitivities (54% to 77%). One maternity hospital in São Paulo and one in Niterói presented, respectively, the lowest and highest rates of infant mortality, near miss, and frequency of births with life-threatening conditions, regardless of the definition. The definitions of near miss based exclusively on pragmatic criteria are valid and can be used for monitoring purposes. Based on the perinatal literature, the cutoff points adopted by Silva et al. were more appropriate. Periodic studies could apply a more complete definition, incorporating clinical, laboratory, and management criteria, including congenital anomalies

Optimized Use of Low-Depth Genotyping-by-Sequencing for Genomic Prediction Among Multi-Parental Family Pools and Single Plants in Perennial Ryegrass (Lolium perenne L.

Directory of Open Access Journals (Sweden)

Fabio Cericola

2018-03-01

Full Text Available Ryegrass single plants, bi-parental family pools, and multi-parental family pools are often genotyped, based on allele-frequencies using genotyping-by-sequencing (GBS assays. GBS assays can be performed at low-coverage depth to reduce costs. However, reducing the coverage depth leads to a higher proportion of missing data, and leads to a reduction in accuracy when identifying the allele-frequency at each locus. As a consequence of the latter, genomic relationship matrices (GRMs will be biased. This bias in GRMs affects variance estimates and the accuracy of GBLUP for genomic prediction (GBLUP-GP. We derived equations that describe the bias from low-coverage sequencing as an effect of binomial sampling of sequence reads, and allowed for any ploidy level of the sample considered. This allowed us to combine individual and pool genotypes in one GRM, treating pool-genotypes as a polyploid genotype, equal to the total ploidy-level of the parents of the pool. Using simulated data, we verified the magnitude of the GRM bias at different coverage depths for three different kinds of ryegrass breeding material: individual genotypes from single plants, pool-genotypes from F2 families, and pool-genotypes from synthetic varieties. To better handle missing data, we also tested imputation procedures, which are suited for analyzing allele-frequency genomic data. The relative advantages of the bias-correction and the imputation of missing data were evaluated using real data. We examined a large dataset, including single plants, F2 families, and synthetic varieties genotyped in three GBS assays, each with a different coverage depth, and evaluated them for heading date, crown rust resistance, and seed yield. Cross validations were used to test the accuracy using GBLUP approaches, demonstrating the feasibility of predicting among different breeding material. Bias-corrected GRMs proved to increase predictive accuracies when compared with standard approaches to

Transposition of a Ds element from a plasmid into the plant genome in Nicotiana plumbaginifolia protoplast-derived cells.

Science.gov (United States)

Houba-Hérin, N; Domin, M; Pédron, J

1994-07-01

Nicotiana plumbaginifolia haploid protoplasts were co-transformed with two plasmids, one with a NPT-II/Ds element and one with a gene encoding an amino-terminal truncated Ac transposase. It is shown that Ds can efficiently transpose from extrachromosomal DNA to N. plumbaginifolia chromosomes when the Ac transposase gene is present in trans. Ds has been shown to have transposed into the plant genome in a limited number of copies (1.9 copies per genome), for 21/32 transgenic lines tested. The flanking sequences present in the original plasmid are missing in these 21 plants. In only two of 21 plants was part of the transposase construct integrated. By segregation analysis of transgenic progeny, Ds was shown to be present in the heterozygous state in 10 lines even though haploid protoplasts had been originally transformed. This observation could indicate that integration occurred after or during DNA replication that leads to protoplast diploidization.

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 ...

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

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...

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…

RPAN: rice pan-genome browser for ∼3000 rice genomes.

Science.gov (United States)

Sun, Chen; Hu, Zhiqiang; Zheng, Tianqing; Lu, Kuangchen; Zhao, Yue; Wang, Wensheng; Shi, Jianxin; Wang, Chunchao; Lu, Jinyuan; Zhang, Dabing; Li, Zhikang; Wei, Chaochun

2017-01-25

A pan-genome is the union of the gene sets of all the individuals of a clade or a species and it provides a new dimension of genome complexity with the presence/absence variations (PAVs) of genes among these genomes. With the progress of sequencing technologies, pan-genome study is becoming affordable for eukaryotes with large-sized genomes. The Asian cultivated rice, Oryza sativa L., is one of the major food sources for the world and a model organism in plant biology. Recently, the 3000 Rice Genome Project (3K RGP) sequenced more than 3000 rice genomes with a mean sequencing depth of 14.3×, which provided a tremendous resource for rice research. In this paper, we present a genome browser, Rice Pan-genome Browser (RPAN), as a tool to search and visualize the rice pan-genome derived from 3K RGP. RPAN contains a database of the basic information of 3010 rice accessions, including genomic sequences, gene annotations, PAV information and gene expression data of the rice pan-genome. At least 12 000 novel genes absent in the reference genome were included. RPAN also provides multiple search and visualization functions. RPAN can be a rich resource for rice biology and rice breeding. It is available at http://cgm.sjtu.edu.cn/3kricedb/ or http://www.rmbreeding.cn/pan3k. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Identification of genomic sites for CRISPR/Cas9-based genome editing in the Vitis vinifera genome

Science.gov (United States)

CRISPR/Cas9 has been recently demonstrated as an effective and popular genome editing tool for modifying genomes of human, animals, microorganisms, and plants. Success of such genome editing is highly dependent on the availability of suitable target sites in the genomes to be edited. Many specific t...

Genomics Portals: integrative web-platform for mining genomics data.

Science.gov (United States)

Shinde, Kaustubh; Phatak, Mukta; Johannes, Freudenberg M; Chen, Jing; Li, Qian; Vineet, Joshi K; Hu, Zhen; Ghosh, Krishnendu; Meller, Jaroslaw; Medvedovic, Mario

2010-01-13

A large amount of experimental data generated by modern high-throughput technologies is available through various public repositories. Our knowledge about molecular interaction networks, functional biological pathways and transcriptional regulatory modules is rapidly expanding, and is being organized in lists of functionally related genes. Jointly, these two sources of information hold a tremendous potential for gaining new insights into functioning of living systems. Genomics Portals platform integrates access to an extensive knowledge base and a large database of human, mouse, and rat genomics data with basic analytical visualization tools. It provides the context for analyzing and interpreting new experimental data and the tool for effective mining of a large number of publicly available genomics datasets stored in the back-end databases. The uniqueness of this platform lies in the volume and the diversity of genomics data that can be accessed and analyzed (gene expression, ChIP-chip, ChIP-seq, epigenomics, computationally predicted binding sites, etc), and the integration with an extensive knowledge base that can be used in such analysis. The integrated access to primary genomics data, functional knowledge and analytical tools makes Genomics Portals platform a unique tool for interpreting results of new genomics experiments and for mining the vast amount of data stored in the Genomics Portals backend databases. Genomics Portals can be accessed and used freely at http://GenomicsPortals.org.

i-Genome: A database to summarize oligonucleotide data in genomes

Directory of Open Access Journals (Sweden)

Chang Yu-Chung

2004-10-01

Full Text Available Abstract Background Information on the occurrence of sequence features in genomes is crucial to comparative genomics, evolutionary analysis, the analyses of regulatory sequences and the quantitative evaluation of sequences. Computing the frequencies and the occurrences of a pattern in complete genomes is time-consuming. Results The proposed database provides information about sequence features generated by exhaustively computing the sequences of the complete genome. The repetitive elements in the eukaryotic genomes, such as LINEs, SINEs, Alu and LTR, are obtained from Repbase. The database supports various complete genomes including human, yeast, worm, and 128 microbial genomes. Conclusions This investigation presents and implements an efficiently computational approach to accumulate the occurrences of the oligonucleotides or patterns in complete genomes. A database is established to maintain the information of the sequence features, including the distributions of oligonucleotide, the gene distribution, the distribution of repetitive elements in genomes and the occurrences of the oligonucleotides. The database can provide more effective and efficient way to access the repetitive features in genomes.

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.

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.

Two-pass imputation algorithm for missing value estimation in gene expression time series.

Science.gov (United States)

Tsiporkova, Elena; Boeva, Veselka

2007-10-01

Gene expression microarray experiments frequently generate datasets with multiple values missing. However, most of the analysis, mining, and classification methods for gene expression data require a complete matrix of gene array values. Therefore, the accurate estimation of missing values in such datasets has been recognized as an important issue, and several imputation algorithms have already been proposed to the biological community. Most of these approaches, however, are not particularly suitable for time series expression profiles. In view of this, we propose a novel imputation algorithm, which is specially suited for the estimation of missing values in gene expression time series data. The algorithm utilizes Dynamic Time Warping (DTW) distance in order to measure the similarity between time expression profiles, and subsequently selects for each gene expression profile with missing values a dedicated set of candidate profiles for estimation. Three different DTW-based imputation (DTWimpute) algorithms have been considered: position-wise, neighborhood-wise, and two-pass imputation. These have initially been prototyped in Perl, and their accuracy has been evaluated on yeast expression time series data using several different parameter settings. The experiments have shown that the two-pass algorithm consistently outperforms, in particular for datasets with a higher level of missing entries, the neighborhood-wise and the position-wise algorithms. The performance of the two-pass DTWimpute algorithm has further been benchmarked against the weighted K-Nearest Neighbors algorithm, which is widely used in the biological community; the former algorithm has appeared superior to the latter one. Motivated by these findings, indicating clearly the added value of the DTW techniques for missing value estimation in time series data, we have built an optimized C++ implementation of the two-pass DTWimpute algorithm. The software also provides for a choice between three different

The Perennial Ryegrass GenomeZipper: Targeted Use of Genome Resources for Comparative Grass Genomics1[C][W

Science.gov (United States)

Pfeifer, Matthias; Martis, Mihaela; Asp, Torben; Mayer, Klaus F.X.; Lübberstedt, Thomas; Byrne, Stephen; Frei, Ursula; Studer, Bruno

2013-01-01

Whole-genome sequences established for model and major crop species constitute a key resource for advanced genomic research. For outbreeding forage and turf grass species like ryegrasses (Lolium spp.), such resources have yet to be developed. Here, we present a model of the perennial ryegrass (Lolium perenne) genome on the basis of conserved synteny to barley (Hordeum vulgare) and the model grass genome Brachypodium (Brachypodium distachyon) as well as rice (Oryza sativa) and sorghum (Sorghum bicolor). A transcriptome-based genetic linkage map of perennial ryegrass served as a scaffold to establish the chromosomal arrangement of syntenic genes from model grass species. This scaffold revealed a high degree of synteny and macrocollinearity and was then utilized to anchor a collection of perennial ryegrass genes in silico to their predicted genome positions. This resulted in the unambiguous assignment of 3,315 out of 8,876 previously unmapped genes to the respective chromosomes. In total, the GenomeZipper incorporates 4,035 conserved grass gene loci, which were used for the first genome-wide sequence divergence analysis between perennial ryegrass, barley, Brachypodium, rice, and sorghum. The perennial ryegrass GenomeZipper is an ordered, information-rich genome scaffold, facilitating map-based cloning and genome assembly in perennial ryegrass and closely related Poaceae species. It also represents a milestone in describing synteny between perennial ryegrass and fully sequenced model grass genomes, thereby increasing our understanding of genome organization and evolution in the most important temperate forage and turf grass species. PMID:23184232

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

Science.gov (United States)

Manolio, Teri A.

2016-01-01

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

Unlocking the diversity of genebanks: whole-genome marker analysis of Swiss bread wheat and spelt

KAUST Repository

Mü ller, Thomas; Schierscher-Viret, Beate; Fossati, Dario; Brabant, Cé cile; Schori, Arnold; Keller, Beat; Krattinger, Simon G.

2017-01-01

Genebanks play a pivotal role in preserving the genetic diversity present among old landraces and wild progenitors of modern crops and they represent sources of agriculturally important genes that were lost during domestication and in modern breeding. However, undesirable genes that negatively affect crop performance are often co-introduced when landraces and wild crop progenitors are crossed with elite cultivars, which often limit the use of genebank material in modern breeding programs. A detailed genetic characterization is an important prerequisite to solve this problem and to make genebank material more accessible to breeding. Here, we genotyped 502 bread wheat and 293 spelt accessions held in the Swiss National Genebank using a 15K wheat SNP array. The material included both spring and winter wheats and consisted of old landraces and modern cultivars. Genome- and sub-genome-wide analyses revealed that spelt and bread wheat form two distinct gene pools. In addition, we identified bread wheat landraces that were genetically distinct from modern cultivars. Such accessions were possibly missed in the early Swiss wheat breeding program and are promising targets for the identification of novel genes. The genetic information obtained in this study is appropriate to perform genome-wide association studies, which will facilitate the identification and transfer of agriculturally important genes from the genebank into modern cultivars through marker-assisted selection.

Unlocking the diversity of genebanks: whole-genome marker analysis of Swiss bread wheat and spelt

KAUST Repository

Müller, Thomas

2017-11-04

Genebanks play a pivotal role in preserving the genetic diversity present among old landraces and wild progenitors of modern crops and they represent sources of agriculturally important genes that were lost during domestication and in modern breeding. However, undesirable genes that negatively affect crop performance are often co-introduced when landraces and wild crop progenitors are crossed with elite cultivars, which often limit the use of genebank material in modern breeding programs. A detailed genetic characterization is an important prerequisite to solve this problem and to make genebank material more accessible to breeding. Here, we genotyped 502 bread wheat and 293 spelt accessions held in the Swiss National Genebank using a 15K wheat SNP array. The material included both spring and winter wheats and consisted of old landraces and modern cultivars. Genome- and sub-genome-wide analyses revealed that spelt and bread wheat form two distinct gene pools. In addition, we identified bread wheat landraces that were genetically distinct from modern cultivars. Such accessions were possibly missed in the early Swiss wheat breeding program and are promising targets for the identification of novel genes. The genetic information obtained in this study is appropriate to perform genome-wide association studies, which will facilitate the identification and transfer of agriculturally important genes from the genebank into modern cultivars through marker-assisted selection.

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.

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”.

Increased Urge to Gamble Following Near-Miss Outcomes May Drive Purchasing Behaviour in Scratch Card Gambling.

Science.gov (United States)

Stange, Madison; Graydon, Candice; Dixon, Mike J

2017-09-01

Previous research into scratch card gambling has highlighted the effects of these games on players' arousal and affective states. Specifically, near-miss outcomes in scratch cards (uncovering 2 of 3 needed jackpot symbols) have been associated with high levels of physiological and subjective arousal and negative emotional evaluations, including increased frustration. We sought to extend this research by examining whether near-misses prompted increases in gambling urge, and the subsequent purchasing of additional scratch cards. Participants played two scratch cards with varying outcomes with half of the sample experiencing a near-miss for the jackpot prize, and the other half experiencing a regular loss. Players rated their urge to continue gambling after each game outcome, and following the initial playing phase, were then able to use their winnings to purchase additional cards. Our results indicated that near-misses increased the urge to gamble significantly more than regular losses, and urge to gamble in the near-miss group was significantly correlated with purchasing at least one additional card. Although some players in the loss group purchased another card, there was no correlation between urge to gamble and purchasing in this group. Additionally, participants in the near-miss group who purchased additional cards reported higher levels of urge than those who did not purchase more cards. This was not true for the loss group: participants who experienced solely losing outcomes reported similar levels of urge regardless of whether or not they purchased more scratch cards. Despite near-misses' objective status as monetary losses, the increased urge that follows near-miss outcomes may translate into further scratch card gambling for a subset of individuals .

Impact of Delayed Time to Advanced Imaging on Missed Appointments Across Different Demographic and Socioeconomic Factors.

Science.gov (United States)

Daye, Dania; Carrodeguas, Emmanuel; Glover, McKinley; Guerrier, Claude Emmanuel; Harvey, H Benjamin; Flores, Efrén J

2018-05-01

The aim of this study was to investigate the impact of wait days (WDs) on missed outpatient MRI appointments across different demographic and socioeconomic factors. An institutional review board-approved retrospective study was conducted among adult patients scheduled for outpatient MRI during a 12-month period. Scheduling data and demographic information were obtained. Imaging missed appointments were defined as missed scheduled imaging encounters. WDs were defined as the number of days from study order to appointment. Multivariate logistic regression was applied to assess the contribution of race and socioeconomic factors to missed appointments. Linear regression was performed to assess the relationship between missed appointment rates and WDs stratified by race, income, and patient insurance groups with analysis of covariance statistics. A total of 42,727 patients met the inclusion criteria. Mean WDs were 7.95 days. Multivariate regression showed increased odds ratio for missed appointments for patients with increased WDs (7-21 days: odds ratio [OR], 1.39; >21 days: OR, 1.77), African American patients (OR, 1.71), Hispanic patients (OR, 1.30), patients with noncommercial insurance (OR, 2.00-2.55), and those with imaging performed at the main hospital campus (OR, 1.51). Missed appointment rate linearly increased with WDs, with analysis of covariance revealing underrepresented minorities and Medicaid insurance as significant effect modifiers. Increased WDs for advanced imaging significantly increases the likelihood of missed appointments. This effect is most pronounced among underrepresented minorities and patients with lower socioeconomic status. Efforts to reduce WDs may improve equity in access to and utilization of advanced diagnostic imaging for all patients. Copyright © 2018. Published by Elsevier Inc.

Comparing Mycobacterium tuberculosis genomes using genome topology networks.

Science.gov (United States)

Jiang, Jianping; Gu, Jianlei; Zhang, Liang; Zhang, Chenyi; Deng, Xiao; Dou, Tonghai; Zhao, Guoping; Zhou, Yan

2015-02-14

Over the last decade, emerging research methods, such as comparative genomic analysis and phylogenetic study, have yielded new insights into genotypes and phenotypes of closely related bacterial strains. Several findings have revealed that genomic structural variations (SVs), including gene gain/loss, gene duplication and genome rearrangement, can lead to different phenotypes among strains, and an investigation of genes affected by SVs may extend our knowledge of the relationships between SVs and phenotypes in microbes, especially in pathogenic bacteria. In this work, we introduce a 'Genome Topology Network' (GTN) method based on gene homology and gene locations to analyze genomic SVs and perform phylogenetic analysis. Furthermore, the concept of 'unfixed ortholog' has been proposed, whose members are affected by SVs in genome topology among close species. To improve the precision of 'unfixed ortholog' recognition, a strategy to detect annotation differences and complete gene annotation was applied. To assess the GTN method, a set of thirteen complete M. tuberculosis genomes was analyzed as a case study. GTNs with two different gene homology-assigning methods were built, the Clusters of Orthologous Groups (COG) method and the orthoMCL clustering method, and two phylogenetic trees were constructed accordingly, which may provide additional insights into whole genome-based phylogenetic analysis. We obtained 24 unfixable COG groups, of which most members were related to immunogenicity and drug resistance, such as PPE-repeat proteins (COG5651) and transcriptional regulator TetR gene family members (COG1309). The GTN method has been implemented in PERL and released on our website. The tool can be downloaded from http://homepage.fudan.edu.cn/zhouyan/gtn/ , and allows re-annotating the 'lost' genes among closely related genomes, analyzing genes affected by SVs, and performing phylogenetic analysis. With this tool, many immunogenic-related and drug resistance-related genes

A universal genomic coordinate translator for comparative genomics.

Science.gov (United States)

Zamani, Neda; Sundström, Görel; Meadows, Jennifer R S; Höppner, Marc P; Dainat, Jacques; Lantz, Henrik; Haas, Brian J; Grabherr, Manfred G

2014-06-30

Genomic duplications constitute major events in the evolution of species, allowing paralogous copies of genes to take on fine-tuned biological roles. Unambiguously identifying the orthology relationship between copies across multiple genomes can be resolved by synteny, i.e. the conserved order of genomic sequences. However, a comprehensive analysis of duplication events and their contributions to evolution would require all-to-all genome alignments, which increases at N2 with the number of available genomes, N. Here, we introduce Kraken, software that omits the all-to-all requirement by recursively traversing a graph of pairwise alignments and dynamically re-computing orthology. Kraken scales linearly with the number of targeted genomes, N, which allows for including large numbers of genomes in analyses. We first evaluated the method on the set of 12 Drosophila genomes, finding that orthologous correspondence computed indirectly through a graph of multiple synteny maps comes at minimal cost in terms of sensitivity, but reduces overall computational runtime by an order of magnitude. We then used the method on three well-annotated mammalian genomes, human, mouse, and rat, and show that up to 93% of protein coding transcripts have unambiguous pairwise orthologous relationships across the genomes. On a nucleotide level, 70 to 83% of exons match exactly at both splice junctions, and up to 97% on at least one junction. We last applied Kraken to an RNA-sequencing dataset from multiple vertebrates and diverse tissues, where we confirmed that brain-specific gene family members, i.e. one-to-many or many-to-many homologs, are more highly correlated across species than single-copy (i.e. one-to-one homologous) genes. Not limited to protein coding genes, Kraken also identifies thousands of newly identified transcribed loci, likely non-coding RNAs that are consistently transcribed in human, chimpanzee and gorilla, and maintain significant correlation of expression levels across

A prospective evaluation of missed injuries in trauma patients, before and after formalising the trauma tertiary survey.

Science.gov (United States)

Keijzers, Gerben B; Campbell, Don; Hooper, Jeffrey; Bost, Nerolie; Crilly, Julia; Steele, Michael Craig; Del Mar, Chris; Geeraedts, Leo M G

2014-01-01

This study prospectively evaluated in-hospital and postdischarge missed injury rates in admitted trauma patients, before and after the formalisation of a trauma tertiary survey (TTS) procedure. Prospective before-and-after cohort study. TTS were formalised in a single regional level II trauma hospital in November 2009. All multitrauma patients admitted between March-October 2009 (preformalisation of TTS) and December 2009-September 2010 (post-) were assessed for missed injury, classified into three types: Type I, in-hospital, (injury missed at initial assessment, detected within 24 h); Type II, in-hospital (detected in hospital after 24 h, missed at initial assessment and by TTS); Type III, postdischarge (detected after hospital discharge). Secondary outcome measures included TTS performance rates and functional outcomes at 1 and 6 months. A total of 487 trauma patients were included (pre-: n = 235; post-: n = 252). In-hospital missed injury rate (Types I and II combined) was similar for both groups (3.8 vs. 4.8 %, P = 0.61), as were postdischarge missed injury rates (Type III) at 1 month (13.7 vs. 11.5 %, P = 0.43), and 6 months (3.8 vs. 3.3 %, P = 0.84) after discharge. TTS performance was substantially higher in the post-group (27 vs. 42 %, P cumulative missed injury rates >15 %. Some of these injuries were clinically relevant. Although TTS performance was significantly improved by formalising the process (from 27 to 42 %), this did not decrease missed injury rates.

Genomics Portals: integrative web-platform for mining genomics data

Directory of Open Access Journals (Sweden)

Ghosh Krishnendu

2010-01-01

Full Text Available Abstract Background A large amount of experimental data generated by modern high-throughput technologies is available through various public repositories. Our knowledge about molecular interaction networks, functional biological pathways and transcriptional regulatory modules is rapidly expanding, and is being organized in lists of functionally related genes. Jointly, these two sources of information hold a tremendous potential for gaining new insights into functioning of living systems. Results Genomics Portals platform integrates access to an extensive knowledge base and a large database of human, mouse, and rat genomics data with basic analytical visualization tools. It provides the context for analyzing and interpreting new experimental data and the tool for effective mining of a large number of publicly available genomics datasets stored in the back-end databases. The uniqueness of this platform lies in the volume and the diversity of genomics data that can be accessed and analyzed (gene expression, ChIP-chip, ChIP-seq, epigenomics, computationally predicted binding sites, etc, and the integration with an extensive knowledge base that can be used in such analysis. Conclusion The integrated access to primary genomics data, functional knowledge and analytical tools makes Genomics Portals platform a unique tool for interpreting results of new genomics experiments and for mining the vast amount of data stored in the Genomics Portals backend databases. Genomics Portals can be accessed and used freely at http://GenomicsPortals.org.

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.

Femoral head avascular necrosis: a frequently missed incidental finding on multidetector CT.

Science.gov (United States)

Barille, M F; Wu, Jim S; McMahon, Colm J

2014-03-01

To determine the incidence of missed femoral head avascular necrosis (AVN) on pelvic computed tomography (CT) performed for clinical indications other than assessment for AVN. The study was a Health Insurance Portability and Accountability Act (HIPAA)-compliant retrospective study. The picture archiving and communication system (PACS) database was queried for patients with diagnosis of femoral head AVN on magnetic resonance imaging (MRI), who also underwent pelvic multidetector CT after or AVN on MRI and 33 age-matched controls; mean age = 60 years, 28 male, 44 female), were reviewed in consensus by two readers in a randomized, blinded manner. Using MRI-proven CT-visible AVN as a reference standard, the incidence of missed AVN on initial CT interpretation was determined. Readers confirmed AVN in 33 patients on the MRI images. Nine hips with AVN underwent joint replacement of the affected joint(s) prior to subsequent CT and were excluded. Forty-three MRI-proven AVN cases in 28 patients (15 bilateral, 13 unilateral) were available for analysis. The study readers diagnosed 35/43 (81%) MRI-proven AVN cases in 22/28 (79%) patients. Four of the 35 (11%) cases of MRI-proven, CT-visible AVN were prospectively reported in 3/22 (14%) patients at initial clinical interpretation, with a miss rate of 89% per hip and 86% per patient. Multidetector CT has high accuracy for detection of AVN; however, this is frequently missed as an incidental finding (89% missed in the present study). Assessment for signs of femoral AVN should be part of routine search pattern in interpretation of pelvic CT. Copyright © 2013 The Royal College of Radiologists. Published by Elsevier Ltd. All rights reserved.

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

Estimation of response from longitudinal binary data with nonignorable missing values in migraine trials

Directory of Open Access Journals (Sweden)

Fang Fang

2016-12-01

Full Text Available In migraine trials pain relief responses from a headache at specific time points and sustained pain relief response over a period of time are important efficacy measures. When there are missing records of individual time point pain scores and/or headache recurrences during a migraine trial, the common approach used in practice to estimate the sustained response is statistically inconsistent even if the data are missing completely at random. Methods dealing with nonignorable longitudinal missing data usually assume certain models for the missing mechanism which can not be checked as they involve unobserved data. Taking advantage of the specific definition of the ‘sustained pain relief’ response, we propose two estimating methods based on intuitive imputation, which do not require model assumptions on the missing probability or specification of the correlation structure among the longitudinal observations. The consistency of the proposed methods is discussed in theory and their empirical performances are assessed through intensive simulation studies. The simulation results show that the proposed methods perform well in terms of reducing bias and mean square error except in several extreme cases which are unlikely to happen in real trials. The application of the proposed methods is illustrated in a real data analysis.

Calibration and analysis of genome-based models for microbial ecology.

Science.gov (United States)

Louca, Stilianos; Doebeli, Michael

2015-10-16

Microbial ecosystem modeling is complicated by the large number of unknown parameters and the lack of appropriate calibration tools. Here we present a novel computational framework for modeling microbial ecosystems, which combines genome-based model construction with statistical analysis and calibration to experimental data. Using this framework, we examined the dynamics of a community of Escherichia coli strains that emerged in laboratory evolution experiments, during which an ancestral strain diversified into two coexisting ecotypes. We constructed a microbial community model comprising the ancestral and the evolved strains, which we calibrated using separate monoculture experiments. Simulations reproduced the successional dynamics in the evolution experiments, and pathway activation patterns observed in microarray transcript profiles. Our approach yielded detailed insights into the metabolic processes that drove bacterial diversification, involving acetate cross-feeding and competition for organic carbon and oxygen. Our framework provides a missing link towards a data-driven mechanistic microbial ecology.

Extraction of the missing low-Q data from small-angle scattering data

International Nuclear Information System (INIS)

Doherty, G.K.; Poland, G.A.

1996-01-01

A new method is presented that recovers the scatter intensity curve at low Q values from small-angle neutron scattering data. The method uses only the measured data, requiring no extrapolation of the scatter curve nor any a priori knowledge of the maximum chord length, radius of gyration or molecular weight of the particle under investigation. It is assumed that the incoherent level would have been extracted from the data in the normal course of events but any errors do not affect the method presented. The distance distribution function of any particle has a restricted extension in real space and any nonzero value beyond the maximum size of the particle is due to the effects of missing data segments and noise on the measured data. The effects due to the missing and noisy data are isolated from the distance distribution of the particle and a suitably scaled template particle is used to fill in the missing distribution data segment. The inverse transform of the new distribution function returns the missing low-Q scatter data and to some extent cancels out the noise. While the method is generally explored using noise-free analytically derived particles, its application to real experimental data is demonstrated. (orig.)

Mercury genomics in the Arctic Ocean

Science.gov (United States)

Bowman, K.; Lamborg, C. H.; Collins, E.; Hammerschmidt, C. R.; Agather, A. M.

2017-12-01

Methyl-mercury production in the ocean is likely dependent on microbial activity, however, methylation pathways remain elusive. In the Arctic, high concentrations of methyl-mercury are found in top predator marine mammals and seabirds. As a result of seafood consumption, pregnant women and women of child-bearing age in the Arctic often have blood Hg concentrations that exceed U.S. and Canadian safety guidelines. To understand the chemical cycling of mercury in the Arctic Ocean we participated in the 2015 U.S. GEOTRACES Arctic expedition (GN01) to measure Hg speciation in the water column of the Bering Sea, Makarov basin, and Canada basin between Dutch Harbor, Alaska and the North Pole. At select stations, seawater was filtered through 0.22 µm Sterivex filters and genomic DNA was collected using a phenol-chloroform extraction. Broad-range degenerate PCR primers were used to detect the presence of hgcAB, and clade-specific degenerate quantitative PCR primers were used to determine the abundance of hgcA. Metagenomic sequencing was done at three stations to identify taxonomic and functional groups, and to search for hgcA-like genes that the PCR primers may have missed.

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...

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...

On a Comparison and Contrast of Sherlock Holmes And Miss Jane Marple

Institute of Scientific and Technical Information of China (English)

张豪若

2014-01-01

In the history of detective stories, Sherlock Holmes and Miss Jane Marple remain as two of the most prominent fig-ures. Focusing on the two detectives' images, personality traits, detective strategies as well as settings of the stories, this study ex-amines the grounds that magnetize readers.The purpose of this research is to inquire into readers' orientations to Sherlock Holm-es and Miss Jane Marple, and to investigate the causes for their views. To fulfill that purpose, a questionnaire was designed and dis-tributed. Sherlock Holmes and Miss Jane Marple prove themselves to be successful detectives. Both of them have distinct images and personality traits as well as plausible detective strategies. The settings, combining reality with imagination, also play a dispens-able role. Besides, reasons given by students who disbelieve that they are real persons fail to convince.

Exploring the Influence of Nursing Work Environment and Patient Safety Culture on Missed Nursing Care in Korea.

Science.gov (United States)

Kim, Kyoung-Ja; Yoo, Moon Sook; Seo, Eun Ji

2018-04-20

This study aimed to explore the influence of nurse work environment and patient safety culture in hospital on instances of missed nursing care in South Korea. A cross-sectional design was used, in which a structured questionnaire was administered to 186 nurses working at a tertiary university hospital. Data were analyzed using descriptive statistics, t-test or ANOVA, Pearson correlation and multiple regression analysis. Missed nursing care was found to be correlated with clinical career, nursing work environment and patient safety culture. The regression model explained approximately 30.3 % of missed nursing care. Meanwhile, staffing and resource adequacy (β = -.31, p = .001), nurse manager ability, leadership and support of nurses (β = -.26, p = .004), clinical career (β = -.21, p = .004), and perception on patient safety culture within unit (β = -.19, p = .041) were determined to be influencing factors on missed nursing care. This study has significance as it suggested that missed nursing care is affected by work environment factors within unit. This means that missed nursing care is a unit outcome affected by nurse work environment factors and patient safety culture. Therefore, missed nursing care can be managed through the implementation of interventions that promote a positive nursing work environment and patient safety culture. Copyright © 2018. Published by Elsevier B.V.

Near Misses in Financial Trading: Skills for Capturing and Averting Error.

Science.gov (United States)

Leaver, Meghan; Griffiths, Alex; Reader, Tom

2018-05-01

The aims of this study were (a) to determine whether near-miss incidents in financial trading contain information on the operator skills and systems that detect and prevent near misses and the patterns and trends revealed by these data and (b) to explore if particular operator skills and systems are found as important for avoiding particular types of error on the trading floor. In this study, we examine a cohort of near-miss incidents collected from a financial trading organization using the Financial Incident Analysis System and report on the nontechnical skills and systems that are used to detect and prevent error in this domain. One thousand near-miss incidents are analyzed using distribution, mean, chi-square, and associative analysis to describe the data; reliability is provided. Slips/lapses (52%) and human-computer interface problems (21%) often occur alone and are the main contributors to error causation, whereas the prevention of error is largely a result of teamwork (65%) and situation awareness (46%) skills. No matter the cause of error, situation awareness and teamwork skills are used most often to detect and prevent the error. Situation awareness and teamwork skills appear universally important as a "last line" of defense for capturing error, and data from incident-monitoring systems can be analyzed in a fashion more consistent with a "Safety-II" approach. This research provides data for ameliorating risk within financial trading organizations, with implications for future risk management programs and regulation.

Missing texture reconstruction method based on error reduction algorithm using Fourier transform magnitude estimation scheme.

Science.gov (United States)

Ogawa, Takahiro; Haseyama, Miki

2013-03-01

A missing texture reconstruction method based on an error reduction (ER) algorithm, including a novel estimation scheme of Fourier transform magnitudes is presented in this brief. In our method, Fourier transform magnitude is estimated for a target patch including missing areas, and the missing intensities are estimated by retrieving its phase based on the ER algorithm. Specifically, by monitoring errors converged in the ER algorithm, known patches whose Fourier transform magnitudes are similar to that of the target patch are selected from the target image. In the second approach, the Fourier transform magnitude of the target patch is estimated from those of the selected known patches and their corresponding errors. Consequently, by using the ER algorithm, we can estimate both the Fourier transform magnitudes and phases to reconstruct the missing areas.

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,…