High-quality permanent draft genome sequence of Bradyrhizobium sp. Tv2a.2, a microsymbiont of Tachigali versicolor discovered in Barro Colorado Island of Panama

DOE PAGES

Tian, Rui; Parker, Matthew; Seshadri, Rekha; ...

2015-05-17

Bradyrhizobiumsp. Tv2a.2 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing root nodule of Tachigali versicolor collected in Barro Colorado Island of Panama. Here we describe the features of Bradyrhizobiumsp. Tv2a.2, together with high-quality permanent draft genome sequence information and annotation. The 8,496,279 bp high-quality draft genome is arranged in 87 scaffolds of 87 contigs, contains 8,109 protein-coding genes and 72 RNA-only encoding genes. In conclusion, this rhizobial genome was sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.

De novo genome assembly of the red silk cotton tree (Bombax ceiba).

PubMed

Gao, Yong; Wang, Haibo; Liu, Chao; Chu, Honglong; Dai, Dongqin; Song, Shengnan; Yu, Long; Han, Lihong; Fu, Yi; Tian, Bin; Tang, Lizhou

2018-05-01

Bombax ceiba L. (the red silk cotton tree) is a large deciduous tree that is distributed in tropical and sub-tropical Asia as well as northern Australia. It has great economic and ecological importance, with several applications in industry and traditional medicine in many Asian countries. To facilitate further utilization of this plant resource, we present here the draft genome sequence for B. ceiba. We assembled a relatively intact genome of B. ceiba by using PacBio single-molecule sequencing and BioNano optical mapping technologies. The final draft genome is approximately 895 Mb long, with contig and scaffold N50 sizes of 1.0 Mb and 2.06 Mb, respectively. The high-quality draft genome assembly of B. ceiba will be a valuable resource enabling further genetic improvement and more effective use of this tree species.

Publication Guidelines for Quality Improvement Studies in Health Care: Evolution of the SQUIRE Project

PubMed Central

Batalden, Paul; Stevens, David; Ogrinc, Greg; Mooney, Susan

2008-01-01

In 2005 we published draft guidelines for reporting studies of quality improvement interventions as the initial step in a consensus process for development of a more definitive version. The current article contains the revised version, which we refer to as SQUIRE (Standards for QUality Improvement Reporting Excellence). We describe the consensus process, which included informal feedback, formal written commentaries, input from publication guideline developers, review of the literature on the epistemology of improvement and on methods for evaluating complex social programs, and a meeting of stakeholders for critical review of the guidelines’ content and wording, followed by commentary on sequential versions from an expert consultant group. Finally, we examine major differences between SQUIRE and the initial draft, and consider limitations of and unresolved questions about SQUIRE; we also describe ancillary supporting documents and alternative versions under development, and plans for dissemination, testing, and further development of SQUIRE. PMID:18830766

High-Quality Draft Genome Sequences of Four Lignocellulose-Degrading Bacteria Isolated from Puerto Rican Forest Soil: Gordonia sp., Paenibacillus sp., Variovorax sp., and Vogesella sp.

DOE PAGES

Woo, Hannah L.; DeAngelis, Kristen M.; Teshima, Hazuki; ...

2017-05-04

In this paper, we report the high-quality draft genome sequences of four phylogenetically diverse lignocellulose-degrading bacteria isolated from tropical soil ( Gordonia sp., Paenibacillus sp., Variovorax sp., and Vogesella sp.) to elucidate the genetic basis of their ability to degrade lignocellulose. These isolates may provide novel enzymes for biofuel production.

High-Quality Draft Genome Sequences of Four Lignocellulose-Degrading Bacteria Isolated from Puerto Rican Forest Soil: Gordonia sp., Paenibacillus sp., Variovorax sp., and Vogesella sp.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Woo, Hannah L.; DeAngelis, Kristen M.; Teshima, Hazuki

In this paper, we report the high-quality draft genome sequences of four phylogenetically diverse lignocellulose-degrading bacteria isolated from tropical soil ( Gordonia sp., Paenibacillus sp., Variovorax sp., and Vogesella sp.) to elucidate the genetic basis of their ability to degrade lignocellulose. These isolates may provide novel enzymes for biofuel production.

Refining a taxonomy for guideline implementation: results of an exercise in abstract classification

PubMed Central

2013-01-01

Background To better understand the efficacy of various implementation strategies, improved methods for describing and classifying the nature of these strategies are urgently required. The aim of this study was to develop and pilot the feasibility of a taxonomy to classify the nature and content of implementation strategies. Methods A draft implementation taxonomy was developed based on the Cochrane Effective Practice and Organisation of Care (EPOC) data collection checklist. The draft taxonomy had four domains (professional, financial, organisational and regulatory) covering 49 distinct strategies. We piloted the draft taxonomy by using it to classify the implementation strategies described in the conference abstracts of the implementation stream of the 2010 Guideline International Network Conference. Five authors classified the strategies in each abstract individually. Final categorisation was then carried out in a face-to-face consensus meeting involving three authors. Results The implementation strategies described in 71 conference abstracts were classified. Approximately 15.5% of abstracts utilised strategies that could not be categorised using the draft taxonomy. Of those strategies that could be categorised, the majority were professionally focused (57%). A total of 41% of projects used only one implementation strategy, with 29% using two and 31% three or more. The three most commonly used strategies were changes in quality assurance, quality improvement and/or performance measurement systems, changes in information and communication technology, and distribution of guideline materials (via hard-copy, audio-visual and/or electronic means). Conclusions Further refinement of the draft taxonomy is required to provide hierarchical dimensions and granularity, particularly in the areas of patient-focused interventions, those concerned with audit and feedback and quality improvement, and electronic forms of implementation, including electronic decision support. PMID:23497520

Refining a taxonomy for guideline implementation: results of an exercise in abstract classification.

PubMed

Mazza, Danielle; Bairstow, Phillip; Buchan, Heather; Chakraborty, Samantha Paubrey; Van Hecke, Oliver; Grech, Cathy; Kunnamo, Ilkka

2013-03-15

To better understand the efficacy of various implementation strategies, improved methods for describing and classifying the nature of these strategies are urgently required. The aim of this study was to develop and pilot the feasibility of a taxonomy to classify the nature and content of implementation strategies. A draft implementation taxonomy was developed based on the Cochrane Effective Practice and Organisation of Care (EPOC) data collection checklist. The draft taxonomy had four domains (professional, financial, organisational and regulatory) covering 49 distinct strategies. We piloted the draft taxonomy by using it to classify the implementation strategies described in the conference abstracts of the implementation stream of the 2010 Guideline International Network Conference. Five authors classified the strategies in each abstract individually. Final categorisation was then carried out in a face-to-face consensus meeting involving three authors. The implementation strategies described in 71 conference abstracts were classified. Approximately 15.5% of abstracts utilised strategies that could not be categorised using the draft taxonomy. Of those strategies that could be categorised, the majority were professionally focused (57%). A total of 41% of projects used only one implementation strategy, with 29% using two and 31% three or more. The three most commonly used strategies were changes in quality assurance, quality improvement and/or performance measurement systems, changes in information and communication technology, and distribution of guideline materials (via hard-copy, audio-visual and/or electronic means). Further refinement of the draft taxonomy is required to provide hierarchical dimensions and granularity, particularly in the areas of patient-focused interventions, those concerned with audit and feedback and quality improvement, and electronic forms of implementation, including electronic decision support.

77 FR 39959 - Draft Guidance To Implement Requirements for the Treatment of Air Quality Monitoring Data...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-06

... of the revised draft High Winds Guidance document, the EPA identifies example technical analyses that... identified analyses and any additional technical analyses that air agencies could use to demonstrate that the... Web site at http://www.epa.gov/ttn/analysis/exevents.htm for additional details on the draft non...

ASCCP Colposcopy Standards: Colposcopy Quality Improvement Recommendations for the United States.

PubMed

Mayeaux, Edward J; Novetsky, Akiva P; Chelmow, David; Garcia, Francisco; Choma, Kim; Liu, Angela H; Papasozomenos, Theognosia; Einstein, Mark H; Massad, L Stewart; Wentzensen, Nicolas; Waxman, Alan G; Conageski, Christine; Khan, Michelle J; Huh, Warner K

2017-10-01

The American Society for Colposcopy and Cervical Pathology (ASCCP) Colposcopy Standards recommendations address the role of and approach to colposcopy and biopsy for cervical cancer prevention in the United States. The recommendations were developed by an expert working group appointed by ASCCP's Board of Directors. The ASCCP Quality Improvement Working Group developed evidence-based guidelines to promote best practices and reduce errors in colposcopy and recommended indicators to measure colposcopy quality. The working group performed a systematic review of existing major society and national guidelines and quality indicators. An initial list of potential quality indicators was developed and refined through successive iterative discussions, and draft quality indicators were proposed. The draft recommendations were then reviewed and commented on by the entire Colposcopy Standards Committee, posted online for public comment, and presented at the International Federation for Cervical Pathology and Colposcopy 2017 World Congress for further comment. All comments were considered, additional adjustments made, and the final recommendations approved by the entire Task Force. Eleven quality indicators were selected spanning documentation, biopsy protocols, and time intervals between index screening tests and completion of diagnostic evaluation. The proposed quality indicators are intended to serve as a starting point for quality improvement in colposcopy at a time when colposcopy volume is decreasing and individual procedures are becoming technically more difficult to perform.

Positional bias in variant calls against draft reference assemblies.

PubMed

Briskine, Roman V; Shimizu, Kentaro K

2017-03-28

Whole genome resequencing projects may implement variant calling using draft reference genomes assembled de novo from short-read libraries. Despite lower quality of such assemblies, they allowed researchers to extend a wide range of population genetic and genome-wide association analyses to non-model species. As the variant calling pipelines are complex and involve many software packages, it is important to understand inherent biases and limitations at each step of the analysis. In this article, we report a positional bias present in variant calling performed against draft reference assemblies constructed from de Bruijn or string overlap graphs. We assessed how frequently variants appeared at each position counted from ends of a contig or scaffold sequence, and discovered unexpectedly high number of variants at the positions related to the length of either k-mers or reads used for the assembly. We detected the bias in both publicly available draft assemblies from Assemblathon 2 competition as well as in the assemblies we generated from our simulated short-read data. Simulations confirmed that the bias causing variants are predominantly false positives induced by reads from spatially distant repeated sequences. The bias is particularly strong in contig assemblies. Scaffolding does not eliminate the bias but tends to mitigate it because of the changes in variants' relative positions and alterations in read alignments. The bias can be effectively reduced by filtering out the variants that reside in repetitive elements. Draft genome sequences generated by several popular assemblers appear to be susceptible to the positional bias potentially affecting many resequencing projects in non-model species. The bias is inherent to the assembly algorithms and arises from their particular handling of repeated sequences. It is recommended to reduce the bias by filtering especially if higher-quality genome assembly cannot be achieved. Our findings can help other researchers to improve the quality of their variant data sets and reduce artefactual findings in downstream analyses.

Access to Quality Early Childhood Care and Education. Background Paper for the Quality Child Care Think Tank. Draft.

ERIC Educational Resources Information Center

Brandon, Richard N.; Smith, Diana

This background paper discusses the current system of child care finance in Washington State and analyzes options for improvement. It describes prominent characteristics of the early childhood care and education system, findings relating program quality to staff/child ratios and staff educational levels, characteristics of quality, parent…

The potential clinical impact of the release of two drafts of the human proteome

PubMed Central

Ezkurdia, Iakes; Calvo, Enrique; Del Pozo, Angela; Vázquez, Jesús; Valencia, Alfonso; Tress, Michael L.

2015-01-01

The authors have carried out an investigation of the two “draft maps of the human proteome” published in 2014 in Nature. The findings include an abundance of poor spectra, low-scoring peptide-spectrum matches and incorrectly identified proteins in both these studies, highlighting clear issues with the application of false discovery rates. This noise means that the claims made by the two papers – the identification of high numbers of protein coding genes, the detection of novel coding regions and the draft tissue maps themselves – should be treated with considerable caution. The authors recommend that clinicians and researchers do not use the unfiltered data from these studies. Despite this these studies will inspire further investigation into tissue-based proteomics. As long as this future work has proper quality controls, it could help produce a consensus map of the human proteome and improve our understanding of the processes that underlie health and disease. PMID:26496066

78 FR 16656 - Draft Damage Assessment and Restoration Plan and Environmental Assessment for Natural Resource...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-18

... may be sent to: Ian Zelo, NOAA Oil Spill Coordinator, Assessment and Restoration Division, 7600 Sand... are: (1) Improve Helmet Creek, restore juvenile and adult fish passage, (2) Improve water quality, and...

Venturia carpophila draft genome sequence

USDA-ARS?s Scientific Manuscript database

Venturia carpophila causes peach scab, a disease that renders peach fruit unmarketable. We report a high-quality draft genome sequence (36.9 Mb) of V. carpophila from an isolate collected from a peach tree in central Georgia in the United States. The genome sequence described will be a useful resour...

Publication guidelines for quality improvement in health care: evolution of the SQUIRE project

PubMed Central

Davidoff, F; Batalden, P; Stevens, D; Ogrinc, G; Mooney, S

2008-01-01

In 2005, draft guidelines were published for reporting studies of quality improvement interventions as the initial step in a consensus process for development of a more definitive version. This article contains the full revised version of the guidelines, which the authors refer to as SQUIRE (Standards for QUality Improvement Reporting Excellence). This paper also describes the consensus process, which included informal feedback from authors, editors and peer reviewers who used the guidelines; formal written commentaries; input from a group of publication guideline developers; ongoing review of the literature on the epistemology of improvement and methods for evaluating complex social programmes; a two-day meeting of stakeholders for critical discussion and debate of the guidelines’ content and wording; and commentary on sequential versions of the guidelines from an expert consultant group. Finally, the authors consider the major differences between SQUIRE and the initial draft guidelines; limitations of and unresolved questions about SQUIRE; ancillary supporting documents and alternative versions that are under development; and plans for dissemination, testing and further development of SQUIRE. PMID:18836063

Evaluation and validation of de novo and hybrid assembly techniques to derive high quality genome sequences

DOE PAGES

Utturkar, Sagar M.; Klingeman, Dawn Marie; Land, Miriam L.; ...

2014-06-14

Our motivation with this work was to assess the potential of different types of sequence data combined with de novo and hybrid assembly approaches to improve existing draft genome sequences. Our results show Illumina, 454 and PacBio sequencing technologies were used to generate de novo and hybrid genome assemblies for four different bacteria, which were assessed for quality using summary statistics (e.g. number of contigs, N50) and in silico evaluation tools. Differences in predictions of multiple copies of rDNA operons for each respective bacterium were evaluated by PCR and Sanger sequencing, and then the validated results were applied as anmore » additional criterion to rank assemblies. In general, assemblies using longer PacBio reads were better able to resolve repetitive regions. In this study, the combination of Illumina and PacBio sequence data assembled through the ALLPATHS-LG algorithm gave the best summary statistics and most accurate rDNA operon number predictions. This study will aid others looking to improve existing draft genome assemblies. As to availability and implementation–all assembly tools except CLC Genomics Workbench are freely available under GNU General Public License.« less

75 FR 16459 - Draft Document Related to the Review of the National Ambient Air Quality Standards for...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-01

... Review of the National Ambient Air Quality Standards for Particulate Matter AGENCY: Environmental... Review of the Particulate Matter National Ambient Air Quality Standards--First External Review Draft (75... Particulate Matter National Ambient Air Quality Standards--First External Review Draft (March 2010), please...

Augmenting Chinese hamster genome assembly by identifying regions of high confidence.

PubMed

Vishwanathan, Nandita; Bandyopadhyay, Arpan A; Fu, Hsu-Yuan; Sharma, Mohit; Johnson, Kathryn C; Mudge, Joann; Ramaraj, Thiruvarangan; Onsongo, Getiria; Silverstein, Kevin A T; Jacob, Nitya M; Le, Huong; Karypis, George; Hu, Wei-Shou

2016-09-01

Chinese hamster Ovary (CHO) cell lines are the dominant industrial workhorses for therapeutic recombinant protein production. The availability of genome sequence of Chinese hamster and CHO cells will spur further genome and RNA sequencing of producing cell lines. However, the mammalian genomes assembled using shot-gun sequencing data still contain regions of uncertain quality due to assembly errors. Identifying high confidence regions in the assembled genome will facilitate its use for cell engineering and genome engineering. We assembled two independent drafts of Chinese hamster genome by de novo assembly from shotgun sequencing reads and by re-scaffolding and gap-filling the draft genome from NCBI for improved scaffold lengths and gap fractions. We then used the two independent assemblies to identify high confidence regions using two different approaches. First, the two independent assemblies were compared at the sequence level to identify their consensus regions as "high confidence regions" which accounts for at least 78 % of the assembled genome. Further, a genome wide comparison of the Chinese hamster scaffolds with mouse chromosomes revealed scaffolds with large blocks of collinearity, which were also compiled as high-quality scaffolds. Genome scale collinearity was complemented with EST based synteny which also revealed conserved gene order compared to mouse. As cell line sequencing becomes more commonly practiced, the approaches reported here are useful for assessing the quality of assembly and potentially facilitate the engineering of cell lines. Copyright © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

75 FR 8045 - National Environmental Policy Act (NEPA) Draft Guidance, Establishing, Applying, and Revising...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-02-23

... COUNCIL ON ENVIRONMENTAL QUALITY National Environmental Policy Act (NEPA) Draft Guidance...: Council on Environmental Quality. ACTION: Notice of Availability, Draft Guidance, ``Establishing, Applying... February 18, 2010, the Council on Environmental Quality (CEQ) announced four steps to modernize...

High-quality permanent draft genome sequence of the Parapiptadenia rigida-nodulating Cupriavidus sp. strain UYPR2.512

DOE Office of Scientific and Technical Information (OSTI.GOV)

De Meyer, Sofie E.; Fabiano, Elena; Tian, Rui

Cupriavidus sp. strain UYPR2.512 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from a root nodule of Parapiptadenia rigida grown in soils from a native forest of Uruguay. Here we describe the features of Cupriavidus sp. strain UYPR2.512, together with sequence and annotation. We find the 7,858,949 bp high-quality permanent draft genome is arranged in 365 scaffolds of 369 contigs, contains 7,411 protein-coding genes and 76 RNA-only encoding genes, and is part of the GEBA-RNB project proposal.

High-quality permanent draft genome sequence of the Parapiptadenia rigida-nodulating Cupriavidus sp. strain UYPR2.512

DOE PAGES

De Meyer, Sofie E.; Fabiano, Elena; Tian, Rui; ...

2015-04-11

Cupriavidus sp. strain UYPR2.512 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from a root nodule of Parapiptadenia rigida grown in soils from a native forest of Uruguay. Here we describe the features of Cupriavidus sp. strain UYPR2.512, together with sequence and annotation. We find the 7,858,949 bp high-quality permanent draft genome is arranged in 365 scaffolds of 369 contigs, contains 7,411 protein-coding genes and 76 RNA-only encoding genes, and is part of the GEBA-RNB project proposal.

Draft genome sequence of Venturia carpophila, the causal agent of peach scab

USDA-ARS?s Scientific Manuscript database

Venturia carpophila causes peach scab, a disease that renders peach fruit unmarketable. We report a high-quality draft genome sequence (36.9 Mb) of V. carpophila from an isolate collected from a peach tree in central Georgia in the United States. The genome sequence described will be a useful resour...

Draft Genome sequence of Frankia sp. Strain QA3, a nitrogen-fixing actinobacterium isolated from the root nodule of Alnus nitida

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sen, Arnab; Beauchemin, Nicholas; Bruce, David

Members of actinomycete genus Frankia form a nitrogen-fixing symbiosis with 8 different families of actinorhizal plants. We report a high-quality draft genome sequence for Frankia sp. stain QA3, a nitrogen-fixing actinobacterium isolated from root nodules of Alnus nitida.

77 FR 38377 - Notice of Availability of the Draft Environmental Impact Statement: Los Angeles County, CA

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-27

... modernize the design at the I-405, SR-91 and a portion of the I-5 interchanges, modernize and reconfigure... Intelligent Transportation Systems (ITS) improvements; improvements to 42 local arterial intersections within the I-710 Corridor; aesthetic enhancements; and, drainage and water quality improvement design...

75 FR 8046 - National Environmental Policy Act (NEPA) Draft Guidance, “NEPA Mitigation and Monitoring.”

Federal Register 2010, 2011, 2012, 2013, 2014

2010-02-23

... COUNCIL ON ENVIRONMENTAL QUALITY National Environmental Policy Act (NEPA) Draft Guidance, ``NEPA Mitigation and Monitoring.'' AGENCY: Council On Environmental Quality. ACTION: Notice of Availability, Draft... Quality (CEQ) announced four steps to modernize, reinvigorate, and ease the use and increase the...

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tian, Rui; Parker, Matthew; Seshadri, Rekha

Bradyrhizobiumsp. Tv2a.2 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing root nodule of Tachigali versicolor collected in Barro Colorado Island of Panama. Here we describe the features of Bradyrhizobiumsp. Tv2a.2, together with high-quality permanent draft genome sequence information and annotation. The 8,496,279 bp high-quality draft genome is arranged in 87 scaffolds of 87 contigs, contains 8,109 protein-coding genes and 72 RNA-only encoding genes. In conclusion, this rhizobial genome was sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.

High quality draft genome of Nakamurella lactea type strain, a rock actinobacterium, and emended description of Nakamurella lactea

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nouioui, Imen; Göker, Markus; Carro, Lorena

Nakamurella lactea DLS-10 T , isolated from rock in Korea, is one of the four type strains of the genus Nakamurella. In this study, we describe the high quality draft genome of N. lactea DLS-10 T and its annotation. A summary of phenotypic data collected from previously published studies was also included. The genome of strain DLS-10 T presents a size of 5.82 Mpb, 5100 protein coding genes, and a C + G content of 68.9%. Based on the genome analysis, emended description of N. lactea in terms of G + C content was also proposed.

High quality draft genome of Nakamurella lactea type strain, a rock actinobacterium, and emended description of Nakamurella lactea

DOE PAGES

Nouioui, Imen; Göker, Markus; Carro, Lorena; ...

2017-01-06

Nakamurella lactea DLS-10 T , isolated from rock in Korea, is one of the four type strains of the genus Nakamurella. In this study, we describe the high quality draft genome of N. lactea DLS-10 T and its annotation. A summary of phenotypic data collected from previously published studies was also included. The genome of strain DLS-10 T presents a size of 5.82 Mpb, 5100 protein coding genes, and a C + G content of 68.9%. Based on the genome analysis, emended description of N. lactea in terms of G + C content was also proposed.

76 FR 63909 - Draft Programmatic Environmental Impact Statement (EIS) for Modernization of Training...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-14

... the training requirements of military units in Hawai`i. This modernization would improve the quality... at PTA are old, are operating beyond their useful life and do not meet current DoD design standards... with the possible effects to air quality, historic resources, and threatened and endangered species...

[How to establish a good acupuncture-moxibustion standard?].

PubMed

Wu, Xiao-dong; Xiao, Hui

2014-10-01

At the beginning of a standard item, the standardized objects and involved contents should be demonstrated thoroughly, which is the precondition of establishing a good standard. After the proposal of this standard, a high-level drafting group should be built, led by top specialists who also draft the standard, which is essential to guarantee the quality of the standard. Before drafting the standard, literature regarding this standard should be searched completely, and Directives for Standardization should be learned to understand the basic requirements of establishing a standard; in the meanwhile, selections on standardized contents and quantitative boundaries of technical indices should be comprehensively and deeply studied. At the stage of consultation, focus should be paid on the scope of the consultation departments, level and personnel quality. As for standard review, it should be precise and truth-seeking. At the stage of submitting and authorization, it is necessary to have timely communication. Only by full cooperations of all parties, and by strictly following the procedure, method and rule of standard establishment, can a high-quality acupuncture-moxibustion standard be established.

A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants.

PubMed

Pilkington, Sarah M; Crowhurst, Ross; Hilario, Elena; Nardozza, Simona; Fraser, Lena; Peng, Yongyan; Gunaseelan, Kularajathevan; Simpson, Robert; Tahir, Jibran; Deroles, Simon C; Templeton, Kerry; Luo, Zhiwei; Davy, Marcus; Cheng, Canhong; McNeilage, Mark; Scaglione, Davide; Liu, Yifei; Zhang, Qiong; Datson, Paul; De Silva, Nihal; Gardiner, Susan E; Bassett, Heather; Chagné, David; McCallum, John; Dzierzon, Helge; Deng, Cecilia; Wang, Yen-Yi; Barron, Lorna; Manako, Kelvina; Bowen, Judith; Foster, Toshi M; Erridge, Zoe A; Tiffin, Heather; Waite, Chethi N; Davies, Kevin M; Grierson, Ella P; Laing, William A; Kirk, Rebecca; Chen, Xiuyin; Wood, Marion; Montefiori, Mirco; Brummell, David A; Schwinn, Kathy E; Catanach, Andrew; Fullerton, Christina; Li, Dawei; Meiyalaghan, Sathiyamoorthy; Nieuwenhuizen, Niels; Read, Nicola; Prakash, Roneel; Hunter, Don; Zhang, Huaibi; McKenzie, Marian; Knäbel, Mareike; Harris, Alastair; Allan, Andrew C; Gleave, Andrew; Chen, Angela; Janssen, Bart J; Plunkett, Blue; Ampomah-Dwamena, Charles; Voogd, Charlotte; Leif, Davin; Lafferty, Declan; Souleyre, Edwige J F; Varkonyi-Gasic, Erika; Gambi, Francesco; Hanley, Jenny; Yao, Jia-Long; Cheung, Joey; David, Karine M; Warren, Ben; Marsh, Ken; Snowden, Kimberley C; Lin-Wang, Kui; Brian, Lara; Martinez-Sanchez, Marcela; Wang, Mindy; Ileperuma, Nadeesha; Macnee, Nikolai; Campin, Robert; McAtee, Peter; Drummond, Revel S M; Espley, Richard V; Ireland, Hilary S; Wu, Rongmei; Atkinson, Ross G; Karunairetnam, Sakuntala; Bulley, Sean; Chunkath, Shayhan; Hanley, Zac; Storey, Roy; Thrimawithana, Amali H; Thomson, Susan; David, Charles; Testolin, Raffaele; Huang, Hongwen; Hellens, Roger P; Schaffer, Robert J

2018-04-16

Most published genome sequences are drafts, and most are dominated by computational gene prediction. Draft genomes typically incorporate considerable sequence data that are not assigned to chromosomes, and predicted genes without quality confidence measures. The current Actinidia chinensis (kiwifruit) 'Hongyang' draft genome has 164 Mb of sequences unassigned to pseudo-chromosomes, and omissions have been identified in the gene models. A second genome of an A. chinensis (genotype Red5) was fully sequenced. This new sequence resulted in a 554.0 Mb assembly with all but 6 Mb assigned to pseudo-chromosomes. Pseudo-chromosomal comparisons showed a considerable number of translocation events have occurred following a whole genome duplication (WGD) event some consistent with centromeric Robertsonian-like translocations. RNA sequencing data from 12 tissues and ab initio analysis informed a genome-wide manual annotation, using the WebApollo tool. In total, 33,044 gene loci represented by 33,123 isoforms were identified, named and tagged for quality of evidential support. Of these 3114 (9.4%) were identical to a protein within 'Hongyang' The Kiwifruit Information Resource (KIR v2). Some proportion of the differences will be varietal polymorphisms. However, as most computationally predicted Red5 models required manual re-annotation this proportion is expected to be small. The quality of the new gene models was tested by fully sequencing 550 cloned 'Hort16A' cDNAs and comparing with the predicted protein models for Red5 and both the original 'Hongyang' assembly and the revised annotation from KIR v2. Only 48.9% and 63.5% of the cDNAs had a match with 90% identity or better to the original and revised 'Hongyang' annotation, respectively, compared with 90.9% to the Red5 models. Our study highlights the need to take a cautious approach to draft genomes and computationally predicted genes. Our use of the manual annotation tool WebApollo facilitated manual checking and correction of gene models enabling improvement of computational prediction. This utility was especially relevant for certain types of gene families such as the EXPANSIN like genes. Finally, this high quality gene set will supply the kiwifruit and general plant community with a new tool for genomics and other comparative analysis.

Resources for Ensuring Quality School-to-Work Opportunities for Young Women. Draft.

ERIC Educational Resources Information Center

Wider Opportunities for Women, Inc., Washington, DC.

This annotated bibliography lists 49 resources for ensuring high quality school-to-work opportunities for young women. These resources are grouped into 10 categories: print material for middle and high school girls; videos for middle and high school girls; administrator/school guides; curriculum guides/resources for teachers; resources for…

Textual analysis of sugar industry influence on the World Health Organization's 2015 sugars intake guideline.

PubMed

Stuckler, David; Reeves, Aaron; Loopstra, Rachel; McKee, Martin

2016-08-01

To determine whether sugar industry-related organizations influenced textual changes between the draft and final versions of the World Health Organization's (WHO's) 2015 guideline Sugars intake for adults and children. Stakeholder consultation submissions on the draft guideline from seven sugar industry-related and 10 public health organizations were assessed using the Wordscores program. Document scores were rescaled using the Martin-Vanberg transformation to improve comparability. Draft and final guidelines were compared to identify changes influenced by the sugar industry and public health organizations. There was a small shift in transformed Wordscores score between the draft and final guidelines, from 0.25 to 0.24, towards the industry position. The change was linked to increased use of the word "low" to describe the quality of the evidence, consistent with industry arguments. There was also a shift from use of the word "consumption" to "intake", irrespective of policy position. Scores for World Sugar Research Organisation and Sugar Nutrition UK submissions ( 0.11 and 0.18, respectively) represented strong pro-industry positions and scores for European Public Health Alliance and Wemos submissions (1.00 and 0.88, respectively) represented the strongest public health positions. Industry tactics included challenging the quality of the evidence, distinguishing between different types of sugar and advocating harm reduction. There was little change between draft and final versions of the WHO sugars intake guideline 2015, following industry consultation. The main change was linked to emphasizing the low quality of the evidence on sugar's adverse effects. Guideline development appeared relatively resistant to industry influence at the stakeholder consultation stage.

Teaching Pharmacology Graduate Students how to Write an NIH Grant Application

PubMed Central

O’Donnell, Lauren A.; Surratt, Christopher K.

2015-01-01

Objective. To fill the gap in grant writing training in pharmacology graduate education using an active-learning strategy. Design. Graduate students wrote subsections of a grant according to NIH guidelines. Students revised their applications based on multiple rounds of critiques from professors and peers throughout a semester-long scientific writing course. Assessment. Prerevision and postrevision grant drafts were graded. Students were provided with questionnaires assessing their perception of the process. To determine the impact of feedback on the proposals, the quality of the pre/postrevision drafts was assessed by professors who were blinded and unaffiliated with the course. Conclusion. Student grades improved significantly upon resubmission. Perceptions of the proposals by blinded faculty members favored revised submissions based on multiple criteria. Survey feedback indicated an increase in student confidence in grant writing ability. The results of 3 independent measures demonstrate that intensive feedback on scientific writing improved the quality of student proposals. PMID:28435165

Teaching Pharmacology Graduate Students how to Write an NIH Grant Application.

PubMed

Leak, Rehana K; O'Donnell, Lauren A; Surratt, Christopher K

2015-11-25

Objective. To fill the gap in grant writing training in pharmacology graduate education using an active-learning strategy. Design. Graduate students wrote subsections of a grant according to NIH guidelines. Students revised their applications based on multiple rounds of critiques from professors and peers throughout a semester-long scientific writing course. Assessment. Prerevision and postrevision grant drafts were graded. Students were provided with questionnaires assessing their perception of the process. To determine the impact of feedback on the proposals, the quality of the pre/postrevision drafts was assessed by professors who were blinded and unaffiliated with the course. Conclusion. Student grades improved significantly upon resubmission. Perceptions of the proposals by blinded faculty members favored revised submissions based on multiple criteria. Survey feedback indicated an increase in student confidence in grant writing ability. The results of 3 independent measures demonstrate that intensive feedback on scientific writing improved the quality of student proposals.

The draft genome of whitefly Bemisia tabaci MEAM1, a global crop pest, provides novel insights into virus transmission, host adaptation, and insecticide resistance

USDA-ARS?s Scientific Manuscript database

Whiteflies are among the most important agricultural pests. They have a broad range of host plants and exceptional ability to transmit a large number of plant viruses, and can rapidly evolve insecticide resistance. Here we present a high-quality draft genome of the whitefly, Bemisia tabaci. Comparat...

Asynchronous Transfer Mode Quality-of-Service Testing

NASA Technical Reports Server (NTRS)

Ivancic, William D.

1998-01-01

In support of satellite-ATM interoperability, researchers at the NASA Lewis Research Center performed asynchronous transfer mode (ATM) quality-of-service experiments using MPEG-2 (ATM application layer 5, AAL5) over ATM over an emulated satellite link. The purpose of these experiments was to determine the free-space link quality necessary to use the ATM protocol to transmit high-quality multimedia information. The experimental results have been submitted to various International Telecommunications Union (ITU) study groups in order to improve and modify current standards and recommendations for the telecommunications industry. Quality-of-service parameters for Class I, stringent class requirements for ITU-T I.356 are currently being debated. The experimental results presented will help to establish these quality-of-service thresholds. This material will also be useful in the development of the ITU-R WP-4B's Draft Preliminary New Recommendation on the Transmission of Asynchronous Transfer Mode Traffic via Satellite (Rec. S.atm).

High quality draft genome sequence of the moderately halophilic bacterium Pontibacillus yanchengensis Y32(T) and comparison among Pontibacillus genomes.

PubMed

Huang, Jing; Qiao, Zi Xu; Tang, Jing Wei; Wang, Gejiao

2015-01-01

Pontibacillus yanchengensis Y32(T) is an aerobic, motile, Gram-positive, endospore-forming, and moderately halophilic bacterium isolated from a salt field. In this study, we describe the features of P. yanchengensis strain Y32(T) together with a comparison with other four Pontibacillus genomes. The 4,281,464 bp high-quality-draft genome of strain Y32(T) is arranged into 153 contigs containing 3,965 protein-coding genes and 77 RNA encoding genes. The genome of strain Y32(T) possesses many genes related to its halophilic character, flagellar assembly and chemotaxis to support its survival in a salt-rich environment.

Draft Genome Sequences of 20 Salmonella enterica subsp. enterica Serovar Typhimurium Strains Isolated from Swine in Santa Catarina, Brazil.

PubMed

Seribelli, Amanda Aparecida; Frazão, Miliane Rodrigues; Gonzales, Júlia Cunha; Cao, Guojie; Leon, Maria Sanchez; Kich, Jalusa Deon; Allard, Marc William; Falcão, Juliana Pfrimer

2018-04-19

Salmonellosis is a disease with a high incidence worldwide, and Salmonella enterica subsp. enterica serovar Typhimurium is one of the most clinically important serovars. We report here the draft genome sequences of 20 S. Typhimurium strains isolated from swine in Santa Catarina, Brazil. These draft genomes will improve our understanding of S. Typhimurium in Brazil.

Application of long sequence reads to improve genomes for Clostridium thermocellum AD2, Clostridium thermocellum LQRI, and Pelosinus fermentans R7

DOE PAGES

Utturkar, Sagar M.; Bayer, Edward A.; Borovok, Ilya; ...

2016-09-29

Here, we and others have shown the utility of long sequence reads to improve genome assembly quality. In this study, we generated PacBio DNA sequence data to improve the assemblies of draft genomes for Clostridium thermocellum AD2, Clostridium thermocellum LQRI, and Pelosinus fermentans R7.

75 FR 69983 - Notice of Intent to Prepare a Draft Environmental Impact Statement (EIS), Initiate the Public...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-11-16

... that water quality has improved, these canals allow the transfer of both indigenous and nonindigenous... Water and Related Land Resource Implementation Studies, Water Resources Council, March 10, 1983. 2...

Tools for Communication: Novel infrastructure to address patient-perceived gaps in oncology care
.

PubMed

McMullen, Suzanne; Szabo, Shelagh; Halbert, Ronald J; Lai, Catherine; Parikh, Aparna; Bunce, Mikele; Khoury, Raya; Small, Art; Masaquel, Anthony

2017-04-01

Healthcare providers (HCPs) and patient communication are integral to high-quality oncology care. The patient and HCP perspectives are needed to identify gaps in care and develop communication tools.
. This study aimed to understand patient- and HCP-perceived elements of and gaps in high-quality care to develop novel communication tools to improve care. 
. Qualitative interviews were conducted among 16 patients with cancer and 10 HCPs in the United States. Trained interviewers elicited patients' and HCPs' concerns, views, and perceived needs for communication tools. A thematic analysis was used to identify four quality of care domains, depicted in a conceptual model, and two draft communication tools were developed to address identified gaps.
. No patients reported previously using a communication tool, and gaps in communication regarding treatment aims and education were evident. Two tools were developed to assess patients' life and treatment goals and the importance of ongoing education.

High-Quality Draft Genomes from Thermus caliditerrae YIM 77777 and T. tengchongensis YIM 77401, Isolates from Tengchong, China

DOE PAGES

Mefferd, Chrisabelle C.; Zhou, En-Min; Yu, Tian-Tian; ...

2016-04-28

The draft genomes ofThermus  tengchongensisYIM 77401 andT. caliditerraeYIM 77777 are 2,562,314 and 2,218,114 bp and encode 2,726 and 2,305 predicted genes, respectively. Gene content and growth experiments demonstrate broad metabolic capacity, including starch hydrolysis, thiosulfate oxidation, arsenite oxidation, incomplete denitrification, and polysulfide reduction.

High-Quality Draft Genome Sequence of Thermocrinis jamiesonii GBS1 T Isolated from Great Boiling Spring, Nevada

DOE PAGES

Ganji, Rakesh; Murugapiran, Senthil K.; Ong, John C.; ...

2016-10-20

The draft genome of Thermocrinis jamiesonii GBS1 T is 1,315,625 bp in 10 contigs and encodes 1,463 predicted genes. The presence of sox genes and various glycoside hydrolases and the absence of uptake NiFe hydrogenases ( hyaB) are consistent with a requirement for thiosulfate and suggest the ability to use carbohydrate polymers.

Draft Genome Sequence of Telmatospirillum siberiense 26-4b1, an Acidotolerant Peatland Alphaproteobacterium Potentially Involved in Sulfur Cycling

PubMed Central

Schreck, Katharina; Herbold, Craig W.; Daims, Holger; Wagner, Michael; Loy, Alexander

2018-01-01

ABSTRACT The facultative anaerobic chemoorganoheterotrophic alphaproteobacterium Telmatospirillum siberiense 26-4b1 was isolated from a Siberian peatland. We report here a 6.20-Mbp near-complete high-quality draft genome sequence of T. siberiense that reveals expected and novel metabolic potential for the genus Telmatospirillum, including genes for sulfur oxidation. PMID:29371357

76 FR 79176 - Notice of Availability of Draft Recreational Water Quality Criteria and Request for Scientific Views

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-21

... ENVIRONMENTAL PROTECTION AGENCY [EPA-OW-2011-0466; FRL-9609-3] Notice of Availability of Draft Recreational Water Quality Criteria and Request for Scientific Views AGENCY: Environmental Protection Agency... Environmental Protection Agency (EPA) is announcing the availability of the draft document Recreational Water...

78 FR 3420 - Office of Environmental Information; Announcement of Availability and Comment Period for the...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-16

...) Organizations and two associated draft QA Handbooks; 1) draft Handbook for Preparing Quality Management Plans... Availability and Comment Period for the Draft Quality Standard for Environmental Data Collection, Production, and Use by Non-EPA (External) Organizations and Two Associated QA Handbooks; Correction AGENCY...

77 FR 22282 - Draft Guidelines on Biologics Quality Monitoring: Testing for the Detection of Mycoplasma...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-04-13

...] Draft Guidelines on Biologics Quality Monitoring: Testing for the Detection of Mycoplasma Contamination... Detection of Mycoplasma Contamination.'' This draft guideline identifies stages of manufacture where... contamination. Because the guidelines apply to final product and master seed/cell testing in veterinary vaccines...

76 FR 35216 - Science Advisory Board Staff Office Notification of a Public Teleconference of the Chartered...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-16

...The EPA Science Advisory Board (SAB) Staff Office announces a public teleconference of the chartered SAB on July 5, 2011 to conduct a quality review of a draft SAB report, Review of EPA's Draft Hydraulic Fracturing Study Plan (Quality Review Draft).

75 FR 71694 - Science Advisory Board Staff Office; Notification of Two Public Quality Review Teleconferences of...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-11-24

... review of EPA's ``Toxicological Review of Trichloroethylene'' on December 15, 2010 and (b) a quality... of Trichloroethylene'' (October 2009), and (2) a draft report peer reviewing EPA's draft document... draft assessment entitled ``Toxicological Review of Trichloroethylene'' (October 2009). EPA's Office of...

High-quality genome of the peach scab pathogen, Venturia carpophila

USDA-ARS?s Scientific Manuscript database

Venturia carpophila causes peach scab, a disease that renders peach (Prunus persica) fruit unmarketable. We report a high-quality draft genome (36.9 Mb) of V. carpophila from an isolate collected from a peach tree in central Georgia. The genome was sequenced by MiSeq using an Illumina paired-end lib...

Extensive Error in the Number of Genes Inferred from Draft Genome Assemblies

PubMed Central

Denton, James F.; Lugo-Martinez, Jose; Tucker, Abraham E.; Schrider, Daniel R.; Warren, Wesley C.; Hahn, Matthew W.

2014-01-01

Current sequencing methods produce large amounts of data, but genome assemblies based on these data are often woefully incomplete. These incomplete and error-filled assemblies result in many annotation errors, especially in the number of genes present in a genome. In this paper we investigate the magnitude of the problem, both in terms of total gene number and the number of copies of genes in specific families. To do this, we compare multiple draft assemblies against higher-quality versions of the same genomes, using several new assemblies of the chicken genome based on both traditional and next-generation sequencing technologies, as well as published draft assemblies of chimpanzee. We find that upwards of 40% of all gene families are inferred to have the wrong number of genes in draft assemblies, and that these incorrect assemblies both add and subtract genes. Using simulated genome assemblies of Drosophila melanogaster, we find that the major cause of increased gene numbers in draft genomes is the fragmentation of genes onto multiple individual contigs. Finally, we demonstrate the usefulness of RNA-Seq in improving the gene annotation of draft assemblies, largely by connecting genes that have been fragmented in the assembly process. PMID:25474019

Extensive error in the number of genes inferred from draft genome assemblies.

PubMed

Denton, James F; Lugo-Martinez, Jose; Tucker, Abraham E; Schrider, Daniel R; Warren, Wesley C; Hahn, Matthew W

2014-12-01

Current sequencing methods produce large amounts of data, but genome assemblies based on these data are often woefully incomplete. These incomplete and error-filled assemblies result in many annotation errors, especially in the number of genes present in a genome. In this paper we investigate the magnitude of the problem, both in terms of total gene number and the number of copies of genes in specific families. To do this, we compare multiple draft assemblies against higher-quality versions of the same genomes, using several new assemblies of the chicken genome based on both traditional and next-generation sequencing technologies, as well as published draft assemblies of chimpanzee. We find that upwards of 40% of all gene families are inferred to have the wrong number of genes in draft assemblies, and that these incorrect assemblies both add and subtract genes. Using simulated genome assemblies of Drosophila melanogaster, we find that the major cause of increased gene numbers in draft genomes is the fragmentation of genes onto multiple individual contigs. Finally, we demonstrate the usefulness of RNA-Seq in improving the gene annotation of draft assemblies, largely by connecting genes that have been fragmented in the assembly process.

Textual analysis of sugar industry influence on the World Health Organization’s 2015 sugars intake guideline

PubMed Central

Reeves, Aaron; Loopstra, Rachel; McKee, Martin

2016-01-01

Abstract Objective To determine whether sugar industry-related organizations influenced textual changes between the draft and final versions of the World Health Organization’s (WHO’s) 2015 guideline Sugars intake for adults and children. Methods Stakeholder consultation submissions on the draft guideline from seven sugar industry-related and 10 public health organizations were assessed using the Wordscores program. Document scores were rescaled using the Martin–Vanberg transformation to improve comparability. Draft and final guidelines were compared to identify changes influenced by the sugar industry and public health organizations. Findings There was a small shift in transformed Wordscores score between the draft and final guidelines, from 0.25 to 0.24, towards the industry position. The change was linked to increased use of the word “low” to describe the quality of the evidence, consistent with industry arguments. There was also a shift from use of the word “consumption” to “intake”, irrespective of policy position. Scores for World Sugar Research Organisation and Sugar Nutrition UK submissions ( 0.11 and 0.18, respectively) represented strong pro-industry positions and scores for European Public Health Alliance and Wemos submissions (1.00 and 0.88, respectively) represented the strongest public health positions. Industry tactics included challenging the quality of the evidence, distinguishing between different types of sugar and advocating harm reduction. Conclusion There was little change between draft and final versions of the WHO sugars intake guideline 2015, following industry consultation. The main change was linked to emphasizing the low quality of the evidence on sugar’s adverse effects. Guideline development appeared relatively resistant to industry influence at the stakeholder consultation stage. PMID:27516634

Use of low-coverage, large-insert, short-read data for rapid and accurate generation of enhanced-quality draft Pseudomonas genome sequences.

PubMed

O'Brien, Heath E; Gong, Yunchen; Fung, Pauline; Wang, Pauline W; Guttman, David S

2011-01-01

Next-generation genomic technology has both greatly accelerated the pace of genome research as well as increased our reliance on draft genome sequences. While groups such as the Genomics Standards Consortium have made strong efforts to promote genome standards there is a still a general lack of uniformity among published draft genomes, leading to challenges for downstream comparative analyses. This lack of uniformity is a particular problem when using standard draft genomes that frequently have large numbers of low-quality sequencing tracts. Here we present a proposal for an "enhanced-quality draft" genome that identifies at least 95% of the coding sequences, thereby effectively providing a full accounting of the genic component of the genome. Enhanced-quality draft genomes are easily attainable through a combination of small- and large-insert next-generation, paired-end sequencing. We illustrate the generation of an enhanced-quality draft genome by re-sequencing the plant pathogenic bacterium Pseudomonas syringae pv. phaseolicola 1448A (Pph 1448A), which has a published, closed genome sequence of 5.93 Mbp. We use a combination of Illumina paired-end and mate-pair sequencing, and surprisingly find that de novo assemblies with 100x paired-end coverage and mate-pair sequencing with as low as low as 2-5x coverage are substantially better than assemblies based on higher coverage. The rapid and low-cost generation of large numbers of enhanced-quality draft genome sequences will be of particular value for microbial diagnostics and biosecurity, which rely on precise discrimination of potentially dangerous clones from closely related benign strains.

Genome sequence of the phylogenetically isolated spirochete Leptonema illini type strain (3055T)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huntemann, Marcel; Stackebrandt, Erko; Held, Brittany

2013-01-01

Leptonema illini Hovind-Hougen 1979 is the type species of the genus Leptonema, family Leptospiraceae, phylum Spirochaetes. Organisms of this family have a Gram-negative-like cell enve- lope consisting of a cytoplasmic membrane and an outer membrane. The peptidoglycan layer is as- sociated with the cytoplasmic rather than the outer membrane. The two flagella of members of Leptospiraceae extend from the cytoplasmic membrane at the ends of the bacteria into the periplasmic space and are necessary for their motility. Here we describe the features of the L. illini type strain, together with the complete genome sequence, and annotation. This is the firstmore » genome sequence (finished at the level of Improved High Quality Draft) to be reported from of a member of the genus Leptonema and a representative of the third genus of the family Leptospiraceae for which complete or draft genome sequences are now available. The three scaffolds of the 4,522,760 bp draft genome sequence reported here, and its 4,230 protein-coding and 47 RNA genes are part of the Ge- nomic Encyclopedia of Bacteria and Archaea project.« less

75 FR 47595 - Science Advisory Board Staff Office; Notification of a Public Teleconference of the Clean Air...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-06

... Air Quality Standards--Second External Review Draft (June 2010). DATES: The teleconference will be... Standards--Second External Review Draft (June 2010). Background information on previous meetings and... Quality Standards--Second External Review Draft (June 2010) should be directed to Ms. Beth Hassett-Sipple...

75 FR 9206 - Science Advisory Board Staff Office; Notification of a Clean Air Scientific Advisory Committee...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-01

...: Second External Review Draft and EPA's Policy Assessment for the Review of the Carbon Monoxide National Ambient Air Quality Standards: External Review Draft. The chartered CASAC will subsequently hold a public... National Ambient Air Quality Standards: Second External Review Draft and the Policy Assessment for the...

75 FR 4067 - Release of Draft Documents Related to the Review of the National Ambient Air Quality Standards...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-01-26

... for public comment a second draft assessment document titled, Quantitative Health Risk Assessment for... quantitative analyses that are being conducted as part of the review of the national ambient air quality...-Focused Visibility Assessment--Second External Review Draft and Quantitative Health Risk Assessment for...

Quality measures for the diagnosis and non-operative management of carpal tunnel syndrome in occupational settings.

PubMed

Nuckols, Teryl; Harber, Philip; Sandin, Karl; Benner, Douglas; Weng, Haoling; Shaw, Rebecca; Griffin, Anne; Asch, Steven

2011-03-01

Providing higher quality medical care to workers with occupationally associated carpal tunnel syndrome (CTS) may reduce disability, facilitate return to work, and lower the associated costs. Although many workers' compensation systems have adopted treatment guidelines to reduce the overuse of unnecessary care, limited attention has been paid to ensuring that the care workers do receive is high quality. Further, guidelines are not designed to enable objective assessments of quality of care. This study sought to develop quality measures for the diagnostic evaluation and non-operative management of CTS, including managing occupational activities and functional limitations. Using a variation of the well-established RAND/UCLA Appropriateness Method, we developed draft quality measures using guidelines and literature reviews. Next, in a two-round modified-Delphi process, a multidisciplinary panel of 11 U.S. experts in CTS rated the measures on validity and feasibility. Of 40 draft measures, experts rated 31 (78%) valid and feasible. Nine measures pertained to diagnostic evaluation, such as assessing symptoms, signs, and risk factors. Eleven pertain to non-operative treatments, such as the use of splints, steroid injections, and medications. Eleven others address assessing the association between symptoms and work, managing occupational activities, and accommodating functional limitations. These measures will complement existing treatment guidelines by enabling providers, payers, policymakers, and researchers to assess quality of care for CTS in an objective, structured manner. Given the characteristics of previous measures developed with these methods, greater adherence to these measures will probably lead to improved patient outcomes at a population level.

Draft Genome Sequence of Telmatospirillum siberiense 26-4b1, an Acidotolerant Peatland Alphaproteobacterium Potentially Involved in Sulfur Cycling.

PubMed

Hausmann, Bela; Pjevac, Petra; Schreck, Katharina; Herbold, Craig W; Daims, Holger; Wagner, Michael; Loy, Alexander

2018-01-25

The facultative anaerobic chemoorganoheterotrophic alphaproteobacterium Telmatospirillum siberiense 26-4b1 was isolated from a Siberian peatland. We report here a 6.20-Mbp near-complete high-quality draft genome sequence of T. siberiense that reveals expected and novel metabolic potential for the genus Telmatospirillum , including genes for sulfur oxidation. Copyright © 2018 Hausmann et al.

The impact of peer review on paediatric forensic reports.

PubMed

Kariyawasam, Uditha

2016-10-01

To retrospectively evaluate the common grammar and spelling errors of the medico-legal reports written by the doctors at the Victorian Forensic Paediatric Medical Service (VFPMS) in both Royal Children's Hospital (RCH) and Monash Medical Centre. The reports were evaluated at two points in time; before and after peer review. The aim of the study was to ascertain whether peer review improved the grammar and spelling in VFPMS medico-legal reports. Draft VFPMS reports are sent to the VFPMS medical director for peer review. The current study sampled 50 reports that were sent consecutively to Dr. Anne Smith from 1st of May 2015. The 50 corresponding final reports were then retrieved from the VFPMS database. The 50 pairs of draft and final reports were scored using a 50-point scoring system. The scores of the draft reports were compared to the scores of the final report to assess if there was a change in quality as measured using an explicit criteria audit of report structure, simple grammar, jargon use and spelling. The audit did not include evaluation of the validity of forensic opinions. The overall scores were statistically analysed using descriptive statistics and a paired T-test. The scores of the reports improved by 2.24% when the final reports were compared to the draft reports (p < 0.001). The peer-review process resulted in a significantly higher quality of medico-legal reports. The report writing and peer-review process could be assisted by an abbreviated version of the checklist used for the audit. Crown Copyright © 2016. Published by Elsevier Ltd. All rights reserved.

Drafting.

ERIC Educational Resources Information Center

Hughes, Larry R.

This guide to teaching drafting, one in a series of instructional materials for junior high industrial arts education, is designed to assist teachers as they plan and implement new courses of study and as they make revisions and improvements in existing courses in order to integrate classroom learning with real-life experiences. This drafting…

High-quality permanent draft genome sequence of the Lebeckia - nodulating Burkholderia dilworthii strain WSM3556T

DOE Office of Scientific and Technical Information (OSTI.GOV)

De Meyer, Sofie E.; Tian, Rui; Seshadri, Rekha

Burkholderia dilworthii strain WSM3556T is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective N2-fixing root nodule of Lebeckia ambigua collected near Grotto Bay Nature Reserve, in the Western Cape of South Africa, in October 2004. This plant persists in infertile and deep sandy soils with acidic pH, and is therefore an ideal candidate for a perennial based agriculture system in Western Australia. WSM3556T thus represents a potential inoculant quality strain for L. ambigua for which we describe the general features, together with genome sequence and annotation. Lastly, the 7,679,067 bp high-quality permanent draft genome is arrangedmore » in 140 scaffolds of 141 contigs, contains 7,059 protein-coding genes and 64 RNA-only encoding genes, and is part of the GEBA-RNB project proposal.« less

High-quality permanent draft genome sequence of the Lebeckia ambigua-nodulating Burkholderia sp. strain WSM4176

DOE Office of Scientific and Technical Information (OSTI.GOV)

De Meyer, Sofie E.; Tian, Rui; Seshadri, Rekha

We report that Burkholderia sp. strain WSM4176 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective N2-fixing root nodule of Lebeckia ambigua collected in Nieuwoudtville, Western Cape of South Africa, in October 2007. This plant persists in infertile, acidic and deep sandy soils, and is therefore an ideal candidate for a perennial based agriculture system in Western Australia. Here we describe the features of Burkholderia sp. strain WSM4176, which represents a potential inoculant quality strain for L. ambigua, together with sequence and annotation. The 9,065,247 bp high-quality-draft genome is arranged in 13 scaffolds of 65 contigs,more » contains 8369 protein-coding genes and 128 RNA-only encoding genes, and is part of the GEBA-RNB project proposal (Project ID 882).« less

High-quality permanent draft genome sequence of the Lebeckia - nodulating Burkholderia dilworthii strain WSM3556T

DOE PAGES

De Meyer, Sofie E.; Tian, Rui; Seshadri, Rekha; ...

2015-09-19

Burkholderia dilworthii strain WSM3556T is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective N2-fixing root nodule of Lebeckia ambigua collected near Grotto Bay Nature Reserve, in the Western Cape of South Africa, in October 2004. This plant persists in infertile and deep sandy soils with acidic pH, and is therefore an ideal candidate for a perennial based agriculture system in Western Australia. WSM3556T thus represents a potential inoculant quality strain for L. ambigua for which we describe the general features, together with genome sequence and annotation. Lastly, the 7,679,067 bp high-quality permanent draft genome is arrangedmore » in 140 scaffolds of 141 contigs, contains 7,059 protein-coding genes and 64 RNA-only encoding genes, and is part of the GEBA-RNB project proposal.« less

High-quality permanent draft genome sequence of the Lebeckia ambigua-nodulating Burkholderia sp. strain WSM4176

DOE PAGES

De Meyer, Sofie E.; Tian, Rui; Seshadri, Rekha; ...

2015-10-16

We report that Burkholderia sp. strain WSM4176 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective N2-fixing root nodule of Lebeckia ambigua collected in Nieuwoudtville, Western Cape of South Africa, in October 2007. This plant persists in infertile, acidic and deep sandy soils, and is therefore an ideal candidate for a perennial based agriculture system in Western Australia. Here we describe the features of Burkholderia sp. strain WSM4176, which represents a potential inoculant quality strain for L. ambigua, together with sequence and annotation. The 9,065,247 bp high-quality-draft genome is arranged in 13 scaffolds of 65 contigs,more » contains 8369 protein-coding genes and 128 RNA-only encoding genes, and is part of the GEBA-RNB project proposal (Project ID 882).« less

Toward Global Comparability of Sexual Orientation Data in Official Statistics: A Conceptual Framework of Sexual Orientation for Health Data Collection in New Zealand's Official Statistics System

PubMed Central

Gray, Alistair; Veale, Jaimie F.; Binson, Diane; Sell, Randell L.

2013-01-01

Objective. Effectively addressing health disparities experienced by sexual minority populations requires high-quality official data on sexual orientation. We developed a conceptual framework of sexual orientation to improve the quality of sexual orientation data in New Zealand's Official Statistics System. Methods. We reviewed conceptual and methodological literature, culminating in a draft framework. To improve the framework, we held focus groups and key-informant interviews with sexual minority stakeholders and producers and consumers of official statistics. An advisory board of experts provided additional guidance. Results. The framework proposes working definitions of the sexual orientation topic and measurement concepts, describes dimensions of the measurement concepts, discusses variables framing the measurement concepts, and outlines conceptual grey areas. Conclusion. The framework proposes standard definitions and concepts for the collection of official sexual orientation data in New Zealand. It presents a model for producers of official statistics in other countries, who wish to improve the quality of health data on their citizens. PMID:23840231

A Draft Conceptual Framework of Relevant Theories to Inform Future Rigorous Research on Student Service-Learning Outcomes

ERIC Educational Resources Information Center

Whitley, Meredith A.

2014-01-01

While the quality and quantity of research on service-learning has increased considerably over the past 20 years, researchers as well as governmental and funding agencies have called for more rigor in service-learning research. One key variable in improving rigor is using relevant existing theories to improve the research. The purpose of this…

75 FR 65480 - Science Advisory Board Staff Office; Notification of Two Public Teleconferences of the Clean Air...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-25

... Quality Standards for NOX and SOX: Second External Review Draft (September 2010) and a teleconference for... the Secondary National Ambient Air Quality Standards for NO X and SO X : Second External Review Draft... External Review Draft (September 2010) should be directed to Dr. Byran Hubbell, OAR, at (919) 541-0621 or...

Comparison of Conventional and Computer-Aided Drafting Methods from the View of Time and Drafting Quality

ERIC Educational Resources Information Center

Ozkan, Aysen; Yildirim, Kemal

2016-01-01

Problem Statement: Drafting course is essential for students in the design disciplines for becoming more organized and for complying with standards in the educational system. Drafting knowledge is crucial, both for comprehension of the issues and for the implementation phase. In any design project, drafting performance and success are as important…

Improved genomic resources and new bioinformatic workflow for the carcinogenic parasite Clonorchis sinensis: Biotechnological implications.

PubMed

Wang, Daxi; Korhonen, Pasi K; Gasser, Robin B; Young, Neil D

Clonorchis sinensis (family Opisthorchiidae) is an important foodborne parasite that has a major socioeconomic impact on ~35 million people predominantly in China, Vietnam, Korea and the Russian Far East. In humans, infection with C. sinensis causes clonorchiasis, a complex hepatobiliary disease that can induce cholangiocarcinoma (CCA), a malignant cancer of the bile ducts. Central to understanding the epidemiology of this disease is knowledge of genetic variation within and among populations of this parasite. Although most published molecular studies seem to suggest that C. sinensis represents a single species, evidence of karyotypic variation within C. sinensis and cryptic species within a related opisthorchiid fluke (Opisthorchis viverrini) emphasise the importance of studying and comparing the genes and genomes of geographically distinct isolates of C. sinensis. Recently, we sequenced, assembled and characterised a draft nuclear genome of a C. sinensis isolate from Korea and compared it with a published draft genome of a Chinese isolate of this species using a bioinformatic workflow established for comparing draft genome assemblies and their gene annotations. We identified that 50.6% and 51.3% of the Korean and Chinese C. sinensis genomic scaffolds were syntenic, respectively. Within aligned syntenic blocks, the genomes had a high level of nucleotide identity (99.1%) and encoded 15 variable proteins likely to be involved in diverse biological processes. Here, we review current technical challenges of using draft genome assemblies to undertake comparative genomic analyses to quantify genetic variation between isolates of the same species. Using a workflow that overcomes these challenges, we report on a high-quality draft genome for C. sinensis from Korea and comparative genomic analyses, as a basis for future investigations of the genetic structures of C. sinensis populations, and discuss the biotechnological implications of these explorations. Copyright © 2018 Elsevier Inc. All rights reserved.

76 FR 5156 - Environmental Impact Statements; Notice of Availability

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-28

... Firm Water Supplies, Improve Water Quality, and to Reduce Water Costs, San Bernardino and Riverside.... 20110020, Draft EIS, NRCS, IA, Clarke County Water Supply, To Construct a Multiple-purpose Structure that Provides for Rural Water Supply and Water Based Recreational Opportunities, Clarke County, IA, Comment...

Socioeconomic Representativeness and the Draft

DTIC Science & Technology

1980-06-01

l that the quality of recruits who enter the services ( especiall the Army) is of lover caliber than historically experienced. Proponents of...the "quality" of recruits who enter the services ( especially the Army) is of lower caliber than historically experienced. Proponents of conscription...draft, especially when considering peacetime conscrip- tion. The strength of the argument for the draft was held to be that all eligible men would serve

76 FR 10892 - Aquatic Ecosystems, Water Quality, and Global Change: Challenges of Conducting Multi-Stressor...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-28

... Ecosystems, Water Quality, and Global Change: Challenges of Conducting Multi-Stressor Vulnerability...: EPA is announcing the release of the draft report titled, ``Aquatic Ecosystems, Water Quality, and... for Environmental Assessment within EPA's Office of Research and Development. This draft report...

Comparative Genomics as a Foundation for Evo-Devo Studies in Birds.

PubMed

Grayson, Phil; Sin, Simon Y W; Sackton, Timothy B; Edwards, Scott V

2017-01-01

Developmental genomics is a rapidly growing field, and high-quality genomes are a useful foundation for comparative developmental studies. A high-quality genome forms an essential reference onto which the data from numerous assays and experiments, including ChIP-seq, ATAC-seq, and RNA-seq, can be mapped. A genome also streamlines and simplifies the development of primers used to amplify putative regulatory regions for enhancer screens, cDNA probes for in situ hybridization, microRNAs (miRNAs) or short hairpin RNAs (shRNA) for RNA interference (RNAi) knockdowns, mRNAs for misexpression studies, and even guide RNAs (gRNAs) for CRISPR knockouts. Finally, much can be gleaned from comparative genomics alone, including the identification of highly conserved putative regulatory regions. This chapter provides an overview of laboratory and bioinformatics protocols for DNA extraction, library preparation, library quantification, and genome assembly, from fresh or frozen tissue to a draft avian genome. Generating a high-quality draft genome can provide a developmental research group with excellent resources for their study organism, opening the doors to many additional assays and experiments.

Report of the international workshop on quality control of monthly climate data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

1993-12-31

The National Climatic Data Center (NCDC), the US Department of Energy`s Carbon Dioxide Information Analysis Center, and the World Meteorological Organization (WMO) cosponsored an international quality control workshop for monthly climate data, October 5--6, 1993, at NCDC. About 40 scientists from around the world participated. The purpose of the meeting was to discuss and compare various quality control methods and to draft recommendations concerning the most successful systems. The near-term goal to improve quality control of CLIMAT messages for the NCDC/WMO publication Monthly Climatic Data for the World was sucessfully met. An electronic bulletin board was established to post errorsmore » and corrections. Improved communications among Global Telecommunication System hubs will be implemented. Advanced quality control algorithms were discussed and improvements were suggested. Further data exchanges were arranged.« less

Permanent draft genome sequence of the gliding predator Saprospira grandis strain Sa g1 (= HR1)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mavromatis, K; Chertkov, Olga; Lapidus, Alla L.

2012-01-01

Saprospira grandis Gross et al. 1911 is a member of the Saprospiraceae, a family in the class 'Sphingobacteria' that remains poorly characterized at the genomic level. The species is known for preying on other marine bacteria via 'ixotrophy'. S. grandis strain Sa g1 was isolated from decaying crab carapace in France and was selected for genome sequencing because of its isolated location in the tree of life. Only one type strain genome has been published so far from the Saprospiraceae, while the sequence of strain Sa g1 represents the second genome to be published from a non-type strain of S.more » grandis. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,495,250 bp long Improved-High-Quality draft of the genome with its 3,536 protein-coding and 62 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.« less

Householder's Perceptions of Insulation Adequacy and Drafts in the Home in 2001

EIA Publications

2004-01-01

In order to improve the estimation of end-use heating consumption, the Energy Information Administration's (EIA), 2001 Residential Energy Consumption Survey (RECS), for the first time, asked respondents to judge how drafty they perceived their homes to be as a measure of insulation quality.

Improving transcriptome construction in non-model organisms: integrating manual and automated gene definition in Emiliania huxleyi.

PubMed

Feldmesser, Ester; Rosenwasser, Shilo; Vardi, Assaf; Ben-Dor, Shifra

2014-02-22

The advent of Next Generation Sequencing technologies and corresponding bioinformatics tools allows the definition of transcriptomes in non-model organisms. Non-model organisms are of great ecological and biotechnological significance, and consequently the understanding of their unique metabolic pathways is essential. Several methods that integrate de novo assembly with genome-based assembly have been proposed. Yet, there are many open challenges in defining genes, particularly where genomes are not available or incomplete. Despite the large numbers of transcriptome assemblies that have been performed, quality control of the transcript building process, particularly on the protein level, is rarely performed if ever. To test and improve the quality of the automated transcriptome reconstruction, we used manually defined and curated genes, several of them experimentally validated. Several approaches to transcript construction were utilized, based on the available data: a draft genome, high quality RNAseq reads, and ESTs. In order to maximize the contribution of the various data, we integrated methods including de novo and genome based assembly, as well as EST clustering. After each step a set of manually curated genes was used for quality assessment of the transcripts. The interplay between the automated pipeline and the quality control indicated which additional processes were required to improve the transcriptome reconstruction. We discovered that E. huxleyi has a very high percentage of non-canonical splice junctions, and relatively high rates of intron retention, which caused unique issues with the currently available tools. While individual tools missed genes and artificially joined overlapping transcripts, combining the results of several tools improved the completeness and quality considerably. The final collection, created from the integration of several quality control and improvement rounds, was compared to the manually defined set both on the DNA and protein levels, and resulted in an improvement of 20% versus any of the read-based approaches alone. To the best of our knowledge, this is the first time that an automated transcript definition is subjected to quality control using manually defined and curated genes and thereafter the process is improved. We recommend using a set of manually curated genes to troubleshoot transcriptome reconstruction.

Integrated editing system for Japanese text and image information "Linernote"

NASA Astrophysics Data System (ADS)

Tanaka, Kazuto

Integrated Japanese text editing system "Linernote" developed by Toyo Industries Co. is explained. The system has been developed on the concept of electronic publishing. It is composed of personal computer NEC PC-9801 VX and other peripherals. Sentence, drawing and image data is inputted and edited under the integrated operating environment in the system and final text is printed out by laser printer. Handling efficiency of time consuming work such as pattern input or page make up has been improved by draft image data indication method on CRT. It is the latest DTP system equipped with three major functions, namly, typesetting for high quality text editing, easy drawing/tracing and high speed image processing.

78 FR 14538 - Notification of a Public Teleconference of the Clean Air Scientific Advisory Committee

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-06

... Assessment for Lead (Third External Review Draft--November 2012) and EPA's Policy Assessment for the Review of the Lead National Ambient Air Quality Standards (First External Review Draft--January 2013). DATES... CASAC will hold a public teleconference review its draft letters on EPA's third external review draft of...

Opera: reconstructing optimal genomic scaffolds with high-throughput paired-end sequences.

PubMed

Gao, Song; Sung, Wing-Kin; Nagarajan, Niranjan

2011-11-01

Scaffolding, the problem of ordering and orienting contigs, typically using paired-end reads, is a crucial step in the assembly of high-quality draft genomes. Even as sequencing technologies and mate-pair protocols have improved significantly, scaffolding programs still rely on heuristics, with no guarantees on the quality of the solution. In this work, we explored the feasibility of an exact solution for scaffolding and present a first tractable solution for this problem (Opera). We also describe a graph contraction procedure that allows the solution to scale to large scaffolding problems and demonstrate this by scaffolding several large real and synthetic datasets. In comparisons with existing scaffolders, Opera simultaneously produced longer and more accurate scaffolds demonstrating the utility of an exact approach. Opera also incorporates an exact quadratic programming formulation to precisely compute gap sizes (Availability: http://sourceforge.net/projects/operasf/ ).

Opera: Reconstructing Optimal Genomic Scaffolds with High-Throughput Paired-End Sequences

PubMed Central

Gao, Song; Sung, Wing-Kin

2011-01-01

Abstract Scaffolding, the problem of ordering and orienting contigs, typically using paired-end reads, is a crucial step in the assembly of high-quality draft genomes. Even as sequencing technologies and mate-pair protocols have improved significantly, scaffolding programs still rely on heuristics, with no guarantees on the quality of the solution. In this work, we explored the feasibility of an exact solution for scaffolding and present a first tractable solution for this problem (Opera). We also describe a graph contraction procedure that allows the solution to scale to large scaffolding problems and demonstrate this by scaffolding several large real and synthetic datasets. In comparisons with existing scaffolders, Opera simultaneously produced longer and more accurate scaffolds demonstrating the utility of an exact approach. Opera also incorporates an exact quadratic programming formulation to precisely compute gap sizes (Availability: http://sourceforge.net/projects/operasf/). PMID:21929371

Draft genome sequence of the marine bacterium Streptomyces griseoaurantiacus M045, which produces novel manumycin-type antibiotics with a pABA core component.

PubMed

Li, Fuchao; Jiang, Peng; Zheng, Huajun; Wang, Shengyue; Zhao, Guoping; Qin, Song; Liu, Zhaopu

2011-07-01

Streptomyces griseoaurantiacus M045, isolated from marine sediment, produces manumycin and chinikomycin antibiotics. Here we present a high-quality draft genome sequence of S. griseoaurantiacus M045, the first marine Streptomyces species to be sequenced and annotated. The genome encodes several gene clusters for biosynthesis of secondary metabolites and has provided insight into genomic islands linking secondary metabolism to functional adaptation in marine S. griseoaurantiacus M045.

Draft Genome Sequence of Streptomyces clavuligerus NRRL 3585, a Producer of Diverse Secondary Metabolites▿

PubMed Central

Song, Ju Yeon; Jeong, Haeyoung; Yu, Dong Su; Fischbach, Michael A.; Park, Hong-Seog; Kim, Jae Jong; Seo, Jeong-Sun; Jensen, Susan E.; Oh, Tae Kwang; Lee, Kye Joon; Kim, Jihyun F.

2010-01-01

Streptomyces clavuligerus is an important industrial strain that produces a number of antibiotics, including clavulanic acid and cephamycin C. A high-quality draft genome sequence of the S. clavuligerus NRRL 3585 strain was produced by employing a hybrid approach that involved Sanger sequencing, Roche/454 pyrosequencing, optical mapping, and partial finishing. Its genome, comprising four linear replicons, one chromosome, and four plasmids, carries numerous sets of genes involved in the biosynthesis of secondary metabolites, including a variety of antibiotics. PMID:20889745

National Policy on Education and Higher Education

ERIC Educational Resources Information Center

Varughese, Rajan

2017-01-01

The Ministry of Human Resource Development (MHRD) has come out with the draft of 'National Education Policy (NEP) 2016' in April 2016. The new NEP 2016 seeks to create conditions to improve the quality of teaching, learning and assessment, and promote transparency in the management of education in the country. The policy prescriptions enunciated…

The Genomics Education Partnership: Successful Integration of Research into Laboratory Classes at a Diverse Group of Undergraduate Institutions

PubMed Central

Shaffer, Christopher D.; Alvarez, Consuelo; Bailey, Cheryl; Barnard, Daron; Bhalla, Satish; Chandrasekaran, Chitra; Chandrasekaran, Vidya; Chung, Hui-Min; Dorer, Douglas R.; Du, Chunguang; Eckdahl, Todd T.; Poet, Jeff L.; Frohlich, Donald; Goodman, Anya L.; Gosser, Yuying; Hauser, Charles; Hoopes, Laura L.M.; Johnson, Diana; Jones, Christopher J.; Kaehler, Marian; Kokan, Nighat; Kopp, Olga R.; Kuleck, Gary A.; McNeil, Gerard; Moss, Robert; Myka, Jennifer L.; Nagengast, Alexis; Morris, Robert; Overvoorde, Paul J.; Shoop, Elizabeth; Parrish, Susan; Reed, Kelynne; Regisford, E. Gloria; Revie, Dennis; Rosenwald, Anne G.; Saville, Ken; Schroeder, Stephanie; Shaw, Mary; Skuse, Gary; Smith, Christopher; Smith, Mary; Spana, Eric P.; Spratt, Mary; Stamm, Joyce; Thompson, Jeff S.; Wawersik, Matthew; Wilson, Barbara A.; Youngblom, Jim; Leung, Wilson; Buhler, Jeremy; Mardis, Elaine R.; Lopatto, David

2010-01-01

Genomics is not only essential for students to understand biology but also provides unprecedented opportunities for undergraduate research. The goal of the Genomics Education Partnership (GEP), a collaboration between a growing number of colleges and universities around the country and the Department of Biology and Genome Center of Washington University in St. Louis, is to provide such research opportunities. Using a versatile curriculum that has been adapted to many different class settings, GEP undergraduates undertake projects to bring draft-quality genomic sequence up to high quality and/or participate in the annotation of these sequences. GEP undergraduates have improved more than 2 million bases of draft genomic sequence from several species of Drosophila and have produced hundreds of gene models using evidence-based manual annotation. Students appreciate their ability to make a contribution to ongoing research, and report increased independence and a more active learning approach after participation in GEP projects. They show knowledge gains on pre- and postcourse quizzes about genes and genomes and in bioinformatic analysis. Participating faculty also report professional gains, increased access to genomics-related technology, and an overall positive experience. We have found that using a genomics research project as the core of a laboratory course is rewarding for both faculty and students. PMID:20194808

Development and Validation of the Scan of Postgraduate Educational Environment Domains (SPEED): A Brief Instrument to Assess the Educational Environment in Postgraduate Medical Education

PubMed Central

Schönrock-Adema, Johanna; Visscher, Maartje; Raat, A. N. Janet; Brand, Paul L. P.

2015-01-01

Introduction Current instruments to evaluate the postgraduate medical educational environment lack theoretical frameworks and are relatively long, which may reduce response rates. We aimed to develop and validate a brief instrument that, based on a solid theoretical framework for educational environments, solicits resident feedback to screen the postgraduate medical educational environment quality. Methods Stepwise, we developed a screening instrument, using existing instruments to assess educational environment quality and adopting a theoretical framework that defines three educational environment domains: content, atmosphere and organization. First, items from relevant existing instruments were collected and, after deleting duplicates and items not specifically addressing educational environment, grouped into the three domains. In a Delphi procedure, the item list was reduced to a set of items considered most important and comprehensively covering the three domains. These items were triangulated against the results of semi-structured interviews with 26 residents from three teaching hospitals to achieve face validity. This draft version of the Scan of Postgraduate Educational Environment Domains (SPEED) was administered to residents in a general and university hospital and further reduced and validated based on the data collected. Results Two hundred twenty-three residents completed the 43-item draft SPEED. We used half of the dataset for item reduction, and the other half for validating the resulting SPEED (15 items, 5 per domain). Internal consistencies were high. Correlations between domain scores in the draft and brief versions of SPEED were high (>0.85) and highly significant (p<0.001). Domain score variance of the draft instrument was explained for ≥80% by the items representing the domains in the final SPEED. Conclusions The SPEED comprehensively covers the three educational environment domains defined in the theoretical framework. Because of its validity and brevity, the SPEED is promising as useful and easily applicable tool to regularly screen educational environment quality in postgraduate medical education. PMID:26413836

Draft genome sequence of the silver pomfret fish, Pampus argenteus.

PubMed

AlMomin, Sabah; Kumar, Vinod; Al-Amad, Sami; Al-Hussaini, Mohsen; Dashti, Talal; Al-Enezi, Khaznah; Akbar, Abrar

2016-01-01

Silver pomfret, Pampus argenteus, is a fish species from coastal waters. Despite its high commercial value, this edible fish has not been sequenced. Hence, its genetic and genomic studies have been limited. We report the first draft genome sequence of the silver pomfret obtained using a Next Generation Sequencing (NGS) technology. We assembled 38.7 Gb of nucleotides into scaffolds of 350 Mb with N50 of about 1.5 kb, using high quality paired end reads. These scaffolds represent 63.7% of the estimated silver pomfret genome length. The newly sequenced and assembled genome has 11.06% repetitive DNA regions, and this percentage is comparable to that of the tilapia genome. The genome analysis predicted 16 322 genes. About 91% of these genes showed homology with known proteins. Many gene clusters were annotated to protein and fatty-acid metabolism pathways that may be important in the context of the meat texture and immune system developmental processes. The reference genome can pave the way for the identification of many other genomic features that could improve breeding and population-management strategies, and it can also help characterize the genetic diversity of P. argenteus.

77 FR 15052 - National Ocean Council-National Ocean Policy Draft Implementation Plan

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-14

... COUNCIL ON ENVIRONMENTAL QUALITY National Ocean Council--National Ocean Policy Draft Implementation Plan AGENCY: Council on Environmental Quality. ACTION: Extension of comment period. SUMMARY: On July 19, 2010, President Obama signed Executive Order 13547 establishing a National Policy for the...

2017 Draft Aquatic Life Criteria for Aluminum in Freshwater

EPA Pesticide Factsheets

EPA has released draft updated aluminum aquatic life ambient water quality criteria for freshwater under Section 304(a)(1) of the Clean Water Act. EPA will accept public comments on the draft criteria for 60 days upon publication in the Federal Register.

Systematic Review of International Colposcopy Quality Improvement Guidelines.

PubMed

Mayeaux, Edward J; Novetsky, Akiva P; Chelmow, David; Choma, Kim; Garcia, Francisco; Liu, Angela H; Papasozomenos, Theognosia; Einstein, Mark H

2017-10-01

The American Society for Colposcopy and Cervical Pathology Colposcopy Standards Committee organized multiple working groups to draft colposcopy standards for the United States. As part of this project, international quality assurance and improvement measures were examined. The quality improvement working group performed a systematic review of the literature to collate international guidelines related to quality improvement. Source guidelines were collected using searches in Medline, Google Scholar, the International Federation of Cervical Pathology and Colposcopy Web site, other regional colposcopy group's Web sites, and communications with International Federation of Cervical Pathology and Colposcopy board of directors' members and other expert members of various national groups. Once identified, the sources were reviewed by multiple workgroup members for potential guideline materials. Fifty-six unique documents were identified, of which 18 met inclusion criteria and contributed data to the analysis. Information was abstracted and grouped by related subject. Wide variation exists in colposcopy guidance and quality indicators from regional and national colposcopy societies. Abstracted international guidelines are presented.

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

PubMed

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).

Lead us not into tanktation: a simulation modelling approach to gain insights into incentives for sporting teams to tank.

PubMed

Tuck, Geoffrey N; Whitten, Athol R

2013-01-01

Annual draft systems are the principal method used by teams in major sporting leagues to recruit amateur players. These draft systems frequently take one of three forms: a lottery style draft, a weighted draft, or a reverse-order draft. Reverse-order drafts can create incentives for teams to deliberately under-perform, or tank, due to the perceived gain from obtaining quality players at higher draft picks. This paper uses a dynamic simulation model that captures the key components of a win-maximising sporting league, including the amateur player draft, draft choice error, player productivity, and between-team competition, to explore how competitive balance and incentives to under-perform vary according to league characteristics. We find reverse-order drafts can lead to some teams cycling between success and failure and to other teams being stuck in mid-ranking positions for extended periods of time. We also find that an incentive for teams to tank exists, but that this incentive decreases (i) as uncertainty in the ability to determine quality players in the draft increases, (ii) as the number of teams in the league reduces, (iii) as team size decreases, and (iv) as the number of teams adopting a tanking strategy increases. Simulation models can be used to explore complex stochastic dynamic systems such as sports leagues, where managers face difficult decisions regarding the structure of their league and the desire to maintain competitive balance.

Lead Us Not into Tanktation: A Simulation Modelling Approach to Gain Insights into Incentives for Sporting Teams to Tank

PubMed Central

Tuck, Geoffrey N.; Whitten, Athol R.

2013-01-01

Annual draft systems are the principal method used by teams in major sporting leagues to recruit amateur players. These draft systems frequently take one of three forms: a lottery style draft, a weighted draft, or a reverse-order draft. Reverse-order drafts can create incentives for teams to deliberately under-perform, or tank, due to the perceived gain from obtaining quality players at higher draft picks. This paper uses a dynamic simulation model that captures the key components of a win-maximising sporting league, including the amateur player draft, draft choice error, player productivity, and between-team competition, to explore how competitive balance and incentives to under-perform vary according to league characteristics. We find reverse-order drafts can lead to some teams cycling between success and failure and to other teams being stuck in mid-ranking positions for extended periods of time. We also find that an incentive for teams to tank exists, but that this incentive decreases (i) as uncertainty in the ability to determine quality players in the draft increases, (ii) as the number of teams in the league reduces, (iii) as team size decreases, and (iv) as the number of teams adopting a tanking strategy increases. Simulation models can be used to explore complex stochastic dynamic systems such as sports leagues, where managers face difficult decisions regarding the structure of their league and the desire to maintain competitive balance. PMID:24312243

High-quality permanent draft genome sequence of Rhizobium leguminosarum bv. viciae strain GB30; an effective microsymbiont of Pisum sativum growing in Poland

DOE PAGES

Mazur, Andrzej; De Meyer, Sofie E.; Tian, Rui; ...

2015-07-16

We report that Rhizobium leguminosarum bv. viciae GB30 is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of Pisum sativum. GB30 was isolated in Poland from a nodule recovered from the roots of Pisum sativum growing at Janow. GB30 is also an effective microsymbiont of the annual forage legumes vetch and pea. Here we describe the features of R. leguminosarum bv. viciae strain GB30, together with sequence and annotation. The 7,468,464 bp high-quality permanent draft genome is arranged in 78 scaffolds of 78 contigs containing 7,227 protein-coding genes and 75more » RNA-only encoding genes, and is part of the GEBA-RNB project proposal.« less

High-Quality draft genome sequence of the Lotus spp. microsymbiont Mesorhizobium loti strain CJ3Sym

DOE PAGES

Reeve, Wayne; Sullivan, John; Ronson, Clive; ...

2015-08-14

Mesorhizobium loti strain CJ3Sym was isolated in 1998 following transfer of the integrative and conjugative element ICE Ml Sym R7A , also known as the R7A symbiosis island, in a laboratory mating from the donor M. loti strain R7A to a nonsymbiotic recipient Mesorhizobium strain CJ3. Strain CJ3 was originally isolated from a field site in the Rocklands range in New Zealand in 1994. CJ3Sym is an aerobic, Gram-negative, non-spore-forming rod. This report reveals the genome of M. loti strain CJ3Sym currently comprises 70 scaffolds totaling 7,563,725 bp. In conclusion, the high-quality draft genome is arranged in 70 scaffolds ofmore » 71 contigs, contains 7,331 protein-coding genes and 70 RNA-only encoding genes, and is part of the GEBA-RNB project proposal.« less

High-Quality draft genome sequence of the Lotus spp. microsymbiont Mesorhizobium loti strain CJ3Sym

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reeve, Wayne; Sullivan, John; Ronson, Clive

Mesorhizobium loti strain CJ3Sym was isolated in 1998 following transfer of the integrative and conjugative element ICE Ml Sym R7A , also known as the R7A symbiosis island, in a laboratory mating from the donor M. loti strain R7A to a nonsymbiotic recipient Mesorhizobium strain CJ3. Strain CJ3 was originally isolated from a field site in the Rocklands range in New Zealand in 1994. CJ3Sym is an aerobic, Gram-negative, non-spore-forming rod. This report reveals the genome of M. loti strain CJ3Sym currently comprises 70 scaffolds totaling 7,563,725 bp. In conclusion, the high-quality draft genome is arranged in 70 scaffolds ofmore » 71 contigs, contains 7,331 protein-coding genes and 70 RNA-only encoding genes, and is part of the GEBA-RNB project proposal.« less

High-quality permanent draft genome sequence of Rhizobium leguminosarum bv. viciae strain GB30; an effective microsymbiont of Pisum sativum growing in Poland

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mazur, Andrzej; De Meyer, Sofie E.; Tian, Rui

We report that Rhizobium leguminosarum bv. viciae GB30 is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of Pisum sativum. GB30 was isolated in Poland from a nodule recovered from the roots of Pisum sativum growing at Janow. GB30 is also an effective microsymbiont of the annual forage legumes vetch and pea. Here we describe the features of R. leguminosarum bv. viciae strain GB30, together with sequence and annotation. The 7,468,464 bp high-quality permanent draft genome is arranged in 78 scaffolds of 78 contigs containing 7,227 protein-coding genes and 75more » RNA-only encoding genes, and is part of the GEBA-RNB project proposal.« less

Emission reduction potentials of improved cookstoves and their issues in adoption: An Indian outlook.

PubMed

Sharma, Monikankana; Dasappa, S

2017-12-15

Biomass as a fuel for cooking is a common practice in rural India, and about 700 million people use traditional stoves to meet their energy demand. However, the thermal and the combustion efficiencies of these stoves are very low, leading to an inefficient use of biomass, and also, resulting in significant indoor air pollution. Research development has however led to the development of some improved stoves viz., natural draft and forced draft for both domestic as well as large scale cooking applications and government is trying to promote them. Forced draft stoves using processed biomass fuels (pellets) have received more prominence due to their superior performance, however, higher initial cost and limited fuel distribution networks have remained the key challenges. Improved natural draft stoves too have gained attention for being relatively inexpensive, and they are more likely to hit the rural households. In this paper, we have examined the environmental benefits obtained by the use of improved stoves for two important scenarios: traditional stoves are replaced by (i)improved natural draft stoves and, (ii) by improved natural draft as well as forced draft stoves. In the best case scenario (case ii), i.e., by shifting 111 million households who currently use wood to the forced draft stoves, and another 45 million households who are dependent on dung cake and agro residues to the improved natural draft stoves, the emission reduction that can be achieved are as follows: particulate matter (PM) 875 kT, black carbon (BC) 229 kT, organic carbon (OC) 525 kT, methane (CH 4 )1178 kT and non methane hydrocarbon (NMHC) of 564 kT. With the promotion of only natural draft improved stoves, the total reductions would be ∼12% lower than the combinational promotion. The CO 2 equivalent reduction is estimated to be ∼70-80 MT per year. Copyright © 2017 Elsevier Ltd. All rights reserved.

Voice recognition software can be used for scientific articles.

PubMed

Pommergaard, Hans-Christian; Huang, Chenxi; Burcharth, Jacob; Rosenberg, Jacob

2015-02-01

Dictation of scientific articles has been recognised as an efficient method for producing high-quality, first article drafts. However, standardised transcription service by a secretary may not be available for all researchers and voice recognition software (VRS) may therefore be an alternative. The purpose of this study was to evaluate the out-of-the-box accuracy of VRS. Eleven young researchers without dictation experience dictated the first draft of their own scientific article after thorough preparation according to a pre-defined schedule. The dictate transcribed by VRS was compared with the same dictate transcribed by an experienced research secretary, and the effect of adding words to the vocabulary of the VRS was investigated. The number of errors per hundred words was used as outcome. Furthermore, three experienced researchers assessed the subjective readability using a Likert scale (0-10). Dragon Nuance Premium version 12.5 was used as VRS. The median number of errors per hundred words was 18 (range: 8.5-24.3), which improved when 15,000 words were added to the vocabulary. Subjective readability assessment showed that the texts were understandable with a median score of five (range: 3-9), which was improved with the addition of 5,000 words. The out-of-the-box performance of VRS was acceptable and improved after additional words were added. Further studies are needed to investigate the effect of additional software accuracy training.

Dramatic improvement in genome assembly achieved using doubled-haploid genomes.

PubMed

Zhang, Hong; Tan, Engkong; Suzuki, Yutaka; Hirose, Yusuke; Kinoshita, Shigeharu; Okano, Hideyuki; Kudoh, Jun; Shimizu, Atsushi; Saito, Kazuyoshi; Watabe, Shugo; Asakawa, Shuichi

2014-10-27

Improvement in de novo assembly of large genomes is still to be desired. Here, we improved draft genome sequence quality by employing doubled-haploid individuals. We sequenced wildtype and doubled-haploid Takifugu rubripes genomes, under the same conditions, using the Illumina platform and assembled contigs with SOAPdenovo2. We observed 5.4-fold and 2.6-fold improvement in the sizes of the N50 contig and scaffold of doubled-haploid individuals, respectively, compared to the wildtype, indicating that the use of a doubled-haploid genome aids in accurate genome analysis.

Assessing the Relationship between Different Types of Student Feedback and the Quality of Revised Writing

ERIC Educational Resources Information Center

Diab, Nuwar Mawlawi

2011-01-01

This paper reports on a quasi-experimental study comparing the effects of peer-editing to self-editing on improving students' revised drafts. The study involved two intact classes (experimental and control groups) of an English course. The experimental group practiced peer-editing while the control group engaged in self-editing. After receiving…

High-quality draft genome sequence of Kocuria marina SO9-6, an actinobacterium isolated from a copper mine

PubMed Central

Castro, Daniel B.A.; Pereira, Letícia Bianca; Silva, Marcus Vinícius M. e; Silva, Bárbara P. da; Palermo, Bruna Rafaella Z.; Carlos, Camila; Belgini, Daiane R.B.; Limache, Elmer Erasmo G.; Lacerda, Gileno V. Jr; Nery, Mariana B.P.; Gomes, Milene B.; Souza, Salatiel S. de; Silva, Thiago M. da; Rodrigues, Viviane D.; Paulino, Luciana C.; Vicentini, Renato; Ferraz, Lúcio F.C.; Ottoboni, Laura M.M.

2015-01-01

An actinobacterial strain, designated SO9-6, was isolated from a copper iron sulfide mineral. The organism is Gram-positive, facultatively anaerobic, and coccoid. Chemotaxonomic and phylogenetic properties were consistent with its classification in the genus Kocuria. Here, we report the first draft genome sequence of Kocuria marina SO9-6 under accession JROM00000000 (http://www.ncbi.nlm.nih.gov/nuccore/725823918), which provides insights for heavy metal bioremediation and production of compounds of biotechnological interest. PMID:26484219

How to Write Your First Research Paper

PubMed Central

Kallestinova, Elena D.

2011-01-01

Writing a research manuscript is an intimidating process for many novice writers in the sciences. One of the stumbling blocks is the beginning of the process and creating the first draft. This paper presents guidelines on how to initiate the writing process and draft each section of a research manuscript. The paper discusses seven rules that allow the writer to prepare a well-structured and comprehensive manuscript for a publication submission. In addition, the author lists different strategies for successful revision. Each of those strategies represents a step in the revision process and should help the writer improve the quality of the manuscript. The paper could be considered a brief manual for publication. PMID:21966034

How to write your first research paper.

PubMed

Kallestinova, Elena D

2011-09-01

Writing a research manuscript is an intimidating process for many novice writers in the sciences. One of the stumbling blocks is the beginning of the process and creating the first draft. This paper presents guidelines on how to initiate the writing process and draft each section of a research manuscript. The paper discusses seven rules that allow the writer to prepare a well-structured and comprehensive manuscript for a publication submission. In addition, the author lists different strategies for successful revision. Each of those strategies represents a step in the revision process and should help the writer improve the quality of the manuscript. The paper could be considered a brief manual for publication. Copyright © 2011.

Air Quality Criteria for Ozone and Related Photochemical Oxidants (First External Review Draft)

EPA Science Inventory

This first external review draft of the Air Quality Criteria for Ozone and Related Photochemical Oxidants (Ozone Criteria Document) is being released in January 2005 for public comment and for review by EPA's Clean A...

Air Quality Criteria for Ozone and Related Photochemical Oxidants (Second External Review Draft)

EPA Science Inventory

This second external review draft of the Air Quality Criteria for Ozone and Related Photochemical Oxidants, Volumes I-III (Ozone Criteria Document) is being released for public comment and for review by EPA's Clean Air Scientific Advisory Committee (CASAC) r...

Aquatic Ecosystems, Water Quality, and Global Change: Challenges of conducting Multi-Stressor Vulnerability Assessments (External Review Draft)

EPA Science Inventory

This draft report investigates the issues and challenges associated with identifying, calculating, and mapping indicators of the relative vulnerability of water quality and aquatic ecosystems, across the United States, to the potential impacts of global change. Using a large set...

Arizona watershed framework in the Verde River watershed

Treesearch

Ren Northrup

2000-01-01

The Arizona Department of Environmental Quality, Water Quality Division drafted a six-step approach to guide its staff and local participants in developing and implementing watershed management plans. From January 1999 through June 2000, the draft Arizona Statewide Watershed Framework will be tested in Arizona's Verde River watershed. This concept proofing...

78 FR 31943 - Draft Guidance for Industry on Contract Manufacturing Arrangements for Drugs: Quality Agreements...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-05-28

... documenting the responsibilities of all parties involved in drug manufacturing, testing, or other support... DEPARTMENT OF HEALTH AND HUMAN SERVICES Food and Drug Administration [Docket No. FDA-2013-D-0558] Draft Guidance for Industry on Contract Manufacturing Arrangements for Drugs: Quality Agreements...

Draft framework for watershed-based trading

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

1996-05-30

Effluent trading is an innovative way for water quality agencies and community stakeholders to develop common-sense, cost-effective solutions for water quality problems in their watersheds. Trading can allow communities to grow and prosper while retaining their commitment to water quality. The bulk of this framework discusses effluent trading in watersheds. Remaining sections discuss transactions that, while not technically fulfilling the definition of `effluent` trade, do involve the exchange of valued water quality or other ecological improvements between partners responding to market initiatives. This document therefore includes activities such as trades within a facility (intra-plant trading) and wetland mitigation banking, effluentmore » trading/watersheds/watershed management/water quality protection/water quality management.« less

The Transcriptomics of Secondary Growth and Wood Formation in Conifers

PubMed Central

Carvalho, Ana; Paiva, Jorge; Louzada, José; Lima-Brito, José

2013-01-01

In the last years, forestry scientists have adapted genomics and next-generation sequencing (NGS) technologies to the search for candidate genes related to the transcriptomics of secondary growth and wood formation in several tree species. Gymnosperms, in particular, the conifers, are ecologically and economically important, namely, for the production of wood and other forestry end products. Until very recently, no whole genome sequencing of a conifer genome was available. Due to the gradual improvement of the NGS technologies and inherent bioinformatics tools, two draft assemblies of the whole genomes sequence of Picea abies and Picea glauca arose in the current year. These draft genome assemblies will bring new insights about the structure, content, and evolution of the conifer genomes. Furthermore, new directions in the forestry, breeding and research of conifers will be discussed in the following. The identification of genes associated with the xylem transcriptome and the knowledge of their regulatory mechanisms will provide less time-consuming breeding cycles and a high accuracy for the selection of traits related to wood production and quality. PMID:24288610

77 FR 42495 - Release of Draft Documents Related to the Review of the National Ambient Air Quality Standards...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-19

... Review Draft. These two draft assessment documents describe the quantitative analyses the EPA is... NAAQS,\\3\\ the Agency is conducting quantitative assessments characterizing the: (1) Health risks... present the initial key results, observations, and related uncertainties associated with the quantitative...

Draft genome of the medaka fish: a comprehensive resource for medaka developmental genetics and vertebrate evolutionary biology.

PubMed

Takeda, Hiroyuki

2008-06-01

The medaka Oryzias latipes is a small egg-laying freshwater teleost, and has become an excellent model system for developmental genetics and evolutionary biology. The medaka genome is relatively small in size, approximately 800 Mb, and the genome sequencing project was recently completed by Japanese research groups, providing a high-quality draft genome sequence of the inbred Hd-rR strain of medaka. In this review, I present an overview of the medaka genome project including genome resources, followed by specific findings obtained with the medaka draft genome. In particular, I focus on the analysis that was done by taking advantage of the medaka system, such as the sex chromosome differentiation and the regional history of medaka species using single nucleotide polymorphisms as genomic markers.

Draft Guidelines for State and Areawide Water Quality Management Program Development.

ERIC Educational Resources Information Center

Environmental Protection Agency, Washington, DC.

This document discusses the draft guidelines formulated by the Environmental Protection Agency (EPA) to assist the states in establishing a management program to integrate water quality and other resource management decisions. These guidelines are pfovided so that the long range goals of the Federal Water Pollution Control Act Amendments of 1972…

Exploiting long read sequencing technologies to establish high quality highly contiguous pig reference genome assemblies

USDA-ARS?s Scientific Manuscript database

The current pig reference genome sequence (Sscrofa10.2) was established using Sanger sequencing and following the clone-by-clone hierarchical shotgun sequencing approach used in the public human genome project. However, as sequence coverage was low (4-6x) the resulting assembly was only of draft qua...

Ten tips for authors of scientific articles.

PubMed

Hong, Sung-Tae

2014-08-01

Writing a good quality scientific article takes experience and skill. I propose 'Ten Tips' that may help to improve the quality of manuscripts for scholarly journals. It is advisable to draft first version of manuscript and revise it repeatedly for consistency and accuracy of the writing. During the drafting and revising the following tips can be considered: 1) focus on design to have proper content, conclusion, points compliant with scope of the target journal, appropriate authors and contributors list, and relevant references from widely visible sources; 2) format the manuscript in accordance with instructions to authors of the target journal; 3) ensure consistency and logical flow of ideas and scientific facts; 4) provide scientific confidence; 5) make your story interesting for your readers; 6) write up short, simple and attractive sentences; 7) bear in mind that properly composed and reflective titles increase chances of attracting more readers; 8) do not forget that well-structured and readable abstracts improve citability of your publications; 9) when revising adhere to the rule of 'First and Last' - open your text with topic paragraph and close it with resolution paragraph; 10) use connecting words linking sentences within a paragraph by repeating relevant keywords.

Ten Tips for Authors of Scientific Articles

PubMed Central

2014-01-01

Writing a good quality scientific article takes experience and skill. I propose 'Ten Tips' that may help to improve the quality of manuscripts for scholarly journals. It is advisable to draft first version of manuscript and revise it repeatedly for consistency and accuracy of the writing. During the drafting and revising the following tips can be considered: 1) focus on design to have proper content, conclusion, points compliant with scope of the target journal, appropriate authors and contributors list, and relevant references from widely visible sources; 2) format the manuscript in accordance with instructions to authors of the target journal; 3) ensure consistency and logical flow of ideas and scientific facts; 4) provide scientific confidence; 5) make your story interesting for your readers; 6) write up short, simple and attractive sentences; 7) bear in mind that properly composed and reflective titles increase chances of attracting more readers; 8) do not forget that well-structured and readable abstracts improve citability of your publications; 9) when revising adhere to the rule of 'First and Last' - open your text with topic paragraph and close it with resolution paragraph; 10) use connecting words linking sentences within a paragraph by repeating relevant keywords. PMID:25120310

76 FR 67437 - Draft Aquatic Life Ambient Water Quality Criteria for Carbaryl-2011

Federal Register 2010, 2011, 2012, 2013, 2014

2011-11-01

... ENVIRONMENTAL PROTECTION AGENCY [EPA-HQ-OW-2011-0787; FRL-9483-8] Draft Aquatic Life Ambient Water... criteria for the protection of aquatic life from effects of carbaryl (EPA-820-D-11-001). The draft criteria document incorporates the latest scientific knowledge on the toxicity of carbaryl to aquatic life. The...

Operational Draft Regional Guidebook for the Functional Assessment of High-Gradient Headwater Streams and Low-Gradient Perennial Streams in Appalachia

DTIC Science & Technology

rapid assessments provided in this guidebook utilize structural components of streams and their watershed and can be used in conjunction with assessment of water quality and biotic communities if desired.

A comprehensive porcine blood transcriptome

USDA-ARS?s Scientific Manuscript database

Blood sample analyses are extensively used in high throughput assays in biomedicine, as well as animal genetics and physiology research. However, the draft quality of the current pig genome (Sscrofa 10.2) is insufficient for accurate interpretation of many of these assays because of incomplete gene ...

DCT based interpolation filter for motion compensation in HEVC

NASA Astrophysics Data System (ADS)

Alshin, Alexander; Alshina, Elena; Park, Jeong Hoon; Han, Woo-Jin

2012-10-01

High Efficiency Video Coding (HEVC) draft standard has a challenging goal to improve coding efficiency twice compare to H.264/AVC. Many aspects of the traditional hybrid coding framework were improved during new standard development. Motion compensated prediction, in particular the interpolation filter, is one area that was improved significantly over H.264/AVC. This paper presents the details of the interpolation filter design of the draft HEVC standard. The coding efficiency improvements over H.264/AVC interpolation filter is studied and experimental results are presented, which show a 4.0% average bitrate reduction for Luma component and 11.3% average bitrate reduction for Chroma component. The coding efficiency gains are significant for some video sequences and can reach up 21.7%.

75 FR 63519 - Notice of Availability of Draft Environmental Assessment and Draft Finding of No Significant...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-15

... significantly affect the quality of the human environment and that a finding of no significant impact should...). Ecology SMALL SMALL SMALL to MODERATE. Noise SMALL SMALL SMALL to MODERATE. Historic & Cultural SMALL..., Tennessee to continue for a period of 40 years would not significantly affect the quality of the human...

Workshop to Obtain Input on Draft Materials for the Integrated Science Assessment (ISA) for Sulfur Oxides (SOx): Health Criteria

EPA Science Inventory

As part of the review of the air quality criteria for sulfur oxides (SO_X) and primary (health-based) National Ambient Air Quality Standards (NAAQS) for sulfur dioxide (SO₂), EPA is announcing a teleconference workshop to evaluate preliminary draft materials ...

Improving draft genome contiguity with reference-derived in silico mate-pair libraries.

PubMed

Grau, José Horacio; Hackl, Thomas; Koepfli, Klaus-Peter; Hofreiter, Michael

2018-05-01

Contiguous genome assemblies are a highly valued biological resource because of the higher number of completely annotated genes and genomic elements that are usable compared to fragmented draft genomes. Nonetheless, contiguity is difficult to obtain if only low coverage data and/or only distantly related reference genome assemblies are available. In order to improve genome contiguity, we have developed Cross-Species Scaffolding-a new pipeline that imports long-range distance information directly into the de novo assembly process by constructing mate-pair libraries in silico. We show how genome assembly metrics and gene prediction dramatically improve with our pipeline by assembling two primate genomes solely based on ∼30x coverage of shotgun sequencing data.

Single-molecule sequencing and optical mapping yields an improved genome of woodland strawberry (Fragaria vesca) with chromosome-scale contiguity.

PubMed

Edger, Patrick P; VanBuren, Robert; Colle, Marivi; Poorten, Thomas J; Wai, Ching Man; Niederhuth, Chad E; Alger, Elizabeth I; Ou, Shujun; Acharya, Charlotte B; Wang, Jie; Callow, Pete; McKain, Michael R; Shi, Jinghua; Collier, Chad; Xiong, Zhiyong; Mower, Jeffrey P; Slovin, Janet P; Hytönen, Timo; Jiang, Ning; Childs, Kevin L; Knapp, Steven J

2018-02-01

Although draft genomes are available for most agronomically important plant species, the majority are incomplete, highly fragmented, and often riddled with assembly and scaffolding errors. These assembly issues hinder advances in tool development for functional genomics and systems biology. Here we utilized a robust, cost-effective approach to produce high-quality reference genomes. We report a near-complete genome of diploid woodland strawberry (Fragaria vesca) using single-molecule real-time sequencing from Pacific Biosciences (PacBio). This assembly has a contig N50 length of ∼7.9 million base pairs (Mb), representing a ∼300-fold improvement of the previous version. The vast majority (>99.8%) of the assembly was anchored to 7 pseudomolecules using 2 sets of optical maps from Bionano Genomics. We obtained ∼24.96 Mb of sequence not present in the previous version of the F. vesca genome and produced an improved annotation that includes 1496 new genes. Comparative syntenic analyses uncovered numerous, large-scale scaffolding errors present in each chromosome in the previously published version of the F. vesca genome. Our results highlight the need to improve existing short-read based reference genomes. Furthermore, we demonstrate how genome quality impacts commonly used analyses for addressing both fundamental and applied biological questions. © The Authors 2017. Published by Oxford University Press.

Phanerochaete chrysosporium genomics

Treesearch

Luis F. Larrondo; Rafael Vicuna; Dan Cullen

2005-01-01

A high quality draft genome sequence has been generated for the lignocellulose-degrading basidiomycete Phanerochaete chrysosporium (Martinez et al. 2004). Analysis of the genome in the context of previously established genetics and physiology is presented. Transposable elements and their potential relationship to genes involved in lignin degradation are systematically...

DOE Office of Scientific and Technical Information (OSTI.GOV)

Isanapong, Jantiya; Goodwin, Lynne A.; Bruce, David

Microbial communities in the termite hindgut are essential for degrading plant material. We present the high-quality draft genome sequence of the Opitutaceae bacterium strain TAV1, the first member of the phylum Verrucomicrobia to be isolated from wood-feeding termites. The genomic analysis reveals genes coding for lignocellulosic degradation and nitrogen fixation.

High-quality permanent draft genome sequence of Bradyrhizobium sp. strain WSM1743 - an effective microsymbiont of an Indigofera sp. growing in Australia

DOE PAGES

Eshraghi, Leila; De Meyer, Sofie E.; Tian, Rui; ...

2015-10-26

Bradyrhizobium sp. strain WSM1743 is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of an Indigofera sp. WSM1743 was isolated from a nodule recovered from the roots of an Indigofera sp. growing 20 km north of Carnarvon in Australia. It is slow growing, tolerates up to 1 % NaCl and is capable of growth at 37 °C. Here we describe the features of Bradyrhizobium sp. strain WSM1743, together with genome sequence information and its annotation. Finally, the 8,341,956 bp high-quality permanent draft genome is arranged into 163 scaffolds and 167more » contigs, contains 7908 protein-coding genes and 75 RNA-only encoding genes and was sequenced as part of the Root Nodule Bacteria chapter of the Genomic Encyclopedia of Bacteria and Archaea project.« less

High-quality permanent draft genome sequence of the Mimosa asperata - nodulating Cupriavidus sp. strain AMP6

DOE PAGES

De Meyer, Sofie E.; Parker, Matthew; Van Berkum, Peter; ...

2015-10-16

Cupriavidus sp. strain AMP6 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from a root nodule of Mimosa asperata collected in Santa Ana National Wildlife Refuge, Texas, in 2005. Mimosa asperata is the only legume described so far to exclusively associates with Cupriavidus symbionts. Furthermore, strain AMP6 represents an early-diverging lineage within the symbiotic Cupriavidus group and has the capacity to develop an effective nitrogen-fixing symbiosis with three other species of Mimosa. Here, we describe the genome of Cupriavidus sp. strain AMP6 which enables comparative analyses of symbiotic trait evolution in this genus; the general features, together withmore » sequence and annotation are further discussed. Finally, the 7,579,563 bp high-quality permanent draft genome is arranged in 260 scaffolds of 262 contigs, contains 7,033 protein-coding genes and 97 RNA-only encoding genes, and is part of the GEBA-RNB project proposal.« less

High-quality permanent draft genome sequence of the Mimosa asperata - nodulating Cupriavidus sp. strain AMP6

DOE Office of Scientific and Technical Information (OSTI.GOV)

De Meyer, Sofie E.; Parker, Matthew; Van Berkum, Peter

Cupriavidus sp. strain AMP6 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from a root nodule of Mimosa asperata collected in Santa Ana National Wildlife Refuge, Texas, in 2005. Mimosa asperata is the only legume described so far to exclusively associates with Cupriavidus symbionts. Furthermore, strain AMP6 represents an early-diverging lineage within the symbiotic Cupriavidus group and has the capacity to develop an effective nitrogen-fixing symbiosis with three other species of Mimosa. Here, we describe the genome of Cupriavidus sp. strain AMP6 which enables comparative analyses of symbiotic trait evolution in this genus; the general features, together withmore » sequence and annotation are further discussed. Finally, the 7,579,563 bp high-quality permanent draft genome is arranged in 260 scaffolds of 262 contigs, contains 7,033 protein-coding genes and 97 RNA-only encoding genes, and is part of the GEBA-RNB project proposal.« less

High-quality permanent draft genome sequence of Bradyrhizobium sp. strain WSM1743 - an effective microsymbiont of an Indigofera sp. growing in Australia

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eshraghi, Leila; De Meyer, Sofie E.; Tian, Rui

Bradyrhizobium sp. strain WSM1743 is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of an Indigofera sp. WSM1743 was isolated from a nodule recovered from the roots of an Indigofera sp. growing 20 km north of Carnarvon in Australia. It is slow growing, tolerates up to 1 % NaCl and is capable of growth at 37 °C. Here we describe the features of Bradyrhizobium sp. strain WSM1743, together with genome sequence information and its annotation. Finally, the 8,341,956 bp high-quality permanent draft genome is arranged into 163 scaffolds and 167more » contigs, contains 7908 protein-coding genes and 75 RNA-only encoding genes and was sequenced as part of the Root Nodule Bacteria chapter of the Genomic Encyclopedia of Bacteria and Archaea project.« less

Quality scores for 32,000 genomes

DOE PAGES

Land, Miriam L.; Hyatt, Doug; Jun, Se-Ran; ...

2014-12-08

More than 80% of the microbial genomes in GenBank are of ‘draft’ quality (12,553 draft vs. 2,679 finished, as of October, 2013). In this study, we have examined all the microbial DNA sequences available for complete, draft, and Sequence Read Archive genomes in GenBank as well as three other major public databases, and assigned quality scores for more than 30,000 prokaryotic genome sequences. Scores were assigned using four categories: the completeness of the assembly, the presence of full-length rRNA genes, tRNA composition and the presence of a set of 102 conserved genes in prokaryotes. Most (~88%) of the genomes hadmore » quality scores of 0.8 or better and can be safely used for standard comparative genomics analysis. We compared genomes across factors that may influence the score. We found that although sequencing depth coverage of over 100x did not ensure a better score, sequencing read length was a better indicator of sequencing quality. With few exceptions, most of the 30,000 genomes have nearly all the 102 essential genes. The score can be used to set thresholds for screening data when analyzing “all published genomes” and reference data is either not available or not applicable. The scores highlighted organisms for which commonly used tools do not perform well. This information can be used to improve tools and to serve a broad group of users as more diverse organisms are sequenced. Finally and unexpectedly, the comparison of predicted tRNAs across 15,000 high quality genomes showed that anticodons beginning with an ‘A’ (codons ending with a ‘U’) are almost non-existent, with the exception of one arginine codon (CGU); this has been noted previously in the literature for a few genomes, but not with the depth found here.« less

Quality scores for 32,000 genomes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Land, Miriam L.; Hyatt, Doug; Jun, Se-Ran

More than 80% of the microbial genomes in GenBank are of ‘draft’ quality (12,553 draft vs. 2,679 finished, as of October, 2013). In this study, we have examined all the microbial DNA sequences available for complete, draft, and Sequence Read Archive genomes in GenBank as well as three other major public databases, and assigned quality scores for more than 30,000 prokaryotic genome sequences. Scores were assigned using four categories: the completeness of the assembly, the presence of full-length rRNA genes, tRNA composition and the presence of a set of 102 conserved genes in prokaryotes. Most (~88%) of the genomes hadmore » quality scores of 0.8 or better and can be safely used for standard comparative genomics analysis. We compared genomes across factors that may influence the score. We found that although sequencing depth coverage of over 100x did not ensure a better score, sequencing read length was a better indicator of sequencing quality. With few exceptions, most of the 30,000 genomes have nearly all the 102 essential genes. The score can be used to set thresholds for screening data when analyzing “all published genomes” and reference data is either not available or not applicable. The scores highlighted organisms for which commonly used tools do not perform well. This information can be used to improve tools and to serve a broad group of users as more diverse organisms are sequenced. Finally and unexpectedly, the comparison of predicted tRNAs across 15,000 high quality genomes showed that anticodons beginning with an ‘A’ (codons ending with a ‘U’) are almost non-existent, with the exception of one arginine codon (CGU); this has been noted previously in the literature for a few genomes, but not with the depth found here.« less

Incentivizing Multiple Revisions Improves Student Writing without Increasing Instructor Workload

ERIC Educational Resources Information Center

Stellmack, Mark A.; Sandidge, Rita R.; Sippl, Amy L.; Miller, Danneka J.

2015-01-01

Previous research has shown that when students are required to submit a draft and a revision of their writing, large proportions of students do not improve across drafts. We implemented a writing assignment in which students were permitted to submit up to four optional drafts. To encourage substantive revisions, students were awarded additional…

Effect of Making an Audio Recording of a Term Paper on Writing Quality

ERIC Educational Resources Information Center

Taxis, Tasia M.; Lannin, Amy A.; Selting, Bonita R.; Lamberson, William R.

2014-01-01

Writing-to-learn assignments engage students with a problem while they develop writing skills. It is difficult in large classes to provide training in proofreading and editing techniques. The purpose of this project was to determine if a term paper was improved after making an audio recording of a draft of the paper. Data from 2 years of papers…

Drafting New Curricula in South-East Europe. Final Report of the Regional Seminar (Bohinj, Slovenia, April 26-28, 2002).

ERIC Educational Resources Information Center

Rozemeijer, Saskia, Ed.

The aim of the regional seminar on curriculum renewal, held in Bohinj, Slovenia in April 2002 was to contribute to human resource development and capacity-building in the field of curriculum development. It is currently widely recognized that curriculum renewal is an important component in the reform and in improving the quality of education. The…

High-quality permanent draft genome sequence of Ensifer meliloti strain 4H41, an effective salt- and drought-tolerant microsymbiont of Phaseolus vulgaris

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mhamdi, Ridha; Ardley, Julie; Tian, Rui

We report that Ensifer meliloti 4H41 is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of common bean (Phaseolus vulgaris). Strain 4H41 was isolated in 2002 from root nodules of P. vulgaris grown in South Tunisia from the oasis of Rjim-Maatoug. Strain 4H41 is salt- and drought-tolerant and highly effective at fixing nitrogen with P. vulgaris. Here we describe the features of E. meliloti 4H41, together with genome sequence information and its annotation. The 6,795,637 bp high-quality permanent draft genome is arranged into 47 scaffolds of 47 contigs containing 6,350more » protein-coding genes and 72 RNA-only encoding genes, and is one of the rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project proposal.« less

High-quality permanent draft genome sequence of Rhizobium sullae strain WSM1592; a Hedysarum coronarium microsymbiont from Sassari, Italy

DOE PAGES

Yates, Ron; Howieson, John; De Meyer, Sofie E.; ...

2015-07-24

Rhizobium sullae strain WSM1592 is an aerobic, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen (N2) fixing root nodule formed on the short-lived perennial legume Hedysarum coronarium (also known as Sulla coronaria or Sulla). WSM1592 was isolated from a nodule recovered from H. coronarium roots located in Ottava, bordering Sassari, Sardinia in 1995. WSM1592 is highly effective at fixing nitrogen with H. coronarium, and is currently the commercial Sulla inoculant strain in Australia. Here we describe the features of R. sullae strain WSM1592, together with genome sequence information and its annotation. The 7,530,820 bp high-quality permanent draft genomemore » is arranged into 118 scaffolds of 118 contigs containing 7.453 protein-coding genes and 73 RNA-only encoding genes. In conclusion, this rhizobial genome is sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.« less

High-quality permanent draft genome sequence of Ensifer meliloti strain 4H41, an effective salt- and drought-tolerant microsymbiont of Phaseolus vulgaris

DOE PAGES

Mhamdi, Ridha; Ardley, Julie; Tian, Rui; ...

2015-07-02

We report that Ensifer meliloti 4H41 is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of common bean (Phaseolus vulgaris). Strain 4H41 was isolated in 2002 from root nodules of P. vulgaris grown in South Tunisia from the oasis of Rjim-Maatoug. Strain 4H41 is salt- and drought-tolerant and highly effective at fixing nitrogen with P. vulgaris. Here we describe the features of E. meliloti 4H41, together with genome sequence information and its annotation. The 6,795,637 bp high-quality permanent draft genome is arranged into 47 scaffolds of 47 contigs containing 6,350more » protein-coding genes and 72 RNA-only encoding genes, and is one of the rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project proposal.« less

Translations on Environmental Quality No. 124.

DTIC Science & Technology

1976-11-01

pollution is being drawn up, the Dewan Rakyat was told today. The programme consists of preventive and restorative measures and would be aimed against all...ENVIRONMENTAL QUALITY No. 124 CONTENTS PAGE ASIA MALAYSIA Malaysia Drafting Antipollution Program (NEW STRAITS TIMES, 17 Jul 76)... 1 EASTERN EUROPE...French, Swiss Experience and Projects Opponents of Nuclear Power Plants Appeal to Bonn Government MALAYSIA MALAYSIA DRAFTING ANTIPOLLUTION

Air Quality Criteria for Particulate Matter (Fourth External Review Draft) [revised Drafts of Chapters 7 and 8, December 2003

EPA Science Inventory

EPA is in the process of updating and revising, where appropriate, its Air Quality Criteria for Particulate Matter as issued in 1996 (usually referred to as the Criteria Document). Sections 108 and 109 of the Clean Air Act require that EPA carry out a periodic review an...

Managing uncertainty in metabolic network structure and improving predictions using EnsembleFBA

PubMed Central

2017-01-01

Genome-scale metabolic network reconstructions (GENREs) are repositories of knowledge about the metabolic processes that occur in an organism. GENREs have been used to discover and interpret metabolic functions, and to engineer novel network structures. A major barrier preventing more widespread use of GENREs, particularly to study non-model organisms, is the extensive time required to produce a high-quality GENRE. Many automated approaches have been developed which reduce this time requirement, but automatically-reconstructed draft GENREs still require curation before useful predictions can be made. We present a novel approach to the analysis of GENREs which improves the predictive capabilities of draft GENREs by representing many alternative network structures, all equally consistent with available data, and generating predictions from this ensemble. This ensemble approach is compatible with many reconstruction methods. We refer to this new approach as Ensemble Flux Balance Analysis (EnsembleFBA). We validate EnsembleFBA by predicting growth and gene essentiality in the model organism Pseudomonas aeruginosa UCBPP-PA14. We demonstrate how EnsembleFBA can be included in a systems biology workflow by predicting essential genes in six Streptococcus species and mapping the essential genes to small molecule ligands from DrugBank. We found that some metabolic subsystems contributed disproportionately to the set of predicted essential reactions in a way that was unique to each Streptococcus species, leading to species-specific outcomes from small molecule interactions. Through our analyses of P. aeruginosa and six Streptococci, we show that ensembles increase the quality of predictions without drastically increasing reconstruction time, thus making GENRE approaches more practical for applications which require predictions for many non-model organisms. All of our functions and accompanying example code are available in an open online repository. PMID:28263984

Managing uncertainty in metabolic network structure and improving predictions using EnsembleFBA.

PubMed

Biggs, Matthew B; Papin, Jason A

2017-03-01

Genome-scale metabolic network reconstructions (GENREs) are repositories of knowledge about the metabolic processes that occur in an organism. GENREs have been used to discover and interpret metabolic functions, and to engineer novel network structures. A major barrier preventing more widespread use of GENREs, particularly to study non-model organisms, is the extensive time required to produce a high-quality GENRE. Many automated approaches have been developed which reduce this time requirement, but automatically-reconstructed draft GENREs still require curation before useful predictions can be made. We present a novel approach to the analysis of GENREs which improves the predictive capabilities of draft GENREs by representing many alternative network structures, all equally consistent with available data, and generating predictions from this ensemble. This ensemble approach is compatible with many reconstruction methods. We refer to this new approach as Ensemble Flux Balance Analysis (EnsembleFBA). We validate EnsembleFBA by predicting growth and gene essentiality in the model organism Pseudomonas aeruginosa UCBPP-PA14. We demonstrate how EnsembleFBA can be included in a systems biology workflow by predicting essential genes in six Streptococcus species and mapping the essential genes to small molecule ligands from DrugBank. We found that some metabolic subsystems contributed disproportionately to the set of predicted essential reactions in a way that was unique to each Streptococcus species, leading to species-specific outcomes from small molecule interactions. Through our analyses of P. aeruginosa and six Streptococci, we show that ensembles increase the quality of predictions without drastically increasing reconstruction time, thus making GENRE approaches more practical for applications which require predictions for many non-model organisms. All of our functions and accompanying example code are available in an open online repository.

A Survey to Evaluate Facilitators and Barriers to Quality Measurement and Improvement: Adapting Tools for Implementation Research in Palliative Care Programs.

PubMed

Dy, Sydney M; Al Hamayel, Nebras Abu; Hannum, Susan M; Sharma, Ritu; Isenberg, Sarina R; Kuchinad, Kamini; Zhu, Junya; Smith, Katherine; Lorenz, Karl A; Kamal, Arif H; Walling, Anne M; Weaver, Sallie J

2017-12-01

Although critical for improving patient outcomes, palliative care quality indicators are not yet widely used. Better understanding of facilitators and barriers to palliative care quality measurement and improvement might improve their use and program quality. Development of a survey tool to assess palliative care team perspectives on facilitators and barriers to quality measurement and improvement in palliative care programs. We used the adapted Consolidated Framework for Implementation Research to define domains and constructs to select instruments. We assembled a draft survey and assessed content validity through pilot testing and cognitive interviews with experts and frontline practitioners for key items. We analyzed responses using a constant comparative process to assess survey item issues and potential solutions. We developed a final survey using these results. The survey includes five published instruments and two additional item sets. Domains include organizational characteristics, individual and team characteristics, intervention characteristics, and process of implementation. Survey modules include Quality Improvement in Palliative Care, Implementing Quality Improvement in the Palliative Care Program, Teamwork and Communication, Measuring the Quality of Palliative Care, and Palliative Care Quality in Your Program. Key refinements from cognitive interviews included item wording on palliative care team members, programs, and quality issues. This novel, adaptable instrument assesses palliative care team perspectives on barriers and facilitators for quality measurement and improvement in palliative care programs. Next steps include evaluation of the survey's construct validity and how survey results correlate with findings from program quality initiatives. Copyright © 2017 American Academy of Hospice and Palliative Medicine. All rights reserved.

Engineering Documentation and Data Control

NASA Technical Reports Server (NTRS)

Matteson, Michael J.; Bramley, Craig; Ciaruffoli, Veronica

2001-01-01

Mississippi Space Services (MSS) the facility services contractor for NASA's John C. Stennis Space Center (SSC), is utilizing technology to improve engineering documentation and data control. Two identified improvement areas, labor intensive documentation research and outdated drafting standards, were targeted as top priority. MSS selected AutoManager(R) WorkFlow from Cyco software to manage engineering documentation. The software is currently installed on over 150 desctops. The outdated SSC drafting standard was written for pre-CADD drafting methods, in other words, board drafting. Implementation of COTS software solutions to manage engineering documentation and update the drafting standard resulted in significant increases in productivity by reducing the time spent searching for documents.

77 FR 52365 - Notice of Availability of the Draft Environmental Impact Statement for the Arkansas Valley...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-29

... Pueblo Reservoir during emergencies or periodic maintenance activities. Interconnect operations would... available space in Pueblo Reservoir would deliver high quality water that would meet Environmental... contract with Southeastern Colorado Water Conservancy District to store water in Pueblo Reservoir. While...

76 FR 50213 - Environmental Impacts Statements; Notice of Availability

Federal Register 2010, 2011, 2012, 2013, 2014

2011-08-12

... Bakersfield Section High-Speed Train, Proposes to Construct, Operate, and Maintain an Electric-Powered High...): Merced to Fresno Section High-Speed Train, Proposes to Construct, Operate, and Maintain an Electric.... 20110190, Draft EIS, FRA, MS, Tupelo Railroad Relocation Planning and Environmental Study, To Improve...

77 FR 22247 - Veterinary Feed Directive; Draft Text for Proposed Regulation

Federal Register 2010, 2011, 2012, 2013, 2014

2012-04-13

.... FDA-2010-N-0155] Veterinary Feed Directive; Draft Text for Proposed Regulation AGENCY: Food and Drug Administration, HHS. ACTION: Notification; draft text for proposed regulation. SUMMARY: The Food and Drug Administration (FDA) is announcing the availability of draft text for a proposed regulation intended to improve...

77 FR 64538 - Tualatin River National Wildlife Refuge, Washington and Yamhill Counties, OR, Draft Comprehensive...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-10-22

... bordered by uplands. Habitats include rivers and streams, seasonal, scrub-shrub, and riparian forests; and... grasses, forbs, shrubs, and trees; and controlling weeds. The Refuge's high quality wildlife observation... (Preferred Alternative) The Tualatin River and Rock Creek Units' riparian forest, scrub- shrub wetland, and...

Genomic Diversity of Biocontrol Strains of Pseudomonas spp. Isolated from Aerial or Root Surfaces of Plants

USDA-ARS?s Scientific Manuscript database

The striking ecological, metabolic, and biochemical diversity of Pseudomonas has intrigued microbiologists for many decades. To explore the genomic diversity of biocontrol strains of Pseudomonas spp., we derived high quality draft sequences of seven strains known to suppress plant disease. The str...

78 FR 18323 - Notice of Availability of a Draft Programmatic Environmental Assessment of the Proposed United...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-26

... Proposed United States Regional Climate Reference Network (USRCRN) AGENCY: National Weather Service (NWS..., is proposing to implement, operate, and manage a USRCRN. With other climate monitoring efforts..., high-quality climate data for use in climate-monitoring activities and for placing current climate...

High-quality draft genome sequence of Effusibacillus lacus strain skLN1T, facultative anaerobic spore-former isolated from freshwater lake sediment.

PubMed

Watanabe, Miho; Tokizawa, Riho; Kojima, Hisaya; Fukui, Manabu

2017-01-01

10.1601/nm.25721 strain skLN1 T is the type strain of the type species in the genus 10.1601/nm.25720 which is the one of the genera in the family 10.1601/nm.5070 within the phylum 10.1601/nm.3874. 10.1601/nm.25721 strain skLN1 T is a Gram-positive, spore-forming thermophilic neutrophile isolated from freshwater lake sediment. Here, we present the draft genome sequence of strain skLN1 T , which consists of 3,902,380 bp with a G + C content of 50.38%.

Executive Summary, Hydraulic Fracturing Study - Draft Assessment 2015

EPA Pesticide Factsheets

In this Executive Summary of the HF Draft report, EPA highlights the reviews of scientific literature to assess the potential for hydraulic fracturing for oil and gas to change the quality or quantity of drinking water resources.

United Kingdom unveils ambitious air pollution plan

NASA Astrophysics Data System (ADS)

Warren, Matthew

2018-06-01

The U.K. government's new strategy to combat air pollution has drawn praise for its ambitious goals—and reservations about whether they will be achieved. Environmental scientists have applauded the aims of the Clean Air Strategy, which include substantially reducing the number of people breathing air containing high levels of fine particulates and curbing ammonia emissions from agriculture. But for now, the document, published as a draft for public consultation on 22 May, remains light on the specific policies that will help the country attain these goals. And although the government has said that with the new strategy it will go further than the European Union in tackling air pollution post-Brexit, scientists say major improvements to air quality will require a coordinated effort across Europe.

An empirical definition of clinical supervision.

PubMed

Milne, Derek

2007-11-01

The growing recognition of clinical supervision as the basis for high-quality mental health services is apparent in policy, research and clinical practice, but an empirical definition is required to progress research and practice. A logical analysis was used to draft a working definition, and then a systematic review of 24 empirical studies of clinical supervision produced a best evidence synthesis, which was used to test and improve this definition. The logical analysis indicated that the most popular definition (Bernard & Goodyear, 1992) failed all four necessary tests of a good definition: precision, specification, operationalization and corroboration. The systematic review synthesis was then used to test the working definition, which passed these tests (with two amendments). These two complementary review approaches created a firmer basis for advancing research and practice.

Redesigning a risk-management process for tracking injuries.

PubMed

Wenzel, G R

1998-01-01

The changing responsibilities of registered nurses are challenging even the most dedicated professionals. To survive within her newly-defined roles, one nurse used a total quality improvement model to understand, analyze, and improve a medical center's system for tracking inpatient injuries. This process led to the drafting of an original software design that implemented a nursing informatics tracking system. It has resulted in significant savings of time and money and has far surpassed the accuracy, efficiency, and scope of the previous method. This article presents an overview of the design process.

A Screening Assessment of the Potential Impacts of Climate Change on the Costs of Implementing Water Quality-Based Effluent Limits at Publicly-Owned Treatment Works (Potws) in the Great Lakes Region (External Review Draft)

EPA Science Inventory

EPA has released this draft document solely for the purpose of pre-dissemination peer review under applicable information quality guidelines. This document has not been formally disseminated by EPA. It does not represent and should not be construed to represent any Agency policy ...

In-field experiment of electro-hydraulic tillage depth draft-position mixed control on tractor

NASA Astrophysics Data System (ADS)

Han, Jiangyi; Xia, Changgao; Shang, Gaogao; Gao, Xiang

2017-12-01

The soil condition and condition of the plow affect the tillage resistance and the maximum traction of tractor. In order to improve the adaptability of tractor tillage depth control, a multi-parameter control strategy is proposed that included tillage depth target, draft force aim and draft-position mixed ratio. In the strategy, the resistance coefficient was used to adjust the draft force target. Then, based on a JINMA1204 tractor, the electro-hydraulic hitch prototype is constructed that could set control parameters.. The fuzzy controller of draft-position mixed control is designed. After that, in-field experiments of position control was carried on, and the result of experiment shows the error of tillage depth was less than ±20mm. The experiment of draft-position control shown that the draft force and the tillage depth could be adjust by multi-parameter such as tillage depth, resistance coefficient and draft-position mixed coefficient. So that, the multi-parameter control strategy could improve the adaptability of tillage depth control in various soils and plow condition.

A review of the FDA draft guidance document for software validation: guidance for industry.

PubMed

Keatley, K L

1999-01-01

A Draft Guidance Document (Version 1.1) was issued by the United States Food and Drug Administration (FDA) to address the software validation requirement of the Quality System Regulation, 21 CFR Part 820, effective June 1, 1997. The guidance document outlines validation considerations that the FDA regards as applicable to both medical device software and software used to "design, develop or manufacture" medical devices. The Draft Guidance is available at the FDA web site http:@www.fda.gov/cdrh/comps/swareval++ +.html. Presented here is a review of the main features of the FDA document for Quality System Regulation (QSR), and some guidance for its implementation in industry.

Design optimization of hydraulic turbine draft tube based on CFD and DOE method

NASA Astrophysics Data System (ADS)

Nam, Mun chol; Dechun, Ba; Xiangji, Yue; Mingri, Jin

2018-03-01

In order to improve performance of the hydraulic turbine draft tube in its design process, the optimization for draft tube is performed based on multi-disciplinary collaborative design optimization platform by combining the computation fluid dynamic (CFD) and the design of experiment (DOE) in this paper. The geometrical design variables are considered as the median section in the draft tube and the cross section in its exit diffuser and objective function is to maximize the pressure recovery factor (Cp). Sample matrixes required for the shape optimization of the draft tube are generated by optimal Latin hypercube (OLH) method of the DOE technique and their performances are evaluated through computational fluid dynamic (CFD) numerical simulation. Subsequently the main effect analysis and the sensitivity analysis of the geometrical parameters of the draft tube are accomplished. Then, the design optimization of the geometrical design variables is determined using the response surface method. The optimization result of the draft tube shows a marked performance improvement over the original.

[Applying the Modified Delphi Technique to Develop the Role of HIV Case Managers and Essential Nursing Competencies in HIV Care].

PubMed

Ko, Nai-Ying; Hsieh, Chia-Yin; Chen, Yen-Chin; Tsai, Chen-Hsi; Liu, Hsiao-Ying; Liu, Li-Fang

2015-08-01

Since 2005, the Taiwan Centers for Disease Control (Taiwan CDC) initiated an HIV case management program in AIDS-designated hospitals to provide integrative services and risk-reduction counseling for HIV-infected individuals. In light of the increasingly complex and highly specialized nature of clinical care, expanding and improving competency-based professional education is important to enhance the quality of HIV/AIDS care. The aim of this study was to develop the essential competency framework for HIV care for HIV case managers in Taiwan. We reviewed essential competencies of HIV care from Canada, the United Kingdom, and several African countries and devised descriptions of the roles of case managers and of the associated core competencies for HIV care in Taiwan. The modified Delphi technique was used to evaluate the draft framework of these roles and core competencies. A total of 15 HIV care experts were invited to join the expert panel to review and rank the draft framework. The final framework consisted of 7 roles and 27 competencies for HIV case managers. In Round 1, only 3 items did not receive consensus approval from the experts. After modification based on opinions of the experts, 7 roles and 27 competencies received 97.06% consensus approval in Round 2 and were organized into the final framework for HIV case managers. These roles and associated core competencies were: HIV Care Expert (9 competencies), Communicator (1 competency), Collaborator (4 competencies), Navigator (2 competencies), Manager (4 competencies), Advocate (2 competencies), and Professional (5 competencies). The authors developed an essential competency framework for HIV care using the consensus of a multidisciplinary expert panel. Curriculum developers and advanced nurses and practitioners may use this framework to support developments and to ensure a high quality of HIV care.

[Quality in the healthcare sector: new strategic measures for new challenges].

PubMed

Larroca, Norberto

2002-01-01

This article reviews the experience of the organizations representing the private healthcare industry in Argentina in their request to improve the quality of care. In it, the author highlights how their collaboration with the PAHO/WHO in the nineties led to the drafting of a Quality Accreditation Handbook, as well as its circulation in most of the countries in the area. Ten years on, the new challenges are analyzed in order to achieve better quality fro all, without limits. With these challenges in mind, the study presents the five programmes being developed at present, by the private health sector as a way of collaborating with society and the government in its progress towards the nationalization of resources and achieving a fairer system and better quality in healthcare.

Draft Genome Sequence of Mycobacterium chimaera Type ...

EPA Pesticide Factsheets

We report the draft genome sequence of the type strain Mycobacterium chimaera Fl-0169T, a member of the Mycobacterium avium complex (MAC). M. chimaera Fl-0169T was isolated from a patient in Italy and is highly similar to strains of M. chimaera isolated in Ireland, though Fl-0169T possesses unique virulence genes. Evidence suggests that M. avium, M. intracellulare, and M. chimaera are differently virulent and a comparative genomic analysis is critically needed to identify diagnostic targets that reliably differentiate species of MAC. With treatment costs for Mycobacterium infections estimated to be >$1.8 B annually in the U.S., correct species identification will result in improved treatment selection, lower costs, and improved patient outcomes.

75 FR 2107 - Notice of Availability of the Draft Environmental Assessment (Draft EA) for the Urban Stream...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-01-14

... discloses any potential significant impacts to the quality of the human environment that may arise from the... augmentation. The Urban Stream Research Center will propagate and augment the population densities and increase...

SQUIRE 2.0 (Standards for QUality Improvement Reporting Excellence): Revised Publication Guidelines from a Detailed Consensus Process

PubMed Central

Ogrinc, Greg; Davies, Louise; Goodman, Daisy; Batalden, Paul; Davidoff, Frank; Stevens, David

2015-01-01

Since the publication of Standards for Quality Improvement Reporting Excellence (SQUIRE 1.0) guidelines in 2008, the science of the field has advanced considerably. In this manuscript we describe the development of SQUIRE 2.0 and its key components. We undertook the revision between 2012 and 2015, using 1) semistructured interviews and focus groups to evaluate SQUIRE 1.0 plus feedback from an international steering group; 2) two face-to-face consensus meetings to develop interim drafts; and 3) pilot testing with authors and a public comment period. SQUIRE 2.0 emphasizes the reporting of three key components of systematic efforts to improve the quality, value, and safety of health care: the use of formal and informal theory in planning, implementing, and evaluating improvement work; the context in which the work is done; and the study of the intervention(s). SQUIRE 2.0 is intended for reporting the range of methods used to improve health care, recognizing that they can be complex and multidimensional. It provides common ground to share these discoveries in the scholarly literature (www.squire-statement.org). PMID:26517437

SQUIRE 2.0 (Standards for QUality Improvement Reporting Excellence): Revised Publication Guidelines from a Detailed Consensus Process.

PubMed

Ogrinc, Greg; Davies, Louise; Goodman, Daisy; Batalden, Paul; Davidoff, Frank; Stevens, David

2015-01-01

Since the publication of Standards for Quality Improvement Reporting Excellence (SQUIRE 1.0) guidelines in 2008, the science of the field has advanced considerably. In this manuscript we describe the development of SQUIRE 2.0 and its key components. We undertook the revision between 2012 and 2015, using 1) semistructured interviews and focus groups to evaluate SQUIRE 1.0 plus feedback from an international steering group; 2) two face-to-face consensus meetings to develop interim drafts; and 3) pilot testing with authors and a public comment period. SQUIRE 2.0 emphasizes the reporting of three key components of systematic efforts to improve the quality, value, and safety of health care: the use of formal and informal theory in planning, implementing, and evaluating improvement work; the context in which the work is done; and the study of the intervention(s). SQUIRE 2.0 is intended for reporting the range of methods used to improve health care, recognizing that they can be complex and multidimensional. It provides common ground to share these discoveries in the scholarly literature (www.squire-statement.org).

Does knowledge brokering improve the quality of rapid review proposals? A before and after study.

PubMed

Moore, Gabriel; Redman, Sally; D'Este, Catherine; Makkar, Steve; Turner, Tari

2017-01-28

Rapid reviews are increasingly being used to help policy makers access research in short time frames. A clear articulation of the review's purpose, questions, scope, methods and reporting format is thought to improve the quality and generalisability of review findings. The aim of the study is to explore the effectiveness of knowledge brokering in improving the perceived clarity of rapid review proposals from the perspective of potential reviewers. To conduct the study, we drew on the Evidence Check program, where policy makers draft a review proposal (a pre knowledge brokering proposal) and have a 1-hour session with a knowledge broker, who re-drafts the proposal based on the discussion (a post knowledge brokering proposal). We asked 30 reviewers who had previously undertaken Evidence Check reviews to examine the quality of 60 pre and 60 post knowledge brokering proposals. Reviewers were blind to whether the review proposals they received were pre or post knowledge brokering. Using a six-point Likert scale, reviewers scored six questions examining clarity of information about the review's purpose, questions, scope, method and format and reviewers' confidence that they could meet policy makers' needs. Each reviewer was allocated two pre and two post knowledge brokering proposals, randomly ordered, from the 60 reviews, ensuring no reviewer received a pre and post knowledge brokering proposal from the same review. The results showed that knowledge brokering significantly improved the scores for all six questions addressing the perceived clarity of the review proposal and confidence in meeting policy makers' needs; with average changes of 0.68 to 1.23 from pre to post across the six domains. This study found that knowledge brokering increased the perceived clarity of information provided in Evidence Check rapid review proposals and the confidence of reviewers that they could meet policy makers' needs. Further research is needed to identify how the knowledge brokering process achieves these improvements and to test the applicability of the findings in other rapid review programs.

Climate Change Impacts on Human Health Due to Changes in Ambient Ozone Concentrations (External Review Draft)

EPA Science Inventory

This report uses results from a previous report titled Assessment of the Impacts of Global Change on Regional U.S. Air Quality: A Synthesis of Climate Change Impacts on Ground-Level Ozone, a number of high-resolution, spatially explicit population projections developed ...

High-quality permanent draft genome sequence of the Parapiptadenia rigida-nodulating Burkholderia sp. strain UYPR1.413

DOE PAGES

De Meyer, Sofie E.; Fabiano, Elena; Tian, Rui; ...

2015-06-04

We report that Burkholderia sp. strain UYPR1.413 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from a root nodule of Parapiptadenia rigida collected at the Angico plantation, Mandiyu, Uruguay, in December 2006. A survey of symbionts of P. rigida in Uruguay demonstrated that this species is nodulated predominantly by Burkholderia microsymbionts. Moreover, Burkholderia sp. strain UYPR1.413 is a highly efficient nitrogen fixing symbiont with this host. Currently, the only other sequenced isolate to fix with this host is Cupriavidus sp. UYPR2.512. Therefore, Burkholderia sp. strain UYPR1.413 was selected for sequencing on the basis of its environmental and agriculturalmore » relevance to issues in global carbon cycling, alternative energy production, and biogeochemical importance, and is part of the GEBA-RNB project. Here we describe the features of Burkholderia sp. strain UYPR1.413, together with sequence and annotation. The 10,373,764 bp high-quality permanent draft genome is arranged in 336 scaffolds of 342 contigs, contains 9759 protein-coding genes and 77 RNA-only encoding genes.« less

High-quality permanent draft genome sequence of the Parapiptadenia rigida-nodulating Burkholderia sp. strain UYPR1.413

DOE Office of Scientific and Technical Information (OSTI.GOV)

De Meyer, Sofie E.; Fabiano, Elena; Tian, Rui

We report that Burkholderia sp. strain UYPR1.413 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from a root nodule of Parapiptadenia rigida collected at the Angico plantation, Mandiyu, Uruguay, in December 2006. A survey of symbionts of P. rigida in Uruguay demonstrated that this species is nodulated predominantly by Burkholderia microsymbionts. Moreover, Burkholderia sp. strain UYPR1.413 is a highly efficient nitrogen fixing symbiont with this host. Currently, the only other sequenced isolate to fix with this host is Cupriavidus sp. UYPR2.512. Therefore, Burkholderia sp. strain UYPR1.413 was selected for sequencing on the basis of its environmental and agriculturalmore » relevance to issues in global carbon cycling, alternative energy production, and biogeochemical importance, and is part of the GEBA-RNB project. Here we describe the features of Burkholderia sp. strain UYPR1.413, together with sequence and annotation. The 10,373,764 bp high-quality permanent draft genome is arranged in 336 scaffolds of 342 contigs, contains 9759 protein-coding genes and 77 RNA-only encoding genes.« less

Development of an Official Guideline for the Economic Evaluation of Drugs/Medical Devices in Japan.

PubMed

Shiroiwa, Takeru; Fukuda, Takashi; Ikeda, Shunya; Takura, Tomoyuki; Moriwaki, Kensuke

2017-03-01

In Japan, cost-effectiveness evaluation was implemented on a trial basis from fiscal year 2016. The results will be applied to the future repricing of drugs and medical devices. On the basis of a request from the Central Social Insurance Medical Council (Chuikyo), our research team drafted the official methodological guideline for trial implementation. Here, we report the process of developing and the contents of the official guideline for cost-effectiveness evaluation. The guideline reflects discussions at the Chuikyo subcommittee (e.g., the role of quality-adjusted life-year) and incorporates our academic perspective. Team members generated research questions for each section of the guideline and discussions on these questions were carried out. A draft guideline was prepared and submitted to the Ministry of Health, Labour and Welfare (MHLW), and then to the subcommittee. The draft guideline was revised on the basis of the discussions at the subcommitte, if appropriate. Although the "public health care payer's perspective" is standard in this guideline, other perspectives can be applied as necessary depending on the objective of analysis. On the basis of the discussions at the subcommittee, quality-adjusted life-year will be used as the basic outcome. A discount rate of 2% per annum for costs and outcomes is recommended. The final guideline was officially approved by the Chuikyo general assembly in February 2016. This is the first officially approved guideline for the economic evaluation of drugs and medical devices in Japan. The guideline is expected to improve the quality and comparability of submitted cost-effectiveness data for decision making. Copyright © 2017 International Society for Pharmacoeconomics and Outcomes Research (ISPOR). Published by Elsevier Inc. All rights reserved.

Reform of general education and vocational training in the U.S.S.R

NASA Technical Reports Server (NTRS)

Spearman, M. L.

1985-01-01

School reform in the Soviet Union is now being carried out in accordance with programmatic directives of the June 1983 plenary session of the CPSU Central Committee. The draft reform was under study and discussion for several months by various groups within the Soviet Union with the participation of about 120 million people. Following the discussion of the draft reform, the basic guidelines for reform were approved by the plenary session of the CPSU Central Committee on April 10, 1984, and by the U.S.S.R. Supreme Soviet on April 12, 1984. The essence of the reform is to improve the quality of instruction (including an added year of compulsory education-from 10 to 11) and to teach young people a profession in addition to the required volume of knowledge and work skills.

Mind-to-paper is an effective method for scientific writing.

PubMed

Rosenberg, Jacob; Burcharth, Jakob; Pommergaard, Hans Christian; Danielsen, Anne Kjærgaard

2013-03-01

The problem of initiating the writing process is a well-known phenomenon, especially for young and inexperienced scientists. The purpose of this paper is to present an effective method to overcome this problem and increase writing efficiency among inexperienced scientists. Twelve young scientists within the medical/surgical fields were introduced to the mind-to-paper concept. The first and last article drafts produced by each of the scientists were scored for language complexity (LIX number, Flesch Reading Ease Scale and Gunning Fog), flow, structure, length and use of references; and the results were compared. All participants produced one full article draft during each of the three dictation days. When comparing the first and last article draft regarding time used, no significant difference was detected. In general, the manuscripts were of high quality on all evaluated parameters, but language complexity had increased in the final manuscript. Mind-to-paper dictation for scientific writing is an effective method for production of scientific papers of good initial quality, even when used for the first time by inexperienced scientists. We conclude that practicing this concept produces papers of an adequate language complexity, and that dictation as a writing tool allows for fast transfer of ideas and thoughts to written text. not relevant. not relevant.

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

PubMed

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 (<450 bps), which are presumed to aid in the analysis of uncharacterized genomes. The array of 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 unknown bacteria with modest effort.

Experimental analysis of the flow pattern of a pump turbine model in pump mode

NASA Astrophysics Data System (ADS)

Guggenberger, Mark; Senn, Florian; Jaberg, Helmut; Gehrer, Arno; Sallaberger, Manfred; Widmer, Christian

2016-11-01

Reversible pump turbines are the only means to store primary energy in an highly efficient way. Within a short time their operation can be switched between the different operational regimes thus enhancing the stabilization of the electric grid. These qualities in combination with the operation even at off-design conditions offer a high flexibility to the energy market. However, pump turbines pass through operational regimes where their behaviour becomes unstable. One of these effects occurs when the flowrate is decreased continuously down to a minimum. This point is the physical limitation of the pump operation and is very difficult to predict properly by numerical design without a model test. The purpose of the present study is to identify the fluid mechanical phenomena leading to the occurrence of instabilities of pump turbines in pump mode. A reduced scale model of a ANDRITZ pump turbine was installed on a 4-quadrant test rig for the experimental investigation of unstable conditions in pump mode. The performed measurements are based on the IEC60193-standard. Characteristic measurements at a single guide vane opening were carried out to get a detailed insight into the instabilities in pump mode. The interaction between runner and guide vane was analysed by Particle Image Velocimetry. Furthermore, high-speed visualizations of the suction side part load flow and the suction recirculation were performed. Like never before the flow pattern in the draft tube cone became visible with the help of a high-speed camera by intentionally caused cavitation effects which allow a qualitative view on the flow pattern in the draft tube cone. Suction recirculation is observed in form of single vortices separating from each runner blade and stretching into the draft tube against the main flow direction. To find an explanation for the flow phenomena responsible for the appearance of the unstable head curve also characteristic velocity distributions on the pressure side were combined with high-speed visualizations on the suction side of the pump turbine model. The results enhance the comprehension of the physical background leading to the instability and improve the numerical predictability of the instability in pump mode.

Programmatic Agreements for Project-Level Air Quality Analyses : NCHRP 25-25 Task 78

DOT National Transportation Integrated Search

2015-09-01

The research performed under Task 78 was divided into two phases. The first phase involved development of a draft Programmatic Agreement (PA) template and a draft Technical Support Document (TSD) template for project-level carbon monoxide (CO) hot-sp...

Analysis of the groundwater monitoring controversy at the Pavillion, Wyoming natural gas field.

PubMed

Stephens, Daniel B

2015-01-01

The U.S. Environmental Protection Agency (EPA) was contacted by citizens of Pavillion, Wyoming 6 years ago regarding taste and odor in their water wells in an area where hydraulic fracturing operations were occurring. EPA conducted a field investigation, including drilling two deep monitor wells, and concluded in a draft report that constituents associated with hydraulic fracturing had impacted the drinking water aquifer. Following extensive media coverage, pressure from state and other federal agencies, and extensive technical criticism from industry, EPA stated the draft report would not undergo peer review, that it would not rely on the conclusions, and that it had relinquished its lead role in the investigation to the State of Wyoming for further investigation without resolving the source of the taste and odor problem. Review of the events leading up to EPA's decision suggests that much of the criticism could have been avoided through improved preproject planning with clear objectives. Such planning would have identified the high national significance and potential implications of the proposed work. Expanded stakeholder involvement and technical input could have eliminated some of the difficulties that plagued the investigation. However, collecting baseline groundwater quality data prior to initiating hydraulic fracturing likely would have been an effective way to evaluate potential impacts. The Pavillion groundwater investigation provides an excellent opportunity for improving field methods, report transparency, clarity of communication, and the peer review process in future investigations of the impacts of hydraulic fracturing on groundwater. © 2014, National Ground Water Association.

Whole Genome Complete Resequencing of Bacillus subtilis Natto by Combining Long Reads with High-Quality Short Reads

PubMed Central

Kamada, Mayumi; Hase, Sumitaka; Sato, Kengo; Toyoda, Atsushi; Fujiyama, Asao; Sakakibara, Yasubumi

2014-01-01

De novo microbial genome sequencing reached a turning point with third-generation sequencing (TGS) platforms, and several microbial genomes have been improved by TGS long reads. Bacillus subtilis natto is closely related to the laboratory standard strain B. subtilis Marburg 168, and it has a function in the production of the traditional Japanese fermented food “natto.” The B. subtilis natto BEST195 genome was previously sequenced with short reads, but it included some incomplete regions. We resequenced the BEST195 genome using a PacBio RS sequencer, and we successfully obtained a complete genome sequence from one scaffold without any gaps, and we also applied Illumina MiSeq short reads to enhance quality. Compared with the previous BEST195 draft genome and Marburg 168 genome, we found that incomplete regions in the previous genome sequence were attributed to GC-bias and repetitive sequences, and we also identified some novel genes that are found only in the new genome. PMID:25329997

Genome sequence of Bradyrhizobium sp. WSM1253; a microsymbiont of Ornithopus compressus from the Greek Island of Sifnos

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tiwari, Ravi; Howieson, John; Yates, Ron

Bradyrhizobium sp. WSM1253 is a novel N 2-fixing bacterium isolated from a root nodule of the herbaceous annual legume Ornithopus compressus that was growing on the Greek Island of Sifnos. WSM1253 emerged as a strain of interest in an Australian program that was selecting inoculant quality bradyrhizobial strains for inoculation of Mediterranean species of lupins ( Lupinus angustifolius, L. princei, L. atlanticus, L. pilosus ). In this report we describe, for the first time, the genome sequence information and annotation of this legume microsymbiont. The 8,719,808 bp genome has a G + C content of 63.09 % with 71 contigsmore » arranged into two scaffolds. The assembled genome contains 8,432 protein-coding genes, 66 RNA genes and a single rRNA operon. In conclusion, this improved-high-quality draft rhizobial genome is one of 20 sequenced through a DOE Joint Genome Institute 2010 Community Sequencing Project.« less

Genome sequence of Bradyrhizobium sp. WSM1253; a microsymbiont of Ornithopus compressus from the Greek Island of Sifnos

DOE PAGES

Tiwari, Ravi; Howieson, John; Yates, Ron; ...

2015-11-30

Bradyrhizobium sp. WSM1253 is a novel N 2-fixing bacterium isolated from a root nodule of the herbaceous annual legume Ornithopus compressus that was growing on the Greek Island of Sifnos. WSM1253 emerged as a strain of interest in an Australian program that was selecting inoculant quality bradyrhizobial strains for inoculation of Mediterranean species of lupins ( Lupinus angustifolius, L. princei, L. atlanticus, L. pilosus ). In this report we describe, for the first time, the genome sequence information and annotation of this legume microsymbiont. The 8,719,808 bp genome has a G + C content of 63.09 % with 71 contigsmore » arranged into two scaffolds. The assembled genome contains 8,432 protein-coding genes, 66 RNA genes and a single rRNA operon. In conclusion, this improved-high-quality draft rhizobial genome is one of 20 sequenced through a DOE Joint Genome Institute 2010 Community Sequencing Project.« less

An improved high-quality draft genome sequence of Carnobacterium inhibens subsp. inhibens strain K1 T

DOE PAGES

Nicholson, Wayne L.; Davis, Christina L.; Shapiro, Nicole; ...

2016-09-08

Despite their ubiquity and their involvement in food spoilage, the genus Carnobacterium remains rather sparsely characterized at the genome level. Carnobacterium inhibens K1 T is a member of the Carnobacteriaceae family within the class Bacilli. This strain is a Gram-positive, rod-shaped bacterium isolated from the intestine of an Atlantic salmon. The present study determined the genome sequence and annotation of Carnobacterium inhibens K1 T. The genome comprised 2,748,608 bp with a G+C content of 34.85 %, which included 2621 protein-coding genes and 116 RNA genes. The strain contained five contigs corresponding to presumptive plasmids of sizes: 19,036; 24,250; 26,581; 65,272;more » and 65,904 bp.« less

An improved high-quality draft genome sequence of Carnobacterium inhibens subsp. inhibens strain K1 T

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nicholson, Wayne L.; Davis, Christina L.; Shapiro, Nicole

Despite their ubiquity and their involvement in food spoilage, the genus Carnobacterium remains rather sparsely characterized at the genome level. Carnobacterium inhibens K1 T is a member of the Carnobacteriaceae family within the class Bacilli. This strain is a Gram-positive, rod-shaped bacterium isolated from the intestine of an Atlantic salmon. The present study determined the genome sequence and annotation of Carnobacterium inhibens K1 T. The genome comprised 2,748,608 bp with a G+C content of 34.85 %, which included 2621 protein-coding genes and 116 RNA genes. The strain contained five contigs corresponding to presumptive plasmids of sizes: 19,036; 24,250; 26,581; 65,272;more » and 65,904 bp.« less

Genome Sequence of the Thermotolerant Yeast Kluyveromyces marxianus var. marxianus KCTC 17555

PubMed Central

Jeong, Haeyoung; Lee, Dae-Hee; Kim, Sun Hong; Kim, Hyun-Jin; Lee, Kyusang; Song, Ju Yeon; Kim, Byung Kwon; Sung, Bong Hyun; Sohn, Jung Hoon; Koo, Hyun Min

2012-01-01

Kluyveromyces marxianus is a thermotolerant yeast that has been explored for potential use in biotechnological applications, such as production of biofuels, single-cell proteins, enzymes, and other heterologous proteins. Here, we present the high-quality draft of the 10.9-Mb genome of K. marxianus var. marxianus KCTC 17555 (= CBS 6556 = ATCC 26548). PMID:23193140

77 FR 3545 - Notice of Availability of the Draft Program Environmental Impact Report (PEIR): Southern...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-01-24

... transportation and urban form strategies that encourage compact growth, increased jobs/housing balance and... DEPARTMENT OF TRANSPORTATION Federal Highway Administration Notice of Availability of the Draft... California Environmental Quality Act for the 2012-2035 Regional Transportation Plan and Sustainable...

75 FR 9878 - Draft Principles and Standards Sections of the “Economic and Environmental Principles and...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-04

... COUNCIL ON ENVIRONMENTAL QUALITY Draft Principles and Standards Sections of the ``Economic and Environmental Principles and Guidelines for Water and Related Land Resources Implementation Studies... the ``Economic and Environmental Principles and Guidelines for Water and Related Land Resources...

Draft EU regulation on paediatric medicines: some improvements but still far from perfect.

PubMed

2006-02-01

(1) In 2004, the European Commission proposed a draft European Regulation on paediatric medicines. This draft was more closely oriented towards defending drug companies' interests than with meeting children's medical needs. (2) Despite pressure from drug companies and their allies, several major improvements were made to the draft at its first reading in the European Parliament, thanks especially to the efforts of the Medicines in Europe Forum. (3) In particular, European deputies pushed for a better definition of children's needs and paediatric research priorities, greater transparency at various important stages of the market authorization procedure, and strengthened pharmacovigilance. (4) Yet the incentives and rewards offered to companies fail to take into account the notion of true therapeutic advantages and R&D expenditure. (5) Unfortunately the Commission refused some important amendments and published a new draft proposal, which was accepted by the Council of Health Ministers at the end of 2005. The new draft will come before the Parliament for a second reading in 2006.

Draft genome and reference transcriptomic resources for the urticating pine defoliator Thaumetopoea pityocampa (Lepidoptera: Notodontidae).

PubMed

Gschloessl, B; Dorkeld, F; Berges, H; Beydon, G; Bouchez, O; Branco, M; Bretaudeau, A; Burban, C; Dubois, E; Gauthier, P; Lhuillier, E; Nichols, J; Nidelet, S; Rocha, S; Sauné, L; Streiff, R; Gautier, M; Kerdelhué, C

2018-05-01

The pine processionary moth Thaumetopoea pityocampa (Lepidoptera: Notodontidae) is the main pine defoliator in the Mediterranean region. Its urticating larvae cause severe human and animal health concerns in the invaded areas. This species shows a high phenotypic variability for various traits, such as phenology, fecundity and tolerance to extreme temperatures. This study presents the construction and analysis of extensive genomic and transcriptomic resources, which are an obligate prerequisite to understand their underlying genetic architecture. Using a well-studied population from Portugal with peculiar phenological characteristics, the karyotype was first determined and a first draft genome of 537 Mb total length was assembled into 68,292 scaffolds (N50 = 164 kb). From this genome assembly, 29,415 coding genes were predicted. To circumvent some limitations for fine-scale physical mapping of genomic regions of interest, a 3X coverage BAC library was also developed. In particular, 11 BACs from this library were individually sequenced to assess the assembly quality. Additionally, de novo transcriptomic resources were generated from various developmental stages sequenced with HiSeq and MiSeq Illumina technologies. The reads were de novo assembled into 62,376 and 63,175 transcripts, respectively. Then, a robust subset of the genome-predicted coding genes, the de novo transcriptome assemblies and previously published 454/Sanger data were clustered to obtain a high-quality and comprehensive reference transcriptome consisting of 29,701 bona fide unigenes. These sequences covered 99% of the cegma and 88% of the busco highly conserved eukaryotic genes and 84% of the busco arthropod gene set. Moreover, 90% of these transcripts could be localized on the draft genome. The described information is available via a genome annotation portal (http://bipaa.genouest.org/sp/thaumetopoea_pityocampa/). © 2018 John Wiley & Sons Ltd.

Biosafety and Biosecurity: A Relative Risk-Based Framework for Safer, More Secure, and Sustainable Laboratory Capacity Building.

PubMed

Dickmann, Petra; Sheeley, Heather; Lightfoot, Nigel

2015-01-01

Laboratory capacity building is characterized by a paradox between endemicity and resources: countries with high endemicity of pathogenic agents often have low and intermittent resources (water, electricity) and capacities (laboratories, trained staff, adequate regulations). Meanwhile, countries with low endemicity of pathogenic agents often have high-containment facilities with costly infrastructure and maintenance governed by regulations. The common practice of exporting high biocontainment facilities and standards is not sustainable and concerns about biosafety and biosecurity require careful consideration. A group at Chatham House developed a draft conceptual framework for safer, more secure, and sustainable laboratory capacity building. The draft generic framework is guided by the phrase "LOCAL - PEOPLE - MAKE SENSE" that represents three major principles: capacity building according to local needs (local) with an emphasis on relationship and trust building (people) and continuous outcome and impact measurement (make sense). This draft generic framework can serve as a blueprint for international policy decision-making on improving biosafety and biosecurity in laboratory capacity building, but requires more testing and detailing development.

Vertical feed stick wood fuel burning furnace system

DOEpatents

Hill, Richard C.

1984-01-01

A new and improved stove or furnace for efficient combustion of wood fuel including a vertical feed combustion chamber for receiving and supporting wood fuel in a vertical attitude or stack, a major upper portion of the combustion chamber column comprising a water jacket for coupling to a source of water or heat transfer fluid and for convection circulation of the fluid for confining the locus of wood fuel combustion to the bottom of the vertical gravity feed combustion chamber. A flue gas propagation delay channel extending from the laterally directed draft outlet affords delayed travel time in a high temperature environment to assure substantially complete combustion of the gaseous products of wood burning with forced air as an actively induced draft draws the fuel gas and air mixture laterally through the combustion and high temperature zone. Active sources of forced air and induced draft are included, multiple use and circuit couplings for the recovered heat, and construction features in the refractory material substructure and metal component superstructure.

Impact of Scribes on Physician Satisfaction, Patient Satisfaction, and Charting Efficiency: A Randomized Controlled Trial

PubMed Central

Gidwani, Risha; Nguyen, Cathina; Kofoed, Alexis; Carragee, Catherine; Rydel, Tracy; Nelligan, Ian; Sattler, Amelia; Mahoney, Megan; Lin, Steven

2017-01-01

PURPOSE Scribes are increasingly being used in clinical practice despite a lack of high-quality evidence regarding their effects. Our objective was to evaluate the effect of medical scribes on physician satisfaction, patient satisfaction, and charting efficiency. METHODS We conducted a randomized controlled trial in which physicians in an academic family medicine clinic were randomized to 1 week with a scribe then 1 week without a scribe for the course of 1 year. Scribes drafted all relevant documentation, which was reviewed by the physician before attestation and signing. In encounters without a scribe, the physician performed all charting duties. Our outcomes were physician satisfaction, measured by a 5-item instrument that included physicians’ perceptions of chart quality and chart accuracy; patient satisfaction, measured by a 6-item instrument; and charting efficiency, measured by time to chart close. RESULTS Scribes improved all aspects of physician satisfaction, including overall satisfaction with clinic (OR = 10.75), having enough face time with patients (OR = 3.71), time spent charting (OR = 86.09), chart quality (OR = 7.25), and chart accuracy (OR = 4.61) (all P values <.001). Scribes had no effect on patient satisfaction. Scribes increased the proportion of charts that were closed within 48 hours (OR =1.18, P =.028). CONCLUSIONS To our knowledge, we have conducted the first randomized controlled trial of scribes. We found that scribes produced significant improvements in overall physician satisfaction, satisfaction with chart quality and accuracy, and charting efficiency without detracting from patient satisfaction. Scribes appear to be a promising strategy to improve health care efficiency and reduce physician burnout. PMID:28893812

Head losses prediction and analysis in a bulb turbine draft tube under different operating conditions using unsteady simulations

NASA Astrophysics Data System (ADS)

Wilhelm, S.; Balarac, G.; Métais, O.; Ségoufin, C.

2016-11-01

Flow prediction in a bulb turbine draft tube is conducted for two operating points using Unsteady RANS (URANS) simulations and Large Eddy Simulations (LES). The inlet boundary condition of the draft tube calculation is a rotating two dimensional velocity profile exported from a RANS guide vane- runner calculation. Numerical results are compared with experimental data in order to validate the flow field and head losses prediction. Velocity profiles prediction is improved with LES in the center of the draft tube compared to URANS results. Moreover, more complex flow structures are obtained with LES. A local analysis of the predicted flow field using the energy balance in the draft tube is then introduced in order to detect the hydrodynamic instabilities responsible for head losses in the draft tube. In particular, the production of turbulent kinetic energy next to the draft tube wall and in the central vortex structure is found to be responsible for a large part of the mean kinetic energy dissipation in the draft tube and thus for head losses. This analysis is used in order to understand the differences in head losses for different operating points. The numerical methodology could then be improved thanks to an in-depth understanding of the local flow topology.

76 FR 72919 - Draft Integrated Science Assessment for Ozone and Related Photochemical Oxidants

Federal Register 2010, 2011, 2012, 2013, 2014

2011-11-28

... Science Assessment for Ozone and Related Photochemical Oxidants AGENCY: Environmental Protection Agency... Draft Integrated Science Assessment for Ozone and Related Photochemical Oxidants'' (EPA/600/R-10/076B... national ambient air quality standards (NAAQS) for ozone. DATES: The public comment period began on...

76 FR 17121 - Draft Integrated Science Assessment for Ozone and Related Photochemical Oxidants

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-28

... Science Assessment for Ozone and Related Photochemical Oxidants AGENCY: Environmental Protection Agency... Draft Integrated Science Assessment for Ozone and Related Photochemical Oxidants'' (EPA/600/R-10/076A... ambient air quality standards (NAAQS) for ozone. DATES: The public comment period began on February 28...

77 FR 76035 - Office of Environmental Information; Announcement of Availability and Comment Period for the...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-12-26

...) Organizations and two associated draft QA Handbooks; 1) draft Handbook for Preparing Quality Management Plans... Data Collection, Production, and Use by Non-EPA (External) Organizations and two associated QA Handbooks AGENCY: Environmental Protection Agency (EPA). ACTION: Notice of availability & request for...

76 FR 51993 - Draft Guidance for Industry on Standards for Clinical Trial Imaging Endpoints; Availability

Federal Register 2010, 2011, 2012, 2013, 2014

2011-08-19

... assist the office in processing your requests. See the SUPPLEMENTARY INFORMATION section for electronic... considerations for standardization of image acquisition, image interpretation methods, and other procedures to help ensure imaging data quality. The draft guidance describes two categories of image acquisition and...

Basins 4.0 Climate Assessment Tool (Cat): Supporting Documentation and User Manual (External Review Draft)

EPA Science Inventory

EPA has released of the draft document solely for the purpose of pre-dissemination peer review under applicable Information Quality Guidelines (IQGs). This document has not been formally disseminated by EPA. It does not represent and should not be construed to represent any Agenc...

Climate Change Vulnerability Assessments: Four Case Studies of Water Utility Practices (External Review Draft)

EPA Science Inventory

EPA has released this draft document solely for the purpose of pre-dissemination peer review under applicable information quality guidelines. This document has not been formally disseminated by EPA. It does not represent and should not be construed to represent any Agency policy ...

75 FR 19971 - Science Advisory Board Staff Office; Notification of a Public Teleconference of the Clean Air...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-16

... Quality Standards--First External Review Draft (March 2010). DATES: The teleconference will be held on May... assessment documents titled Particulate Matter Urban-Focused Visibility Assessment: Second External Review Draft (January 2010) and Quantitative Health Risk Assessment for Particulate Matter: Second External...

AIR QUALITY CRITERIA FOR PARTICULATE MATTER DOCUMENT

EPA Science Inventory

A Planning Document was produced by NCEA/RTP and reviewed by the Clean Air Scientific Advisory Committee (CASAC) (62 FR 55201, October 23, 1997). In FY99, a workshop draft of the PM AQCD was completed, a peer input workshop held, and an External Review Draft released for public ...

75 FR 10252 - Release of Draft Documents Related to the Review of the National Ambient Air Quality Standards...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-05

.... This draft document describes the quantitative analyses that are being conducted as part of the review... primary (health-based) CO NAAQS, the Agency is conducting qualitative and quantitative assessments... results, observations, and related uncertainties associated with the quantitative analyses performed. An...

Draft Plan for Development of the Integrated Science Assessment for Nitrogen Oxides - Health Criteria

EPA Science Inventory

EPA has announced a draft development plan for the next Integrated Science Assessment (ISA) for the health effects of nitrogen oxides (NOX) which will serve as the scientific basis for review of the primary (health-based) National Ambient Air Quality Standard for nitrogen dioxide...

75 FR 44790 - Second Draft Document Related to the Review of the National Ambient Air Quality Standards for...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-29

... characters, any form of encryption, and be free of any defects or viruses. Docket: All documents in the... EPA's TTN website at: http://www.epa.gov/ttn/naaqs/standards/pm/s_pm_2007_pa.html . The draft document...

77 FR 5797 - Draft Toxicological Review of Vanadium Pentoxide: In Support of Summary Information on the...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-06

... Office of Research and Development. EPA is releasing this draft assessment for the purposes of public... health assessment program that evaluates quantitative and qualitative risk information on effects that..., EPA provides the highest quality science- based human health assessments to support the Agency's...

76 FR 36542 - Draft Guidance for Industry and Food and Drug Administration Staff: The Content of...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-22

...The Food and Drug Administration (FDA) is announcing the availability of the draft guidance document entitled ``Draft Guidance for Industry and Food and Drug Administration Staff: The Content of Investigational Device Exemption (IDE) and Premarket Approval (PMA) Applications for Low Glucose Suspend (LGS) Device Systems.'' This draft guidance document provides industry and Agency staff with recommendations that are intended to improve the safety and effectiveness of LGS Device Systems. This draft guidance is not final nor is it in effect at this time.

Draft Detailed Project Report and Draft Environmental Assessment. Neah Bay Navigation Improvements, Neah Bay, Washington

DTIC Science & Technology

1993-11-01

navigation improvements for Neah Bay, Clallam Bay, and Port Angeles was begun under the Puget Sound and Adjacent Waters, General Investigations authority. The...Regonnaissance Report and Plan of Study. Puget Sound and Adjacent Waters. Washington. Northern Olympic Peninsula Shallow-Draft Naviaation Study, August 1983...operators from having to make long trips from the fishing grounds near Neah Bay to ports farther east in the Strait of Juan de Fuca or in Puget Sound . 9 9

Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database.

PubMed

Winsor, Geoffrey L; Griffiths, Emma J; Lo, Raymond; Dhillon, Bhavjinder K; Shay, Julie A; Brinkman, Fiona S L

2016-01-04

The Pseudomonas Genome Database (http://www.pseudomonas.com) is well known for the application of community-based annotation approaches for producing a high-quality Pseudomonas aeruginosa PAO1 genome annotation, and facilitating whole-genome comparative analyses with other Pseudomonas strains. To aid analysis of potentially thousands of complete and draft genome assemblies, this database and analysis platform was upgraded to integrate curated genome annotations and isolate metadata with enhanced tools for larger scale comparative analysis and visualization. Manually curated gene annotations are supplemented with improved computational analyses that help identify putative drug targets and vaccine candidates or assist with evolutionary studies by identifying orthologs, pathogen-associated genes and genomic islands. The database schema has been updated to integrate isolate metadata that will facilitate more powerful analysis of genomes across datasets in the future. We continue to place an emphasis on providing high-quality updates to gene annotations through regular review of the scientific literature and using community-based approaches including a major new Pseudomonas community initiative for the assignment of high-quality gene ontology terms to genes. As we further expand from thousands of genomes, we plan to provide enhancements that will aid data visualization and analysis arising from whole-genome comparative studies including more pan-genome and population-based approaches. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

QUALITY CONTROLS FOR PCR

EPA Science Inventory

The purpose of this presentation is to present an overview of the quality control (QC) sections of a draft EPA document entitled, "Quality Assurance/Quality Control Guidance for Laboratories Performing PCR Analyses on Environmental Samples." This document has been prepared by th...

Standards for QUality Improvement Reporting Excellence 2.0: revised publication guidelines from a detailed consensus process.

PubMed

Ogrinc, Greg; Davies, Louise; Goodman, Daisy; Batalden, Paul; Davidoff, Frank; Stevens, David

2016-02-01

Since the publication of Standards for QUality Improvement Reporting Excellence (SQUIRE 1.0) guidelines in 2008, the science of the field has advanced considerably. In this article, we describe the development of SQUIRE 2.0 and its key components. We undertook the revision between 2012 and 2015 using (1) semistructured interviews and focus groups to evaluate SQUIRE 1.0 plus feedback from an international steering group, (2) two face-to-face consensus meetings to develop interim drafts, and (3) pilot testing with authors and a public comment period. SQUIRE 2.0 emphasizes the reporting of three key components of systematic efforts to improve the quality, value, and safety of health care: the use of formal and informal theory in planning, implementing, and evaluating improvement work; the context in which the work is done; and the study of the intervention(s). SQUIRE 2.0 is intended for reporting the range of methods used to improve health care, recognizing that they can be complex and multidimensional. It provides common ground to share these discoveries in the scholarly literature (www.squire-statement.org). Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

The Asian arowana (Scleropages formosus) genome provides new insights into the evolution of an early lineage of teleosts

PubMed Central

Bian, Chao; Hu, Yinchang; Ravi, Vydianathan; Kuznetsova, Inna S.; Shen, Xueyan; Mu, Xidong; Sun, Ying; You, Xinxin; Li, Jia; Li, Xiaofeng; Qiu, Ying; Tay, Boon-Hui; Thevasagayam, Natascha May; Komissarov, Aleksey S.; Trifonov, Vladimir; Kabilov, Marsel; Tupikin, Alexey; Luo, Jianren; Liu, Yi; Song, Hongmei; Liu, Chao; Wang, Xuejie; Gu, Dangen; Yang, Yexin; Li, Wujiao; Polgar, Gianluca; Fan, Guangyi; Zeng, Peng; Zhang, He; Xiong, Zijun; Tang, Zhujing; Peng, Chao; Ruan, Zhiqiang; Yu, Hui; Chen, Jieming; Fan, Mingjun; Huang, Yu; Wang, Min; Zhao, Xiaomeng; Hu, Guojun; Yang, Huanming; Wang, Jian; Wang, Jun; Xu, Xun; Song, Linsheng; Xu, Gangchun; Xu, Pao; Xu, Junmin; O’Brien, Stephen J.; Orbán, László; Venkatesh, Byrappa; Shi, Qiong

2016-01-01

The Asian arowana (Scleropages formosus), one of the world’s most expensive cultivated ornamental fishes, is an endangered species. It represents an ancient lineage of teleosts: the Osteoglossomorpha. Here, we provide a high-quality chromosome-level reference genome of a female golden-variety arowana using a combination of deep shotgun sequencing and high-resolution linkage mapping. In addition, we have also generated two draft genome assemblies for the red and green varieties. Phylogenomic analysis supports a sister group relationship between Osteoglossomorpha (bonytongues) and Elopomorpha (eels and relatives), with the two clades together forming a sister group of Clupeocephala which includes all the remaining teleosts. The arowana genome retains the full complement of eight Hox clusters unlike the African butterfly fish (Pantodon buchholzi), another bonytongue fish, which possess only five Hox clusters. Differential gene expression among three varieties provides insights into the genetic basis of colour variation. A potential heterogametic sex chromosome is identified in the female arowana karyotype, suggesting that the sex is determined by a ZW/ZZ sex chromosomal system. The high-quality reference genome of the golden arowana and the draft assemblies of the red and green varieties are valuable resources for understanding the biology, adaptation and behaviour of Asian arowanas. PMID:27089831

High-quality permanent draft genome sequence of the Bradyrhizobium elkanii type strain USDA 76T, isolated from Glycine max (L.) Merr

USDA-ARS?s Scientific Manuscript database

Bradyrhizobium elkanii USDA 76T (INSCD = ARAG00000000), the type strain for Bradyrhizobium elkanii, is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing root nodule of Glycine max (L. Merr) grown in the USA. Because of its significance as a ...

Genome Sequence of Enterohemorrhagic Escherichia coli NCCP15658

PubMed Central

Song, Ju Yeon; Yoo, Ran Hee; Jang, Song Yee; Seong, Won-Keun; Kim, Seon-Young; Jeong, Haeyoung; Kang, Sung Gyun; Kim, Byung Kwon; Kwon, Soon-Kyeong; Lee, Choong Hoon; Yu, Dong Su; Park, Mi-Sun

2012-01-01

Enterohemorrhagic Escherichia coli causes severe food-borne disease in the guts of humans and animals. Here, we report the high-quality draft genome sequence of E. coli NCCP15658 isolated from a patient in the Republic of Korea. Its genome size was determined to be 5.46 Mb, and its genomic features, including genes encoding virulence factors, were analyzed. PMID:22740673

High quality draft genome sequences of Pseudomonas fulva DSM 17717 T, Pseudomonas parafulva DSM 17004 T and Pseudomonas cremoricolorata DSM 17059 T type strains

DOE PAGES

Peña, Arantxa; Busquets, Antonio; Gomila, Margarita; ...

2016-09-01

Pseudomonas has the highest number of species out of any genus of Gram-negative bacteria and is phylogenetically divided into several groups. The Pseudomonas putida phylogenetic branch includes at least 13 species of environmental and industrial interest, plant-associated bacteria, insect pathogens, and even some members that have been found in clinical specimens. In the context of the Genomic Encyclopedia of Bacteria and Archaea project, we present the permanent, high-quality draft genomes of the type strains of 3 taxonomically and ecologically closely related species in the Pseudomonas putida phylogenetic branch: Pseudomonas fulva DSM 17717 T, Pseudomonas parafulva DSM 17004 T and Pseudomonasmore » cremoricolorata DSM 17059T. All three genomes are comparable in size (4.6-4.9Mb), with 4,119-4,459 protein-coding genes. Average nucleotide identity based on BLAST comparisons and digital genome-to-genome distance calculations are in good agreement with experimental DNA-DNA hybridization results. The genome sequences presented here will be very helpful in elucidating the taxonomy, phylogeny and evolution of the Pseudomonas putida species complex.« less

High-quality permanent draft genome sequence of Ensifer sp. PC2, isolated from a nitrogen-fixing root nodule of the legume tree (Khejri) native to the Thar Desert of India

DOE PAGES

Gehlot, Hukam Singh; Ardley, Julie; Tak, Nisha; ...

2016-06-23

Ensifer sp. PC2 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from a nitrogen-fixing nodule of the tree legume P. cineraria (L.) Druce (Khejri), which is a keystone species that grows in arid and semi-arid regions of the Indian Thar desert. Strain PC2 exists as a dominant saprophyte in alkaline soils of Western Rajasthan. It is fast growing, well-adapted to arid conditions and is able to form an effective symbiosis with several annual crop legumes as well as species of mimosoid trees and shrubs. Here we describe the features of Ensifer sp. PC2, together with genome sequence informationmore » and its annotation. The 8,458,965 bp high-quality permanent draft genome is arranged into 171 scaffolds of 171 contigs containing 8,344 protein-coding genes and 139 RNA-only encoding genes, and is one of the rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project proposal.« less

High-quality permanent draft genome sequence of Ensifer sp. PC2, isolated from a nitrogen-fixing root nodule of the legume tree (Khejri) native to the Thar Desert of India

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gehlot, Hukam Singh; Ardley, Julie; Tak, Nisha

Ensifer sp. PC2 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from a nitrogen-fixing nodule of the tree legume P. cineraria (L.) Druce (Khejri), which is a keystone species that grows in arid and semi-arid regions of the Indian Thar desert. Strain PC2 exists as a dominant saprophyte in alkaline soils of Western Rajasthan. It is fast growing, well-adapted to arid conditions and is able to form an effective symbiosis with several annual crop legumes as well as species of mimosoid trees and shrubs. Here we describe the features of Ensifer sp. PC2, together with genome sequence informationmore » and its annotation. The 8,458,965 bp high-quality permanent draft genome is arranged into 171 scaffolds of 171 contigs containing 8,344 protein-coding genes and 139 RNA-only encoding genes, and is one of the rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project proposal.« less

High quality draft genome sequences of Pseudomonas fulva DSM 17717 T, Pseudomonas parafulva DSM 17004 T and Pseudomonas cremoricolorata DSM 17059 T type strains

DOE Office of Scientific and Technical Information (OSTI.GOV)

Peña, Arantxa; Busquets, Antonio; Gomila, Margarita

Pseudomonas has the highest number of species out of any genus of Gram-negative bacteria and is phylogenetically divided into several groups. The Pseudomonas putida phylogenetic branch includes at least 13 species of environmental and industrial interest, plant-associated bacteria, insect pathogens, and even some members that have been found in clinical specimens. In the context of the Genomic Encyclopedia of Bacteria and Archaea project, we present the permanent, high-quality draft genomes of the type strains of 3 taxonomically and ecologically closely related species in the Pseudomonas putida phylogenetic branch: Pseudomonas fulva DSM 17717 T, Pseudomonas parafulva DSM 17004 T and Pseudomonasmore » cremoricolorata DSM 17059T. All three genomes are comparable in size (4.6-4.9Mb), with 4,119-4,459 protein-coding genes. Average nucleotide identity based on BLAST comparisons and digital genome-to-genome distance calculations are in good agreement with experimental DNA-DNA hybridization results. The genome sequences presented here will be very helpful in elucidating the taxonomy, phylogeny and evolution of the Pseudomonas putida species complex.« less

Environmental Impact Analysis Process. Preliminary Draft Environmental Impact Statement. Construction and Operation of Space Launch Complex 7. Volume 2. Appendices.

DTIC Science & Technology

1989-03-15

non -point source pollution managementprograms, and implement controls to improve water quality. Controls should be implemented for any project...Businesses or other for- Vandenberg AFB, and the launching of on the proposed information collection profit, non -profit institutions Ithe Titan Centaur. In...communications. The Titan Centaur launch vehicle is a modified Titan 34D designed to deliver a payload of up to U 32,000 pounds directly into polar orbit from VAFB

Motivation for documentation.

PubMed

Graham, Denise H

2004-11-01

The quality improvement plan relies on controlling quality of care through improving the process or system as a whole. Your ongoing data collection is paramount to the process of system-wide improvement and performance, enhancement of financial performance, operational performance and overall service performance and satisfaction. The threat of litigation and having to defend yourself from a claim of wrongdoing still looms every time your wheels turn. Your runsheet must serve and protect you. Look at the NFPA 1710 standard, which was enacted to serve and protect firefighters. This standard was enacted with their personal safety and well-being as the principle behind staffing requirements. At what stage of draft do you suppose the NFPA 1710 standard would be today if the relative data were collected sporadically or were not tracked for each service-related death? It may have taken many more service-related deaths to effect change for a system-wide improvement in operational performance. Every call merits documentation and data collection. Your data are catalysts for change.

77 FR 12853 - Draft Guidances Relating to the Development of Biosimilar Products; Public Hearing; Request for...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-02

... Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Ave., Bldg. 51, Rm. 6340, Silver... the review of 351(k) applications and general scientific principles in conducting comparative analyses... specific, on the scientific considerations, Q&A, and quality considerations draft guidances. For example...

75 FR 8046 - National Environmental Policy Act (NEPA) Draft Guidance, “Consideration of the Effects of Climate...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-02-23

..., ``Consideration of the Effects of Climate Change and Greenhouse Gas Emissions.'' AGENCY: Council On Environmental Quality. ACTION: Notice of Availability, Draft Guidance, ``Consideration of the Effects of Climate Change... Effects of Climate Change and Greenhouse Gas Emissions'' should be submitted electronically to GCC...

76 FR 21346 - Science Advisory Board Staff Office, Notification of a Public Teleconference of the Clean Air...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-04-15

... a Public Teleconference of the Clean Air Scientific Advisory Committee (CASAC) Lead Review Panel... (CASAC) Lead Review Panel to provide consultative advice on EPA's draft Integrated Review Plan for the National Ambient Air Quality Standards for Lead (draft IRP). DATES: The public teleconference will be held...

Memoranda Associated with the Second External Review Draft of Health Risk and Exposure Assessments from the Current Review of Ozone NAAQS

EPA Pesticide Factsheets

EPA's Health and Environmental Impacts Division had to make corrections to some of the risk results included in earlier drafts of the Health Risk and Exposure Assessment from the current review of ozone national ambient air quality standards (NAAQS).

75 FR 59716 - Draft Toxicological Review of Urea: In Support of Summary Information on the Integrated Risk...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-09-28

... environment. Through the IRIS Program, EPA provides the highest quality science- based human health... external review draft human health assessment titled, ``Toxicological Review of Urea: In Support of Summary... register, please indicate if you will need audio-visual equipment (e.g., laptop computer and slide...

77 FR 47067 - Notification of Two Public Quality Review Teleconferences of the Chartered Science Advisory Board

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-07

... Assessment in Environmental Decision- Making'' (EPA-SAB-08-002). Background information about this advisory... ecological assessment action plan and (2) an SAB draft review report on EPA's accounting framework for... ``SAB Review (7-26-12 Draft) of EPA's Accounting Framework for Biogenic CO 2 Emissions from Stationary...

76 FR 60825 - Draft Toxicological Review of Vanadium Pentoxide: In Support of Summary Information on the...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-09-30

...) within the EPA Office of Research and Development (ORD). EPA is releasing this draft assessment solely... quantitative and qualitative risk information on effects that may result from exposure to chemical substances found in the environment. Through the IRIS Program, EPA provides the highest quality science- based...

Findings from a novel approach to publication guideline revision: user road testing of a draft version of SQUIRE 2.0.

PubMed

Davies, Louise; Donnelly, Kyla Z; Goodman, Daisy J; Ogrinc, Greg

2016-04-01

The Standards for Quality Improvement Reporting Excellence (SQUIRE) Guideline was published in 2008 (SQUIRE 1.0) and was the first publication guideline specifically designed to advance the science of healthcare improvement. Advances in the discipline of improvement prompted us to revise it. We adopted a novel approach to the revision by asking end-users to 'road test' a draft version of SQUIRE 2.0. The aim was to determine whether they understood and implemented the guidelines as intended by the developers. Forty-four participants were assigned a manuscript section (ie, introduction, methods, results, discussion) and asked to use the draft Guidelines to guide their writing process. They indicated the text that corresponded to each SQUIRE item used and submitted it along with a confidential survey. The survey examined usability of the Guidelines using Likert-scaled questions and participants' interpretation of key concepts in SQUIRE using open-ended questions. On the submitted text, we evaluated concordance between participants' item usage/interpretation and the developers' intended application. For the survey, the Likert-scaled responses were summarised using descriptive statistics and the open-ended questions were analysed by content analysis. Consistent with the SQUIRE Guidelines' recommendation that not every item be included, less than one-third (n=14) of participants applied every item in their section in full. Of the 85 instances when an item was partially used or was omitted, only 7 (8.2%) of these instances were due to participants not understanding the item. Usage of Guideline items was highest for items most similar to standard scientific reporting (ie, 'Specific aim of the improvement' (introduction), 'Description of the improvement' (methods) and 'Implications for further studies' (discussion)) and lowest (<20% of the time) for those unique to healthcare improvement (ie, 'Assessment methods for context factors that contributed to success or failure' and 'Costs and strategic trade-offs'). Items unique to healthcare improvement, specifically 'Evolution of the improvement', 'Context elements that influenced the improvement', 'The logic on which the improvement was based', 'Process and outcome measures', demonstrated poor concordance between participants' interpretation and developers' intended application. User testing of a draft version of SQUIRE 2.0 revealed which items have poor concordance between developer intent and author usage, which will inform final editing of the Guideline and development of supporting supplementary materials. It also identified the items that require special attention when teaching about scholarly writing in healthcare improvement. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

How Learners Use Automated Computer-Based Feedback to Produce Revised Drafts of Essays

ERIC Educational Resources Information Center

Laing, Jonny; El Ebyary, Khaled; Windeatt, Scott

2012-01-01

Our previous results suggest that the use of "Criterion", an automatic writing evaluation (AWE) system, is particularly successful in encouraging learners to produce amended drafts of their essays, and that those amended drafts generally represent an improvement on the original submission. Our analysis of the submitted essays and the…

75 FR 69449 - Draft Guidance for Industry and Food and Drug Administration Staff on Dear Health Care Provider...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-11-12

...] Draft Guidance for Industry and Food and Drug Administration Staff on Dear Health Care Provider Letters... a draft guidance for industry and FDA staff entitled ``Dear Health Care Provider Letters: Improving Communication of Important Safety Information.'' Dear Health Care Provider (DHCP) Letters are correspondence...

77 FR 64836 - Notice of Availability of Draft Environmental Impact Statement (DEIS), Draft Section 4(f...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-10-23

... DEIS for Proposed Runway Safety Area Improvements at the Kodiak Airport, Kodiak, AK AGENCY: Federal... advise the public that a Draft Environmental Impact Statement (DEIS) for proposed Runway Safety Area... the DEIS can be submitted to the individual listed in the section, FOR FURTHER INFORMATION CONTACT. A...

Findings from a novel approach to publication guideline revision: user road testing of a draft version of SQUIRE 2.0

PubMed Central

Davies, Louise; Donnelly, Kyla Z; Goodman, Daisy J; Ogrinc, Greg

2016-01-01

Background The Standards for Quality Improvement Reporting Excellence (SQUIRE) Guideline was published in 2008 (SQUIRE 1.0) and was the first publication guideline specifically designed to advance the science of healthcare improvement. Advances in the discipline of improvement prompted us to revise it. We adopted a novel approach to the revision by asking end-users to ‘road test’ a draft version of SQUIRE 2.0. The aim was to determine whether they understood and implemented the guidelines as intended by the developers. Methods Forty-four participants were assigned a manuscript section (ie, introduction, methods, results, discussion) and asked to use the draft Guidelines to guide their writing process. They indicated the text that corresponded to each SQUIRE item used and submitted it along with a confidential survey. The survey examined usability of the Guidelines using Likert-scaled questions and participants’ interpretation of key concepts in SQUIRE using open-ended questions. On the submitted text, we evaluated concordance between participants’ item usage/interpretation and the developers’ intended application. For the survey, the Likert-scaled responses were summarised using descriptive statistics and the open-ended questions were analysed by content analysis. Results Consistent with the SQUIRE Guidelines’ recommendation that not every item be included, less than one-third (n=14) of participants applied every item in their section in full. Of the 85 instances when an item was partially used or was omitted, only 7 (8.2%) of these instances were due to participants not understanding the item. Usage of Guideline items was highest for items most similar to standard scientific reporting (ie, ‘Specific aim of the improvement’ (introduction), ‘Description of the improvement’ (methods) and ‘Implications for further studies’ (discussion)) and lowest (<20% of the time) for those unique to healthcare improvement (ie, ‘Assessment methods for context factors that contributed to success or failure’ and ‘Costs and strategic trade-offs’). Items unique to healthcare improvement, specifically ‘Evolution of the improvement’, ‘Context elements that influenced the improvement’, ‘The logic on which the improvement was based’, ‘Process and outcome measures’, demonstrated poor concordance between participants’ interpretation and developers’ intended application. Conclusions User testing of a draft version of SQUIRE 2.0 revealed which items have poor concordance between developer intent and author usage, which will inform final editing of the Guideline and development of supporting supplementary materials. It also identified the items that require special attention when teaching about scholarly writing in healthcare improvement. PMID:26263916

The Nuclear and Mitochondrial Genomes of the Facultatively Eusocial Orchid Bee Euglossa dilemma

PubMed Central

Brand, Philipp; Saleh, Nicholas; Pan, Hailin; Li, Cai; Kapheim, Karen M.; Ramírez, Santiago R.

2017-01-01

Bees provide indispensable pollination services to both agricultural crops and wild plant populations, and several species of bees have become important models for the study of learning and memory, plant–insect interactions, and social behavior. Orchid bees (Apidae: Euglossini) are especially important to the fields of pollination ecology, evolution, and species conservation. Here we report the nuclear and mitochondrial genome sequences of the orchid bee Euglossa dilemma Bembé & Eltz. E. dilemma was selected because it is widely distributed, highly abundant, and it was recently naturalized in the southeastern United States. We provide a high-quality assembly of the 3.3 Gb genome, and an official gene set of 15,904 gene annotations. We find high conservation of gene synteny with the honey bee throughout 80 MY of divergence time. This genomic resource represents the first draft genome of the orchid bee genus Euglossa, and the first draft orchid bee mitochondrial genome, thus representing a valuable resource to the research community. PMID:28701376

The Nuclear and Mitochondrial Genomes of the Facultatively Eusocial Orchid Bee Euglossa dilemma.

PubMed

Brand, Philipp; Saleh, Nicholas; Pan, Hailin; Li, Cai; Kapheim, Karen M; Ramírez, Santiago R

2017-09-07

Bees provide indispensable pollination services to both agricultural crops and wild plant populations, and several species of bees have become important models for the study of learning and memory, plant-insect interactions, and social behavior. Orchid bees (Apidae: Euglossini) are especially important to the fields of pollination ecology, evolution, and species conservation. Here we report the nuclear and mitochondrial genome sequences of the orchid bee Euglossa dilemma Bembé & Eltz. E. dilemma was selected because it is widely distributed, highly abundant, and it was recently naturalized in the southeastern United States. We provide a high-quality assembly of the 3.3 Gb genome, and an official gene set of 15,904 gene annotations. We find high conservation of gene synteny with the honey bee throughout 80 MY of divergence time. This genomic resource represents the first draft genome of the orchid bee genus Euglossa , and the first draft orchid bee mitochondrial genome, thus representing a valuable resource to the research community. Copyright © 2017 Brand et al.

Draft Genome Sequence of Bifidobacterium animalis subsp. lactis Strain CECT 8145, Able To Improve Metabolic Syndrome In Vivo.

PubMed

Chenoll, E; Codoñer, F M; Silva, A; Martinez-Blanch, J F; Martorell, P; Ramón, D; Genovés, S

2014-03-27

Bifidobacterium animalis subsp. lactis strain CECT 8145 is able to reduce body fat content and improve metabolic syndrome biomarkers. Here, we report the draft genome sequence of this strain, which may provide insights into its safety status and functional role.

High-quality draft genome sequence of Rhizobium mesoamericanum strain STM6155, a Mimosa pudica microsymbiont from New Caledonia

DOE PAGES

Klonowska, Agnieszka; López-López, Aline; Moulin, Lionel; ...

2017-01-17

Rhizobium mesoamericanum STM6155 (INSCD=ATYY01000000) is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as an effective nitrogen fixing microsymbiont of the legume Mimosa pudica L.. STM6155 was isolated in 2009 from a nodule of the trap host M. pudica grown in nickel-rich soil collected near Mont Dore, New Caledonia. R. mesoamericanum STM6155 was selected as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) genome sequencing project. Here we describe the symbiotic properties of R. mesoamericanum STM6155, together with its genome sequence information and annotation. Themore » 6,927,906bp high-quality draft genome is arranged into 147 scaffolds of 152 contigs containing 6855 protein-coding genes and 71 RNA-only encoding genes. Strain STM6155 forms an ANI clique (ID 2435) with the sequenced R. mesoamericanum strain STM3625, and the nodulation genes are highly conserved in these strains and the type strain of Rhizobium grahamii CCGE501 T . Within the STM6155 genome, we have identified a chr chromate efflux gene cluster of six genes arranged into two putative operons and we postulate that this cluster is important for the survival of STM6155 in ultramafic soils containing high concentrations of chromate.« less

High-quality draft genome sequence of Rhizobium mesoamericanum strain STM6155, a Mimosa pudica microsymbiont from New Caledonia

DOE Office of Scientific and Technical Information (OSTI.GOV)

Klonowska, Agnieszka; López-López, Aline; Moulin, Lionel

Rhizobium mesoamericanum STM6155 (INSCD=ATYY01000000) is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as an effective nitrogen fixing microsymbiont of the legume Mimosa pudica L.. STM6155 was isolated in 2009 from a nodule of the trap host M. pudica grown in nickel-rich soil collected near Mont Dore, New Caledonia. R. mesoamericanum STM6155 was selected as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) genome sequencing project. Here we describe the symbiotic properties of R. mesoamericanum STM6155, together with its genome sequence information and annotation. Themore » 6,927,906bp high-quality draft genome is arranged into 147 scaffolds of 152 contigs containing 6855 protein-coding genes and 71 RNA-only encoding genes. Strain STM6155 forms an ANI clique (ID 2435) with the sequenced R. mesoamericanum strain STM3625, and the nodulation genes are highly conserved in these strains and the type strain of Rhizobium grahamii CCGE501 T . Within the STM6155 genome, we have identified a chr chromate efflux gene cluster of six genes arranged into two putative operons and we postulate that this cluster is important for the survival of STM6155 in ultramafic soils containing high concentrations of chromate.« less

78 FR 22269 - International Conference on Harmonisation; Draft Guidance on M7 Assessment and Control of DNA...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-15

...The Food and Drug Administration (FDA) is announcing the availability of a draft guidance entitled ``M7 Assessment and Control of DNA Reactive (Mutagenic) Impurities in Pharmaceuticals to Limit Potential Carcinogenic Risk.'' The draft guidance was prepared under the auspices of the International Conference on Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH). The draft guidance emphasizes considerations of both safety and quality risk management in establishing levels of mutagenic impurities that are expected to pose negligible carcinogenic risk. It outlines recommendations for assessment and control of mutagenic impurities that reside or are reasonably expected to reside in a final drug substance or product, taking into consideration the intended conditions of human use. The draft guidance is intended to provide guidance for new drug substances and new drug products during their clinical development and subsequent applications for marketing.

Improved motors for utility applications: Volume 6, Squirrel-cage rotor analysis: Final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Griffith, J.W.; McCoy, R.M.

1986-11-01

An analysis of squirrel cage induction motor rotors was undertaken in response to an Industry Assessment Study finding 10% of motor failures to be rotor related. The analysis focuses on evaluating rotor design life. The evaluation combines state-of-the-art electromagnetic, thermal, and structural solution techniques into an integrated analysis and presents a simple summary. Finite element techniques are central tools in the analysis. The analysis is applied to a specific forced draft fan drive design. Fans as a category of application have a higher failure rate than other categories of power station auxiliary motor applications. Forced-draft fan drives are one ofmore » the major fan drives which accelerate a relatively high value of rotor load inertia. Various starting and operating conditions are studied for this forced-draft fan drive motor including a representative application duty cycle.« less

76 FR 41554 - Notice To Rescind a Notice of Intent and Draft Environmental Impact Statement: Highway 35...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-14

... and Draft Environmental Impact Statement: Highway 35, Between Norfolk and South Sioux City, NE AGENCY... Environmental Impact Statement. SUMMARY: The FHWA is issuing this notice to advise the public that we are rescinding the Notice of Intent (NOI) and Draft Environmental Impact Statement (DEIS) for improvements that...

Development of a mental health action checklist for improving workplace environment as means of job stress prevention.

PubMed

Yoshikawa, Toru; Kawakami, Norito; Kogi, Kazutaka; Tsutsumi, Akizumi; Shimazu, Miyuki; Nagami, Makiko; Shimazu, Akihito

2007-07-01

An action checklist for improving the workplace environment by means of enhancing mental health of workers (Mental Health Action Check List: MHACL) was developed. The use of the checklist for primary prevention was examined. MHACL was developed through three steps: (1) Review of related references and collection of improvement examples for designing a draft MHACL; (2) pilot application of the draft at industrial workplaces and trials at workshops of occupational health staff; and (3) proposing a new MHACL for general use in industry. Workplace improvement actions related to mental health were listed in eight technical areas. From 84 workplaces in Japan, 201 such actions were collected. Typical improvement action phrases were extracted based on these examples, and a draft MHACL containing 40 generally applicable actions were prepared. This draft was applied to selected workplaces for its use as a tool for group discussion. Then, the utility of the checklist was discussed by 105 occupational health staff working in public service offices. The workshop suggested modifications of the draft MHACL including improved check items and usage procedures and the need to use easy-to-understand actions. The final version of the MHACL comprised 30 items in six technical areas: A) sharing work planning, B) work time and organization, C) ergonomic work methods, D) workplace environment, E) mutual support in the workplace, and F) preparedness and care. A new action checklist was proposed for use as a means of changing existing workplace environments and proposing practical actions for improving it. The checklist was confirmed to be useful for organizing workplace-level discussion for identifying immediate improvements at the workplace. The checklist is expected to be widely applied for promoting primary prevention measures in terms of better mental health.

78 FR 2394 - Release of Draft Document Related to the Review of the National Ambient Air Quality Standards for...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-11

... technical difficulties and cannot contact you for clarification, the EPA may not be able to consider your... docket number and other identifying information (subject heading, Federal Register date and page number... information presented in the third draft Integrated Science Assessment for Lead \\2\\ and health and ecological...

77 FR 12579 - Notification of a Public Meeting of the Chartered Science Advisory Board

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-01

... the Chartered SAB to conduct quality reviews of a draft report on the President's requested FY 2013 budget for EPA research and a draft report on science integration at EPA; to plan for a joint meeting of... receive a briefing on ORD and sustainability science; and to discuss the scientific and technical bases...

76 FR 54227 - Draft Toxicological Review of n-Butanol: In Support of Summary Information on the Integrated Risk...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-08-31

... found in the environment. Through the IRIS Program, EPA provides the highest quality science-based human... for the external review draft human health assessment titled, ``Toxicological Review of n-Butanol: In... will need audio-visual equipment (e.g., laptop computer and slide projector). In general, each...

76 FR 62087 - Draft Conservation Plan and Draft Environmental Assessment; Dunes Sagebrush Lizard, Texas

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-06

... known as the sand dune lizard, and the lesser prairie-chicken, among the Service, the Bureau of Land... southeastern New Mexico and west Texas. The species only occurs in sand dune complexes associated with shinnery... direct, indirect, and cumulative impacts of the TCP on the quality of the human environment and other...

Problem Formulation for Human Health Risk Assessments of Pathogens in Land-Applied Biosolids (External Review Draft)

EPA Science Inventory

This is a draft document and as such has not been formally disseminated by the U.S. EPA; it does not represent - and should not be construed to represent - any U.S. EPA policy or determination. Under applicable information quality guidelines, the document is being released for a...

Genome Sequence of an Oligohaline Hyperthermophilic Archaeon, Thermococcus zilligii AN1, Isolated from a Terrestrial Geothermal Freshwater Spring

PubMed Central

Kim, Byung Kwon; Lee, Seong Hyuk; Kim, Seon-Young; Jeong, Haeyoung; Kwon, Soon-Kyeong; Lee, Choong Hoon; Song, Ju Yeon; Yu, Dong Su

2012-01-01

Thermococcus zilligii, a thermophilic anaerobe in freshwater, is useful for physiological research and biotechnological applications. Here we report the high-quality draft genome sequence of T. zilligii AN1T. The genome contains a number of genes for an immune system and adaptation to a microbial biomass-rich environment as well as hydrogenase genes. PMID:22740682

Genomes of Salmonella with diverse patterns of antibiotic resistance (AR) revealed the dynamics of AR gene organization and detected resistance gene families found in Salmonella

USDA-ARS?s Scientific Manuscript database

We produced and assembled high quality draft genomes (~100X coverage) for 305 Salmonella from a diverse a group of over 100 serovars and diverse sources. Of these isolates, 119 were selected to capture a wide variety of different AR patterns. In our subsequent analyses we included 285 additional pub...

A high-coverage draft genome of the mycalesine butterfly Bicyclus anynana.

PubMed

Nowell, Reuben W; Elsworth, Ben; Oostra, Vicencio; Zwaan, Bas J; Wheat, Christopher W; Saastamoinen, Marjo; Saccheri, Ilik J; Van't Hof, Arjen E; Wasik, Bethany R; Connahs, Heidi; Aslam, Muhammad L; Kumar, Sujai; Challis, Richard J; Monteiro, Antónia; Brakefield, Paul M; Blaxter, Mark

2017-07-01

The mycalesine butterfly Bicyclus anynana, the "Squinting bush brown," is a model organism in the study of lepidopteran ecology, development, and evolution. Here, we present a draft genome sequence for B. anynana to serve as a genomics resource for current and future studies of this important model species. Seven libraries with insert sizes ranging from 350 bp to 20 kb were constructed using DNA from an inbred female and sequenced using both Illumina and PacBio technology; 128 Gb of raw Illumina data was filtered to 124 Gb and assembled to a final size of 475 Mb (∼×260 assembly coverage). Contigs were scaffolded using mate-pair, transcriptome, and PacBio data into 10 800 sequences with an N50 of 638 kb (longest scaffold 5 Mb). The genome is comprised of 26% repetitive elements and encodes a total of 22 642 predicted protein-coding genes. Recovery of a BUSCO set of core metazoan genes was almost complete (98%). Overall, these metrics compare well with other recently published lepidopteran genomes. We report a high-quality draft genome sequence for Bicyclus anynana. The genome assembly and annotated gene models are available at LepBase (http://ensembl.lepbase.org/index.html). © The Authors 2017. Published by Oxford University Press.

A high-coverage draft genome of the mycalesine butterfly Bicyclus anynana

PubMed Central

Elsworth, Ben; Oostra, Vicencio; Zwaan, Bas J.; Wheat, Christopher W.; Saastamoinen, Marjo; Saccheri, Ilik J.; van’t Hof, Arjen E.; Wasik, Bethany R.; Connahs, Heidi; Aslam, Muhammad L.; Kumar, Sujai; Challis, Richard J.; Monteiro, Antónia; Brakefield, Paul M.

2017-01-01

Abstract The mycalesine butterfly Bicyclus anynana, the “Squinting bush brown,” is a model organism in the study of lepidopteran ecology, development, and evolution. Here, we present a draft genome sequence for B. anynana to serve as a genomics resource for current and future studies of this important model species. Seven libraries with insert sizes ranging from 350 bp to 20 kb were constructed using DNA from an inbred female and sequenced using both Illumina and PacBio technology; 128 Gb of raw Illumina data was filtered to 124 Gb and assembled to a final size of 475 Mb (∼×260 assembly coverage). Contigs were scaffolded using mate-pair, transcriptome, and PacBio data into 10 800 sequences with an N50 of 638 kb (longest scaffold 5 Mb). The genome is comprised of 26% repetitive elements and encodes a total of 22 642 predicted protein-coding genes. Recovery of a BUSCO set of core metazoan genes was almost complete (98%). Overall, these metrics compare well with other recently published lepidopteran genomes. We report a high-quality draft genome sequence for Bicyclus anynana. The genome assembly and annotated gene models are available at LepBase (http://ensembl.lepbase.org/index.html). PMID:28486658

Patient-reported quality indicators for osteoarthritis: a patient and public generated self-report measure for primary care.

PubMed

Blackburn, Steven; Higginbottom, Adele; Taylor, Robert; Bird, Jo; Østerås, Nina; Hagen, Kåre Birger; Edwards, John J; Jordan, Kelvin P; Jinks, Clare; Dziedzic, Krysia

2016-01-01

People with osteoarthritis desire high quality care, support and information. However, the quality of care for people with OA in general practice is not routinely collected. Quality Indicators can be used to benefit patients by measuring whether minimum standards of quality care are being met from a patient perspective. The aim of this study was to describe how a Research User Group (RUG) worked alongside researchers to co-produce a set of self-reported quality indicators for people with osteoarthritis when visiting their general practitioner or practice nurse (primary care). These were required in the MOSAICS study, which developed and evaluated a new model of supported self-management of OA to implement the NICE quality standards for OA. This article describes the public involvement in the MOSAICS study. This was 1) the co-development by RUG members and researchers of an Osteoarthritis Quality Indicators United Kingdom (OA QI (UK)) questionnaire for use in primary care, and 2) the comparison of the OA QI (UK) with a similar questionnaire developed in Norway. This study shows how important and effective a research user group can be in working with researchers in developing quality care indicators for osteoarthritis for use in a research study and, potentially, routine use in primary care. The questionnaire is intended to benefit patients by enabling the assessment of the quality of primary care for osteoarthritis from a patient's perspective. The OA QI (UK) has been used to examine differences in the quality of osteoarthritis care in four European countries. Background People with osteoarthritis (OA) desire high quality care, support and information about OA. However, the quality of care for people with OA in general practice is not routinely collected. Quality Indicators (QI) can be used to benefit patients by measuring whether minimum standards of quality care (e.g. NICE quality standards) are being met from a patient perspective. A Research User Group (RUG) worked with researchers to co-produce a set of self-report, patient-generated QIs for OA. The QIs were intended for use in the MOSAICS study, which developed and evaluated a new model of supported self-management of OA to implement the NICE guidelines. We report on 1) the co-development of the OA QI (UK) questionnaire for primary care; and 2) the comparison of the content of the OA QI (UK) questionnaire with a parallel questionnaire developed in Norway for the Musculoskeletal Pain in Ullensaker (MUST) study. Methods Researchers were invited to OA RUG meetings. Firstly, RUG members were asked to consider factors important to patients consulting their general practitioner (GP) for OA and then each person rated their five most important. RUG members then discussed these in relation to a systematic review of OA QIs in order to form a list of OA QIs from a patient perspective. RUG members suggested wording and response options for a draft OA QI (UK) questionnaire to assess the QIs. Finally RUG members commented on draft and final versions of the questionnaire and how it compared with a translated Norwegian OA-QI questionnaire. Results RUG members (5 males, 5 females; aged 52-80 years) attended up to four meetings. RUG members ranked 20 factors considered most important to patients consulting their GP for joint pain. Following discussion, a list of eleven patient-reported QIs for OA consultations were formed. RUG members then suggested the wording and response options of 16 draft items - four QIs were split into two or more questionnaire items to avoid multiple dimensions of care quality within a single item. On comparison of this to the Norwegian OA-QI questionnaire, RUG members commented that both questionnaires contained seven similar QIs. The RUG members and researchers agreed to adopt the Norwegian OA-QI wording for four of these items. RUG members also recommended adopting an additional seven items from the Norwegian OA-QI with some minor word changes to improve their suitability for patients in the UK. One other item from the draft OA QI (UK) questionnaire was retained and eight items were excluded, resulting in a 15-item final version. Conclusions This study describes the development of patient-reported quality indicators for OA primary care derived by members of a RUG group, working in partnership with the research team throughout the study. The OA QI (UK) supports the NICE quality standards for OA and they have been successfully used to assess the quality of OA consultations in primary care in the MOSAICS study. The OA QI (UK) has the potential for routine use in primary care to assess the quality of OA care provided to patients. Ongoing research using both the UK and Norwegian OA-QI questionnaires is assessing the self-reported quality of OA care in different European populations.

SQUIRE 2.0 (Standards for QUality Improvement Reporting Excellence): revised publication guidelines from a detailed consensus process.

PubMed

Ogrinc, Greg; Davies, Louise; Goodman, Daisy; Batalden, Paul; Davidoff, Frank; Stevens, David

2015-01-01

In the past several years, the science of health care improvement has advanced considerably. In this article, we describe the development of SQUIRE 2.0 and its key components. We undertook the revision between 2012 and 2015 using (1) interviews and focus groups to evaluate SQUIRE 1.0 plus feedback from an international steering group, (2) face-to-face consensus meetings to develop interim drafts, and (3) pilot testing with authors and a public comment period. SQUIRE 2.0 emphasizes 3 key components of systematic efforts to improve the quality, value, and safety of health care: formal and informal theory in planning, implementing, and evaluating improvement work; the context in which the work is done; and the study of the intervention(s). SQUIRE 2.0 is intended for reporting the range of methods used to improve health care, recognizing that they can be complex and multidimensional. It provides common ground to share these discoveries in the scholarly literature (www.squire-statement.org). © The Author(s) 2015.

Quality of care in the intensive care unit from the perspective of patient's relatives: development and psychometric evaluation of the consumer quality index 'R-ICU'.

PubMed

Rensen, Ans; van Mol, Margo M; Menheere, Ilse; Nijkamp, Marjan D; Verhoogt, Ellen; Maris, Bea; Manders, Willeke; Vloet, Lilian; Verharen, Lisbeth

2017-01-24

The quality standards of the Dutch Society of Intensive Care require monitoring of the satisfaction of patient's relatives with respect to care. Currently, no suitable instrument is available in the Netherlands to measure this. This study describes the development and psychometric evaluation of the questionnaire-based Consumer Quality Index 'Relatives in Intensive Care Unit' (CQI 'R-ICU'). The CQI 'R-ICU' measures the perceived quality of care from the perspective of patients' relatives, and identifies aspects of care that need improvement. The CQI 'R-ICU' was developed using a mixed method design. Items were based on quality of care aspects from earlier studies and from focus group interviews with patients' relatives. The time period for the data collection of the psychometric evaluation was from October 2011 until July 2012. Relatives of adult intensive care patients in one university hospital and five general hospitals in the Netherlands were approached to participate. Psychometric evaluation included item analysis, inter-item analysis, and factor analysis. Twelve aspects were noted as being indicators of quality of care, and were subsequently selected for the questionnaire's vocabulary. The response rate of patients' relatives was 81% (n = 455). Quality of care was represented by two clusters, each showing a high reliability: 'Communication' (α = .80) and 'Participation' (α = .84). Relatives ranked the following aspects for quality of care as most important: no conflicting information, information from doctors and nurses is comprehensive, and health professionals take patients' relatives seriously. The least important care aspects were: need for contact with peers, nuisance, and contact with a spiritual counsellor. Aspects that needed the most urgent improvement (highest quality improvement scores) were: information about how relatives can contribute to the care of the patient, information about the use of meal-facilities in the hospital, and involvement in decision-making on the medical treatment of the patient. The CQI 'R-ICU' evaluates quality of care from the perspective of relatives of intensive care patients and provides practical information for quality assurance and improvement programs. The development and psychometric evaluation of the CQI 'R-ICU' led to a draft questionnaire, sufficient to justify further research into the reliability, validity, and the discriminative power of the questionnaire.

Scenario drafting to anticipate future developments in technology assessment.

PubMed

Retèl, Valesca P; Joore, Manuela A; Linn, Sabine C; Rutgers, Emiel J T; van Harten, Wim H

2012-08-16

Health Technology Assessment (HTA) information, and in particular cost-effectiveness data is needed to guide decisions, preferably already in early stages of technological development. However, at that moment there is usually a high degree of uncertainty, because evidence is limited and different development paths are still possible. We developed a multi-parameter framework to assess dynamic aspects of a technology -still in development-, by means of scenario drafting to determine the effects, costs and cost-effectiveness of possible future diffusion patterns. Secondly, we explored the value of this method on the case of the clinical implementation of the 70-gene signature for breast cancer, a gene expression profile for selecting patients who will benefit most from chemotherapy. To incorporate process-uncertainty, ten possible scenarios regarding the introduction of the 70-gene signature were drafted with European experts. Out of 5 most likely scenarios, 3 drivers of diffusion (non-compliance, technical failure, and uptake) were quantitatively integrated in a decision-analytical model. For these scenarios, the cost-effectiveness of the 70-gene signature expressed in Incremental Cost-Effectiveness Ratios (ICERs) was compared to clinical guidelines, calculated from the past (2005) until the future (2020). In 2005 the ICER was €1,9 million/quality-adjusted-life-year (QALY), meaning that the 70-gene signature was not yet cost-effective compared to the current clinical guideline. The ICER for the 70-gene signature improved over time with a range of €1,9 million to €26,145 in 2010 and €1,9 million to €11,123/QALY in 2020 depending on the separate scenario used. From 2010, the 70-gene signature should be cost-effective, based on the combined scenario. The uptake-scenario had strongest influence on the cost-effectiveness. When optimal diffusion of a technology is sought, incorporating process-uncertainty by means of scenario drafting into a decision model may reveal unanticipated developments and can demonstrate a range of possible cost-effectiveness outcomes. The effect of scenarios give additional information on the speed with cost effectiveness might be reached and thus provide a more realistic picture for policy makers, opinion leaders and manufacturers.

Scenario drafting to anticipate future developments in technology assessment

PubMed Central

2012-01-01

Background Health Technology Assessment (HTA) information, and in particular cost-effectiveness data is needed to guide decisions, preferably already in early stages of technological development. However, at that moment there is usually a high degree of uncertainty, because evidence is limited and different development paths are still possible. We developed a multi-parameter framework to assess dynamic aspects of a technology -still in development-, by means of scenario drafting to determine the effects, costs and cost-effectiveness of possible future diffusion patterns. Secondly, we explored the value of this method on the case of the clinical implementation of the 70-gene signature for breast cancer, a gene expression profile for selecting patients who will benefit most from chemotherapy. Methods To incorporate process-uncertainty, ten possible scenarios regarding the introduction of the 70-gene signature were drafted with European experts. Out of 5 most likely scenarios, 3 drivers of diffusion (non-compliance, technical failure, and uptake) were quantitatively integrated in a decision-analytical model. For these scenarios, the cost-effectiveness of the 70-gene signature expressed in Incremental Cost-Effectiveness Ratios (ICERs) was compared to clinical guidelines, calculated from the past (2005) until the future (2020). Results In 2005 the ICER was €1,9 million/quality-adjusted-life-year (QALY), meaning that the 70-gene signature was not yet cost-effective compared to the current clinical guideline. The ICER for the 70-gene signature improved over time with a range of €1,9 million to €26,145 in 2010 and €1,9 million to €11,123/QALY in 2020 depending on the separate scenario used. From 2010, the 70-gene signature should be cost-effective, based on the combined scenario. The uptake-scenario had strongest influence on the cost-effectiveness. Conclusions When optimal diffusion of a technology is sought, incorporating process-uncertainty by means of scenario drafting into a decision model may reveal unanticipated developments and can demonstrate a range of possible cost-effectiveness outcomes. The effect of scenarios give additional information on the speed with cost effectiveness might be reached and thus provide a more realistic picture for policy makers, opinion leaders and manufacturers. PMID:22894140

76 FR 57751 - Notice of Availability of a Draft Programmatic Environmental Impact Statement for Northern Border...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-09-16

... particular place. Because this effort is programmatic in nature, the Draft PEIS does not define effects for a... the purposes of the PEIS, the Northern Border is defined as the area between the United States and... environmental quality and the government's role in protecting it. The essence of NEPA is the requirement that...

76 FR 30149 - Science Advisory Board Staff Office Notification of a Public Teleconference of the Chartered...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-24

... of ballast water treatment systems; A Report by the EPA Science Advisory Board (May 2011 Draft... Board can be found on the EPA Web site at http://www.epa.gov/sab . SUPPLEMENTARY INFORMATION: The SAB... quality review of a draft report entitled Efficacy of ballast water treatment systems; a report by the EPA...

A Screening Assessment of the Potential Impacts of Climate Change on Combined Sewer Overflow (Cso) Mitigation in the Great Lakes and New England Regions (External Review Draft)

EPA Science Inventory

EPA has released this draft document solely for the purpose of pre-dissemination peer review under applicable information quality guidelines. This document has not been formally disseminated by EPA. It does not represent and should not be construed to represent any Agency policy ...

SPIRIT 2013 explanation and elaboration: guidance for protocols of clinical trials

PubMed Central

Tetzlaff, Jennifer M; Gøtzsche, Peter C; Altman, Douglas G; Mann, Howard; Berlin, Jesse A; Dickersin, Kay; Hróbjartsson, Asbjørn; Schulz, Kenneth F; Parulekar, Wendy R; Krleža-Jerić, Karmela; Laupacis, Andreas; Moher, David

2013-01-01

High quality protocols facilitate proper conduct, reporting, and external review of clinical trials. However, the completeness of trial protocols is often inadequate. To help improve the content and quality of protocols, an international group of stakeholders developed the SPIRIT 2013 Statement (Standard Protocol Items: Recommendations for Interventional Trials). The SPIRIT Statement provides guidance in the form of a checklist of recommended items to include in a clinical trial protocol. This SPIRIT 2013 Explanation and Elaboration paper provides important information to promote full understanding of the checklist recommendations. For each checklist item, we provide a rationale and detailed description; a model example from an actual protocol; and relevant references supporting its importance. We strongly recommend that this explanatory paper be used in conjunction with the SPIRIT Statement. A website of resources is also available (www.spirit-statement.org). The SPIRIT 2013 Explanation and Elaboration paper, together with the Statement, should help with the drafting of trial protocols. Complete documentation of key trial elements can facilitate transparency and protocol review for the benefit of all stakeholders. PMID:23303884

SPIRIT 2013 explanation and elaboration: guidance for protocols of clinical trials.

PubMed

Chan, An-Wen; Tetzlaff, Jennifer M; Gøtzsche, Peter C; Altman, Douglas G; Mann, Howard; Berlin, Jesse A; Dickersin, Kay; Hróbjartsson, Asbjørn; Schulz, Kenneth F; Parulekar, Wendy R; Krleza-Jeric, Karmela; Laupacis, Andreas; Moher, David

2013-01-08

High quality protocols facilitate proper conduct, reporting, and external review of clinical trials. However, the completeness of trial protocols is often inadequate. To help improve the content and quality of protocols, an international group of stakeholders developed the SPIRIT 2013 Statement (Standard Protocol Items: Recommendations for Interventional Trials). The SPIRIT Statement provides guidance in the form of a checklist of recommended items to include in a clinical trial protocol. This SPIRIT 2013 Explanation and Elaboration paper provides important information to promote full understanding of the checklist recommendations. For each checklist item, we provide a rationale and detailed description; a model example from an actual protocol; and relevant references supporting its importance. We strongly recommend that this explanatory paper be used in conjunction with the SPIRIT Statement. A website of resources is also available (www.spirit-statement.org). The SPIRIT 2013 Explanation and Elaboration paper, together with the Statement, should help with the drafting of trial protocols. Complete documentation of key trial elements can facilitate transparency and protocol review for the benefit of all stakeholders.

Standardized Methods for Enhanced Quality and Comparability of Tuberculous Meningitis Studies.

PubMed

Marais, Ben J; Heemskerk, Anna D; Marais, Suzaan S; van Crevel, Reinout; Rohlwink, Ursula; Caws, Maxine; Meintjes, Graeme; Misra, Usha K; Mai, Nguyen T H; Ruslami, Rovina; Seddon, James A; Solomons, Regan; van Toorn, Ronald; Figaji, Anthony; McIlleron, Helen; Aarnoutse, Robert; Schoeman, Johan F; Wilkinson, Robert J; Thwaites, Guy E

2017-02-15

Tuberculous meningitis (TBM) remains a major cause of death and disability in tuberculosis-endemic areas, especially in young children and immunocompromised adults. Research aimed at improving outcomes is hampered by poor standardization, which limits study comparison and the generalizability of results. We propose standardized methods for the conduct of TBM clinical research that were drafted at an international tuberculous meningitis research meeting organized by the Oxford University Clinical Research Unit in Vietnam. We propose a core dataset including demographic and clinical information to be collected at study enrollment, important aspects related to patient management and monitoring, and standardized reporting of patient outcomes. The criteria proposed for the conduct of observational and intervention TBM studies should improve the quality of future research outputs, can facilitate multicenter studies and meta-analyses of pooled data, and could provide the foundation for a global TBM data repository.

77 FR 1913 - Notice of Meeting of the Agricultural Air Quality Task Force

Federal Register 2010, 2011, 2012, 2013, 2014

2012-01-12

... Conservation Service Notice of Meeting of the Agricultural Air Quality Task Force AGENCY: Natural Resources...), Agricultural Air Quality Task Force (AAQTF) will meet to continue discussions on critical air quality issues... relationship between agricultural production and air quality. The meeting is open to the public, and a draft...

78 FR 52602 - Notice To Rescind a Notice of Intent and Draft Environmental Impact Statement: I-17 Corridor...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-23

... and Draft Environmental Impact Statement: I-17 Corridor Improvement Study; Maricopa County, Arizona... Corridor Improvement Study was published in the Federal Register on January 6, 2010. FOR FURTHER... Corridor is located in the city of Phoenix, and the study area limits for the EIS consisted of...

Draft genome of the Northern snakehead, Channa argus.

PubMed

Xu, Jian; Bian, Chao; Chen, Kunci; Liu, Guiming; Jiang, Yanliang; Luo, Qing; You, Xinxin; Peng, Wenzhu; Li, Jia; Huang, Yu; Yi, Yunhai; Dong, Chuanju; Deng, Hua; Zhang, Songhao; Zhang, Hanyuan; Shi, Qiong; Xu, Peng

2017-04-01

The Northern snakehead (Channa argus), a member of the Channidae family of the Perciformes, is an economically important freshwater fish native to East Asia. In North America, it has become notorious as an intentionally released invasive species. Its ability to breathe air with gills and migrate short distances over land makes it a good model for bimodal breath research. Therefore, recent research has focused on the identification of relevant candidate genes. Here, we performed whole genome sequencing of C. argus to construct its draft genome, aiming to offer useful information for further functional studies and identification of target genes related to its unusual facultative air breathing. Findings: We assembled the C. argus genome with a total of 140.3 Gb of raw reads, which were sequenced using the Illumina HiSeq2000 platform. The final draft genome assembly was approximately 615.3 Mb, with a contig N50 of 81.4 kb and scaffold N50 of 4.5 Mb. The identified repeat sequences account for 18.9% of the whole genome. The 19 877 protein-coding genes were predicted from the genome assembly, with an average of 10.5 exons per gene. Conclusion: We generated a high-quality draft genome of C. argus, which will provide a valuable genetic resource for further biomedical investigations of this economically important teleost fish. © The Author 2017. Published by Oxford University Press.

SQUIRE 2.0 (Standards for QUality Improvement Reporting Excellence): revised publication guidelines from a detailed consensus process.

PubMed

Ogrinc, Greg; Davies, Louise; Goodman, Daisy; Batalden, Paul; Davidoff, Frank; Stevens, David

2016-12-01

Since the publication of Standards for QUality Improvement Reporting Excellence (SQUIRE 1.0) guidelines in 2008, the science of the field has advanced considerably. In this manuscript, we describe the development of SQUIRE 2.0 and its key components. We undertook the revision between 2012 and 2015 using (1) semistructured interviews and focus groups to evaluate SQUIRE 1.0 plus feedback from an international steering group, (2) two face-to-face consensus meetings to develop interim drafts and (3) pilot testing with authors and a public comment period. SQUIRE 2.0 emphasises the reporting of three key components of systematic efforts to improve the quality, value and safety of healthcare: the use of formal and informal theory in planning, implementing and evaluating improvement work; the context in which the work is done and the study of the intervention(s). SQUIRE 2.0 is intended for reporting the range of methods used to improve healthcare, recognising that they can be complex and multidimensional. It provides common ground to share these discoveries in the scholarly literature (http://www.squire-statement.org). Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

AIR QUALITY CRITERIA CARBON MONOXIDE, EXTERNAL REVIEW DRAFT

EPA Science Inventory

The U.S. Environmental Protection Agency (EPA) promulgates the National Ambient Air Quality Standards (NAAQS) on the basis of scientific information contained in criteria documents. The last air quality criteria document for carbon monoxide (CO) was completed by EPA in 1991. This...

Molecular Markers and Cotton Genetic Improvement: Current Status and Future Prospects

PubMed Central

Malik, Waqas; Iqbal, Muhammad Zaffar; Ali Khan, Asif; Qayyum, Abdul; Ali Abid, Muhammad; Noor, Etrat; Qadir Ahmad, Muhammad; Hasan Abbasi, Ghulam

2014-01-01

Narrow genetic base and complex allotetraploid genome of cotton (Gossypium hirsutum L.) is stimulating efforts to avail required polymorphism for marker based breeding. The availability of draft genome sequence of G. raimondii and G. arboreum and next generation sequencing (NGS) technologies facilitated the development of high-throughput marker technologies in cotton. The concepts of genetic diversity, QTL mapping, and marker assisted selection (MAS) are evolving into more efficient concepts of linkage disequilibrium, association mapping, and genomic selection, respectively. The objective of the current review is to analyze the pace of evolution in the molecular marker technologies in cotton during the last ten years into the following four areas: (i) comparative analysis of low- and high-throughput marker technologies available in cotton, (ii) genetic diversity in the available wild and improved gene pools of cotton, (iii) identification of the genomic regions within cotton genome underlying economic traits, and (iv) marker based selection methodologies. Moreover, the applications of marker technologies to enhance the breeding efficiency in cotton are also summarized. Aforementioned genomic technologies and the integration of several other omics resources are expected to enhance the cotton productivity and meet the global fiber quantity and quality demands. PMID:25401149

High-quality draft genome sequence of Ensifer meliloti Mlalz-1, a microsymbiont of Medicago laciniata (L.) miller collected in Lanzarote, Canary Islands, Spain.

PubMed

Osman, Wan Adnawani Meor; van Berkum, Peter; León-Barrios, Milagros; Velázquez, Encarna; Elia, Patrick; Tian, Rui; Ardley, Julie; Gollagher, Margaret; Seshadri, Rekha; Reddy, T B K; Ivanova, Natalia; Woyke, Tanja; Pati, Amrita; Markowitz, Victor; Baeshen, Mohamed N; Baeshen, Naseebh Nabeeh; Kyrpides, Nikos; Reeve, Wayne

2017-01-01

10.1601/nm.1335 Mlalz-1 (INSDC = ATZD00000000) is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing nodule of Medicago laciniata (L.) Miller from a soil sample collected near the town of Guatiza on the island of Lanzarote, the Canary Islands, Spain. This strain nodulates and forms an effective symbiosis with the highly specific host M. laciniata . This rhizobial genome was sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) sequencing project. Here the features of 10.1601/nm.1335 Mlalz-1 are described, together with high-quality permanent draft genome sequence information and annotation. The 6,664,116 bp high-quality draft genome is arranged in 99 scaffolds of 100 contigs, containing 6314 protein-coding genes and 74 RNA-only encoding genes. Strain Mlalz-1 is closely related to 10.1601/nm.1335 10.1601/strainfinder?urlappend=%3Fid%3DIAM+12611 T , 10.1601/nm.1334 A 321 T and 10.1601/nm.17831 10.1601/strainfinder?urlappend=%3Fid%3DORS+1407 T , based on 16S rRNA gene sequences. gANI values of ≥98.1% support the classification of strain Mlalz-1 as 10.1601/nm.1335. Nodulation of M. laciniata requires a specific nodC allele, and the nodC gene of strain Mlalz-1 shares ≥98% sequence identity with nodC of M. laciniata -nodulating 10.1601/nm.1328 strains, but ≤93% with nodC of 10.1601/nm.1328 strains that nodulate other Medicago species. Strain Mlalz-1 is unique among sequenced 10.1601/nm.1335 strains in possessing genes encoding components of a T2SS and in having two versions of the adaptive acid tolerance response lpiA-acvB operon. In 10.1601/nm.1334 strain 10.1601/strainfinder?urlappend=%3Fid%3DWSM+419, lpiA is essential for enhancing survival in lethal acid conditions. The second copy of the lpiA-acvB operon of strain Mlalz-1 has highest sequence identity (> 96%) with that of 10.1601/nm.1334 strains, which suggests genetic recombination between strain Mlalz-1 and 10.1601/nm.1334 and the horizontal gene transfer of lpiA-acvB .

The Virtual Pelvic Floor, a tele-immersive educational environment.

PubMed Central

Pearl, R. K.; Evenhouse, R.; Rasmussen, M.; Dech, F.; Silverstein, J. C.; Prokasy, S.; Panko, W. B.

1999-01-01

This paper describes the development of the Virtual Pelvic Floor, a new method of teaching the complex anatomy of the pelvic region utilizing virtual reality and advanced networking technology. Virtual reality technology allows improved visualization of three-dimensional structures over conventional media because it supports stereo vision, viewer-centered perspective, large angles of view, and interactivity. Two or more ImmersaDesk systems, drafting table format virtual reality displays, are networked together providing an environment where teacher and students share a high quality three-dimensional anatomical model, and are able to converse, see each other, and to point in three dimensions to indicate areas of interest. This project was realized by the teamwork of surgeons, medical artists and sculptors, computer scientists, and computer visualization experts. It demonstrates the future of virtual reality for surgical education and applications for the Next Generation Internet. Images Figure 1 Figure 2 Figure 3 PMID:10566378

High quality permanent draft genome sequence of Chryseobacterium bovis DSM 19482 T, isolated from raw cow milk

DOE PAGES

Laviad-Shitrit, Sivan; Göker, Markus; Huntemann, Marcel; ...

2017-05-08

Chryseobacterium bovis DSM 19482 T (Hantsis-Zacharov et al., Int J Syst Evol Microbiol 58:1024-1028, 2008) is a Gram-negative, rod shaped, non-motile, facultative anaerobe, chemoorganotroph bacterium. C. bovis is a member of the Flavobacteriaceae, a family within the phylum Bacteroidetes. It was isolated when psychrotolerant bacterial communities in raw milk and their proteolytic and lipolytic traits were studied. Here we describe the features of this organism, together with the draft genome sequence and annotation. The DNA G + C content is 38.19%. The chromosome length is 3,346,045 bp. It encodes 3236 proteins and 105 RNA genes. The C. bovis genome ismore » part of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes study.« less

High quality permanent draft genome sequence of Chryseobacterium bovis DSM 19482 T, isolated from raw cow milk

DOE Office of Scientific and Technical Information (OSTI.GOV)

Laviad-Shitrit, Sivan; Göker, Markus; Huntemann, Marcel

Chryseobacterium bovis DSM 19482 T (Hantsis-Zacharov et al., Int J Syst Evol Microbiol 58:1024-1028, 2008) is a Gram-negative, rod shaped, non-motile, facultative anaerobe, chemoorganotroph bacterium. C. bovis is a member of the Flavobacteriaceae, a family within the phylum Bacteroidetes. It was isolated when psychrotolerant bacterial communities in raw milk and their proteolytic and lipolytic traits were studied. Here we describe the features of this organism, together with the draft genome sequence and annotation. The DNA G + C content is 38.19%. The chromosome length is 3,346,045 bp. It encodes 3236 proteins and 105 RNA genes. The C. bovis genome ismore » part of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes study.« less

78 FR 68852 - Draft Guidance for Industry on Acrylamide in Foods; Availability

Federal Register 2010, 2011, 2012, 2013, 2014

2013-11-15

... high-temperature cooking. The draft guidance is intended to suggest a range of possible approaches to... during certain types of high-temperature cooking, and is a concern because it can cause cancer in... placing preparation and cooking instructions on frozen French fry packages. Lastly, the draft guidance is...

2016 Draft Estuarine/Marine Copper Aquatic Life Ambient Water Quality Criteria

EPA Pesticide Factsheets

Documents pertain to Aquatic Life Ambient Water Quality criteria for Copper (2016 Estuarine/marine). These documents contain the safe levels of Copper in water that should protect to the majority of species.

dBBQs: dataBase of Bacterial Quality scores.

PubMed

Wanchai, Visanu; Patumcharoenpol, Preecha; Nookaew, Intawat; Ussery, David

2017-12-28

It is well-known that genome sequencing technologies are becoming significantly cheaper and faster. As a result of this, the exponential growth in sequencing data in public databases allows us to explore ever growing large collections of genome sequences. However, it is less known that the majority of available sequenced genome sequences in public databases are not complete, drafts of varying qualities. We have calculated quality scores for around 100,000 bacterial genomes from all major genome repositories and put them in a fast and easy-to-use database. Prokaryotic genomic data from all sources were collected and combined to make a non-redundant set of bacterial genomes. The genome quality score for each was calculated by four different measurements: assembly quality, number of rRNA and tRNA genes, and the occurrence of conserved functional domains. The dataBase of Bacterial Quality scores (dBBQs) was designed to store and retrieve quality scores. It offers fast searching and download features which the result can be used for further analysis. In addition, the search results are shown in interactive JavaScript chart framework using DC.js. The analysis of quality scores across major public genome databases find that around 68% of the genomes are of acceptable quality for many uses. dBBQs (available at http://arc-gem.uams.edu/dbbqs ) provides genome quality scores for all available prokaryotic genome sequences with a user-friendly Web-interface. These scores can be used as cut-offs to get a high-quality set of genomes for testing bioinformatics tools or improving the analysis. Moreover, all data of the four measurements that were combined to make the quality score for each genome, which can potentially be used for further analysis. dBBQs will be updated regularly and is freely use for non-commercial purpose.

Emission reduction by multipurpose buffer strips on arable fields.

PubMed

Sloots, K; van der Vlies, A W

2007-01-01

In the area managed by Hollandse Delta, agriculture is under great pressure and the social awareness of the agricultural sector is increasing steadily. In recent years, a stand-still has been observed in water quality, in terms of agrochemicals, and concentrations even exceed the standard. To improve the waterquality a multi-purpose Field Margin Regulation was drafted for the Hoeksche Waard island in 2005. The regulation prescribes a crop-free strip, 3.5 m wide, alongside wet drainage ditches. The strip must be sown with mixtures of grasses, flowers or herbs. No crop protection chemicals or fertilizer may be used on the strips. A total length of approximately 200 km of buffer strip has now been laid. Besides reducing emissions, the buffer strips also stimulate natural pest control methods and encourage local tourism. Finally, the strips should lead to an improvement in the farmers' image. The regulation has proved to be successful. The buffer strips boosted both local tourism and the image of the agricultural sector. Above all, the strips provided a natural shield for emission to surface water, which will lead to an improvement of the water quality and raise the farmers' awareness of water quality and the environment.

Health impact assessment as an agent of policy change: improving the health impacts of the mayor of London's draft transport strategy.

PubMed

Mindell, J; Sheridan, L; Joffe, M; Samson-Barry, H; Atkinson, S

2004-03-01

To increase the positive and mitigate the negative health impacts of the mayor's draft transport strategy for London. A rapid prospective health impact assessment (HIA) of the penultimate draft of the strategy, using a review commissioned by the regional director of public health; an appraisal of congestion charging; and a participatory workshop. Two audits of changes were performed to assess the impact on policy of the HIA process. Regional government policy development. Recommendations from the rapid HIA were fed back into the drafting process. Changes (a) between the penultimate draft and the draft for public consultation and (b) between that and the final mayoral strategy. The draft transport strategy published for consultation differed in a number of respects from the previous version. Almost all the recommendations from the HIA were incorporated into the final strategy. Significant changes included promoting sustainable travel plans for workplaces and schools; giving priority to infrastructure and services that benefit London's deprived communities; increased emphasis on promoting walking and cycling and reducing reliance on private cars; and a commitment to track the health impacts of the final strategy and its implementation. Specific additions included re-allocating road space. HIA was successful in influencing the transport strategy for London, resulting in several improvements from a health viewpoint. HIA is an effective method both for bringing about significant change in policy proposals and in increasing policy makers' understanding of determinants of health and hence in changing attitudes of policy makers.

The SDM 3 Circle Model: A Literature Synthesis and Adaptation for Shared Decision Making in the Hospital.

PubMed

Rennke, Stephanie; Yuan, Patrick; Monash, Brad; Blankenburg, Rebecca; Chua, Ian; Harman, Stephanie; Sakai, Debbie S; Khan, Adeena; Hilton, Joan F; Shieh, Lisa; Satterfield, Jason

2017-12-01

Patient engagement through shared decision-making (SDM) is increasingly seen as a key component for patient safety, patient satisfaction, and quality of care. Current SDM models do not adequately account for medical and environmental contexts, which may influence medical decisions in the hospital. We identified leading SDM models and reviews to inductively construct a novel SDM model appropriate for the inpatient setting. A team of medicine and pediatric hospitalists reviewed the literature to integrate core SDM concepts and processes and iteratively constructed a synthesized draft model. We then solicited broad SDM expert feedback on the draft model for validation and further refinement. The SDM 3 Circle Model identifies 3 core categories of variables that dynamically interact within an "environmental frame." The resulting Venn diagram includes overlapping circles for (1) patient/family, (2) provider/team, and (3) medical context. The environmental frame includes all external, contextual factors that may influence any of the 3 circles. Existing multistep SDM process models were then rearticulated and contextualized to illustrate how a shared decision might be made. The SDM 3 Circle Model accounts for important environmental and contextual characteristics that vary across settings. The visual emphasis generated by each "circle" and by the environmental frame direct attention to often overlooked interactive forces and has the potential to more precisely define, promote, and improve SDM. This model provides a framework to develop interventions to improve quality and patient safety through SDM and patient engagement for hospitalists. © 2017 Society of Hospital Medicine.

Tribal Air Grants Framework - Menu of Options

EPA Pesticide Factsheets

Tool to assist tribes that apply for CAA funding to draft moreeffective work plans for projects that will develop tribal knowledge of air quality issues andbuild tribal expertise to manage air quality on reservations and tribal trust land

77 FR 74729 - Notice To Rescind a Notice of Intent and Draft Environmental Impact Statement: I-10 Corridor...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-12-17

... and Draft Environmental Impact Statement: I-10 Corridor Improvement Study; Maricopa County, AZ AGENCY..., Arizona. A NOI to prepare an EIS for the I-10 Corridor Improvement Study was published in the Federal..., Arizona. The I-10 Corridor is in or adjacent to the cities of Phoenix, Tempe, and Chandler, as well as the...

Communicating data quality through Web Map Services

NASA Astrophysics Data System (ADS)

Blower, Jon; Roberts, Charles; Griffiths, Guy; Lewis, Jane; Yang, Kevin

2013-04-01

The sharing and visualization of environmental data through spatial data infrastructures is becoming increasingly common. However, information about the quality of data is frequently unavailable or presented in an inconsistent fashion. ("Data quality" is a phrase with many possible meanings but here we define it as "fitness for purpose" - therefore different users have different notions of what constitutes a "high quality" dataset.) The GeoViQua project (www.geoviqua.org) is developing means for eliciting, formatting, discovering and visualizing quality information using ISO and Open Geospatial Consortium (OGC) standards. Here we describe one aspect of the innovations of the GeoViQua project. In this presentation, we shall demonstrate new developments in using Web Map Services to communicate data quality at the level of datasets, variables and individual samples. We shall outline a new draft set of conventions (known as "WMS-Q"), which describe a set of rules for using WMS to convey quality information (OGC draft Engineering Report 12-160). We shall demonstrate these conventions through new prototype software, based upon the widely-used ncWMS software, that applies these rules to enable the visualization of uncertainties in raster data such as satellite products and the results of numerical simulations. Many conceptual and practical issues have arisen from these experiments. How can source data be formatted so that a WMS implementation can detect the semantic links between variables (e.g. the links between a mean field and its variance)? The visualization of uncertainty can be a complex task - how can we provide users with the power and flexibility to choose an optimal strategy? How can we maintain compatibility (as far as possible) with existing WMS clients? We explore these questions with reference to existing standards and approaches, including UncertML, NetCDF-U and Styled Layer Descriptors.

Draft genome of the Peruvian scallop Argopecten purpuratus.

PubMed

Li, Chao; Liu, Xiao; Liu, Bo; Ma, Bin; Liu, Fengqiao; Liu, Guilong; Shi, Qiong; Wang, Chunde

2018-04-01

The Peruvian scallop, Argopecten purpuratus, is mainly cultured in southern Chile and Peru was introduced into China in the last century. Unlike other Argopecten scallops, the Peruvian scallop normally has a long life span of up to 7 to 10 years. Therefore, researchers have been using it to develop hybrid vigor. Here, we performed whole genome sequencing, assembly, and gene annotation of the Peruvian scallop, with an important aim to develop genomic resources for genetic breeding in scallops. A total of 463.19-Gb raw DNA reads were sequenced. A draft genome assembly of 724.78 Mb was generated (accounting for 81.87% of the estimated genome size of 885.29 Mb), with a contig N50 size of 80.11 kb and a scaffold N50 size of 1.02 Mb. Repeat sequences were calculated to reach 33.74% of the whole genome, and 26,256 protein-coding genes and 3,057 noncoding RNAs were predicted from the assembly. We generated a high-quality draft genome assembly of the Peruvian scallop, which will provide a solid resource for further genetic breeding and for the analysis of the evolutionary history of this economically important scallop.

Using an e-Portfolio System to Improve the Academic Writing Performance of ESL Students

ERIC Educational Resources Information Center

Alshahrani, Ali; Windeatt, Scott

2012-01-01

Many intensive English language programmes that English second language (ESL) students enrol in adopt a process approach to writing, interpreting writing as a cognitive process that is highly private or individualistic (Atkinson, 2003), where writers use specific cognitive phases, such as pre-writing, drafting, and revising, to generate their…

Single-molecule sequencing and optical mapping yields an improved genome of woodland strawberry (Fragaria vesca) with chromosome-scale contiguity

USDA-ARS?s Scientific Manuscript database

Although draft genomes are available for most agronomically important plant species, the majority are incomplete, highly fragmented, and often riddled with assembly and scaffolding errors. These assembly issues hinder advances in tool development for functional genomics and systems biology. Here we ...

Development of the First Guideline for Professional Conduct in Medical Practice in Iran.

PubMed

Saeedi Tehrani, Saeedeh; Nayeri, Fatemeh; Parsapoor, Alireza; Jafarian, Ali; Labaf, Ali; Mirzazadeh, Azim; Emadi Kouchak, Hamid; Shahi, Farhad; Ghasemzadeh, Nazafarin; Asghari, Fariba

2017-01-01

Professional behavior is first learned at the university. One of the necessary considerations in maintaining the professional environment of the university is establishing a set of codes for the behavior of physicians and medical students. This paper describes the process of developing the professional code of conduct in Tehran University of Medical Sciences, Tehran, Iran. A review of Iranian and international literature was performed to develop the first draft of the guideline. In sessions of group discussion by the authors, the articles of the draft were evaluated for relevancy, clarity, and lack of repetition. The draft was sent for evaluation to all participants, including the medical faculty members, residents, and medical students, four times and necessary corrections were made according to the comments received. The final guideline included 76 behavior codes in 6 categories, including altruism, honor and integrity, responsibility, respect, justice, and excellence. The codes of the guideline cover the physicians' commitments in the physician-patient, physician-colleague, and instructor-student relationships in order to improve the quality of the services. The Islamic and Iranian culture were taken into consideration in developing the guideline. Accordance with the administrative and educational conditions of the universities was ensured in developing the guideline and its acceptance was ensured through extensive surveys. Thus, it is expected that this guideline will be very effective in enhancing professional commitment in medical universities.

Sequence-based Network Completion Reveals the Integrality of Missing Reactions in Metabolic Networks*

PubMed Central

Krumholz, Elias W.; Libourel, Igor G. L.

2015-01-01

Genome-scale metabolic models are central in connecting genotypes to metabolic phenotypes. However, even for well studied organisms, such as Escherichia coli, draft networks do not contain a complete biochemical network. Missing reactions are referred to as gaps. These gaps need to be filled to enable functional analysis, and gap-filling choices influence model predictions. To investigate whether functional networks existed where all gap-filling reactions were supported by sequence similarity to annotated enzymes, four draft networks were supplemented with all reactions from the Model SEED database for which minimal sequence similarity was found in their genomes. Quadratic programming revealed that the number of reactions that could partake in a gap-filling solution was vast: 3,270 in the case of E. coli, where 72% of the metabolites in the draft network could connect a gap-filling solution. Nonetheless, no network could be completed without the inclusion of orphaned enzymes, suggesting that parts of the biochemistry integral to biomass precursor formation are uncharacterized. However, many gap-filling reactions were well determined, and the resulting networks showed improved prediction of gene essentiality compared with networks generated through canonical gap filling. In addition, gene essentiality predictions that were sensitive to poorly determined gap-filling reactions were of poor quality, suggesting that damage to the network structure resulting from the inclusion of erroneous gap-filling reactions may be predictable. PMID:26041773

Health system guidance appraisal--concept evaluation and usability testing.

PubMed

Ako-Arrey, Denis E; Brouwers, Melissa C; Lavis, John N; Giacomini, Mita K

2016-01-05

Health system guidance (HSG) provides recommendations aimed to address health system challenges. However, there is a paucity of methods to direct, appraise, and report HSG. Earlier research identified 30 candidate criteria (concepts) that can be used to evaluate the quality of HSG and guide development and reporting requirements. The objective of this paper was to describe two studies aimed at evaluating the importance of these 30 criteria, design a draft HSG appraisal tool, and test its usability. This study involved a two-step survey process. In step 1, respondents rated the 30 concepts for appropriateness to, relevance to, and priority for health system decisions and HSG. This led to a draft tool. In step 2, respondents reviewed HSG documents, appraised them using the tool, and answered a series of questions. Descriptive analyses were computed. Fifty participants were invited in step 1, and we had a response rate of 82 %. The mean response rates for each concept within each survey question were universally favorable. There was also an overall agreement about the need for a high-quality tool to systematically direct the development, appraisal, and reporting of HSG. Qualitative feedback and a consensus process by the team led to refinements to some of the concepts and the creation of a beta (draft) version of the HSG tool. In step 2, 35 participants were invited and we had a response rate of 74 %. Exploratory analyses showed that the quality of the HSGs reviewed varied as a function of the HSG item and the specific document assessed. A favorable consensus was reached with participants agreeing that the HSG items were easy to understand and easy to apply. Moreover, the overall agreement was high for the usability of the tool to systematically direct the development (85 %), appraisal (92 %), and reporting (81 %) of HSG. From this process, version 1.0 of the HSG appraisal tool was generated complete with 32 items (and their descriptions) and 4 domains. The final tool, named the Appraisal of Guidelines for Research and Evaluation for Health Systems (AGREE-HS) (version 1), defines expectations of HSG and facilitates informed decisions among policymakers on health system delivery, financial, and governance arrangements.

Jobs and the Quality of Life in Cities: Local Government's Role in Full Employment.

ERIC Educational Resources Information Center

Newport, Eugene "Gus"

1986-01-01

"The Quality-of-Life Action" conference was held to: (1) involve more people in activities relating to economic well-being; (2) plan for responsible growth and environmental preservation; and (3) involve people in quality-of-life legislation. Included is the conference's draft of a "Proposed Berkeley Ordinance on Quality-of-Life…

Fact Sheet: Revised Draft Ambient Water Quality Criteria Document for Atrazine and Request for Scientific Views

EPA Pesticide Factsheets

Documents pertaining to Acute and Chronic Ambient Water Quality Aquatic Life Criteria for Atrazine (Freshwater and Salt Water) and revised Ecological Fate and Effects Risk Assessment for Atrazine. (Fact Sheet)

77 FR 41442 - Notice of Availability of the Draft Order of the Secretary on Oil and Gas and Potash Development...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-13

... protection of other mineral resources, other natural resources, environmental quality, life, health, safety... sufficient thickness and quality to be mineable), the Development Areas would generally be larger...

21 CFR 26.6 - Equivalence assessment.

Code of Federal Regulations, 2010 CFR

2010-04-01

... OF PHARMACEUTICAL GOOD MANUFACTURING PRACTICE REPORTS, MEDICAL DEVICE QUALITY SYSTEM AUDIT REPORTS... draft programs for assessing the equivalence of the respective regulatory systems in terms of quality... inspection reports), joint training, and joint inspections for the purpose of assessing regulatory systems...

AN ECOEPIDEMIOLOGICAL APPROACH FOR DEVELOPING WATER QUALITY CRITERIA

EPA Science Inventory

The USEPA's Draft Framework for Developing Suspended and Bedded Sediments Water Quality Criteria is based on an ecoepidemiological approach that is potentially applicable to any chemical or non-chemical agent. An ecoepidemiological approach infers associations from the co-occurre...

RAPADAPTE for rapid guideline development: high-quality clinical guidelines can be rapidly developed with limited resources.

PubMed

Alper, Brian S; Tristan, Mario; Ramirez-Morera, Anggie; Vreugdenhil, Maria M T; Van Zuuren, Esther J; Fedorowicz, Zbys

2016-06-01

Guideline development is challenging, expensive and labor-intensive. A high-quality guideline with 90 recommendations for breast cancer treatment was developed within 6 months with limited resources in Costa Rica. We describe the experience and propose a process others can use and adapt.The ADAPTE method (using existing guidelines to minimize repeating work that has been done) was used but existing guidelines were not current. The method was extended to use databases that systematically identify, appraise and synthesize evidence for clinical application (DynaMed, EBM Guidelines) to provide current evidence searches and critical appraisal of evidence. The Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach was used to rate the quality of evidence and the strength of recommendations. Draft recommendations with supporting evidence were provided to panel members for facilitated voting to target panel discussion to areas necessary for reaching consensus.Training panelists in guideline development methodology facilitated rapid consensus development. Extending 'guideline adaptation' to 'evidence database adaptation' was highly effective and efficient. Methods were created to simplify mapping DynaMed evidence ratings to GRADE ratings. Twelve steps are presented to facilitate rapid guideline development and enable further adaptation by others.This is a case report and the RAPADAPTE method was retrospectively derived. Prospective replication and validation will support advances for the guideline development community. If guideline development can be accelerated without compromising validity and relevance of the resulting recommendations this would greatly improve our ability to impact clinical care. © The Author 2016. Published by Oxford University Press in association with the International Society for Quality in Health Care; all rights reserved.

High-quality draft genome sequence of Ensifer meliloti Mlalz-1, a microsymbiont of Medicago laciniata (L.) miller collected in Lanzarote, Canary Islands, Spain

DOE Office of Scientific and Technical Information (OSTI.GOV)

Osman, Wan Adnawani Meor; van Berkum, Peter; León-Barrios, Milagros

Ensifer meliloti Mlalz-1 (INSDC = ATZD00000000) is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing nodule of Medicago laciniata (L.) Miller from a soil sample collected near the town of Guatiza on the island of Lanzarote, the Canary Islands, Spain. This strain nodulates and forms an effective symbiosis with the highly specific host M. laciniata. This rhizobial genome was sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) sequencing project. Here in this paper, the features of E. meliloti Mlalz-1 are described, together with high-qualitymore » permanent draft genome sequence information and annotation. The 6,664,116 bp high-quality draft genome is arranged in 99 scaffolds of 100 contigs, containing 6314 protein-coding genes and 74 RNA-only encoding genes. Strain Mlalz-1 is closely related to Ensifer meliloti IAM 12611 T, Ensifer medicae A 321T and Ensifer numidicus ORS 1407 T, based on 16S rRNA gene sequences. gANI values of ≥98.1% support the classification of strain Mlalz-1 as E. meliloti . Nodulation of M. laciniata requires a specific nodC allele, and the nodC gene of strain Mlalz-1 shares ≥98% sequence identity with nodC of M. laciniata-nodulating Ensifer strains, but ≤93% with nodC of Ensifer strains that nodulate other Medicago species. Strain Mlalz-1 is unique among sequenced E. meliloti strains in possessing genes encoding components of a T2SS and in having two versions of the adaptive acid tolerance response lpiA-acvB operon. In E. medicae strain WSM419, lpiA is essential for enhancing survival in lethal acid conditions. The second copy of the lpiA-acvB operon of strain Mlalz-1 has highest sequence identity (> 96%) with that of E. medicae strains, which suggests genetic recombination between strain Mlalz-1 and E. medicae and the horizontal gene transfer of lpiA-acvB.« less

High-quality draft genome sequence of Ensifer meliloti Mlalz-1, a microsymbiont of Medicago laciniata (L.) miller collected in Lanzarote, Canary Islands, Spain

DOE PAGES

Osman, Wan Adnawani Meor; van Berkum, Peter; León-Barrios, Milagros; ...

2017-09-25

Ensifer meliloti Mlalz-1 (INSDC = ATZD00000000) is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing nodule of Medicago laciniata (L.) Miller from a soil sample collected near the town of Guatiza on the island of Lanzarote, the Canary Islands, Spain. This strain nodulates and forms an effective symbiosis with the highly specific host M. laciniata. This rhizobial genome was sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) sequencing project. Here in this paper, the features of E. meliloti Mlalz-1 are described, together with high-qualitymore » permanent draft genome sequence information and annotation. The 6,664,116 bp high-quality draft genome is arranged in 99 scaffolds of 100 contigs, containing 6314 protein-coding genes and 74 RNA-only encoding genes. Strain Mlalz-1 is closely related to Ensifer meliloti IAM 12611 T, Ensifer medicae A 321T and Ensifer numidicus ORS 1407 T, based on 16S rRNA gene sequences. gANI values of ≥98.1% support the classification of strain Mlalz-1 as E. meliloti . Nodulation of M. laciniata requires a specific nodC allele, and the nodC gene of strain Mlalz-1 shares ≥98% sequence identity with nodC of M. laciniata-nodulating Ensifer strains, but ≤93% with nodC of Ensifer strains that nodulate other Medicago species. Strain Mlalz-1 is unique among sequenced E. meliloti strains in possessing genes encoding components of a T2SS and in having two versions of the adaptive acid tolerance response lpiA-acvB operon. In E. medicae strain WSM419, lpiA is essential for enhancing survival in lethal acid conditions. The second copy of the lpiA-acvB operon of strain Mlalz-1 has highest sequence identity (> 96%) with that of E. medicae strains, which suggests genetic recombination between strain Mlalz-1 and E. medicae and the horizontal gene transfer of lpiA-acvB.« less

Introduction to MacDraft. High-Technology Training Module.

ERIC Educational Resources Information Center

Traxler, Gene

This training module on MacDraft is part of a computer drafting skills unit on communications technology for grades 9-12. The objective is for each student to complete a drawing on the MacIntosh computer using the MacDraft software program. This drawing is to be dimensioned with a dual system and is to include a border and title block. This module…

Design of a Kaplan turbine for a wide range of operating head -Curved draft tube design and model test verification-

NASA Astrophysics Data System (ADS)

KO, Pohan; MATSUMOTO, Kiyoshi; OHTAKE, Norio; DING, Hua

2016-11-01

As for turbomachine off-design performance improvement is challenging but critical for maximising the performing area. In this paper, a curved draft tube for a medium head Kaplan type hydro turbine is introduced and discussed for its significant effect on expanding operating head range. Without adding any extra structure and working fluid for swirl destruction and damping, a carefully designed outline shape of draft tube with the selected placement of center-piers successfully supresses the growth of turbulence eddy and the transport of the swirl to the outlet. Also, more kinetic energy is recovered and the head lost is improved. Finally, the model test results are also presented. The obvious performance improvement was found in the lower net head area, where the maximum efficiency improvement was measured up to 20% without compromising the best efficiency point. Additionally, this design results in a new draft tube more compact in size and so leads to better construction and manufacturing cost performance for prototype. The draft tube geometry parameter designing process was concerning the best efficiency point together with the off-design points covering various water net heads and discharges. The hydraulic performance and flow behavior was numerically previewed and visualized by solving Reynolds-Averaged Navier-Stokes equations with Shear Stress Transport turbulence model. The simulation was under the assumption of steady-state incompressible turbulence flow inside the flow passage, and the inlet boundary condition was the carefully simulated flow pattern from the runner outlet. For confirmation, the corresponding turbine efficiency performance of the entire operating area was verified by model test.

High-quality draft genome sequence of Sedimenticola selenatireducens strain AK4OH1T, a gammaproteobacterium isolated from estuarine sediment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Louie, Tiffany S.; Giovannelli, Donato; Yee, Nathan

Sedimenticola selenatireducens strain AK4OH1 T (= DSM 17993 T = ATCC BAA-1233 T) is a microaerophilic bacterium isolated from sediment from the Arthur Kill intertidal strait between New Jersey and Staten Island, NY. S. selenatireducens is Gram-negative and belongs to the Gammaproteobacteria. Strain AK4OH1 T was the first representative of its genus to be isolated for its unique coupling of the oxidation of aromatic acids to the respiration of selenate. It is a versatile heterotroph and can use a variety of carbon compounds, but can also grow lithoautotrophically under hypoxic and anaerobic conditions. Furthermore, the draft genome comprises 4,588,530 bpmore » and 4276 predicted protein-coding genes including genes for the anaerobic degradation of 4-hydroxybenzoate and benzoate. We report the main features of the genome of S. selenatireducens strain AK4OH1 T.« less

ABACAS: algorithm-based automatic contiguation of assembled sequences

PubMed Central

Assefa, Samuel; Keane, Thomas M.; Otto, Thomas D.; Newbold, Chris; Berriman, Matthew

2009-01-01

Summary: Due to the availability of new sequencing technologies, we are now increasingly interested in sequencing closely related strains of existing finished genomes. Recently a number of de novo and mapping-based assemblers have been developed to produce high quality draft genomes from new sequencing technology reads. New tools are necessary to take contigs from a draft assembly through to a fully contiguated genome sequence. ABACAS is intended as a tool to rapidly contiguate (align, order, orientate), visualize and design primers to close gaps on shotgun assembled contigs based on a reference sequence. The input to ABACAS is a set of contigs which will be aligned to the reference genome, ordered and orientated, visualized in the ACT comparative browser, and optimal primer sequences are automatically generated. Availability and Implementation: ABACAS is implemented in Perl and is freely available for download from http://abacas.sourceforge.net Contact: sa4@sanger.ac.uk PMID:19497936

Draft genome sequence of the novel strain Pseudomonas sp. 10B238 with potential ability to produce antibiotics from deep-sea sediment.

PubMed

Pan, Hua-Qi; Hu, Jiang-Chun

2015-10-01

Pseudomonas sp. 10B238 was a putatively novel species of Pseudomonas, isolated from a deep-sea sediment of the South China Sea, which had the genetic potential to produce secondary metabolites related to nonribosomal peptides (NRPs), as well as showed moderate antimicrobial activities. Here we report a high quality draft genome of Pseudomonas sp. 10B238, which comprises 4,933,052bp with the G+C content of 60.23%. A total of 11 potential secondary metabolite biosynthetic gene clusters were predicted, including a NRP for new peptide siderophore. And many anaerobic respiratory terminal enzymes were found for life in deep-sea environments. Our results may provide insights into biosynthetic pathway for antimicrobial bioactive compounds and be helpful to understand the physiological characteristic of this species. Copyright © 2015 Elsevier B.V. All rights reserved.

High quality permanent draft genome sequence of Phaseolibacter flectens ATCC 12775 T, a plant pathogen of French bean pods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aizenberg-Gershtein, Yana; Izhaki, Ido; Lapidus, Alla

We report that the Phaseolibacter flectens strain ATCC 12775 T (Halpern et al., Int J Syst Evol Microbiol 63:268–273, 2013) is a Gram-negative, rod shaped, motile, aerobic, chemoorganotroph bacterium. Ph. flectens is as a plant-pathogenic bacterium on pods of French bean and was first identified by Johnson (1956) as Pseudomonas flectens. After its phylogenetic position was reexamined, Pseudomonas flectens was transferred to the family Enterobacteriaceae as Phaseolibacter flectens gen. nov., comb. nov. Here we describe the features of this organism, together with the draft genome sequence and annotation. The DNA GC content is 44.34 mol%. The chromosome length is 2,748,442more » bp. It encodes 2,437 proteins and 89 RNA genes. Ph. flectens genome is part of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes study.« less

High quality draft genome sequence and analysis of Pontibacter roseus type strain SRC-1T (DSM 17521T) isolated from muddy waters of a drainage system in Chandigarh, India

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mukherjee, Supratim; Lapidus, Alla; Shapiro, Nicole

2015-01-01

Pontibacter roseus Suresh et al 2006 is a member of genus Pontibacter family Cytophagaceae, class Cytophagia. While the type species of the genus Pontibacter actiniarum was isolated in 2005 from a marine environment, subsequent species of the same genus have been found in different types of habitats ranging from seawater, sediment, desert soil, rhizosphere, contaminated sites, solar saltern and muddy water. Here we describe the features of Pontibacter roseus strain SRC-1T along with its complete genome sequence and annotation from a culture of DSM 17521T. The 4,581,480 bp long draft genome consists of 12 scaffolds with 4,003 protein-coding and 50more » RNA genes and is a part of Genomic encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG-I) project.« less

High-quality draft genome sequence of Sedimenticola selenatireducens strain AK4OH1T, a gammaproteobacterium isolated from estuarine sediment

DOE PAGES

Louie, Tiffany S.; Giovannelli, Donato; Yee, Nathan; ...

2016-09-08

Sedimenticola selenatireducens strain AK4OH1 T (= DSM 17993 T = ATCC BAA-1233 T) is a microaerophilic bacterium isolated from sediment from the Arthur Kill intertidal strait between New Jersey and Staten Island, NY. S. selenatireducens is Gram-negative and belongs to the Gammaproteobacteria. Strain AK4OH1 T was the first representative of its genus to be isolated for its unique coupling of the oxidation of aromatic acids to the respiration of selenate. It is a versatile heterotroph and can use a variety of carbon compounds, but can also grow lithoautotrophically under hypoxic and anaerobic conditions. Furthermore, the draft genome comprises 4,588,530 bpmore » and 4276 predicted protein-coding genes including genes for the anaerobic degradation of 4-hydroxybenzoate and benzoate. We report the main features of the genome of S. selenatireducens strain AK4OH1 T.« less

High quality permanent draft genome sequence of Phaseolibacter flectens ATCC 12775 T, a plant pathogen of French bean pods

DOE PAGES

Aizenberg-Gershtein, Yana; Izhaki, Ido; Lapidus, Alla; ...

2016-01-13

We report that the Phaseolibacter flectens strain ATCC 12775 T (Halpern et al., Int J Syst Evol Microbiol 63:268–273, 2013) is a Gram-negative, rod shaped, motile, aerobic, chemoorganotroph bacterium. Ph. flectens is as a plant-pathogenic bacterium on pods of French bean and was first identified by Johnson (1956) as Pseudomonas flectens. After its phylogenetic position was reexamined, Pseudomonas flectens was transferred to the family Enterobacteriaceae as Phaseolibacter flectens gen. nov., comb. nov. Here we describe the features of this organism, together with the draft genome sequence and annotation. The DNA GC content is 44.34 mol%. The chromosome length is 2,748,442more » bp. It encodes 2,437 proteins and 89 RNA genes. Ph. flectens genome is part of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes study.« less

High quality draft genome sequence and analysis of Pontibacter roseus type strain SRC-1T (DSM 17521T) isolated from muddy waters of a drainage system in Chandigarh, India

DOE PAGES

Mukherjee, Supratim; Lapidus, Alla; Shapiro, Nicole; ...

2015-02-09

Pontibacter roseus is a member of genus Pontibacter family Cytophagaceae, class Cytophagia. While the type species of the genus Pontibacter actiniarum was isolated in 2005 from a marine environment, subsequent species of the same genus have been found in different types of habitats ranging from seawater, sediment, desert soil, rhizosphere, contaminated sites, solar saltern and muddy water. Here we describe the features of Pontibacter roseus strain SRC-1 T along with its complete genome sequence and annotation from a culture of DSM 17521 T. In conclusion, the 4,581,480 bp long draft genome consists of 12 scaffolds with 4,003 protein-coding and 50more » RNA genes and is a part of Genomic Encyclopedia of Type Strains: KMG-I project.« less

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds.

PubMed

Dudchenko, Olga; Batra, Sanjit S; Omer, Arina D; Nyquist, Sarah K; Hoeger, Marie; Durand, Neva C; Shamim, Muhammad S; Machol, Ido; Lander, Eric S; Aiden, Aviva Presser; Aiden, Erez Lieberman

2017-04-07

The Zika outbreak, spread by the Aedes aegypti mosquito, highlights the need to create high-quality assemblies of large genomes in a rapid and cost-effective way. Here we combine Hi-C data with existing draft assemblies to generate chromosome-length scaffolds. We validate this method by assembling a human genome, de novo, from short reads alone (67× coverage). We then combine our method with draft sequences to create genome assemblies of the mosquito disease vectors Ae aegypti and Culex quinquefasciatus , each consisting of three scaffolds corresponding to the three chromosomes in each species. These assemblies indicate that almost all genomic rearrangements among these species occur within, rather than between, chromosome arms. The genome assembly procedure we describe is fast, inexpensive, and accurate, and can be applied to many species. Copyright © 2017, American Association for the Advancement of Science.

Genome sequence of the dark pink pigmented Listia bainesii microsymbiont Methylobacterium sp. WSM2598

PubMed Central

2014-01-01

Strains of a pink-pigmented Methylobacterium sp. are effective nitrogen- (N2) fixing microsymbionts of species of the African crotalarioid genus Listia. Strain WSM2598 is an aerobic, motile, Gram-negative, non-spore-forming rod isolated in 2002 from a Listia bainesii root nodule collected at Estcourt Research Station in South Africa. Here we describe the features of Methylobacterium sp. WSM2598, together with information and annotation of a high-quality draft genome sequence. The 7,669,765 bp draft genome is arranged in 5 scaffolds of 83 contigs, contains 7,236 protein-coding genes and 18 RNA-only encoding genes. This rhizobial genome is one of 100 sequenced as part of the DOE Joint Genome Institute 2010 G enomic E ncyclopedia for B acteria and A rchaea- R oot N odule B acteria (GEBA-RNB) project. PMID:25780498

Genome sequence of the dark pink pigmented Listia bainesii microsymbiont Methylobacterium sp. WSM2598.

PubMed

Ardley, Julie; Tian, Rui; Howieson, John; Yates, Ron; Bräu, Lambert; Han, James; Lobos, Elizabeth; Huntemann, Marcel; Chen, Amy; Mavromatis, Konstantinos; Markowitz, Victor; Ivanova, Natalia; Pati, Amrita; Goodwin, Lynne; Woyke, Tanja; Kyrpides, Nikos; Reeve, Wayne

2014-01-01

Strains of a pink-pigmented Methylobacterium sp. are effective nitrogen- (N2) fixing microsymbionts of species of the African crotalarioid genus Listia. Strain WSM2598 is an aerobic, motile, Gram-negative, non-spore-forming rod isolated in 2002 from a Listia bainesii root nodule collected at Estcourt Research Station in South Africa. Here we describe the features of Methylobacterium sp. WSM2598, together with information and annotation of a high-quality draft genome sequence. The 7,669,765 bp draft genome is arranged in 5 scaffolds of 83 contigs, contains 7,236 protein-coding genes and 18 RNA-only encoding genes. This rhizobial genome is one of 100 sequenced as part of the DOE Joint Genome Institute 2010 G enomic E ncyclopedia for B acteria and A rchaea- R oot N odule B acteria (GEBA-RNB) project.

Climate and Land Use Change Effects on Ecological Resources in Three Watersheds: A Synthesis Report (External Review Draft)

EPA Science Inventory

The purpose of this draft report is to provide a summary of climate change impacts to selected watersheds and recommendations for how to improve the process of conducting watershed assessments in the future.

Clinical Practice Guideline: Safe Medication Use in the ICU.

PubMed

Kane-Gill, Sandra L; Dasta, Joseph F; Buckley, Mitchell S; Devabhakthuni, Sandeep; Liu, Michael; Cohen, Henry; George, Elisabeth L; Pohlman, Anne S; Agarwal, Swati; Henneman, Elizabeth A; Bejian, Sharon M; Berenholtz, Sean M; Pepin, Jodie L; Scanlon, Mathew C; Smith, Brian S

2017-09-01

To provide ICU clinicians with evidence-based guidance on safe medication use practices for the critically ill. PubMed, Cochrane Database of Systematic Reviews, Cochrane Central Register of Controlled Trials, CINAHL, Scopus, and ISI Web of Science for relevant material to December 2015. Based on three key components: 1) environment and patients, 2) the medication use process, and 3) the patient safety surveillance system. The committee collectively developed Population, Intervention, Comparator, Outcome questions and quality of evidence statements pertaining to medication errors and adverse drug events addressing the key components. A total of 34 Population, Intervention, Comparator, Outcome questions, five quality of evidence statements, and one commentary on disclosure was developed. Subcommittee members were assigned selected Population, Intervention, Comparator, Outcome questions or quality of evidence statements. Subcommittee members completed their Grading of Recommendations Assessment, Development, and Evaluation of the question with his/her quality of evidence assessment and proposed strength of recommendation, then the draft was reviewed by the relevant subcommittee. The subcommittee collectively reviewed the evidence profiles for each question they developed. After the draft was discussed and approved by the entire committee, then the document was circulated among all members for voting on the quality of evidence and strength of recommendation. The committee followed the principles of the Grading of Recommendations Assessment, Development, and Evaluation system to determine quality of evidence and strength of recommendations. This guideline evaluates the ICU environment as a risk for medication-related events and the environmental changes that are possible to improve safe medication use. Prevention strategies for medication-related events are reviewed by medication use process node (prescribing, distribution, administration, monitoring). Detailed considerations to an active surveillance system that includes reporting, identification, and evaluation are discussed. Also, highlighted is the need for future research for safe medication practices that is specific to critically ill patients.

NIH state-of-the-science conference statement: Enhancing use and quality of colorectal cancer screening.

PubMed

Steinwachs, Donald; Allen, Jennifer Dacey; Barlow, William Eric; Duncan, R Paul; Egede, Leonard E; Friedman, Lawrence S; Keating, Nancy L; Kim, Paula; Lave, Judith R; LaVeist, Thomas A; Ness, Roberta B; Optican, Robert J; Virnig, Beth A

2010-02-04

To provide health care providers, patients, and the general public with a responsible assessment of currently available data on enhancing use and quality of colorectal cancer screening. A non-DHHS, nonadvocate 13-member panel representing the fields of cancer surveillance, health services research, community-based research, informed decision-making, access to care, health care policy, health communication, health economics, health disparities, epidemiology, statistics, thoracic radiology, internal medicine, gastroenterology, public health, end-of-life care, and a public representative. In addition, 20 experts from pertinent fields presented data to the panel and conference audience. Presentations by experts and a systematic review of the literature prepared by the RTI International-University of North Carolina Evidence-based Practice Center, through the Agency for Healthcare Research and Quality. Scientific evidence was given precedence over anecdotal experience. The panel drafted its statement based on scientific evidence presented in open forum and on published scientific literature. The draft statement was presented on the final day of the conference and circulated to the audience for comment. The panel released a revised statement later that day at http://consensus.nih.gov. This statement is an independent report of the panel and is not a policy statement of the NIH or the Federal Government. The panel found that despite substantial progress toward higher colorectal cancer screening rates nationally, screening rates fall short of desirable levels. Targeted initiatives to improve screening rates and reduce disparities in underscreened communities and population subgroups could further reduce colorectal cancer morbidity and mortality. This could be achieved by utilizing the full range of screening options and evidence-based interventions for increasing screening rates. With additional investments in quality monitoring, Americans could be assured that all screening achieves high rates of cancer prevention and early detection. To close the gap in screening, this report identifies the following priority areas for implementation and research to enhance the use and quality of colorectal cancer screening: • Eliminate financial barriers to colorectal cancer screening and appropriate follow up. • Widely implement interventions that have proven effective at increasing colorectal cancer screening, including patient reminder systems and one-on-one interactions with providers, educators, or navigators. • Conduct research to assess the effectiveness of tailoring programs to match the characteristics and preferences of target population groups to increase colorectal cancer screening. • Implement systems to ensure appropriate follow-up of positive colorectal cancer screening results. • Develop systems to assure high quality of colorectal cancer screening programs. • Conduct studies to determine the comparative effectiveness of the various colorectal cancer screening methods in usual practice settings.

Automated drafting system uses computer techniques

NASA Technical Reports Server (NTRS)

Millenson, D. H.

1966-01-01

Automated drafting system produces schematic and block diagrams from the design engineers freehand sketches. This system codes conventional drafting symbols and their coordinate locations on standard size drawings for entry on tapes that are used to drive a high speed photocomposition machine.

Advancing palliative care in the Uganda health system: an evidence-based policy brief.

PubMed

Nabudere, Harriet; Obuku, Ekwaro; Lamorde, Mohammed

2014-12-01

This paper describes the development and findings for a policy brief on "Advancing the Integration of Palliative Care into the National Health System" and the subsequent use of this report. Key stakeholders involved with palliative care helped identify the problem and potential policy solutions to scale up these services within the health system. A working group of national stakeholder representatives and external reviewers commented on and contributed to successive drafts of the report. Research describing the problem, policy options and implementation considerations was identified by reviewing government documents, routinely collected data, electronic literature searches, contact with key informants, and reviewing the reference lists of relevant documents that were retrieved. The palliative burden is not only high but increasing due to the rise in population and life expectancy. A few options for holistic, supportive care include: Home-based care increases chances of a peaceful death for the terminally ill surrounded by their loved ones; supporting informal caregivers improves their quality of life and discharge planning reduces unscheduled admissions and has the potential to free up capacity for acute care services. A combination of strategies is needed to effectively implement the proposed options as discussed further in this article. The policy brief report was used as a background document for two stakeholder dialogues whose main outcome was that a comprehensive national palliative care policy should be instituted to include all the options, which need to be integrated within the public health system. A draft policy is now in process.

Genome sequence of the mud-dwelling archaeon Methanoplanus limicola type strain (DSM 2279 T), reclassification of Methanoplanus petrolearius as Methanolacinia petrolearia and emended descriptions of the genera Methanoplanus and Methanolacinia

DOE PAGES

Goker, Markus; Lu, Megan; Fiebig, Anne; ...

2014-06-15

Methanoplanus limicola Wildgruber et al. 1984 is a mesophilic methanogen that was isolated from a swamp composed of drilling waste near Naples, Italy, shortly after the Archaea were recognized as a separate domain of life. Methanoplanus is the type genus in the family Methanoplanaceae, a taxon that felt into disuse since modern 16S rRNA gene sequences-based taxonomy was established. Methanoplanus is now placed within the Methanomicrobiaceae, a family that is so far poorly characterized at the genome level. The only other type strain of the genus with a sequenced genome, Methanoplanus petrolearius SEBR 4847 T, turned out to be misclassifiedmore » and required reclassification to Methanolacinia. Both, Methanoplanus and Methanolacinia, needed taxonomic emendations due to a significant deviation of the G+C content of their genomes from previously published (pregenome-sequence era) values. Until now genome sequences were published for only four of the 33 species with validly published names in the Methanomicrobiaceae. Here we describe the features of M. limicola, together with the improved-high-quality draft genome sequence and an notation of the type strain, M3 T. The 3,200,946 bp long chromosome (permanent draft sequence) with its 3,064 protein-coding and 65 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.« less

High-Quality Draft Genome Sequence of Desulfovibrio carbinoliphilus FW-101-2B, an Organic Acid-Oxidizing Sulfate-Reducing Bacterium Isolated from Uranium(VI)-Contaminated Groundwater

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ramsay, Bradley D.; Hwang, Chiachi; Woo, Hannah L.

2015-03-12

Desulfovibrio carbinoliphilus subsp. oakridgensis FW-101-2B is an anaerobic, organic acid/alcohol-oxidizing, sulfate-reducing δ-proteobacterium. FW-101-2B was isolated from contaminated groundwater at The Field Research Center at Oak Ridge National Lab after in situ stimulation for heavy metal-reducing conditions. The genome will help elucidate the metabolic potential of sulfate-reducing bacteria during uranium reduction.

Early Childhood Standards of Quality for Prekindergarten through Second Grade.

ERIC Educational Resources Information Center

Michigan State Board of Education, Lansing.

Recognizing the value and need for quality early childhood education programs for children ages four through eight years, the Michigan State Board of Education appointed an ad hoc committee to develop standards of quality. Based on the draft developed by this committee, this standards guide is designed to assist administrators, teachers, and…

78 FR 29016 - Establishing Quality Assurance Programs for Packaging Used in Transport of Radioactive Material

Federal Register 2010, 2011, 2012, 2013, 2014

2013-05-16

... Establishing Quality Assurance Programs for Packaging Used in Transport of Radioactive Material AGENCY: Nuclear..., ``Establishing Quality Assurance Programs for Packaging Used in Transport of Radioactive Material.'' This draft... regulations for the packaging and transportation of radioactive material in Part 71 of Title 10 of the Code of...

78 FR 53777 - Notice of Availability of the Draft Visual Resource Management and Areas of Critical...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-30

... species, a unique sand dune community and habitat, the desert kangaroo rat, and for scenic quality. The... criteria: McCarty Canyon; for scenic quality and wildlife habitat; Seminoe and Pathfinder Reservoirs; for sensitive plant species, scenic quality, and wildlife habitat; Flattop Mountain; for sensitive plant species...

High-quality permanent draft genome sequence of Ensifer medicae strain WSM244, a microsymbiont isolated from Medicago polymorpha growing in alkaline soil

DOE PAGES

Ardley, Julie; Tian, Rui; O’Hara, Graham; ...

2015-12-01

We report that Ensifer medicae WSM244 is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of Medicago species. WSM244 was isolated in 1979 from a nodule recovered from the roots of the annual Medicago polymorpha L. growing in alkaline soil (pH 8.0) in Tel Afer, Iraq. WSM244 is the only acid-sensitive E. medicae strain that has been sequenced to date. It is effective at fixing nitrogen with M. polymorpha L., as well as with more alkaline-adapted Medicago spp. such as M. littoralis Loisel., M. scutellata (L.) Mill., M. tornata (L.)more » Mill. and M. truncatula Gaertn. This strain is also effective with the perennial M. sativa L. Here we describe the features of E. medicae WSM244, together with genome sequence information and its annotation. The 6,650,282 bp high-quality permanent draft genome is arranged into 91 scaffolds of 91 contigs containing 6,427 protein-coding genes and 68 RNA-only encoding genes, and is one of the rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project proposal.« less

High-quality permanent draft genome sequence of Ensifer medicae strain WSM244, a microsymbiont isolated from Medicago polymorpha growing in alkaline soil

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ardley, Julie; Tian, Rui; O’Hara, Graham

We report that Ensifer medicae WSM244 is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of Medicago species. WSM244 was isolated in 1979 from a nodule recovered from the roots of the annual Medicago polymorpha L. growing in alkaline soil (pH 8.0) in Tel Afer, Iraq. WSM244 is the only acid-sensitive E. medicae strain that has been sequenced to date. It is effective at fixing nitrogen with M. polymorpha L., as well as with more alkaline-adapted Medicago spp. such as M. littoralis Loisel., M. scutellata (L.) Mill., M. tornata (L.)more » Mill. and M. truncatula Gaertn. This strain is also effective with the perennial M. sativa L. Here we describe the features of E. medicae WSM244, together with genome sequence information and its annotation. The 6,650,282 bp high-quality permanent draft genome is arranged into 91 scaffolds of 91 contigs containing 6,427 protein-coding genes and 68 RNA-only encoding genes, and is one of the rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project proposal.« less

Emerging Genomic Tools for Legume Breeding: Current Status and Future Prospects

PubMed Central

Pandey, Manish K.; Roorkiwal, Manish; Singh, Vikas K.; Ramalingam, Abirami; Kudapa, Himabindu; Thudi, Mahendar; Chitikineni, Anu; Rathore, Abhishek; Varshney, Rajeev K.

2016-01-01

Legumes play a vital role in ensuring global nutritional food security and improving soil quality through nitrogen fixation. Accelerated higher genetic gains is required to meet the demand of ever increasing global population. In recent years, speedy developments have been witnessed in legume genomics due to advancements in next-generation sequencing (NGS) and high-throughput genotyping technologies. Reference genome sequences for many legume crops have been reported in the last 5 years. The availability of the draft genome sequences and re-sequencing of elite genotypes for several important legume crops have made it possible to identify structural variations at large scale. Availability of large-scale genomic resources and low-cost and high-throughput genotyping technologies are enhancing the efficiency and resolution of genetic mapping and marker-trait association studies. Most importantly, deployment of molecular breeding approaches has resulted in development of improved lines in some legume crops such as chickpea and groundnut. In order to support genomics-driven crop improvement at a fast pace, the deployment of breeder-friendly genomics and decision support tools seems appear to be critical in breeding programs in developing countries. This review provides an overview of emerging genomics and informatics tools/approaches that will be the key driving force for accelerating genomics-assisted breeding and ultimately ensuring nutritional and food security in developing countries. PMID:27199998

Adding Realism to Technical Drafting Programs

ERIC Educational Resources Information Center

Weaver, Gerald L.

1976-01-01

Suggestions for improved, relevant technical drafting programs are presented: (1) making realistic assignments, (2) viewing real projects, (3) duplicating industrial projects, (4) practicing lettering, (5) conducting research, (6) engaging in teamwork, (7) adapting to change, (8) learning to meet deadlines, and (9) stressing the importance of…

Alliance Helps States Map New Terrain in Educator Evaluation. REL West Research Digest

ERIC Educational Resources Information Center

Regional Educational Laboratory West, 2014

2014-01-01

About five years ago, states across the country took on the huge, complex task of developing and implementing new systems to evaluate teacher and principal performance in public schools. In response to a federal mandate aimed at improving student achievement, especially in the lowest performing schools, state boards of education drafted high-level…

75 FR 39325 - Notice of Draft Finding of No Significant Impact for the Washington State Portion of the Pacific...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-08

... Washington State is to improve intercity passenger rail service by reducing travel times, achieving greater... intercity travel demand. To achieve these goals WSDOT applied for federal funding through the High Speed Intercity Passenger Rail Program (HSIPR Program) administered by the FRA and funded by the American Recovery...

Iterative Design and Classroom Evaluation of Automated Formative Feedback for Improving Peer Feedback Localization

ERIC Educational Resources Information Center

Nguyen, Huy; Xiong, Wenting; Litman, Diane

2017-01-01

A peer-review system that automatically evaluates and provides formative feedback on free-text feedback comments of students was iteratively designed and evaluated in college and high-school classrooms. Classroom assignments required students to write paper drafts and submit them to a peer-review system. When student peers later submitted feedback…

Microbiological diversity and prevalence of spoilage and pathogenic bacteria in commercial fermented alcoholic beverages (beer, fruit wine, refined rice wine, and yakju).

PubMed

Jeon, Se Hui; Kim, Nam Hee; Shim, Moon Bo; Jeon, Young Wook; Ahn, Ji Hye; Lee, Soon Ho; Hwang, In Gyun; Rhee, Min Suk

2015-04-01

The present study examined 469 commercially available fermented alcoholic beverages (FABs), including beer (draft, microbrewed, and pasteurized), fruit wine (grape and others), refined rice wine, and yakju (raw and pasteurized). Samples were screened for Escherichia coli and eight foodborne pathogens (Bacillus cereus, Campylobacter jejuni, Clostridium perfringens, Escherichia coli O157:H7, Listeria monocytogenes, Salmonella spp., Staphylococcus aureus, and Yersinia enterocolitica), and the aerobic plate count, lactic acid bacteria, acetic acid bacteria, fungi, and total coliforms were also enumerated. Microbrewed beer contained the highest number of microorganisms (average aerobic plate count, 3.5; lactic acid bacteria, 2.1; acetic acid bacteria, 2.0; and fungi, 3.6 log CFU/ml), followed by draft beer and yakju (P < 0.05), whereas the other FABs contained , 25 CFU/25 ml microorganisms. Unexpectedly, neither microbial diversity nor microbial count correlated with the alcohol content (4.7 to 14.1%) or pH (3.4 to 4.2) of the product. Despite the harsh conditions, coliforms (detected in 23.8% of microbrewed beer samples) and B. cereus (detected in all FABs) were present in some products. B. cereus was detected most frequently in microbrewed beer (54.8% of samples) and nonpasteurized yakju (50.0%), followed by pasteurized yakju (28.8%), refined rice wine (25.0%), other fruit wines (12.3%), grape wine (8.6%), draft beer (5.6%), and pasteurized beer (2.2%) (P < 0.05). The finding that spore-forming B. cereus and coliform bacteria can survive the harsh conditions present in alcoholic beverages should be taken into account (alongside traditional quality indicators such as the presence of lactic acid-producing bacteria, acetic acid-producing bacteria, or both) when developing manufacturing systems and methods to prolong the shelf life of high-quality FAB products. New strategic quality management plans for various FABs are needed.

Air Quality Criteria for Lead (First External Review Draft)

EPA Science Inventory

Background:

The Clean Air Act mandates periodic review of the National Ambient Air Quality Standards (NAAQS) for six common air pollutants, also referred to as criteria pollutants, including lead. Under the review process, EPA's Office of Research and Development d...

Develop nondestructive rapid pavement quality assurance/quality control evaluation test methods and supporting technology : project summary.

DOT National Transportation Integrated Search

2017-01-01

The findings from the proof of concept with mechanics-based models for flexible base suggest additional validation work should be performed, draft construction specification frameworks should be developed, and work extending the technology to stabili...

Develop nondestructive rapid pavement quality Assurance/quality control evaluation test methods and supporting technology : project summary.

DOT National Transportation Integrated Search

2017-01-01

The findings from the proof of concept with mechanics-based models for flexible base suggest additional validation work should be performed, draft construction specification frameworks should be developed, and work extending the technology to stabili...

Reducing assembly complexity of microbial genomes with single-molecule sequencing.

PubMed

Koren, Sergey; Harhay, Gregory P; Smith, Timothy P L; Bono, James L; Harhay, Dayna M; Mcvey, Scott D; Radune, Diana; Bergman, Nicholas H; Phillippy, Adam M

2013-01-01

The short reads output by first- and second-generation DNA sequencing instruments cannot completely reconstruct microbial chromosomes. Therefore, most genomes have been left unfinished due to the significant resources required to manually close gaps in draft assemblies. Third-generation, single-molecule sequencing addresses this problem by greatly increasing sequencing read length, which simplifies the assembly problem. To measure the benefit of single-molecule sequencing on microbial genome assembly, we sequenced and assembled the genomes of six bacteria and analyzed the repeat complexity of 2,267 complete bacteria and archaea. Our results indicate that the majority of known bacterial and archaeal genomes can be assembled without gaps, at finished-grade quality, using a single PacBio RS sequencing library. These single-library assemblies are also more accurate than typical short-read assemblies and hybrid assemblies of short and long reads. Automated assembly of long, single-molecule sequencing data reduces the cost of microbial finishing to $1,000 for most genomes, and future advances in this technology are expected to drive the cost lower. This is expected to increase the number of completed genomes, improve the quality of microbial genome databases, and enable high-fidelity, population-scale studies of pan-genomes and chromosomal organization.

A High-Resolution SNP Array-Based Linkage Map Anchors a New Domestic Cat Draft Genome Assembly and Provides Detailed Patterns of Recombination.

PubMed

Li, Gang; Hillier, LaDeana W; Grahn, Robert A; Zimin, Aleksey V; David, Victor A; Menotti-Raymond, Marilyn; Middleton, Rondo; Hannah, Steven; Hendrickson, Sher; Makunin, Alex; O'Brien, Stephen J; Minx, Pat; Wilson, Richard K; Lyons, Leslie A; Warren, Wesley C; Murphy, William J

2016-06-01

High-resolution genetic and physical maps are invaluable tools for building accurate genome assemblies, and interpreting results of genome-wide association studies (GWAS). Previous genetic and physical maps anchored good quality draft assemblies of the domestic cat genome, enabling the discovery of numerous genes underlying hereditary disease and phenotypes of interest to the biomedical science and breeding communities. However, these maps lacked sufficient marker density to order thousands of shorter scaffolds in earlier assemblies, which instead relied heavily on comparative mapping with related species. A high-resolution map would aid in validating and ordering chromosome scaffolds from existing and new genome assemblies. Here, we describe a high-resolution genetic linkage map of the domestic cat genome based on genotyping 453 domestic cats from several multi-generational pedigrees on the Illumina 63K SNP array. The final maps include 58,055 SNP markers placed relative to 6637 markers with unique positions, distributed across all autosomes and the X chromosome. Our final sex-averaged maps span a total autosomal length of 4464 cM, the longest described linkage map for any mammal, confirming length estimates from a previous microsatellite-based map. The linkage map was used to order and orient the scaffolds from a substantially more contiguous domestic cat genome assembly (Felis catus v8.0), which incorporated ∼20 × coverage of Illumina fragment reads. The new genome assembly shows substantial improvements in contiguity, with a nearly fourfold increase in N50 scaffold size to 18 Mb. We use this map to report probable structural errors in previous maps and assemblies, and to describe features of the recombination landscape, including a massive (∼50 Mb) recombination desert (of virtually zero recombination) on the X chromosome that parallels a similar desert on the porcine X chromosome in both size and physical location. Copyright © 2016 Li et al.

Draft Genome Sequence of Lactobacillus helveticus ATCC 12046

PubMed Central

2018-01-01

ABSTRACT Lactobacillus helveticus is a lactic acid bacterium used traditionally in the dairy industry, especially in the manufacture of cheeses. We present here the 2,141,841-bp draft genome sequence of L. helveticus strain ATCC 12046, a potential starter strain for improving cheese production. PMID:29449405

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

PubMed Central

Parks, Donovan H.; Imelfort, Michael; Skennerton, Connor T.; Hugenholtz, Philip; Tyson, Gene W.

2015-01-01

Large-scale recovery of genomes from isolates, single cells, and metagenomic data has been made possible by advances in computational methods and substantial reductions in sequencing costs. Although this increasing breadth of draft genomes is providing key information regarding the evolutionary and functional diversity of microbial life, it has become impractical to finish all available reference genomes. Making robust biological inferences from draft genomes requires accurate estimates of their completeness and contamination. Current methods for assessing genome quality are ad hoc and generally make use of a limited number of “marker” genes conserved across all bacterial or archaeal genomes. Here we introduce CheckM, an automated method for assessing the quality of a genome using a broader set of marker genes specific to the position of a genome within a reference genome tree and information about the collocation of these genes. We demonstrate the effectiveness of CheckM using synthetic data and a wide range of isolate-, single-cell-, and metagenome-derived genomes. CheckM is shown to provide accurate estimates of genome completeness and contamination and to outperform existing approaches. Using CheckM, we identify a diverse range of errors currently impacting publicly available isolate genomes and demonstrate that genomes obtained from single cells and metagenomic data vary substantially in quality. In order to facilitate the use of draft genomes, we propose an objective measure of genome quality that can be used to select genomes suitable for specific gene- and genome-centric analyses of microbial communities. PMID:25977477

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes.

PubMed

Parks, Donovan H; Imelfort, Michael; Skennerton, Connor T; Hugenholtz, Philip; Tyson, Gene W

2015-07-01

Large-scale recovery of genomes from isolates, single cells, and metagenomic data has been made possible by advances in computational methods and substantial reductions in sequencing costs. Although this increasing breadth of draft genomes is providing key information regarding the evolutionary and functional diversity of microbial life, it has become impractical to finish all available reference genomes. Making robust biological inferences from draft genomes requires accurate estimates of their completeness and contamination. Current methods for assessing genome quality are ad hoc and generally make use of a limited number of "marker" genes conserved across all bacterial or archaeal genomes. Here we introduce CheckM, an automated method for assessing the quality of a genome using a broader set of marker genes specific to the position of a genome within a reference genome tree and information about the collocation of these genes. We demonstrate the effectiveness of CheckM using synthetic data and a wide range of isolate-, single-cell-, and metagenome-derived genomes. CheckM is shown to provide accurate estimates of genome completeness and contamination and to outperform existing approaches. Using CheckM, we identify a diverse range of errors currently impacting publicly available isolate genomes and demonstrate that genomes obtained from single cells and metagenomic data vary substantially in quality. In order to facilitate the use of draft genomes, we propose an objective measure of genome quality that can be used to select genomes suitable for specific gene- and genome-centric analyses of microbial communities. © 2015 Parks et al.; Published by Cold Spring Harbor Laboratory Press.

Strategies for addressing barriers to publishing pediatric quality improvement research.

PubMed

Van Cleave, Jeanne; Dougherty, Denise; Perrin, James M

2011-09-01

Advancing the science of quality improvement (QI) requires dissemination of the results of QI. However, the results of few QI interventions reach publication. To identify barriers to publishing results of pediatric QI research and provide practical strategies that QI researchers can use to enhance publishability of their work. We reviewed and summarized a workshop conducted at the Pediatric Academic Societies 2007 meeting in Toronto, Ontario, Canada, on conducting and publishing QI research. We also interviewed 7 experts (QI researchers, administrators, journal editors, and health services researchers who have reviewed QI manuscripts) about common reasons that QI research fails to reach publication. We also reviewed recently published pediatric QI articles to find specific examples of tactics to enhance publishability, as identified in interviews and the workshop. We found barriers at all stages of the QI process, from identifying an appropriate quality issue to address to drafting the manuscript. Strategies for overcoming these barriers included collaborating with research methodologists, creating incentives to publish, choosing a study design to include a control group, increasing sample size through research networks, and choosing appropriate process and clinical quality measures. Several well-conducted, successfully published QI studies in pediatrics offer guidance to other researchers in implementing these strategies in their own work. Specific, feasible approaches can be used to improve opportunities for publication in pediatric, QI, and general medical journals.

Thermo-hydrological and chemical (THC) modeling to support Field Test Design

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stauffer, Philip H.; Jordan, Amy B.; Harp, Dylan Robert

This report summarizes ongoing efforts to simulate coupled thermal-hydrological-chemical (THC) processes occurring within a hypothetical high-level waste (HLW) repository in bedded salt. The report includes work completed since the last project deliverable, “Coupled model for heat and water transport in a high level waste repository in salt”, a Level 2 milestone submitted to DOE in September 2013 (Stauffer et al., 2013). Since the last deliverable, there have been code updates to improve the integration of the salt module with the pre-existing code and development of quality assurance (QA) tests of constitutive functions and precipitation/dissolution reactions. Simulations of bench-scale experiments, bothmore » historical and currently in the planning stages have been performed. Additional simulations have also been performed on the drift-scale model that incorporate new processes, such as an evaporation function to estimate water vapor removal from the crushed salt backfill and isotopic fractionation of water isotopes. Finally, a draft of a journal paper on the importance of clay dehydration on water availability is included as Appendix I.« less

Quantitative and qualitative analysis on the legislative production relating to healthcare in passage in the National Congress in the years 2007 and 2008.

PubMed

Santos, Viviane Cristina dos; Ferraz, Marcos Bosi

2013-01-01

The Federal Constitution of 1988 allowed the National Congress to contribute towards formulation of new public policies. The objective of this study was to analyze the legislative production that dealt with health issues that was in passage in the National Congress between January 2007 and December 2008. Descriptive-exploratory cross-sectional study with quantitative and qualitative approaches, conducted in a federal university. The analysis material for the study comprised 144 draft bills that were classified and subsequently randomly evaluated by 155 professionals working within the healthcare system. The analysis showed that the Workers' Party (PT) and Brazilian Democratic Movement Party (PMDB) were the parties that presented the largest proportions of the draft bills (12.5% and 11.1%); 25.4% of the draft bills were presented by congress members with academic qualifications within healthcare and only 1.4% of the draft bills became transformed into legal regulations. In questionnaire responses, 51.5% of the evaluators did not consider the draft bills to be viable, 40.6% did not consider them to be relevant and 52.5% said that if the draft bills were not approved it would not be harmful to Brazilian society. In analyzing the data from this study, it was noted that the legislative production relating to healthcare was low and the transformation rate from draft bill to legal regulation was negligible. The results from the evaluation showed that the quality of legislative production was impaired.

AIR QUALITY CRITERIA FOR LEAD, VOLUMES 1-4. (1983) FIRST EXTERNAL REVIEW DRAFT

EPA Science Inventory

The document evaluates and assesses scientific information on the health and welfare effects associated with exposure to various concentrations of lead in ambient air. The literature through 1983 has been reviewed thoroughly for information relevant to air quality criteria, altho...

AIR QUALITY CRITERIA FOR LEAD (SECOND EXTERNAL REVIEW DRAFT)

EPA Science Inventory

The Clean Air Act mandates periodic review of the National Ambient Air Quality Standards (NAAQS) for six common air pollutants, also referred to as criteria pollutants, including lead. Under the review process, EPA's Office of Research and Development develops a criteria docu...