Methodology to Estimate the Quantity, Composition, and ...

EPA Pesticide Factsheets

This report, Methodology to Estimate the Quantity, Composition and Management of Construction and Demolition Debris in the US, was developed to expand access to data on CDD in the US and to support research on CDD and sustainable materials management. Since past US EPA CDD estimates have been limited to building-related CDD, a goal in the development of this methodology was to use data originating from CDD facilities and contractors to better capture the current picture of total CDD management, including materials from roads, bridges and infrastructure. This report, Methodology to Estimate the Quantity, Composition and Management of Construction and Demolition Debris in the US, was developed to expand access to data on CDD in the US and to support research on CDD and sustainable materials management. Since past US EPA CDD estimates have been limited to building-related CDD, a goal in the development of this methodology was to use data originating from CDD facilities and contractors to better capture the current picture of total CDD management, including materials from roads, bridges and infrastructure.

Automated hierarchical classification of protein domain subfamilies based on functionally-divergent residue signatures

PubMed Central

2012-01-01

Background The NCBI Conserved Domain Database (CDD) consists of a collection of multiple sequence alignments of protein domains that are at various stages of being manually curated into evolutionary hierarchies based on conserved and divergent sequence and structural features. These domain models are annotated to provide insights into the relationships between sequence, structure and function via web-based BLAST searches. Results Here we automate the generation of conserved domain (CD) hierarchies using a combination of heuristic and Markov chain Monte Carlo (MCMC) sampling procedures and starting from a (typically very large) multiple sequence alignment. This procedure relies on statistical criteria to define each hierarchy based on the conserved and divergent sequence patterns associated with protein functional-specialization. At the same time this facilitates the sequence and structural annotation of residues that are functionally important. These statistical criteria also provide a means to objectively assess the quality of CD hierarchies, a non-trivial task considering that the protein subgroups are often very distantly related—a situation in which standard phylogenetic methods can be unreliable. Our aim here is to automatically generate (typically sub-optimal) hierarchies that, based on statistical criteria and visual comparisons, are comparable to manually curated hierarchies; this serves as the first step toward the ultimate goal of obtaining optimal hierarchical classifications. A plot of runtimes for the most time-intensive (non-parallelizable) part of the algorithm indicates a nearly linear time complexity so that, even for the extremely large Rossmann fold protein class, results were obtained in about a day. Conclusions This approach automates the rapid creation of protein domain hierarchies and thus will eliminate one of the most time consuming aspects of conserved domain database curation. At the same time, it also facilitates protein domain annotation by identifying those pattern residues that most distinguish each protein domain subgroup from other related subgroups. PMID:22726767

A Computational Framework for Design and Development of Novel Prostate Cancer Therapies

DTIC Science & Technology

2014-09-01

kinase Inhibitors, Late-stage Prostate Cancer 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT 18 . NUMBER OF PAGES 19a. NAME OF...calculate an evolutionary distance matrix(16- 18 ). We used the conserved domains identified from CDD to generate domain specific PSSM library, which were...prostate cancer cells from apoptosis induced by photodynamic therapy or thapsigargin. Oncogene 18 , 3391 (Jun 3, 1999). 7. Y. Qiu, H. J. Kung, Signaling

Logistic LASSO regression for the diagnosis of breast cancer using clinical demographic data and the BI-RADS lexicon for ultrasonography.

PubMed

Kim, Sun Mi; Kim, Yongdai; Jeong, Kuhwan; Jeong, Heeyeong; Kim, Jiyoung

2018-01-01

The aim of this study was to compare the performance of image analysis for predicting breast cancer using two distinct regression models and to evaluate the usefulness of incorporating clinical and demographic data (CDD) into the image analysis in order to improve the diagnosis of breast cancer. This study included 139 solid masses from 139 patients who underwent a ultrasonography-guided core biopsy and had available CDD between June 2009 and April 2010. Three breast radiologists retrospectively reviewed 139 breast masses and described each lesion using the Breast Imaging Reporting and Data System (BI-RADS) lexicon. We applied and compared two regression methods-stepwise logistic (SL) regression and logistic least absolute shrinkage and selection operator (LASSO) regression-in which the BI-RADS descriptors and CDD were used as covariates. We investigated the performances of these regression methods and the agreement of radiologists in terms of test misclassification error and the area under the curve (AUC) of the tests. Logistic LASSO regression was superior (P<0.05) to SL regression, regardless of whether CDD was included in the covariates, in terms of test misclassification errors (0.234 vs. 0.253, without CDD; 0.196 vs. 0.258, with CDD) and AUC (0.785 vs. 0.759, without CDD; 0.873 vs. 0.735, with CDD). However, it was inferior (P<0.05) to the agreement of three radiologists in terms of test misclassification errors (0.234 vs. 0.168, without CDD; 0.196 vs. 0.088, with CDD) and the AUC without CDD (0.785 vs. 0.844, P<0.001), but was comparable to the AUC with CDD (0.873 vs. 0.880, P=0.141). Logistic LASSO regression based on BI-RADS descriptors and CDD showed better performance than SL in predicting the presence of breast cancer. The use of CDD as a supplement to the BI-RADS descriptors significantly improved the prediction of breast cancer using logistic LASSO regression.

Improvement of liver injury and survival by JNK2 and iNOS deficiency in liver transplants from cardiac death mice.

PubMed

Liu, Qinlong; Rehman, Hasibur; Krishnasamy, Yasodha; Schnellmann, Rick G; Lemasters, John J; Zhong, Zhi

2015-07-01

Inclusion of liver grafts from cardiac death donors (CDD) would increase the availability of donor livers but is hampered by a higher risk of primary non-function. Here, we seek to determine mechanisms that contribute to primary non-function of liver grafts from CDD with the goal to develop strategies for improved function and outcome, focusing on c-Jun-N-terminal kinase (JNK) activation and mitochondrial depolarization, two known mediators of graft failure. Livers explanted from wild-type, inducible nitric oxide synthase knockout (iNOS(-/-)), JNK1(-/-) or JNK2(-/-) mice after 45-min aorta clamping were implanted into wild-type recipients. Mitochondrial depolarization was detected by intravital confocal microscopy in living recipients. After transplantation of wild-type CDD livers, graft iNOS expression and 3-nitrotyrosine adducts increased, but hepatic endothelial NOS expression was unchanged. Graft injury and dysfunction were substantially higher in CDD grafts than in non-CDD grafts. iNOS deficiency and inhibition attenuated injury and improved function and survival of CDD grafts. JNK1/2 and apoptosis signal-regulating kinase-1 activation increased markedly in wild-type CDD grafts, which was blunted by iNOS deficiency. JNK inhibition and JNK2 deficiency, but not JNK1 deficiency, decreased injury and improved function and survival of CDD grafts. Mitochondrial depolarization and binding of phospho-JNK2 to Sab, a mitochondrial protein linked to the mitochondrial permeability transition, were higher in CDD than in non-CDD grafts. iNOS deficiency, JNK inhibition and JNK2 deficiency all decreased mitochondrial depolarization and blunted ATP depletion in CDD grafts. JNK inhibition and deficiency did not decrease 3-nitrotyrosine adducts in CDD grafts. The iNOS-JNK2-Sab pathway promotes CDD graft failure via increased mitochondrial depolarization, and is an attractive target to improve liver function and survival in CDD liver transplantation recipients. Copyright © 2015 European Association for the Study of the Liver. Published by Elsevier B.V. All rights reserved.

Cross Domain Deterrence: Livermore Technical Report, 2014-2016

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

Barnes, Peter D.; Bahney, Ben; Matarazzo, Celeste

2016-08-03

Lawrence Livermore National Laboratory (LLNL) is an original collaborator on the project titled “Deterring Complex Threats: The Effects of Asymmetry, Interdependence, and Multi-polarity on International Strategy,” (CDD Project) led by the UC Institute on Global Conflict and Cooperation at UCSD under PIs Jon Lindsay and Erik Gartzke , and funded through the DoD Minerva Research Initiative. In addition to participating in workshops and facilitating interaction among UC social scientists, LLNL is leading the computational modeling effort and assisting with empirical case studies to probe the viability of analytic, modeling and data analysis concepts. This report summarizes LLNL work on themore » CDD Project to date, primarily in Project Years 1-2, corresponding to Federal fiscal year 2015. LLNL brings two unique domains of expertise to bear on this Project: (1) access to scientific expertise on the technical dimensions of emerging threat technology, and (2) high performance computing (HPC) expertise, required for analyzing the complexity of bargaining interactions in the envisioned threat models. In addition, we have a small group of researchers trained as social scientists who are intimately familiar with the International Relations research. We find that pairing simulation scientists, who are typically trained in computer science, with domain experts, social scientists in this case, is the most effective route to developing powerful new simulation tools capable of representing domain concepts accurately and answering challenging questions in the field.« less

Roles of the C-terminal domains of human dihydrodiol dehydrogenase isoforms in the binding of substrates and modulators: probing with chimaeric enzymes.

PubMed Central

Matsuura, K; Hara, A; Deyashiki, Y; Iwasa, H; Kume, T; Ishikura, S; Shiraishi, H; Katagiri, Y

1998-01-01

Human liver dihydrodiol dehydrogenase (DD; EC 1.3.1.20) exists in isoforms (DD1, DD2 and DD4) composed of 323 amino acids. DD1 and DD2 share 98% amino acid sequence identity, but show lower identities (approx. 83%) with DD4, in which a marked difference is seen in the C-terminal ten amino acids. DD4 exhibits unique catalytic properties, such as the ability to oxidize both (R)- and (S)-alicyclic alcohols equally, high dehydrogenase activity for bile acids, potent inhibition by steroidal anti-inflammatory drugs and activation by sulphobromophthalein and clofibric acid derivatives. In this study, we have prepared chimaeric enzymes, in which we exchanged the C-terminal 39 residues between the two enzymes. Compared with DD1, CDD1-4 (DD1 with the C-terminal sequence of DD4) had increased kcat/Km values for 3alpha-hydroxy-5beta-androstanes and bile acids of 3-9-fold and decreased values for the other substrates by 5-100-fold. It also became highly sensitive to DD4 inhibitors such as phenolphthalein and hexoestrol. Another chimaeric enzyme, CDD4-1 (DD4 with the C-terminal sequence of DD1), showed the same (S)-stereospecificity for the alicyclic alcohols as DD1, had decreased kcat/Km values for bile acids with 7beta- or 12alpha-hydroxy groups by more than 120-fold and was resistant to inhibition by betamethasone. In addition, the activation effects of sulphobromophthalein and bezafibrate decreased or disappeared for CDD4-1. The recombinant DD4 with the His314-->Pro (the corresponding residue of DD1) mutation showed intermediate changes in the properties between those of wild-type DD4 and CDD4-1. The results indicate that the binding of substrates, inhibitors and activators to the enzymes is controlled by residues in their C-terminal domains; multiple residues co-ordinately act as determinants for substrate specificity and inhibitor sensitivity. PMID:9820821

Metabolic pathway reconstruction of eugenol to vanillin bioconversion in Aspergillus niger

PubMed Central

Srivastava, Suchita; Luqman, Suaib; Khan, Feroz; Chanotiya, Chandan S; Darokar, Mahendra P

2010-01-01

Identification of missing genes or proteins participating in the metabolic pathways as enzymes are of great interest. One such class of pathway is involved in the eugenol to vanillin bioconversion. Our goal is to develop an integral approach for identifying the topology of a reference or known pathway in other organism. We successfully identify the missing enzymes and then reconstruct the vanillin biosynthetic pathway in Aspergillus niger. The procedure combines enzyme sequence similarity searched through BLAST homology search and orthologs detection through COG & KEGG databases. Conservation of protein domains and motifs was searched through CDD, PFAM & PROSITE databases. Predictions regarding how proteins act in pathway were validated experimentally and also compared with reported data. The bioconversion of vanillin was screened on UV-TLC plates and later confirmed through GC and GC-MS techniques. We applied a procedure for identifying missing enzymes on the basis of conserved functional motifs and later reconstruct the metabolic pathway in target organism. Using the vanillin biosynthetic pathway of Pseudomonas fluorescens as a case study, we indicate how this approach can be used to reconstruct the reference pathway in A. niger and later results were experimentally validated through chromatography and spectroscopy techniques. PMID:20978605

Nutritional models for space travel from chemically defined diets

NASA Technical Reports Server (NTRS)

Dufour, P. A.

1984-01-01

Human nutritional requirements are summarized, including recommended daily intake and maximum safe chronic intake of nutrients. The biomedical literature on various types of chemically defined diets (CDD's), which are liquid, formulated diets for enteral and total parenteral nutrition, is reviewed. The chemical forms of the nutrients in CDD's are detailed, and the compositions and sources of representative commercial CDD's are tabulated. Reported effects of CDD's in medical patients, healthy volunteers, and laboratory animals are discussed. The effects include gastrointestinal side effects, metabolic imbalances, nutrient deficiencies and excesses, and psychological problems. Dietary factors contributing to the side effects are examined. Certain human nutrient requirements have been specified more precisely as a result of long-term use of CDD's, and related studies are included. CDD's are the most restricted yet nutritionally complete diets available.

Outcome of metronidazole therapy for Clostridium difficile disease and correlation with a scoring system.

PubMed

Belmares, Jaime; Gerding, Dale N; Parada, Jorge P; Miskevics, Scott; Weaver, Frances; Johnson, Stuart

2007-12-01

To determine the response rate of Clostridium difficile disease (CDD) to treatment with metronidazole and assess a scoring system to predict response to treatment with metronidazole when applied at the time of CDD diagnosis. Retrospective review of patients with CDD who received primary treatment with metronidazole. We defined success as diarrhea resolution within 6 days of therapy. A CDD score was defined prospectively using variables suggested to correlate with disease severity. Among 102 evaluable patients, 72 had a successful response (70.6%). Twenty-one of the remaining 30 patients eventually responded to metronidazole, but required longer treatment, leaving 9 'true failures'. The mean CDD score was higher among true failures (2.89+/-1.4) than among all metronidazole responders (0.77+/-1.0) (p<.0001). The score was greater than 2 in 67% of true failures and 2 or less in 94% of metronidazole responders. Leukocytosis and abnormal CT scan findings were individual factors associated with a higher risk of metronidazole failure. Only 71% of CDD patients responded to metronidazole within 6 days, but the overall response rate was 91%. A CDD score greater than 2 was associated with metronidazole failure in 6 of 9 true failures. The CDD score will require prospective validation.

Arabidopsis thaliana cdd1 mutant uncouples the constitutive activation of salicylic acid signalling from growth defects.

PubMed

Swain, Swadhin; Roy, Shweta; Shah, Jyoti; Van Wees, Saskia; Pieterse, Corné M; Nandi, Ashis K

2011-12-01

Arabidopsis genotypes with a hyperactive salicylic acid-mediated signalling pathway exhibit enhanced disease resistance, which is often coupled with growth and developmental defects, such as dwarfing and spontaneous necrotic lesions on the leaves, resulting in reduced biomass yield. In this article, we report a novel recessive mutant of Arabidopsis, cdd1 (constitutive defence without defect in growth and development1), that exhibits enhanced disease resistance associated with constitutive salicylic acid signalling, but without any observable pleiotropic phenotype. Both NPR1 (NON-EXPRESSOR OF PATHOGENESIS-RELATED GENES1)-dependent and NPR1-independent salicylic acid-regulated defence pathways are hyperactivated in cdd1 mutant plants, conferring enhanced resistance against bacterial pathogens. However, a functional NPR1 allele is required for the cdd1-conferred heightened resistance against the oomycete pathogen Hyaloperonospora arabidopsidis. Salicylic acid accumulates at elevated levels in cdd1 and cdd1 npr1 mutant plants and is necessary for cdd1-mediated PR1 expression and disease resistance phenotypes. In addition, we provide data which indicate that the cdd1 mutation negatively regulates the npr1 mutation-induced hyperactivation of ethylene/jasmonic acid signalling. © 2011 The Authors. Molecular Plant Pathology © 2011 BSPP and Blackwell Publishing Ltd.

Factors affecting the attrition of community-directed distributors of ivermectin, in an onchocerciasis-control programme in the Imo and Abia states of south-eastern Nigeria.

PubMed

Emukah, E C; Enyinnaya, U; Olaniran, N S; Akpan, E A; Hopkins, D R; Miri, E S; Amazigo, U; Okoronkwo, C; Stanley, A; Rakers, L; Richards, F O; Katabarwa, M N

2008-01-01

In areas of Nigeria where onchocerciasis is endemic, community-directed distributors (CDD) distribute ivermectin annually, as part of the effort to control the disease. Unfortunately, it has been reported that at least 35% of the distributors who have been trained in Nigeria are unwilling to participate further as CDD. The selection and training of new CDD, to replace those unwilling to continue, leads to annual expense that the national onchocerciasis-programme is finding difficult to meet, given other programme priorities and the limited resources. If the reported levels of attrition are true, they seriously threaten the sustainability of community-directed treatment with ivermectin (CDTI) in Nigeria. In 2002, interviews were held with 101 people who had been trained as CDD, including those who had stopped serving their communities, from 12 communities in south-eastern Nigeria that had high rates of CDD attrition. The results showed that, although the overall reported CDD attrition was 40.6%, the actual rate was only 10.9%. The CDD who had ceased participating in the annual rounds of ivermectin blamed a lack of incentives (65.9%), the demands of other employment (14.6%), the long distances involved in the house-to-house distribution (12.2%) or marital duties (7.3%). Analysis of the data obtained from all the interviewed CDD showed that inadequate supplies of ivermectin (P<0.01), lack of supervision (P<0.05) and a lack of monetary incentives (P<0.001) led to significant increases in attrition. Conversely, CDD retention was significantly enhanced when the distributors were selected by their community members (P<0.001), supervised (P<0.001), supplied with adequate ivermectin tablets (P<0.05), involved in educating their community members (P<0.05), and/or involved in other health programmes (P<0.001). Although CDD who were involved in other health programmes were relatively unlikely to cease participating in the distributions, they were more likely to take longer than 14 days to complete ivermectin distribution than other CDD, who only distributed ivermectin. Data obtained in interviews with present and past CDD appear vital for informing, directing, protecting and enhancing the performance of CDTI programmes, in Nigeria and elsewhere.

Simulated Extreme Prepitation Indices over Northeast Brasil in Current Climate and Future Scenarios RCP4.5 and RCP8.5

NASA Astrophysics Data System (ADS)

Wender Santiago Marinho, Marcos; Araújo Costa, Alexandre; Cassain Sales, Domingo; Oliveira Guimarães, Sullyandro; Mariano da Silva, Emerson; das Chagas Vasconcelos Júnior, Francisco

2013-04-01

In this study, we analyzed extreme precipitation indices, for present and future modeled climates over Northeast of Brazil (NEB), from CORDEX simulations over the domain of Tropical Americas. The period for the model validation was from 1989-2007, using data from the European Center (ECWMF) Reanalysis, ERA-INTERIM, as input to drive the regional model (RAMS 6.0). Reanalysis data were assimilated via both lateral boundaries and the entire domain (a much weaker "central nudging"). Six indices of extreme precipitation were calculated over NEB: the average number of days above 10, 20 and 30 mm in one year (R10, R20, R30), the number of consecutive dry days (CDD), the number of consecutive wet days (CWD) and the maximum rainfall in five consecutive days (RX5). Those indices were compared against two independent databases: MERRA (Modern Era Retrospective analysis for Research and Applications) and TRMM (Tropical Rainfall Measuring Mission). After validation, climate simulations were performed for the present climate (1985-2005) and short-term (2015-2035), mid-term (2045-2065) and long-term (2079 to 2099) future climates for two scenarios: RCP 4.5 and RCP 8.5, nesting RAMS into HadGEM2-ES global model (a participant of CMIP5). Along with the indices, we also calculated Probability Distribution Functions (PDFs) to study the behavior of daily precipitation in the present and by the end of the 21st century (2079 to 2099) to assess possible changes under RCPs 4.5 and 8.5. The regional model is capable of representing relatively well the extreme precipitation indices for current climate, but there is some difficulties in performing a proper validation since the observed databases disagree significantly. Future projections show significant changes in most extreme indices. Rnn generally tend to increase, especially under RCP8.5. More significant changes are projected for the long-term period, under RCP8.5, which shows a pronounced R30 enhancement over northern states. CDD tends to decrease over most of NEB in the short but this trend is reverted toward the end of the century in both scenarios with a significant increase in the duration of the dry season over Northwestern and Eastern NEB (exceeding 50 days over certain areas), whereas projected CWD changes are smaller. Rx5 shows a general increasing trend especially in the long term period,under RCP8.5.

Cancer diagnosis disclosure preferences of family caregivers of cancer patients in Egypt.

PubMed

Alsirafy, Samy A; Abdel-Kareem, Shady S; Ibrahim, Noha Y; Abolkasem, Mohamed A; Farag, Dina E

2017-11-01

Family caregivers (FCs) of cancer patients are frequently seen as a barrier to honest communication with patients in Egypt. This study was conducted to investigate the attitude of FCs of cancer patients toward cancer diagnosis disclosure (CDD) and its determinants. A structured interview was used to assess the preferences of 288 FCs regarding CDD. According to the FCs, 85% of patients were aware of their diagnosis. The majority (81%) of FCs preferred CDD to patients. In case they developed cancer, 92% of FCs wanted to know their diagnosis and 88% wanted to inform their families. In a univariate analysis, factors associated with FCs' negative attitude toward CDD to patients were as follows: patient's lower level of education (P = .001), patient's rural residence (P < .001), hematological malignancies (P < .001), FC's belief that the patient is unaware of diagnosis (P < .001), FC's unwillingness to know his/her own cancer diagnosis (P < .001), and FC's unwillingness to inform his/her family about his/her cancer diagnosis (P < .001). Only 2 factors predicted independently the negative attitude of FCs toward CDD, the FC's belief that the patient is unaware of diagnosis (P < .001), and the FC's unwillingness to know his/her own cancer diagnosis (P = .049). The results suggest that the majority of FCs of Egyptian cancer patients prefer CDD to patients. The finding that the vast majority of FCs of aware patients preferred CDD suggests that the reaction of Egyptian patients to CDD is acceptable by FCs. Family caregivers with a negative attitude toward CDD may be reflecting their own fears. Copyright © 2016 John Wiley & Sons, Ltd.

The selective M1 muscarinic cholinergic agonist CDD-0102A enhances working memory and cognitive flexibility.

PubMed

Ragozzino, Michael E; Artis, Sonja; Singh, Amritha; Twose, Trevor M; Beck, Joseph E; Messer, William S

2012-03-01

Various neurodegenerative diseases and psychiatric disorders are marked by alterations in brain cholinergic function and cognitive deficits. Efforts to alleviate such deficits have been limited by a lack of selective M(1) muscarinic agonists. 5-(3-Ethyl-1,2,4-oxadiazol-5-yl)-1,4,5,6-tetrahydropyrimidine hydrochloride (CDD-0102A) is a partial agonist at M(1) muscarinic receptors with limited activity at other muscarinic receptor subtypes. The present studies investigated the effects of CDD-0102A on working memory and strategy shifting in rats. CDD-0102A administered intraperitoneally 30 min before testing at 0.1, 0.3, and 1 mg/kg significantly enhanced delayed spontaneous alternation performance in a four-arm cross maze, suggesting improvement in working memory. In separate experiments, CDD-0102A had potent enhancing effects on learning and switching between a place and visual cue discrimination. Treatment with CDD-0102A did not affect acquisition of either a place or visual cue discrimination. In contrast, CDD-0102A at 0.03 and 0.1 mg/kg significantly enhanced a shift between a place and visual cue discrimination. Analysis of the errors in the shift to the place or shift to the visual cue strategy revealed that in both cases CDD-0102A significantly increased the ability to initially inhibit a previously relevant strategy and maintain a new, relevant strategy once selected. In anesthetized rats, the minimum dose required to induce salivation was approximately 0.3 mg/kg i.p. Salivation increased with dose, and the estimated ED(50) was 2.0 mg/kg. The data suggest that CDD-0102A has unique memory and cognitive enhancing properties that might be useful in the treatment of neurological disorders at doses that do not produce adverse effects such as salivation.

Genetic study of congenital bile-duct dilatation identifies de novo and inherited variants in functionally related genes.

PubMed

Wong, John K L; Campbell, Desmond; Ngo, Ngoc Diem; Yeung, Fanny; Cheng, Guo; Tang, Clara S M; Chung, Patrick H Y; Tran, Ngoc Son; So, Man-Ting; Cherny, Stacey S; Sham, Pak C; Tam, Paul K; Garcia-Barcelo, Maria-Mercè

2016-12-12

Congenital dilatation of the bile-duct (CDD) is a rare, mostly sporadic, disorder that results in bile retention with severe associated complications. CDD affects mainly Asians. To our knowledge, no genetic study has ever been conducted. We aim to identify genetic risk factors by a "trio-based" exome-sequencing approach, whereby 31 CDD probands and their unaffected parents were exome-sequenced. Seven-hundred controls from the local population were used to detect gene-sets significantly enriched with rare variants in CDD patients. Twenty-one predicted damaging de novo variants (DNVs; 4 protein truncating and 17 missense) were identified in several evolutionarily constrained genes (p < 0.01). Six genes carrying DNVs were associated with human developmental disorders involving epithelial, connective or bone morphologies (PXDN, RTEL1, ANKRD11, MAP2K1, CYLD, ACAN) and four linked with cholangio- and hepatocellular carcinomas (PIK3CA, TLN1 CYLD, MAP2K1). Importantly, CDD patients have an excess of DNVs in cancer-related genes (p < 0.025). Thirteen genes were recurrently mutated at different sites, forming compound heterozygotes or functionally related complexes within patients. Our data supports a strong genetic basis for CDD and show that CDD is not only genetically heterogeneous but also non-monogenic, requiring mutations in more than one genes for the disease to develop. The data is consistent with the rarity and sporadic presentation of CDD.

How robust is the pre-1931 National Climatic Data Center—climate divisional dataset? Examples from Georgia and Louisiana

NASA Astrophysics Data System (ADS)

Allard, Jason; Thompson, Clint; Keim, Barry D.

2015-04-01

The National Climatic Data Center's climate divisional dataset (CDD) is commonly used in climate change analyses. This dataset is a spatially continuous dataset for the conterminous USA from 1895 to the present. The CDD since 1931 is computed by averaging all available representative cooperative weather station data into a single monthly value for each of the 344 climate divisions of the conterminous USA, while pre-1931 data for climate divisions are derived from statewide averages using regression equations. This study examines the veracity of these pre-1931 data. All available Cooperative Observer Program (COOP) stations within each climate division in Georgia and Louisiana were averaged into a single monthly value for each month and each climate division from 1897 to 1930 to generate a divisional dataset (COOP DD), using similar methods to those used by the National Climatic Data Center to generate the post-1931 CDD. The reliability of the official CDD—derived from statewide averages—to produce temperature and precipitation means and trends prior to 1931 are then evaluated by comparing that dataset with the COOP DD with difference-of-means tests, correlations, and linear regression techniques. The CDD and the COOP DD are also compared to a divisional dataset derived from the United States Historical Climatology Network (USHCN) data (USHCN DD), with difference of means and correlation techniques, to demonstrate potential impacts of inhomogeneities within the CDD and the COOP DD. The statistical results, taken as a whole, not only indicate broad similarities between the CDD and COOP DD but also show that the CDD does not adequately portray pre-1931 temperature and precipitation in certain climate divisions within Georgia and Louisiana. In comparison with the USHCN DD, both the CDD and the COOP DD appear to be subject to biases that probably result from changing stations within climate divisions. As such, the CDD should be used judiciously for long-term studies of climate change, and past studies using the CDD should be evaluated in the context of these new findings.

Methodology to Estimate the Quantity, Composition, and Management of Construction and Demolition Debris in the United States

EPA Science Inventory

This report, Methodology to Estimate the Quantity, Composition and Management of Construction and Demolition Debris in the US, was developed to expand access to data on CDD in the US and to support research on CDD and sustainable materials management. Since past US EPA CDD estima...

Diarrhoeal diseases and the global health agenda: measuring and changing priority.

PubMed

Bump, Jesse B; Reich, Michael R; Johnson, Anne M

2013-12-01

We investigate priority setting and the global health agenda by analysing the control of diarrhoeal diseases (CDD). CDD was one of the 'twin engines' of the 1980s' child survival movement, but now has a low priority on the global health agenda, even though diarrhoeal diseases still claim around 1.5 million children annually. In this article, we develop a framework and four indicators of priority to measure CDD's overall prominence on the global health agenda over the last three decades: trends in treatment coverage, changes in perceived priority, changes in financial support and institutional involvement and bibliographic trends. We find that CDD's priority is now one-sixth to one-third of its level in 1985. We then use political analysis to suggest strategies for reframing CDD as an issue and promoting its priority on the global health agenda.

External Validity of Childhood Disintegrative Disorder in Comparison with Autistic Disorder

ERIC Educational Resources Information Center

Kurita, Hiroshi; Osada, Hirokazu; Miyake, Yuko

2004-01-01

To examine the external validity of DSM-IV childhood disintegrative disorder (CDD), 10 children (M = 8.2 yrs) with CDD and 152 gender- and age-matched children with autistic disorder (AD) were compared on 24 variables. The CDD children had a significantly higher rate of epilepsy, significantly less uneven intellectual functioning, and a tendency…

Creatine supplementation prevents fatty liver in rats fed choline-deficient diet: a burden of one-carbon and fatty acid metabolism.

PubMed

Deminice, Rafael; de Castro, Gabriela Salim Ferreira; Francisco, Lucas Vieira; da Silva, Lilian Eslaine Costa Mendes; Cardoso, João Felipe Rito; Frajacomo, Fernando Tadeu Trevisan; Teodoro, Bruno Gonzaga; Dos Reis Silveira, Leonardo; Jordao, Alceu Afonso

2015-04-01

To examine the effects of creatine (Cr) supplementation on liver fat accumulation in rats fed a choline-deficient diet. Twenty-four rats were divided into 3 groups of 8 based on 4 weeks of feeding an AIN-93 control diet (C), a choline-deficient diet (CDD) or a CDD supplemented with 2% Cr. The CDD diet was AIN-93 without choline. The CDD significantly increased plasma homocysteine and TNFα concentration, as well as ALT activity. In liver, the CDD enhanced concentrations of total fat (55%), cholesterol (25%), triglycerides (87%), MDA (30%), TNFα (241%) and decreased SAM concentrations (25%) and the SAM/SAH ratio (33%). Cr supplementation prevented all these metabolic changes, except for hepatic SAM and the SAM/SAH ratio. However, no changes in PEMT gene expression or liver phosphatidylcholine levels were observed among the three experimental groups, and there were no changes in hepatic triglyceride transfer protein (MTP) mRNA level. On the contrary, Cr supplementation normalized expression of the transcription factors PPARα and PPARγ that were altered by the CDD. Further, the downstream targets and fatty acids metabolism genes, UCP2, LCAD and CPT1a, were also normalized in the Cr group as compared to CDD-fed rats. Cr supplementation prevented fat liver accumulation and hepatic injures in rats fed with a CDD for 4 weeks. Our results demonstrated that one-carbon metabolism may have a small role in mitigating hepatic fat accumulation by Cr supplementation. The modulation of key genes related to fatty acid oxidation pathway suggests a new mechanism by which Cr prevents liver fat accumulation. Copyright © 2015 Elsevier Inc. All rights reserved.

cis-chlorobenzene dihydrodiol dehydrogenase (TcbB) from Pseudomonas sp. strain P51, expressed in Escherichia coli DH5alpha(pTCB149), catalyzes enantioselective dehydrogenase reactions.

PubMed

Raschke, H; Fleischmann, T; Van Der Meer, J R; Kohler, H P

1999-12-01

cis-Chlorobenzene dihydrodiol dehydrogenase (CDD) from Pseudomonas sp. strain P51, cloned into Escherichia coli DH5alpha(pTCB149) was able to oxidize cis-dihydrodihydroxy derivatives (cis-dihydrodiols) of dihydronaphthalene, indene, and four para-substituted toluenes to the corresponding catechols. During the incubation of a nonracemic mixture of cis-1,2-indandiol, only the (+)-cis-(1R,2S) enantiomer was oxidized; the (-)-cis-(S,2R) enantiomer remained unchanged. CDD oxidized both enantiomers of cis-1,2-dihydroxy-1,2,3, 4-tetrahydronaphthalene, but oxidation of the (+)-cis-(1S,2R) enantiomer was delayed until the (-)-cis-(1R,2S) enantiomer was completely depleted. When incubated with nonracemic mixtures of para-substituted cis-toluene dihydrodiols, CDD always oxidized the major enantiomer at a higher rate than the minor enantiomer. When incubated with racemic 1-indanol, CDD enantioselectively transformed the (+)-(1S) enantiomer to 1-indanone. This stereoselective transformation shows that CDD also acted as an alcohol dehydrogenase. Additionally, CDD was able to oxidize (+)-cis-(1R,2S)-dihydroxy-1, 2-dihydronaphthalene, (+)-cis-monochlorobiphenyl dihydrodiols, and (+)-cis-toluene dihydrodiol to the corresponding catechols.

cis-Chlorobenzene Dihydrodiol Dehydrogenase (TcbB) from Pseudomonas sp. Strain P51, Expressed in Escherichia coli DH5α(pTCB149), Catalyzes Enantioselective Dehydrogenase Reactions

PubMed Central

Raschke, Henning; Fleischmann, Thomas; Van Der Meer, Jan Roelof; Kohler, Hans-Peter E.

1999-01-01

cis-Chlorobenzene dihydrodiol dehydrogenase (CDD) from Pseudomonas sp. strain P51, cloned into Escherichia coli DH5α(pTCB149) was able to oxidize cis-dihydrodihydroxy derivatives (cis-dihydrodiols) of dihydronaphthalene, indene, and four para-substituted toluenes to the corresponding catechols. During the incubation of a nonracemic mixture of cis-1,2-indandiol, only the (+)-cis-(1R,2S) enantiomer was oxidized; the (−)-cis-(S,2R) enantiomer remained unchanged. CDD oxidized both enantiomers of cis-1,2-dihydroxy-1,2,3,4-tetrahydronaphthalene, but oxidation of the (+)-cis-(1S,2R) enantiomer was delayed until the (−)-cis-(1R,2S) enantiomer was completely depleted. When incubated with nonracemic mixtures of para-substituted cis-toluene dihydrodiols, CDD always oxidized the major enantiomer at a higher rate than the minor enantiomer. When incubated with racemic 1-indanol, CDD enantioselectively transformed the (+)-(1S) enantiomer to 1-indanone. This stereoselective transformation shows that CDD also acted as an alcohol dehydrogenase. Additionally, CDD was able to oxidize (+)-cis-(1R,2S)-dihydroxy-1,2-dihydronaphthalene, (+)-cis-monochlorobiphenyl dihydrodiols, and (+)-cis-toluene dihydrodiol to the corresponding catechols. PMID:10583971

Lipid peroxidation in mice fed a choline-deficient diet as evaluated by total hydroxyoctadecadienoic acid.

PubMed

Yoshida, Yasukazu; Itoh, Nanako; Hayakawa, Mieko; Habuchi, Yoko; Inoue, Ruriko; Chen, Zhi-Hua; Cao, Jiaofei; Cynshi, Osamu; Niki, Etsuo

2006-03-01

The relevance of oxidative stress in mice fed a choline-deficient diet (CDD) was investigated in relation to the oxidative stress marker, hydroxyoctadecadienoic acid (HODE) in comparison with F2-isoprostanes. Further, the protective effects of antioxidants against oxidative damage were assessed by using HODE. We recently proposed total HODE as a biomarker for oxidative stress in vivo. Biological samples such as plasma, urine, and tissues were first reduced and then saponified to convert various oxidation products of linoleates to HODE. In the present study, this method was applied to measure oxidative damage in mice induced by CDD for 1 mo. CDD, when compared with choline-controlled diet (CCD), increased liver weight and fatty acid accumulation but the increase in body weight was less significant. Remarkable increases in HODE and 8-iso-prostaglandin F(2alpha) in liver and plasma were observed when mice were fed with the CDD for 1 mo compared with the CCD. The HODE level was about two to three orders higher than the F2-isoprostane level. This increase was decreased to the level of the CCD when alpha-tocopherol or 2,3-dihydro-5-hydroxy-4,6-di-tert-butyl-2,2-dipentylbenzofuran, a potent synthetic antioxidant, was mixed with the CDD. The stereoisomer ratio of HODE (9-and-13 (Z,E)-HODE/9-and-13 (E,E)-HODE) was decreased by CDD compared with CCD, which was spared by the addition of alpha-tocopherol and 2,3-dihydro-5-hydroxy-4,6-di-tert-butyl-2,2-dipentylbenzofuran. However, the increase in plasma glutamic-pyruvic transaminase and fatty acids in liver induced by the CDD was not recovered by any antioxidant. This study clearly demonstrated that oxidative stress was involved in fatty liver formation induced by the CDD and that HODE was a good biomarker for an oxidative stress in vivo.

Identifying different transcribed proteins in the newly described Theraphosidae Pamphobeteus verdolaga.

PubMed

Estrada-Gómez, Sebastian; Vargas-Muñoz, Leidy Johana; Saldarriaga-Córdoba, Mónica; Cifuentes, Yeimy; Perafan, Carlos

2017-04-01

Theraphosidae spider venoms are well known for possess a complex mixture of protein and non-protein compounds in their venom. The objective of this study was to report and identify different proteins translated from the venom gland DNA information of the recently described Theraphosidae spider Pamphobeteus verdolaga. Using a venom gland transcriptomic analysis, we reported a set of the first complete sequences of seven different proteins of the recenlty described Theraphosidae spider P. verdolaga. Protein analysis indicates the presence of different proteins on the venom composition of this new spider, some of them uncommon in the Theraphosidae family. MS/MS analysis of P. verdolaga showed different fragments matching sphingomyelinases (sicaritoxin), barytoxins, hexatoxins, latroinsectotoxins, and linear (zadotoxins) peptides. Only four of the MS/MS fragments showed 100% sequence similarity with one of the transcribed proteins. Transcriptomic analysis showed the presence of different groups of proteins like phospholipases, hyaluronidases, inhibitory cysteine knots (ICK) peptides among others. The three database of protein domains used in this study (Pfam, SMART and CDD) showed congruency in the search of unique conserved protein domain for only four of the translated proteins. Those proteins matched with EF-hand proteins, cysteine rich secretory proteins, jingzhaotoxins, theraphotoxins and hexatoxins, from different Mygalomorphae spiders belonging to the families Theraphosidae, Barychelidae and Hexathelidae. None of the analyzed sequences showed a complete 100% similarity. Copyright © 2017 Elsevier Ltd. All rights reserved.

Cervical disc arthroplasty for symptomatic cervical disc disease: Traditional and Bayesian meta-analysis with trial sequential analysis.

PubMed

Kan, Shun-Li; Yuan, Zhi-Fang; Ning, Guang-Zhi; Liu, Fei-Fei; Sun, Jing-Cheng; Feng, Shi-Qing

2016-11-01

Cervical disc arthroplasty (CDA) has been designed as a substitute for anterior cervical discectomy and fusion (ACDF) in the treatment of symptomatic cervical disc disease (CDD). Several researchers have compared CDA with ACDF for the treatment of symptomatic CDD; however, the findings of these studies are inconclusive. Using recently published evidence, this meta-analysis was conducted to further verify the benefits and harms of using CDA for treatment of symptomatic CDD. Relevant trials were identified by searching the PubMed, EMBASE, and Cochrane Library databases. Outcomes were reported as odds ratio or standardized mean difference. Both traditional frequentist and Bayesian approaches were used to synthesize evidence within random-effects models. Trial sequential analysis (TSA) was applied to test the robustness of our findings and obtain more conservative estimates. Nineteen trials were included. The findings of this meta-analysis demonstrated better overall, neck disability index (NDI), and neurological success; lower NDI and neck and arm pain scores; higher 36-Item Short Form Health Survey (SF-36) Physical Component Summary (PCS) and Mental Component Summary (MCS) scores; more patient satisfaction; greater range of motion at the operative level; and fewer secondary surgical procedures (all P < 0.05) in the CDA group compared with the ACDF group. CDA was not significantly different from ACDF in the rate of adverse events (P > 0.05). TSA of overall success suggested that the cumulative z-curve crossed both the conventional boundary and the trial sequential monitoring boundary for benefit, indicating sufficient and conclusive evidence had been ascertained. For treating symptomatic CDD, CDA was superior to ACDF in terms of overall, NDI, and neurological success; NDI and neck and arm pain scores; SF-36 PCS and MCS scores; patient satisfaction; ROM at the operative level; and secondary surgical procedures rate. Additionally, there was no significant difference between CDA and ACDF in the rate of adverse events. However, as the CDA procedure is a relatively newer operative technique, long-term results and evaluation are necessary before CDA is routinely used in clinical practice. Copyright © 2016 IJS Publishing Group Ltd. Published by Elsevier Ltd. All rights reserved.

Colonic wall changes in patients with diverticular disease - is there a predisposition for a complicated course?

PubMed

Ulmer, T F; Rosch, R; Mossdorf, A; Alizai, H; Binnebösel, M; Neumann, U

2014-01-01

The aim of this study was to evaluate colonic wall changes and enteric neuropathy in patients with either uncomplicated (UDD) or complicated diverticular disease (CDD). Furthermore, we evaluated the presence of an anatomic sphincter at the rectosigmoid junction (RSJ). Samples of colonic tissue from fifteen patients with UDD, fifteen patients with CDD and fifteen patients as control were collected. Collagen quotient I/III was measured with the Sirius-red test, expression of MMP-1, MMP-13, innervation (S100), proliferation (Ki67) and apoptosis (TUNEL) in the colonic wall were investigated by immunohistochemical studies. Furthermore, measurements of the different layers were performed to investigate the RSJ. Patients with either UDD or CDD had lower collagen I/III quotients compared to the control group, significant for CDD (p = 0.007). For MMP-1 and MMP-13 only a slight increase for patients with CDD was found. The percentage of proliferating (Ki67) and apoptotic (TUNEL) cells was significantly higher for patients with CDD than in the control group (p = 0.016; p = 0.037). Upon investigating the S100-expression a significant reduce in glial cells density was found in the myenteric and mucosal plexus for both groups (UDD and CDD) compared to the control group. Measurements of the different colon layers oral, aboral and at the RSJ revealed equal values. This study has shown that colonic wall changes and enteric neuropathy seem to play a role in the pathogenesis of colonic diverticulosis. None of our results suggest a predisposition for a complicated diverticular disease. Furthermore, the presence of an anatomic sphincter at the rectosigmoid junction could not be detected. Copyright © 2014 Surgical Associates Ltd. Published by Elsevier Ltd. All rights reserved.

Simultaneous degradation of commercially produced CNP herbicide and of contaminated dioxin by treatment using the white-rot fungus Phlebia brevispora.

PubMed

Kamei, Ichiro; Kondo, Ryuichiro

2006-11-01

An experiment was carried out to study the degradation of commercially produced chlornitrofen (2,4,6-trichlorophenyl p-nitrophenyl ether; CNP) herbicide contaminated with 1,3,6,8-tetrachlorodibenzo-p-dioxin (1,3,6,8-tetraCDD) by means of the white rot fungus Phlebia brevispora TMIC33929. Recently, we reported that 1,3,6,8-tetraCDD was degraded by P. brevispora. In the degradation experiment using CNP standard compounds, CNP was transformed into several metabolites including monomethoxylated compounds and 2,4,6-trichlorophenol by P. brevispora. When the mixture of CNP and 1,3,6,8-tetraCDD was treated with P. brevispora, each substrate was degraded and metabolites were detected. The treatment of the commercially produced CNP herbicide by P. brevispora led to the degradation of CNP and contaminated 1,3,6,8-tetraCDD as a result. These results indicate that P. brevispora can degrade CNP and 1,3,6,8-tetraCDD at the same time, and that biological treatment of commercially produced CNP herbicide is possible.

Cadmium and phosphate variability during algal blooms of the dinoflagellate Lingulodinium polyedrum in Todos Santos Bay, Baja California, Mexico.

PubMed

Gutierrez-Mejia, E; Lares, M L; Huerta-Diaz, M A; Delgadillo-Hinojosa, F

2016-01-15

Dinoflagellate algal blooms (DABs), with Lingulodinium polyedrum as the dominant species, have increased over the past few years in coastal areas off Baja California, Mexico. Vertical and temporal variability of particulate cadmium (Cdp), dissolved Cd (Cdd), PO4(3-) and Cdd/PO4(3-) were investigated during two intense DABs of L. polyedrum that occurred during the fall of 2011 and 2012 in Todos Santos Bay. Results were then, compared with data gathered in the absence of algal blooms during the autumn of 2013. In both algal blooms, L. polyedrum tended to be concentrated near the surface throughout the duration; however, during DAB 2011 the number of cells was twice as abundant ([10.0 ± 8.0] × 10(5) cells L(-1)) as in DAB 2012 ([5.0 ± 4.4] × 10(5) cells L(-1)). During DAB 2011, Cdp increased significantly (up to 1.02 ± 0.99 nmol kg(-1)) and was positively correlated with the cell abundance of L. polyedrum, suggesting that this dinoflagellate is able to assimilate and concentrate Cdd. Likewise, Cdd (up to 0.71 ± 0.17 nM) increased in the days of highest cell abundance, which could be attributed to uptake and subsequent regeneration of Cdd resulting from the remineralization of organic particulate matter produced during the bloom, as well as with the presence of organic ligands secreted by L. polyedrum that could keep Cdd in solution. During DAB 2011, dissolved Cdd/PO4(3-) ratios exhibited high vertical and temporal variability in the upper 5 m of the water column, but remained virtually constant near the bottom, suggesting a depth-dependent decoupling between these two dissolved components during the bloom development. Given the observed differences in the vertical and temporal variability of Cdd, Cdp, and PO4(3-) between these two intense DABs, we propose the existence of an abundance threshold of approximately 10(6) cells L(-1) of L. polyedrum above which Cd and PO4(3-) significantly increased due to remineralization in coastal waters during the bloom development.

ANALYSIS OF ANIMAL- AND PLANT-DERIVED FEED ...

EPA Pesticide Factsheets

During a national survey of polychlorinated dibenzo-p-dioxins (CDD), dibenzofurans (CDF), and dioxin-like coplanar PCBs (PCB) in poultry, elevated concentrations above 20 parts per trillion (ppt) toxic equivalents (TEQ) were found in the fat of 2 broilers. These TEQ values were driven by very high concentrations of CDD. A team comprised of individuals from the United States (US) Environmental Protection Agency (EPA), the US Food and Drug Administration (FDA), and the US Department of Agriculture (DA) traced the source of elevated CDD to a minor component in the poultry feed. This component was ball clay and it was used as an anti-caking agent in the soybean meal. The ball clay often comprised less than 0.2% of the dry weight of the complete ration in contaminated poultry. The investigation traced the ball clay to a mine in Mississippi. After learning that other ball clay mines in Kentucky and Tennessee also contained elevated CDD levels, the FDA issued a letter to producers or users of clay products in animal feeds asking that they cease using ball clay in any animal feed or feed ingredient. Subsequent contaminations of animal feed in Belgium with PCB and of citrus pulp from Brazil with CDD and CDF alerted countries worldwide that animal feeds can become contaminated with CDD/CDF/PCB (DFP) via contamination of minor feed components. This type of contamination can overshadow the normal air-to-leaf process that is thought to dominate the food chain for terr

Conventional and high-dose daunorubicin and idarubicin in acute myeloid leukaemia remission induction treatment: a mixed treatment comparison meta-analysis of 7258 patients.

PubMed

Sekine, Leo; Morais, Vinícius Daudt; Lima, Karine Margarites; Onsten, Tor Gunnar Hugo; Ziegelmann, Patrícia Klarmann; Ribeiro, Rodrigo Antonini

2015-12-01

Previous meta-analyses suggested that acute myeloid leukaemia induction regimens containing idarubicin (IDA) or high-dose daunorubicin (HDD) induce higher rates of complete remission (CR) than conventional-dose daunorubicin (CDD), with a possible benefit in overall survival. However, robust comparisons between these regimens are still lacking. We conducted a mixed treatment comparison meta-analysis regarding these three regimens. Mixed treatment comparison is a statistical method of data summarization that aggregates data from both direct and indirect effect estimates. Literature search strategy included MEDLINE, EMBASE, Cochrane, Scielo and LILACS, from inception until August 2013 and resulted in the inclusion of 17 trials enrolling 7258 adult patients. HDD [relative risk (RR) 1.13; 95% credible interval (CrI) 1.02-1.26] and IDA (RR 1.13; 95% CrI 1.05-1.23) showed higher CR rates than CDD. IDA also led to lower long-term overall mortality rates when compared with CDD (RR 0.93, 95% CrI 0.86-0.99), whereas HDD and CDD were no different (RR 0.94, 95% CrI 0.85-1.02). HDD and IDA comparison did not reach statistically significant differences in CR (RR 1.00; 95% CrI 0.89-1.11) and in long-term mortality (RR 1.01, 95% CrI 0.91-1.11). IDA and HDD are consistently superior to CDD in inducing CR, and IDA was associated with lower long-term mortality. On the basis of these findings, we recommend incorporation of IDA and HDD instead of the traditional CDD as standard treatments for acute myeloid leukaemia induction. The lack of HDD benefit on mortality, when compared with CDD in this study, should be cautiously addressed, because it may have been susceptible to underestimation because of statistical power limitations. Copyright © 2014 John Wiley & Sons, Ltd.

Candidate Mission from Planet Earth control and data delivery system architecture

NASA Technical Reports Server (NTRS)

Shapiro, Phillip; Weinstein, Frank C.; Hei, Donald J., Jr.; Todd, Jacqueline

1992-01-01

Using a structured, experienced-based approach, Goddard Space Flight Center (GSFC) has assessed the generic functional requirements for a lunar mission control and data delivery (CDD) system. This analysis was based on lunar mission requirements outlined in GSFC-developed user traffic models. The CDD system will facilitate data transportation among user elements, element operations, and user teams by providing functions such as data management, fault isolation, fault correction, and link acquisition. The CDD system for the lunar missions must not only satisfy lunar requirements but also facilitate and provide early development of data system technologies for Mars. Reuse and evolution of existing data systems can help to maximize system reliability and minimize cost. This paper presents a set of existing and currently planned NASA data systems that provide the basic functionality. Reuse of such systems can have an impact on mission design and significantly reduce CDD and other system development costs.

Structure of hadron resonances with a nearby zero of the amplitude

NASA Astrophysics Data System (ADS)

Kamiya, Yuki; Hyodo, Tetsuo

2018-03-01

We discuss the relation between the analytic structure of the scattering amplitude and the origin of an eigenstate represented by a pole of the amplitude. If the eigenstate is not dynamically generated by the interaction in the channel of interest, the residue of the pole vanishes in the zero coupling limit. Based on the topological nature of the phase of the scattering amplitude, we show that the pole must encounter with the Castillejo-Dalitz-Dyson (CDD) zero in this limit. It is concluded that the dynamical component of the eigenstate is small if a CDD zero exists near the eigenstate pole. We show that the line shape of the resonance is distorted from the Breit-Wigner form as an observable consequence of the nearby CDD zero. Finally, studying the positions of poles and CDD zeros of the K ¯ N -π Σ amplitude, we discuss the origin of the eigenstates in the Λ (1405 ) region.

A FORTRAN IV Computer Program for the Time Domain Analysis of the Two- Dimensional Dynamic Motions of General Buoy-Cable-Body Systems

DTIC Science & Technology

1977-06-01

SPHEROIDAL BUOYS As mentioned previously, for the limiting case of zero ; educed frequency where tile free surface behaves as a rigid plane, the...4P ) -4 -4 ft O D - % Cdd :# P) fy ou Cd 1d Cd’. . 6 - C3 ’o .. eg S w Cd *g.4C~dI~**II~.a Ký 0 4 : 10 In H-C IV ..4 _ C) bu 0 40 la W C2C W cc lp lqa

Dioxins and Nonortho PCBs in Breast Milk of Vietnamese Mothers Living in the Largest Hot Spot of Dioxin Contamination.

PubMed

Nghi, Tran Ngoc; Nishijo, Muneko; Manh, Ho Dung; Tai, Pham The; Van Luong, Hoang; Anh, Tran Hai; Thao, Pham Ngoc; Trung, Nguyen Viet; Waseda, Tomoo; Nakagawa, Hideaki; Kido, Teruhiko; Nishijo, Hisao

2015-05-05

Bien Hoa Air Base is the largest dioxin contamination hot spot in Vietnam. In 2012, we recruited 216 mothers who were living in 10 communities around Bien Hoa Air Base and had delivered newborns at a prefecture hospital, and we investigated recent exposure levels of dioxins and nonortho PCBs in their breast milk. 2,3,7,8-Tetrachlorodibenzo-p-dioxin (2,3,7,8-tetraCDD) was present at 2.6 pg/g lipid in primiparae and 2.2 pg/g lipid in multiparae. Among multiparae and total subjects, significant high prevalence of 2,3,7,8-tetraCDD≥5 pg/g lipid and 2,3,7,8-tetraCDD contribution≥40% were observed in mothers living in the five communities closest to Bien Hoa Air Base. The TEQ for nonortho PCBs was 1.6 pg-TEQ/g lipid for primiparae, and this was even lower than that in the unsprayed area. The length of residency was a strong factor to increase dioxins, including 2,3,7,8-tetraCDD. Residency in the five communities with the highest exposure was a specific risk factor for increased 2,3,7,8-tetraCDD in breast milk. Food intake might contribute partly to the increased levels of dioxin congeners other than 2,3,7,8-tetraCDD in breast milk. These results suggest that Bien Hoa Air Base has led to elevated 2,3,7,8-tetraCDD levels in breast milk of mothers in nearby areas even in the recent years.

Microstructural comparison of the kinematics of discrete and continuum dislocations models

NASA Astrophysics Data System (ADS)

Sandfeld, Stefan; Po, Giacomo

2015-12-01

The Continuum Dislocation Dynamics (CDD) theory and the Discrete Dislocation Dynamics (DDD) method are compared based on concise mathematical formulations of the coarse graining of discrete data. A numerical tool for converting from a discrete to a continuum representation of a given dislocation configuration is developed, which allows to directly compare both simulation approaches based on continuum quantities (e.g. scalar density, geometrically necessary densities, mean curvature). Investigating the evolution of selected dislocation configurations within analytically given velocity fields for both DDD and CDD reveals that CDD contains a surprising number of important microstructural details.

Impacts of global warming on residential heating and cooling degree-days in the United States

PubMed Central

Petri, Yana; Caldeira, Ken

2015-01-01

Climate change is expected to decrease heating demand and increase cooling demand for buildings and affect outdoor thermal comfort. Here, we project changes in residential heating degree-days (HDD) and cooling degree-days (CDD) for the historical (1981–2010) and future (2080–2099) periods in the United States using median results from the Climate Model Intercomparison Project phase 5 (CMIP5) simulations under the Representation Concentration Pathway 8.5 (RCP8.5) scenario. We project future HDD and CDD values by adding CMIP5 projected changes to values based on historical observations of US climate. The sum HDD + CDD is an indicator of locations that are thermally comfortable, with low heating and cooling demand. By the end of the century, station median HDD + CDD will be reduced in the contiguous US, decreasing in the North and increasing in the South. Under the unmitigated RCP8.5 scenario, by the end of this century, in terms of HDD and CDD values considered separately, future New York, NY, is anticipated to become more like present Oklahoma City, OK; Denver, CO, becomes more like Raleigh, NC, and Seattle, WA, becomes more like San Jose, CA. These results serve as an indicator of projected climate change and can help inform decision-making. PMID:26238673

Impacts of global warming on residential heating and cooling degree-days in the United States.

PubMed

Petri, Yana; Caldeira, Ken

2015-08-04

Climate change is expected to decrease heating demand and increase cooling demand for buildings and affect outdoor thermal comfort. Here, we project changes in residential heating degree-days (HDD) and cooling degree-days (CDD) for the historical (1981-2010) and future (2080-2099) periods in the United States using median results from the Climate Model Intercomparison Project phase 5 (CMIP5) simulations under the Representation Concentration Pathway 8.5 (RCP8.5) scenario. We project future HDD and CDD values by adding CMIP5 projected changes to values based on historical observations of US climate. The sum HDD + CDD is an indicator of locations that are thermally comfortable, with low heating and cooling demand. By the end of the century, station median HDD + CDD will be reduced in the contiguous US, decreasing in the North and increasing in the South. Under the unmitigated RCP8.5 scenario, by the end of this century, in terms of HDD and CDD values considered separately, future New York, NY, is anticipated to become more like present Oklahoma City, OK; Denver, CO, becomes more like Raleigh, NC, and Seattle, WA, becomes more like San Jose, CA. These results serve as an indicator of projected climate change and can help inform decision-making.

MOnthly TEmperature DAtabase of Spain 1951-2010: MOTEDAS (2): The Correlation Decay Distance (CDD) and the spatial variability of maximum and minimum monthly temperature in Spain during (1981-2010).

NASA Astrophysics Data System (ADS)

Cortesi, Nicola; Peña-Angulo, Dhais; Simolo, Claudia; Stepanek, Peter; Brunetti, Michele; Gonzalez-Hidalgo, José Carlos

2014-05-01

One of the key point in the develop of the MOTEDAS dataset (see Poster 1 MOTEDAS) in the framework of the HIDROCAES Project (Impactos Hidrológicos del Calentamiento Global en España, Spanish Ministery of Research CGL2011-27574-C02-01) is the reference series for which no generalized metadata exist. In this poster we present an analysis of spatial variability of monthly minimum and maximum temperatures in the conterminous land of Spain (Iberian Peninsula, IP), by using the Correlation Decay Distance function (CDD), with the aim of evaluating, at sub-regional level, the optimal threshold distance between neighbouring stations for producing the set of reference series used in the quality control (see MOTEDAS Poster 1) and the reconstruction (see MOREDAS Poster 3). The CDD analysis for Tmax and Tmin was performed calculating a correlation matrix at monthly scale between 1981-2010 among monthly mean values of maximum (Tmax) and minimum (Tmin) temperature series (with at least 90% of data), free of anomalous data and homogenized (see MOTEDAS Poster 1), obtained from AEMEt archives (National Spanish Meteorological Agency). Monthly anomalies (difference between data and mean 1981-2010) were used to prevent the dominant effect of annual cycle in the CDD annual estimation. For each station, and time scale, the common variance r2 (using the square of Pearson's correlation coefficient) was calculated between all neighbouring temperature series and the relation between r2 and distance was modelled according to the following equation (1): Log (r2ij) = b*°dij (1) being Log(rij2) the common variance between target (i) and neighbouring series (j), dij the distance between them and b the slope of the ordinary least-squares linear regression model applied taking into account only the surrounding stations within a starting radius of 50 km and with a minimum of 5 stations required. Finally, monthly, seasonal and annual CDD values were interpolated using the Ordinary Kriging with a spherical variogram over conterminous land of Spain, and converted on a regular 10 km2 grid (resolution similar to the mean distance between stations) to map the results. In the conterminous land of Spain the distance at which couples of stations have a common variance in temperature (both maximum Tmax, and minimum Tmin) above the selected threshold (50%, r Pearson ~0.70) on average does not exceed 400 km, with relevant spatial and temporal differences. The spatial distribution of the CDD shows a clear coastland-to-inland gradient at annual, seasonal and monthly scale, with highest spatial variability along the coastland areas and lower variability inland. The highest spatial variability coincide particularly with coastland areas surrounded by mountain chains and suggests that the orography is one of the most driving factor causing higher interstation variability. Moreover, there are some differences between the behaviour of Tmax and Tmin, being Tmin spatially more homogeneous than Tmax, but its lower CDD values indicate that night-time temperature is more variable than diurnal one. The results suggest that in general local factors affects the spatial variability of monthly Tmin more than Tmax and then higher network density would be necessary to capture the higher spatial variability highlighted for Tmin respect to Tmax. The results suggest that in general local factors affects the spatial variability of Tmin more than Tmax and then higher network density would be necessary to capture the higher spatial variability highlighted for minimum temperature respect to maximum temperature. A conservative distance for reference series could be evaluated in 200 km, that we propose for continental land of Spain and use in the development of MOTEDAS.

Heart dysfunction induced by choline-deficiency in adult rats: the protective role of L-carnitine.

PubMed

Strilakou, Athina A; Lazaris, Andreas C; Perelas, Apostolos I; Mourouzis, Iordanis S; Douzis, Ioannis Ch; Karkalousos, Petros L; Stylianaki, Aikaterini Th; Pantos, Costas I; Liapi, Charis A

2013-06-05

Choline is a B vitamin co-factor and its deficiency seems to impair heart function. Carnitine, a chemical analog of choline, has been used as adjunct in the management of cardiac diseases. The study investigates the effects of choline deficiency on myocardial performance in adult rats and the possible modifications after carnitine administration. Wistar Albino rats (n=24), about 3 months old, were randomized into four groups fed with: (a) standard diet (control-CA), (b) choline deficient diet (CDD), (c) standard diet and carnitine in drinking water 0.15% w/v (CARN) and (d) choline deficient diet and carnitine (CDD+CARN). After four weeks of treatment, we assessed cardiac function under isometric conditions using the Langendorff preparations [Left Ventricular Developed Pressure (LVDP-mmHg), positive and negative first derivative of LVDP were evaluated], measured serum homocysteine and brain natriuretic peptide (BNP) levels and performed histopathology analyses. In the CDD group a compromised myocardium contractility compared to control (P=0.01), as assessed by LVDP, was noted along with a significantly impaired diastolic left ventricular function, as assessed by (-) dp/dt (P=0.02) that were prevented by carnitine. Systolic force, assessed by (+) dp/dt, showed no statistical difference between groups. A significant increase in serum BNP concentration was found in the CDD group (P<0.004) which was attenuated by carnitine (P<0.05), whereas homocysteine presented contradictory results (higher in the CDD+CARN group). Heart histopathology revealed a lymphocytic infiltration of myocardium and valves in the CDD group that was reduced by carnitine. In conclusion, choline deficiency in adult rats impairs heart performance; carnitine acts against these changes. Copyright © 2013 Elsevier B.V. All rights reserved.

Testing the distance-duality relation in the Rh = ct universe

NASA Astrophysics Data System (ADS)

Hu, J.; Wang, F. Y.

2018-07-01

In this paper, we test the cosmic distance-duality (CDD) relation using the luminosity distances from joint light-curve analysis Type Ia supernovae (SNe Ia) sample and angular diameter distance sample from galaxy clusters. The Rh = ct and Λ cold dark matter (CDM) models are considered. In order to compare the two models, we constrain the CDD relation and the SNe Ia light-curve parameters simultaneously. Considering the effects of Hubble constant, we find that η ≡ DA(1 + z)2/DL = 1 is valid at the 2σ confidence level in both models with H0= 67.8 ± 0.9 km -1s-1 Mpc. However, the CDD relation is valid at 3σ confidence level with H0= 73.45 ± 1.66 km -1s-1Mpc. Using the Akaike Information Criterion and the Bayesian Information Criterion, we find that the ΛCDM model is very stongly preferred over the Rh = ct model with these data sets for the CDD relation test.

A most spectrum-efficient duplexing system: CDD

NASA Astrophysics Data System (ADS)

Lee, William C. Y.

2001-10-01

The game to play in wireless communications when it comes to increasing spectrum efficiency is to eliminate interference. Currently, all cellular systems use FDD (Frequency Division Duplexing) in an attempt to eliminate the interference from the adjacent cells. Through the use of many technologies only one type of interference remains and that is the adjacent base-tohome mobile interference. TDD (Time Division Duplexing) has not been used for mobile cellular systems, not only because of the adjacent base-to-home mobile interference, but also because of the additional adjacent base-to-home base interference, and adjacent mobile-to-home mobile interference. Therefore, TDD can only be used for small, confined area systems. CDD (Code Division Duplexing) can eliminate all three kinds of interference; the adjacent base-to-home mobile, the adjacent baseto-home base, and the adjacent mobile- to- home in cellular systems. Eliminating each of these interferences makes CDD the most spectrum efficient duplexing system. This talk will elaborate on a set of smart codes, which will make an efficient CDD system a reality.

76 FR 33342 - Final Supplementary Rules for Public Lands Managed by the California Desert District

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-08

... DEPARTMENT OF THE INTERIOR Bureau of Land Management [L12200000.NO0000.LLCAD00000] Final Supplementary Rules for Public Lands Managed by the California Desert District AGENCY: Bureau of Land Management... Land Management (BLM), CDD office and the five field offices within the CDD, are issuing Final...

Prevalence of Childhood Disintegrative Disorder.

ERIC Educational Resources Information Center

Fombonne, Eric

2002-01-01

A review of 32 epidemiological surveys of autism and pervasive developmental disorders found four surveys yielded estimates for childhood disintegrative disorder (CDD) ranging from 1.1 to 6.4 per 100,000. It is concluded that CDD is very rare and its prevalence is 60 times less than that of autistic disorder. (Contains references.) (Author/CR)

Treating multi-level cervical disc disease with hybrid surgery compared to anterior cervical discectomy and fusion: a systematic review and meta-analysis.

PubMed

Lu, Victor M; Zhang, Lucy; Scherman, Daniel B; Rao, Prashanth J; Mobbs, Ralph J; Phan, Kevin

2017-02-01

The traditional surgical approach to treat multi-level cervical disc disease (mCDD) has been anterior cervical discectomy and fusion (ACDF). There has been recent development of other surgical approaches to further improve clinical outcomes. Collectively, when elements of these different approaches are combined in surgery, it is known as hybrid surgery (HS) which remains a novel treatment option. A systematic review and meta-analysis was conducted to compare the outcomes of HS versus ACDF for the treatment of mCDD. Relevant articles were identified from six electronic databases from their inception to January 2016. From 8 relevant studies identified, 169 patients undergoing HS were compared with 193 ACDF procedures. Operative time was greater after HS by 42 min (p < 0.00001), with less intraoperative blood loss by 26 mL (p < 0.00001) and shorter return to work by 32 days (p < 0.00001). In terms of clinical outcomes, HS was associated with greater C2-C7 range of motion (ROM) preservation (p < 0.00001) and less functional impairment (p = 0.008) after surgery compared to ACDF. There was no significant difference between HS and ACDF with respect to postoperative pain (p = 0.12). The postoperative course following HS was not significantly different to ACDF in terms of length of stay (p = 0.24) and postoperative complication rates (p = 0.18). HS is a novel surgical approach to treat mCDD, associated with a greater operative time, less intraoperative blood loss and comparable if not superior clinical outcomes compared to ACDF. While it remains a viable consideration, there is a lack of robust clinical evidence in the literature. Future large prospective registries and randomised trials are warranted to validate the findings of this study.

Degree Day Requirements for Kudzu Bug (Hemiptera: Plataspidae), a Pest of Soybeans.

PubMed

Grant, Jessica I; Lamp, William O

2018-04-02

Understanding the phenology of a new potential pest is fundamental for the development of a management program. Megacopta cribraria Fabricius (Hemiptera: Plataspidae), kudzu bug, is a pest of soybeans first detected in the United States in 2009 and in Maryland in 2013. We observed the phenology of kudzu bug life stages in Maryland, created a Celsius degree-day (CDD) model for development, and characterized the difference between microhabitat and ambient temperatures of both kudzu, Pueraria montana (Lour.) Merr. (Fabales: Fabaceae) and soybeans, Glycine max (L.) Merrill (Fabales: Fabaceae). In 2014, low population numbers yielded limited resolution from field phenology observations. We observed kudzu bug populations persisting within Maryland; but between 2013 and 2016, populations were low compared to populations in the southeastern United States. Based on the degree-day model, kudzu bug eggs require 80 CDD at a minimum temperature of 14°C to hatch. Nymphs require 545 CDD with a minimum temperature of 16°C for development. The CDD model matches field observations when factoring a biofix date of April 1 and a minimum preoviposition period of 17 d. The model suggests two full generations per year in Maryland. Standard air temperature monitors do not affect model predictions for pest management, as microhabitat temperature differences did not show a clear trend between kudzu and soybeans. Ultimately, producers can predict the timing of kudzu bug life stages with the CDD model for the use of timing management plans in soybean fields.

Detecting modulated signals in modulated noise: (II) neural thresholds in the songbird forebrain.

PubMed

Bee, Mark A; Buschermöhle, Michael; Klump, Georg M

2007-10-01

Sounds in the real world fluctuate in amplitude. The vertebrate auditory system exploits patterns of amplitude fluctuations to improve signal detection in noise. One experimental paradigm demonstrating these general effects has been used in psychophysical studies of 'comodulation detection difference' (CDD). The CDD effect refers to the fact that thresholds for detecting a modulated, narrowband noise signal are lower when the envelopes of flanking bands of modulated noise are comodulated with each other, but fluctuate independently of the signal compared with conditions in which the envelopes of the signal and flanking bands are all comodulated. Here, we report results from a study of the neural correlates of CDD in European starlings (Sturnus vulgaris). We manipulated: (i) the envelope correlations between a narrowband noise signal and a masker comprised of six flanking bands of noise; (ii) the signal onset delay relative to masker onset; (iii) signal duration; and (iv) masker spectrum level. Masked detection thresholds were determined from neural responses using signal detection theory. Across conditions, the magnitude of neural CDD ranged between 2 and 8 dB, which is similar to that reported in a companion psychophysical study of starlings [U. Langemann & G.M. Klump (2007) Eur. J. Neurosci., 26, 1969-1978]. We found little evidence to suggest that neural CDD resulted from the across-channel processing of auditory grouping cues related to common envelope fluctuations and synchronous onsets between the signal and flanking bands. We discuss a within-channel model of peripheral processing that explains many of our results.

Potencies of red seabream AHR1- and AHR2-mediated transactivation by dioxins: implication of both AHRs in dioxin toxicity.

PubMed

Bak, Su-Min; Iida, Midori; Hirano, Masashi; Iwata, Hisato; Kim, Eun-Young

2013-03-19

To evaluate species- and isoform-specific responses to dioxins and related compounds (DRCs) via aryl hydrocarbon receptor (AHR) in the red seabream ( Pagrus major ), we constructed a reporter gene assay system. Each expression plasmid of red seabream AHR1 (rsAHR1) and AHR2 (rsAHR2) together with a reporter plasmid containing red seabream CYP1A 5'-flanking region were transfected into COS-7 cells. The cells were treated with graded concentrations of seven DRC congeners including 2,3,7,8-TCDD, 1,2,3,7,8-PeCDD, 1,2,3,4,7,8-HxCDD, 2,3,7,8-TCDF, 2,3,4,7,8-PeCDF, 1,2,3,4,7,8-HxCDF, and PCB126. Both rsAHR1 and rsAHR2 exhibited dose-dependent responses for all the tested congeners. The rsAHR isoform-specific TCDD induction equivalency factors (rsAHR1- and rsAHR2-IEFs) were calculated on the basis of 2,3,7,8-TCDD relative potency derived from the dose-response of each congener. The rsAHR1-IEFs of PeCDD, HxCDD, TCDF, PeCDF, and HxCDF were estimated as 0.17, 0.29, 2.5, 1.5, and 0.27, respectively. For PCB126, no rsAHR1-IEF was given because of less than 10% 2,3,7,8-TCDD maximum response. The rsAHR2-IEFs of PeCDD, HxCDD, TCDF, PeCDF, HxCDF, and PCB126 were estimated as 0.38, 0.13, 1.5, 0.93, 0.20, and 0.0085, respectively. The rsAHR1/2-IEF profiles were different from WHO toxic equivalency factors for fish. In silico docking simulations supported that both rsAHRs have potentials to bind to these congeners. These results suggest that dioxin toxicities may be mediated by both rsAHRs in red seabreams.

A Game Theoretic Model of Thermonuclear Cyberwar

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

Soper, Braden C.

In this paper we propose a formal game theoretic model of thermonuclear cyberwar based on ideas found in [1] and [2]. Our intention is that such a game will act as a first step toward building more complete formal models of Cross-Domain Deterrence (CDD). We believe the proposed thermonuclear cyberwar game is an ideal place to start on such an endeavor because the game can be fashioned in a way that is closely related to the classical models of nuclear deterrence [4–6], but with obvious modifications that will help to elucidate the complexities introduced by a second domain. We startmore » with the classical bimatrix nuclear deterrence game based on the game of chicken, but introduce uncertainty via a left-of-launch cyber capability that one or both players may possess.« less

Simplified Paper Format for Detecting HIV Drug Resistance in Clinical Specimens by Oligonucleotide Ligation

PubMed Central

Panpradist, Nuttada; Beck, Ingrid A.; Chung, Michael H.; Kiarie, James N.; Frenkel, Lisa M.; Lutz, Barry R.

2016-01-01

Human immunodeficiency virus (HIV) is a chronic infection that can be managed by antiretroviral treatment (ART). However, periods of suboptimal viral suppression during lifelong ART can select for HIV drug resistant (DR) variants. Transmission of drug resistant virus can lessen or abrogate ART efficacy. Therefore, testing of individuals for drug resistance prior to initiation of treatment is recommended to ensure effective ART. Sensitive and inexpensive HIV genotyping methods are needed in low-resource settings where most HIV infections occur. The oligonucleotide ligation assay (OLA) is a sensitive point mutation assay for detection of drug resistance mutations in HIV pol. The current OLA involves four main steps from sample to analysis: (1) lysis and/or nucleic acid extraction, (2) amplification of HIV RNA or DNA, (3) ligation of oligonucleotide probes designed to detect single nucleotide mutations that confer HIV drug resistance, and (4) analysis via oligonucleotide surface capture, denaturation, and detection (CDD). The relative complexity of these steps has limited its adoption in resource-limited laboratories. Here we describe a simplification of the 2.5-hour plate-format CDD to a 45-minute paper-format CDD that eliminates the need for a plate reader. Analysis of mutations at four HIV-1 DR codons (K103N, Y181C, M184V, and G190A) in 26 blood specimens showed a strong correlation of the ratios of mutant signal to total signal between the paper CDD and the plate CDD. The assay described makes the OLA easier to perform in low resource laboratories. PMID:26751207

2011 Chemical, Biological, Radiological, and Nuclear Survivability Conference

DTIC Science & Technology

2011-05-18

Protection (barrier, sorptive and reactive material technologies) o Top surface antimicrobial treatments (kills spores, bacteria, fungi, viruses ) o...Warning System (TWS) CDD - Countermeasure Anti-Torpedo ( CAT ) CDD UNCLASSIFIED Joint Program Executive Office for Chemical and Biological Defense May...Creating viruses de novo Biological Threats UNCLASSIFIED JPEO-CBD Radiological/Nuclear (RN) Status and Path Forward • Issue: No identified DoD

A high-dose preparation of lactobacilli and bifidobacteria in the prevention of antibiotic-associated and Clostridium difficile diarrhoea in older people admitted to hospital: a multicentre, randomised, double-blind, placebo-controlled, parallel arm trial (PLACIDE).

PubMed

Allen, S J; Wareham, K; Wang, D; Bradley, C; Sewell, B; Hutchings, H; Harris, W; Dhar, A; Brown, H; Foden, A; Gravenor, M B; Mack, D; Phillips, C J

2013-12-01

Antibiotic-associated diarrhoea (AAD) occurs most commonly in older people admitted to hospital and within 12 weeks of exposure to broad-spectrum antibiotics. Although usually a mild and self-limiting illness, the 15-39% of cases caused by Clostridium difficile infection [C. difficile diarrhoea (CDD)] may result in severe diarrhoea and death. Previous research has shown that probiotics, live microbial organisms that, when administered in adequate numbers, are beneficial to health, may be effective in preventing AAD and CDD. To determine the clinical effectiveness and cost-effectiveness of a high-dose, multistrain probiotic in the prevention of AAD and CDD in older people admitted to hospital. A multicentre, randomised, double-blind, placebo-controlled, parallel-arm trial. Medical, surgical and elderly care inpatient wards in five NHS hospitals in the UK. Eligible patients were aged ≥ 65 years, were exposed to one or more oral or parenteral antibiotics and were without pre-existing diarrhoeal disorders, recent CDD or at risk of probiotic adverse effects. Out of 17,420 patients screened, 2981 (17.1%) were recruited. Participants were allocated sequentially according to a computer-generated random allocation sequence; 1493 (50.1%) were allocated to the probiotic and 1488 (49.9%) to the placebo arm. Vegetarian capsules containing two strains of lactobacilli and two strains of bifidobacteria (a total of 6 × 10(10) organisms per day) were taken daily for 21 days. The placebo was inert maltodextrin powder in identical capsules. The occurrence of AAD within 8 weeks and CDD within 12 weeks of recruitment was determined by participant follow-up and checking hospital laboratory records by research nurses who were blind to arm allocation. Analysis based on the treatment allocated included 2941 (98.7%) participants. Potential risk factors for AAD at baseline were similar in the two study arms. Frequency of AAD (including CDD) was similar in the probiotic (159/1470, 10.8%) and placebo arms [153/1471, 10.4%; relative risk (RR) 1.04; 95% confidence interval (CI) 0.84 to 1.28; p = 0.71]. CDD was an uncommon cause of AAD and occurred in 12/1470 (0.8%) participants in the probiotic and 17/1471 (1.2%) in the placebo arm (RR 0.71; 95% CI 0.34 to 1.47; p = 0.35). Duration and severity of diarrhoea, common gastrointestinal symptoms, serious adverse events and quality of life measures were also similar in the two arms. Total health-care costs per patient did not differ significantly between the probiotic (£8020; 95% CI £7620 to £8420) and placebo (£8010; 95% CI £7600 to £8420) arms. We found no evidence that probiotic administration was effective in preventing AAD. Although there was a trend towards reduced CDD in the probiotic arm, on balance, the administration of this probiotic seems unlikely to benefit older patients exposed to antibiotics. A better understanding of the pathogenesis of AAD and CDD and the strain-specific effects of probiotics is needed before further clinical trials of specific microbial preparations are undertaken. Evaluation of the effectiveness of other probiotics will be difficult where other measures, such as antibiotic stewardship, have reduced CDD rates. This trial is registered as ISRCTN70017204. This project was funded by the NIHR Health Technology Assessment programme and will be published in full in Health Technology Assessment; Vol. 17, No. 57. See the NIHR Journals Library website for further project information.

[Anti-NMDA-receptor encephalitis: a new axis-III disorder in the differential diagnosis of childhood disintegrative disorder, early onset schizophrenia and late onset autism].

PubMed

Creten, C; van der Zwaan, S; Blankespoor, R J; Maatkamp, A; Klinkenberg, S; van Kranen-Mastenbroek, V H J M; Nicolai, J; Dhossche, D M; van Os, J; Schieveld, J N M

2012-01-01

Childhood disintegrative disorder (CDD), early onset schizophrenia (EOS), and late onset autism (LOA) often follow a similar course: initially, development is normal, then there is a sudden neuropsychiatric deterioration of social interaction and communication skills, which is combined with a decline in intelligence and reduction in daily activities. A 9-year-old boy was admitted to the paediatric ward with acute onset of secondary epileptic seizures. It was not long until the boy's symptoms resembled that of patients with cdd, eos and loa. Intensive tests led to the diagnosis of anti-NMDA-receptor encephalitis. Anti-NMDA-receptor encephalitis should be regarded as a possible organic cause underlying the syndromal presentation of CDD, EOS and LOA.

Collaborative drug discovery for More Medicines for Tuberculosis (MM4TB)

PubMed Central

Ekins, Sean; Spektor, Anna Coulon; Clark, Alex M.; Dole, Krishna; Bunin, Barry A.

2016-01-01

Neglected disease drug discovery is generally poorly funded compared with major diseases and hence there is an increasing focus on collaboration and precompetitive efforts such as public–private partnerships (PPPs). The More Medicines for Tuberculosis (MM4TB) project is one such collaboration funded by the EU with the goal of discovering new drugs for tuberculosis. Collaborative Drug Discovery has provided a commercial web-based platform called CDD Vault which is a hosted collaborative solution for securely sharing diverse chemistry and biology data. Using CDD Vault alongside other commercial and free cheminformatics tools has enabled support of this and other large collaborative projects, aiding drug discovery efforts and fostering collaboration. We will describe CDD's efforts in assisting with the MM4TB project. PMID:27884746

Quantitative mRNA analysis of muscarinic acetylcholine receptors in the intestine of dairy cows with spontaneous caecal dilatation-dislocation.

PubMed

Ontsouka, E C; Steiner, A; Bruckmaier, R M; Blum, J W; Meylan, M

2009-05-01

Muscarinic receptors mediate acetylcholine-induced muscular contractions. In this study, mRNA levels of muscarinic receptor subtypes 2 and 3 (M(2) and M(3)) in the ileum, caecum, proximal loop of the ascending colon (PLAC) and external loop of the spiral colon (ELSC) were determined by quantitative polymerase chain reaction in seven cows with caecal dilatation-dislocation (CDD) and seven healthy control cows. Levels of M(2) were significantly lower in the caecum, PLAC and ELSC and levels of M(3) were significantly lower in the ileum, caecum, PLAC and ELSC of cows with CDD compared to healthy cows (P<0.05). Down-regulation of M(3) may play a role in the pathogenesis of CDD.

Modulation of the Effect of l‐β‐D‐Arabinofuranosylcytosine by 6‐Mercaptopurine in L1210 Cells

PubMed Central

Kawai, Yasukazu; Ueda, Takanori; Nakamura, Toru

1994-01-01

In L1210 cells incubated with l‐β‐D‐arabinofuranosylcytosine (ara‐C), 6‐mercaptopurine (6‐MP) significantly potentiated 1‐β‐D‐arabinofuranosylcytosme 5′‐triphosphate (ara‐CTP) accumulation and ara‐C incorporation into DNA (ara‐C/DNA). The cytotoxicity of these two drugs was assessed to be at least additive by clonogenic assay. l‐β‐D‐Arabinofuranosylnracil (ara‐U) level in a cell suspension was suppressed by 6‐MP in a concentration‐dependent fashion, though intracellular cytidine deaminase (CDD) activity was not affected by 6‐MP. In addition, extracted CDD activity was not directly inhibited by 6‐MP or by its intracellular metabolites in vitro. After preincubation in the presence or absence of 6‐MP, the cell suspension was fractionated to obtain the spent medium and cell pellet. Then, each fraction was incubated with ara‐C. Ara‐U formation in the spent medium was found to increase conspicuously in relation to the time of preincubation in the control and it was suppressed by 6‐MP pretreatment. Ara‐U formation in the cell compartment increased slightly in relation to the time of preincubation in the control and substantially no suppression of ara‐U formation was observed in spite of 6‐MP pretreatment. In conclusion, intracellularly synthesized CDD was thought to be rapidly shed into the medium and the released CDD could play an important role in ara‐C inactivation. 6‐MP interrupted some step between synthesis and shedding of CDD, resulting in a decrease of the ara‐C deamination in the medium and enhancement of its antileukemic effect. PMID:7961129

Relationship of polychlorinated dibenzo-p-dioxin and polychlorinated dibenzofuran levels to stable-nitrogen isotope abundance in marine birds and mammals in coastal California

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

Jarman, W.M.; Sydeman, W.J.; Hobson, K.A.

1997-05-01

Levels of polychlorinated dibenzo-p-dioxins (PCDDs) and polychlorinated dibenzofurans (PCDFs) were determined in common murre (Uria aalge), Brandt`s cormorant (Phalacrocorax penicillatus), rhinoceros auklet (Cerorhinca monocerata), and pigeon guillemot (Cepphus columba) eggs, and Steller sea lion (Eumetopias jubatus) blubber collected from the Gulf of the Farallones National Marine Sanctuary in 1993. In addition, the samples were analyzed for stable-nitrogen isotopes ({delta}{sup 15}N). Of the PCDDs and PCDFs, the 2,3,7,8-TCDD (TCDD) and 2,3,7,8-TCDF (TCDF) congeners were the most prominent in the birds. The levels of TCDD in the eggs ranged from 0.2 to 6.6 ng/wet kg in the pigeon guillemot and Brandt`s cormorant,more » respectively. The TCDF ranged from 0.30 to 2.25 ng/kg in the pigeon guillemot and Brandt`s cormorant eggs, respectively. Other prominent PCDD and PCDF congeners detected in all bird species were 1,2,3,6,7,8-HxCDD, 2,3,4,7,8-PeCDF, 1,2,3,7,8-PeCDD and 1,2,3,4,6,7,8-HpCDD. In the Steller sea lion the most prominent congeners were 1,2,3,7,8-PeCDD at 3.2 ng/kg, 2,3,7,8-TCDD at 2.9 ng/kg, OCDF at 2.2 ng/kg, 1,2,3,6,7,8-HxCDD at 1.92 ng/kg, and 1,2,3,4,7,8-HxCDF at 1.3 ng/kg. Stable-nitrogen values ranged from 16.9% in the pigeon guillemot and rhinoceros auklet to 19.8% in the Steller sea lion.« less

Using XML Configuration-Driven Development to Create a Customizable Ground Data System

NASA Technical Reports Server (NTRS)

Nash, Brent; DeMore, Martha

2009-01-01

The Mission data Processing and Control Subsystem (MPCS) is being developed as a multi-mission Ground Data System with the Mars Science Laboratory (MSL) as the first fully supported mission. MPCS is a fully featured, Java-based Ground Data System (GDS) for telecommand and telemetry processing based on Configuration-Driven Development (CDD). The eXtensible Markup Language (XML) is the ideal language for CDD because it is easily readable and editable by all levels of users and is also backed by a World Wide Web Consortium (W3C) standard and numerous powerful processing tools that make it uniquely flexible. The CDD approach adopted by MPCS minimizes changes to compiled code by using XML to create a series of configuration files that provide both coarse and fine grained control over all aspects of GDS operation.

Cyclododecane exposure in the field of conservation and restoration of art objects.

PubMed

Vernez, David; Wognin, Barthélémy; Tomicic, Catherine; Plateel, Gregory; Charrière, Nicole; Bruhin, Stefanie

2011-04-01

Recent work practices in the conservation and restoration involve the use of cyclododecane (CDD, CAS 294-62-2) to protect fragile artifacts during their handling or transportation. Little is known about its toxicity, and no previous exposure has been reported. A short field investigation was conducted to characterize the exposure conditions to both CDD vapors and aerosols. Measurements were conducted in the laboratory of conservation and restoration of the archeological service in Bern (Switzerland). Three indoor and four outdoor typical work situations, either during brush or spray gun applications, were investigated. Measurements were performed on charcoal adsorbent tube and analyzed by a gas chromatograph equipped with a flame ionization detector. Measurements have been conducted during both brush and spray gun applications. Indoor exposures were of 0.75-15.5 mg/m(3), while outdoors exposures were 19.5-53.9 mg/m(3). Exposures appear to be extremely localized due to both physicochemical properties and application methods of the CDD. Vapor exposure increases dramatically with the confinement of the workplace. Preventive measures should be undertaken to limit as much as possible these exposures. Field work in confined areas (ditches, underground) is of particular concern. CDD-coated artifacts or materials should be stored in ventilated areas to avoid delayed exposures.

Fabrication of large area Si cylindric drift detectors

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

Chen, W.; Kraner, H.W.; Li, Z.

1993-04-01

Advanced Si drift detector, a large area cylindrical drift detector (CDD), processing steps, with the exception of the ion implantation, were carried out in the BNL class 100 cleanroom. The double-side planer process technique was developed for the fabrication of CDD. Important improvements of the double-side planer process in this fabrication are the introduction of Al implantation protection mask and the remaining of a 1000 Angstroms oxide layer in the p-window during the implantation. Another important design of the CDD is the structure called ``river,`` which ,allows the current generated on Si-SiO{sub 2} interface to ``flow`` into the guard anode,more » and thus can minimize the leakage current at the signed anode. The test result showed that most of the signal anodes have the leakage current about 0.3 nA/cm{sup 2} for the best detector.« less

Quantitative coronary angiography using image recovery techniques for background estimation in unsubtracted images

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

Wong, Jerry T.; Kamyar, Farzad; Molloi, Sabee

2007-10-15

Densitometry measurements have been performed previously using subtracted images. However, digital subtraction angiography (DSA) in coronary angiography is highly susceptible to misregistration artifacts due to the temporal separation of background and target images. Misregistration artifacts due to respiration and patient motion occur frequently, and organ motion is unavoidable. Quantitative densitometric techniques would be more clinically feasible if they could be implemented using unsubtracted images. The goal of this study is to evaluate image recovery techniques for densitometry measurements using unsubtracted images. A humanoid phantom and eight swine (25-35 kg) were used to evaluate the accuracy and precision of the followingmore » image recovery techniques: Local averaging (LA), morphological filtering (MF), linear interpolation (LI), and curvature-driven diffusion image inpainting (CDD). Images of iodinated vessel phantoms placed over the heart of the humanoid phantom or swine were acquired. In addition, coronary angiograms were obtained after power injections of a nonionic iodinated contrast solution in an in vivo swine study. Background signals were estimated and removed with LA, MF, LI, and CDD. Iodine masses in the vessel phantoms were quantified and compared to known amounts. Moreover, the total iodine in left anterior descending arteries was measured and compared with DSA measurements. In the humanoid phantom study, the average root mean square errors associated with quantifying iodine mass using LA and MF were approximately 6% and 9%, respectively. The corresponding average root mean square errors associated with quantifying iodine mass using LI and CDD were both approximately 3%. In the in vivo swine study, the root mean square errors associated with quantifying iodine in the vessel phantoms with LA and MF were approximately 5% and 12%, respectively. The corresponding average root mean square errors using LI and CDD were both 3%. The standard deviations in the differences between measured iodine mass in left anterior descending arteries using DSA and LA, MF, LI, or CDD were calculated. The standard deviations in the DSA-LA and DSA-MF differences (both {approx}21 mg) were approximately a factor of 3 greater than that of the DSA-LI and DSA-CDD differences (both {approx}7 mg). Local averaging and morphological filtering were considered inadequate for use in quantitative densitometry. Linear interpolation and curvature-driven diffusion image inpainting were found to be effective techniques for use with densitometry in quantifying iodine mass in vitro and in vivo. They can be used with unsubtracted images to estimate background anatomical signals and obtain accurate densitometry results. The high level of accuracy and precision in quantification associated with using LI and CDD suggests the potential of these techniques in applications where background mask images are difficult to obtain, such as lumen volume and blood flow quantification using coronary arteriography.« less

Childhood disintegrative disorder with seasonal total mutism: A rare clinical presentation

PubMed Central

Shirazi, Elham; Hosseinpoor, Sara; Mirhosseini, Seyyed Mohammad Mahdy; Bidaki, Reza

2016-01-01

Childhood disintegrative disorder (CDD) is a rare autistic-like clinical condition with unknown etiology, in that previously acquired age-appropriate language, social and adaptive abilities deteriorate significantly in 2-10-year-old healthy children, although physical and neurological evaluations display no observable abnormality. Our case is a 22-year-old female born of a consanguineous marriage, with the appearance of CDD symptoms in her fifth year of age following normal mental and physical development during her initial four years of life. Without any precipitating factor, she gradually lost her language abilities, social relational skills, affectionate behavior, adaptive capacities, peer play and meaningful interest in her surrounding, friends and family members over a period of 4 years, reaching a plateau in her ninth year of age. The unique special clinical symptom in this case is a seasonal total mutism, which after the beginning of her CDD symptoms is revealing every year covering the spring. As no additional physical or psychological change accompanies her total seasonal speech loss, it cannot be attributed to any mental condition known as having a seasonal pattern. Because in the literature CDD is presented mostly as case reports with lacking of advanced research data, describing any new case is recommended to improve the knowledge about this rare condition, especially if it displays some new unusual signs, not reported till now. PMID:27069898

Does Disposing of Construction and Demolition Debris in Unlined Landfills Impact Groundwater Quality? Evidence from 91 Landfill Sites in Florida.

PubMed

Powell, Jon T; Jain, Pradeep; Smith, Justin; Townsend, Timothy G; Tolaymat, Thabet M

2015-08-04

More than 1,500 construction and demolition debris (CDD) landfills operate in the United States (U.S.), and U.S. federal regulations do not require containment features such as low-permeability liners and leachate collection systems for these facilities. Here we evaluate groundwater quality from samples collected in groundwater monitoring networks at 91 unlined, permitted CDD landfills in Florida, U.S. A total of 460,504 groundwater sample results were analyzed, with a median of 10 years of quarterly or semiannual monitoring data per site including more than 400 different chemical constituents. Downgradient concentrations of total dissolved solids, sulfate, chloride, iron, ammonia-nitrogen, and aluminum were greater than upgradient concentrations (p < 0.05). At downgradient wells where sulfate concentrations were greater than 150 mg/L (approximately 10% of the maximum dissolved sulfate concentration in water, which suggests the presence of leachate from the landfill), iron and arsenic were detected in 91% and 43% of samples, with median concentrations of 1,900 μg/L and 11 μg/L, respectively. These results show that although health-based standards can be exceeded at unlined CDD landfills, the magnitude of detected chemical concentrations is generally small and reflective of leached minerals from components (wood, concrete, and gypsum drywall) that comprise the bulk of discarded CDD by mass.

Using exterior building surface films to assess human exposure and health risks from PCDD/Fs in New York City, USA, after the World Trade Center attacks.

PubMed

Rayne, Sierra

2005-12-09

Concentrations of tetra- through octa-chlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) were determined in exterior window films from Manhattan and Brooklyn in New York City (NYC), USA, 6 weeks after the World Trade Center (WTC) attacks of 11 September 2001. High concentrations of the 2,3,7,8-substituted congeners (P(2378)CDD/Fs) were observed, at levels up to 6600 pg-TEQ g(-1) nearest the WTC site. An equilibrium partitioning model was developed to reconstruct total gas + particle-phase atmospheric concentrations of P(2378)CDD/Fs at each site. The reconstructed atmospheric and window film concentrations were subsequently used in a preliminary human health risk assessment to estimate the potential cancer and non-cancer risks posed to residents of lower Manhattan from these contaminants over the 6 week exposure period between the WTC attacks and sampling dates. Residents of lower Manhattan appear to have a slightly elevated cancer risk (up to 1.6% increase over background) and increased P(2378)CDD/F body burden (up to 8.0% increase over background) because of above-background exposure to high concentrations of P(2378)CDD/Fs produced from the WTC attacks during the short period between 11 September 2001, and window film sampling 6 weeks later.

Testing the Distance-Duality Relation in the Rh = ct Universe

NASA Astrophysics Data System (ADS)

Hu, J.; Wang, F. Y.

2018-04-01

In this paper, we test the cosmic distance duality (CDD) relation using the luminosity distances from joint light-curve analysis (JLA) type Ia supernovae (SNe Ia) sample and angular diameter distance sample from galaxy clusters. The Rh = ct and ΛCDM models are considered. In order to compare the two models, we constrain the CCD relation and the SNe Ia light-curve parameters simultaneously. Considering the effects of Hubble constant, we find that η ≡ DA(1 + z)2/DL = 1 is valid at the 2σ confidence level in both models with H0 = 67.8 ± 0.9 km/s/Mpc. However, the CDD relation is valid at 3σ confidence level with H0 = 73.45 ± 1.66 km/s/Mpc. Using the Akaike Information Criterion (AIC) and the Bayesian Information Criterion (BIC), we find that the ΛCDM model is very strongly preferred over the Rh = ct model with these data sets for the CDD relation test.

Spondyloarthritis, diffuse idiopathic skeletal hyperostosis (DISH) and chondrocalcinosis.

PubMed

Armas, Jácome Brugues; Couto, Ana Rita; Bettencourt, Bruno Filipe

2009-01-01

The authors describe the main clinical and radiological findings of common enthesopathic disorders-spondylarthritis (SpA), chondrocalcinosis/calcium pyrophosphate dehydrate crystal deposition disease (CPPD CDD) and diffuse idiopathic skeletal hyperostosis (DISH), stressing similarities and differences which may help in the differential diagnosis. They emphasize the clinical presentation of the "pseudoankylosing spondylitis" forms of CPPD CDD. They also review the most relevant genes and molecular mechanisms associated with these conditions and with another enthesopathic disorder with high prevalence in the Japanese population-ossification of the posterior longitudinal ligament (OPLL).

Enhanced Polar System (EPS)

DTIC Science & Technology

2015-12-01

Aug 2014 Aug 2014 Feb 2015 Jul 2014 DT&E Completion for Single String May 2017 May 2017 Nov 2017 May 2017 RAA Jun 2018 Jun 2018 Jun 2019 Jun 2018 Change...as defined by Section 12.0 of the EPS CDD dated September 15, 2011 in support of IOC. RAA is the date two hosted payloads, T&C-T, CAPS, and the Gateway...system with the three NMTs are available for operational use per Section 12.3 of the EPS CDD dated September 15, 2011, in support of FOC. The RAA

Metabolic pathways promoting intrahepatic fatty acid accumulation in methionine and choline deficiency: implications for the pathogenesis of steatohepatitis.

PubMed

Macfarlane, David P; Zou, Xiantong; Andrew, Ruth; Morton, Nicholas M; Livingstone, Dawn E W; Aucott, Rebecca L; Nyirenda, Moffat J; Iredale, John P; Walker, Brian R

2011-02-01

The pathological mechanisms that distinguish simple steatosis from steatohepatitis (or NASH, with consequent risk of cirrhosis and hepatocellular cancer) remain incompletely defined. Whereas both a methionine- and choline-deficient diet (MCDD) and a choline-deficient diet (CDD) lead to hepatic triglyceride accumulation, MCDD alone is associated with hepatic insulin resistance and inflammation (steatohepatitis). We used metabolic tracer techniques, including stable isotope ([¹³C₄]palmitate) dilution and mass isotopomer distribution analysis (MIDA) of [¹³C₂]acetate, to define differences in intrahepatic fatty acid metabolism that could explain the contrasting effect of MCDD and CDD on NASH in C57Bl6 mice. Compared with control-supplemented (CS) diet, liver triglyceride pool sizes were similarly elevated in CDD and MCDD groups (24.37 ± 2.4, 45.94 ± 3.9, and 43.30 ± 3.5 μmol/liver for CS, CDD, and MCDD, respectively), but intrahepatic neutrophil infiltration and plasma alanine aminotransferase (31 ± 3, 48 ± 4, 231 ± 79 U/l, P < 0.05) were elevated only in MCDD mice. However, despite loss of peripheral fat in MCDD mice, neither the rate of appearance of palmitate (27.2 ± 3.5, 26.3 ± 2.3, and 28.3 ± 3.5 μmol·kg⁻¹·min⁻¹) nor the contribution of circulating fatty acids to the liver triglyceride pool differed between groups. Unlike CDD, MCDD had a defect in hepatic triglyceride export that was confirmed using intravenous tyloxapol (142 ± 21, 122 ± 15, and 80 ± 7 mg·kg⁻¹·h⁻¹, P < 0.05). Moreover, hepatic de novo lipogenesis was significantly elevated in the MCDD group only (1.4 ± 0.3, 2.3 ± 0.4, and 3.4 ± 0.4 μmol/day, P < 0.01). These findings suggest that important alterations in hepatic fatty acid metabolism may promote the development of steatohepatitis. Similar mechanisms may predispose to hepatocyte damage in human NASH.

Potential impact of 1.5 °C and 2 °C global warming on consecutive dry and wet days over West Africa

NASA Astrophysics Data System (ADS)

Ama Browne Klutse, Nana; Ajayi, Vincent O.; Olabode Gbobaniyi, Emiola; Egbebiyi, Temitope S.; Kouadio, Kouakou; Nkrumah, Francis; Akumenyi Quagraine, Kwesi; Olusegun, Christiana; Diasso, Ulrich; Abiodun, Babatunde J.; Lawal, Kamoru; Nikulin, Grigory; Lennard, Christopher; Dosio, Alessandro

2018-05-01

We examine the impact of +1.5 °C and +2 °C global warming levels above pre-industrial levels on consecutive dry days (CDD) and consecutive wet days (CWD), two key indicators for extreme precipitation and seasonal drought. This is done using climate projections from a multi-model ensemble of 25 regional climate model (RCM) simulations. The RCMs take boundary conditions from ten global climate models (GCMs) under the RCP8.5 scenario. We define CDD as the maximum number of consecutive days with rainfall amount less than 1 mm and CWD as the maximum number of consecutive days with rainfall amount more than 1 mm. The differences in model representations of the change in CDD and CWD, at 1.5 °C and 2 °C global warming, and based on the control period 1971‑2000 are reported. The models agree on a noticeable response to both 1.5 °C and 2 °C warming for each index. Enhanced warming results in a reduction in mean rainfall across the region. More than 80% of ensemble members agree that CDD will increase over the Guinea Coast, in tandem with a projected decrease in CWD at both 1.5 °C and 2 °C global warming levels. These projected changes may influence already fragile ecosystems and agriculture in the region, both of which are strongly affected by mean rainfall and the length of wet and dry periods.

Removal of dibenzofuran, dibenzo-p-dioxin, and 2-chlorodibenzo-p-dioxin from soils inoculated with Sphingomonas sp. strain RW1

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

Halden, R.U.; Halden, B.G.; Dwyer, D.F.

Removal of dibenzofuran, dibenzo-p-dioxin, and 2-chlorodibenzo-p-dioxin (2-CDD) (10 ppm each) from soil microcosms to final concentrations in the parts-per-billion range was affected by the addition of Sphingomonas sp. strain RW1. Rates and extents of removal were influenced by the density of RW1 organisms. For 2-CDD, the rate of removal was dependent on the content of soil organic matter (SOM), with half-life values ranging from 5.8 h (0% SOM) to 26.3 h (5.5% SOM).

Autism and Related Disorders

PubMed Central

McPartland, James; Volkmar, Fred R.

2012-01-01

The Pervasive Developmental Disorders are a group of neurodevelopmental disorders that include Autistic Disorder, Asperger’s Disorder, Pervasive Developmental Disorder - Not Otherwise Specified (PDD-NOS), Childhood Disintegrative Disorder (CDD), and Rett’s Disorder. All feature childhood onset with a constellation of symptoms spanning social interaction and communication and including atypical behavior patterns. The first three disorders (Autistic Disorder, Asperger’s Disorder, and PDD-NOS) are currently referred to as Autism Spectrum Disorders, reflecting divergent phenotypic and etiologic characteristics compared to Rett’s Disorder and CDD. This chapter reviews relevant research and clinical information relevant to appropriate medical diagnosis and treatment. PMID:22608634

Sequencing and functional annotation of the whole genome of the filamentous fungus Aspergillus westerdijkiae.

PubMed

Han, Xiaolong; Chakrabortti, Alolika; Zhu, Jindong; Liang, Zhao-Xun; Li, Jinming

2016-08-15

Aspergillus westerdijkiae produces ochratoxin A (OTA) in Aspergillus section Circumdati. It is responsible for the contamination of agricultural crops, fruits, and food commodities, as its secondary metabolite OTA poses a potential threat to animals and humans. As a member of the filamentous fungi family, its capacity for enzymatic catalysis and secondary metabolite production is valuable in industrial production and medicine. To understand the genetic factors underlying its pathogenicity, enzymatic degradation, and secondary metabolism, we analysed the whole genome of A. westerdijkiae and compared it with eight other sequenced Aspergillus species. We sequenced the complete genome of A. westerdijkiae and assembled approximately 36 Mb of its genomic DNA, in which we identified 10,861 putative protein-coding genes. We constructed a phylogenetic tree of A. westerdijkiae and eight other sequenced Aspergillus species and found that the sister group of A. westerdijkiae was the A. oryzae - A. flavus clade. By searching the associated databases, we identified 716 cytochrome P450 enzymes, 633 carbohydrate-active enzymes, and 377 proteases. By combining comparative analysis with Kyoto Encyclopaedia of Genes and Genomes (KEGG), Conserved Domains Database (CDD), and Pfam annotations, we predicted 228 potential carbohydrate-active enzymes related to plant polysaccharide degradation (PPD). We found a large number of secondary biosynthetic gene clusters, which suggested that A. westerdijkiae had a remarkable capacity to produce secondary metabolites. Furthermore, we obtained two more reliable and integrated gene sequences containing the reported portions of OTA biosynthesis and identified their respective secondary metabolite clusters. We also systematically annotated these two hybrid t1pks-nrps gene clusters involved in OTA biosynthesis. These two clusters were separate in the genome, and one of them encoded a couple of GH3 and AA3 enzyme genes involved in sucrose and glucose metabolism. The genomic information obtained in this study is valuable for understanding the life cycle and pathogenicity of A. westerdijkiae. We identified numerous enzyme genes that are potentially involved in host invasion and pathogenicity, and we provided a preliminary prediction for each putative secondary metabolite (SM) gene cluster. In particular, for the OTA-related SM gene clusters, we delivered their components with domain and pathway annotations. This study sets the stage for experimental verification of the biosynthetic and regulatory mechanisms of OTA and for the discovery of new secondary metabolites.

Research priorities on diarrhoeal diseases to support the Control of Diarrhoeal Diseases (CDD) programme in Indonesia.

PubMed

Sunoto

1986-01-01

A comprehensive program review of Indonesia's Control of Diarrheal Diseases (CDD) program conducted in 1983 indicated that considerable success has been achieved in this area. Oral rehydration solution (ORS) is widely available, there has been community involvement, a strong managerial structure has developed, baseline data on diarrhea morbidity and mortality are being collected, and staff have received adequate training. At the same time, there have been some problems: inadequate use of ORS, a lack of coordination among CDD programs, insufficient surveillance, budgetary problems, and a lack of laboratory support. During the last 10 years, diarrhea mortality in Indonesia has been reduced by 50-70%, to about 20,000 (20% of child mortality). The Government has established the goal of reducing mortality from diarrhea to less than 1% of child deaths by the year 2000. A major strategy for achieving this goal is integrating family planning, nutrition, maternal-child health, immunization, and CDD programs. Another strategy involves improving research in this area. Areas for further research include: epidemiologic studies, rehydration treatment, antidiarrheal agents, social aspects, immunity and vaccine development, and laboratory examination. The cause of diarrheal diseases is not only enteric infection, it is indirectly caused by acute respiratory infection, malnutrition, measles and other systemic infection as well as the health knowledge and education of the mother. Priority is to be given to 7 areas of research: 1) the use of home-prepared rehydration fluids, 2) feeding practices during acute diarrhea that can prevent chronic diarrhea and malnutrition, 3) the determinants of progression to chronic diarrhea, 4) the impact of simple health information on hygienic and feeding practices on mortality, 5) the potential of using traditional birth attendants in ORS campaigns, 6) traditional attitudes and practices, and 7) the effectiveness of traditional medicines in diarrhea treatment.

Modelling the potential impacts of afforestation on extreme precipitation over West Africa

NASA Astrophysics Data System (ADS)

Odoulami, Romaric C.; Abiodun, Babatunde J.; Ajayi, Ayodele E.

2018-05-01

This study examines how afforestation in West Africa could influence extreme precipitation over the region, with a focus on widespread extreme rainfall events (WEREs) over the afforestation area. Two regional climate models (RegCM and WRF) were applied to simulate the present-day climate (1971-2000) and future climate (2031-2060, under IPCC RCP 4.5 emission scenario) with and without afforestation of the Savannah zone in West Africa. The models give a realistic simulation of precipitation indices and WEREs over the subcontinent. On average, the regional models projected future decreases in total annual wet day precipitation (PRCPTOT) and total annual daily precipitation greater than or equal to the 95th percentile of daily precipitation threshold (R95pTOT) and increases in maximum number of consecutive dry days (CDD) over Sahel. Over Savannah, the models projected decreases in PRCPTOT but increases in R95pTOT and CDD. Also, an increase in WEREs frequency is projected over west, central and east Savannah, except that RegCM simulated a decrease in WEREs over east Savannah. In general, afforestation increases PRCPTOT and R95pTOT but decreases CDD over the afforestation area. The forest-induced increases in PRCPTOT and decreases in CDD affect all ecological zones in West Africa. However, the simulations show that afforestation of Savannah also decreases R95pTOT over the Guinea Coast. It further increases WEREs over west and central Savannah and decreases them over east Savannah because of the local decrease in R95pTOT. Results of this study suggest that the future changes in characteristics of extreme precipitation events over West Africa are sensitive to the ongoing land modification.

Controlled population-based comparative study of USA and international adult [55-74] neurological deaths 1989-2014.

PubMed

Pritchard, C; Rosenorn-Lanng, E; Silk, A; Hansen, L

2017-12-01

A population-based controlled study to determine whether adult (55-74 years) neurological disease deaths are continuing to rise and are there significant differences between America and the twenty developed countries 1989-91 and 2012-14. Total Neurological Deaths (TND) rates contrasted against control Cancer and Circulatory Disease Deaths (CDD) extrapolated from WHO data. Confidence intervals compare USA and the other countries over the period. The Over-75's TND and population increases are examined as a context for the 55-74 outcomes. Male neurological deaths rose >10% in eleven countries, the other countries average rose 20% the USA 43% over the period. Female neurological deaths rose >10% in ten counties, averaging 14%, the USA up 68%. USA male and female neurological deaths increased significantly more than twelve and seventeen countries, respectively. USA over-75s population increased by 49%, other countries 56%. Other countries TND up 187% the USA rose fourfold. Male and female cancer and CDD fell in every country averaging 26% and 21%, respectively, and 64% and 67% for CDD. Male neurological rates rose significantly more than Cancer and CCD in every country; Female neurological deaths rose significantly more than cancer in 17 countries and every country for CDD. There was no significant correlation between increases in neurological deaths and decreases in control mortalities. There are substantial increases in neurological deaths in most countries, significantly so in America. Rises in the 55-74 and over-75's rates are not primarily due to demographic changes and are a matter of concern warranting further investigation. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

The behaviour of health care providers in managing diarrheal disease in Palembang City, south Sumatera, Indonesia.

PubMed

Ismail, R; Bakri, A; Nazir, M; Pardede, N

1991-01-01

A study on knowledge, attitude and practice of health care providers in Palembang had been conducted at the end of 1989 and beginning of 1990. Four approaches were carried out: (1) by recording the help obtained by cases who consulted researchers for further help for the same diarrheal diseases (DD) episode, (2) by studying the medical records of DD cases admitted to three hospitals, (3) by studying prescriptions dispensed by three pharmacies and (4) by focus group discussions. The findings were analysed to evaluate the achievement of the Indonesian Diarrheal Diseases Control Program (CDD). ORT, avoiding antimotility drugs and appropriated feeding have been accepted and practiced by the providers in Palembang. The target of promotion now is to support the acquisition of these behaviours to be implemented as a routine habit of the providers and as a part of the ongoing system of health care delivery system. Specifically the danger of loperamide promotion to the policy on antimotility must be stressed. Rapid iv rehydration and avoiding surface precipitating agents have been accepted, but are not practiced consistently yet due to practical considerations. It seems that there is no impact at all of CDD towards the rate of antibiotic therapy in DD. Besides intensifying the campaign, enforcing group pressure, may be we have to elaborate more the perception of health care provider as a practitioner, and conforming the strategy of the CDD campaign towards the findings. Health education had not been practiced effectively yet. Morale and value system of the providers are important for the success of this program. In general the medical-technic aspect of the CDD has been accepted by the providers, but there is still a lot to do in communicating them to be adopted as an effective behaviour.

Reductive transformation of dioxins: An assessment of the contribution of dissolved organic matter to dechlorination reactions

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

Fu, Q.S.; Barkovskii, A.L.; Adriaens, P.

1999-11-01

The susceptibility of dioxins to dissolved organic carbon (DOC)-mediated dechlorination reactions was investigated using 1,2,3,4,6,7,9-heptachlorodibenzo-p-dioxin (HpCDD), Aldrich humic acid (AHA), and polymaleic acid (PMA) as model compounds. The dechlorination yields were on the order of 4--20% which, when normalized to phenolic acidity, was comparable to yields observed in the presence of the humic constituents catechol and resorcinol. Based on the ratio of dechlorination yields as a function of phenolic acidity and electron transfer capacity, differences in electron transfer efficiency to dioxins are likely combined effects of specific interactions with the functional groups and nonspecific hydrophobic interactions. Hexa- and pentaCDD homologuesmore » were dominant in all incubations, and diCDD constituted the final product of dechlorination. The rates of appearance of lesser chlorinated products were similar to those observed in sediment systems and followed thermodynamic considerations as they decreased with a decrease in level of chlorination. Generally, both absolute and phenolic acidity-normalized rate constants for AHA-mediated reactions were up to 2-fold higher than those effected by PMA. These results indicate that the electron shuttling capacity of sediment DOC may significantly affect the fate of dioxins, in part through dechlorination reactions.« less

Deriving the real-ear SPL of audiometric data using the "coupler to dial difference" and the "real ear to coupler difference".

PubMed

Munro, K J; Davis, J

2003-04-01

The purpose of the study was to compare the measured real-ear sound pressure level (SPL) of audiometer output with the derived real-ear SPL obtained by adding the coupler to dial difference (CDD) and real-ear to coupler difference (RECD) to the audiometer dial reading. The real-ear SPL and RECD were measured in one ear of 16 normally hearing subjects using a probe-tube microphone. The CDD transform and the RECD transfer function were measured in an HA1 and an HA2 2-cc coupler using an EAR-LINK foam ear-tip or a customized earmold. The RECD transfer function was measured using the EARTone ER 3A and the Audioscan RE770 insert earphone. The procedures were very reliable with mean differences on retest of less than 1 dB. The mean difference between the measured and derived real-ear SPL was generally less than 1 dB and rarely exceeded 3 dB in any subject. The CDD measured for an individual audiometer and the RECD measured for an individual ear can be used to derive a valid estimate of real-ear SPL when it has not been possible to measure this directly.

Estimation of dioxin and furan elimination rates with a pharmacokinetic model.

PubMed

Van der Molen, G W; Kooijman, B A; Wittsiepe, J; Schrey, P; Flesch-Janys, D; Slob, W

2000-01-01

Quantitative description of the pharmacokinetics of dioxins and furans in humans can be of great help for the assessment of health risks posed by these compounds. To that the elimination rates of sixteen 2,3,7,8-chlorinated dibenzodioxins and dibenzofurans are estimated from both a longitudinal and a cross-sectional data set using the model of Van der Molen et al. [Van der Molen G.W., Kooijman S.A.L.M., and Slob W. A generic toxicokinetic model for persistent lipophilic compounds in humans: an application to TCDD. Fundam Appl Toxicol 1996: 31: 83-94]. In this model the elimination rate is given by the (constant) specific elimination rate multiplied with the ratio between the lipid weight of the liver and total body lipid weight. Body composition, body weight and intake are assumed to depend on age. The elimination rate is, therefore, not constant. For 49-year-old males, the elimination rate estimates range between 0.03 per year for 1,2,3,6,7,8-hexaCDF to 1.0 per year for octaCDF. The elimination rates of the most toxic congeners, 2,3,7,8-tetraCDD, 1,2,3,7,8-pentaCDD, and 2,3,4,7,8-pentaCDF, were estimated at 0.09, 0.06, and 0.07, respectively, based on the cross-sectional data, and 0.11, 0.09, and 0.09 based on the longitudinal data. The elimination rates of dioxins decrease with age between 0.0011 per year for 1,2,3,6,7,8-hexaCDD and 0.0035 per year for 1,2,3,4,6,7,8-heptaCDD. For furans the average decrease is 0.0033 per year. The elimination rates were estimated both from a longitudinal and a cross-sectional data set, and agreed quite well with each other, after taking account of historical changes in average intake levels.

Serum Concentrations of Selected Persistent Organic Pollutants in a Sample of Pregnant Females and Changes in Their Concentrations during Gestation

PubMed Central

Wang, Richard Y.; Jain, Ram B.; Wolkin, Amy F.; Rubin, Carol H.; Needham, Larry L.

2009-01-01

Objectives In this study we evaluated the concentrations of selected persistent organic pollutants in a sample of first-time pregnant females residing in the United States and assessed differences in these concentrations in all pregnant females during gestation. Methods We reviewed demographic and laboratory data for pregnant females participating in the National Health and Nutrition Examination Survey, including concentrations of 25 polychlorinated biphenyls (PCBs), 6 polychlorinated dibenzo-p-dioxins (PCDDs), 9 polychlorinated dibenzofurans (PCDFs), and 9 organochlorine pesticides. We report serum concentrations for first-time pregnant females (2001–2002; n = 49) and evaluate these concentrations in all pregnant females by trimester (1999–2002; n = 203) using a cross-sectional analysis. Results The chemicals with ≥ 60% detection included PCBs (congeners 126, 138/158, 153, 180), PCDDs/PCDFs [1,2,3,4,6,7,8-heptachlorodibenzo-p-dioxin (1234678HpCDD), 1,2,3,6,7,8-hexachlorodibenzo-p-dioxin (123678HxCDD), 1,2,3,4,6,7,8-heptachlorodibenzofuran (1234678HpCDF), 1,1′-(2,2-dichloroethenylidene)-bis(4-chlorobenzene) (p,p′-DDE)], and trans-nonachlor. The geometric mean concentration (95% confidence intervals) for 1234678HpCDD was 15.9 pg/g lipid (5.0–50.6 pg/g); for 123678HxCDD, 9.7 pg/g (5.5–17.1 pg/g); and for 1234678HpCDF, 5.4 pg/g (3.3–8.7 pg/g). The differences in concentrations of these chemicals by trimester were better accounted for with the use of lipid-adjusted units than with whole-weight units; however, the increase in the third-trimester concentration was greater for PCDDs/PCDFs (123678HxCDD, 1234678HpCDF) than for the highest concentration of indicator PCBs (138/158, 153, 180), even after adjusting for potential confounders. Conclusion The concentrations of these persistent organic pollutants in a sample of first-time pregnant females living in the United States suggest a decline in exposures to these chemicals since their ban or restricted use and emission. The redistribution of body burden for these and other persistent organic pollutants during pregnancy needs to be more carefully defined to improve the assessment of fetal exposure to them based on maternal serum concentrations. Additional studies are needed to further the understanding of the potential health consequences to the fetus from persistent organic pollutants. PMID:19672404

Daily intake of vitamin D- or calcium-vitamin D-fortified Persian yogurt drink (doogh) attenuates diabetes-induced oxidative stress: evidence for antioxidative properties of vitamin D.

PubMed

Nikooyeh, B; Neyestani, T R; Tayebinejad, N; Alavi-Majd, H; Shariatzadeh, N; Kalayi, A; Zahedirad, M; Heravifard, S; Salekzamani, S

2014-04-01

Both poor vitamin D status and oxidative stress (OS) have been independently associated with late diabetic complications, including cardiovascular disease (CVD). The present study aimed to examine the effect of daily intake of vitamin D alone or in combination with calcium as a fortified Persian yogurt drink (doogh) on OS over 12 weeks. Ninety patients with type 2 diabetes aged 30-50 years from both sexes were randomly allocated to one of the three groups to receive two 250-mL bottles of doogh a day, which was either plain (PD; containing 150 mg per 250 mL of calcium and no detectable vitamin D), vitamin D-fortified (DD; containing 150 mg of calcium + 500 IU vitamin D per 250 mL) or calcium-vitamin D-fortified (CDD; 250 mg od calcium + 500 IU vitamin D per 250 mL). Although mean (SD) serum concentrations of protein carbonyl significantly decreased in both DD and CDD groups [-2.07 (4.39) nm, P = 0.015 and -4.4 (7.64) nm, P = 0.003, respectively], the change in PD group was not significant [-0.54 (6.96) nm, P = 0.674]. A similar pattern was observed for cardiac myeloperoxidase [PD: -19.4 (75.9) μg L(-1) , P = 0.173; DD: -21.8 (54.2) μg L(-1) , P = 0.035, CDD: -48.5 (76.9) μg L(-1) , P = 0.002]. Superoxide dismutase increased significantly only in DD and CDD [56.9 (74.0) U L(-1) , P < 0.001 and 51.6 (119.9) U L(-1) , P = 0.025, respectively]. Changes of serum advanced glycation end-products showed a significant between-group difference among PD, DD and CDD [239.4 (388.4) U L(-1) , -58.1 (147.6) U L(-1) and -143.7 (475.9) U L(-1)  × 10(3) , respectively, P = 0.003], which remained significant after controlling for changes of fasting serum glucose (P = 0.013) and glycated haemoglobin (P = 0.015). The findings of the present study demonstrated an OS attenuating effect of vitamin D. However, extra calcium did not convey additional benefit. © 2013 The British Dietetic Association Ltd.

Domain fusion analysis by applying relational algebra to protein sequence and domain databases

PubMed Central

Truong, Kevin; Ikura, Mitsuhiko

2003-01-01

Background Domain fusion analysis is a useful method to predict functionally linked proteins that may be involved in direct protein-protein interactions or in the same metabolic or signaling pathway. As separate domain databases like BLOCKS, PROSITE, Pfam, SMART, PRINTS-S, ProDom, TIGRFAMs, and amalgamated domain databases like InterPro continue to grow in size and quality, a computational method to perform domain fusion analysis that leverages on these efforts will become increasingly powerful. Results This paper proposes a computational method employing relational algebra to find domain fusions in protein sequence databases. The feasibility of this method was illustrated on the SWISS-PROT+TrEMBL sequence database using domain predictions from the Pfam HMM (hidden Markov model) database. We identified 235 and 189 putative functionally linked protein partners in H. sapiens and S. cerevisiae, respectively. From scientific literature, we were able to confirm many of these functional linkages, while the remainder offer testable experimental hypothesis. Results can be viewed at . Conclusion As the analysis can be computed quickly on any relational database that supports standard SQL (structured query language), it can be dynamically updated along with the sequence and domain databases, thereby improving the quality of predictions over time. PMID:12734020

Mobile social network services for families with children with developmental disabilities.

PubMed

Chou, Li-Der; Lai, Nien-Hwa; Chen, Yen-Wen; Chang, Yao-Jen; Yang, Jyun-Yan; Huang, Lien-Fu; Chiang, Wen-Ling; Chiu, Hung-Yi; Shin, Haw-Yun

2011-07-01

As Internet technologies evolve, their applications have changed various aspects of human life. Here, we attempt to examine their potential impact on services for families with developmentally delayed children. Our research is thus designed to utilize wireless mobile communication technologies, location services, and search technology in an effort to match families of specific needs with potential care providers. Based on the investigation conducted by our counselors, this paper describes a platform for smooth communication between professional communities and families with children with developmental disabilities (CDD). This research also looks into the impact of management of mobile social network services and training on the operation of these services. Interaction opportunities, care, and support to families with CDD are introduced.

Domain fusion analysis by applying relational algebra to protein sequence and domain databases.

PubMed

Truong, Kevin; Ikura, Mitsuhiko

2003-05-06

Domain fusion analysis is a useful method to predict functionally linked proteins that may be involved in direct protein-protein interactions or in the same metabolic or signaling pathway. As separate domain databases like BLOCKS, PROSITE, Pfam, SMART, PRINTS-S, ProDom, TIGRFAMs, and amalgamated domain databases like InterPro continue to grow in size and quality, a computational method to perform domain fusion analysis that leverages on these efforts will become increasingly powerful. This paper proposes a computational method employing relational algebra to find domain fusions in protein sequence databases. The feasibility of this method was illustrated on the SWISS-PROT+TrEMBL sequence database using domain predictions from the Pfam HMM (hidden Markov model) database. We identified 235 and 189 putative functionally linked protein partners in H. sapiens and S. cerevisiae, respectively. From scientific literature, we were able to confirm many of these functional linkages, while the remainder offer testable experimental hypothesis. Results can be viewed at http://calcium.uhnres.utoronto.ca/pi. As the analysis can be computed quickly on any relational database that supports standard SQL (structured query language), it can be dynamically updated along with the sequence and domain databases, thereby improving the quality of predictions over time.

Cerebral creatine deficiencies: a group of treatable intellectual developmental disorders.

PubMed

Stockler-Ipsiroglu, Sylvia; van Karnebeek, Clara D M

2014-07-01

Currently there are 91 treatable inborn errors of metabolism that cause intellectual developmental disorders. Cerebral creatine deficiencies (CDD) comprise three of these: arginine: glycine amidinotransferase [AGAT], guanidinoacetate methyltransferase [GAMT], and X-linked creatine transporter deficiency [SLC6A8]. Intellectual developmental disorder and cerebral creatine deficiency are the hallmarks of CDD. Additional clinical features include prominent speech delay, autism, epilepsy, extrapyramidal movement disorders, and signal changes in the globus pallidus. Patients with GAMT deficiency exhibit the most severe clinical spectrum. Myopathy is a distinct feature in AGAT deficiency. Guanidinoacetate (GAA) is the immediate product in the creatine biosynthetic pathway. Low GAA concentrations in urine, plasma, and cerebrospinal fluid are characteristic diagnostic markers for AGAT deficiency, while high GAA concentrations are characteristic markers for GAMT deficiency. An elevated ratio of urinary creatine /creatinine excretion serves as a diagnostic marker in males with SLC6A8 deficiency. Treatment strategies include oral supplementation of high-dose creatine-monohydrate for all three CDD. Guanidinoacetate-reducing strategies (high-dose ornithine, arginine-restricted diet) are additionally employed in GAMT deficiency. Supplementation of substrates for intracerebral creatine synthesis (arginine, glycine) has been used additionally to treat SLC6A8 deficiency. Early recognition and treatment improves outcomes. Normal outcomes in neonatally ascertained siblings from index families with AGAT and GAMT deficiency suggest a potential benefit of newborn screening for these disorders. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

An approach to quantify the heat wave strength and price a heat derivative for risk hedging

NASA Astrophysics Data System (ADS)

Shen, Samuel S. P.; Kramps, Benedikt; Sun, Shirley X.; Bailey, Barbara

2012-01-01

Mitigating the heat stress via a derivative policy is a vital financial option for agricultural producers and other business sectors to strategically adapt to the climate change scenario. This study has provided an approach to identifying heat stress events and pricing the heat stress weather derivative due to persistent days of high surface air temperature (SAT). Cooling degree days (CDD) are used as the weather index for trade. In this study, a call-option model was used as an example for calculating the price of the index. Two heat stress indices were developed to describe the severity and physical impact of heat waves. The daily Global Historical Climatology Network (GHCN-D) SAT data from 1901 to 2007 from the southern California, USA, were used. A major California heat wave that occurred 20-25 October 1965 was studied. The derivative price was calculated based on the call-option model for both long-term station data and the interpolated grid point data at a regular 0.1°×0.1° latitude-longitude grid. The resulting comparison indicates that (a) the interpolated data can be used as reliable proxy to price the CDD and (b) a normal distribution model cannot always be used to reliably calculate the CDD price. In conclusion, the data, models, and procedures described in this study have potential application in hedging agricultural and other risks.

Thigh muscle segmentation of chemical shift encoding-based water-fat magnetic resonance images: The reference database MyoSegmenTUM.

PubMed

Schlaeger, Sarah; Freitag, Friedemann; Klupp, Elisabeth; Dieckmeyer, Michael; Weidlich, Dominik; Inhuber, Stephanie; Deschauer, Marcus; Schoser, Benedikt; Bublitz, Sarah; Montagnese, Federica; Zimmer, Claus; Rummeny, Ernst J; Karampinos, Dimitrios C; Kirschke, Jan S; Baum, Thomas

2018-01-01

Magnetic resonance imaging (MRI) can non-invasively assess muscle anatomy, exercise effects and pathologies with different underlying causes such as neuromuscular diseases (NMD). Quantitative MRI including fat fraction mapping using chemical shift encoding-based water-fat MRI has emerged for reliable determination of muscle volume and fat composition. The data analysis of water-fat images requires segmentation of the different muscles which has been mainly performed manually in the past and is a very time consuming process, currently limiting the clinical applicability. An automatization of the segmentation process would lead to a more time-efficient analysis. In the present work, the manually segmented thigh magnetic resonance imaging database MyoSegmenTUM is presented. It hosts water-fat MR images of both thighs of 15 healthy subjects and 4 patients with NMD with a voxel size of 3.2x2x4 mm3 with the corresponding segmentation masks for four functional muscle groups: quadriceps femoris, sartorius, gracilis, hamstrings. The database is freely accessible online at https://osf.io/svwa7/?view_only=c2c980c17b3a40fca35d088a3cdd83e2. The database is mainly meant as ground truth which can be used as training and test dataset for automatic muscle segmentation algorithms. The segmentation allows extraction of muscle cross sectional area (CSA) and volume. Proton density fat fraction (PDFF) of the defined muscle groups from the corresponding images and quadriceps muscle strength measurements/neurological muscle strength rating can be used for benchmarking purposes.

Quadrupole-octupole coupled states in 112Cd populated in the 111Cd(d ⃗,p ) reaction

NASA Astrophysics Data System (ADS)

Jamieson, D. S.; Garrett, P. E.; Bildstein, V.; Demand, G. A.; Finlay, P.; Green, K. L.; Leach, K. G.; Phillips, A. A.; Sumithrarachchi, C. S.; Svensson, C. E.; Triambak, S.; Ball, G. C.; Faestermann, T.; Hertenberger, R.; Wirth, H.-F.

2014-11-01

States in 112Cd have been studied with the 111Cd(d ⃗,p ) 12Cd reaction using 22 MeV polarized deuterons. The protons from the reaction were momentum analyzed with a Q3D magnetic spectrograph, and spectra have been recorded with a position-sensitive detector located on the focal plane. Angular distributions of cross sections and analyzing powers have been constructed for the low-lying negative-parity states observed, including the 3-,4-, and 5- members of the previously assigned quadrupole-octupole quintuplet. The 5- member at 2373-keV possess the second largest spectroscopic strength observed, and is reassigned as having the s1/2⊗h11/2 two-quasineutron configuration as the dominate component of its wave function.

Gradient Plasticity Model and its Implementation into MARMOT

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

Barker, Erin I.; Li, Dongsheng; Zbib, Hussein M.

2013-08-01

The influence of strain gradient on deformation behavior of nuclear structural materials, such as boby centered cubic (bcc) iron alloys has been investigated. We have developed and implemented a dislocation based strain gradient crystal plasticity material model. A mesoscale crystal plasticity model for inelastic deformation of metallic material, bcc steel, has been developed and implemented numerically. Continuum Dislocation Dynamics (CDD) with a novel constitutive law based on dislocation density evolution mechanisms was developed to investigate the deformation behaviors of single crystals, as well as polycrystalline materials by coupling CDD and crystal plasticity (CP). The dislocation density evolution law in thismore » model is mechanism-based, with parameters measured from experiments or simulated with lower-length scale models, not an empirical law with parameters back-fitted from the flow curves.« less

A sublimate sorbent for stir-bar sorptive extraction of aqueous endocrine disruptor pesticides for gas chromatography-electron capture detection.

PubMed

Huang, Yu-Wen; Lee, Hua Kwang; Shih, Hou-Kuang; Jen, Jen-Fon

2018-06-06

A dumbbell-shaped magnetic stir-bar with sublimate sorbent was prepared for the stir bar sorptive extraction (SBSE) of pesticides in an aqueous sample prior to gas chromatography-micro-electron capture detection (GC-μECD). Cyclododecane (CDD) was coated onto a magnetic stir-bar surface as a sublimate sorbent, and steel balls were placed on both ends to form a dumbbell-shaped magnetic stir-bar for SBSE. Four EDC pesticides including chlorpyrifos, ethion, bromopropylate, and λ-cyhalothrin in aqueous samples were selected as model species to examine the proposed SBSE and the following desorption. The parameters studied were those affecting the extraction efficiencies including the coating (solvent for CDD and thickness), extraction (sample pH, stirring rate, time, and salting out effect), dissolution solvent volume, and the loss of CDD sublimated in air. The maximum extraction efficiency was obtained under the following conditions. The stir bar (with CDD thickness of 5.2 μm) was added into a 10 mL sample solution (at pH 7) for a 20-min extraction at 600 rpm. Then, the stir bar was gently removed from the sample solution, disassembled, and immersed into a 0.2 mL insert tube consisting of 3 μL hexane to dissolve; 1 μL was used for GC-ECD analysis. The linear ranges were 0.005-5 μg L -1 with coefficients of determination ranging from 0.9950 - 0.9994. Detection limits (based on S/N = 3) of the four EDCs were 0.4-4.5 ngL -1 with a relative standard deviation (RSD) of 2.4-6.3%, and quantitation limits (based on S/N = 5) were 1-15 ngL -1 . The relative recoveries of the spiked samples were in the range of 83.2-98.7% with RSDs of 2.1-8.4% in farm field waters. The proposed sublimation sorbent obtained excellent enrichment factors (101-834) and provided a simple, rapid, sensitive, and eco-friendly sample preparation method. Copyright © 2018 Elsevier B.V. All rights reserved.

The impact of generalized joint laxity (GJL) on the posterior neck pain, cervical disc herniation, and cervical disc degeneration in the cervical spine.

PubMed

Lee, Sun-Mi; Oh, Su Chan; Yeom, Jin S; Shin, Ji-Hoon; Park, Sam-Guk; Shin, Duk-Seop; Ahn, Myun-Whan; Lee, Gun Woo

2016-12-01

Generalized joint laxity (GJL) can have a negative impact on lumbar spine pathology, including low back pain, disc degeneration, and disc herniation, but the relationship between GJL and cervical spine conditions remains unknown. To investigate the relationship between GJL and cervical spine conditions, including the prevalence of posterior neck pain (PNP), cervical disc herniation (CDH), and cervical disc degeneration (CDD), in a young, active population. Retrospective 1:2 matched cohort (case-control) study from prospectively collected data PATIENT SAMPLE: Of a total of 1853 individuals reviewed, 73 individuals with GJL (study group, gruop A) and 146 without GJL (control group, Group B) were included in the study according to a 1:2 case-control matched design for age, sex, and body mass index. The primary outcome measure was the prevalence and intensity of PNP at enrollment based on a visual analogue scale score for pain. The secondary outcome measures were (1) clinical outcomes as measured with the neck disability index (NDI) and 12-item short form health survey (SF-12) at enrollment, and (2) radiological outcomes of CDH and CDD at enrollment. We compared baseline data between groups. Descriptive statistical analyses were performed to compare the 2 groups in terms of the outcome measures. The prevalence and intensity of PNP were significantly greater in group A (patients with GJL) than in group B (patients without GJL) (prevalence: p=.02; intensity: p=.001). Clinical outcomes as measured with NDI and SF-12 did not differ significantly between groups. For radiologic outcomes, the prevalence of CDD was significantly greater in group A than in group B (p=.04), whereas the prevalence of CDH did not differ significantly between groups (p=.91). The current study revealed that GJL was closely related to the prevalence and intensity of PNP, suggesting that GJL may be a causative factor for PNP. In addition, GJL may contribute to the occurrence of CDD, but not CDH. Spine surgeons should screen for GJL in patientswith PNP and inform patients of its potential negative impact on disc degeneration of the cervical spine. Copyright © 2016 Elsevier Inc. All rights reserved.

ActRII blockade protects mice from cancer cachexia and prolongs survival in the presence of anti-cancer treatments.

PubMed

Hatakeyama, Shinji; Summermatter, Serge; Jourdain, Marie; Melly, Stefan; Minetti, Giulia C; Lach-Trifilieff, Estelle

2016-01-01

Cachexia affects the majority of patients with advanced cancer and is associated with reduced treatment tolerance, response to therapy, quality of life, and life expectancy. Cachectic patients with advanced cancer often receive anti-cancer therapies against their specific cancer type as a standard of care, and whether specific ActRII inhibition is efficacious when combined with anti-cancer agents has not been elucidated yet. In this study, we evaluated interactions between ActRII blockade and anti-cancer agents in CT-26 mouse colon cancer-induced cachexia model. CDD866 (murinized version of bimagrumab) is a neutralizing antibody against the activin receptor type II (ActRII) preventing binding of ligands such as myostatin and activin A, which are involved in cancer cachexia. CDD866 was evaluated in association with cisplatin as a standard cytotoxic agent or with everolimus, a molecular-targeted agent against mammalian target of rapamycin (mTOR). In the early studies, the treatment effect on cachexia was investigated, and in the additional studies, the treatment effect on progression of cancer and the associated cachexia was evaluated using body weight loss or tumor volume as interruption criteria. Cisplatin accelerated body weight loss and tended to exacerbate skeletal muscle loss in cachectic animals, likely due to some toxicity of this anti-cancer agent. Administration of CDD866 alone or in combination with cisplatin protected from skeletal muscle weight loss compared to animals receiving only cisplatin, corroborating that ActRII inhibition remains fully efficacious under cisplatin treatment. In contrast, everolimus treatment alone significantly protected the tumor-bearing mice against skeletal muscle weight loss caused by CT-26 tumor. CDD866 not only remains efficacious in the presence of everolimus but also showed a non-significant trend for an additive effect on reversing skeletal muscle weight loss. Importantly, both combination therapies slowed down time-to-progression. Anti-ActRII blockade is an effective intervention against cancer cachexia providing benefit even in the presence of anti-cancer therapies. Co-treatment comprising chemotherapies and ActRII inhibitors might constitute a promising new approach to alleviate chemotherapy- and cancer-related wasting conditions and extend survival rates in cachectic cancer patients.

Computer-determined dosage of insulin in the management of neonatal hyperglycaemia (HINT2): protocol of a randomised controlled trial.

PubMed

Alsweiler, Jane; Williamson, Kathryn; Bloomfield, Frank; Chase, Geoffrey; Harding, Jane

2017-03-06

Neonatal hyperglycaemia is frequently treated with insulin, which may increase the risk of hypoglycaemia. Computer-determined dosage of insulin (CDD) with the STAR-GRYPHON program uses a computer model to predict an effective dose of insulin to treat hyperglycaemia while minimising the risk of hypoglycaemia. However, CDD models can require more frequent blood glucose testing than common clinical protocols. The aim of this trial is to determine if CDD using STAR-GRYPHON reduces hypoglycaemia in hyperglycaemic preterm babies treated with insulin independent of the frequency of blood glucose testing. Design: Multicentre, non-blinded, randomised controlled trial. Neonatal intensive care units in New Zealand and Australia. 138 preterm babies ≤30 weeks' gestation or ≤1500 g at birth who develop hyperglycaemia (two consecutive blood glucose concentrations ≥10 mmol/L, at least 4 hours apart) will be randomised to one of three groups: (1) CDD using the STAR-GRYPHON model-based decision support system: insulin dose and frequency of blood glucose testing advised by STAR-GRYPHON, with a maximum testing interval of 4 hours; (2) bedside titration: insulin dose determined by medical staff, maximum blood glucose testing interval of 4 hours; (3) standard care: insulin dose and frequency of blood glucose testing determined by medical staff. The target range for blood glucose concentrations is 5-8 mmol/L in all groups. A subset of babies will have masked continuous glucose monitoring. is the number of babies with one or more episodes of hypoglycaemia (blood glucose concentration <2.6 mmol/L), during treatment with insulin. This protocol has been approved by New Zealand's Health and Disability Ethics Committee: 14/STH/26. A data safety monitoring committee has been appointed to oversee the trial. Findings will be disseminated to participants and carers, peer-reviewed journals, guideline developers and the public. 12614000492651. 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/.

DIMA 3.0: Domain Interaction Map.

PubMed

Luo, Qibin; Pagel, Philipp; Vilne, Baiba; Frishman, Dmitrij

2011-01-01

Domain Interaction MAp (DIMA, available at http://webclu.bio.wzw.tum.de/dima) is a database of predicted and known interactions between protein domains. It integrates 5807 structurally known interactions imported from the iPfam and 3did databases and 46,900 domain interactions predicted by four computational methods: domain phylogenetic profiling, domain pair exclusion algorithm correlated mutations and domain interaction prediction in a discriminative way. Additionally predictions are filtered to exclude those domain pairs that are reported as non-interacting by the Negatome database. The DIMA Web site allows to calculate domain interaction networks either for a domain of interest or for entire organisms, and to explore them interactively using the Flash-based Cytoscape Web software.

Impact of estuarine gradients on reductive dechlorination of 1,2,3,4-tetrachlorodibenzo-p-dioxin in river sediment enrichment cultures.

PubMed

Dam, Hang T; Häggblom, Max M

2017-02-01

Polychlorinated dibenzo-p-dioxins (PCDDs) are among the most persistent organic pollutants. Although the total input of PCDDs into the environment has decreased substantially over the past four decades, their input via non-point sources is still increasing, especially in estuarine metropolitan areas. Here we report on the microbially mediated reductive dechlorination of PCDDs in anaerobic enrichment cultures established from sediments collected from five locations along the Hackensack River, NJ and investigate the impacts of sediment physicochemical characteristics on dechlorination activity. Dechlorination of 1,2,3,4-tetrachlorodibenzo-p-dioxin (1,2,3,4-TeCDD) and abundance of Dehalococcoides spp. negatively correlated with salinity and sulfate concentration in sediments used to establish the cultures. 1,2,3,4-TeCDD was dechlorinated to a lesser extent in cultures established from sediments from the tidally influenced estuarine mouth of the river. In cultures established from low salinity sediments, 1,2,3,4-TeCDD was reductively dechlorinated with the accumulation of 2-monochlorodibenzo-p-dioxin as the major product. Sulfate concentrations above 2 mM inhibited 1,2,3,4-TecDD dechlorination activity. Consecutive lateral- and peri- dechlorination took place in enrichment cultures with a minimal accumulation of 2,3-dichlorodibenzo-p-dioxin in active cultures. A Dehalococcoides spp. community was enriched and accounted for up to 64% of Chloroflexi detected in these sediment cultures. Copyright © 2016 Elsevier Ltd. All rights reserved.

Open Source Bayesian Models. 1. Application to ADME/Tox and Drug Discovery Datasets.

PubMed

Clark, Alex M; Dole, Krishna; Coulon-Spektor, Anna; McNutt, Andrew; Grass, George; Freundlich, Joel S; Reynolds, Robert C; Ekins, Sean

2015-06-22

On the order of hundreds of absorption, distribution, metabolism, excretion, and toxicity (ADME/Tox) models have been described in the literature in the past decade which are more often than not inaccessible to anyone but their authors. Public accessibility is also an issue with computational models for bioactivity, and the ability to share such models still remains a major challenge limiting drug discovery. We describe the creation of a reference implementation of a Bayesian model-building software module, which we have released as an open source component that is now included in the Chemistry Development Kit (CDK) project, as well as implemented in the CDD Vault and in several mobile apps. We use this implementation to build an array of Bayesian models for ADME/Tox, in vitro and in vivo bioactivity, and other physicochemical properties. We show that these models possess cross-validation receiver operator curve values comparable to those generated previously in prior publications using alternative tools. We have now described how the implementation of Bayesian models with FCFP6 descriptors generated in the CDD Vault enables the rapid production of robust machine learning models from public data or the user's own datasets. The current study sets the stage for generating models in proprietary software (such as CDD) and exporting these models in a format that could be run in open source software using CDK components. This work also demonstrates that we can enable biocomputation across distributed private or public datasets to enhance drug discovery.

Open Source Bayesian Models. 1. Application to ADME/Tox and Drug Discovery Datasets

PubMed Central

2015-01-01

On the order of hundreds of absorption, distribution, metabolism, excretion, and toxicity (ADME/Tox) models have been described in the literature in the past decade which are more often than not inaccessible to anyone but their authors. Public accessibility is also an issue with computational models for bioactivity, and the ability to share such models still remains a major challenge limiting drug discovery. We describe the creation of a reference implementation of a Bayesian model-building software module, which we have released as an open source component that is now included in the Chemistry Development Kit (CDK) project, as well as implemented in the CDD Vault and in several mobile apps. We use this implementation to build an array of Bayesian models for ADME/Tox, in vitro and in vivo bioactivity, and other physicochemical properties. We show that these models possess cross-validation receiver operator curve values comparable to those generated previously in prior publications using alternative tools. We have now described how the implementation of Bayesian models with FCFP6 descriptors generated in the CDD Vault enables the rapid production of robust machine learning models from public data or the user’s own datasets. The current study sets the stage for generating models in proprietary software (such as CDD) and exporting these models in a format that could be run in open source software using CDK components. This work also demonstrates that we can enable biocomputation across distributed private or public datasets to enhance drug discovery. PMID:25994950

Polychlorinated dibenzo-p-dioxin and dibenzofuran concentrations in serum samples of workers at intermittently burning municipal waste incinerators in Japan

PubMed Central

Kumagai, S; Koda, S; Miyakita, T; Ueno, M

2002-01-01

Objectives: To find whether or not incinerator workers employed at intermittently burning municipal incineration plants are exposed to high concentrations of polychlorinated dibenzo-p-dioxins (PCDDs) and polychlorinated dibenzofurans (PCDFs). Methods: 20 Workers employed at three municipal waste incineration plants (incinerator workers) and 20 controls were studied. The previous job, dietary, smoking, and body weight and height were obtained from a questionnaire survey. Concentrations of PCDDs and PCDFs were measured in serum samples of the workers and the deposited dust of the plants. The influence of occupational exposure on concentrations of PCDDs and PCDFs in serum samples was examined by multiple regression analysis. Results: Dust analysis showed that dominant constituents were octachlorodibenzo-p-dioxin (OCDD) and 1,2,3,4,6,7,8-heptachlorodibenzo-p-dioxin (HpCDD) among the PCDDs, and 1,2,3,4,6,7,8-heptachlorodibenzofuran (HpCDF) and octachlorodibenzofuran (OCDF) among the PCDFs. The toxicity equivalents (TEQs) of summed PCDDs and PCDFs in the deposited dust were 0.91, 33, and 11 ng TEQ/g, respectively, for plants I, II, and III. The means of TEQ in serum samples of summed PCDDs and PCDFs in the incinerator workers and controls were 22.8 and 16.4 pg TEQ/g lipid for area I, 29.4 and 19.3 pg TEQ/g lipid for area II, and 22.8 and 24.9 pg TEQ/g lipid for area III, which were almost the same as for the general population of Japan. No significant differences in the TEQ of PCDDs and TEQ of PCDDs and PCDDs were found between the incinerator workers and the controls. However, the TEQ of PCDFs was significantly higher among the incinerator workers in areas I and II, and the 1,2,3,4,6,7,8-HpCDF concentration was also significantly higher for all three areas. When the occupational exposure index for each constituent of PCDDs and PCDFs was defined as the product of the duration of employment at the incineration plant and the concentration of the constituent in the deposited dust, multiple regression analysis showed that the concentrations of HxCDF, HpCDF, and TEQ of PCDFs in serum samples increased with the occupational exposure index. The multiple regression analysis also suggested that significant factors affecting the concentrations in serum samples were area for HxCDD, age for TCDD, PeCDD, PeCDF, TEQ of PCDDs, TEQ of PCDFs, and TEQ of summed PCDDs and PCDFs, and BMI for HxCDD, HpCDD, and OCDD. Conclusion: This study showed that incinerator workers employed at intermittently burning incineration plants were not necessarily exposed to high concentrations of PCDDs and PCDFs. However, the increases in the concentrations in serum of HxCDF, HpCDF and TEQ of PCDFs with the occupational exposure index suggest that the incinerator workers had inhaled dust containing PCDDs and PCDFs during their work. PMID:12040109

Comprehensive assessment of drought from 1960 to 2013 in China based on different perspectives

NASA Astrophysics Data System (ADS)

Lai, Wenli; Wang, Hongrui; Zhang, Jie

2017-10-01

Using daily and monthly precipitation data collected from 520 meteorological stations from 1960 to 2013, we compared a widely used drought index, the standardized precipitation index (SPI), with an extreme index, the maximum consecutive dry days index (CDD). Two other homogeneity test methods, namely the Gini coefficient (including both Total-Gini and Wet-Gini) and the precipitation concentration degree (PCD) were also applied to indirectly estimate extreme droughts. The changes in droughts determined using the SPI and the CDD exhibited similar spatial and temporal patterns throughout most parts of China, with the exception of Southwestern China. Comparison of the five indices indicated that Wet-Gini exhibited different or even opposite trends of drought across all of China. Finally, a trend analysis from 2000 to 2013 was applied to perform a regional empirical analysis of a classic extreme drought event in Southwestern China. All indices, except for Wet-Gini, indicated increasing drought risk.

Perinatal dioxin exposure and the neurodevelopment of Vietnamese toddlers at 1 year of age.

PubMed

Pham, Tai The; Nishijo, Muneko; Nguyen, Anh Thi Nguyet; Tran, Nghi Ngoc; Hoang, Luong Van; Tran, Anh Hai; Nguyen, Trung Viet; Nishijo, Hisao

2015-12-01

Dioxin concentrations remain elevated in both the environment and in humans residing near former US Air Force bases in South Vietnam. This may potentially have adverse health effects, particularly on infant neurodevelopment. We followed 214 infants whose mothers resided in a dioxin-contaminated area in Da Nang, Vietnam, from birth until 1 year of age. Perinatal exposure to dioxins was estimated from toxic equivalent (TEQ) levels of polychlorinated dibenzodioxins and polychlorinated dibenzofurans (PCDDs/Fs-TEQ), and 2,3,7,8-tetrachlorodibenzo-p-dioxin (2,3,7,8-TetraCDD) concentrations in breast milk. In infants, daily dioxin intake (DDI) was used as an index of postnatal exposure through breastfeeding. Neurodevelopment of toddlers was assessed using the Bayley Scales of Infant and Toddler Development, Third Edition (Bayley-III). No significant differences in neurodevelopmental scores were exhibited for cognitive, language or motor functions between four exposure groups of PCDDs/Fs-TEQ or 2,3,7,8-TetraCDD. However, social-emotional scores were decreased in the high PCDDs/Fs-TEQ group and the high 2,3,7,8-TetraCDD group compared with those with mild exposure, after adjusting for confounding factors. Cognitive scores in the mild, moderate, and high DDI groups were significantly higher than those in low DDI group, but there were no differences in cognitive scores among the three higher DDI groups. These results suggest that perinatal exposure to dioxins may affect social-emotional development of 1-year-old toddlers, without diminishing global neurodevelopmental function. Crown Copyright © 2015. Published by Elsevier B.V. All rights reserved.

Dynamics of Copy Number Variation in Host Races of the Pea Aphid

PubMed Central

Duvaux, Ludovic; Geissmann, Quentin; Gharbi, Karim; Zhou, Jing-Jiang; Ferrari, Julia; Smadja, Carole M.; Butlin, Roger K.

2015-01-01

Copy number variation (CNV) makes a major contribution to overall genetic variation and is suspected to play an important role in adaptation. However, aside from a few model species, the extent of CNV in natural populations has seldom been investigated. Here, we report on CNV in the pea aphid Acyrthosiphon pisum, a powerful system for studying the genetic architecture of host-plant adaptation and speciation thanks to multiple host races forming a continuum of genetic divergence. Recent studies have highlighted the potential importance of chemosensory genes, including the gustatory and olfactory receptor gene families (Gr and Or, respectively), in the process of host race formation. We used targeted resequencing to achieve a very high depth of coverage, and thereby revealed the extent of CNV of 434 genes, including 150 chemosensory genes, in 104 individuals distributed across eight host races of the pea aphid. We found that CNV was widespread in our global sample, with a significantly higher occurrence in multigene families, especially in Ors. We also observed a decrease in the gene probability of being completely duplicated or deleted (CDD) with increase in coding sequence length. Genes with CDD variants were usually more polymorphic for copy number, especially in the P450 gene family where toxin resistance may be related to gene dosage. We found that Gr were overrepresented among genes discriminating host races, as were CDD genes and pseudogenes. Our observations shed new light on CNV dynamics and are consistent with CNV playing a role in both local adaptation and speciation. PMID:25234705

Department of Defense Enterprise Requirements and Acquisition Model

DTIC Science & Technology

2011-06-01

Laboratories’ Center for Reengineering and Enabling Technology ( CRET ) to develop the APM. The APM is a compilation of policy, instructions, and...CDD Capabilities Development Document CBA Capabilities-Based Assessment CPD Capability Production Document CRET Center for Re-engineering

Contaminants in ospreys from the Pacific Northwest: I. Trends and Patterns in polychlorinated dibenzo-p-dioxins and -dibenzofurans in eggs and plasma

USGS Publications Warehouse

Elliott, J.E.; Machmer, M.M.; Henny, Charles J.; Wilson, L.K.; Norstrom, R.J.

1998-01-01

Osprey (Pandion haliaetus) eggs were collected from 1991 to 1997 at nests (na??=a??121) upstream and downstream of bleached kraft pulp mills and at reference sites in the Fraser and Columbia River drainage systems of British Columbia, Washington, and Oregon. Blood samples were collected from nestling ospreys during the 1992 breeding season on the Thompson River. Samples were analyzed for polychlorinated dibenzo-p-dioxins (PCDDs) and -dibenzofurans (PCDFs). Mean concentrations of 2,3,7,8-TCDD were significantly higher in eggs collected in 1991 at downstream compared to upstream nests near pulp mills at Kamloops and Castlegar, British Columbia. There were no significant temporal trends in 2,3,7,8-TCDD, -TCDF or other measured compounds at a sample of nests monitored between 1991 and 1994 downstream of the Castlegar pulp mill, despite changes in bleaching technology (CIO2 substitution). However, by 1997 concentrations of 2,3,7,8-TCDD and -TCDF were significantly lower than previous years in nests sampled downstream at both Castlegar and Kamloops. An unusual pattern of higher chlorinated PCDDs and PCDFs was found in many of the osprey eggs collected in this study, and considerable individual variation in the pattern existed among eggs from the same site. For example, eggs from four different nests at one study area (Quesnel) on the Fraser River had concentrations of 1,2,3,4,6,7,8-HpCDD ranging from <1 to 1,100 ng/kg and OCDD from <1 to 7,000 ng/kg wet weight. Higher mean concentrations of HpCDD and OCDD were found in eggs from the Thompson River, a tributary of the Fraser, compared to the Columbia River, and concentrations were generally higher at nests upstream of pulp mills. In plasma samples, 1,2,3,4,6,7,8-HpCDD and OCDD were the main compounds detected, with no significant differences measured between samples upstream versus downstream or earlier versus later in the breeding season. Use of chlorophenolic wood preservatives by lumber processors was considered the main source of higher chlorinated PCDD/Fs throughout the systems, based on patterns of trace PCDFs in eggs and significant correlations between egg concentrations of pentachlorophenol and both HpCDD (ra??=a??0.891, pa??

Contaminants in ospreys from the Pacific Northwest: I. Trends and patterns in polychlorinated dibenzo-p-dioxins and -dibenzofurans in eggs and plasma.

PubMed

Elliott, J E; Machmer, M M; Henny, C J; Wilson, L K; Norstrom, R J

1998-11-01

Osprey (Pandion haliaetus) eggs were collected from 1991 to 1997 at nests (n = 121) upstream and downstream of bleached kraft pulp mills and at reference sites in the Fraser and Columbia River drainage systems of British Columbia, Washington, and Oregon. Blood samples were collected from nestling ospreys during the 1992 breeding season on the Thompson River. Samples were analyzed for polychlorinated dibenzo-p-dioxins (PCDDs) and -dibenzofurans (PCDFs). Mean concentrations of 2,3,7,8-TCDD were significantly higher in eggs collected in 1991 at downstream compared to upstream nests near pulp mills at Kamloops and Castlegar, British Columbia. There were no significant temporal trends in 2,3,7,8-TCDD, -TCDF or other measured compounds at a sample of nests monitored between 1991 and 1994 downstream of the Castlegar pulp mill, despite changes in bleaching technology (CIO2 substitution). However, by 1997 concentrations of 2, 3,7,8-TCDD and -TCDF were significantly lower than previous years in nests sampled downstream at both Castlegar and Kamloops. An unusual pattern of higher chlorinated PCDDs and PCDFs was found in many of the osprey eggs collected in this study, and considerable individual variation in the pattern existed among eggs from the same site. For example, eggs from four different nests at one study area (Quesnel) on the Fraser River had concentrations of 1,2,3,4,6,7,8-HpCDD ranging from <1 to 1,100 ng/kg and OCDD from <1 to 7,000 ng/kg wet weight. Higher mean concentrations of HpCDD and OCDD were found in eggs from the Thompson River, a tributary of the Fraser, compared to the Columbia River, and concentrations were generally higher at nests upstream of pulp mills. In plasma samples, 1,2,3,4,6,7,8-HpCDD and OCDD were the main compounds detected, with no significant differences measured between samples upstream versus downstream or earlier versus later in the breeding season. Use of chlorophenolic wood preservatives by lumber processors was considered the main source of higher chlorinated PCDD/Fs throughout the systems, based on patterns of trace PCDFs in eggs and significant correlations between egg concentrations of pentachlorophenol and both HpCDD (r = 0.891, p < 0.01) and OCDD (r = 0.870, p < 0.01).

Anterior cervical discectomy and fusion (ACDF) versus cervical disc arthroplasty (CDA) for two contiguous levels cervical disc degenerative disease: a meta-analysis of randomized controlled trials.

PubMed

Zou, Shihua; Gao, Junyi; Xu, Bin; Lu, Xiangdong; Han, Yongbin; Meng, Hui

2017-04-01

Anterior cervical discectomy and fusion (ACDF) has been considered as a gold standard for symptomatic cervical disc degeneration (CDD), which may result in progressive degeneration of the adjacent segments. The artificial cervical disc was designed to reduce the number of lesions in the adjacent segments. Clinical studies have demonstrated equivalence of cervical disc arthroplasty (CDA) for anterior cervical discectomy and fusion in single segment cervical disc degeneration. But for two contiguous levels cervical disc degeneration (CDD), which kind of treatment method is better is controversial. To evaluate the clinical effects requiring surgical intervention between anterior cervical discectomy and fusion (ACDF) and cervical disc arthroplasty (CDA) at two contiguous levels cervical disc degeneration. We conducted a comprehensive search in multiple databases, including PubMed, Cochrane Central Register of Controlled Trials, EBSCO and EMBASE. We identified that six reports meet inclusion criteria. Two independent reviewers performed the data extraction from archives. Data analysis was conducted with RevMan 5.3. After applying inclusion and exclusion criteria, six papers were included in meta-analyses. The overall sample size at baseline was 650 patients (317 in the TDR group and 333 in the ACDF group). The results of the meta-analysis indicated that the CDA patients had significant superiorities in mean blood loss (P < 0.00001, standard mean differences (SMD) = -0.85, 95 % confidence interval (CI) = -1.22 to -0.48); reoperation (P = 0.0009, risk ratio (RR) = 0.28, 95 % confidence interval (CI) = 0.13-0.59), adjacent segment degeneration (P < 0.00001, risk ratio (RR) = 0.48, 95 % confidence interval (CI) = 0.40-0.58) and Neck Disability Index (P = 0.002, SMD = 0.31, 95 % CI = 0.12-0.50). No significant difference was identified between the two groups regarding mean surgical time (P = 0.84, SMD = -0.04, 95 % CI = -0.40 to 0.32), neck and arm pain scores (P = 0.52, SMD = 0.06, 95 % CI = -0.13 to 0.25) reported on a visual analog scale and rate of postoperative complications [risk ratio (RR) = 0.79; 95 % CI = 0.50-1.25; P = 0.31]. The CDA group of sagittal range of motion (ROM) of the operated and adjacent levels, functional segment units (FSU) and C2-7 is superior to ACDF group by radiographic data of peroperation, postoperation and follow-up. We can learn from this meta-analysis that the cervical disc arthroplasty (CDA) group is equivalent and in some aspects has more significant clinical outcomes than the ACDF group at two contiguous levels CDD.

Space Based Infrared System High (SBIRS High)

DTIC Science & Technology

2015-12-01

Cost Assessment and Program Evaluation CARD - Cost Analysis Requirements Description CDD - Capability Development Document CLIN - Contract Line Item...Funds for the Commercially Hosted Infrared Payload ( CHIRP ), project number A040, were excluded from this report. Those RDT&E funds are not associated

THE APPLICATION OF JET REMPI/TOFMS TO REAL-TIME MONITORING OF DIOXINS

EPA Science Inventory

An advanced rapid monitoring technology, Jet Resonance Enhanced Multi-Photon Ionization, (Jet REMPI) is being applied to the measurement of air toxics, including chlorinated dibenzodioxins and dibenzofurans (CDD/CDF), for mechanistic understanding, process monitoring, and regulat...

A Collaborative Web-Based Architecture For Sharing ToxCast Data

EPA Science Inventory

Collaborative Drug Discovery (CDD) has created a scalable platform that combines traditional drug discovery informatics with Web2.0 features. Traditional drug discovery capabilities include substructure, similarity searching and export to excel or sdf formats. Web2.0 features inc...

Childhood Disintegrative Disorder.

ERIC Educational Resources Information Center

Malhotra, Savita; Gupta, Nitin

1999-01-01

This article reviews what is known about childhood distintegrative disorder (CDD), a clinical syndrome characterized by disintegration of mental functions and regression of acquired language and intellectual functions after a period (usually 3-4 years) of normal development. It reviews the condition's epidemiology, onset and progression,…

Dalhousie Fire

ERIC Educational Resources Information Center

Matthews, Fred W.

1986-01-01

Describes steps taken by the Weldon Law Library at Dalhousie University in salvaging books damaged in a major fire, including procedures and processes used in packing, sorting, drying, and cleaning the books. The need for a disaster plan for specific libraries is emphasized, and some suggestions are made. (CDD)

Coping with Information Load: User Strategies and Implications for Librarians.

ERIC Educational Resources Information Center

Rudd, Joel; Rudd, Mary Jo

1986-01-01

Describes important techniques by which library users avoid information overload, clarifies the terminology in the information overload literature, and reviews the major findings of this literature in the context of library applications. Implications for users and librarians are discussed. (CDD)

Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea.

PubMed

Makarova, Kira S; Sorokin, Alexander V; Novichkov, Pavel S; Wolf, Yuri I; Koonin, Eugene V

2007-11-27

An evolutionary classification of genes from sequenced genomes that distinguishes between orthologs and paralogs is indispensable for genome annotation and evolutionary reconstruction. Shortly after multiple genome sequences of bacteria, archaea, and unicellular eukaryotes became available, an attempt on such a classification was implemented in Clusters of Orthologous Groups of proteins (COGs). Rapid accumulation of genome sequences creates opportunities for refining COGs but also represents a challenge because of error amplification. One of the practical strategies involves construction of refined COGs for phylogenetically compact subsets of genomes. New Archaeal Clusters of Orthologous Genes (arCOGs) were constructed for 41 archaeal genomes (13 Crenarchaeota, 27 Euryarchaeota and one Nanoarchaeon) using an improved procedure that employs a similarity tree between smaller, group-specific clusters, semi-automatically partitions orthology domains in multidomain proteins, and uses profile searches for identification of remote orthologs. The annotation of arCOGs is a consensus between three assignments based on the COGs, the CDD database, and the annotations of homologs in the NR database. The 7538 arCOGs, on average, cover approximately 88% of the genes in a genome compared to a approximately 76% coverage in COGs. The finer granularity of ortholog identification in the arCOGs is apparent from the fact that 4538 arCOGs correspond to 2362 COGs; approximately 40% of the arCOGs are new. The archaeal gene core (protein-coding genes found in all 41 genome) consists of 166 arCOGs. The arCOGs were used to reconstruct gene loss and gene gain events during archaeal evolution and gene sets of ancestral forms. The Last Archaeal Common Ancestor (LACA) is conservatively estimated to possess 996 genes compared to 1245 and 1335 genes for the last common ancestors of Crenarchaeota and Euryarchaeota, respectively. It is inferred that LACA was a chemoautotrophic hyperthermophile that, in addition to the core archaeal functions, encoded more idiosyncratic systems, e.g., the CASS systems of antivirus defense and some toxin-antitoxin systems. The arCOGs provide a convenient, flexible framework for functional annotation of archaeal genomes, comparative genomics and evolutionary reconstructions. Genomic reconstructions suggest that the last common ancestor of archaea might have been (nearly) as advanced as the modern archaeal hyperthermophiles. ArCOGs and related information are available at: ftp://ftp.ncbi.nih.gov/pub/koonin/arCOGs/.

Distribution and Classification of Serine β-Lactamases in Brazilian Hospital Sewage and Other Environmental Metagenomes Deposited in Public Databases.

PubMed

Fróes, Adriana M; da Mota, Fábio F; Cuadrat, Rafael R C; Dávila, Alberto M R

2016-01-01

β-lactam is the most used antibiotic class in the clinical area and it acts on blocking the bacteria cell wall synthesis, causing cell death. However, some bacteria have evolved resistance to these antibiotics mainly due the production of enzymes known as β-lactamases. Hospital sewage is an important source of dispersion of multidrug-resistant bacteria in rivers and oceans. In this work, we used next-generation DNA sequencing to explore the diversity and dissemination of serine β-lactamases in two hospital sewage from Rio de Janeiro, Brazil (South Zone, SZ and North Zone, NZ), presenting different profiles, and to compare them with public environmental data available. Also, we propose a Hidden-Markov-Model approach to screen potential serine β-lactamases genes (in public environments samples and generated hospital sewage data), exploring its evolutionary relationships. Due to the high variability in β-lactamases, we used a position-specific scoring matrix search method (RPS-BLAST) against conserved domain database profiles (CDD, Pfam, and COG) followed by visual inspection to detect conserved motifs, to increase the reliability of the results and remove possible false positives. We were able to identify novel β-lactamases from Brazilian hospital sewage and to estimate relative abundance of its types. The highest relative abundance found in SZ was the Class A (50%), while Class D is predominant in NZ (55%). CfxA (65%) and ACC (47%) types were the most abundant genes detected in SZ, while in NZ the most frequent were OXA-10 (32%), CfxA (28%), ACC (21%), CEPA (20%), and FOX (19%). Phylogenetic analysis revealed β-lactamases from Brazilian hospital sewage grouped in the same clade and close to sequences belonging to Firmicutes and Bacteroidetes groups, but distant from potential β-lactamases screened from public environmental data, that grouped closer to β-lactamases of Proteobacteria. Our results demonstrated that HMM-based approach identified homologs of serine β-lactamases, indicating the specificity and high sensitivity of this approach in large datasets, contributing for the identification and classification of a large number of homologous genes, comprising possible new ones. Phylogenetic analysis revealed the potential reservoir of β-lactam resistance genes in the environment, contributing to understanding the evolution and dissemination of these genes.

Distribution and Classification of Serine β-Lactamases in Brazilian Hospital Sewage and Other Environmental Metagenomes Deposited in Public Databases

PubMed Central

Fróes, Adriana M.; da Mota, Fábio F.; Cuadrat, Rafael R. C.; Dávila, Alberto M. R.

2016-01-01

β-lactam is the most used antibiotic class in the clinical area and it acts on blocking the bacteria cell wall synthesis, causing cell death. However, some bacteria have evolved resistance to these antibiotics mainly due the production of enzymes known as β-lactamases. Hospital sewage is an important source of dispersion of multidrug-resistant bacteria in rivers and oceans. In this work, we used next-generation DNA sequencing to explore the diversity and dissemination of serine β-lactamases in two hospital sewage from Rio de Janeiro, Brazil (South Zone, SZ and North Zone, NZ), presenting different profiles, and to compare them with public environmental data available. Also, we propose a Hidden-Markov-Model approach to screen potential serine β-lactamases genes (in public environments samples and generated hospital sewage data), exploring its evolutionary relationships. Due to the high variability in β-lactamases, we used a position-specific scoring matrix search method (RPS-BLAST) against conserved domain database profiles (CDD, Pfam, and COG) followed by visual inspection to detect conserved motifs, to increase the reliability of the results and remove possible false positives. We were able to identify novel β-lactamases from Brazilian hospital sewage and to estimate relative abundance of its types. The highest relative abundance found in SZ was the Class A (50%), while Class D is predominant in NZ (55%). CfxA (65%) and ACC (47%) types were the most abundant genes detected in SZ, while in NZ the most frequent were OXA-10 (32%), CfxA (28%), ACC (21%), CEPA (20%), and FOX (19%). Phylogenetic analysis revealed β-lactamases from Brazilian hospital sewage grouped in the same clade and close to sequences belonging to Firmicutes and Bacteroidetes groups, but distant from potential β-lactamases screened from public environmental data, that grouped closer to β-lactamases of Proteobacteria. Our results demonstrated that HMM-based approach identified homologs of serine β-lactamases, indicating the specificity and high sensitivity of this approach in large datasets, contributing for the identification and classification of a large number of homologous genes, comprising possible new ones. Phylogenetic analysis revealed the potential reservoir of β-lactam resistance genes in the environment, contributing to understanding the evolution and dissemination of these genes. PMID:27895627

Congenital Sodium Diarrhea: A Form of Intractable Diarrhea, With a Link to Inflammatory Bowel Disease.

PubMed

Janecke, Andreas R; Heinz-Erian, Peter; Müller, Thomas

2016-08-01

Congenital diarrheal disorders (CDDs) represent a group of challenging clinical conditions for pediatricians because of the severity of the presentation and the broad range of possible differential diagnoses. CDDs arise from alterations in the transport of nutrients and electrolytes across the intestinal mucosa, from enterocyte and enteroendocrine cell differentiation and/or polarization defects, and from the modulation of the intestinal immune response. Advances were made recently in deciphering the etiology and pathophysiology of one of these disorders, congenital sodium diarrhea (CSD). CSD refers to an intractable diarrhea of intrauterine onset with high fecal sodium loss. CSD is clinically and genetically heterogeneous. A syndromic form of CSD features choanal and intestinal atresias as well as recurrent corneal erosions. Small bowel histology frequently detects an epithelial "tufting" dysplasia. It is autosomal recessively inherited, and caused by SPINT2 mutations. The nonsyndromic form of CSD can be caused by dominant activating mutations in GUCY2C, encoding intestinal receptor guanylate cyclase C (GC-C), and by autosomal recessive SLC9A3 loss-of-function mutations. SLC9A3 encodes Na/H antiporter 3, the major intestinal brush border Na/H exchanger, and a downstream target of GC-C. A number of patients with GUCY2C and SLC9A3 mutations developed inflammatory bowel disease. Both the number of recognized CDD forms as well as the number of underlying disease genes are gradually increasing. Knowledge of these CDD genes enables noninvasive, next-generation gene panel-based testing to facilitate an early diagnosis in CDD. Primary Na/H antiporter 3 and GC-C malfunction is implicated as a predisposition for inflammatory bowel disease in subset of patients.

Transient and Prolonged Response of Chicken Cecum Mucosa to Colonization with Different Gut Microbiota

PubMed Central

Volf, Jiri; Polansky, Ondrej; Varmuzova, Karolina; Gerzova, Lenka; Sekelova, Zuzana; Faldynova, Marcela; Babak, Vladimir; Medvecky, Matej; Smith, Adrian L.; Kaspers, Bernd; Velge, Philippe; Rychlik, Ivan

2016-01-01

In this study we determined protein and gene expression in the caeca of newly hatched chickens inoculated with cecal contents sourced from hens of different ages. Over 250 proteins exhibited modified expression levels in response to microbiota inoculation. The most significant inductions were observed for ISG12-2, OASL, ES1, LYG2, DMBT1-L, CDD, ANGPTL6, B2M, CUZD1, IgM and Ig lambda chain. Of these, ISG12-2, ES1 and both immunoglobulins were expressed at lower levels in germ-free chickens compared to conventional chickens. In contrast, CELA2A, BRT-2, ALDH1A1, ADH1C, AKR1B1L, HEXB, ALDH2, ALDOB, CALB1 and TTR were expressed at lower levels following inoculation of microbiota. When chicks were given microbiota preparations from different age donors, the recipients mounted differential responses to the inoculation which also differed from the response profile in naturally colonised birds. For example, B2M, CUZD1 and CELA2A responded differently to the inoculation with microbiota of 4- or 40-week-old hens. The increased or decreased gene expression could be recorded 6 weeks after the inoculation of newly hatched chickens. To characterise the proteins that may directly interact with the microbiota we characterised chicken proteins that co-purified with the microbiota and identified a range of host proteins including CDD, ANGPTL6, DMBT1-L, MEP1A and Ig lambda. We propose that induction of ISG12-2 results in reduced apoptosis of host cells exposed to the colonizing commensal microbiota and that CDD, ANGPTL6, DMBT1-L, MEP1A and Ig lambda reduce contact of luminal microbiota with the gut epithelium thereby reducing the inflammatory response. PMID:27685470

Global Warming Impacts on Heating and Cooling Degree-Days in the United States

NASA Astrophysics Data System (ADS)

Petri, Y.; Caldeira, K.

2014-12-01

Anthropogenic climate change is expected to significantly alter residential air conditioning and space heating requirements, which account for 41% of U.S. household energy expenditures. The degree-day method can be used for reliable estimation of weather related building energy consumption and costs, as well as outdoor climatic thermal comfort. Here, we use U.S. Climate Normals developed by NOAA based on weather station observations along with Climate Model Intercomparison Project phase 5 (CMIP5) multi-model ensemble simulations. We add the projected change in heating and cooling degree-days based on the climate models to the estimates based on the NOAA U.S. Climate Normals to project future heating and cooling degree-days. We find locations with the lowest and highest combined index of cooling (CDDs) and heating degree-days (HDDs) for the historical period (1981 - 2010) and future period (2080 - 2099) under the Representation Concentration Pathway 8.5 (RCP8.5) climate change scenario. Our results indicate that in both time frames and among the lower 48 states, coastal areas in the West and South California will have the smallest degree-day sum (CDD + HDD), and hence from a climatic perspective become the best candidates for residential real estate. The Rocky Mountains region in Wyoming, in addition to northern Minnesota and North Dakota, will have the greatest CDD + HDD. While global warming is projected to reduce the median heating and cooling demand (- 5%) at the end of the century, CDD + HDD will decrease in the North, with an opposite effect in the South. This work could be helpful in deciding where to live in the United States based on present and future thermal comfort, and could also provide a basis for estimates of changes in heating and cooling energy demand.

Photocatalytic reductive dechlorination of 2-chlorodibenzo-p-dioxin by Pd modified g-C3N4 photocatalysts under UV-vis irradiation: Efficacy, kinetics and mechanism.

PubMed

Ding, Jiafeng; Long, Gaoyuan; Luo, Yang; Sun, Runze; Chen, Mengxia; Li, Yajun; Zhou, Yanfang; Xu, Xinhua; Zhao, Weirong

2018-05-09

Polychlorinated dibenzo-p-dioxins (PCDDs), as a group of notorious anthropogenic environmental toxicants, are arguably ubiquitous in nature. In this study, we investigated the photocatalytic reductive dechlorination of 2-chlorodibenzo-p-dioxin (2-CDD) over Pd/g-C 3 N 4 catalysts under UV-vis irradiation. The g-C 3 N 4 and a series of Pd/g-C 3 N 4 catalysts were prepared by thermal polymerization and mechanical mixing-illumination method and characterized by XRD, TEM, BET, SEM and UV-vis DRS analyses. Among all the samples, the Pd/g-C 3 N 4 (5 wt%) yielded the optimal dechlorination activity with a total 2-CDD conversion of 54% within 4 h, and 76% of those converted 2-CDD were evolved to dibenzo-p-dioxin (DD). The kinetics of dechlorination could be described as pseudo-first-order decay model (R 2  > 0.84). Corresponding rate constants (k) increased from 0.052 to 0.17 h -1 with Pd contents up to 5 wt% and decreased to 0.13 h -1 with a 10 wt% of Pd. The enhanced activities originated from the surface plasmonic resonance (SPR) effect of Pd nanoparticles and the formation of Schottky barrier between Pd and g-C 3 N 4 , which extend the spectrum responsive range and suppress the charge recombination of g-C 3 N 4 . This is the first report on the photocatalytic reductive removal of PCDDs and may provide a new approach for PCDDs pollution control. Copyright © 2018 Elsevier B.V. All rights reserved.

Effects of Perinatal Dioxin Exposure on Development of Children during the First 3 Years of Life.

PubMed

Tai, Pham The; Nishijo, Muneko; Nghi, Tran Ngoc; Nakagawa, Hideaki; Van Luong, Hoang; Anh, Tran Hai; Nishijo, Hisao

2016-08-01

To investigate the longitudinal effects of perinatal exposure to dioxin on neurodevelopment and physical growth of a birth cohort during the first 3 years of life. A total of 217 mother-infant pairs living in a dioxin-contaminated area in Vietnam were followed up. Perinatal dioxin exposure of infants was estimated by the measurement of dioxin levels in breast milk of nursing mothers. Neurodevelopment of infants and children, including cognitive, language, and motor development, was determined at 4 months, 1 year, and 3 years of age. Physical growth, including weight, height, and head and abdominal circumferences, was measured at birth, 1 and 4 months, and 1 and 3 years of age. Multivariate mixed models were applied for analyzing repeated measures. In boys, composite motor and gross motor scores were decreased with increasing exposure of 2,3,7,8-tetrachlorodibenzo-p-dioxin (2,3,7,8-TetraCDD). The high toxic equivalent of polychlorinated dibenzo-p-dioxins and polychlorinated dibenzofurans (PCDDs/PCDFs-TEQ) group showed a significant decrease in expressive communication score. In girls, there was no decreased score in any neurodevelopment aspects in high-exposure groups. All body size measures in boys were decreased in the high-exposure groups of 2,3,7,8-TetraCDD and PCDDs/PCDFs-TEQ. In girls, high 2,3,7,8-TetraCDD and PCDDs/PCDFs-TEQ exposure was associated with increased head and abdominal circumferences. Perinatal dioxin exposure affects physical growth and neurodevelopment of infants and children in the first 3 years of life in a sex-specific manner. Copyright © 2016 Elsevier Inc. All rights reserved.

Photolysis of polychlorinated dibenzo-p-dioxins and dibenzofurans dissolved in vegetable oils: influence of oil quality.

PubMed

Isosaari, Pirjo; Laine, Olli; Tuhkanen, Tuula; Vartiainen, Terttu

2005-03-20

Sunlight or ultraviolet light irradiation of polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) in the presence of vegetable oil offers a potential method for the cleanup of contaminated soil. In this study, the effects of different types of vegetable oils on the photochemical degradation of 1,2,3,4,6,7,8-heptachlorodibenzofuran and heptachlorodibenzo-p-dioxin (1,2,3,4,6,7,8-HpCDF/HpCDD) were investigated in the laboratory. Using a blacklight lamp as a source of ultraviolet light, 93-100% of 1,2,3,4,6,7,8-HpCDF degraded in 60 min in rapeseed oil, extra virgin olive oil and olive oil. Less degradation occurred in palm oil (59%), toluene (39%) and hexane (20%). The better degradation in vegetable oils in comparison with organic solvents was attributed to the photooxidation of lipids producing hydrogen for PCDD/F dechlorination. In addition to the hydrogen donor capacity, permeability of ultraviolet light was involved in the differences between vegetable oils. alpha-Tocopherol and chlorophyll did not influence the performance of oil at concentrations normally present in vegetable oils, whereas beta-carotene had an inhibitory effect on the degradation of 1,2,3,4,6,7,8-HpCDF. Up to 28% of the degradation products of 1,2,3,4,6,7,8-HpCDF were formed via the dechlorination pathway. Products included both toxic (2,3,7,8-chlorinated) and non-toxic PCDD/Fs, the toxic PCDD/Fs being more stable. Irradiation of 1,2,3,4,6,7,8-HpCDD yielded only non-toxic dechlorination products. Polychlorinated hydroxybiphenyls (OH-PCBs), polychlorinated dihydroxybiphenyls (DOH-PCBs) and polychlorinated hydroxydiphenylethers (OH-PCDEs) containing one to seven chlorine atoms were not detected in irradiated HpCDF/HpCDD samples.

Closed Incision Negative Pressure Wound Therapy vs Conventional Dry Dressings After Primary Knee Arthroplasty: A Randomized Controlled Study.

PubMed

Manoharan, Varaguna; Grant, Andrea L; Harris, Alicia C; Hazratwala, Kaushik; Wilkinson, Matthew P R; McEwen, Peter J C

2016-11-01

The purpose of this study was to assess the effect of negative pressure wound therapy (NPWT) on quality of life (QoL), wound complications, and cost after primary knee arthroplasty. A prospective analysis of 33 patients undergoing primary knee arthroplasty performed by 3 surgeons in one institution. The first 12 patients (3 bilateral and 9 unilateral) had conventional dry dressings (CDD) applied and cost of dressings was assessed. The other 21 patients all underwent bilateral knee arthroplasty and had either side randomized to receiving NPWT or CDD. Cost of dressings, wound complications, and QoL were compared. One patient had a reaction to the NPWT requiring readmission. Another had persistent wound drainage that required NPWT application. There were no wound issues in the remaining 31 patients. The average cost in the first 12 patients was Australian dollar $48.70 with an average of 1.5 changes on ward. In the 21 patients receiving both dressings, the average cost for CDD was less (Australian dollar $43.51 vs $396.02, P ≤ .011, effect size [ES] = 1.06). When comparing QoL factors, wound leakage (0.14 vs 0.39 P = .019, ES = 1.02), and wound protection (0.16 vs 0.33, P = .001, ES = 0.021) were better in the NPWT group. There was no other significant difference in QoL factors. The average number of changes on the ward was less for the NPWT group (1.19 vs 1.38, P = .317, ES = 1.02). We found no benefit in wound healing or cost with NPWT post knee arthroplasty. There was some benefit in NPWT QoL factors less wound leakage and better protection. Crown Copyright © 2016. Published by Elsevier Inc. All rights reserved.

Disposal of historically contaminated soil in the cement industry and the evaluation of environmental performance.

PubMed

Li, Yeqing; Zhang, Jiang; Miao, Wenjuan; Wang, Huanzhong; Wei, Mao

2015-09-01

Approximately 400000t of DDTs/HCHs-contaminated soil (CS) needed to be co-processed in a cement kiln with a time limitation of 2y. A new pre-processing facility with a "drying, grinding and DDTs/HCHs vaporizing" ability was equipped to meet the technical requirements for processing cement raw meal and the environmental standards for stack emissions. And the bottom of the precalciner with high temperatures >1000°C was chosen as the CS feeding point for co-processing, which has rarely been reported. To assess the environmental performance of CS pre- and co-processing technologies, according to the local regulation, a test burn was performed by independent and accredited institutes systematically for determination of the clinker quality, kiln stack gas emissions and destruction efficiency of the pollutant. The results demonstrated that the clinker was of high quality and not adversely affected by CS co-processing. Stack emissions were all below the limits set by Chinese standards. Particularly, PCDD/PCDF emissions ranged from 0.0023 to 0.0085ngI-TEQNm(-3). The less toxic OCDD was the peak congener for CS co-processing procedure, while the most toxic congeners (i.e. 2,3,7,8-TeCDD, 1,2,3,7,8-PeCDD and 2,3,4,7,8-PeCDD) remained in a minor proportion. Destruction and removal efficiency (DRE) and destruction efficiency (DE) of the kiln system were better than 99.9999% and 99.99%, respectively, at the highest CS feeding rate during normal production. To guarantee the environmental performance of the system the quarterly stack gas emission was also monitored during the whole period. And all of the results can meet the national standards requirements. Copyright © 2015 Elsevier Ltd. All rights reserved.

Patients with chronic insomnia have selective impairments in memory that are modulated by cortisol.

PubMed

Chen, Gui-Hai; Xia, Lan; Wang, Fang; Li, Xue-Wei; Jiao, Chuan-An

2016-10-01

Memory impairment is a frequent complaint in insomniacs; however, it is not consistently demonstrated. It is unknown whether memory impairment in insomniacs involves neuroendocrine dysfunction. The participants in this study were selected from the clinical setting and included 21 patients with chronic insomnia disorder (CID), 25 patients with insomnia and comorbid depressive disorder (CDD), and 20 control participants without insomnia. We evaluated spatial working and reference memory, object working and reference memory, and object recognition memory using the Nine Box Maze Test. We also evaluated serum neuroendocrine hormone levels. Compared to the controls, the CID patients made significantly more errors in spatial working and object recognition memory (p < .05), whereas the CDD patients performed poorly in all the assessed memory types (p < .05). In addition, the CID patients had higher levels (mean difference [95% CI]) of corticotrophin-releasing hormone, cortisol (31.98 [23.97, 39.98] μg/l), total triiodothyronine (667.58 [505.71, 829.45] μg/l), and total thyroxine (41.49 [33.23, 49.74] μg/l) (p < .05), and lower levels of thyrotropin-releasing hormone (-35.93 [-38.83, -33.02] ng/l), gonadotropin-releasing hormone (-4.50 [-5.02, -3.98] ng/l) (p < .05), and adrenocorticotropic hormone compared to the CDD patients. After controlling for confounding variables, the partial correlation analysis revealed that the levels of cortisol positively correlated with the errors in object working memory (r = .534, p = .033) and negatively correlated with the errors in object recognition memory (r = -.659, p = .006) in the CID patients. The results suggest that the CID patients had selective memory impairment, which may be mediated by increased cortisol levels. © 2016 Society for Psychophysiological Research.

TOPDOM: database of conservatively located domains and motifs in proteins.

PubMed

Varga, Julia; Dobson, László; Tusnády, Gábor E

2016-09-01

The TOPDOM database-originally created as a collection of domains and motifs located consistently on the same side of the membranes in α-helical transmembrane proteins-has been updated and extended by taking into consideration consistently localized domains and motifs in globular proteins, too. By taking advantage of the recently developed CCTOP algorithm to determine the type of a protein and predict topology in case of transmembrane proteins, and by applying a thorough search for domains and motifs as well as utilizing the most up-to-date version of all source databases, we managed to reach a 6-fold increase in the size of the whole database and a 2-fold increase in the number of transmembrane proteins. TOPDOM database is available at http://topdom.enzim.hu The webpage utilizes the common Apache, PHP5 and MySQL software to provide the user interface for accessing and searching the database. The database itself is generated on a high performance computer. tusnady.gabor@ttk.mta.hu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Armored Multi Purpose Vehicle (AMPV)

DTIC Science & Technology

2015-12-01

Procurement Contracting Officer ( PCO ) notified BAE of PDR completion on January 21, 2016. The FY 2016 Omnibus Appropriations Bill decremented FY 2016...CDD requirements and under configuration control. All PDR items were closed by the PCO on January 21, 2016. AMPV December 2015 SAR March 21, 2016 18

COMBUSTION CONTROL OF ORGANIC EMISSIONS FROM MUNICIPAL WASTE COMBUSTORS

EPA Science Inventory

More than two decades ago, researchers identified benzo(a)pyrene and other organic species in the emissions from incineration of solid waste. Chlorinated dibenzo-p-dioxins and-furans (CDD/CDF) were first detected in municipal waste combustor (MWC) emissions in 1977. Since then, C...

High Functioning Autism and Childhood Disintegrative Disorder in Half Brothers.

ERIC Educational Resources Information Center

Zwaigenbaum, L.; Szatmari, P.; Mahoney, W.; Bryson, S.; Bartolucci, G.; MacLean, J.

2000-01-01

This case report describes the presence of autism and Childhood Disintegrative Disorder (CDD) cosegregating within a sibship of half-brothers with the same mother. The report suggests that the rarity of the two conditions suggests a shared transmissible mechanism. (Contains references.) (Author/DB)

Ambient air concentrations of PCDDs, PCDFs, coplanar PCBs, and PAHs at the Mississippi Sandhill Crane National Wildlife Refuge, Jackson County, Mississippi

USGS Publications Warehouse

White, D.H.; Hardy, J.W.

1994-01-01

Our objective was to determine the levels of selected airborne contaminants in ambient air at the Mississippi Sandhill Crane National Wildlife Refuge, Mississippi, that might be affecting the health of endangered cranes living there. Two high-volume air samplers were operated at separate locations on the Refuge during May?September 1991. The sampling media were micro-quartz filters in combination with polyurethane foam plugs. Composite bimonthly samples from each station were analyzed for polychlorinated dibenzo-p-dioxins (PCDDs), dibenzofurans (PCDFs), coplanar polychlorinated biphenyls (PCBs), and polycyclic aromatic hydrocarbons (PAHs). Overall, residue concentrations were low. The toxic PCDD isomer 2,3,7,8-tetra-CDD was not detected, nor was penta-CDD. There was no difference (P>0.05) in residue concentrations between stations or over time and meteorological parameters were not correlated with residue concentrations. Because contaminant levels and patterns may differ seasonally, we recommend that air samples collected during winter months also be analyzed for these same chemical groups.

Methods and apparatus for constructing and implementing a universal extension module for processing objects in a database

NASA Technical Reports Server (NTRS)

Li, Chung-Sheng (Inventor); Smith, John R. (Inventor); Chang, Yuan-Chi (Inventor); Jhingran, Anant D. (Inventor); Padmanabhan, Sriram K. (Inventor); Hsiao, Hui-I (Inventor); Choy, David Mun-Hien (Inventor); Lin, Jy-Jine James (Inventor); Fuh, Gene Y. C. (Inventor); Williams, Robin (Inventor)

2004-01-01

Methods and apparatus for providing a multi-tier object-relational database architecture are disclosed. In one illustrative embodiment of the present invention, a multi-tier database architecture comprises an object-relational database engine as a top tier, one or more domain-specific extension modules as a bottom tier, and one or more universal extension modules as a middle tier. The individual extension modules of the bottom tier operationally connect with the one or more universal extension modules which, themselves, operationally connect with the database engine. The domain-specific extension modules preferably provide such functions as search, index, and retrieval services of images, video, audio, time series, web pages, text, XML, spatial data, etc. The domain-specific extension modules may include one or more IBM DB2 extenders, Oracle data cartridges and/or Informix datablades, although other domain-specific extension modules may be used.

ANALYSIS OF ANIMAL- AND PLANT-DERIVED FEED INGREDIENTS FOR DIOXIN-LIKE COMPOUNDS

EPA Science Inventory

During a national survey of polychlorinated dibenzo-p-dioxins (CDD), dibenzofurans (CDF), and dioxin-like coplanar PCBs (PCB) in poultry, elevated concentrations above 20 parts per trillion (ppt) toxic equivalents (TEQ) were found in the fat of 2 broilers. These TEQ values were ...

Capability Portfolio Analysis Tool (CPAT) Verification and Validation Report

DTIC Science & Technology

2013-01-01

BFSB Battlefield Surveillance Brigade BFV Bradley Fighting Vehicle BMOD Bradley Modernization C2 (H) Command and Control (HBCT) C2 (S...Fire Infantry Fighting Vehicle (IFV); Fire Integrated Support Team (FIST); Engineer (Eng); Cavalry (CAV) BFV FOV CDD Block II - 16 Apr 2010 GCV FOV

Case Study of Childhood Disintegrative Disorder--Heller's Syndrome.

ERIC Educational Resources Information Center

Bray, Melissa A.; Kehle, Thomas J.; Theodore, Lea A.; Broudy, Matthew S.

2002-01-01

Discusses the case of a 25-year-old male with childhood disintegrative disorder (CDD), or Heller's syndrome, in terms of differential diagnosis, progression of the disorder, and suggestions for home- and school-based interventions. Documents the progressive deterioration of cognitive and social competencies. (Contains 23 references.) (GCP)

The Managerial Roles of Academic Library Directors: The Mintzberg Model.

ERIC Educational Resources Information Center

Moskowitz, Michael Ann

1986-01-01

A study based on a model developed by Henry Mintzberg examined the internal and external managerial roles of 126 New England college and university library directors. Survey results indicate that the 97 responding directors were primarily involved with internal managerial roles and work contacts. (CDD)

The ASTRAL Compendium in 2004

DOE R&D Accomplishments Database

Chandonia, John-Marc; Hon, Gary; Walker, Nigel S.; Lo Conte, Loredana; Koehl, Patrice; Levitt, Michael; Brenner, Steven E.

2003-09-15

The ASTRAL compendium provides several databases and tools to aid in the analysis of protein structures, particularly through the use of their sequences. Partially derived from the SCOP database of protein structure domains, it includes sequences for each domain and other resources useful for studying these sequences and domain structures. The current release of ASTRAL contains 54,745 domains, more than three times as many as the initial release four years ago. ASTRAL has undergone major transformations in the past two years. In addition to several complete updates each year, ASTRAL is now updated on a weekly basis with preliminary classifications of domains from newly released PDB structures. These classifications are available as a stand-alone database, as well as available integrated into other ASTRAL databases such as representative subsets. To enhance the utility of ASTRAL to structural biologists, all SCOP domains are now made available as PDB-style coordinate files as well as sequences. In addition to sequences and representative subsets based on SCOP domains, sequences and subsets based on PDB chains are newly included in ASTRAL. Several search tools have been added to ASTRAL to facilitate retrieval of data by individual users and automated methods.

SNAPPI-DB: a database and API of Structures, iNterfaces and Alignments for Protein–Protein Interactions

PubMed Central

Jefferson, Emily R.; Walsh, Thomas P.; Roberts, Timothy J.; Barton, Geoffrey J.

2007-01-01

SNAPPI-DB, a high performance database of Structures, iNterfaces and Alignments of Protein–Protein Interactions, and its associated Java Application Programming Interface (API) is described. SNAPPI-DB contains structural data, down to the level of atom co-ordinates, for each structure in the Protein Data Bank (PDB) together with associated data including SCOP, CATH, Pfam, SWISSPROT, InterPro, GO terms, Protein Quaternary Structures (PQS) and secondary structure information. Domain–domain interactions are stored for multiple domain definitions and are classified by their Superfamily/Family pair and interaction interface. Each set of classified domain–domain interactions has an associated multiple structure alignment for each partner. The API facilitates data access via PDB entries, domains and domain–domain interactions. Rapid development, fast database access and the ability to perform advanced queries without the requirement for complex SQL statements are provided via an object oriented database and the Java Data Objects (JDO) API. SNAPPI-DB contains many features which are not available in other databases of structural protein–protein interactions. It has been applied in three studies on the properties of protein–protein interactions and is currently being employed to train a protein–protein interaction predictor and a functional residue predictor. The database, API and manual are available for download at: . PMID:17202171

Pricing for Efficiency, Equity, and Simplicity: A Model Policy for an Interlibrary Courier Service.

ERIC Educational Resources Information Center

Gassler, Robert Scott

1985-01-01

Presents an example of a pricing policy for any interlibrary courier service which (1) calculates fixed, travelling, and stopping costs; (2) charges by how often the courier stops at each participating library; and (3) uses any subsidies for costs libraries cannot control. (CDD)

MONSOON Image Acquisition System | CTIO

Science.gov Websites

Visitor's Computer Guidelines Network Connection Request Instruments Instruments by Telescope IR Instruments flexible solution for the acquisition of pixel data from scientific CDD and IR detectors. The architecture requirements for both IR and CCD large focal planes that NOAO developed for instrumentation efforts in the

Cost Allocation Issues in Interlibrary Systems.

ERIC Educational Resources Information Center

Alexander, Ernest R.

1985-01-01

In comparing methods of allocating service transaction costs among member libraries of interlibrary systems, questions of how costs are to be estimated, and what cost elements are to be included are critical. Different approaches of estimation yield varying results. Actual distribution of units accounts for greatest variance in allocations. (CDD)

Interoperability, Integration, and Interdependence Between the United States and Canadian Forces: Recreating the Devil’s Brigade

DTIC Science & Technology

2016-05-26

www.arcic.army.mil/Articles/cdd-Force-Design-in-a-Constrained­ Environment.aspx. 45 Tzu , Sun . The Art of War... Bibliography Army Capabilities Integration Center. “Force 2025 and Beyond.” US Army. February 18, 2016. Accessed February 20, 2016. http

Oral History in Louisiana Libraries.

ERIC Educational Resources Information Center

Gardner, Joel, Ed.

1985-01-01

Theme issue shares experiences of librarians who have done oral history projects in school, parish, and university libraries throughout Louisiana. Articles cover the roles of the library and of oral history, how to begin projects, and how to involve students in the production of tapes and their organization for retrieval. (CDD)

A web-based system architecture for ontology-based data integration in the domain of IT benchmarking

NASA Astrophysics Data System (ADS)

Pfaff, Matthias; Krcmar, Helmut

2018-03-01

In the domain of IT benchmarking (ITBM), a variety of data and information are collected. Although these data serve as the basis for business analyses, no unified semantic representation of such data yet exists. Consequently, data analysis across different distributed data sets and different benchmarks is almost impossible. This paper presents a system architecture and prototypical implementation for an integrated data management of distributed databases based on a domain-specific ontology. To preserve the semantic meaning of the data, the ITBM ontology is linked to data sources and functions as the central concept for database access. Thus, additional databases can be integrated by linking them to this domain-specific ontology and are directly available for further business analyses. Moreover, the web-based system supports the process of mapping ontology concepts to external databases by introducing a semi-automatic mapping recommender and by visualizing possible mapping candidates. The system also provides a natural language interface to easily query linked databases. The expected result of this ontology-based approach of knowledge representation and data access is an increase in knowledge and data sharing in this domain, which will enhance existing business analysis methods.

Conducting a Competitive Prototype Acquisition Program: An Account of the Joint Light Tactical Vehicle (JLTV) Technology Development Phase

DTIC Science & Technology

2013-03-01

9  B.  REQUIREMENTS ANALYSIS PROCESS ..................................................9  1.  Requirements Management and... Analysis Plan ................................9  2.  Knowledge Point Reviews .................................................................11  3...are Identified .......12  5.  RMAP/CDD Process Analysis and Results......................................13  IV.  TD PHASE BEGINS

Brief Report: Childhood Disintegrative Disorder--A Brief Examination of Eight Case Studies

ERIC Educational Resources Information Center

Homan, Kendra J.; Mellon, Michael W.; Houlihan, Daniel; Katusic, Maja Z.

2011-01-01

Childhood disintegrative disorder (CDD) is a rare condition characterized by distinct regression of developmental and behavioral functioning following a period of apparently normal development for at least 2 years. The purpose of this article is to present the developmental, behavioral, psychosocial, and medical histories of eight children who…

Modeling end-of-life pathways of construction and demolition debris in the United States (poster for LCM 2017)

EPA Science Inventory

In 2013, the United States generated 530 million tons of construction and demolition debris (CDD), 90% of which was related to demolition. Despite this major contribution to national waste streams, Life Cycle Assessment (LCA) studies and product declarations of buildings and buil...

Dioxins in cigarette smoke

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

Muto, H.; Takizawa, Y.

Dioxins in cigarettes, smoke, and ash were determined using gas chromatography/mass spectrometry. The total concentration of polychlorinated dibenzo-p-dioxins (PCDDs) in cigarette smoke was approximately 5.0 micrograms/m3 at the maximum level, whereas various congeners from tetra-octa-chlorodibenzo-p-dioxin (-CDD) were detected. Particullary, the total concentration of hepta-CDD congeners was the highest among these congeners. Mass fragmentograms of various PCDD congeners were similar to those in flue gas samples collected from a municipal waste incinerator. The PCDD congeners that were not present in the cigarettes were found in the smoke samples. The 2,3,7,8-TCDD toxic equivalent value--an index for effects on humans--for total PCDDs inmore » smoke was 1.81 ng/m3 using the toxic factor of the United States Environment Protection Agency. Daily intake of PCDDs by smoking 20 cigarettes was estimated to be approximately 4.3 pg.kg body weight/day. This value was close to that of the ADIs: 1-5 pg.kg body weight/day reported in several countries. A heretofore unrecognized health risk was represented by the presence of PCDDs in cigarette smoke.« less

A framework for organizing cancer-related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE).

PubMed

Wu, Tsung-Jung; Shamsaddini, Amirhossein; Pan, Yang; Smith, Krista; Crichton, Daniel J; Simonyan, Vahan; Mazumder, Raja

2014-01-01

Years of sequence feature curation by UniProtKB/Swiss-Prot, PIR-PSD, NCBI-CDD, RefSeq and other database biocurators has led to a rich repository of information on functional sites of genes and proteins. This information along with variation-related annotation can be used to scan human short sequence reads from next-generation sequencing (NGS) pipelines for presence of non-synonymous single-nucleotide variations (nsSNVs) that affect functional sites. This and similar workflows are becoming more important because thousands of NGS data sets are being made available through projects such as The Cancer Genome Atlas (TCGA), and researchers want to evaluate their biomarkers in genomic data. BioMuta, an integrated sequence feature database, provides a framework for automated and manual curation and integration of cancer-related sequence features so that they can be used in NGS analysis pipelines. Sequence feature information in BioMuta is collected from the Catalogue of Somatic Mutations in Cancer (COSMIC), ClinVar, UniProtKB and through biocuration of information available from publications. Additionally, nsSNVs identified through automated analysis of NGS data from TCGA are also included in the database. Because of the petabytes of data and information present in NGS primary repositories, a platform HIVE (High-performance Integrated Virtual Environment) for storing, analyzing, computing and curating NGS data and associated metadata has been developed. Using HIVE, 31 979 nsSNVs were identified in TCGA-derived NGS data from breast cancer patients. All variations identified through this process are stored in a Curated Short Read archive, and the nsSNVs from the tumor samples are included in BioMuta. Currently, BioMuta has 26 cancer types with 13 896 small-scale and 308 986 large-scale study-derived variations. Integration of variation data allows identifications of novel or common nsSNVs that can be prioritized in validation studies. Database URL: BioMuta: http://hive.biochemistry.gwu.edu/tools/biomuta/index.php; CSR: http://hive.biochemistry.gwu.edu/dna.cgi?cmd=csr; HIVE: http://hive.biochemistry.gwu.edu.

From data repositories to submission portals: rethinking the role of domain-specific databases in CollecTF.

PubMed

Kılıç, Sefa; Sagitova, Dinara M; Wolfish, Shoshannah; Bely, Benoit; Courtot, Mélanie; Ciufo, Stacy; Tatusova, Tatiana; O'Donovan, Claire; Chibucos, Marcus C; Martin, Maria J; Erill, Ivan

2016-01-01

Domain-specific databases are essential resources for the biomedical community, leveraging expert knowledge to curate published literature and provide access to referenced data and knowledge. The limited scope of these databases, however, poses important challenges on their infrastructure, visibility, funding and usefulness to the broader scientific community. CollecTF is a community-oriented database documenting experimentally validated transcription factor (TF)-binding sites in the Bacteria domain. In its quest to become a community resource for the annotation of transcriptional regulatory elements in bacterial genomes, CollecTF aims to move away from the conventional data-repository paradigm of domain-specific databases. Through the adoption of well-established ontologies, identifiers and collaborations, CollecTF has progressively become also a portal for the annotation and submission of information on transcriptional regulatory elements to major biological sequence resources (RefSeq, UniProtKB and the Gene Ontology Consortium). This fundamental change in database conception capitalizes on the domain-specific knowledge of contributing communities to provide high-quality annotations, while leveraging the availability of stable information hubs to promote long-term access and provide high-visibility to the data. As a submission portal, CollecTF generates TF-binding site information through direct annotation of RefSeq genome records, definition of TF-based regulatory networks in UniProtKB entries and submission of functional annotations to the Gene Ontology. As a database, CollecTF provides enhanced search and browsing, targeted data exports, binding motif analysis tools and integration with motif discovery and search platforms. This innovative approach will allow CollecTF to focus its limited resources on the generation of high-quality information and the provision of specialized access to the data.Database URL: http://www.collectf.org/. © The Author(s) 2016. Published by Oxford University Press.

Missing Modality Transfer Learning via Latent Low-Rank Constraint.

PubMed

Ding, Zhengming; Shao, Ming; Fu, Yun

2015-11-01

Transfer learning is usually exploited to leverage previously well-learned source domain for evaluating the unknown target domain; however, it may fail if no target data are available in the training stage. This problem arises when the data are multi-modal. For example, the target domain is in one modality, while the source domain is in another. To overcome this, we first borrow an auxiliary database with complete modalities, then consider knowledge transfer across databases and across modalities within databases simultaneously in a unified framework. The contributions are threefold: 1) a latent factor is introduced to uncover the underlying structure of the missing modality from the known data; 2) transfer learning in two directions allows the data alignment between both modalities and databases, giving rise to a very promising recovery; and 3) an efficient solution with theoretical guarantees to the proposed latent low-rank transfer learning algorithm. Comprehensive experiments on multi-modal knowledge transfer with missing target modality verify that our method can successfully inherit knowledge from both auxiliary database and source modality, and therefore significantly improve the recognition performance even when test modality is inaccessible in the training stage.

Inverse association of highly chlorinated dioxin congeners in maternal breast milk with dehydroepiandrosterone levels in three-year-old Vietnamese children.

PubMed

Kido, Teruhiko; Honma, Seijiro; Nhu, Dang Duc; Manh, Ho Dung; Van Tung, Dao; Liang, Sun Xian; Anh, Le Thai; Okamoto, Rie; Maruzeni, Shoko; Nakagawa, Hideaki; Hung, Nguyen Ngoc; Son, Le Ke

2016-04-15

This study aims to evaluate the endocrine-disrupting effect of dioxin congeners on adrenal steroid hormones in mother-child pairs. In our previous study, we found that cortisol and cortisone levels were higher in the blood and the saliva of mothers living in a dioxin hotspot area than in mothers from a non-exposed region in Vietnam. In this follow-up study, we determined the salivary steroid hormone levels in 49 and 55 three-year-old children of these mothers in the hotspot and non-exposed region, respectively. Steroid hormones were determined by liquid chromatography-tandem mass spectrometry, and dioxin in the maternal breast milk was determined by gas chromatography-mass spectrometry. Dioxin levels in the breast milk of mothers from the hotspot (median total toxic equivalents polychlorinated dibenzodioxins/polychlorinated dibenzofurans; (TEQ PCDD/Fs) of 11pg/g lipid) were three to four times higher than those of mothers in the non-exposed region (median TEQ PCDD/Fs of 3.07pg/g lipid). Salivary dehydroepiandrosterone (DHEA) levels in children were found to be significantly lower in the hotspot than in the non-exposed region, while cortisol and cortisone levels were not different between the two regions. Highly chlorinated dioxin congeners, such as octacholorodibenzodioxin (OCDD), 1,2,3,4,6,7,8-heptacholorodibenzodioxin (HpCDD) and 1,2,3,4 (or 6), 7,8-hexachlorodibenzodioxin Hx(CDD), showed stronger inverse associations with the children's salivary DHEA than other lowly chlorinated dioxin congeners. Glucocorticoid levels in the mothers exhibited a significantly positive correlation with OCDD and HpCDD/F (polychlorinated dibenzofurans). In conclusion, highly chlorinated dioxin congeners are more strongly correlated with endocrine-disrupting effects on adrenal hormones, resulting in high cortisol levels in the mothers and low DHEA levels in their three-year-old children. Copyright © 2016 Elsevier B.V. All rights reserved.

Urodilatin, a natriuretic peptide with clinical implications.

PubMed

Meyer, M; Richter, R; Forssmann, W G

1998-02-21

Natriuretic peptides (NP) constitute hormonal systems of great clinical impact. This report deals with Urodilatin (URO), a renal natriuretic peptide type A. From the gene of NP type A, a message for the preprohormone is transcribed in heart and kidney. The cardiac prohormone CDD/ANP-1-126 is synthesized in the heart atrium and processed during exocytosis forming the circulating hormone CDD/ANP-99-126. URO (CDD/ANP 95-126) is a product from the same gene, but differentially processed in the kidney and detected only in urine. Physiologically, URO acts in a paracrine fashion. After release from distal tubular kidney cells into the tubular lumen, URO binds to luminal receptors (NPR-A) in the collecting duct resulting in a cGMP-dependent signal transduction. cGMP generation is followed by an interaction with the amiloriode-sensitive sodium channel which induces diuresis and natriuresis. In this way, URO physiologically regulates fluid balance and sodium homeostasis. Moreover, URO excretion and natriuresis are in turn dependent on several physiological states, such as directly by sodium homeostasis. Pharmacologically, URO at low dose administered intravenously shows a strong diuretic and natriuretic effect and a low hypotensive effect. Renal, pulmonary, and cardiovascular effects evoked by pharmacological doses indicate that URO is a putative drug for several related diseases. Clinical trials show promising results for various clinical indications. However, the reduction in hemodialysis/hemofiltration in patients suffering from ARF following heart and liver transplantation, derived from preliminary trials recruiting a small number of patients, was not confirmed by a multicenter phase II study. In contrast, data for the prophylactic use of URO in this clinical setting suggest a better outcome for the patients. Furthermore, treatment of asthmatic patients showed a convincingly beneficial effect of URO on pulmonary function. Patients with congestive heart failure may also profit from URO treatment, as it increases stroke volume and PCWP. Moreover, preliminary results from recent studies indicate that URO may also be effective in patients suffering from hepato-renal syndrome.

Improving The Prototyping Process In Department Of Defense Acquisition

DTIC Science & Technology

2014-06-01

System Flow Chart ................................................. 39 Figure 13. TRL Definitions (from ASD [R&E] 2011... ASD (R&E) Assistant Secretary of Defense for Research and Engineering BCL Business Capability Life cycle CDD Capability Development Document CDR...TRL 6 cannot be attained until the technology has been demonstrated in a relevant operational environment ( ASD [R&E] 2011). A technology that has

Global Hawk: Root Cause Analysis of Projected Unit Cost Growth

DTIC Science & Technology

2011-05-01

December 2009 Selected Acquisition Report (SAR), an Initial Operational Test & v Evaluation (“ IOT &E Phase II”) was planned for July–October 2010. The...PAT & mod facility 8% Diminishing Mfg Sources 3% “ IOT &E Replan” 3% ASIP calibration facility 1% Revised Cost Estimates Missing CDD Content...Diminishing Manufacturing Sources (DMS) ..............................................20 j. “ IOT &E Replan

Applying Early Systems Engineering: Injecting Knowledge into the Capability Development Process

DTIC Science & Technology

2012-10-01

involves early use of systems engi- neering and technical analyses to supplement the existing operational analysis techniques currently used in...complexity, and costs of systems now being developed require tight coupling between operational requirements stated in the CDD, system requirements...Fleischer » Keywords: Capability Development, Competitive Prototyping, Knowledge Points, Early Systems Engineering Applying Early Systems

A Case Study of Childhood Disintegrative Disorder Using Systematic Analysis of Family Home Movies

ERIC Educational Resources Information Center

Palomo, Ruben; Thompson, Meagan; Colombi, Costanza; Cook, Ian; Goldring, Stacy; Young, Gregory S.; Ozonoff, Sally

2008-01-01

Childhood disintegrative disorder (CDD) is a rare pervasive developmental disorder that involves regression after a period of at least 2 years of typical development. This case study presents data from family home movies, coded by reliable raters using an objective coding system, to examine the trajectory of development in one child with a…

ExDom: an integrated database for comparative analysis of the exon–intron structures of protein domains in eukaryotes

PubMed Central

Bhasi, Ashwini; Philip, Philge; Manikandan, Vinu; Senapathy, Periannan

2009-01-01

We have developed ExDom, a unique database for the comparative analysis of the exon–intron structures of 96 680 protein domains from seven eukaryotic organisms (Homo sapiens, Mus musculus, Bos taurus, Rattus norvegicus, Danio rerio, Gallus gallus and Arabidopsis thaliana). ExDom provides integrated access to exon-domain data through a sophisticated web interface which has the following analytical capabilities: (i) intergenomic and intragenomic comparative analysis of exon–intron structure of domains; (ii) color-coded graphical display of the domain architecture of proteins correlated with their corresponding exon-intron structures; (iii) graphical analysis of multiple sequence alignments of amino acid and coding nucleotide sequences of homologous protein domains from seven organisms; (iv) comparative graphical display of exon distributions within the tertiary structures of protein domains; and (v) visualization of exon–intron structures of alternative transcripts of a gene correlated to variations in the domain architecture of corresponding protein isoforms. These novel analytical features are highly suited for detailed investigations on the exon–intron structure of domains and make ExDom a powerful tool for exploring several key questions concerning the function, origin and evolution of genes and proteins. ExDom database is freely accessible at: http://66.170.16.154/ExDom/. PMID:18984624

FARE-CAFE: a database of functional and regulatory elements of cancer-associated fusion events.

PubMed

Korla, Praveen Kumar; Cheng, Jack; Huang, Chien-Hung; Tsai, Jeffrey J P; Liu, Yu-Hsuan; Kurubanjerdjit, Nilubon; Hsieh, Wen-Tsong; Chen, Huey-Yi; Ng, Ka-Lok

2015-01-01

Chromosomal translocation (CT) is of enormous clinical interest because this disorder is associated with various major solid tumors and leukemia. A tumor-specific fusion gene event may occur when a translocation joins two separate genes. Currently, various CT databases provide information about fusion genes and their genomic elements. However, no database of the roles of fusion genes, in terms of essential functional and regulatory elements in oncogenesis, is available. FARE-CAFE is a unique combination of CTs, fusion proteins, protein domains, domain-domain interactions, protein-protein interactions, transcription factors and microRNAs, with subsequent experimental information, which cannot be found in any other CT database. Genomic DNA information including, for example, manually collected exact locations of the first and second break points, sequences and karyotypes of fusion genes are included. FARE-CAFE will substantially facilitate the cancer biologist's mission of elucidating the pathogenesis of various types of cancer. This database will ultimately help to develop 'novel' therapeutic approaches. Database URL: http://ppi.bioinfo.asia.edu.tw/FARE-CAFE. © The Author(s) 2015. Published by Oxford University Press.

The study of co-citation analysis and knowledge structure on healthcare domain

NASA Astrophysics Data System (ADS)

Chu, Kuo-Chung; Liu, Wen-I.; Tsai, Ming-Yu

2012-11-01

With the prevalence of Internet and digital archives, the online e-journal database facilitates scholars to search literature in a research domain, or to cross-search an inter-disciplined field; the key literature can be efficiently traced out. This study intends to build a Web-based citation analysis system, which consists of four modules, they are: 1) literature search module; (2) statistics module; (3) articles analysis module; and (4) co-citation analysis module. The system focuses on PubMed Central dataset that has 170,000 records. In a research domain, a specific keyword searches in terms of authors, journals, and core issues. In addition, we use data mining techniques for co-citation analysis. The results assist researchers with in-depth understanding of the domain knowledge. Having an automated system for co-citation analysis, it helps to understand changes, trends, and knowledge structure of research domain. For the best of our knowledge, the proposed system differentiates from existing online electronic retrieval database analysis function. Perhaps, the proposed system is going to be a value-added database of healthcare domain, and hope to contribute the researchers.

Fullerene data mining using bibliometrics and database tomography

PubMed

Kostoff; Braun; Schubert; Toothman; Humenik

2000-01-01

Database tomography (DT) is a textual database analysis system consisting of two major components: (1) algorithms for extracting multiword phrase frequencies and phrase proximities (physical closeness of the multiword technical phrases) from any type of large textual database, to augment (2) interpretative capabilities of the expert human analyst. DT was used to derive technical intelligence from a fullerenes database derived from the Science Citation Index and the Engineering Compendex. Phrase frequency analysis by the technical domain experts provided the pervasive technical themes of the fullerenes database, and phrase proximity analysis provided the relationships among the pervasive technical themes. Bibliometric analysis of the fullerenes literature supplemented the DT results with author/journal/institution publication and citation data. Comparisons of fullerenes results with past analyses of similarly structured near-earth space, chemistry, hypersonic/supersonic flow, aircraft, and ship hydrodynamics databases are made. One important finding is that many of the normalized bibliometric distribution functions are extremely consistent across these diverse technical domains and could reasonably be expected to apply to broader chemical topics than fullerenes that span multiple structural classes. Finally, lessons learned about integrating the technical domain experts with the data mining tools are presented.

Childhood Disintegrative Disorder as a Complication of Chicken Pox.

PubMed

Verma, Jitendra Kumar; Mohapatra, Satyakam

2016-01-01

Childhood disintegrative disorder (CDD) is characterized by late onset (>3 years of age) of developmental delays in language, social function and motor skills. Commonly there is no antecedent physical disorder leading to childhood disintegrative disorder. The present case report describes a child who developed childhood disintegrative disorder at the age of 6 years after an episode of chicken pox.

Assessing Weapon System Acquisition Cycle Times: Setting Program Schedules

DTIC Science & Technology

2015-06-01

kits begins in FY16 – “Required Assets Available ( RAA )” Sepember 2019 (means first unit equipped) *RDT&E exceeds threshold 22 C. Summary and...July 2013 CPD 2006 CDD by USMC Apr. 2014a F-22 3.2B Mod RAA : 4QFY19 None identified None identified Enhanced Global Strike 2007a Incr. 3.2B KSAs

Ballistic Missile Defense System (BMDS)

DTIC Science & Technology

2015-12-01

Assessment and Program Evaluation CARD - Cost Analysis Requirements Description CDD - Capability Development Document CLIN - Contract Line Item Number CPD...Estimate RDT&E - Research, Development, Test, and Evaluation SAR - Selected Acquisition Report SCP - Service Cost Position TBD - To Be Determined TY - Then...BMDS December 2015 SAR March 23, 2016 16:29:09 UNCLASSIFIED 5 Mission and Description Mission and Description To develop, test, and field a layered

Complex dynamics in the Leslie-Gower type of the food chain system with multiple delays

NASA Astrophysics Data System (ADS)

Guo, Lei; Song, Zi-Gen; Xu, Jian

2014-08-01

In this paper, we present a Leslie-Gower type of food chain system composed of three species, which are resource, consumer, and predator, respectively. The digestion time delays corresponding to consumer-eat-resource and predator-eat-consumer are introduced for more realistic consideration. It is called the resource digestion delay (RDD) and consumer digestion delay (CDD) for simplicity. Analyzing the corresponding characteristic equation, the stabilities of the boundary and interior equilibrium points are studied. The food chain system exhibits the species coexistence for the small values of digestion delays. Large RDD/CDD may destabilize the species coexistence and induce the system dynamic into recurrent bloom or system collapse. Further, the present of multiple delays can control species population into the stable coexistence. To investigate the effect of time delays on the recurrent bloom of species population, the Hopf bifurcation and periodic solution are investigated in detail in terms of the central manifold reduction and normal form method. Finally, numerical simulations are performed to display some complex dynamics, which include multiple periodic solution and chaos motion for the different values of system parameters. The system dynamic behavior evolves into the chaos motion by employing the period-doubling bifurcation.

Impact of forest fires on the concentrations of polychlorinated dibenzo-p-dioxin and dibenzofurans in coastal waters of central Chile.

PubMed

Salamanca, Marco; Chandía, Cristian; Hernández, Aldo

2016-12-15

The relationship between the occurrence of forest fires in central Chile and the total concentration of dioxins and furans (PCDD/F) in nearby coastal waters was analyzed. The data for this analysis was obtained from a long-term environmental monitoring program (PROMNA) in the Bio-Bio Region. Quantification of PCDD/F was performed using HRGC/HRMS at the MSS laboratory in England. Between 2006 and 2014, peaks were observed in February 2007 and 2012. These concentration maxima coincided with major forest fires in the Bio-Bio Region and particularly with those in the Itata River Basin. The January 2012 fires generated an intense short-term response that was associated with atmospheric transport which increases medium toxicity furan-type congeners concentrations (TCDF, PCDF and HxCDF) and six months later a concentration increase of low toxicity dioxin-type congeners was observed (OCDD, HpCDD and HxCDD) coinciding with maximum winter river flow. These results suggest that forest fires near the coastal zone are responsible for increases in PCDD/F concentration observed in the study area. Copyright © 2016 Elsevier B.V. All rights reserved.

Landscape features, standards, and semantics in U.S. national topographic mapping databases

USGS Publications Warehouse

Varanka, Dalia

2009-01-01

The objective of this paper is to examine the contrast between local, field-surveyed topographical representation and feature representation in digital, centralized databases and to clarify their ontological implications. The semantics of these two approaches are contrasted by examining the categorization of features by subject domains inherent to national topographic mapping. When comparing five USGS topographic mapping domain and feature lists, results indicate that multiple semantic meanings and ontology rules were applied to the initial digital database, but were lost as databases became more centralized at national scales, and common semantics were replaced by technological terms.

Using a Relational Database to Index Infectious Disease Information

PubMed Central

Brown, Jay A.

2010-01-01

Mapping medical knowledge into a relational database became possible with the availability of personal computers and user-friendly database software in the early 1990s. To create a database of medical knowledge, the domain expert works like a mapmaker to first outline the domain and then add the details, starting with the most prominent features. The resulting “intelligent database” can support the decisions of healthcare professionals. The intelligent database described in this article contains profiles of 275 infectious diseases. Users can query the database for all diseases matching one or more specific criteria (symptom, endemic region of the world, or epidemiological factor). Epidemiological factors include sources (patients, water, soil, or animals), routes of entry, and insect vectors. Medical and public health professionals could use such a database as a decision-support software tool. PMID:20623018

Variability in CitXET expression and XET activity in Citrus cultivar Huangguogan seedlings with differed degrees of etiolation

PubMed Central

Xiong, Bo; Gu, Xianjie; Qiu, Xia; Dong, Zhixiang; Ye, Shuang; Sun, Guochao; Huang, Shengjia; Liu, Xinya; Xi, Lijuan

2017-01-01

Considering the known effects of xyloglucan endotransglycosylase (XET) on plant growth and development, we aimed to determine whether XETs help to regulate the growth and elongation of Huangguogan shoots and roots. We confirmed a possible role for XET during seedling etiolation. Our results revealed that the roots of etiolated seedlings (H-E) were longer than those of green seedlings (H-G). However, shoot length exhibited the opposite pattern. We also observed positive and negative effects on the xyloglucan-degrading activity of XET in the root sub-apical region and shoots of etiolated Huangguogan seedling, respectively. There was a significant down-regulation in CitXET expression in the etiolated shoots at 15 days after seed germination. On the contrary, it was significantly increased in the root sub-apical region of etiolated and multicolored seedlings at 15 days after seed germination. The XET coding sequence (i.e., CitXET) was cloned from Huangguogan seedlings using gene-specific primers. The encoded amino acid sequence was predicted by using bioinformatics-based methods. The 990-bp CitXET gene was highly homologous to other XET genes. The CitXET protein was predicted to contain 319 amino acids, with a molecular mass of 37.45 kDa and an isoelectric point of 9.05. The predicted molecular formula was C1724H2548N448O466S14, and the resulting protein included only one transmembrane structure. The CitXET secondary structure consisted of four main structures (i.e., 21% α-helix, 30.72% extended strand, 9.09% β-turn, and 39.18% random coil). Analyses involving the NCBI Conserved Domains Database (NCBI-CDD), InterPro, and ScanProsite revealed that CitXET was a member of the glycosyl hydrolase family 16 (GH16), and included the DEIDFEFLG motif. Our results indicate that the differed degrees of etiolation influenced the CitXET expression pattern and XET activity in Huangguogan seedlings. The differential changes in XET activity and CitXET expression levels in Huangguogan seedlings may influence the regulation of root and shoot development, and may be important for seedling etiolation. PMID:28617857

Teaching Case: Adapting the Access Northwind Database to Support a Database Course

ERIC Educational Resources Information Center

Dyer, John N.; Rogers, Camille

2015-01-01

A common problem encountered when teaching database courses is that few large illustrative databases exist to support teaching and learning. Most database textbooks have small "toy" databases that are chapter objective specific, and thus do not support application over the complete domain of design, implementation and management concepts…

Joint Space Operations Center (JSpOC) Mission System (JMS)

NASA Astrophysics Data System (ADS)

Morton, M.; Roberts, T.

2011-09-01

US space capabilities benefit the economy, national security, international relationships, scientific discovery, and our quality of life. Realizing these space responsibilities is challenging not only because the space domain is increasingly congested, contested, and competitive but is further complicated by the legacy space situational awareness (SSA) systems approaching end of life and inability to provide the breadth of SSA and command and control (C2) of space forces in this challenging domain. JMS will provide the capabilities to effectively employ space forces in this challenging domain. Requirements for JMS were developed based on regular, on-going engagement with the warfighter. The use of DoD Architecture Framework (DoDAF) products facilitated requirements scoping and understanding and transferred directly to defining and documenting the requirements in the approved Capability Development Document (CDD). As part of the risk reduction efforts, the Electronic System Center (ESC) JMS System Program Office (SPO) fielded JMS Capability Package (CP) 0 which includes an initial service oriented architecture (SOA) and user defined operational picture (UDOP) along with force status, sensor management, and analysis tools. Development efforts are planned to leverage and integrate prototypes and other research projects from Defense Advanced Research Projects Agency, Air Force Research Laboratories, Space Innovation and Development Center, and Massachusetts Institute of Technology/Lincoln Laboratories. JMS provides a number of benefits to the space community: a reduction in operational “transaction time” to accomplish key activities and processes; ability to process the increased volume of metric observations from new sensors (e.g., SBSS, SST, Space Fence), as well as owner/operator ephemerides thus enhancing the high accuracy near-real-time catalog, and greater automation of SSA data sharing supporting collaboration with government, civil, commercial, and foreign entities. Continued success in JMS depends on continued support from across the space community. Key activities where community participation is essential include the C2 SSA Community of Interest (COI) development and refinement, creative strategies for faster, better, cheaper development, and defining the next set of capabilities.

Evaluation of relative potencies for in vitro transactivation of the baikal seal aryl hydrocarbon receptor by dioxin-like compounds.

PubMed

Kim, Eun-Young; Suda, Tomoko; Tanabe, Shinsuke; Batoev, Valeriy B; Petrov, Evgeny A; Iwata, Hisato

2011-02-15

To evaluate the sensitivity and responses to dioxins and related compounds (DRCs) via aryl hydrocarbon receptor (AHR) in Baikal seals (Pusa sibirica), we constructed an in vitro reporter gene assay system. Baikal seal AHR (BS AHR) expression plasmid and a reporter plasmid containing CYP1A1 promoter were transfected in COS-7 cells. The cells were treated with six representative congeners, and dose-dependent responses were obtained for all the congeners. EC50 values of 2,3,7,8-TCDD, 1,2,3,7,8-PeCDD, 2,3,7,8-TCDF, 2,3,4,7,8-PeCDF, and PCB126 were found to be 0.021, 1.8, 0.16, 2.4, and 2.5 nM, respectively. As the response did not reach the maximal plateau, EC50 value for PCB118 could not be obtained. The TCDD-EC50 for BS AHR was as high as that for dioxin sensitive C57BL/6 mouse AHR. The in vitro dose responses were further analyzed following an established systematic framework and multiple (20, 50, and 80%) relative potencies (REPs) to the maximum TCDD response. The estimates revealed lower REP ranges (20-80%) of PeCDD and PeCDF for BS AHR than for mouse AHR. Average of the 20, 50, and 80% REPs was designated as Baikal seal specific TCDD induction equivalency factor (BS IEF). The BS IEFs of PeCDD, TCDF, PeCDF, PCB126, and PCB118 were estimated as 0.010, 0.018, 0.0078, 0.0059, and 0.00010, respectively. Total TCDD induction equivalents (IEQs) that were calculated using BS IEFs and hepatic concentrations in wild Baikal seals corresponded to only 12-31% of 2005 WHO TEF-derived TEQs. Nevertheless, about 50% of Baikal seals accumulated IEQs over the TCDD-EC50 obtained in this study. This assessment was supported by the enhanced CYP1A1 mRNA expression found in 50% of the specimens contaminated over the TCDD-EC50. These findings suggest that the IEFs proposed from this in vitro assay could be used to predict AHR-mediated responses in wild seals.

Analysis of satellite precipitation over East Africa during last decades

NASA Astrophysics Data System (ADS)

Cattani, Elsa; Wenhaji Ndomeni, Claudine; Merino, Andrés; Levizzani, Vincenzo

2016-04-01

Daily accumulated precipitation time series from satellite retrieval algorithms (e.g., ARC2 and TAMSAT) are exploited to extract the spatial and temporal variability of East Africa (EA - 5°S-20°N, 28°E-52°E) precipitation during last decades (1983-2013). The Empirical Orthogonal Function (EOF) analysis is applied to precipitation time series to investigate the spatial and temporal variability in particular for October-November-December referred to as the short rain season. Moreover, the connection among EA's precipitation, sea surface temperature, and soil moisture is analyzed through the correlation with the dominant EOF modes of variability. Preliminary results concern the first two EOF's modes for the ARC2 data set. EOF1 is characterized by an inter-annual variability and a positive correlation between precipitation and El Niño, positive Indian Ocean Dipole mode, and soil moisture, while EOF2 shows a dipole structure of spatial variability associated with a longer scale temporal variability. This second dominant mode is mostly linked to sea surface temperature variations in the North Atlantic Ocean. Further analyses are carried out by computing the time series of the joint CCI/CLIVAR/JCOMM Expert Team on Climate Change Detection and Indices (ETCCDI, http://etccdi.pacificclimate.org/index.shtml), i.e. RX1day, RX5day, CDD, CDD, CWD, SDII, PRCPTOT, R10, R20. The purpose is to identify the occurrenes of extreme events (droughts and floods) and extract precipitation temporal variation by trend analysis (Mann-Kendall technique). Results for the ARC2 data set demonstrate the existence of a dipole spatial pattern in the linear trend of the time series of PRCPTOT (annual precipitation considering days with a rain rate > 1 mm) and SDII (average precipitation on wet days over a year). A negative trend is mainly present over West Ethiopia and Sudan, whereas a positive trend is exhibited over East Ethiopia and Somalia. CDD (maximum number of consecutive dry days) and CWD (maximum number of consecutive wet days) time series do not exhibit a similar behavior and trends are generally weaker with a lower significance level with respect to PRCPTOT and SDII.

Searching Across the International Space Station Databases

NASA Technical Reports Server (NTRS)

Maluf, David A.; McDermott, William J.; Smith, Ernest E.; Bell, David G.; Gurram, Mohana

2007-01-01

Data access in the enterprise generally requires us to combine data from different sources and different formats. It is advantageous thus to focus on the intersection of the knowledge across sources and domains; keeping irrelevant knowledge around only serves to make the integration more unwieldy and more complicated than necessary. A context search over multiple domain is proposed in this paper to use context sensitive queries to support disciplined manipulation of domain knowledge resources. The objective of a context search is to provide the capability for interrogating many domain knowledge resources, which are largely semantically disjoint. The search supports formally the tasks of selecting, combining, extending, specializing, and modifying components from a diverse set of domains. This paper demonstrates a new paradigm in composition of information for enterprise applications. In particular, it discusses an approach to achieving data integration across multiple sources, in a manner that does not require heavy investment in database and middleware maintenance. This lean approach to integration leads to cost-effectiveness and scalability of data integration with an underlying schemaless object-relational database management system. This highly scalable, information on demand system framework, called NX-Search, which is an implementation of an information system built on NETMARK. NETMARK is a flexible, high-throughput open database integration framework for managing, storing, and searching unstructured or semi-structured arbitrary XML and HTML used widely at the National Aeronautics Space Administration (NASA) and industry.

The history of the CATH structural classification of protein domains.

PubMed

Sillitoe, Ian; Dawson, Natalie; Thornton, Janet; Orengo, Christine

2015-12-01

This article presents a historical review of the protein structure classification database CATH. Together with the SCOP database, CATH remains comprehensive and reasonably up-to-date with the now more than 100,000 protein structures in the PDB. We review the expansion of the CATH and SCOP resources to capture predicted domain structures in the genome sequence data and to provide information on the likely functions of proteins mediated by their constituent domains. The establishment of comprehensive function annotation resources has also meant that domain families can be functionally annotated allowing insights into functional divergence and evolution within protein families. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

USACE AIS Transmit Technical Support Summary Report

DTIC Science & Technology

2014-09-01

the TAG block for the correct transmitters, and then send to the USACE AIS network. B. Outbound openings in the USCG firewall for the USCG Message...USACE AIS Transmit Technical Support Summary Report Distribution Statement A: Approved for public release; distribution is unlimited...September 2014 Report No. CD-D-09-15 USACE AIS Transmit Technical Support Summary Report ii UNCLAS//Public | CG-926 RDC | I. Gonin et al. Public

Distributed Common Ground System-Navy Increment 2 (DCGS-N Inc 2)

DTIC Science & Technology

2016-03-01

15 minutes Enter and be Managed in the Network: Reference SvcV-7, Consolidated Afloat Networks and Enterprise Services ( CANES ) CDD, DCGS-N Inc 2...Red, White , Gray Data and Tracks to Command and Control System. Continuous Stream from SCI Common Intelligence Picture to General Service (GENSER...AIS - Automatic Information System AOC - Air Operations Command CANES - Consolidated Afloat Networks and Enterprise Services CID - Center for

Determination of relative assay response factors for toxic chlorinated and brominated dioxins/furans using an enzyme immunoassay (EIA) and a chemically-activated luciferase gene expression cell bioassay (CALUX).

PubMed

Samara, Fatin; Gullett, Brian K; Harrison, Robert O; Chu, Andrew; Clark, George C

2009-04-01

Determination of toxic activity requires knowledge of both the concentration and toxicity to evaluate the risk for adverse human health and environmental effects. A chemically-activated luciferase gene expression cell bioassay system (CALUX) and an antibody-based method enzyme immunoassay (EIA) were used to detect the dioxin-like response of several polybrominated, polychlorinated, and polybrominated/chlorinated dibenzo-p-dioxins/furans (PBDDs/Fs, PCDDs/Fs, and PBCDDs/Fs, respectively). It has been suggested that the biological activity of the brominated and mixed bromo/chloro compounds is similar to their chlorinated analogues (measured by binding to the Ah receptor). PBDD/F, PCDD/F, and PBCDD/F laboratory standards exhibited biological activity ranging over three orders of magnitude. The highest relative potency (REP) values from CALUX analysis, when compared to 2,3,7,8-TCDD, were 2,3,7,8-TBDD at 0.99 (+/-0.07), 1,2,3,7,8-PeCDD at 0.69, and 2-Br-3,7,8-TriCDD at 0.72 (+/-0.02). Cross-reactivities were calculated using EIA for several PBDDs/Fs and PBCDDs. The highest percent cross-reactivity was found for 2,3,7,8-TBDD at 138 (+/-34%), and 2,3,7-TriBDD at 84 (+/-36%).

Emissions of PCDD/Fs, PCBs, and PAHs from a modern diesel engine equipped with catalyzed emission control systems.

PubMed

Laroo, Christopher A; Schenk, Charles R; Sanchez, L James; McDonald, Joseph

2011-08-01

Exhaust emissions of 17 2,3,7,8-substituted chlorinated dibenzo-p-dioxin/furan (CDD/F) congeners, tetra-octa CDD/F homologues, 12 2005 WHO chlorinated biphenyls (CB) congeners, mono-nona CB homologues, and 19 polycyclic aromatic hydrocarbons (PAHs) from a model year 2008 Cummins ISB engine were investigated. Testing included configurations composed of different combinations of aftertreatment including a diesel oxidation catalyst (DOC), catalyzed diesel particulate filter (CDPF), copper zeolite urea selective catalytic reduction (SCR), iron zeolite SCR, and ammonia slip catalyst. Results were compared to a baseline engine out configuration. Testing included the use of fuel that contained the maximum expected chlorine (Cl) concentration of U.S. highway diesel fuel and a Cl level 1.5 orders of magnitude above. Results indicate there is no risk for an increase in polychlorinated dibenzo-p-dioxin/furan and polychlorinated biphenyl emissions from modern diesel engines with catalyzed aftertreatment when compared to engine out emissions for configurations tested in this program. These results, along with PAH results, compare well with similar results from modern diesel engines in the literature. The results further indicate that polychlorinated dibenzo-p-dioxin/furan emissions from modern diesel engines both with and without aftertreatment are below historical values reported in the literature as well as the current inventory value.

Cholesky-decomposed density MP2 with density fitting: Accurate MP2 and double-hybrid DFT energies for large systems

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

Maurer, Simon A.; Clin, Lucien; Ochsenfeld, Christian, E-mail: christian.ochsenfeld@uni-muenchen.de

2014-06-14

Our recently developed QQR-type integral screening is introduced in our Cholesky-decomposed pseudo-densities Møller-Plesset perturbation theory of second order (CDD-MP2) method. We use the resolution-of-the-identity (RI) approximation in combination with efficient integral transformations employing sparse matrix multiplications. The RI-CDD-MP2 method shows an asymptotic cubic scaling behavior with system size and a small prefactor that results in an early crossover to conventional methods for both small and large basis sets. We also explore the use of local fitting approximations which allow to further reduce the scaling behavior for very large systems. The reliability of our method is demonstrated on test sets formore » interaction and reaction energies of medium sized systems and on a diverse selection from our own benchmark set for total energies of larger systems. Timings on DNA systems show that fast calculations for systems with more than 500 atoms are feasible using a single processor core. Parallelization extends the range of accessible system sizes on one computing node with multiple cores to more than 1000 atoms in a double-zeta basis and more than 500 atoms in a triple-zeta basis.« less

Biological sulfate removal from construction and demolition debris leachate: effect of bioreactor configuration.

PubMed

Kijjanapanich, Pimluck; Do, Anh Tien; Annachhatre, Ajit P; Esposito, Giovanni; Yeh, Daniel H; Lens, Piet N L

2014-03-30

Due to the contamination of construction and demolition debris (CDD) by gypsum drywall, especially, its sand fraction (CDD sand, CDDS), the sulfate content in CDDS exceeds the posed limit of the maximum amount of sulfate present in building sand (1.73 g sulfate per kg of sand for the Netherlands). Therefore, the CDDS cannot be reused for construction. The CDDS has to be washed in order to remove most of the impurities and to obtain the right sulfate content, thus generating a leachate, containing high sulfate and calcium concentrations. This study aimed at developing a biological sulfate reduction system for CDDS leachate treatment and compared three different reactor configurations for the sulfate reduction step: the upflow anaerobic sludge blanket (UASB) reactor, inverse fluidized bed (IFB) reactor and gas lift anaerobic membrane bioreactor (GL-AnMBR). This investigation demonstrated that all three systems can be applied for the treatment of CDDS leachate. The highest sulfate removal efficiency of 75-85% was achieved at a hydraulic retention time (HRT) of 15.5h. A high calcium concentration up to 1,000 mg L(-1) did not give any adverse effect on the sulfate removal efficiency of the IFB and GL-AnMBR systems. Copyright © 2013 Elsevier B.V. All rights reserved.

Serum concentrations of polychlorinated dibenzo-p-dioxins among ceramicists.

PubMed

Demond, Avery; Jiang, Xiaohui; Broadwater, Kendra; Meeker, John; Luksemburg, William; Maier, Martha; Garabrant, David; Franzblau, Alfred

2015-01-01

Polychlorinated dibenzo-p-dioxins (PCDDs) occur naturally in ball clay at elevated concentrations. Thus, persons who habitually work with clay may be at risk for exposure to PCDDs. An earlier case report provided some evidence of elevated PCDD levels in serum for long-term hobby ceramicists; however, no previous study has measured serum dioxin concentrations among ceramicists. This study measured PCDD serum levels for 27 individuals involved in ceramics making. The average residual, defined as the average of the [log measured serum lipid concentration – log background serum lipid concentration], was calculated and then tested to determine whether it was significantly different from zero. The p-values for the average residuals indicated that the serum lipid concentrations for several PCDD congeners were elevated relative to background. The number of significant residuals increased dramatically if the background concentrations were adjusted to account for the fact that they were not contemporaneous with the measurements for the ceramicists. The ratio of the 1,2,3,6,7,8-HxCDD concentration to the 1,2,3,7,8,9-HxCDD concentration was greater than 1.0, unlike in ball clay, suggesting that although long-term working with ball clay elevates the PCDD levels in serum somewhat, it is not the predominant source of the PCDD body burden for ceramicists.

The Nuclear Protein Database (NPD): sub-nuclear localisation and functional annotation of the nuclear proteome

PubMed Central

Dellaire, G.; Farrall, R.; Bickmore, W.A.

2003-01-01

The Nuclear Protein Database (NPD) is a curated database that contains information on more than 1300 vertebrate proteins that are thought, or are known, to localise to the cell nucleus. Each entry is annotated with information on predicted protein size and isoelectric point, as well as any repeats, motifs or domains within the protein sequence. In addition, information on the sub-nuclear localisation of each protein is provided and the biological and molecular functions are described using Gene Ontology (GO) terms. The database is searchable by keyword, protein name, sub-nuclear compartment and protein domain/motif. Links to other databases are provided (e.g. Entrez, SWISS-PROT, OMIM, PubMed, PubMed Central). Thus, NPD provides a gateway through which the nuclear proteome may be explored. The database can be accessed at http://npd.hgu.mrc.ac.uk and is updated monthly. PMID:12520015

Navigation Performance of Global Navigation Satellite Systems in the Space Service Volume

NASA Technical Reports Server (NTRS)

Force, Dale A.

2013-01-01

This paper extends the results I reported at this year's ION International Technical Meeting on multi-constellation GNSS coverage by showing how the use of multi-constellation GNSS improves Geometric Dilution of Precision (GDOP). Originally developed to provide position, navigation, and timing for terrestrial users, GPS has found increasing use for in space for precision orbit determination, precise time synchronization, real-time spacecraft navigation, and three-axis attitude control of Earth orbiting satellites. With additional Global Navigation Satellite Systems (GNSS) coming into service (GLONASS, Galileo, and Beidou) and the development of Satellite Based Augmentation Services, it is possible to obtain improved precision by using evolving multi-constellation receiver. The Space Service Volume formally defined as the volume of space between three thousand kilometers altitude and geosynchronous altitude ((is) approximately 36,500 km), with the volume below three thousand kilometers defined as the Terrestrial Service Volume (TSV). The USA has established signal requirements for the Space Service Volume (SSV) as part of the GPS Capability Development Documentation (CDD). Diplomatic efforts are underway to extend Space service Volume commitments to the other Position, Navigation, and Timing (PNT) service providers in an effort to assure that all space users will benefit from the enhanced capabilities of interoperating GNSS services in the space domain.

A Comparison of Selected Bibliographic Database Subject Overlap for Agricultural Information

ERIC Educational Resources Information Center

Ritchie, Stephanie M.; Young, Lauren M.; Sigman, Jessica

2018-01-01

Agricultural researchers and science librarians must understand which research literature databases provide the most comprehensive coverage of agricultural subjects to support their inquiries. Once the domain of a few specialized databases, agricultural research literature is now covered by broad, multidisciplinary databases. The purpose of this…

Molecular scaffold analysis of natural products databases in the public domain.

PubMed

Yongye, Austin B; Waddell, Jacob; Medina-Franco, José L

2012-11-01

Natural products represent important sources of bioactive compounds in drug discovery efforts. In this work, we compiled five natural products databases available in the public domain and performed a comprehensive chemoinformatic analysis focused on the content and diversity of the scaffolds with an overview of the diversity based on molecular fingerprints. The natural products databases were compared with each other and with a set of molecules obtained from in-house combinatorial libraries, and with a general screening commercial library. It was found that publicly available natural products databases have different scaffold diversity. In contrast to the common concept that larger libraries have the largest scaffold diversity, the largest natural products collection analyzed in this work was not the most diverse. The general screening library showed, overall, the highest scaffold diversity. However, considering the most frequent scaffolds, the general reference library was the least diverse. In general, natural products databases in the public domain showed low molecule overlap. In addition to benzene and acyclic compounds, flavones, coumarins, and flavanones were identified as the most frequent molecular scaffolds across the different natural products collections. The results of this work have direct implications in the computational and experimental screening of natural product databases for drug discovery. © 2012 John Wiley & Sons A/S.

Mapping small molecule binding data to structural domains

PubMed Central

2012-01-01

Background Large-scale bioactivity/SAR Open Data has recently become available, and this has allowed new analyses and approaches to be developed to help address the productivity and translational gaps of current drug discovery. One of the current limitations of these data is the relative sparsity of reported interactions per protein target, and complexities in establishing clear relationships between bioactivity and targets using bioinformatics tools. We detail in this paper the indexing of targets by the structural domains that bind (or are likely to bind) the ligand within a full-length protein. Specifically, we present a simple heuristic to map small molecule binding to Pfam domains. This profiling can be applied to all proteins within a genome to give some indications of the potential pharmacological modulation and regulation of all proteins. Results In this implementation of our heuristic, ligand binding to protein targets from the ChEMBL database was mapped to structural domains as defined by profiles contained within the Pfam-A database. Our mapping suggests that the majority of assay targets within the current version of the ChEMBL database bind ligands through a small number of highly prevalent domains, and conversely the majority of Pfam domains sampled by our data play no currently established role in ligand binding. Validation studies, carried out firstly against Uniprot entries with expert binding-site annotation and secondly against entries in the wwPDB repository of crystallographic protein structures, demonstrate that our simple heuristic maps ligand binding to the correct domain in about 90 percent of all assessed cases. Using the mappings obtained with our heuristic, we have assembled ligand sets associated with each Pfam domain. Conclusions Small molecule binding has been mapped to Pfam-A domains of protein targets in the ChEMBL bioactivity database. The result of this mapping is an enriched annotation of small molecule bioactivity data and a grouping of activity classes following the Pfam-A specifications of protein domains. This is valuable for data-focused approaches in drug discovery, for example when extrapolating potential targets of a small molecule with known activity against one or few targets, or in the assessment of a potential target for drug discovery or screening studies. PMID:23282026

Polychlorinated dibenzo-p-dioxin and dibenzofuran concentrations in the serum samples of workers at continuously burning municipal waste incinerators in Japan

PubMed Central

Kumagai, S.; Koda, S.; Miyakita, T.; Yamaguchi, H.; Katagi, K.; Yasuda, N.

2000-01-01

OBJECTIVES—To find whether concentrations of polychlorinated dibenzo-p-dioxins (PCDDs) and polychlorinated dibenzofurans (PCDFs) in serum increased in workers at municipal incinerators that burn continuously.
METHODS—30 Workers employed at three municipal waste incineration plants (incinerator workers) and 30 control workers were studied. The incinerator workers had worn dust masks or airline masks during the periodic repair work inside the incinerators. Previous job, dietary habit, smoking habit, distance from residence to the incineration plant, and body weight and height were obtained from a questionnaire survey. Concentrations of PCDDs/PCDFs were measured in the serum of the workers and the dust deposited in the plants. The influence of various factors on serum concentrations of PCDDs/PCDFs was examined by multiple regression analysis.
RESULTS—Dust analysis showed the greatest amount of octachlorodibenzo-p-dioxin (OCDD), followed by 1,2,3,4,6,7,8-heptachlorodibenzo-p-dioxin (HpCDD), 1,2,3,4,6,7,8-heptachlorodibenzofuran (HpCDF), and octachlorodibenzofuran (OCDF). The toxicity equivalents (TEQs) of PCDDs and PCDFs in the deposited dust were 4.8, 1.0, and 6.4 ng TEQs/g, respectively, for plants A, B, and C. The mean serum TEQs of PCDDs and PCDFs in the incinerator workers and control workers were 19.2 and 22.9 pg TEQs/g lipid, respectively, for area A, 28.8 and 24.5 pg TEQs/g lipid for area B, and 23.4 and 23.6 pg TEQs/g lipid for area C. No significant differences were found between the incinerator workers and the controls for TEQs of PCDDs and PCDFs separately, and TEQs of PCDDs and PCDFs together. However, the serum 1,2,3,4,6,7,8-HpCDF concentration was significantly higher in the incinerator workers than in the controls for all the three areas. When the exposure index to 1,2,3,4,6,7,8-HpCDF is defined as the product of the concentration of 1,2,3,4,6,7,8-HpCDF in the deposited dust and duration of employment, the concentration of 1,2,3,4,6,7,8-HpCDF in serum increased as the exposure index increased. Multivariate analysis suggested that the serum concentration of HpCDF increased with duration of employment at the incineration plants and OCDF increased with employment of ⩾21 years. The other significant variables (p<0.01 or p<0.001) were area for hexachlorodibenzo-p-dioxin (HxCDD) and tetrachlorodibenzofuran (TCDF), Brinkman index for HpCDD, and body mass index (BMI) for tetrachlorodibenzo-p-dioxin (TCDD), HpCDD, and TEQs of PCDDs.
CONCLUSION—The serum TEQs of PCDDs and PCDFs was not significantly higher among the incinerator workers, but the serum concentration of 1,2,3,4,6,7,8-HpCDF was. This suggests that the incinerator workers had inhaled dust containing PCDDs and PCDFs while working in plants equipped with incinerators that burn continuously.


Keywords: serum dioxins; municipal waste incinerators; continuous burning; heptachlorodibenzofuran PMID:10810104

The chordate proteome history database.

PubMed

Levasseur, Anthony; Paganini, Julien; Dainat, Jacques; Thompson, Julie D; Poch, Olivier; Pontarotti, Pierre; Gouret, Philippe

2012-01-01

The chordate proteome history database (http://ioda.univ-provence.fr) comprises some 20,000 evolutionary analyses of proteins from chordate species. Our main objective was to characterize and study the evolutionary histories of the chordate proteome, and in particular to detect genomic events and automatic functional searches. Firstly, phylogenetic analyses based on high quality multiple sequence alignments and a robust phylogenetic pipeline were performed for the whole protein and for each individual domain. Novel approaches were developed to identify orthologs/paralogs, and predict gene duplication/gain/loss events and the occurrence of new protein architectures (domain gains, losses and shuffling). These important genetic events were localized on the phylogenetic trees and on the genomic sequence. Secondly, the phylogenetic trees were enhanced by the creation of phylogroups, whereby groups of orthologous sequences created using OrthoMCL were corrected based on the phylogenetic trees; gene family size and gene gain/loss in a given lineage could be deduced from the phylogroups. For each ortholog group obtained from the phylogenetic or the phylogroup analysis, functional information and expression data can be retrieved. Database searches can be performed easily using biological objects: protein identifier, keyword or domain, but can also be based on events, eg, domain exchange events can be retrieved. To our knowledge, this is the first database that links group clustering, phylogeny and automatic functional searches along with the detection of important events occurring during genome evolution, such as the appearance of a new domain architecture.

EvoDB: a database of evolutionary rate profiles, associated protein domains and phylogenetic trees for PFAM-A

PubMed Central

Ndhlovu, Andrew; Durand, Pierre M.; Hazelhurst, Scott

2015-01-01

The evolutionary rate at codon sites across protein-coding nucleotide sequences represents a valuable tier of information for aligning sequences, inferring homology and constructing phylogenetic profiles. However, a comprehensive resource for cataloguing the evolutionary rate at codon sites and their corresponding nucleotide and protein domain sequence alignments has not been developed. To address this gap in knowledge, EvoDB (an Evolutionary rates DataBase) was compiled. Nucleotide sequences and their corresponding protein domain data including the associated seed alignments from the PFAM-A (protein family) database were used to estimate evolutionary rate (ω = dN/dS) profiles at codon sites for each entry. EvoDB contains 98.83% of the gapped nucleotide sequence alignments and 97.1% of the evolutionary rate profiles for the corresponding information in PFAM-A. As the identification of codon sites under positive selection and their position in a sequence profile is usually the most sought after information for molecular evolutionary biologists, evolutionary rate profiles were determined under the M2a model using the CODEML algorithm in the PAML (Phylogenetic Analysis by Maximum Likelihood) suite of software. Validation of nucleotide sequences against amino acid data was implemented to ensure high data quality. EvoDB is a catalogue of the evolutionary rate profiles and provides the corresponding phylogenetic trees, PFAM-A alignments and annotated accession identifier data. In addition, the database can be explored and queried using known evolutionary rate profiles to identify domains under similar evolutionary constraints and pressures. EvoDB is a resource for evolutionary, phylogenetic studies and presents a tier of information untapped by current databases. Database URL: http://www.bioinf.wits.ac.za/software/fire/evodb PMID:26140928

Understanding the productive author who published papers in medicine using National Health Insurance Database: A systematic review and meta-analysis.

PubMed

Chien, Tsair-Wei; Chang, Yu; Wang, Hsien-Yi

2018-02-01

Many researchers used National Health Insurance database to publish medical papers which are often retrospective, population-based, and cohort studies. However, the author's research domain and academic characteristics are still unclear.By searching the PubMed database (Pubmed.com), we used the keyword of [Taiwan] and [National Health Insurance Research Database], then downloaded 2913 articles published from 1995 to 2017. Social network analysis (SNA), Gini coefficient, and Google Maps were applied to gather these data for visualizing: the most productive author; the pattern of coauthor collaboration teams; and the author's research domain denoted by abstract keywords and Pubmed MESH (medical subject heading) terms.Utilizing the 2913 papers from Taiwan's National Health Insurance database, we chose the top 10 research teams shown on Google Maps and analyzed one author (Dr. Kao) who published 149 papers in the database in 2015. In the past 15 years, we found Dr. Kao had 2987 connections with other coauthors from 13 research teams. The cooccurrence abstract keywords with the highest frequency are cohort study and National Health Insurance Research Database. The most coexistent MESH terms are tomography, X-ray computed, and positron-emission tomography. The strength of the author research distinct domain is very low (Gini < 0.40).SNA incorporated with Google Maps and Gini coefficient provides insight into the relationships between entities. The results obtained in this study can be applied for a comprehensive understanding of other productive authors in the field of academics.

Comprehensive analysis of orthologous protein domains using the HOPS database.

PubMed

Storm, Christian E V; Sonnhammer, Erik L L

2003-10-01

One of the most reliable methods for protein function annotation is to transfer experimentally known functions from orthologous proteins in other organisms. Most methods for identifying orthologs operate on a subset of organisms with a completely sequenced genome, and treat proteins as single-domain units. However, it is well known that proteins are often made up of several independent domains, and there is a wealth of protein sequences from genomes that are not completely sequenced. A comprehensive set of protein domain families is found in the Pfam database. We wanted to apply orthology detection to Pfam families, but first some issues needed to be addressed. First, orthology detection becomes impractical and unreliable when too many species are included. Second, shorter domains contain less information. It is therefore important to assess the quality of the orthology assignment and avoid very short domains altogether. We present a database of orthologous protein domains in Pfam called HOPS: Hierarchical grouping of Orthologous and Paralogous Sequences. Orthology is inferred in a hierarchic system of phylogenetic subgroups using ortholog bootstrapping. To avoid the frequent errors stemming from horizontally transferred genes in bacteria, the analysis is presently limited to eukaryotic genes. The results are accessible in the graphical browser NIFAS, a Java tool originally developed for analyzing phylogenetic relations within Pfam families. The method was tested on a set of curated orthologs with experimentally verified function. In comparison to tree reconciliation with a complete species tree, our approach finds significantly more orthologs in the test set. Examples for investigating gene fusions and domain recombination using HOPS are given.

Protein Information Resource: a community resource for expert annotation of protein data

PubMed Central

Barker, Winona C.; Garavelli, John S.; Hou, Zhenglin; Huang, Hongzhan; Ledley, Robert S.; McGarvey, Peter B.; Mewes, Hans-Werner; Orcutt, Bruce C.; Pfeiffer, Friedhelm; Tsugita, Akira; Vinayaka, C. R.; Xiao, Chunlin; Yeh, Lai-Su L.; Wu, Cathy

2001-01-01

The Protein Information Resource, in collaboration with the Munich Information Center for Protein Sequences (MIPS) and the Japan International Protein Information Database (JIPID), produces the most comprehensive and expertly annotated protein sequence database in the public domain, the PIR-International Protein Sequence Database. To provide timely and high quality annotation and promote database interoperability, the PIR-International employs rule-based and classification-driven procedures based on controlled vocabulary and standard nomenclature and includes status tags to distinguish experimentally determined from predicted protein features. The database contains about 200 000 non-redundant protein sequences, which are classified into families and superfamilies and their domains and motifs identified. Entries are extensively cross-referenced to other sequence, classification, genome, structure and activity databases. The PIR web site features search engines that use sequence similarity and database annotation to facilitate the analysis and functional identification of proteins. The PIR-Inter­national databases and search tools are accessible on the PIR web site at http://pir.georgetown.edu/ and at the MIPS web site at http://www.mips.biochem.mpg.de. The PIR-International Protein Sequence Database and other files are also available by FTP. PMID:11125041

Structure-Based Design of Molecules to Reactivate Tumor-Derived p53 Mutations

DTIC Science & Technology

2007-06-01

cluster in conserved regions or “hot spots” (Hainaut and Hollstein, 2000). Missense mutations leading to amino acid changes are the most common p53...domain stabilization compounds. Analysis of the residue-specific temperature factors of the high resolution core domain structure, coupled with a...second scoring results, 13 compounds (10 from the SPECS database and 3 from the TimTec database) were selected for further analysis using solution

PrionScan: an online database of predicted prion domains in complete proteomes.

PubMed

Espinosa Angarica, Vladimir; Angulo, Alfonso; Giner, Arturo; Losilla, Guillermo; Ventura, Salvador; Sancho, Javier

2014-02-05

Prions are a particular type of amyloids related to a large variety of important processes in cells, but also responsible for serious diseases in mammals and humans. The number of experimentally characterized prions is still low and corresponds to a handful of examples in microorganisms and mammals. Prion aggregation is mediated by specific protein domains with a remarkable compositional bias towards glutamine/asparagine and against charged residues and prolines. These compositional features have been used to predict new prion proteins in the genomes of different organisms. Despite these efforts, there are only a few available data sources containing prion predictions at a genomic scale. Here we present PrionScan, a new database of predicted prion-like domains in complete proteomes. We have previously developed a predictive methodology to identify and score prionogenic stretches in protein sequences. In the present work, we exploit this approach to scan all the protein sequences in public databases and compile a repository containing relevant information of proteins bearing prion-like domains. The database is updated regularly alongside UniprotKB and in its present version contains approximately 28000 predictions in proteins from different functional categories in more than 3200 organisms from all the taxonomic subdivisions. PrionScan can be used in two different ways: database query and analysis of protein sequences submitted by the users. In the first mode, simple queries allow to retrieve a detailed description of the properties of a defined protein. Queries can also be combined to generate more complex and specific searching patterns. In the second mode, users can submit and analyze their own sequences. It is expected that this database would provide relevant insights on prion functions and regulation from a genome-wide perspective, allowing researches performing cross-species prion biology studies. Our database might also be useful for guiding experimentalists in the identification of new candidates for further experimental characterization.

Trends in cooling degree-days for five locations in Croatia

NASA Astrophysics Data System (ADS)

Cvitan, L.

2010-09-01

The cooling degree-days (CDD) and number of cooling days (CD) over the period 1901-2008 are analyzed at five stations that represent different climatic regions in Croatia. The stations under consideration are: Osijek in the southern lowland of Pannonian Plain, Zagreb - Grič at the furthest south-eastern edge of the Julian Alps, Gospić in highland - hinterland of the Dinaric Alps, Crikvenica on the north-eastern Adriatic coast and Hvar on the mid - Adriatic island with the same name. Calculation of CDDs and counting of CDs are performed for the 18° C, 21° C and 23° C temperature thresholds that represent daily mean air temperature. Daily mean temperature (M) is calculated by using daily temperatures measured at 7 a.m. (t7), 2 p.m. (t14) and 9 p.m. (t21), in the following way: M=(t7+t14+2t21)/4. Linear trends over the period 1901-2008 are determined for each month as well as for the whole year (annual trend). Statistical significances of the trends are tested using the non-parametric Mann - Kendal test. For the months with the greatest potential cooling demands - June, July and August, the increasing trend is detected for almost all analyzed values at five locations. Namely, only for the August CD (threshold 18° C) for Hvar area and for the June and August CDDs (threshold 23° C) for Gospić area are detected slightly decreasing trends. Most slightly decreasing trends are discovered for September for both parameters at Osijek, Zagreb and Gospić area. Annual trends in both parameters for all locations are increasing, except the annual Gospić CDD (threshold 23° C) trend that is slightly decreasing. According to the Mann - Kendal test neither of the annual trends in CDD and CD for three temperature thresholds are statistically significant at 0.05 significance level in Gospić and Osijek. On the contrary, all of the mentioned annual trends are significant in Zagreb and Crikvenica, and almost all in Hvar (except trends in CD for the 21° C and 23° C thresholds). Months with the significant trends in most of analyzed values are: May and June in Osijek, May, June and July in Zagreb, June in Gospić, June, July and August in Crikvenica and July in Hvar.

Diet matters: Glucocorticoid-related neuroadaptations associated with calorie intake in female rhesus monkeys.

PubMed

Godfrey, Jodi R; Diaz, Maylen Perez; Pincus, Melanie; Kovacs-Balint, Zsofia; Feczko, Eric; Earl, Eric; Miranda-Dominguez, Oscar; Fair, Damien; Sanchez, Mar M; Wilson, Mark E; Michopoulos, Vasiliki

2018-05-01

Exposure to psychosocial stressors increases consumption of palatable, calorically dense diets (CDD) and the risk for obesity, especially in females. While consumption of an obesogenic diet and chronic stress have both been shown to decrease dopamine 2 receptor (D2R) binding and alter functional connectivity (FC) within the prefrontal cortex (PFC) and the nucleus accumbens (NAcc), it remains uncertain how social experience and dietary environment interact to affect reward pathways critical for the regulation of motivated behavior. Using positron emission tomography (PET) and resting state functional connectivity magnetic resonance neuroimaging (rs-fMRI), in female rhesus monkeys maintained in a low calorie chow (n = 18) or a dietary choice condition (chow and a CDD; n = 16) for 12 months, the current study tested the overarching hypothesis that the adverse social experience resulting from subordinate social status would interact with consumption of an obesogenic diet to increase caloric intake that would be predicted by greater cortisol, lower prefrontal D2R binding potential (D2R-BP) and lower PFC-NAcc FC. Results showed that the consequences of adverse social experience imposed by chronic social subordination vary significantly depending on the dietary environment and are associated with alterations in prefrontal D2R-BP and FC in NAcc-PFC sub-regions that predict differences in caloric intake, body weight gain, and fat accumulation. Higher levels of cortisol in the chow-only condition were associated with mild inappetence, as well as increased orbitofrontal (OFC) D2R-BP and greater FC between the NAcc and the dorsolateral PFC (dlPFC) and ventromedial PFC (vmPFC). However, increased cortisol release in females in the dietary choice condition was associated with reduced prefrontal D2R-BP, and opposite FC between the NAcc and the vmPFC and dlPFC observed in the chow-only females. Importantly, the degree of these glucocorticoid-related neuroadaptations predicted significantly more total calorie intake as well as more consumption of the CDD for females having a dietary choice, but had no relation to calorie intake in the chow-only condition. Overall, the current findings suggest that dietary environment modifies the consequences of adverse social experience on reward pathways and appetite regulation and, in an obesogenic dietary environment, may reflect impaired cognitive control of food intake. Copyright © 2018 Elsevier Ltd. All rights reserved.

SIMS: addressing the problem of heterogeneity in databases

NASA Astrophysics Data System (ADS)

Arens, Yigal

1997-02-01

The heterogeneity of remotely accessible databases -- with respect to contents, query language, semantics, organization, etc. -- presents serious obstacles to convenient querying. The SIMS (single interface to multiple sources) system addresses this global integration problem. It does so by defining a single language for describing the domain about which information is stored in the databases and using this language as the query language. Each database to which SIMS is to provide access is modeled using this language. The model describes a database's contents, organization, and other relevant features. SIMS uses these models, together with a planning system drawing on techniques from artificial intelligence, to decompose a given user's high-level query into a series of queries against the databases and other data manipulation steps. The retrieval plan is constructed so as to minimize data movement over the network and maximize parallelism to increase execution speed. SIMS can recover from network failures during plan execution by obtaining data from alternate sources, when possible. SIMS has been demonstrated in the domains of medical informatics and logistics, using real databases.

SynechoNET: integrated protein-protein interaction database of a model cyanobacterium Synechocystis sp. PCC 6803.

PubMed

Kim, Woo-Yeon; Kang, Sungsoo; Kim, Byoung-Chul; Oh, Jeehyun; Cho, Seongwoong; Bhak, Jong; Choi, Jong-Soon

2008-01-01

Cyanobacteria are model organisms for studying photosynthesis, carbon and nitrogen assimilation, evolution of plant plastids, and adaptability to environmental stresses. Despite many studies on cyanobacteria, there is no web-based database of their regulatory and signaling protein-protein interaction networks to date. We report a database and website SynechoNET that provides predicted protein-protein interactions. SynechoNET shows cyanobacterial domain-domain interactions as well as their protein-level interactions using the model cyanobacterium, Synechocystis sp. PCC 6803. It predicts the protein-protein interactions using public interaction databases that contain mutually complementary and redundant data. Furthermore, SynechoNET provides information on transmembrane topology, signal peptide, and domain structure in order to support the analysis of regulatory membrane proteins. Such biological information can be queried and visualized in user-friendly web interfaces that include the interactive network viewer and search pages by keyword and functional category. SynechoNET is an integrated protein-protein interaction database designed to analyze regulatory membrane proteins in cyanobacteria. It provides a platform for biologists to extend the genomic data of cyanobacteria by predicting interaction partners, membrane association, and membrane topology of Synechocystis proteins. SynechoNET is freely available at http://synechocystis.org/ or directly at http://bioportal.kobic.kr/SynechoNET/.

Genome-Wide Identification of Arabidopsis Coiled-Coil Proteins and Establishment of the ARABI-COIL Database1

PubMed Central

Rose, Annkatrin; Manikantan, Sankaraganesh; Schraegle, Shannon J.; Maloy, Michael A.; Stahlberg, Eric A.; Meier, Iris

2004-01-01

Increasing evidence demonstrates the importance of long coiled-coil proteins for the spatial organization of cellular processes. Although several protein classes with long coiled-coil domains have been studied in animals and yeast, our knowledge about plant long coiled-coil proteins is very limited. The repeat nature of the coiled-coil sequence motif often prevents the simple identification of homologs of animal coiled-coil proteins by generic sequence similarity searches. As a consequence, counterparts of many animal proteins with long coiled-coil domains, like lamins, golgins, or microtubule organization center components, have not been identified yet in plants. Here, all Arabidopsis proteins predicted to contain long stretches of coiled-coil domains were identified by applying the algorithm MultiCoil to a genome-wide screen. A searchable protein database, ARABI-COIL (http://www.coiled-coil.org/arabidopsis), was established that integrates information on number, size, and position of predicted coiled-coil domains with subcellular localization signals, transmembrane domains, and available functional annotations. ARABI-COIL serves as a tool to sort and browse Arabidopsis long coiled-coil proteins to facilitate the identification and selection of candidate proteins of potential interest for specific research areas. Using the database, candidate proteins were identified for Arabidopsis membrane-bound, nuclear, and organellar long coiled-coil proteins. PMID:15020757

Toward More Accurate Iris Recognition Using Cross-Spectral Matching.

PubMed

Nalla, Pattabhi Ramaiah; Kumar, Ajay

2017-01-01

Iris recognition systems are increasingly deployed for large-scale applications such as national ID programs, which continue to acquire millions of iris images to establish identity among billions. However, with the availability of variety of iris sensors that are deployed for the iris imaging under different illumination/environment, significant performance degradation is expected while matching such iris images acquired under two different domains (either sensor-specific or wavelength-specific). This paper develops a domain adaptation framework to address this problem and introduces a new algorithm using Markov random fields model to significantly improve cross-domain iris recognition. The proposed domain adaptation framework based on the naive Bayes nearest neighbor classification uses a real-valued feature representation, which is capable of learning domain knowledge. Our approach to estimate corresponding visible iris patterns from the synthesis of iris patches in the near infrared iris images achieves outperforming results for the cross-spectral iris recognition. In this paper, a new class of bi-spectral iris recognition system that can simultaneously acquire visible and near infra-red images with pixel-to-pixel correspondences is proposed and evaluated. This paper presents experimental results from three publicly available databases; PolyU cross-spectral iris image database, IIITD CLI and UND database, and achieve outperforming results for the cross-sensor and cross-spectral iris matching.

Exploring the dark foldable proteome by considering hydrophobic amino acids topology

PubMed Central

Bitard-Feildel, Tristan; Callebaut, Isabelle

2017-01-01

The protein universe corresponds to the set of all proteins found in all organisms. A way to explore it is by taking into account the domain content of the proteins. However, some part of sequences and many entire sequences remain un-annotated despite a converging number of domain families. The un-annotated part of the protein universe is referred to as the dark proteome and remains poorly characterized. In this study, we quantify the amount of foldable domains within the dark proteome by using the hydrophobic cluster analysis methodology. These un-annotated foldable domains were grouped using a combination of remote homology searches and domain annotations, leading to define different levels of darkness. The dark foldable domains were analyzed to understand what make them different from domains stored in databases and thus difficult to annotate. The un-annotated domains of the dark proteome universe display specific features relative to database domains: shorter length, non-canonical content and particular topology in hydrophobic residues, higher propensity for disorder, and a higher energy. These features make them hard to relate to known families. Based on these observations, we emphasize that domain annotation methodologies can still be improved to fully apprehend and decipher the molecular evolution of the protein universe. PMID:28134276

Characterization of the Pathological and Biochemical Markers that Correlate to the Clinical Features of Autism

DTIC Science & Technology

2009-10-01

Specified (PDD-NOS), Asperger disorder, Childhood Disintegrative Disorder (CDD) and Rett syndrome . According to the Centers for Disease Control (CDC), 1 in...induced epilepsy (Fernandes et al., 1996; Reime et al., 2007), and in Crush syndrome (Desai and Desai, 2007). In chronic fatigue syndrome , the...the gene encoding the L-type voltage-gated Ca2+channel CaV1.2 (CACNA1C) cause Timothy syndrome , a multisystem disorder that includes cardiac

Hot flashes and midlife symptoms in relation to levels of salivary cortisol.

PubMed

Gerber, Linda M; Sievert, Lynnette L; Schwartz, Joseph E

2017-02-01

This study examined the relationship between salivary cortisol levels and hot flashes during midlife. Previous studies have shown that cortisol levels increase with hot flashes in the laboratory, and higher cortisol levels have been associated with more severe hot flashes. Salivary cortisol levels were also examined in relation to total number of midlife symptoms. Women aged 40-60 years (n=109) reported the presence or absence of 23 symptoms, including hot flashes, during the previous 2 weeks. Salivary samples were collected at waking, 30min after waking, 1h before bedtime, and at bedtime. The cortisol awakening response (CAR), cortisol daily decline (CDD), log transformed salivary cortisol levels at each time point, and mean cortisol levels were compared by hot flash report using t-tests. Logistic regression analyses were performed to assess the association between each cortisol measure and the presence or absence of hot flashes, after controlling for potential covariates. Salivary cortisol levels were not significantly associated with hot flashes or sum of symptoms. Hot flash report did not differentiate women who had a positive CAR from those who did not, or women who showed strong CDD from those who did not. Symptomatic women - defined by hot flash report or symptom total - were not found to have higher salivary cortisol levels. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

The Effect of AGN Heating on the Low-redshift Lyα Forest

NASA Astrophysics Data System (ADS)

Gurvich, Alex; Burkhart, Blakesley; Bird, Simeon

2017-02-01

We investigate the effects of AGN heating and the ultraviolet background on the low-redshift Lyα forest column density distribution (CDD) using the Illustris simulation. We show that Illustris reproduces observations at z = 0.1 in the column density range {10}12.5{--}{10}13.5 cm-2, relevant for the “photon underproduction crisis.” We attribute this to the inclusion of AGN feedback, which changes the gas distribution so as to mimic the effect of extra photons, as well as the use of the Faucher-Giguère ultraviolet background, which is more ionizing at z = 0.1 than the Haardt & Madau background previously considered. We show that the difference between simulations run with smoothed particle hydrodynamics and simulations using a moving mesh is small in this column density range but can be more significant at larger column densities. We further consider the effect of supernova feedback, Voigt profile fitting, and finite resolution, all of which we show to have little influence on the CDD. Finally, we identify a discrepancy between our simulations and observations at column densities {10}14{--}{10}16 cm-2, where Illustris produces too few absorbers, which suggests the AGN feedback model should be further refined. Since the “photon underproduction crisis” primarily affects lower column density systems, we conclude that AGN feedback and standard ionizing background models can resolve the crisis.

Fuzzy queries above relational database

NASA Astrophysics Data System (ADS)

Smolka, Pavel; Bradac, Vladimir

2017-11-01

The aim of the theme is to introduce a possibility of fuzzy queries implemented in relational databases. The issue is described on a model which identifies the appropriate part of the problem domain for fuzzy approach. The model is demonstrated on a database of wines focused on searching in it. The construction of the database complies with the Law of the Czech Republic.

Concomitant prediction of function and fold at the domain level with GO-based profiles.

PubMed

Lopez, Daniel; Pazos, Florencio

2013-01-01

Predicting the function of newly sequenced proteins is crucial due to the pace at which these raw sequences are being obtained. Almost all resources for predicting protein function assign functional terms to whole chains, and do not distinguish which particular domain is responsible for the allocated function. This is not a limitation of the methodologies themselves but it is due to the fact that in the databases of functional annotations these methods use for transferring functional terms to new proteins, these annotations are done on a whole-chain basis. Nevertheless, domains are the basic evolutionary and often functional units of proteins. In many cases, the domains of a protein chain have distinct molecular functions, independent from each other. For that reason resources with functional annotations at the domain level, as well as methodologies for predicting function for individual domains adapted to these resources are required.We present a methodology for predicting the molecular function of individual domains, based on a previously developed database of functional annotations at the domain level. The approach, which we show outperforms a standard method based on sequence searches in assigning function, concomitantly predicts the structural fold of the domains and can give hints on the functionally important residues associated to the predicted function.

TB Mobile: a mobile app for anti-tuberculosis molecules with known targets

PubMed Central

2013-01-01

Background An increasing number of researchers are focused on strategies for developing inhibitors of Mycobacterium tuberculosis (Mtb) as tuberculosis (TB) drugs. Results In order to learn from prior work we have collated information on molecules screened versus Mtb and their targets which has been made available in the Collaborative Drug Discovery (CDD) database. This dataset contains published data on target, essentiality, links to PubMed, TBDB, TBCyc (which provides a pathway-based visualization of the entire cellular biochemical network) and human homolog information. The development of mobile cheminformatics apps could lower the barrier to drug discovery and promote collaboration. Therefore we have used this set of over 700 molecules screened versus Mtb and their targets to create a free mobile app (TB Mobile) that displays molecule structures and links to the bioinformatics data. By input of a molecular structures and performing a similarity search within the app we can infer potential targets or search by targets to retrieve compounds known to be active. Conclusions TB Mobile may assist researchers as part of their workflow in identifying potential targets for hits generated from phenotypic screening and in prioritizing them for further follow-up. The app is designed to lower the barriers to accessing this information, so that all researchers with an interest in combatting this deadly disease can use it freely to the benefit of their own efforts. PMID:23497706

Database resources of the National Center for Biotechnology Information

PubMed Central

Wheeler, David L.; Barrett, Tanya; Benson, Dennis A.; Bryant, Stephen H.; Canese, Kathi; Chetvernin, Vyacheslav; Church, Deanna M.; DiCuccio, Michael; Edgar, Ron; Federhen, Scott; Geer, Lewis Y.; Helmberg, Wolfgang; Kapustin, Yuri; Kenton, David L.; Khovayko, Oleg; Lipman, David J.; Madden, Thomas L.; Maglott, Donna R.; Ostell, James; Pruitt, Kim D.; Schuler, Gregory D.; Schriml, Lynn M.; Sequeira, Edwin; Sherry, Stephen T.; Sirotkin, Karl; Souvorov, Alexandre; Starchenko, Grigory; Suzek, Tugba O.; Tatusov, Roman; Tatusova, Tatiana A.; Wagner, Lukas; Yaschenko, Eugene

2006-01-01

In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI's Web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups, Retroviral Genotyping Tools, HIV-1, Human Protein Interaction Database, SAGEmap, Gene Expression Omnibus, Entrez Probe, GENSAT, Online Mendelian Inheritance in Man, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized datasets. All of the resources can be accessed through the NCBI home page at: . PMID:16381840

FARE-CAFE: a database of functional and regulatory elements of cancer-associated fusion events

PubMed Central

Korla, Praveen Kumar; Cheng, Jack; Huang, Chien-Hung; Tsai, Jeffrey J. P.; Liu, Yu-Hsuan; Kurubanjerdjit, Nilubon; Hsieh, Wen-Tsong; Chen, Huey-Yi; Ng, Ka-Lok

2015-01-01

Chromosomal translocation (CT) is of enormous clinical interest because this disorder is associated with various major solid tumors and leukemia. A tumor-specific fusion gene event may occur when a translocation joins two separate genes. Currently, various CT databases provide information about fusion genes and their genomic elements. However, no database of the roles of fusion genes, in terms of essential functional and regulatory elements in oncogenesis, is available. FARE-CAFE is a unique combination of CTs, fusion proteins, protein domains, domain–domain interactions, protein–protein interactions, transcription factors and microRNAs, with subsequent experimental information, which cannot be found in any other CT database. Genomic DNA information including, for example, manually collected exact locations of the first and second break points, sequences and karyotypes of fusion genes are included. FARE-CAFE will substantially facilitate the cancer biologist’s mission of elucidating the pathogenesis of various types of cancer. This database will ultimately help to develop ‘novel’ therapeutic approaches. Database URL: http://ppi.bioinfo.asia.edu.tw/FARE-CAFE PMID:26384373

Database resources of the National Center for Biotechnology Information

PubMed Central

Acland, Abigail; Agarwala, Richa; Barrett, Tanya; Beck, Jeff; Benson, Dennis A.; Bollin, Colleen; Bolton, Evan; Bryant, Stephen H.; Canese, Kathi; Church, Deanna M.; Clark, Karen; DiCuccio, Michael; Dondoshansky, Ilya; Federhen, Scott; Feolo, Michael; Geer, Lewis Y.; Gorelenkov, Viatcheslav; Hoeppner, Marilu; Johnson, Mark; Kelly, Christopher; Khotomlianski, Viatcheslav; Kimchi, Avi; Kimelman, Michael; Kitts, Paul; Krasnov, Sergey; Kuznetsov, Anatoliy; Landsman, David; Lipman, David J.; Lu, Zhiyong; Madden, Thomas L.; Madej, Tom; Maglott, Donna R.; Marchler-Bauer, Aron; Karsch-Mizrachi, Ilene; Murphy, Terence; Ostell, James; O'Sullivan, Christopher; Panchenko, Anna; Phan, Lon; Pruitt, Don Preussm Kim D.; Rubinstein, Wendy; Sayers, Eric W.; Schneider, Valerie; Schuler, Gregory D.; Sequeira, Edwin; Sherry, Stephen T.; Shumway, Martin; Sirotkin, Karl; Siyan, Karanjit; Slotta, Douglas; Soboleva, Alexandra; Soussov, Vladimir; Starchenko, Grigory; Tatusova, Tatiana A.; Trawick, Bart W.; Vakatov, Denis; Wang, Yanli; Ward, Minghong; John Wilbur, W.; Yaschenko, Eugene; Zbicz, Kerry

2014-01-01

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI, http://www.ncbi.nlm.nih.gov) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI Web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, PubReader, Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link, Primer-BLAST, COBALT, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, the Genetic Testing Registry, Genome and related tools, the Map Viewer, Trace Archive, Sequence Read Archive, BioProject, BioSample, ClinVar, MedGen, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus, Probe, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool, Biosystems, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All these resources can be accessed through the NCBI home page. PMID:24259429

Systems Engineering of Unmanned DoD Systems: Following the Joint Capabilities Integration and Development System/Defense Acquisition System Process to Develop an Unmanned Ground Vehicle System

DTIC Science & Technology

2015-12-01

Manual D-A-1). APAs are “Performance attributes of a system not important enough to be considered KPPs or KSAs, but still appropriate to include in...the CDD or CPD are designated as APAs ” (JCIDS Manual D-A-1). The requirements are expressed using Thresholds (T) and Objectives (O). “Performance...NAVAL POSTGRADUATE SCHOOL MONTEREY, CALIFORNIA SYSTEMS ENGINEERING CAPSTONE PROJECT REPORT Approved for public release; distribution is

COMPARISON OF OVERALL METABOLISM OF 1, 2, 7, 8-PECDD IN CYP1A2(-L-) KNOCKOUT AND C57BL/6N PARENTAL STRAINS OF MICE

EPA Science Inventory

COMPARISON OF OVERALL METABOLISM OF 1,2,3,7,8-PeCDD
IN CYP1A2 (-/-) KNOCKOUT AND C57BL/6N PARENTAL
STRAINS OF MICE

Heldur Hakk1 and Janet J. Diliberto2

1 USDA-ARS, Biosciences Research Laboratory, P.O. Box 5674, Fargo, ND, USA
2 US EPA, ORD, National Heal...

EvoDB: a database of evolutionary rate profiles, associated protein domains and phylogenetic trees for PFAM-A.

PubMed

Ndhlovu, Andrew; Durand, Pierre M; Hazelhurst, Scott

2015-01-01

The evolutionary rate at codon sites across protein-coding nucleotide sequences represents a valuable tier of information for aligning sequences, inferring homology and constructing phylogenetic profiles. However, a comprehensive resource for cataloguing the evolutionary rate at codon sites and their corresponding nucleotide and protein domain sequence alignments has not been developed. To address this gap in knowledge, EvoDB (an Evolutionary rates DataBase) was compiled. Nucleotide sequences and their corresponding protein domain data including the associated seed alignments from the PFAM-A (protein family) database were used to estimate evolutionary rate (ω = dN/dS) profiles at codon sites for each entry. EvoDB contains 98.83% of the gapped nucleotide sequence alignments and 97.1% of the evolutionary rate profiles for the corresponding information in PFAM-A. As the identification of codon sites under positive selection and their position in a sequence profile is usually the most sought after information for molecular evolutionary biologists, evolutionary rate profiles were determined under the M2a model using the CODEML algorithm in the PAML (Phylogenetic Analysis by Maximum Likelihood) suite of software. Validation of nucleotide sequences against amino acid data was implemented to ensure high data quality. EvoDB is a catalogue of the evolutionary rate profiles and provides the corresponding phylogenetic trees, PFAM-A alignments and annotated accession identifier data. In addition, the database can be explored and queried using known evolutionary rate profiles to identify domains under similar evolutionary constraints and pressures. EvoDB is a resource for evolutionary, phylogenetic studies and presents a tier of information untapped by current databases. © The Author(s) 2015. Published by Oxford University Press.

Database resources of the National Center for Biotechnology Information

PubMed Central

Wheeler, David L.; Barrett, Tanya; Benson, Dennis A.; Bryant, Stephen H.; Canese, Kathi; Chetvernin, Vyacheslav; Church, Deanna M.; DiCuccio, Michael; Edgar, Ron; Federhen, Scott; Feolo, Michael; Geer, Lewis Y.; Helmberg, Wolfgang; Kapustin, Yuri; Khovayko, Oleg; Landsman, David; Lipman, David J.; Madden, Thomas L.; Maglott, Donna R.; Miller, Vadim; Ostell, James; Pruitt, Kim D.; Schuler, Gregory D.; Shumway, Martin; Sequeira, Edwin; Sherry, Steven T.; Sirotkin, Karl; Souvorov, Alexandre; Starchenko, Grigory; Tatusov, Roman L.; Tatusova, Tatiana A.; Wagner, Lukas; Yaschenko, Eugene

2008-01-01

In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data available through NCBI's web site. NCBI resources include Entrez, the Entrez Programming Utilities, My NCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link, Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genome, Genome Project and related tools, the Trace, Assembly, and Short Read Archives, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups, Influenza Viral Resources, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus, Entrez Probe, GENSAT, Database of Genotype and Phenotype, Online Mendelian Inheritance in Man, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool and the PubChem suite of small molecule databases. Augmenting the web applications are custom implementations of the BLAST program optimized to search specialized data sets. These resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov. PMID:18045790

Multiple graph regularized protein domain ranking.

PubMed

Wang, Jim Jing-Yan; Bensmail, Halima; Gao, Xin

2012-11-19

Protein domain ranking is a fundamental task in structural biology. Most protein domain ranking methods rely on the pairwise comparison of protein domains while neglecting the global manifold structure of the protein domain database. Recently, graph regularized ranking that exploits the global structure of the graph defined by the pairwise similarities has been proposed. However, the existing graph regularized ranking methods are very sensitive to the choice of the graph model and parameters, and this remains a difficult problem for most of the protein domain ranking methods. To tackle this problem, we have developed the Multiple Graph regularized Ranking algorithm, MultiG-Rank. Instead of using a single graph to regularize the ranking scores, MultiG-Rank approximates the intrinsic manifold of protein domain distribution by combining multiple initial graphs for the regularization. Graph weights are learned with ranking scores jointly and automatically, by alternately minimizing an objective function in an iterative algorithm. Experimental results on a subset of the ASTRAL SCOP protein domain database demonstrate that MultiG-Rank achieves a better ranking performance than single graph regularized ranking methods and pairwise similarity based ranking methods. The problem of graph model and parameter selection in graph regularized protein domain ranking can be solved effectively by combining multiple graphs. This aspect of generalization introduces a new frontier in applying multiple graphs to solving protein domain ranking applications.

Multiple graph regularized protein domain ranking

PubMed Central

2012-01-01

Background Protein domain ranking is a fundamental task in structural biology. Most protein domain ranking methods rely on the pairwise comparison of protein domains while neglecting the global manifold structure of the protein domain database. Recently, graph regularized ranking that exploits the global structure of the graph defined by the pairwise similarities has been proposed. However, the existing graph regularized ranking methods are very sensitive to the choice of the graph model and parameters, and this remains a difficult problem for most of the protein domain ranking methods. Results To tackle this problem, we have developed the Multiple Graph regularized Ranking algorithm, MultiG-Rank. Instead of using a single graph to regularize the ranking scores, MultiG-Rank approximates the intrinsic manifold of protein domain distribution by combining multiple initial graphs for the regularization. Graph weights are learned with ranking scores jointly and automatically, by alternately minimizing an objective function in an iterative algorithm. Experimental results on a subset of the ASTRAL SCOP protein domain database demonstrate that MultiG-Rank achieves a better ranking performance than single graph regularized ranking methods and pairwise similarity based ranking methods. Conclusion The problem of graph model and parameter selection in graph regularized protein domain ranking can be solved effectively by combining multiple graphs. This aspect of generalization introduces a new frontier in applying multiple graphs to solving protein domain ranking applications. PMID:23157331

Emergency preparedness for the accidental release of radionuclides from the Uljin Nuclear Power Plant in Korea.

PubMed

Park, Soon-Ung; Lee, In-Hye; Joo, Seung Jin; Ju, Jae-Won

2017-12-01

Site specific radionuclide dispersion databases were archived for the emergency response to the hypothetical releases of 137 Cs from the Uljin nuclear power plant in Korea. These databases were obtained with the horizontal resolution of 1.5 km in the local domain centered the power plant site by simulations of the Lagrangian Particle Dispersion Model (LPDM) with the Unified Model (UM)-Local Data Assimilation Prediction System (LDAPS). The Eulerian Dispersion Model-East Asia (EDM-EA) with the UM-Global Data Assimilation Prediction System (UM-GDAPS) meteorological models was used to get dispersion databases in the regional domain. The LPDM model was performed for a year with a 5-day interval yielding 72 synoptic time-scale cases in a year. For each case hourly mean near surface concentrations, hourly mean column integrated concentrations, hourly total depositions for 5 consecutive days were archived by the LPDM model in the local domain and by the EDM-EA model in the regional domain of Asia. Among 72 synoptic cases in a year the worst synoptic case that showed the highest mean surface concentration averaged for 5 days in the LPDM model domain was chosen to illustrate the emergency preparedness to the hypothetical accident at the site. The simulated results by the LPDM model with the 137 Cs emission rate of the Fukushima nuclear power plant accident for the first 5-day period were found to be able to provide prerequisite information for the emergency response to the early phase of the accident whereas those of the EDM-EA model could provide information required for the environmental impact assessment of the accident in the regional domain. The archived site-specific database of 72 synoptic cases in a year could have a great potential to be used as a prognostic information on the emergency preparedness for the early phase of accident. Copyright © 2017 Elsevier Ltd. All rights reserved.

LenVarDB: database of length-variant protein domains.

PubMed

Mutt, Eshita; Mathew, Oommen K; Sowdhamini, Ramanathan

2014-01-01

Protein domains are functionally and structurally independent modules, which add to the functional variety of proteins. This array of functional diversity has been enabled by evolutionary changes, such as amino acid substitutions or insertions or deletions, occurring in these protein domains. Length variations (indels) can introduce changes at structural, functional and interaction levels. LenVarDB (freely available at http://caps.ncbs.res.in/lenvardb/) traces these length variations, starting from structure-based sequence alignments in our Protein Alignments organized as Structural Superfamilies (PASS2) database, across 731 structural classification of proteins (SCOP)-based protein domain superfamilies connected to 2 730 625 sequence homologues. Alignment of sequence homologues corresponding to a structural domain is available, starting from a structure-based sequence alignment of the superfamily. Orientation of the length-variant (indel) regions in protein domains can be visualized by mapping them on the structure and on the alignment. Knowledge about location of length variations within protein domains and their visual representation will be useful in predicting changes within structurally or functionally relevant sites, which may ultimately regulate protein function. Non-technical summary: Evolutionary changes bring about natural changes to proteins that may be found in many organisms. Such changes could be reflected as amino acid substitutions or insertions-deletions (indels) in protein sequences. LenVarDB is a database that provides an early overview of observed length variations that were set among 731 protein families and after examining >2 million sequences. Indels are followed up to observe if they are close to the active site such that they can affect the activity of proteins. Inclusion of such information can aid the design of bioengineering experiments.

Advanced Traffic Management Systems (ATMS) research analysis database system

DOT National Transportation Integrated Search

2001-06-01

The ATMS Research Analysis Database Systems (ARADS) consists of a Traffic Software Data Dictionary (TSDD) and a Traffic Software Object Model (TSOM) for application to microscopic traffic simulation and signal optimization domains. The purpose of thi...

The identification of complete domains within protein sequences using accurate E-values for semi-global alignment

PubMed Central

Kann, Maricel G.; Sheetlin, Sergey L.; Park, Yonil; Bryant, Stephen H.; Spouge, John L.

2007-01-01

The sequencing of complete genomes has created a pressing need for automated annotation of gene function. Because domains are the basic units of protein function and evolution, a gene can be annotated from a domain database by aligning domains to the corresponding protein sequence. Ideally, complete domains are aligned to protein subsequences, in a ‘semi-global alignment’. Local alignment, which aligns pieces of domains to subsequences, is common in high-throughput annotation applications, however. It is a mature technique, with the heuristics and accurate E-values required for screening large databases and evaluating the screening results. Hidden Markov models (HMMs) provide an alternative theoretical framework for semi-global alignment, but their use is limited because they lack heuristic acceleration and accurate E-values. Our new tool, GLOBAL, overcomes some limitations of previous semi-global HMMs: it has accurate E-values and the possibility of the heuristic acceleration required for high-throughput applications. Moreover, according to a standard of truth based on protein structure, two semi-global HMM alignment tools (GLOBAL and HMMer) had comparable performance in identifying complete domains, but distinctly outperformed two tools based on local alignment. When searching for complete protein domains, therefore, GLOBAL avoids disadvantages commonly associated with HMMs, yet maintains their superior retrieval performance. PMID:17596268

SkyDOT: a publicly accessible variability database, containing multiple sky surveys and real-time data

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

Starr, D. L.; Wozniak, P. R.; Vestrand, W. T.

2002-01-01

SkyDOT (Sky Database for Objects in Time-Domain) is a Virtual Observatory currently comprised of data from the RAPTOR, ROTSE I, and OGLE I1 survey projects. This makes it a very large time domain database. In addition, the RAPTOR project provides SkyDOT with real-time variability data as well as stereoscopic information. With its web interface, we believe SkyDOT will be a very useful tool for both astronomers, and the public. Our main task has been to construct an efficient relational database containing all existing data, while handling a real-time inflow of data. We also provide a useful web interface allowing easymore » access to both astronomers and the public. Initially, this server will allow common searches, specific queries, and access to light curves. In the future we will include machine learning classification tools and access to spectral information.« less

Basement domain map of the conterminous United States and Alaska

USGS Publications Warehouse

Lund, Karen; Box, Stephen E.; Holm-Denoma, Christopher S.; San Juan, Carma A.; Blakely, Richard J.; Saltus, Richard W.; Anderson, Eric D.; DeWitt, Ed

2015-01-01

The tectonic settings for crustal types represented in the basement domains are subdivided into constituent geologic environments and the types of primary metals endowments and deposits in them are documented. The compositions, architecture, and original metals endowments are potentially important to assessments of primary mineral deposits and to the residence and recycling of metals in the crust of the United States portion of the North American continent. The databases can be configured to demonstrate the construction of the United States through time, to identify specific types of crust, or to identify domains potentially containing metal endowments of specific genetic types or endowed with specific metals. The databases can also be configured to illustrate other purposes chosen by users.

A structural portrait of the PDZ domain family.

PubMed

Ernst, Andreas; Appleton, Brent A; Ivarsson, Ylva; Zhang, Yingnan; Gfeller, David; Wiesmann, Christian; Sidhu, Sachdev S

2014-10-23

PDZ (PSD-95/Discs-large/ZO1) domains are interaction modules that typically bind to specific C-terminal sequences of partner proteins and assemble signaling complexes in multicellular organisms. We have analyzed the existing database of PDZ domain structures in the context of a specificity tree based on binding specificities defined by peptide-phage binding selections. We have identified 16 structures of PDZ domains in complex with high-affinity ligands and have elucidated four additional structures to assemble a structural database that covers most of the branches of the PDZ specificity tree. A detailed comparison of the structures reveals features that are responsible for the diverse specificities across the PDZ domain family. Specificity differences can be explained by differences in PDZ residues that are in contact with the peptide ligands, but these contacts involve both side-chain and main-chain interactions. Most PDZ domains bind peptides in a canonical conformation in which the ligand main chain adopts an extended β-strand conformation by interacting in an antiparallel fashion with a PDZ β-strand. However, a subset of PDZ domains bind peptides with a bent main-chain conformation and the specificities of these non-canonical domains could not be explained based on canonical structures. Our analysis provides a structural portrait of the PDZ domain family, which serves as a guide in understanding the structural basis for the diverse specificities across the family. Copyright © 2014 Elsevier Ltd. All rights reserved.

Nuclear model calculation and targetry recipe for production of 110mIn.

PubMed

Kakavand, T; Mirzaii, M; Eslami, M; Karimi, A

2015-10-01

(110m)In is potentially an important positron emitting that can be used in positron emission tomography. In this work, the excitation functions and production yields of (110)Cd(d, 2n), (111)Cd(d, 3n), (nat)Cd(d, xn), (110)Cd(p, n), (111)Cd(p, 2n), (112)Cd(p, 3n) and (nat)Cd(p, xn) reactions to produce the (110m)In were calculated using nuclear model code TALYS and compared with the experimental data. The yield of isomeric state production of (110)In was also compared with ground state production ones to reach the optimal energy range of projectile for the high yield production of metastable state. The results indicate that the (110)Cd(p, n)(110m)In is a high yield reaction with an isomeric ratio (σ(m)/σ(g)) of about 35 within the optimal incident energy range of 15-5 MeV. To make the target, cadmium was electroplated on a copper substrate in varying electroplating conditions such as PH, DC current density, temperature and time. A set of cold tests were also performed on the final sample under several thermal shocks to verify target resistance. The best electroplated cadmium target was irradiated with 15 MeV protons at current of 100 µA for one hour and the production yield of (110m)In and other byproducts were measured. Copyright © 2015 Elsevier Ltd. All rights reserved.

[Dioxins in agricultural soil of Poland].

PubMed

Wyrzykowska, Barbara; Falandysz, Jerzy; Hanari, Nobuyashi; Yamashita, Nobuyoshi

2006-01-01

Total PCDDs concentration ranged from 6.8 to 41 pg g d.w. and for PCDFs from 3.9 to 19 pg/g d.w. with total toxic equivalency within a range 0.023-5.9 pg TEQ/g d.w. A somewhat elevated concentrations of PCDDs and PCDFs were found in the samples collected from the south of Poland in the vicinity of highly industrialized regions known for former extensive mining industry of hard coal and metallurgy, as well as for regions with high rates of urbanization in central Poland and in the vicinity of the western border of the country. Nevertheless, if consider homologue specific pattern of PCDDs and PCDFs no major differences were noted between spatially scattered sampling sites. In all samples highly chlorinated PCDDs/DFs dominated (12345678-OcCDD, 1234678-HpCDD, 12346789-OcCDF, 1234789-HpCDF, 1234678-HpCDF were found in all investigated soils). Their similar pattern can suggest that formation of these chemicals occur in similar conditions. Energy production and fossil fuel co-fired power boilers, chemical industry, metallurgical industry are probably the main sources in industrial regions, however heating of houses by small stoves and hard coal with added household wastes, and former use of agrochemical formulations consisting byimpurities of PCDD/F may also play important role at rural sites. The particularly elevated concentrations of OcCDF in some samples might be connected to the former production and use of highly chlorinated polychlorinated biphenyl formulation--Chlorofen.

CicerTransDB 1.0: a resource for expression and functional study of chickpea transcription factors.

PubMed

Gayali, Saurabh; Acharya, Shankar; Lande, Nilesh Vikram; Pandey, Aarti; Chakraborty, Subhra; Chakraborty, Niranjan

2016-07-29

Transcription factor (TF) databases are major resource for systematic studies of TFs in specific species as well as related family members. Even though there are several publicly available multi-species databases, the information on the amount and diversity of TFs within individual species is fragmented, especially for newly sequenced genomes of non-model species of agricultural significance. We constructed CicerTransDB (Cicer Transcription Factor Database), the first database of its kind, which would provide a centralized putatively complete list of TFs in a food legume, chickpea. CicerTransDB, available at www.cicertransdb.esy.es , is based on chickpea (Cicer arietinum L.) annotation v 1.0. The database is an outcome of genome-wide domain study and manual classification of TF families. This database not only provides information of the gene, but also gene ontology, domain and motif architecture. CicerTransDB v 1.0 comprises information of 1124 genes of chickpea and enables the user to not only search, browse and download sequences but also retrieve sequence features. CicerTransDB also provides several single click interfaces, transconnecting to various other databases to ease further analysis. Several webAPI(s) integrated in the database allow end-users direct access of data. A critical comparison of CicerTransDB with PlantTFDB (Plant Transcription Factor Database) revealed 68 novel TFs in the chickpea genome, hitherto unexplored. Database URL: http://www.cicertransdb.esy.es.

The Protein Information Resource: an integrated public resource of functional annotation of proteins

PubMed Central

Wu, Cathy H.; Huang, Hongzhan; Arminski, Leslie; Castro-Alvear, Jorge; Chen, Yongxing; Hu, Zhang-Zhi; Ledley, Robert S.; Lewis, Kali C.; Mewes, Hans-Werner; Orcutt, Bruce C.; Suzek, Baris E.; Tsugita, Akira; Vinayaka, C. R.; Yeh, Lai-Su L.; Zhang, Jian; Barker, Winona C.

2002-01-01

The Protein Information Resource (PIR) serves as an integrated public resource of functional annotation of protein data to support genomic/proteomic research and scientific discovery. The PIR, in collaboration with the Munich Information Center for Protein Sequences (MIPS) and the Japan International Protein Information Database (JIPID), produces the PIR-International Protein Sequence Database (PSD), the major annotated protein sequence database in the public domain, containing about 250 000 proteins. To improve protein annotation and the coverage of experimentally validated data, a bibliography submission system is developed for scientists to submit, categorize and retrieve literature information. Comprehensive protein information is available from iProClass, which includes family classification at the superfamily, domain and motif levels, structural and functional features of proteins, as well as cross-references to over 40 biological databases. To provide timely and comprehensive protein data with source attribution, we have introduced a non-redundant reference protein database, PIR-NREF. The database consists of about 800 000 proteins collected from PIR-PSD, SWISS-PROT, TrEMBL, GenPept, RefSeq and PDB, with composite protein names and literature data. To promote database interoperability, we provide XML data distribution and open database schema, and adopt common ontologies. The PIR web site (http://pir.georgetown.edu/) features data mining and sequence analysis tools for information retrieval and functional identification of proteins based on both sequence and annotation information. The PIR databases and other files are also available by FTP (ftp://nbrfa.georgetown.edu/pir_databases). PMID:11752247

A Chronostratigraphic Relational Database Ontology

NASA Astrophysics Data System (ADS)

Platon, E.; Gary, A.; Sikora, P.

2005-12-01

A chronostratigraphic research database was donated by British Petroleum to the Stratigraphy Group at the Energy and Geoscience Institute (EGI), University of Utah. These data consists of over 2,000 measured sections representing over three decades of research into the application of the graphic correlation method. The data are global and includes both microfossil (foraminifera, calcareous nannoplankton, spores, pollen, dinoflagellate cysts, etc) and macrofossil data. The objective of the donation was to make the research data available to the public in order to encourage additional chronostratigraphy studies, specifically regarding graphic correlation. As part of the National Science Foundation's Cyberinfrastructure for the Geosciences (GEON) initiative these data have been made available to the public at http://css.egi.utah.edu. To encourage further research using the graphic correlation method, EGI has developed a software package, StrataPlot that will soon be publicly available from the GEON website as a standalone software download. The EGI chronostratigraphy research database, although relatively large, has many data holes relative to some paleontological disciplines and geographical areas, so the challenge becomes how do we expand the data available for chronostratigrahic studies using graphic correlation. There are several public or soon-to-be public databases available to chronostratigraphic research, but they have their own data structures and modes of presentation. The heterogeneous nature of these database schemas hinders their integration and makes it difficult for the user to retrieve and consolidate potentially valuable chronostratigraphic data. The integration of these data sources would facilitate rapid and comprehensive data searches, thus helping advance studies in chronostratigraphy. The GEON project will host a number of databases within the geology domain, some of which contain biostratigraphic data. Ontologies are being developed to provide an integrated query system for the searching across GEON's biostratigraphy databases, as well as databases available in the public domain. Although creating an ontology directly from the existing database metadata would have been effective and straightforward, our effort was directed towards creating a more efficient representation of our database, as well as a general representation of the biostratigraphic domain.

The Council on Quality and Leadership in Supports for People with Disabilities: Personal Outcomes Chart Book.

ERIC Educational Resources Information Center

National Center on Outcomes Research, Council on Quality and Leadership, Towson, MD.

This report describes the genesis, definition and use of the Personal Outcomes database, a database designed to assess whether programs and services are being effective in helping individuals with disabilities. The database is based on 25 outcome measures in seven domains, including: (1) identity, which is designed to provide a sense of how people…

Database resources of the National Center for Biotechnology Information

PubMed Central

2013-01-01

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI, http://www.ncbi.nlm.nih.gov) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, the Genetic Testing Registry, Genome and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, BioProject, BioSample, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus, Probe, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool, Biosystems, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page. PMID:23193264

BioFrameNet: A FrameNet Extension to the Domain of Molecular Biology

ERIC Educational Resources Information Center

Dolbey, Andrew Eric

2009-01-01

In this study I introduce BioFrameNet, an extension of the Berkeley FrameNet lexical database to the domain of molecular biology. I examine the syntactic and semantic combinatorial possibilities exhibited in the lexical items used in this domain in order to get a better understanding of the grammatical properties of the language used in scientific…

An Evaluation of Database Solutions to Spatial Object Association

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

Kumar, V S; Kurc, T; Saltz, J

2008-06-24

Object association is a common problem encountered in many applications. Spatial object association, also referred to as crossmatch of spatial datasets, is the problem of identifying and comparing objects in two datasets based on their positions in a common spatial coordinate system--one of the datasets may correspond to a catalog of objects observed over time in a multi-dimensional domain; the other dataset may consist of objects observed in a snapshot of the domain at a time point. The use of database management systems to the solve the object association problem provides portability across different platforms and also greater flexibility. Increasingmore » dataset sizes in today's applications, however, have made object association a data/compute-intensive problem that requires targeted optimizations for efficient execution. In this work, we investigate how database-based crossmatch algorithms can be deployed on different database system architectures and evaluate the deployments to understand the impact of architectural choices on crossmatch performance and associated trade-offs. We investigate the execution of two crossmatch algorithms on (1) a parallel database system with active disk style processing capabilities, (2) a high-throughput network database (MySQL Cluster), and (3) shared-nothing databases with replication. We have conducted our study in the context of a large-scale astronomy application with real use-case scenarios.« less

A Standardized Protocol for the Prospective Follow-Up of Cleft Lip and Palate Patients.

PubMed

Salimi, Negar; Jolanta, Aleksejūnienė; Edwin, Yen; Angelina, Loo

2018-01-01

To develop a standardized all-encompassing protocol for the assessment of cleft lip and palate patients with clinical and research implications. Electronic database searches were conducted and 13 major cleft centers worldwide were contacted in order to prepare for the development of the protocol. In preparation, the available evidence was reviewed and potential fistula-related risk determinants from 4 different domains were identified. No standardized protocol for the assessment of cleft patients could be found in any of the electronic database searches that were conducted. Interviews with representatives from several major centers revealed that the majority of centers do not have a standardized comprehensive strategy for the reporting and follow-up of cleft lip and palate patients. The protocol was developed and consisted of the following domains of determinants: (1) the sociodemographic domain, (2) the cleft defect domain, (3) the surgery domain, and (4) the fistula domain. The proposed protocol has the potential to enhance the quality of patient care by ensuring that multiple patient-related aspects are consistently reported. It may also facilitate future multicenter research, which could contribute to the reduction of fistula occurrence in cleft lip and palate patients.

A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3

PubMed Central

Dietmann, Sabine; Park, Jong; Notredame, Cedric; Heger, Andreas; Lappe, Michael; Holm, Liisa

2001-01-01

The Dali Domain Dictionary (http://www.ebi.ac.uk/dali/domain) is a numerical taxonomy of all known structures in the Protein Data Bank (PDB). The taxonomy is derived fully automatically from measurements of structural, functional and sequence similarities. Here, we report the extension of the classification to match the traditional four hierarchical levels corresponding to: (i) supersecondary structural motifs (attractors in fold space), (ii) the topology of globular domains (fold types), (iii) remote homologues (functional families) and (iv) homologues with sequence identity above 25% (sequence families). The computational definitions of attractors and functional families are new. In September 2000, the Dali classification contained 10 531 PDB entries comprising 17 101 chains, which were partitioned into five attractor regions, 1375 fold types, 2582 functional families and 3724 domain sequence families. Sequence families were further associated with 99 582 unique homologous sequences in the HSSP database, which increases the number of effectively known structures several-fold. The resulting database contains the description of protein domain architecture, the definition of structural neighbours around each known structure, the definition of structurally conserved cores and a comprehensive library of explicit multiple alignments of distantly related protein families. PMID:11125048

Numerical Model Sensitivity to Heterogeneous Satellite Derived Vegetation Roughness

NASA Technical Reports Server (NTRS)

Jasinski, Michael; Eastman, Joseph; Borak, Jordan

2011-01-01

The sensitivity of a mesoscale weather prediction model to a 1 km satellite-based vegetation roughness initialization is investigated for a domain within the south central United States. Three different roughness databases are employed: i) a control or standard lookup table roughness that is a function only of land cover type, ii) a spatially heterogeneous roughness database, specific to the domain, that was previously derived using a physically based procedure and Moderate Resolution Imaging Spectroradiometer (MODIS) imagery, and iii) a MODIS climatologic roughness database that like (i) is a function only of land cover type, but possesses domain specific mean values from (ii). The model used is the Weather Research and Forecast Model (WRF) coupled to the Community Land Model within the Land Information System (LIS). For each simulation, a statistical comparison is made between modeled results and ground observations within a domain including Oklahoma, Eastern Arkansas, and Northwest Louisiana during a 4-day period within IHOP 2002. Sensitivity analysis compares the impact the three roughness initializations on time-series temperature, precipitation probability of detection (POD), average wind speed, boundary layer height, and turbulent kinetic energy (TKE). Overall, the results indicate that, for the current investigation, replacement of the standard look-up table values with the satellite-derived values statistically improves model performance for most observed variables. Such natural roughness heterogeneity enhances the surface wind speed, PBL height and TKE production up to 10 percent, with a lesser effect over grassland, and greater effect over mixed land cover domains.

Localizome: a server for identifying transmembrane topologies and TM helices of eukaryotic proteins utilizing domain information

PubMed Central

Lee, Sunghoon; Lee, Byungwook; Jang, Insoo; Kim, Sangsoo; Bhak, Jong

2006-01-01

The Localizome server predicts the transmembrane (TM) helix number and TM topology of a user-supplied eukaryotic protein and presents the result as an intuitive graphic representation. It utilizes hmmpfam to detect the presence of Pfam domains and a prediction algorithm, Phobius, to predict the TM helices. The results are combined and checked against the TM topology rules stored in a protein domain database called LocaloDom. LocaloDom is a curated database that contains TM topologies and TM helix numbers of known protein domains. It was constructed from Pfam domains combined with Swiss-Prot annotations and Phobius predictions. The Localizome server corrects the combined results of the user sequence to conform to the rules stored in LocaloDom. Compared with other programs, this server showed the highest accuracy for TM topology prediction: for soluble proteins, the accuracy and coverage were 99 and 75%, respectively, while for TM protein domain regions, they were 96 and 68%, respectively. With a graphical representation of TM topology and TM helix positions with the domain units, the Localizome server is a highly accurate and comprehensive information source for subcellular localization for soluble proteins as well as membrane proteins. The Localizome server can be found at . PMID:16845118

Using the structure-function linkage database to characterize functional domains in enzymes.

PubMed

Brown, Shoshana; Babbitt, Patricia

2014-12-12

The Structure-Function Linkage Database (SFLD; http://sfld.rbvi.ucsf.edu/) is a Web-accessible database designed to link enzyme sequence, structure, and functional information. This unit describes the protocols by which a user may query the database to predict the function of uncharacterized enzymes and to correct misannotated functional assignments. The information in this unit is especially useful in helping a user discriminate functional capabilities of a sequence that is only distantly related to characterized sequences in publicly available databases. Copyright © 2014 John Wiley & Sons, Inc.

[Public scientific knowledge distribution in health information, communication and information technology indexed in MEDLINE and LILACS databases].

PubMed

Packer, Abel Laerte; Tardelli, Adalberto Otranto; Castro, Regina Célia Figueiredo

2007-01-01

This study explores the distribution of international, regional and national scientific output in health information and communication, indexed in the MEDLINE and LILACS databases, between 1996 and 2005. A selection of articles was based on the hierarchical structure of Information Science in MeSH vocabulary. Four specific domains were determined: health information, medical informatics, scientific communications on healthcare and healthcare communications. The variables analyzed were: most-covered subjects and journals, author affiliation and publication countries and languages, in both databases. The Information Science category is represented in nearly 5% of MEDLINE and LILACS articles. The four domains under analysis showed a relative annual increase in MEDLINE. The Medical Informatics domain showed the highest number of records in MEDLINE, representing about half of all indexed articles. The importance of Information Science as a whole is more visible in publications from developed countries and the findings indicate the predominance of the United States, with significant growth in scientific output from China and South Korea and, to a lesser extent, Brazil.

GExplore: a web server for integrated queries of protein domains, gene expression and mutant phenotypes

PubMed Central

2009-01-01

Background The majority of the genes even in well-studied multi-cellular model organisms have not been functionally characterized yet. Mining the numerous genome wide data sets related to protein function to retrieve potential candidate genes for a particular biological process remains a challenge. Description GExplore has been developed to provide a user-friendly database interface for data mining at the gene expression/protein function level to help in hypothesis development and experiment design. It supports combinatorial searches for proteins with certain domains, tissue- or developmental stage-specific expression patterns, and mutant phenotypes. GExplore operates on a stand-alone database and has fast response times, which is essential for exploratory searches. The interface is not only user-friendly, but also modular so that it accommodates additional data sets in the future. Conclusion GExplore is an online database for quick mining of data related to gene and protein function, providing a multi-gene display of data sets related to the domain composition of proteins as well as expression and phenotype data. GExplore is publicly available at: http://genome.sfu.ca/gexplore/ PMID:19917126

Combined Global Navigation Satellite Systems in the Space Service Volume

NASA Technical Reports Server (NTRS)

Force, Dale A.; Miller, James J.

2015-01-01

Besides providing position, navigation, and timing (PNT) services to traditional terrestrial and airborne users, GPS is also being increasingly used as a tool to enable precision orbit determination, precise time synchronization, real-time spacecraft navigation, and three-axis attitude control of Earth orbiting satellites. With additional Global Navigation Satellite System (GNSS) constellations being replenished and coming into service (GLONASS, Beidou, and Galileo), it will become possible to benefit from greater signal availability and robustness by using evolving multi-constellation receivers. The paper, "GPS in the Space Service Volume," presented at the ION GNSS 19th International Technical Meeting in 2006 (Ref. 1), defined the Space Service Volume, and analyzed the performance of GPS out to seventy thousand kilometers. This paper will report a similar analysis of the signal coverage of GPS in the space domain; however, the analyses will also consider signal coverage from each of the additional GNSS constellations noted earlier to specifically demonstrate the expected benefits to be derived from using GPS in conjunction with other foreign systems. The Space Service Volume is formally defined as the volume of space between three thousand kilometers altitude and geosynchronous altitude circa 36,000 km, as compared with the Terrestrial Service Volume between 3,000 km and the surface of the Earth. In the Terrestrial Service Volume, GNSS performance is the same as on or near the Earth's surface due to satellite vehicle availability and geometry similarities. The core GPS system has thereby established signal requirements for the Space Service Volume as part of technical Capability Development Documentation (CDD) that specifies system performance. Besides the technical discussion, we also present diplomatic efforts to extend the GPS Space Service Volume concept to other PNT service providers in an effort to assure that all space users will benefit from the enhanced interoperability of GNSS services in the space domain. A separate paper presented at the conference covers the individual GNSS performance parameters for respective Space Service Volumes.

Digital Array Radar for Ballistic Missile Defense and Counter-Stealth Systems Analysis and Parameter Tradeoff Study

DTIC Science & Technology

2006-09-14

specified time. In general the combined vector traces an ellipse when observed in the x-y plane , as illustrated in the following figure.82 176...STANDARD Missile 3 (SM-3) launched from Aegis ships. Depth of fire with SM-3 is limited during an engagement from one 10 platform– generally one, max...will be the technical requirements for the system so that it will be capable of achieving the KPPs specified in the CDD2. Equation 3.1 is the radar

Developing an ontological explosion knowledge base for business continuity planning purposes.

PubMed

Mohammadfam, Iraj; Kalatpour, Omid; Golmohammadi, Rostam; Khotanlou, Hasan

2013-01-01

Industrial accidents are among the most known challenges to business continuity. Many organisations have lost their reputation following devastating accidents. To manage the risks of such accidents, it is necessary to accumulate sufficient knowledge regarding their roots, causes and preventive techniques. The required knowledge might be obtained through various approaches, including databases. Unfortunately, many databases are hampered by (among other things) static data presentations, a lack of semantic features, and the inability to present accident knowledge as discrete domains. This paper proposes the use of Protégé software to develop a knowledge base for the domain of explosion accidents. Such a structure has a higher capability to improve information retrieval compared with common accident databases. To accomplish this goal, a knowledge management process model was followed. The ontological explosion knowledge base (EKB) was built for further applications, including process accident knowledge retrieval and risk management. The paper will show how the EKB has a semantic feature that enables users to overcome some of the search constraints of existing accident databases.

Noise Radiation From a Leading-Edge Slat

NASA Technical Reports Server (NTRS)

Lockard, David P.; Choudhari, Meelan M.

2009-01-01

This paper extends our previous computations of unsteady flow within the slat cove region of a multi-element high-lift airfoil configuration, which showed that both statistical and structural aspects of the experimentally observed unsteady flow behavior can be captured via 3D simulations over a computational domain of narrow spanwise extent. Although such narrow domain simulation can account for the spanwise decorrelation of the slat cove fluctuations, the resulting database cannot be applied towards acoustic predictions of the slat without invoking additional approximations to synthesize the fluctuation field over the rest of the span. This deficiency is partially alleviated in the present work by increasing the spanwise extent of the computational domain from 37.3% of the slat chord to nearly 226% (i.e., 15% of the model span). The simulation database is used to verify consistency with previous computational results and, then, to develop predictions of the far-field noise radiation in conjunction with a frequency-domain Ffowcs-Williams Hawkings solver.

Toward An Unstructured Mesh Database

NASA Astrophysics Data System (ADS)

Rezaei Mahdiraji, Alireza; Baumann, Peter Peter

2014-05-01

Unstructured meshes are used in several application domains such as earth sciences (e.g., seismology), medicine, oceanography, cli- mate modeling, GIS as approximate representations of physical objects. Meshes subdivide a domain into smaller geometric elements (called cells) which are glued together by incidence relationships. The subdivision of a domain allows computational manipulation of complicated physical structures. For instance, seismologists model earthquakes using elastic wave propagation solvers on hexahedral meshes. The hexahedral con- tains several hundred millions of grid points and millions of hexahedral cells. Each vertex node in the hexahedrals stores a multitude of data fields. To run simulation on such meshes, one needs to iterate over all the cells, iterate over incident cells to a given cell, retrieve coordinates of cells, assign data values to cells, etc. Although meshes are used in many application domains, to the best of our knowledge there is no database vendor that support unstructured mesh features. Currently, the main tool for querying and manipulating unstructured meshes are mesh libraries, e.g., CGAL and GRAL. Mesh li- braries are dedicated libraries which includes mesh algorithms and can be run on mesh representations. The libraries do not scale with dataset size, do not have declarative query language, and need deep C++ knowledge for query implementations. Furthermore, due to high coupling between the implementations and input file structure, the implementations are less reusable and costly to maintain. A dedicated mesh database offers the following advantages: 1) declarative querying, 2) ease of maintenance, 3) hiding mesh storage structure from applications, and 4) transparent query optimization. To design a mesh database, the first challenge is to define a suitable generic data model for unstructured meshes. We proposed ImG-Complexes data model as a generic topological mesh data model which extends incidence graph model to multi-incidence relationships. We instrument ImG model with sets of optional and application-specific constraints which can be used to check validity of meshes for a specific class of object such as manifold, pseudo-manifold, and simplicial manifold. We conducted experiments to measure the performance of the graph database solution in processing mesh queries and compare it with GrAL mesh library and PostgreSQL database on synthetic and real mesh datasets. The experiments show that each system perform well on specific types of mesh queries, e.g., graph databases perform well on global path-intensive queries. In the future, we investigate database operations for the ImG model and design a mesh query language.

Organization of Heterogeneous Scientific Data Using the EAV/CR Representation

PubMed Central

Nadkarni, Prakash M.; Marenco, Luis; Chen, Roland; Skoufos, Emmanouil; Shepherd, Gordon; Miller, Perry

1999-01-01

Entity-attribute-value (EAV) representation is a means of organizing highly heterogeneous data using a relatively simple physical database schema. EAV representation is widely used in the medical domain, most notably in the storage of data related to clinical patient records. Its potential strengths suggest its use in other biomedical areas, in particular research databases whose schemas are complex as well as constantly changing to reflect evolving knowledge in rapidly advancing scientific domains. When deployed for such purposes, the basic EAV representation needs to be augmented significantly to handle the modeling of complex objects (classes) as well as to manage interobject relationships. The authors refer to their modification of the basic EAV paradigm as EAV/CR (EAV with classes and relationships). They describe EAV/CR representation with examples from two biomedical databases that use it. PMID:10579606

Financing a future for public biological data.

PubMed

Ellis, L B; Kalumbi, D

1999-09-01

The public web-based biological database infrastructure is a source of both wonder and worry. Users delight in the ever increasing amounts of information available; database administrators and curators worry about long-term financial support. An earlier study of 153 biological databases (Ellis and Kalumbi, Nature Biotechnol., 16, 1323-1324, 1998) determined that near future (1-5 year) funding for over two-thirds of them was uncertain. More detailed data are required to determine the magnitude of the problem and offer possible solutions. This study examines the finances and use statistics of a few of these organizations in more depth, and reviews several economic models that may help sustain them. Six organizations were studied. Their administrative overhead is fairly low; non-administrative personnel and computer-related costs account for 77% of expenses. One smaller, more specialized US database, in 1997, had 60% of total access from US domains; a majority (56%) of its US accesses came from commercial domains, although only 2% of the 153 databases originally studied received any industrial support. The most popular model used to gain industrial support is asymmetric pricing: preferentially charging the commercial users of a database. At least five biological databases have recently begun using this model. Advertising is another model which may be useful for the more general, more heavily used sites. Microcommerce has promise, especially for databases that do not attract advertisers, but needs further testing. The least income reported for any of the databases studied was $50,000/year; applying this rate to 400 biological databases (a lower limit of the number of such databases, many of which require far larger resources) would mean annual support need of at least $20 million. To obtain this level of support is challenging, yet failure to accept the challenge could be catastrophic. lynda@tc.umn. edu

MMDB: Entrez’s 3D-structure database

PubMed Central

Wang, Yanli; Anderson, John B.; Chen, Jie; Geer, Lewis Y.; He, Siqian; Hurwitz, David I.; Liebert, Cynthia A.; Madej, Thomas; Marchler, Gabriele H.; Marchler-Bauer, Aron; Panchenko, Anna R.; Shoemaker, Benjamin A.; Song, James S.; Thiessen, Paul A.; Yamashita, Roxanne A.; Bryant, Stephen H.

2002-01-01

Three-dimensional structures are now known within many protein families and it is quite likely, in searching a sequence database, that one will encounter a homolog with known structure. The goal of Entrez’s 3D-structure database is to make this information, and the functional annotation it can provide, easily accessible to molecular biologists. To this end Entrez’s search engine provides three powerful features. (i) Sequence and structure neighbors; one may select all sequences similar to one of interest, for example, and link to any known 3D structures. (ii) Links between databases; one may search by term matching in MEDLINE, for example, and link to 3D structures reported in these articles. (iii) Sequence and structure visualization; identifying a homolog with known structure, one may view molecular-graphic and alignment displays, to infer approximate 3D structure. In this article we focus on two features of Entrez’s Molecular Modeling Database (MMDB) not described previously: links from individual biopolymer chains within 3D structures to a systematic taxonomy of organisms represented in molecular databases, and links from individual chains (and compact 3D domains within them) to structure neighbors, other chains (and 3D domains) with similar 3D structure. MMDB may be accessed at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Structure. PMID:11752307

Biological Databases for Behavioral Neurobiology

PubMed Central

Baker, Erich J.

2014-01-01

Databases are, at their core, abstractions of data and their intentionally derived relationships. They serve as a central organizing metaphor and repository, supporting or augmenting nearly all bioinformatics. Behavioral domains provide a unique stage for contemporary databases, as research in this area spans diverse data types, locations, and data relationships. This chapter provides foundational information on the diversity and prevalence of databases, how data structures support the various needs of behavioral neuroscience analysis and interpretation. The focus is on the classes of databases, data curation, and advanced applications in bioinformatics using examples largely drawn from research efforts in behavioral neuroscience. PMID:23195119

A conserved gene family encodes transmembrane proteins with fibronectin, immunoglobulin and leucine-rich repeat domains (FIGLER)

PubMed Central

Munfus, Delicia L; Haga, Christopher L; Burrows, Peter D; Cooper, Max D

2007-01-01

Background In mouse the cytokine interleukin-7 (IL-7) is required for generation of B lymphocytes, but human IL-7 does not appear to have this function. A bioinformatics approach was therefore used to identify IL-7 receptor related genes in the hope of identifying the elusive human cytokine. Results Our database search identified a family of nine gene candidates, which we have provisionally named fibronectin immunoglobulin leucine-rich repeat (FIGLER). The FIGLER 1–9 genes are predicted to encode type I transmembrane glycoproteins with 6–12 leucine-rich repeats (LRR), a C2 type Ig domain, a fibronectin type III domain, a hydrophobic transmembrane domain, and a cytoplasmic domain containing one to four tyrosine residues. Members of this multichromosomal gene family possess 20–47% overall amino acid identity and are differentially expressed in cell lines and primary hematopoietic lineage cells. Genes for FIGLER homologs were identified in macaque, orangutan, chimpanzee, mouse, rat, dog, chicken, toad, and puffer fish databases. The non-human FIGLER homologs share 38–99% overall amino acid identity with their human counterpart. Conclusion The extracellular domain structure and absence of recognizable cytoplasmic signaling motifs in members of the highly conserved FIGLER gene family suggest a trophic or cell adhesion function for these molecules. PMID:17854505

An updated version of NPIDB includes new classifications of DNA–protein complexes and their families

PubMed Central

Zanegina, Olga; Kirsanov, Dmitriy; Baulin, Eugene; Karyagina, Anna; Alexeevski, Andrei; Spirin, Sergey

2016-01-01

The recent upgrade of nucleic acid–protein interaction database (NPIDB, http://npidb.belozersky.msu.ru/) includes a newly elaborated classification of complexes of protein domains with double-stranded DNA and a classification of families of related complexes. Our classifications are based on contacting structural elements of both DNA: the major groove, the minor groove and the backbone; and protein: helices, beta-strands and unstructured segments. We took into account both hydrogen bonds and hydrophobic interaction. The analyzed material contains 1942 structures of protein domains from 748 PDB entries. We have identified 97 interaction modes of individual protein domain–DNA complexes and 17 DNA–protein interaction classes of protein domain families. We analyzed the sources of diversity of DNA–protein interaction modes in different complexes of one protein domain family. The observed interaction mode is sometimes influenced by artifacts of crystallization or diversity in secondary structure assignment. The interaction classes of domain families are more stable and thus possess more biological sense than a classification of single complexes. Integration of the classification into NPIDB allows the user to browse the database according to the interacting structural elements of DNA and protein molecules. For each family, we present average DNA shape parameters in contact zones with domains of the family. PMID:26656949

Polychlorinated dibenzo-p-dioxins and the human immune system: 4 studies on two Spanish families with increased body burdens of highly chlorinated PCDDs.

PubMed

Smith, Andrew G; Hansson, Marriane; Rodriguez-Pichardo, Antonio; Ferrer-Dufol, Ana; Neubert, Reinhard T; Webb, Jessie R; Rappe, Christopher; Neubert, Diether

2008-04-01

The consequences of exposure of people to highly chlorinated polychlorodibenzo-p-dioxins (PCDDs) are much less known than those of TCDD. We report on levels of PCDDs (and PCDFs) in 13 members of two families poisoned by contaminated cooking oil. Originally, all persons displayed chloracne as an early symptom. Persisting hexa- and higher chlorinated PCDDs could be analysed many years after exposure. Highest values found in blood lipids were: OCDD 660,000 pg/g; HpCDD 58,000 pg/g; HxCDDs: 3500 pg/g. None of the participants exhibited increased TCDD levels at the time of study. During a period of 6 years, HpCDD and OCDD disappeared from the blood lipids much faster in persons exposed as children or young adults, than from lipids of their parents. Surface receptors on blood lymphocytes of the members of the two families and the proliferative capacity of these blood cells in the presence of typical stimulants were analysed. Even in family members with the highest body burdens of hexa- to octachlorinated PCDDs we could not detect pronounced changes from a reference population with respect to the immunological markers. Minor deviations of levels of some receptors in a few, but not all, highly exposed persons suggested a similar trend to those reported in previous studies of persons with body burdens of > or =3000 pg TCDD/g blood lipids. An increase in the number of total blood lymphocytes in some subjects exposed as children may have similarity with highly TCDD-exposed children in Seveso.

Theater dramatizes ORT message.

PubMed

White, K

1990-04-01

The Zambian Control of Diarrheal Diseases (CDD) Program sought the assistance of 2 popular theater groups to develop a play on diarrhea including messages on using oral rehydration therapy (ORT), breast feeding, continued feeding, and using fluids. This was a more appropriate channel for promoting ORT because only 30% of the population had access to a radio and even less to a television set. The groups performed their 35-40 minute plays, complete with dancing and singing, in the local language for 40 different high density communities in Lusaka 6 times/week for 3 months. Before each play, 1 group went door to door telling the occupants that they were going to perform a play about diarrhea management, specifically ORT. If no one could come, the group described ORT for the occupants. The other group held discussions after each performance to determine what learned and to correct any misconceptions about ORT. 1 group concentrated on bottle feeding as the cause of diarrhea while the other group concentrated on poor sanitation and personal hygiene. The groups always performed in locations convenient to mothers, such as markets, outside clinics, and schools, thereby reaching an estimated 10,000 people. Men also attended the plays which was good because fathers often decide whether or not to use ORT for a sick child. Several performances were recorded and aired on local language radio programs to increase awareness of ORT. The entire 1989 campaign of the CDD Program cost $3000 while radio spots for the same period cost the program $8000-10,000. Popular theater is now being used to publicize many other health messages, such as AIDS-prevention.

Onchocerciasis control in the Democratic Republic of Congo (DRC): challenges in a post-war environment.

PubMed

Makenga Bof, J-C; Maketa, V; Bakajika, D K; Ntumba, F; Mpunga, D; Murdoch, M E; Hopkins, A; Noma, M M; Zouré, H; Tekle, A H; Katabarwa, M N; Lutumba, P

2015-01-01

To evaluate onchocerciasis control activities in the Democratic Republic of Congo (DRC) in the first 12 years of community-directed treatment with ivermectin (CDTI). Data from the National Programme for Onchocerciasis (NPO) provided by the National Onchocerciasis Task Force (NOTF) through the annual reports of the 21 CDTI projects for the years 2001-2012 were reviewed retrospectively. A hypothetical-inputs-process-outputs-outcomes table was constructed. Community-directed treatment with ivermectin expanded from 1968 communities in 2001 to 39 100 communities by 2012 while the number of community-directed distributors (CDD) and health workers (HW) multiplied. By 2012, there were ratios of 1 CDD per 262 persons and 1 HW per 2318 persons at risk. More than 80% of the funding came from the fiduciary funds of the African Programme for Onchocerciasis Control. The cost of treatment per person treated fell from US$ 1.1 in 2001 to US$ 0.1 in 2012. The therapeutic coverage increased from 2.7% (2001) to 74.2% (2012); the geographical coverage, from 4.7% (2001) to 93.9% (2012). Geographical coverage fell in 2005 due to deaths in loiasis co-endemic areas, and the therapeutic coverage fell in 2008 due to insecurity. Challenges to CDTI in DRC have been serious adverse reactions to ivermectin in loiasis co-endemic areas and political conflict. Targets for personnel or therapeutic and geographical coverages were not met. Longer term funding and renewed efforts are required to achieve control and elimination of onchocerciasis in DRC. © 2014 John Wiley & Sons Ltd.

The ID Database: Managing the Instructional Development Process

ERIC Educational Resources Information Center

Piña, Anthony A.; Sanford, Barry K.

2017-01-01

Management is evolving as a foundational domain to the field of instructional design and technology. However, there are few tools dedicated to the management of instructional design and development projects and activities. In this article, we describe the development, features and implementation of an instructional design database--built from a…

Browsing a Database of Multimedia Learning Material.

ERIC Educational Resources Information Center

Persico, Donatella; And Others

1992-01-01

Describes a project that addressed the problem of courseware reusability by developing a database structure suitable for organizing multimedia learning material in a given content domain. A prototype system that allows browsing a DBLM (Data Base of Learning Material) on earth science is described, and future plans are discussed. (five references)…

HOED: Hypermedia Online Educational Database.

ERIC Educational Resources Information Center

Duval, E.; Olivie, H.

This paper presents HOED, a distributed hypermedia client-server system for educational resources. The aim of HOED is to provide a library facility for hyperdocuments that is accessible via the world wide web. Its main application domain is education. The HOED database not only holds the educational resources themselves, but also data describing…

Saving the Information Commons.

ERIC Educational Resources Information Center

Bollier, David

2003-01-01

Discusses the control of digital content and the stakes for libraries and our democratic culture. Highlights include copyright term extension, the Digital Millennium Copyright Act, use of contract law to limit the public domain, database legislation, trademarks versus the public domain, the void in our cultural vocabulary, and the concept of the…

A novel approach: chemical relational databases, and the role of the ISSCAN database on assessing chemical carcinogenicity.

PubMed

Benigni, Romualdo; Bossa, Cecilia; Richard, Ann M; Yang, Chihae

2008-01-01

Mutagenicity and carcinogenicity databases are crucial resources for toxicologists and regulators involved in chemicals risk assessment. Until recently, existing public toxicity databases have been constructed primarily as "look-up-tables" of existing data, and most often did not contain chemical structures. Concepts and technologies originated from the structure-activity relationships science have provided powerful tools to create new types of databases, where the effective linkage of chemical toxicity with chemical structure can facilitate and greatly enhance data gathering and hypothesis generation, by permitting: a) exploration across both chemical and biological domains; and b) structure-searchability through the data. This paper reviews the main public databases, together with the progress in the field of chemical relational databases, and presents the ISSCAN database on experimental chemical carcinogens.

Computer-Aided Clinical Trial Recruitment Based on Domain-Specific Language Translation: A Case Study of Retinopathy of Prematurity

PubMed Central

2017-01-01

Reusing the data from healthcare information systems can effectively facilitate clinical trials (CTs). How to select candidate patients eligible for CT recruitment criteria is a central task. Related work either depends on DBA (database administrator) to convert the recruitment criteria to native SQL queries or involves the data mapping between a standard ontology/information model and individual data source schema. This paper proposes an alternative computer-aided CT recruitment paradigm, based on syntax translation between different DSLs (domain-specific languages). In this paradigm, the CT recruitment criteria are first formally represented as production rules. The referenced rule variables are all from the underlying database schema. Then the production rule is translated to an intermediate query-oriented DSL (e.g., LINQ). Finally, the intermediate DSL is directly mapped to native database queries (e.g., SQL) automated by ORM (object-relational mapping). PMID:29065644

Computer-Aided Clinical Trial Recruitment Based on Domain-Specific Language Translation: A Case Study of Retinopathy of Prematurity.

PubMed

Zhang, Yinsheng; Zhang, Guoming; Shang, Qian

2017-01-01

Reusing the data from healthcare information systems can effectively facilitate clinical trials (CTs). How to select candidate patients eligible for CT recruitment criteria is a central task. Related work either depends on DBA (database administrator) to convert the recruitment criteria to native SQL queries or involves the data mapping between a standard ontology/information model and individual data source schema. This paper proposes an alternative computer-aided CT recruitment paradigm, based on syntax translation between different DSLs (domain-specific languages). In this paradigm, the CT recruitment criteria are first formally represented as production rules. The referenced rule variables are all from the underlying database schema. Then the production rule is translated to an intermediate query-oriented DSL (e.g., LINQ). Finally, the intermediate DSL is directly mapped to native database queries (e.g., SQL) automated by ORM (object-relational mapping).

Identification of divergent protein domains by combining HMM-HMM comparisons and co-occurrence detection.

PubMed

Ghouila, Amel; Florent, Isabelle; Guerfali, Fatma Zahra; Terrapon, Nicolas; Laouini, Dhafer; Yahia, Sadok Ben; Gascuel, Olivier; Bréhélin, Laurent

2014-01-01

Identification of protein domains is a key step for understanding protein function. Hidden Markov Models (HMMs) have proved to be a powerful tool for this task. The Pfam database notably provides a large collection of HMMs which are widely used for the annotation of proteins in sequenced organisms. This is done via sequence/HMM comparisons. However, this approach may lack sensitivity when searching for domains in divergent species. Recently, methods for HMM/HMM comparisons have been proposed and proved to be more sensitive than sequence/HMM approaches in certain cases. However, these approaches are usually not used for protein domain discovery at a genome scale, and the benefit that could be expected from their utilization for this problem has not been investigated. Using proteins of P. falciparum and L. major as examples, we investigate the extent to which HMM/HMM comparisons can identify new domain occurrences not already identified by sequence/HMM approaches. We show that although HMM/HMM comparisons are much more sensitive than sequence/HMM comparisons, they are not sufficiently accurate to be used as a standalone complement of sequence/HMM approaches at the genome scale. Hence, we propose to use domain co-occurrence--the general domain tendency to preferentially appear along with some favorite domains in the proteins--to improve the accuracy of the approach. We show that the combination of HMM/HMM comparisons and co-occurrence domain detection boosts protein annotations. At an estimated False Discovery Rate of 5%, it revealed 901 and 1098 new domains in Plasmodium and Leishmania proteins, respectively. Manual inspection of part of these predictions shows that it contains several domain families that were missing in the two organisms. All new domain occurrences have been integrated in the EuPathDomains database, along with the GO annotations that can be deduced.

Identification of Divergent Protein Domains by Combining HMM-HMM Comparisons and Co-Occurrence Detection

PubMed Central

Ghouila, Amel; Florent, Isabelle; Guerfali, Fatma Zahra; Terrapon, Nicolas; Laouini, Dhafer; Yahia, Sadok Ben; Gascuel, Olivier; Bréhélin, Laurent

2014-01-01

Identification of protein domains is a key step for understanding protein function. Hidden Markov Models (HMMs) have proved to be a powerful tool for this task. The Pfam database notably provides a large collection of HMMs which are widely used for the annotation of proteins in sequenced organisms. This is done via sequence/HMM comparisons. However, this approach may lack sensitivity when searching for domains in divergent species. Recently, methods for HMM/HMM comparisons have been proposed and proved to be more sensitive than sequence/HMM approaches in certain cases. However, these approaches are usually not used for protein domain discovery at a genome scale, and the benefit that could be expected from their utilization for this problem has not been investigated. Using proteins of P. falciparum and L. major as examples, we investigate the extent to which HMM/HMM comparisons can identify new domain occurrences not already identified by sequence/HMM approaches. We show that although HMM/HMM comparisons are much more sensitive than sequence/HMM comparisons, they are not sufficiently accurate to be used as a standalone complement of sequence/HMM approaches at the genome scale. Hence, we propose to use domain co-occurrence — the general domain tendency to preferentially appear along with some favorite domains in the proteins — to improve the accuracy of the approach. We show that the combination of HMM/HMM comparisons and co-occurrence domain detection boosts protein annotations. At an estimated False Discovery Rate of 5%, it revealed 901 and 1098 new domains in Plasmodium and Leishmania proteins, respectively. Manual inspection of part of these predictions shows that it contains several domain families that were missing in the two organisms. All new domain occurrences have been integrated in the EuPathDomains database, along with the GO annotations that can be deduced. PMID:24901648

An intelligent user interface for browsing satellite data catalogs

NASA Technical Reports Server (NTRS)

Cromp, Robert F.; Crook, Sharon

1989-01-01

A large scale domain-independent spatial data management expert system that serves as a front-end to databases containing spatial data is described. This system is unique for two reasons. First, it uses spatial search techniques to generate a list of all the primary keys that fall within a user's spatial constraints prior to invoking the database management system, thus substantially decreasing the amount of time required to answer a user's query. Second, a domain-independent query expert system uses a domain-specific rule base to preprocess the user's English query, effectively mapping a broad class of queries into a smaller subset that can be handled by a commercial natural language processing system. The methods used by the spatial search module and the query expert system are explained, and the system architecture for the spatial data management expert system is described. The system is applied to data from the International Ultraviolet Explorer (IUE) satellite, and results are given.

Real-time high-resolution PC-based system for measurement of errors on compact disks

NASA Astrophysics Data System (ADS)

Tehranchi, Babak; Howe, Dennis G.

1994-10-01

Hardware and software utilities are developed to directly monitor the Eight-to-Fourteen (EFM) demodulated data bytes at the input of a CD player's Cross-Interleaved Reed-Solomon Code (CIRC) block decoder. The hardware is capable of identifying erroneous data with single-byte resolution in the serial data stream read from a Compact Disc by a CDD 461 Philips CD-ROM drive. In addition, the system produces graphical maps that show the physical location of the measured errors on the entire disc, or via a zooming and planning feature, on user selectable local disc regions.

Relative congener scaling of Polychlorinated dibenzo-p-dioxins and dibenzofurans to estimate building fire contributions in air, surface wipes, and dust samples.

PubMed

Pleil, Joachim D; Lorber, Matthew N

2007-11-01

The United States Environmental Protection Agency collected ambient air samples in lower Manhattan for about 9 months following the September 11, 2001 World Trade Center (WTC) attacks. Measurements were made of a host of airborne contaminants including volatile organic compounds, polycyclic aromatic hydrocarbons, asbestos, lead, and other contaminants of concern. The present study focuses on the broad class of polychlorinated dibenzo-p-dioxins (CDDs) and dibenzofurans (CDFs) with specific emphasis on the 17 CDD/CDF congeners that exhibit mammalian toxicity. This work is a statistical study comparing the internal patterns of CDD/CDFs using data from an unambiguous fire event (WTC) and other data sets to help identify their sources. A subset of 29 samples all taken between September 16 and October 31, 2001 were treated as a basis set known to be heavily impacted by the WTC building fire source. A second basis set was created using data from Los Angeles and Oakland, CA as published by the California Air Resources Board (CARB) and treated as the archetypical background pattern for CDD/CDFs. The CARB data had a congener profile appearing similar to background air samples from different locations in America and around the world and in different matrices, such as background soils. Such disparate data would normally be interpreted with a qualitative pattern recognition based on congener bar graphs or other forms of factor or cluster analysis that group similar samples together graphically. The procedure developed here employs aspects of those statistical methods to develop a single continuous output variable per sample. Specifically, a form of variance structure-based cluster analysis is used to group congeners within samples to reduce collinearity in the basis sets, new variables are created based on these groups, and multivariate regression is applied to the reduced variable set to determine a predictive equation. This equation predicts a value for an output variable, OPT: the predicted value of OPT is near zero (0.00) for a background congener profile and near one (1.00) forthe profile characterized by the WTC air profile. Although this empirical method is calibrated with relatively small sets of airborne samples, it is shown to be generalizable to other WTC, fire source, and background air samples as well as other sample matrices including soils, window films and other dust wipes, and bulk dusts. However, given the limited data set examined, the method does not allow further discrimination between the WTC data and the other fire sources. This type of analysis is demonstrated to be useful for complex trace-level data sets with limited data and some below-detection entries.

Managing Heterogeneous Information Systems through Discovery and Retrieval of Generic Concepts.

ERIC Educational Resources Information Center

Srinivasan, Uma; Ngu, Anne H. H.; Gedeon, Tom

2000-01-01

Introduces a conceptual integration approach to heterogeneous databases or information systems that exploits the similarity in metalevel information and performs metadata mining on database objects to discover a set of concepts that serve as a domain abstraction and provide a conceptual layer above existing legacy systems. Presents results of…

LISLEX: Legal Issues of Concern to the Library and Information Sector.

ERIC Educational Resources Information Center

Oppenheim, Charles

1998-01-01

Examines paparazzi and copyright law, regulation of the Internet, the European Union Database Directive and U.S. efforts to change database laws, Tasini v. The New York Times, freedom of information and access to public sector information, company law and e-mail messages, electronic commerce, cryptography export controls, domain names and trade…

Flight testing and frequency domain analysis for rotorcraft handling qualities characteristics

NASA Technical Reports Server (NTRS)

Ham, Johnnie A.; Gardner, Charles K.; Tischler, Mark B.

1993-01-01

A demonstration of frequency domain flight testing techniques and analyses was performed on a U.S. Army OH-58D helicopter in support of the OH-58D Airworthiness and Flight Characteristics Evaluation and the Army's development and ongoing review of Aeronautical Design Standard 33C, Handling Qualities Requirements for Military Rotorcraft. Hover and forward flight (60 knots) tests were conducted in 1 flight hour by Army experimental test pilots. Further processing of the hover data generated a complete database of velocity, angular rate, and acceleration frequency responses to control inputs. A joint effort was then undertaken by the Airworthiness Qualification Test Directorate (AQTD) and the U.S. Army Aeroflightdynamics Directorate (AFDD) to derive handling qualities information from the frequency response database. A significant amount of information could be extracted from the frequency domain database using a variety of approaches. This report documents numerous results that have been obtained from the simple frequency domain tests; in many areas, these results provide more insight into the aircraft dynamics that affect handling qualities than to traditional flight tests. The handling qualities results include ADS-33C bandwidth and phase delay calculations, vibration spectral determinations, transfer function models to examine single axis results, and a six degree of freedom fully coupled state space model. The ability of this model to accurately predict aircraft responses was verified using data from pulse inputs. This report also documents the frequency-sweep flight test technique and data analysis used to support the tests.

A Recommender System in the Cyber Defense Domain

DTIC Science & Technology

2014-03-27

monitoring software is a java based program sending updates to the database on the sensor machine. The host monitoring program gathers information about...3.2.2 Database. A MySQL database located on the sensor machine acts as the storage for the sensors on the network. Snort, Nmap, vulnerability scores, and...machine with the IDS and the recommender is labeled “sensor”. The recommender system code is written in java and compiled using java version 1.6.024

Pulling on the Long Tail with Flyover Country, a Mobile App to Expose, Visualize, Discover, and Explore Open Geoscience Data

NASA Astrophysics Data System (ADS)

Myrbo, A.; Loeffler, S.; Ai, S.; McEwan, R.

2015-12-01

The ultimate EarthCube product has been described as a mobile app that provides all of the known geoscience data for a geographic point or polygon, from the top of the atmosphere to the core of the Earth, throughout geologic time. The database queries are hidden from the user, and the data are visually rendered for easy recognition of patterns and associations. This fanciful vision is not so remote: NSF EarthCube and Geoinformatics support has already fostered major advances in database interoperability and harmonization of APIs; numerous "domain repositories," databases curated by subject matter experts, now provide a vast wealth of open, easily-accessible georeferenced data on rock and sediment chemistry and mineralogy, paleobiology, stratigraphy, rock magnetics, and more. New datasets accrue daily, including many harvested from the literature by automated means. None of these constitute big data - all are part of the long tail of geoscience, heterogeneous data consisting of relatively small numbers of measurements made by a large number of people, typically on physical samples. This vision of mobile data discovery requires a software package to cleverly expose these domain repositories' holdings; currently, queries mainly come from single investigators to single databases. The NSF-funded mobile app Flyover Country (FC; fc.umn.edu), developed for geoscience outreach and education, has been welcomed by data curators and cyberinfrastructure developers as a testing ground for their API services, data provision, and scalability. FC pulls maps and data within a bounding envelope and caches them for offline use; location-based services alert users to nearby points of interest (POI). The incorporation of data from multiple databases across domains requires parsimonious data requests and novel visualization techniques, especially for mapping of data with a time or stratigraphic depth component. The preservation of data provenance and authority is critical for researcher buy-in to all community databases, and further allows exploration and suggestions of collaborators, based upon geography and topical relevance.

Application of new type of distributed multimedia databases to networked electronic museum

NASA Astrophysics Data System (ADS)

Kuroda, Kazuhide; Komatsu, Naohisa; Komiya, Kazumi; Ikeda, Hiroaki

1999-01-01

Recently, various kinds of multimedia application systems have actively been developed based on the achievement of advanced high sped communication networks, computer processing technologies, and digital contents-handling technologies. Under this background, this paper proposed a new distributed multimedia database system which can effectively perform a new function of cooperative retrieval among distributed databases. The proposed system introduces a new concept of 'Retrieval manager' which functions as an intelligent controller so that the user can recognize a set of distributed databases as one logical database. The logical database dynamically generates and performs a preferred combination of retrieving parameters on the basis of both directory data and the system environment. Moreover, a concept of 'domain' is defined in the system as a managing unit of retrieval. The retrieval can effectively be performed by cooperation of processing among multiple domains. Communication language and protocols are also defined in the system. These are used in every action for communications in the system. A language interpreter in each machine translates a communication language into an internal language used in each machine. Using the language interpreter, internal processing, such internal modules as DBMS and user interface modules can freely be selected. A concept of 'content-set' is also introduced. A content-set is defined as a package of contents. Contents in the content-set are related to each other. The system handles a content-set as one object. The user terminal can effectively control the displaying of retrieved contents, referring to data indicating the relation of the contents in the content- set. In order to verify the function of the proposed system, a networked electronic museum was experimentally built. The results of this experiment indicate that the proposed system can effectively retrieve the objective contents under the control to a number of distributed domains. The result also indicate that the system can effectively work even if the system becomes large.

Cazymes Analysis Toolkit (CAT): Webservice for searching and analyzing carbohydrateactive enzymes in a newly sequenced organism using CAZy database

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

Karpinets, Tatiana V; Park, Byung; Syed, Mustafa H

2010-01-01

The Carbohydrate-Active Enzyme (CAZy) database provides a rich set of manually annotated enzymes that degrade, modify, or create glycosidic bonds. Despite rich and invaluable information stored in the database, software tools utilizing this information for annotation of newly sequenced genomes by CAZy families are limited. We have employed two annotation approaches to fill the gap between manually curated high-quality protein sequences collected in the CAZy database and the growing number of other protein sequences produced by genome or metagenome sequencing projects. The first approach is based on a similarity search against the entire non-redundant sequences of the CAZy database. Themore » second approach performs annotation using links or correspondences between the CAZy families and protein family domains. The links were discovered using the association rule learning algorithm applied to sequences from the CAZy database. The approaches complement each other and in combination achieved high specificity and sensitivity when cross-evaluated with the manually curated genomes of Clostridium thermocellum ATCC 27405 and Saccharophagus degradans 2-40. The capability of the proposed framework to predict the function of unknown protein domains (DUF) and of hypothetical proteins in the genome of Neurospora crassa is demonstrated. The framework is implemented as a Web service, the CAZymes Analysis Toolkit (CAT), and is available at http://cricket.ornl.gov/cgi-bin/cat.cgi.« less

SInCRe—structural interactome computational resource for Mycobacterium tuberculosis

PubMed Central

Metri, Rahul; Hariharaputran, Sridhar; Ramakrishnan, Gayatri; Anand, Praveen; Raghavender, Upadhyayula S.; Ochoa-Montaño, Bernardo; Higueruelo, Alicia P.; Sowdhamini, Ramanathan; Chandra, Nagasuma R.; Blundell, Tom L.; Srinivasan, Narayanaswamy

2015-01-01

We have developed an integrated database for Mycobacterium tuberculosis H37Rv (Mtb) that collates information on protein sequences, domain assignments, functional annotation and 3D structural information along with protein–protein and protein–small molecule interactions. SInCRe (Structural Interactome Computational Resource) is developed out of CamBan (Cambridge and Bangalore) collaboration. The motivation for development of this database is to provide an integrated platform to allow easily access and interpretation of data and results obtained by all the groups in CamBan in the field of Mtb informatics. In-house algorithms and databases developed independently by various academic groups in CamBan are used to generate Mtb-specific datasets and are integrated in this database to provide a structural dimension to studies on tuberculosis. The SInCRe database readily provides information on identification of functional domains, genome-scale modelling of structures of Mtb proteins and characterization of the small-molecule binding sites within Mtb. The resource also provides structure-based function annotation, information on small-molecule binders including FDA (Food and Drug Administration)-approved drugs, protein–protein interactions (PPIs) and natural compounds that bind to pathogen proteins potentially and result in weakening or elimination of host–pathogen protein–protein interactions. Together they provide prerequisites for identification of off-target binding. Database URL: http://proline.biochem.iisc.ernet.in/sincre PMID:26130660

CAZymes Analysis Toolkit (CAT): web service for searching and analyzing carbohydrate-active enzymes in a newly sequenced organism using CAZy database.

PubMed

Park, Byung H; Karpinets, Tatiana V; Syed, Mustafa H; Leuze, Michael R; Uberbacher, Edward C

2010-12-01

The Carbohydrate-Active Enzyme (CAZy) database provides a rich set of manually annotated enzymes that degrade, modify, or create glycosidic bonds. Despite rich and invaluable information stored in the database, software tools utilizing this information for annotation of newly sequenced genomes by CAZy families are limited. We have employed two annotation approaches to fill the gap between manually curated high-quality protein sequences collected in the CAZy database and the growing number of other protein sequences produced by genome or metagenome sequencing projects. The first approach is based on a similarity search against the entire nonredundant sequences of the CAZy database. The second approach performs annotation using links or correspondences between the CAZy families and protein family domains. The links were discovered using the association rule learning algorithm applied to sequences from the CAZy database. The approaches complement each other and in combination achieved high specificity and sensitivity when cross-evaluated with the manually curated genomes of Clostridium thermocellum ATCC 27405 and Saccharophagus degradans 2-40. The capability of the proposed framework to predict the function of unknown protein domains and of hypothetical proteins in the genome of Neurospora crassa is demonstrated. The framework is implemented as a Web service, the CAZymes Analysis Toolkit, and is available at http://cricket.ornl.gov/cgi-bin/cat.cgi.

ASGARD: an open-access database of annotated transcriptomes for emerging model arthropod species.

PubMed

Zeng, Victor; Extavour, Cassandra G

2012-01-01

The increased throughput and decreased cost of next-generation sequencing (NGS) have shifted the bottleneck genomic research from sequencing to annotation, analysis and accessibility. This is particularly challenging for research communities working on organisms that lack the basic infrastructure of a sequenced genome, or an efficient way to utilize whatever sequence data may be available. Here we present a new database, the Assembled Searchable Giant Arthropod Read Database (ASGARD). This database is a repository and search engine for transcriptomic data from arthropods that are of high interest to multiple research communities but currently lack sequenced genomes. We demonstrate the functionality and utility of ASGARD using de novo assembled transcriptomes from the milkweed bug Oncopeltus fasciatus, the cricket Gryllus bimaculatus and the amphipod crustacean Parhyale hawaiensis. We have annotated these transcriptomes to assign putative orthology, coding region determination, protein domain identification and Gene Ontology (GO) term annotation to all possible assembly products. ASGARD allows users to search all assemblies by orthology annotation, GO term annotation or Basic Local Alignment Search Tool. User-friendly features of ASGARD include search term auto-completion suggestions based on database content, the ability to download assembly product sequences in FASTA format, direct links to NCBI data for predicted orthologs and graphical representation of the location of protein domains and matches to similar sequences from the NCBI non-redundant database. ASGARD will be a useful repository for transcriptome data from future NGS studies on these and other emerging model arthropods, regardless of sequencing platform, assembly or annotation status. This database thus provides easy, one-stop access to multi-species annotated transcriptome information. We anticipate that this database will be useful for members of multiple research communities, including developmental biology, physiology, evolutionary biology, ecology, comparative genomics and phylogenomics. Database URL: asgard.rc.fas.harvard.edu.

Identification and correction of abnormal, incomplete and mispredicted proteins in public databases.

PubMed

Nagy, Alinda; Hegyi, Hédi; Farkas, Krisztina; Tordai, Hedvig; Kozma, Evelin; Bányai, László; Patthy, László

2008-08-27

Despite significant improvements in computational annotation of genomes, sequences of abnormal, incomplete or incorrectly predicted genes and proteins remain abundant in public databases. Since the majority of incomplete, abnormal or mispredicted entries are not annotated as such, these errors seriously affect the reliability of these databases. Here we describe the MisPred approach that may provide an efficient means for the quality control of databases. The current version of the MisPred approach uses five distinct routines for identifying abnormal, incomplete or mispredicted entries based on the principle that a sequence is likely to be incorrect if some of its features conflict with our current knowledge about protein-coding genes and proteins: (i) conflict between the predicted subcellular localization of proteins and the absence of the corresponding sequence signals; (ii) presence of extracellular and cytoplasmic domains and the absence of transmembrane segments; (iii) co-occurrence of extracellular and nuclear domains; (iv) violation of domain integrity; (v) chimeras encoded by two or more genes located on different chromosomes. Analyses of predicted EnsEMBL protein sequences of nine deuterostome (Homo sapiens, Mus musculus, Rattus norvegicus, Monodelphis domestica, Gallus gallus, Xenopus tropicalis, Fugu rubripes, Danio rerio and Ciona intestinalis) and two protostome species (Caenorhabditis elegans and Drosophila melanogaster) have revealed that the absence of expected signal peptides and violation of domain integrity account for the majority of mispredictions. Analyses of sequences predicted by NCBI's GNOMON annotation pipeline show that the rates of mispredictions are comparable to those of EnsEMBL. Interestingly, even the manually curated UniProtKB/Swiss-Prot dataset is contaminated with mispredicted or abnormal proteins, although to a much lesser extent than UniProtKB/TrEMBL or the EnsEMBL or GNOMON-predicted entries. MisPred works efficiently in identifying errors in predictions generated by the most reliable gene prediction tools such as the EnsEMBL and NCBI's GNOMON pipelines and also guides the correction of errors. We suggest that application of the MisPred approach will significantly improve the quality of gene predictions and the associated databases.

An approach in building a chemical compound search engine in oracle database.

PubMed

Wang, H; Volarath, P; Harrison, R

2005-01-01

A searching or identifying of chemical compounds is an important process in drug design and in chemistry research. An efficient search engine involves a close coupling of the search algorithm and database implementation. The database must process chemical structures, which demands the approaches to represent, store, and retrieve structures in a database system. In this paper, a general database framework for working as a chemical compound search engine in Oracle database is described. The framework is devoted to eliminate data type constrains for potential search algorithms, which is a crucial step toward building a domain specific query language on top of SQL. A search engine implementation based on the database framework is also demonstrated. The convenience of the implementation emphasizes the efficiency and simplicity of the framework.

AGM: A DSL for mobile cloud computing based on directed graph

NASA Astrophysics Data System (ADS)

Tanković, Nikola; Grbac, Tihana Galinac

2016-06-01

This paper summarizes a novel approach for consuming a domain specific language (DSL) by transforming it to a directed graph representation persisted by a graph database. Using such specialized database enables advanced navigation trough the stored model exposing only relevant subsets of meta-data to different involved services and components. We applied this approach in a mobile cloud computing system and used it to model several mobile applications in retail, supply chain management and merchandising domain. These application are distributed in a Software-as-a-Service (SaaS) fashion and used by thousands of customers in Croatia. We report on lessons learned and propose further research on this topic.

Documentation for the U.S. Geological Survey Public-Supply Database (PSDB): A database of permitted public-supply wells, surface-water intakes, and systems in the United States

USGS Publications Warehouse

Price, Curtis V.; Maupin, Molly A.

2014-01-01

The purpose of this report is to document the PSDB and explain the methods used to populate and update the data from the SDWIS, State datasets, and map and geospatial imagery. This report describes 3 data tables and 11 domain tables, including field contents, data sources, and relations between tables. Although the PSDB database is not available to the general public, this information should be useful for others who are developing other database systems to store and analyze public-supply system and facility data.

Multidomain, multirecord-type Datatrieve-11 databases

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

Horning, R.R.

1983-01-01

Data bases consisting of multiple domains and multirecord-type domains present special problems in design, loading, maintenance, and report generation. The logical association of records is a fundamental concern in all these problem areas. This paper describes techniques for dealing with this and other specifics using Datatrieve-11, Sort-11, FORTRAN 77, and the RSX-11M Indirect Command File Processor.

Precipitation Extremes in Dynamically Downscaled Climate Scenarios over the Greater Horn of Africa

NASA Astrophysics Data System (ADS)

Shiferaw, A. S.; Tadesse, T.; Oglesby, R. J.; Rowe, C. M.

2017-12-01

The precipitation extremes were generated over the Greater Horn of Africa (GHA) using the Regional Climate Models (RCMs) simulations from the Coordinated Regional Downscaling Experiment (CORDEX). To assess how well the RCM simulations are capturing the historical observed precipitation extremes, they were compared with the precipitation extremes derived from Climate Hazards Group InfraRed Precipitation with Station data (CHIRPS v2). The result shows that RCM simulations have reasonably captured observed patterns of the precipitation extremes (i.e., the pattern correlation is greater than 0.5). However, significant overestimations or underestimations were observed over some localized areas in the region. The study then assessed the projected changes in these precipitation extremes during 2069-2098 and compared to the 1976-2005 period that were both derived from the RCM simulations. Projected changes in total annual precipitation (PRCPTOT), annual number of heavy (>10mm) and very heavy (>20mm) precipitation days by 2069-2098 show a general north-south pattern with a decrease over southern-half and increase over the northern-half of GHA. These changes are often greatest over parts of Somalia, Eritrea, Ethiopian highlands and southern Tanzania. Maximum 1 and 5-day total precipitation in a year and "Simple Daily Precipitation Intensity Index" (ratio of PRCPTOT to rainy days) are projected to increase over majority of GHA, including areas where PRCPTOT is projected to decrease, suggesting fewer but heavier rainy days in the future. Changes in annual sum of daily precipitation above 95th and 99th percentile are not statistically significant except Eritrea and northwestern Sudan/Somalia. Projected changes in consecutive dry days (CDD) suggest longer periods of dryness over majority of GHA. Among these areas, a substantial increases in CDD are located over southern Tanzania and Ethiopian highlands.

Searching for evidence of changes in extreme rainfall indices in the Central Rift Valley of Ethiopia

NASA Astrophysics Data System (ADS)

Muluneh, Alemayehu; Bewket, Woldeamlak; Keesstra, Saskia; Stroosnijder, Leo

2017-05-01

Extreme rainfall events have serious implications for economic sectors with a close link to climate such as agriculture and food security. This holds true in the Central Rift Valley (CRV) of Ethiopia where communities rely on highly climate-sensitive rainfed subsistence farming for livelihoods. This study investigates changes in ten extreme rainfall indices over a period of 40 years (1970-2009) using 14 meteorological stations located in the CRV. The CRV consists of three landscape units: the valley floor, the escarpments, and the highlands all of which are considered in our data analysis. The Belg (March-May) and Kiremt (June-September) seasons are also considered in the analysis. The Mann-Kendall test was used to detect trends of the rainfall indices. The results indicated that at the annual time scale, more than half (57 %) of the stations showed significant trends in total wet-day precipitation (PRCPTOT) and heavy precipitation days (R10mm). Only 7-35 % of stations showed significant trends, for the other rainfall indices. Spatially, the valley floor received increasing annual rainfall while the escarpments and the highlands received decreasing annual rainfall over the last 40 years. During Belg, 50 % of the stations showed significant increases in the maximum number of consecutive dry days (CDD) in all parts of the CRV. However, most other rainfall indices during Belg showed no significant changes. During Kiremt, considering both significant and non-significant trends, almost all rainfall indices showed an increasing trend in the valley floor and a decreasing trend in the escarpment and highlands. During Belg and Kiremt, the CDD generally showed increasing tendency in the CRV.

CSF N-glycan profile reveals sialylation deficiency in a patient with GM2 gangliosidosis presenting as childhood disintegrative disorder.

PubMed

Barone, Rita; Sturiale, Luisella; Fiumara, Agata; Palmigiano, Angelo; Bua, Rosaria O; Rizzo, Renata; Zappia, Mario; Garozzo, Domenico

2016-04-01

Protein N-glycosylation consists in the synthesis and processing of the oligosaccharide moiety (N-glycan) linked to a protein and it serves several functions for the proper central nervous system (CNS) development and function. Previous experimental and clinical studies have shown the importance of proper glycoprotein sialylation for the synaptic function and the occurrence of autism spectrum disorders (ASD) in the presence of sialylation deficiency in the CNS. Late-onset Tay Sachs disease (LOTSD) is a lysosomal disorder caused by mutations in the HEXA gene resulting in GM2-ganglioside storage in the CNS. It is characterized by progressive neurological impairment and high co-occurrence of psychiatric disturbances. We studied the N-glycome profile of the cerebrospinal fluid (CSF) in a 14 year-old patient with GM2-gangliosidosis (LOTSD). At the age of 4, the patient presented regressive autism fulfilling criteria for childhood disintegrative disorder (CDD). A CSF sample was obtained in the course of diagnostic work-up for the suspicion of an underlying neurodegenerative disorder. We found definite changes of CSF N-glycans due to a dramatic decrease of sialylated biantennary and triantennary structures and an increase of asialo-core fucosylated bisected N-glycans. No changes of total plasma N-glycans were found. Herein findings highlight possible relationships between the early onset psychiatric disturbance featuring CDD in the patient and defective protein sialylation in the CNS. In conclusion, the study first shows aberrant N-glycan structures of CSF proteins in LOTSD; unveils possible pathomechanisms of GM2-gangliosidosis; supports existing relationships between neuropsychiatric disorders and unproper protein glycosylation in the CNS. © 2015 International Society for Autism Research, Wiley Periodicals, Inc.

Cortisol awakening response is decreased in patients with first-episode psychosis and increased in healthy controls with a history of severe childhood abuse.

PubMed

Ciufolini, Simone; Gayer-Anderson, Charlotte; Fisher, Helen L; Marques, Tiago Reis; Taylor, Heather; Di Forti, Marta; Zunszain, Patricia; Morgan, Craig; Murray, Robin M; Pariante, Carmine M; Dazzan, Paola; Mondelli, Valeria

2018-05-15

Childhood abuse is highly prevalent in psychosis patients, but whether/how it affects hypothalamic-pituitary-adrenal (HPA) axis at the onset of psychosis remains unclear. We aimed to investigate the effects of severity of childhood abuse on HPA axis activity, in first-episode psychosis (FEP) and healthy controls. We recruited 169 FEP patients and 133 controls with different degrees of childhood physical and sexual abuse (i.e. no abuse exposure, non-severe abuse exposure, and severe abuse exposure). Saliva samples were collected to measure cortisol awakening response with respect to ground (CARg), increase (CARi) and diurnal (CDD) cortisol levels. Two-way ANOVA analyses were conducted to test the relationships between severity of childhood abuse and psychosis on cortisol levels in individuals with psychosis and healthy controls with and without childhood abuse history. A statistically significant interaction between childhood abuse and psychosis on CARg was found (F (2,262)  = 4.60, p = 0.011, ω 2  = 0.42). Overall, controls showed a U-shaped relationship between abuse exposure and CARg, while patients showed an inverted U-shaped relationship. CARg values were markedly different between patients and controls with either no abuse history or exposure to severe childhood abuse. No significant differences were found when looking at CARi and CDD. Our results show a divergent effect of severe childhood abuse on HPA axis activity in patients with first-episode psychosis and in controls. In the presence of exposure to severe childhood abuse, a blunted CARg and a less reactive HPA axis may represent one of the biological mechanisms involved in the development of psychosis. Copyright © 2018. Published by Elsevier B.V.

A rapid and reagent-free bioassay for the detection of dioxin-like compounds and other aryl hydrocarbon receptor (AhR) agonists using autobioluminescent yeast.

PubMed

Xu, Tingting; Young, Anna; Marr, Enolia; Sayler, Gary; Ripp, Steven; Close, Dan

2018-02-01

An autonomously bioluminescent Saccharomyces cerevisiae BLYAhS bioreporter was developed in this study for the simple and rapid detection of dioxin-like compounds (DLCs) and aryl hydrocarbon receptor (AhR) agonists. This recombinant yeast reporter was based on a synthetic bacterial luciferase reporter gene cassette (lux) that can produce the luciferase as well as the enzymes capable of self-synthesizing the requisite substrates for bioluminescent production from endogenous cellular metabolites. As a result, bioluminescent signal production is generated continuously and autonomously without cell lysis or exogenous reagent addition. By linking the expression of the autobioluminescent lux reporter cassette to AhR activation via the use of a dioxin-responsive promoter, the S. cerevisiae BLYAhS bioreporter emitted a bioluminescent signal in response to DLC exposure in a dose-responsive manner. The model dioxin, 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), could be detected within 4 h with a half maximal effective concentration (EC 50 ) of ~ 8.1 nM and a lower detection limit of 500 pM. The autobioluminescent response of BLYAhS to other AhR agonists, including 2,3,7,8-tetrachlorodibenzofuran (TCDF), polychlorinated bisphenyl congener 126 (PCB-126) and 169 (PCB-169), 1,2,3,6,7,8-hexachlorodibenzo-p-dioxin (HxCDD), 1,2,3,4,6,7,8-heptachlorodibenzo-p-dioxin (HpCDD), benzo[a]pyrene (BaP), and β-naphthoflavone (bNF), were also characterized in this study. The non-destructive and reagent-free nature of the BLYAhS reporter assay facilitated near-continuous, automated signal acquisition without additional hands-on effort and cost, providing a simple and cost-effective method for rapid DLC detection.

Polychlorinated dibenzo-p-dioxins, polychlorinated dibenzofurans and dioxin-like coplanar polychlorinated biphenyls in mackerel obtained from the Japanese market, 1999-2003.

PubMed

Nakatani, Tadashi; Yamano, Testuo

2017-09-01

This study analysed the concentrations and toxic-equivalent (TEQ) levels of dioxin congeners in mackerel commercially available in Japan in early 2000s. The content of polychlorinated dibenzo-p-dioxins (PCDDs), polychlorinated dibenzofurans (PCDFs) and dioxin-like coplanar polychlorinated biphenyls (DL-PCBs) was determined in 17 mackerel samples from different areas. TEQ levels in mackerel muscle were 0.78 pg TEQ g - 1 wet weight (wt) on average (range = 0.21-2.26 pg TEQ g - 1 wet wt) for PCDD/Fs (PCDDs plus PCDFs), 2.81 pg TEQ g - 1 wet wt on average (range = 1.02-8.5 pg TEQ g - 1 wet wt) for DL-PCBs, and 3.59 pg TEQ g - 1 wet wt on average (range = 1.24-10.8 pg g - 1 wet wt) for dioxins (PCDD/Fs plus DL-PCBs). The results revealed somewhat higher TEQ levels for dioxins compared with the other data for fish and shellfish in the Japanese market. TEQ levels were well correlated with mackerel body weight; the main contributors were tetra- and penta-CDD/Fs, some hexa-CDD/Fs, and all 12 DL-PCBs, which are known to have high bioaccumulation potential. In particular, PCB 126 was mostly responsible for the observed correlation of DL-PCB and dioxins-TEQ levels with mackerel body weight. The average daily intake of dioxins in terms of TEQ through mackerel consumption was estimated to be 4.81 pg TEQ/person/day, accounting for 7% of the total intake of dioxins-TEQ through fish and shellfish in Japan.

Projected Changes in Temperature and Precipitation Extremes over China as Measured by 50-yr Return Values and Periods Based on a CMIP5 Ensemble

NASA Astrophysics Data System (ADS)

Xu, Ying; Gao, Xuejie; Giorgi, Filippo; Zhou, Botao; Shi, Ying; Wu, Jie; Zhang, Yongxiang

2018-04-01

Future changes in the 50-yr return level for temperature and precipitation extremes over mainland China are investigated based on a CMIP5 multi-model ensemble for RCP2.6, RCP4.5 and RCP8.5 scenarios. The following indices are analyzed: TXx and TNn (the annual maximum and minimum of daily maximum and minimum surface temperature), RX5day (the annual maximum consecutive 5-day precipitation) and CDD (maximum annual number of consecutive dry days). After first validating the model performance, future changes in the 50-yr return values and return periods for these indices are investigated along with the inter-model spread. Multi-model median changes show an increase in the 50-yr return values of TXx and a decrease for TNn, more specifically, by the end of the 21st century under RCP8.5, the present day 50-yr return period of warm events is reduced to 1.2 yr, while extreme cold events over the country are projected to essentially disappear. A general increase in RX5day 50-yr return values is found in the future. By the end of the 21st century under RCP8.5, events of the present RX5day 50-yr return period are projected to reduce to < 10 yr over most of China. Changes in CDD-50 show a dipole pattern over China, with a decrease in the values and longer return periods in the north, and vice versa in the south. Our study also highlights the need for further improvements in the representation of extreme events in climate models to assess the future risks and engineering design related to large-scale infrastructure in China.

Schistosomiasis and soil-transmitted helminth control in Niger: cost effectiveness of school based and community distributed mass drug administration [corrected].

PubMed

Leslie, Jacqueline; Garba, Amadou; Oliva, Elisa Bosque; Barkire, Arouna; Tinni, Amadou Aboubacar; Djibo, Ali; Mounkaila, Idrissa; Fenwick, Alan

2011-10-01

In 2004 Niger established a large scale schistosomiasis and soil-transmitted helminths control programme targeting children aged 5-14 years and adults. In two years 4.3 million treatments were delivered in 40 districts using school based and community distribution. Four districts were surveyed in 2006 to estimate the economic cost per district, per treatment and per schistosomiasis infection averted. The study compares the costs of treatment at start up and in a subsequent year, identifies the allocation of costs by activity, input and organisation, and assesses the cost of treatment. The cost of delivery provided by teachers is compared to cost of delivery by community distributers (CDD). The total economic cost of the programme including programmatic, national and local government costs and international support in four study districts, over two years, was US$ 456,718; an economic cost/treatment of $0.58. The full economic delivery cost of school based treatment in 2005/06 was $0.76, and for community distribution was $0.46. Including only the programme costs the figures are $0.47 and $0.41 respectively. Differences at sub-district are more marked. This is partly explained by the fact that a CDD treats 5.8 people for every one treated in school. The range in cost effectiveness for both direct and direct and indirect treatments is quantified and the need to develop and refine such estimates is emphasised. The relative cost effectiveness of school and community delivery differs by country according to the composition of the population treated, the numbers targeted and treated at school and in the community, the cost and frequency of training teachers and CDDs. Options analysis of technical and implementation alternatives including a financial analysis should form part of the programme design process.

Polychlorinated dioxins and furans from the World Trade Center attacks in exterior window films from lower Manhattan in New York City.

PubMed

Rayne, Sierra; Ikonomou, Michael G; Butt, Craig M; Diamond, Miriam L; Truong, Jennifer

2005-04-01

Samples of ambient organic films deposited on exterior window surfaces from lower Manhattan and Brooklyn in New York City were collected six weeks after the terrorist attacks at the World Trade Center (WTC) on September 11, 2001 and analyzed for polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs). Total tetra- through octa-CDD/F concentrations in window films within 1 km of the WTC site in lower Manhattan ranged up to 630,000 pg/m2 (estimated as a mass concentration of ca. 1,300,000 pg/ g) and a maximum toxic equivalent (TEQ) concentration of 4700 TEQ/m2 (ca. 10 000 pg TEQ/g). Measurements at a background site 3.5 km away in Brooklyn showed lower concentrations at 130 pg TEQ/m2 (260 pg TEQ/g). Ambient gas-phase PCDD/F concentrations estimated for each site using an equilibrium partitioning model suggested concentrations ranging from ca. 2700 fg-TEQ/m3 near the WTC site to the more typical urban concentration of 20 fg-TEQ/m3 atthe Brooklyn site. Multivariate analyses of 2,3,7,8-substitued congeners and homologue group profiles suggested unique patterns in films near the WTC site compared to that observed at background sites in the study area and in other literature-derived combustion source profiles. Homologue profiles near the WTC site were dominated by tetra-, penta-, and Hexa-CDD/Fs, and 2,3,7,8-substituted profiles contained mostly octa- and hexachlorinated congeners. In comparison, profiles in Brooklyn and near mid-Manhattan exhibited congener and homologue patterns comprised mainly of hepta- and octa-CDDs, similar to that commonly reported in background air and soil.

Influence of variation in the operating conditions on PCDD/F distribution in a full-scale MSW incinerator.

PubMed

Zhang, Hai-Jun; Ni, Yu-Wen; Chen, Ji-Ping; Zhang, Qing

2008-01-01

Optimizing the operating parameters to minimize polychlorodibenzo-p-dioxins and polychlorodibenzofurans (PCDD/F) emission is the common interest of the municipal solid waste (MSW) incineration industry. In this study, we investigated the distribution of tetra- to octa-CDD/F along the flue gas line in a full-scale reciprocating grate incinerator and evaluated the effects of temperature control and O(2) level on PCDD/F formation. Six runs were laid out and all performed under sufficient burning conditions, in which the combustion efficiency of MSW was more than 99.9%. The total concentration of tetra- to octa-CDD/F measured at the boiler outlet showed an increasing tendency with the increase of boiler outlet temperature (T(B)) from 214 degrees C to 264 degrees C. When flue gas ran across the semi-dry scrubber and cyclone precipitator, in which the temperature varied from 264 degrees C to 162 degrees C, the concentrations of the lower chlorinated dioxins and furans were significantly raised, especially for the TCDF. Increasing O(2) supply from 6.0% to 10.5% essentially led to a higher yield of tetra- to octa-PCDD/F, suggested that under sufficient burning conditions the lower O(2) level was favorable for reducing PCDD/F formation and emission. The variation of O(2) level did not give rise to a systematical change of PCDD/F homologue pattern. For all measurements, the isomer distributions of tetra- to hepta-PCDD/F were more or less the same, nearly independent of variations in the operating conditions and sampling positions. Only the significant increase of the sum of 1,3,7,8-TCDF and 1,3,7,9-TCDF was found in the zone after the boiler section.

Knowledge, attitude and practice of community drug distributors' about onchocerciasis and community directed treatment with ivermectin in Quara district, North Western Ethiopia.

PubMed

Weldegebreal, Fitsum; Medhin, Girmay; Weldegebriel, Zemichael; Legesse, Mengistu

2016-04-06

Onchocerciasis is one of the most important public health problems over large areas of tropical Africa countries including Ethiopia. The African Program for Onchocerciasis Control (APOC) has been working with ultimate goal of reducing the public health and socio-economic problems of onchocerciasis through administration of the tablet for continuous 12-15 years using the strategy of yearly community-directed treatment with ivermectin (CDTI) in endemic areas of Africa to kill the microfilariae that invade the eyes and are present in the skin to be transported to another victim by the black fly. The objective of this study was to assess knowledge, attitude and practice of community drug distributors (CDDs) towards onchocerciasis and CDTI in Quara district. Of all the study participating CDD 11.4% (9/79) said that they knew about the etiology of the disease, 35.4% (28/79) had good level of knowledge, 19 (24.1%) had good level of positive attitude and 18 (22.8%) had good level of positive practice about onchocerciasis. Similarly, 45.6% (36/79), 81.0% (64/79) and 29.1% (23/79) had good level of knowledge, attitude and practice about CDTIP, respectively. Being a female CDD (adjusted OR 7.246, P = 0.035, 95% CI 1.147, 45.455) and being older than 35 years (adjusted OR 8.435, P = 0.001, 95% CI 4.53, 9.003) were significantly associated with the likelihood of having good level of knowledge about the disease. Although onchocerciasis is endemic in Quara district, large proportion of the CDDs had misconceptions about its causation, transmission and prevention. Therefore, CDTIP for onchocerciasis control need to be supported by proper and continuous training, and health education about different aspects of the disease.

Object-oriented structures supporting remote sensing databases

NASA Technical Reports Server (NTRS)

Wichmann, Keith; Cromp, Robert F.

1995-01-01

Object-oriented databases show promise for modeling the complex interrelationships pervasive in scientific domains. To examine the utility of this approach, we have developed an Intelligent Information Fusion System based on this technology, and applied it to the problem of managing an active repository of remotely-sensed satellite scenes. The design and implementation of the system is compared and contrasted with conventional relational database techniques, followed by a presentation of the underlying object-oriented data structures used to enable fast indexing into the data holdings.

Sharing and executing linked data queries in a collaborative environment.

PubMed

García Godoy, María Jesús; López-Camacho, Esteban; Navas-Delgado, Ismael; Aldana-Montes, José F

2013-07-01

Life Sciences have emerged as a key domain in the Linked Data community because of the diversity of data semantics and formats available through a great variety of databases and web technologies. Thus, it has been used as the perfect domain for applications in the web of data. Unfortunately, bioinformaticians are not exploiting the full potential of this already available technology, and experts in Life Sciences have real problems to discover, understand and devise how to take advantage of these interlinked (integrated) data. In this article, we present Bioqueries, a wiki-based portal that is aimed at community building around biological Linked Data. This tool has been designed to aid bioinformaticians in developing SPARQL queries to access biological databases exposed as Linked Data, and also to help biologists gain a deeper insight into the potential use of this technology. This public space offers several services and a collaborative infrastructure to stimulate the consumption of biological Linked Data and, therefore, contribute to implementing the benefits of the web of data in this domain. Bioqueries currently contains 215 query entries grouped by database and theme, 230 registered users and 44 end points that contain biological Resource Description Framework information. The Bioqueries portal is freely accessible at http://bioqueries.uma.es. Supplementary data are available at Bioinformatics online.

HMMerThread: detecting remote, functional conserved domains in entire genomes by combining relaxed sequence-database searches with fold recognition.

PubMed

Bradshaw, Charles Richard; Surendranath, Vineeth; Henschel, Robert; Mueller, Matthias Stefan; Habermann, Bianca Hermine

2011-03-10

Conserved domains in proteins are one of the major sources of functional information for experimental design and genome-level annotation. Though search tools for conserved domain databases such as Hidden Markov Models (HMMs) are sensitive in detecting conserved domains in proteins when they share sufficient sequence similarity, they tend to miss more divergent family members, as they lack a reliable statistical framework for the detection of low sequence similarity. We have developed a greatly improved HMMerThread algorithm that can detect remotely conserved domains in highly divergent sequences. HMMerThread combines relaxed conserved domain searches with fold recognition to eliminate false positive, sequence-based identifications. With an accuracy of 90%, our software is able to automatically predict highly divergent members of conserved domain families with an associated 3-dimensional structure. We give additional confidence to our predictions by validation across species. We have run HMMerThread searches on eight proteomes including human and present a rich resource of remotely conserved domains, which adds significantly to the functional annotation of entire proteomes. We find ∼4500 cross-species validated, remotely conserved domain predictions in the human proteome alone. As an example, we find a DNA-binding domain in the C-terminal part of the A-kinase anchor protein 10 (AKAP10), a PKA adaptor that has been implicated in cardiac arrhythmias and premature cardiac death, which upon stress likely translocates from mitochondria to the nucleus/nucleolus. Based on our prediction, we propose that with this HLH-domain, AKAP10 is involved in the transcriptional control of stress response. Further remotely conserved domains we discuss are examples from areas such as sporulation, chromosome segregation and signalling during immune response. The HMMerThread algorithm is able to automatically detect the presence of remotely conserved domains in proteins based on weak sequence similarity. Our predictions open up new avenues for biological and medical studies. Genome-wide HMMerThread domains are available at http://vm1-hmmerthread.age.mpg.de.

HMMerThread: Detecting Remote, Functional Conserved Domains in Entire Genomes by Combining Relaxed Sequence-Database Searches with Fold Recognition

PubMed Central

Bradshaw, Charles Richard; Surendranath, Vineeth; Henschel, Robert; Mueller, Matthias Stefan; Habermann, Bianca Hermine

2011-01-01

Conserved domains in proteins are one of the major sources of functional information for experimental design and genome-level annotation. Though search tools for conserved domain databases such as Hidden Markov Models (HMMs) are sensitive in detecting conserved domains in proteins when they share sufficient sequence similarity, they tend to miss more divergent family members, as they lack a reliable statistical framework for the detection of low sequence similarity. We have developed a greatly improved HMMerThread algorithm that can detect remotely conserved domains in highly divergent sequences. HMMerThread combines relaxed conserved domain searches with fold recognition to eliminate false positive, sequence-based identifications. With an accuracy of 90%, our software is able to automatically predict highly divergent members of conserved domain families with an associated 3-dimensional structure. We give additional confidence to our predictions by validation across species. We have run HMMerThread searches on eight proteomes including human and present a rich resource of remotely conserved domains, which adds significantly to the functional annotation of entire proteomes. We find ∼4500 cross-species validated, remotely conserved domain predictions in the human proteome alone. As an example, we find a DNA-binding domain in the C-terminal part of the A-kinase anchor protein 10 (AKAP10), a PKA adaptor that has been implicated in cardiac arrhythmias and premature cardiac death, which upon stress likely translocates from mitochondria to the nucleus/nucleolus. Based on our prediction, we propose that with this HLH-domain, AKAP10 is involved in the transcriptional control of stress response. Further remotely conserved domains we discuss are examples from areas such as sporulation, chromosome segregation and signalling during immune response. The HMMerThread algorithm is able to automatically detect the presence of remotely conserved domains in proteins based on weak sequence similarity. Our predictions open up new avenues for biological and medical studies. Genome-wide HMMerThread domains are available at http://vm1-hmmerthread.age.mpg.de. PMID:21423752

Structural diversity of domain superfamilies in the CATH database.

PubMed

Reeves, Gabrielle A; Dallman, Timothy J; Redfern, Oliver C; Akpor, Adrian; Orengo, Christine A

2006-07-14

The CATH database of domain structures has been used to explore the structural variation of homologous domains in 294 well populated domain structure superfamilies, each containing at least three sequence diverse relatives. Our analyses confirm some previously detected trends relating sequence divergence to structural variation but for a much larger dataset and in some superfamilies the new data reveal exceptional structural variation. Use of a new algorithm (2DSEC) to analyse variability in secondary structure compositions across a superfamily sheds new light on how structures evolve. 2DSEC detects inserted secondary structures that embellish the core of conserved secondary structures found throughout the superfamily. Analysis showed that for 56% of highly populated superfamilies (>9 sequence diverse relatives), there are twofold or more increases in the numbers of secondary structures in some relatives. In some families fivefold increases occur, sometimes modifying the fold of the domain. Manual inspection of secondary structure insertions or embellishments in 48 particularly variable superfamilies revealed that although these insertions were usually discontiguous in the sequence they were often co-located in 3D resulting in a larger structural motif that often modified the geometry of the active site or the surface conformation promoting diverse domain partnerships and protein interactions. These observations, supported by automatic analysis of all well populated CATH families, suggest that accretion of small secondary structure insertions may provide a simple mechanism for evolving new functions in diverse relatives. Some layered domain architectures (e.g. mainly-beta and alpha-beta sandwiches) that recur highly in the genomes more frequently exploit these types of embellishments to modify function. In these architectures, aggregation occurs most often at the edges, top or bottom of the beta-sheets. Information on structural variability across domain superfamilies has been made available through the CATH Dictionary of Homologous Structures (DHS).

Quantile Mapping Bias correction for daily precipitation over Vietnam in a regional climate model

NASA Astrophysics Data System (ADS)

Trinh, L. T.; Matsumoto, J.; Ngo-Duc, T.

2017-12-01

In the past decades, Regional Climate Models (RCMs) have been developed significantly, allowing climate simulation to be conducted at a higher resolution. However, RCMs often contained biases when comparing with observations. Therefore, statistical correction methods were commonly employed to reduce/minimize the model biases. In this study, outputs of the Regional Climate Model (RegCM) version 4.3 driven by the CNRM-CM5 global products were evaluated with and without the Quantile Mapping (QM) bias correction method. The model domain covered the area from 90oE to 145oE and from 15oS to 40oN with a horizontal resolution of 25km. The QM bias correction processes were implemented by using the Vietnam Gridded precipitation dataset (VnGP) and the outputs of RegCM historical run in the period 1986-1995 and then validated for the period 1996-2005. Based on the statistical quantity of spatial correlation and intensity distributions, the QM method showed a significant improvement in rainfall compared to the non-bias correction method. The improvements both in time and space were recognized in all seasons and all climatic sub-regions of Vietnam. Moreover, not only the rainfall amount but also some extreme indices such as R10m, R20mm, R50m, CDD, CWD, R95pTOT, R99pTOT were much better after the correction. The results suggested that the QM correction method should be taken into practice for the projections of the future precipitation over Vietnam.

Donor cycle and donor segmentation: new tools for improving blood donor management.

PubMed

Veldhuizen, I; Folléa, G; de Kort, W

2013-07-01

An adequate donor population is of key importance for the entire blood transfusion chain. For good donor management, a detailed overview of the donor database is therefore imperative. This study offers a new description of the donor cycle related to the donor management process. It also presents the outcomes of a European Project, Donor Management IN Europe (DOMAINE), regarding the segmentation of the donor population into donor types. Blood establishments (BEs) from 18 European countries, the Thalassaemia International Federation and a representative from the South-Eastern Europe Health Network joined forces in DOMAINE. A questionnaire assessed blood donor management practices and the composition of the donor population using the newly proposed DOMAINE donor segmentation. 48 BEs in 34 European countries were invited to participate. The response rate was high (88%). However, only 14 BEs could deliver data on the composition of their donor population. The data showed large variations and major imbalances in the donor population. In 79% of the countries, inactive donors formed the dominant donor type. Only in 21%, regular donors were the largest subgroup, and in 29%, the proportion of first-time donors was higher than the proportion of regular donors. Good donor management depends on a thorough insight into the flow of donors through their donor career. Segmentation of the donor database is an essential tool to understand the influx and efflux of donors. The DOMAINE donor segmentation helps BEs in understanding their donor database and to adapt their donor recruitment and retention practices accordingly. Ways to use this new tool are proposed. © 2013 International Society of Blood Transfusion.

Computer programs to characterize alloys and predict cyclic life using the total strain version of strainrange partitioning: Tutorial and users manual, version 1.0

NASA Technical Reports Server (NTRS)

Saltsman, James F.

1992-01-01

This manual presents computer programs for characterizing and predicting fatigue and creep-fatigue resistance of metallic materials in the high-temperature, long-life regime for isothermal and nonisothermal fatigue. The programs use the total strain version of Strainrange Partitioning (TS-SRP). An extensive database has also been developed in a parallel effort. This database is probably the largest source of high-temperature, creep-fatigue test data available in the public domain and can be used with other life prediction methods as well. This users manual, software, and database are all in the public domain and are available through COSMIC (382 East Broad Street, Athens, GA 30602; (404) 542-3265, FAX (404) 542-4807). Two disks accompany this manual. The first disk contains the source code, executable files, and sample output from these programs. The second disk contains the creep-fatigue data in a format compatible with these programs.

Gene: a gene-centered information resource at NCBI.

PubMed

Brown, Garth R; Hem, Vichet; Katz, Kenneth S; Ovetsky, Michael; Wallin, Craig; Ermolaeva, Olga; Tolstoy, Igor; Tatusova, Tatiana; Pruitt, Kim D; Maglott, Donna R; Murphy, Terence D

2015-01-01

The National Center for Biotechnology Information's (NCBI) Gene database (www.ncbi.nlm.nih.gov/gene) integrates gene-specific information from multiple data sources. NCBI Reference Sequence (RefSeq) genomes for viruses, prokaryotes and eukaryotes are the primary foundation for Gene records in that they form the critical association between sequence and a tracked gene upon which additional functional and descriptive content is anchored. Additional content is integrated based on the genomic location and RefSeq transcript and protein sequence data. The content of a Gene record represents the integration of curation and automated processing from RefSeq, collaborating model organism databases, consortia such as Gene Ontology, and other databases within NCBI. Records in Gene are assigned unique, tracked integers as identifiers. The content (citations, nomenclature, genomic location, gene products and their attributes, phenotypes, sequences, interactions, variation details, maps, expression, homologs, protein domains and external databases) is available via interactive browsing through NCBI's Entrez system, via NCBI's Entrez programming utilities (E-Utilities and Entrez Direct) and for bulk transfer by FTP. Published by Oxford University Press on behalf of Nucleic Acids Research 2014. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Massive Scale Cyber Traffic Analysis: A Driver for Graph Database Research

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

Joslyn, Cliff A.; Choudhury, S.; Haglin, David J.

2013-06-19

We describe the significance and prominence of network traffic analysis (TA) as a graph- and network-theoretical domain for advancing research in graph database systems. TA involves observing and analyzing the connections between clients, servers, hosts, and actors within IP networks, both at particular times and as extended over times. Towards that end, NetFlow (or more generically, IPFLOW) data are available from routers and servers which summarize coherent groups of IP packets flowing through the network. IPFLOW databases are routinely interrogated statistically and visualized for suspicious patterns. But the ability to cast IPFLOW data as a massive graph and query itmore » interactively, in order to e.g.\\ identify connectivity patterns, is less well advanced, due to a number of factors including scaling, and their hybrid nature combining graph connectivity and quantitative attributes. In this paper, we outline requirements and opportunities for graph-structured IPFLOW analytics based on our experience with real IPFLOW databases. Specifically, we describe real use cases from the security domain, cast them as graph patterns, show how to express them in two graph-oriented query languages SPARQL and Datalog, and use these examples to motivate a new class of "hybrid" graph-relational systems.« less

Applications of Sentinel-2 data for agriculture and forest monitoring using the absolute difference (ZABUD) index derived from the AgroEye software (ESA)

NASA Astrophysics Data System (ADS)

de Kok, R.; WeŻyk, P.; PapieŻ, M.; Migo, L.

2017-10-01

To convince new users of the advantages of the Sentinel_2 sensor, a simplification of classic remote sensing tools allows to create a platform of communication among domain specialists of agricultural analysis, visual image interpreters and remote sensing programmers. An index value, known in the remote sensing user domain as "Zabud" was selected to represent, in color, the essentials of a time series analysis. The color index used in a color atlas offers a working platform for an agricultural field control. This creates a database of test and training areas that enables rapid anomaly detection in the agricultural domain. The use cases and simplifications now function as an introduction to Sentinel_2 based remote sensing, in an area that before relies on VHR imagery and aerial data, to serve mainly the visual interpretation. The database extension with detected anomalies allows developers of open source software to design solutions for further agricultural control with remote sensing.

Interaction Domains and Suicide: A Population-Based Panel Study of Suicides in Stockholm, 1991-1999

ERIC Educational Resources Information Center

Hedstrom, Peter; Liu, Ka-Yuet; Nordvik, Monica K.

2008-01-01

This article examines how suicides influence suicide risks of others within two interaction domains: the family and the workplace. A distinction is made between dyad-based social-interaction effects and degree-based exposure effects. A unique database including all individuals who ever lived in Stockholm during the 1990s is analyzed. For about 5.6…

Using Simulation to Determine a Strategy for Positively Tracking a Cruise Missile by CMMCA

DTIC Science & Technology

1990-03-01

ANPOS/SS(6),ATC/SS(7),ATAS/ SS(8),ABANGLE/SS(9),CBANGLE/DD(1),CEVEL/ DD(2),CNVEL/DD(3),CTCC/DD(4),AEVEL/ DD(5), ANVEL /DD(6),ATCC RECORD,TNOW,MINUTES,20...ABANGLE),(SS(9),CBANGLE), & (DD(1),CEVEL),(DD(2),CNVEL).(DD(3),CTCC), & (DD(4),AEVEL),(DD(5), ANVEL ),(DD(6).ATCC) GOTO(l,2,3,4,5,6) ,I 1IF (XX(14) *EQ. 1...ABANGLE),(SS(9),CBANGLE), & (DD(l),CEVEL),(DD(2),CNVEL),(DD(3),CTCG), & (DD(4),AEVEL),(DD(5), ANVEL ),CDD(6),ATCC) REAL COSD EXTERNAL COSD REAL SIND

Full-Scale Incineration System Demonstration Verification Test Burns at the Naval Battalion Construction Center, Gulfport, Mississippi. Volume 3. Treatability Tests. Part 1

DTIC Science & Technology

1991-07-01

for archive. b. Except where noted, includes 2,3,7,8-TCDO, 2,3,7,8-TCOF, and total PCOD /PCOF. c. Except where noted, includes acid-type semivolatiles...TCDD- 3 7C14, P5CDD- 13 C12 , H pCOD - 13 C12, CD-13 C12, and P5CDF-13C 12 were used to calculate the accuracy of recovery efficiencies. Whereas for...burns are shown in Table 17. None of these PCOD congeners were detected, including the specific analysis for 2,3,7,8-TCDD. DLVs ranged between 30.02 and

Orchestrating the Development of a Complex System of Systems: Systems Engineering Tools and Methodologies

DTIC Science & Technology

2015-04-30

MCM MP  SSS SUW MP  SSS ASW MP  SSS Level 3: Mission Package Level MM MM MM MM MPAS  4a: Common MM 4b: MMs MM MM MM MM MPAS  4a: Common MM 4b: MMs MM...documented within the standard section of the System/Sub-System Specification ( SSS ) and flowed down to Sub-system Specification (SS) and other...typically contract to a prime developer and find it sufficient to decompose the CDD into a System/Sub-System Specification ( SSS ) or an A-Spec, which is then

COPPERHEAD Operational Performance Evaluation (COPE): Computer Program User and Analyst Manual.

DTIC Science & Technology

1981-03-01

I - ft N C * % S C.󈧬 4 ft - 2 4 4 0. 44 ft 2 -J 𔃾- OIl . ft...C CDD)( A - 4 I < 4- 0 C) C LUV ) I < C)(. I -L =L I - >C) =~ LU;- CU "-. I -7 CiWC n Li u <E m C) mw. vi tl <LU ~J 0- C-W CI- CD C)0 Li0 ( 0 C-j C- Li w...creating a new TAPL II; when PREPMS is modifying an 14-1 Initlaii..-eand uperl f i 1,- oil TAPE 11 ,L ,, Ittempt to read Print "Creation Run" Pj_, N P C

The methodology of database design in organization management systems

NASA Astrophysics Data System (ADS)

Chudinov, I. L.; Osipova, V. V.; Bobrova, Y. V.

2017-01-01

The paper describes the unified methodology of database design for management information systems. Designing the conceptual information model for the domain area is the most important and labor-intensive stage in database design. Basing on the proposed integrated approach to design, the conceptual information model, the main principles of developing the relation databases are provided and user’s information needs are considered. According to the methodology, the process of designing the conceptual information model includes three basic stages, which are defined in detail. Finally, the article describes the process of performing the results of analyzing user’s information needs and the rationale for use of classifiers.

The androgen receptor gene mutations database.

PubMed

Gottlieb, B; Trifiro, M; Lumbroso, R; Vasiliou, D M; Pinsky, L

1996-01-01

The current version of the androgen receptor (AR) gene mutations database is described. We have added (if available) data on the androgen binding phenotype of the mutant AR, the clinical phenotype of the affected persons, the family history and whether the pathogenicity of a mutation has been proven. Exonic mutations are now listed in 5'-->3' sequence regardless of type and single base pair changes are presented in codon context. Splice site and intronic mutations are listed separately. The database has allowed us to substantiate and amplify the observation of mutational hot spots within exons encoding the AR androgen binding domain. The database is available from EML (ftp://www.ebi.ac.uk/pub/databases/androgen) or as a Macintosh Filemaker file (MC33@musica.mcgill.ca).

Multi-Domain Transfer Learning for Early Diagnosis of Alzheimer's Disease.

PubMed

Cheng, Bo; Liu, Mingxia; Shen, Dinggang; Li, Zuoyong; Zhang, Daoqiang

2017-04-01

Recently, transfer learning has been successfully applied in early diagnosis of Alzheimer's Disease (AD) based on multi-domain data. However, most of existing methods only use data from a single auxiliary domain, and thus cannot utilize the intrinsic useful correlation information from multiple domains. Accordingly, in this paper, we consider the joint learning of tasks in multi-auxiliary domains and the target domain, and propose a novel Multi-Domain Transfer Learning (MDTL) framework for early diagnosis of AD. Specifically, the proposed MDTL framework consists of two key components: 1) a multi-domain transfer feature selection (MDTFS) model that selects the most informative feature subset from multi-domain data, and 2) a multi-domain transfer classification (MDTC) model that can identify disease status for early AD detection. We evaluate our method on 807 subjects from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database using baseline magnetic resonance imaging (MRI) data. The experimental results show that the proposed MDTL method can effectively utilize multi-auxiliary domain data for improving the learning performance in the target domain, compared with several state-of-the-art methods.

Classification of proteins with shared motifs and internal repeats in the ECOD database

PubMed Central

Kinch, Lisa N.; Liao, Yuxing

2016-01-01

Abstract Proteins and their domains evolve by a set of events commonly including the duplication and divergence of small motifs. The presence of short repetitive regions in domains has generally constituted a difficult case for structural domain classifications and their hierarchies. We developed the Evolutionary Classification Of protein Domains (ECOD) in part to implement a new schema for the classification of these types of proteins. Here we document the ways in which ECOD classifies proteins with small internal repeats, widespread functional motifs, and assemblies of small domain‐like fragments in its evolutionary schema. We illustrate the ways in which the structural genomics project impacted the classification and characterization of new structural domains and sequence families over the decade. PMID:26833690

Reconstituting protein interaction networks using parameter-dependent domain-domain interactions

PubMed Central

2013-01-01

Background We can describe protein-protein interactions (PPIs) as sets of distinct domain-domain interactions (DDIs) that mediate the physical interactions between proteins. Experimental data confirm that DDIs are more consistent than their corresponding PPIs, lending support to the notion that analyses of DDIs may improve our understanding of PPIs and lead to further insights into cellular function, disease, and evolution. However, currently available experimental DDI data cover only a small fraction of all existing PPIs and, in the absence of structural data, determining which particular DDI mediates any given PPI is a challenge. Results We present two contributions to the field of domain interaction analysis. First, we introduce a novel computational strategy to merge domain annotation data from multiple databases. We show that when we merged yeast domain annotations from six annotation databases we increased the average number of domains per protein from 1.05 to 2.44, bringing it closer to the estimated average value of 3. Second, we introduce a novel computational method, parameter-dependent DDI selection (PADDS), which, given a set of PPIs, extracts a small set of domain pairs that can reconstruct the original set of protein interactions, while attempting to minimize false positives. Based on a set of PPIs from multiple organisms, our method extracted 27% more experimentally detected DDIs than existing computational approaches. Conclusions We have provided a method to merge domain annotation data from multiple sources, ensuring large and consistent domain annotation for any given organism. Moreover, we provided a method to extract a small set of DDIs from the underlying set of PPIs and we showed that, in contrast to existing approaches, our method was not biased towards DDIs with low or high occurrence counts. Finally, we used these two methods to highlight the influence of the underlying annotation density on the characteristics of extracted DDIs. Although increased annotations greatly expanded the possible DDIs, the lack of knowledge of the true biological false positive interactions still prevents an unambiguous assignment of domain interactions responsible for all protein network interactions. Executable files and examples are given at: http://www.bhsai.org/downloads/padds/ PMID:23651452

Item response theory analysis of the Amyotrophic Lateral Sclerosis Functional Rating Scale-Revised in the Pooled Resource Open-Access ALS Clinical Trials Database.

PubMed

Bacci, Elizabeth D; Staniewska, Dorota; Coyne, Karin S; Boyer, Stacey; White, Leigh Ann; Zach, Neta; Cedarbaum, Jesse M

2016-01-01

Our objective was to examine dimensionality and item-level performance of the Amyotrophic Lateral Sclerosis Functional Rating Scale-Revised (ALSFRS-R) across time using classical and modern test theory approaches. Confirmatory factor analysis (CFA) and Item Response Theory (IRT) analyses were conducted using data from patients with amyotrophic lateral sclerosis (ALS) Pooled Resources Open-Access ALS Clinical Trials (PRO-ACT) database with complete ALSFRS-R data (n = 888) at three time-points (Time 0, Time 1 (6-months), Time 2 (1-year)). Results demonstrated that in this population of 888 patients, mean age was 54.6 years, 64.4% were male, and 93.7% were Caucasian. The CFA supported a 4* individual-domain structure (bulbar, gross motor, fine motor, and respiratory domains). IRT analysis within each domain revealed misfitting items and overlapping item response category thresholds at all time-points, particularly in the gross motor and respiratory domain items. Results indicate that many of the items of the ALSFRS-R may sub-optimally distinguish among varying levels of disability assessed by each domain, particularly in patients with less severe disability. Measure performance improved across time as patient disability severity increased. In conclusion, modifications to select ALSFRS-R items may improve the instrument's specificity to disability level and sensitivity to treatment effects.

SAbDab: the structural antibody database

PubMed Central

Dunbar, James; Krawczyk, Konrad; Leem, Jinwoo; Baker, Terry; Fuchs, Angelika; Georges, Guy; Shi, Jiye; Deane, Charlotte M.

2014-01-01

Structural antibody database (SAbDab; http://opig.stats.ox.ac.uk/webapps/sabdab) is an online resource containing all the publicly available antibody structures annotated and presented in a consistent fashion. The data are annotated with several properties including experimental information, gene details, correct heavy and light chain pairings, antigen details and, where available, antibody–antigen binding affinity. The user can select structures, according to these attributes as well as structural properties such as complementarity determining region loop conformation and variable domain orientation. Individual structures, datasets and the complete database can be downloaded. PMID:24214988

Data exploration systems for databases

NASA Technical Reports Server (NTRS)

Greene, Richard J.; Hield, Christopher

1992-01-01

Data exploration systems apply machine learning techniques, multivariate statistical methods, information theory, and database theory to databases to identify significant relationships among the data and summarize information. The result of applying data exploration systems should be a better understanding of the structure of the data and a perspective of the data enabling an analyst to form hypotheses for interpreting the data. This paper argues that data exploration systems need a minimum amount of domain knowledge to guide both the statistical strategy and the interpretation of the resulting patterns discovered by these systems.

Relational Databases and Biomedical Big Data.

PubMed

de Silva, N H Nisansa D

2017-01-01

In various biomedical applications that collect, handle, and manipulate data, the amounts of data tend to build up and venture into the range identified as bigdata. In such occurrences, a design decision has to be taken as to what type of database would be used to handle this data. More often than not, the default and classical solution to this in the biomedical domain according to past research is relational databases. While this used to be the norm for a long while, it is evident that there is a trend to move away from relational databases in favor of other types and paradigms of databases. However, it still has paramount importance to understand the interrelation that exists between biomedical big data and relational databases. This chapter will review the pros and cons of using relational databases to store biomedical big data that previous researches have discussed and used.

Integrating heterogeneous databases in clustered medic care environments using object-oriented technology

NASA Astrophysics Data System (ADS)

Thakore, Arun K.; Sauer, Frank

1994-05-01

The organization of modern medical care environments into disease-related clusters, such as a cancer center, a diabetes clinic, etc., has the side-effect of introducing multiple heterogeneous databases, often containing similar information, within the same organization. This heterogeneity fosters incompatibility and prevents the effective sharing of data amongst applications at different sites. Although integration of heterogeneous databases is now feasible, in the medical arena this is often an ad hoc process, not founded on proven database technology or formal methods. In this paper we illustrate the use of a high-level object- oriented semantic association method to model information found in different databases into an integrated conceptual global model that integrates the databases. We provide examples from the medical domain to illustrate an integration approach resulting in a consistent global view, without attacking the autonomy of the underlying databases.

Design and Implementation of a Prototype Microcomputer Database Management System for the Standardization of Data Elements for the Department of Defense

DTIC Science & Technology

1990-09-01

Justification Cat: Left Timeliness Identifier: Qwe (FI] Domain I Def Text: -Press [F3 to nove in/out of the fields below. Use ARROW keys to scroll- Rec: Host...Delete a record Elemont Creator ID: Justification Cat: Left Timeliness Identifier: Qwe [FI) Domain Def Text: - Press (F3) to move in/out of the...Number: 1 Alias Name: Accounting Code Data Value Type ID: QL Max Length Characters: 34 Timeliness ID: Qwe Justification Category: Left Creator ID: Domain

Domain Hierarchy and closed Loops (DHcL): a server for exploring hierarchy of protein domain structure

PubMed Central

Koczyk, Grzegorz; Berezovsky, Igor N.

2008-01-01

Domain hierarchy and closed loops (DHcL) (http://sitron.bccs.uib.no/dhcl/) is a web server that delineates energy hierarchy of protein domain structure and detects domains at different levels of this hierarchy. The server also identifies closed loops and van der Waals locks, which constitute a structural basis for the protein domain hierarchy. The DHcL can be a useful tool for an express analysis of protein structures and their alternative domain decompositions. The user submits a PDB identifier(s) or uploads a 3D protein structure in a PDB format. The results of the analysis are the location of domains at different levels of hierarchy, closed loops, van der Waals locks and their interactive visualization. The server maintains a regularly updated database of domains, closed loop and van der Waals locks for all X-ray structures in PDB. DHcL server is available at: http://sitron.bccs.uib.no/dhcl. PMID:18502776

Quality of clinical practice guidelines in delirium: a systematic appraisal

PubMed Central

Marchington, Katie L; Agar, Meera; Davis, Daniel H J; Sikora, Lindsey; Tsang, Tammy W Y

2017-01-01

Objective To determine the accessibility and currency of delirium guidelines, guideline summary papers and evaluation studies, and critically appraise guideline quality. Design Systematic literature search for formal guidelines (in English or French) with focus on delirium assessment and/or management in adults (≥18 years), guideline summary papers and evaluation studies. Full appraisal of delirium guidelines published between 2008 and 2013 and obtaining a ‘Rigour of Development’ domain screening score cut-off of >40% using the Appraisal of Guidelines for Research and Evaluation (AGREE II) instrument. Data sources Multiple bibliographic databases, guideline organisation databases, complemented by a grey literature search. Results 3327 database citations and 83 grey literature links were identified. A total of 118 retrieved delirium guidelines and related documents underwent full-text screening. A final 21 delirium guidelines (with 10 being >5 years old), 12 guideline summary papers and 3 evaluation studies were included. For 11 delirium guidelines published between 2008 and 2013, the screening AGREE II ‘Rigour’ scores ranged from 3% to 91%, with seven meeting the cut-off score of >40%. Overall, the highest rating AGREE II domains were ‘Scope and Purpose’ (mean 80.1%, range 64–100%) and ‘Clarity and Presentation’ (mean 76.7%, range 38–97%). The lowest rating domains were ‘Applicability’ (mean 48.7%, range 8–81%) and ‘Editorial Independence’ (mean 53%, range 2–90%). The three highest rating guidelines in the ‘Applicability’ domain incorporated monitoring criteria or audit and costing templates, and/or implementation strategies. Conclusions Delirium guidelines are best sourced by a systematic grey literature search. Delirium guideline quality varied across all six AGREE II domains, demonstrating the importance of using a formal appraisal tool prior to guideline adaptation and implementation into clinical settings. Adding more knowledge translation resources to guidelines may improve their practical application and effective monitoring. More delirium guideline evaluation studies are needed to determine their effect on clinical practice. PMID:28283488

Computer-Based and Paper-Based Measurement of Recognition Performance

DTIC Science & Technology

1989-03-01

domains (e.g., ship silhouettes, electronic schemata, human anatomy ) to ascertain the universality of the validity and reliability results...specific graphic 4 database (e.g., ship silhouettes, human anatomy , electronic circuits, topography), con- tributes to its wide applicability. The game, then...seek implementation of FLASH and PICTURE in other content areas or subject-matter domains (e.g., ship silhouettes, electronic schemata, human anatomy ) to

Personal domains assessed in multiple mini interviews (MMIs) for healthcare student selection: A narrative synthesis systematic review.

PubMed

Callwood, Alison; Jeevaratnam, Kamalan; Kotronoulas, Grigorios; Schneider, Annegret; Lewis, Liane; Nadarajah, Vishna Devi

2018-05-01

To examine the personal domains multiple mini interviews (MMIs) are being designed to assess, explore how they were determined and contextualise such domains in current and future healthcare student selection processes DESIGN: A systematic review of empirical research reporting on MMI model design was conducted from database inception to November 2017. Twelve electronic bibliographic databases. Evidence was extracted from original studies, and integrated in a narrative synthesis guided by the PRISMA statement for reporting systematic reviews. Personal domains were clustered into themes using a modified Delphi technique. A total of 584 articles were screened. 65 unique studies (80 articles) matched our inclusion criteria of which seven were conducted within nursing/midwifery faculties. Six in 10 studies featured applicants to medical school. Across selection processes, we identified 32 personal domains assessed by MMIs, the most frequent being: communication skills (84%), teamwork/collaboration (70%), and ethical/moral judgement (65%). Domains capturing ability to cope with stressful situations (14%), make decisions (14%), and resolve conflict in the workplace (13%) featured in fewer than ten studies overall. Intra- and inter-disciplinary inconsistencies in domain profiles were noted, as well as differences by entry level. MMIs deployed in nursing and midwifery assessed compassion and decision-making more frequently than in all other disciplines. Own programme philosophy and professional body guidance were most frequently cited (~50%) as sources for personal domains; a blueprinting process was reported in only 8% of studies. Nursing, midwifery and allied healthcare professionals should develop their theoretical frameworks for MMIs to ensure they are evidence-based and fit-for-purpose. We suggest a re-evaluation of domain priorities to ensure that students who are selected, not only have the capacity to offer the highest standards of care provision, but are able to maintain these standards when facing clinical practice and organisational pressures. Copyright © 2018 Elsevier Ltd. All rights reserved.

DOMMINO 2.0: integrating structurally resolved protein-, RNA-, and DNA-mediated macromolecular interactions

PubMed Central

Kuang, Xingyan; Dhroso, Andi; Han, Jing Ginger; Shyu, Chi-Ren; Korkin, Dmitry

2016-01-01

Macromolecular interactions are formed between proteins, DNA and RNA molecules. Being a principle building block in macromolecular assemblies and pathways, the interactions underlie most of cellular functions. Malfunctioning of macromolecular interactions is also linked to a number of diseases. Structural knowledge of the macromolecular interaction allows one to understand the interaction’s mechanism, determine its functional implications and characterize the effects of genetic variations, such as single nucleotide polymorphisms, on the interaction. Unfortunately, until now the interactions mediated by different types of macromolecules, e.g. protein–protein interactions or protein–DNA interactions, are collected into individual and unrelated structural databases. This presents a significant obstacle in the analysis of macromolecular interactions. For instance, the homogeneous structural interaction databases prevent scientists from studying structural interactions of different types but occurring in the same macromolecular complex. Here, we introduce DOMMINO 2.0, a structural Database Of Macro-Molecular INteractiOns. Compared to DOMMINO 1.0, a comprehensive database on protein-protein interactions, DOMMINO 2.0 includes the interactions between all three basic types of macromolecules extracted from PDB files. DOMMINO 2.0 is automatically updated on a weekly basis. It currently includes ∼1 040 000 interactions between two polypeptide subunits (e.g. domains, peptides, termini and interdomain linkers), ∼43 000 RNA-mediated interactions, and ∼12 000 DNA-mediated interactions. All protein structures in the database are annotated using SCOP and SUPERFAMILY family annotation. As a result, protein-mediated interactions involving protein domains, interdomain linkers, C- and N- termini, and peptides are identified. Our database provides an intuitive web interface, allowing one to investigate interactions at three different resolution levels: whole subunit network, binary interaction and interaction interface. Database URL: http://dommino.org PMID:26827237

Multi-Domain Transfer Learning for Early Diagnosis of Alzheimer’s Disease

PubMed Central

Cheng, Bo; Liu, Mingxia; Li, Zuoyong

2017-01-01

Recently, transfer learning has been successfully applied in early diagnosis of Alzheimer’s Disease (AD) based on multi-domain data. However, most of existing methods only use data from a single auxiliary domain, and thus cannot utilize the intrinsic useful correlation information from multiple domains. Accordingly, in this paper, we consider the joint learning of tasks in multi-auxiliary domains and the target domain, and propose a novel Multi-Domain Transfer Learning (MDTL) framework for early diagnosis of AD. Specifically, the proposed MDTL framework consists of two key components: 1) a multi-domain transfer feature selection (MDTFS) model that selects the most informative feature subset from multi-domain data, and 2) a multidomain transfer classification (MDTC) model that can identify disease status for early AD detection. We evaluate our method on 807 subjects from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) database using baseline magnetic resonance imaging (MRI) data. The experimental results show that the proposed MDTL method can effectively utilize multi-auxiliary domain data for improving the learning performance in the target domain, compared with several state-of-the-art methods. PMID:27928657

Stackfile Database

NASA Technical Reports Server (NTRS)

deVarvalho, Robert; Desai, Shailen D.; Haines, Bruce J.; Kruizinga, Gerhard L.; Gilmer, Christopher

2013-01-01

This software provides storage retrieval and analysis functionality for managing satellite altimetry data. It improves the efficiency and analysis capabilities of existing database software with improved flexibility and documentation. It offers flexibility in the type of data that can be stored. There is efficient retrieval either across the spatial domain or the time domain. Built-in analysis tools are provided for frequently performed altimetry tasks. This software package is used for storing and manipulating satellite measurement data. It was developed with a focus on handling the requirements of repeat-track altimetry missions such as Topex and Jason. It was, however, designed to work with a wide variety of satellite measurement data [e.g., Gravity Recovery And Climate Experiment -- GRACE). The software consists of several command-line tools for importing, retrieving, and analyzing satellite measurement data.

Assignment of protein sequences to existing domain and family classification systems: Pfam and the PDB.

PubMed

Xu, Qifang; Dunbrack, Roland L

2012-11-01

Automating the assignment of existing domain and protein family classifications to new sets of sequences is an important task. Current methods often miss assignments because remote relationships fail to achieve statistical significance. Some assignments are not as long as the actual domain definitions because local alignment methods often cut alignments short. Long insertions in query sequences often erroneously result in two copies of the domain assigned to the query. Divergent repeat sequences in proteins are often missed. We have developed a multilevel procedure to produce nearly complete assignments of protein families of an existing classification system to a large set of sequences. We apply this to the task of assigning Pfam domains to sequences and structures in the Protein Data Bank (PDB). We found that HHsearch alignments frequently scored more remotely related Pfams in Pfam clans higher than closely related Pfams, thus, leading to erroneous assignment at the Pfam family level. A greedy algorithm allowing for partial overlaps was, thus, applied first to sequence/HMM alignments, then HMM-HMM alignments and then structure alignments, taking care to join partial alignments split by large insertions into single-domain assignments. Additional assignment of repeat Pfams with weaker E-values was allowed after stronger assignments of the repeat HMM. Our database of assignments, presented in a database called PDBfam, contains Pfams for 99.4% of chains >50 residues. The Pfam assignment data in PDBfam are available at http://dunbrack2.fccc.edu/ProtCid/PDBfam, which can be searched by PDB codes and Pfam identifiers. They will be updated regularly.

NPIDB: Nucleic acid-Protein Interaction DataBase.

PubMed

Kirsanov, Dmitry D; Zanegina, Olga N; Aksianov, Evgeniy A; Spirin, Sergei A; Karyagina, Anna S; Alexeevski, Andrei V

2013-01-01

The Nucleic acid-Protein Interaction DataBase (http://npidb.belozersky.msu.ru/) contains information derived from structures of DNA-protein and RNA-protein complexes extracted from the Protein Data Bank (3846 complexes in October 2012). It provides a web interface and a set of tools for extracting biologically meaningful characteristics of nucleoprotein complexes. The content of the database is updated weekly. The current version of the Nucleic acid-Protein Interaction DataBase is an upgrade of the version published in 2007. The improvements include a new web interface, new tools for calculation of intermolecular interactions, a classification of SCOP families that contains DNA-binding protein domains and data on conserved water molecules on the DNA-protein interface.

Genome-wide analysis of the Zn(II)2Cys6 zinc cluster-encoding gene family in Aspergillus flavus

USDA-ARS?s Scientific Manuscript database

Proteins with a Zn(II)2Cys6 domain, Cys-X2-Cys-X6-Cys-X5-12-Cys-X2-Cys-X6-9-Cys (hereafter, referred to as the C6 domain), form a subclass of zinc finger proteins found exclusively in fungi and yeast. Genome sequence databases of Saccharomyces cerevisiae and Candida albicans have provided an overvie...

Making a web based ulcer record work by aligning architecture, legislation and users - a formative evaluation study.

PubMed

Ekeland, Anne G; Skipenes, Eva; Nyheim, Beate; Christiansen, Ellen K

2011-01-01

The University Hospital of North Norway selected a web-based ulcer record used in Denmark, available from mobile phones. Data was stored in a common database and easily accessible. According to Norwegian legislation, only employees of the organization that owns an IT system can access the system, and use of mobile units requires strong security solutions. The system had to be changed. The paper addresses interactions in order to make the system legal, and assesses regulations that followed. By addressing conflicting scripts and the contingent nature of knowledge, we conducted a formative evaluation aiming at improving the object being studied. Participatory observation in a one year process, minutes from meetings and information from participants, constitute the data material. In the technological domain, one database was replaced by four. In the health care delivery domain, easy access was replaced by a more complicated log on procedure, and in the domain of law and security, a clarification of risk levels was obtained, thereby allowing for access by mobile phones with today's authentication mechanisms. Flexibility concerning predefined scripts was important in all domains. Changes were made that improved the platform for further development of legitimate communication of patient data via mobile units. The study also shows the value of formative evaluations in innovations.

A Web-based open-source database for the distribution of hyperspectral signatures

NASA Astrophysics Data System (ADS)

Ferwerda, J. G.; Jones, S. D.; Du, Pei-Jun

2006-10-01

With the coming of age of field spectroscopy as a non-destructive means to collect information on the physiology of vegetation, there is a need for storage of signatures, and, more importantly, their metadata. Without the proper organisation of metadata, the signatures itself become limited. In order to facilitate re-distribution of data, a database for the storage & distribution of hyperspectral signatures and their metadata was designed. The database was built using open-source software, and can be used by the hyperspectral community to share their data. Data is uploaded through a simple web-based interface. The database recognizes major file-formats by ASD, GER and International Spectronics. The database source code is available for download through the hyperspectral.info web domain, and we happily invite suggestion for additions & modification for the database to be submitted through the online forums on the same website.

SalmonDB: a bioinformatics resource for Salmo salar and Oncorhynchus mykiss

PubMed Central

Di Génova, Alex; Aravena, Andrés; Zapata, Luis; González, Mauricio; Maass, Alejandro; Iturra, Patricia

2011-01-01

SalmonDB is a new multiorganism database containing EST sequences from Salmo salar, Oncorhynchus mykiss and the whole genome sequence of Danio rerio, Gasterosteus aculeatus, Tetraodon nigroviridis, Oryzias latipes and Takifugu rubripes, built with core components from GMOD project, GOPArc system and the BioMart project. The information provided by this resource includes Gene Ontology terms, metabolic pathways, SNP prediction, CDS prediction, orthologs prediction, several precalculated BLAST searches and domains. It also provides a BLAST server for matching user-provided sequences to any of the databases and an advanced query tool (BioMart) that allows easy browsing of EST databases with user-defined criteria. These tools make SalmonDB database a valuable resource for researchers searching for transcripts and genomic information regarding S. salar and other salmonid species. The database is expected to grow in the near feature, particularly with the S. salar genome sequencing project. Database URL: http://genomicasalmones.dim.uchile.cl/ PMID:22120661

SalmonDB: a bioinformatics resource for Salmo salar and Oncorhynchus mykiss.

PubMed

Di Génova, Alex; Aravena, Andrés; Zapata, Luis; González, Mauricio; Maass, Alejandro; Iturra, Patricia

2011-01-01

SalmonDB is a new multiorganism database containing EST sequences from Salmo salar, Oncorhynchus mykiss and the whole genome sequence of Danio rerio, Gasterosteus aculeatus, Tetraodon nigroviridis, Oryzias latipes and Takifugu rubripes, built with core components from GMOD project, GOPArc system and the BioMart project. The information provided by this resource includes Gene Ontology terms, metabolic pathways, SNP prediction, CDS prediction, orthologs prediction, several precalculated BLAST searches and domains. It also provides a BLAST server for matching user-provided sequences to any of the databases and an advanced query tool (BioMart) that allows easy browsing of EST databases with user-defined criteria. These tools make SalmonDB database a valuable resource for researchers searching for transcripts and genomic information regarding S. salar and other salmonid species. The database is expected to grow in the near feature, particularly with the S. salar genome sequencing project. Database URL: http://genomicasalmones.dim.uchile.cl/

Component Database for the APS Upgrade

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

Veseli, S.; Arnold, N. D.; Jarosz, D. P.

The Advanced Photon Source Upgrade (APS-U) project will replace the existing APS storage ring with a multi-bend achromat (MBA) lattice to provide extreme transverse coherence and extreme brightness x-rays to its users. As the time to replace the existing storage ring accelerator is of critical concern, an aggressive one-year removal/installation/testing period is being planned. To aid in the management of the thousands of components to be installed in such a short time, the Component Database (CDB) application is being developed with the purpose to identify, document, track, locate, and organize components in a central database. Three major domains are beingmore » addressed: Component definitions (which together make up an exhaustive "Component Catalog"), Designs (groupings of components to create subsystems), and Component Instances (“Inventory”). Relationships between the major domains offer additional "system knowledge" to be captured that will be leveraged with future tools and applications. It is imperative to provide sub-system engineers with a functional application early in the machine design cycle. Topics discussed in this paper include the initial design and deployment of CDB, as well as future development plans.« less

3D-SURFER 2.0: web platform for real-time search and characterization of protein surfaces.

PubMed

Xiong, Yi; Esquivel-Rodriguez, Juan; Sael, Lee; Kihara, Daisuke

2014-01-01

The increasing number of uncharacterized protein structures necessitates the development of computational approaches for function annotation using the protein tertiary structures. Protein structure database search is the basis of any structure-based functional elucidation of proteins. 3D-SURFER is a web platform for real-time protein surface comparison of a given protein structure against the entire PDB using 3D Zernike descriptors. It can smoothly navigate the protein structure space in real-time from one query structure to another. A major new feature of Release 2.0 is the ability to compare the protein surface of a single chain, a single domain, or a single complex against databases of protein chains, domains, complexes, or a combination of all three in the latest PDB. Additionally, two types of protein structures can now be compared: all-atom-surface and backbone-atom-surface. The server can also accept a batch job for a large number of database searches. Pockets in protein surfaces can be identified by VisGrid and LIGSITE (csc) . The server is available at http://kiharalab.org/3d-surfer/.

Bioinformatic flowchart and database to investigate the origins and diversity of Clan AA peptidases

PubMed Central

Llorens, Carlos; Futami, Ricardo; Renaud, Gabriel; Moya, Andrés

2009-01-01

Background Clan AA of aspartic peptidases relates the family of pepsin monomers evolutionarily with all dimeric peptidases encoded by eukaryotic LTR retroelements. Recent findings describing various pools of single-domain nonviral host peptidases, in prokaryotes and eukaryotes, indicate that the diversity of clan AA is larger than previously thought. The ensuing approach to investigate this enzyme group is by studying its phylogeny. However, clan AA is a difficult case to study due to the low similarity and different rates of evolution. This work is an ongoing attempt to investigate the different clan AA families to understand the cause of their diversity. Results In this paper, we describe in-progress database and bioinformatic flowchart designed to characterize the clan AA protein domain based on all possible protein families through ancestral reconstructions, sequence logos, and hidden markov models (HMMs). The flowchart includes the characterization of a major consensus sequence based on 6 amino acid patterns with correspondence with Andreeva's model, the structural template describing the clan AA peptidase fold. The set of tools is work in progress we have organized in a database within the GyDB project, referred to as Clan AA Reference Database . Conclusion The pre-existing classification combined with the evolutionary history of LTR retroelements permits a consistent taxonomical collection of sequence logos and HMMs. This set is useful for gene annotation but also a reference to evaluate the diversity of, and the relationships among, the different families. Comparisons among HMMs suggest a common ancestor for all dimeric clan AA peptidases that is halfway between single-domain nonviral peptidases and those coded by Ty3/Gypsy LTR retroelements. Sequence logos reveal how all clan AA families follow similar protein domain architecture related to the peptidase fold. In particular, each family nucleates a particular consensus motif in the sequence position related to the flap. The different motifs constitute a network where an alanine-asparagine-like variable motif predominates, instead of the canonical flap of the HIV-1 peptidase and closer relatives. Reviewers This article was reviewed by Daniel H. Haft, Vladimir Kapitonov (nominated by Jerry Jurka), and Ben M. Dunn (nominated by Claus Wilke). PMID:19173708

A high level interface to SCOP and ASTRAL implemented in python.

PubMed

Casbon, James A; Crooks, Gavin E; Saqi, Mansoor A S

2006-01-10

Benchmarking algorithms in structural bioinformatics often involves the construction of datasets of proteins with given sequence and structural properties. The SCOP database is a manually curated structural classification which groups together proteins on the basis of structural similarity. The ASTRAL compendium provides non redundant subsets of SCOP domains on the basis of sequence similarity such that no two domains in a given subset share more than a defined degree of sequence similarity. Taken together these two resources provide a 'ground truth' for assessing structural bioinformatics algorithms. We present a small and easy to use API written in python to enable construction of datasets from these resources. We have designed a set of python modules to provide an abstraction of the SCOP and ASTRAL databases. The modules are designed to work as part of the Biopython distribution. Python users can now manipulate and use the SCOP hierarchy from within python programs, and use ASTRAL to return sequences of domains in SCOP, as well as clustered representations of SCOP from ASTRAL. The modules make the analysis and generation of datasets for use in structural genomics easier and more principled.

A Data Preparation Methodology in Data Mining Applied to Mortality Population Databases.

PubMed

Pérez, Joaquín; Iturbide, Emmanuel; Olivares, Víctor; Hidalgo, Miguel; Martínez, Alicia; Almanza, Nelva

2015-11-01

It is known that the data preparation phase is the most time consuming in the data mining process, using up to 50% or up to 70% of the total project time. Currently, data mining methodologies are of general purpose and one of their limitations is that they do not provide a guide about what particular task to develop in a specific domain. This paper shows a new data preparation methodology oriented to the epidemiological domain in which we have identified two sets of tasks: General Data Preparation and Specific Data Preparation. For both sets, the Cross-Industry Standard Process for Data Mining (CRISP-DM) is adopted as a guideline. The main contribution of our methodology is fourteen specialized tasks concerning such domain. To validate the proposed methodology, we developed a data mining system and the entire process was applied to real mortality databases. The results were encouraging because it was observed that the use of the methodology reduced some of the time consuming tasks and the data mining system showed findings of unknown and potentially useful patterns for the public health services in Mexico.

Recent research in data description of the measurement property resource on common data dictionary

NASA Astrophysics Data System (ADS)

Lu, Tielin; Fan, Zitian; Wang, Chunxi; Liu, Xiaojing; Wang, Shuo; Zhao, Hua

2018-03-01

A method for measurement equipment data description has been proposed based on the property resource analysis. The applications of common data dictionary (CDD) to devices and equipment is mainly used in digital factory to advance the management not only in the enterprise, also to the different enterprise in the same data environment. In this paper, we can make a brief of the data flow in the whole manufacture enterprise and the automatic trigger the process of the data exchange. Furthermore,the application of the data dictionary is available for the measurement and control equipment, which can also be used in other different industry in smart manufacture.

Low dose CT image restoration using a database of image patches

NASA Astrophysics Data System (ADS)

Ha, Sungsoo; Mueller, Klaus

2015-01-01

Reducing the radiation dose in CT imaging has become an active research topic and many solutions have been proposed to remove the significant noise and streak artifacts in the reconstructed images. Most of these methods operate within the domain of the image that is subject to restoration. This, however, poses limitations on the extent of filtering possible. We advocate to take into consideration the vast body of external knowledge that exists in the domain of already acquired medical CT images, since after all, this is what radiologists do when they examine these low quality images. We can incorporate this knowledge by creating a database of prior scans, either of the same patient or a diverse corpus of different patients, to assist in the restoration process. Our paper follows up on our previous work that used a database of images. Using images, however, is challenging since it requires tedious and error prone registration and alignment. Our new method eliminates these problems by storing a diverse set of small image patches in conjunction with a localized similarity matching scheme. We also empirically show that it is sufficient to store these patches without anatomical tags since their statistics are sufficiently strong to yield good similarity matches from the database and as a direct effect, produce image restorations of high quality. A final experiment demonstrates that our global database approach can recover image features that are difficult to preserve with conventional denoising approaches.

Allie: a database and a search service of abbreviations and long forms.

PubMed

Yamamoto, Yasunori; Yamaguchi, Atsuko; Bono, Hidemasa; Takagi, Toshihisa

2011-01-01

Many abbreviations are used in the literature especially in the life sciences, and polysemous abbreviations appear frequently, making it difficult to read and understand scientific papers that are outside of a reader's expertise. Thus, we have developed Allie, a database and a search service of abbreviations and their long forms (a.k.a. full forms or definitions). Allie searches for abbreviations and their corresponding long forms in a database that we have generated based on all titles and abstracts in MEDLINE. When a user query matches an abbreviation, Allie returns all potential long forms of the query along with their bibliographic data (i.e. title and publication year). In addition, for each candidate, co-occurring abbreviations and a research field in which it frequently appears in the MEDLINE data are displayed. This function helps users learn about the context in which an abbreviation appears. To deal with synonymous long forms, we use a dictionary called GENA that contains domain-specific terms such as gene, protein or disease names along with their synonymic information. Conceptually identical domain-specific terms are regarded as one term, and then conceptually identical abbreviation-long form pairs are grouped taking into account their appearance in MEDLINE. To keep up with new abbreviations that are continuously introduced, Allie has an automatic update system. In addition, the database of abbreviations and their long forms with their corresponding PubMed IDs is constructed and updated weekly. Database URL: The Allie service is available at http://allie.dbcls.jp/.

Automatic prediction of protein domains from sequence information using a hybrid learning system.

PubMed

Nagarajan, Niranjan; Yona, Golan

2004-06-12

We describe a novel method for detecting the domain structure of a protein from sequence information alone. The method is based on analyzing multiple sequence alignments that are derived from a database search. Multiple measures are defined to quantify the domain information content of each position along the sequence and are combined into a single predictor using a neural network. The output is further smoothed and post-processed using a probabilistic model to predict the most likely transition positions between domains. The method was assessed using the domain definitions in SCOP and CATH for proteins of known structure and was compared with several other existing methods. Our method performs well both in terms of accuracy and sensitivity. It improves significantly over the best methods available, even some of the semi-manual ones, while being fully automatic. Our method can also be used to suggest and verify domain partitions based on structural data. A few examples of predicted domain definitions and alternative partitions, as suggested by our method, are also discussed. An online domain-prediction server is available at http://biozon.org/tools/domains/

The Design and Development of a Potent and Selective Novel Diprolyl Derivative That Binds to the N-Domain of Angiotensin-I Converting Enzyme.

PubMed

Fienberg, Stephen; Cozier, Gyles E; Acharya, K Ravi; Chibale, Kelly; Sturrock, Edward D

2018-01-11

Angiotensin-I converting enzyme (ACE) is a zinc metalloprotease consisting of two catalytic domains (N- and C-). Most clinical ACE inhibitor(s) (ACEi) have been shown to inhibit both domains nonselectively, resulting in adverse effects such as cough and angioedema. Selectively inhibiting the individual domains is likely to reduce these effects and potentially treat fibrosis in addition to hypertension. ACEi from the GVK Biosciences database were inspected for possible N-domain selective binding patterns. From this set, a diprolyl chemical series was modeled using docking simulations. The series was expanded based on key target interactions involving residues known to impart N-domain selectivity. In total, seven diprolyl compounds were synthesized and tested for N-domain selective ACE inhibition. One compound with an aspartic acid in the P 2 position (compound 16) displayed potent inhibition (K i = 11.45 nM) and was 84-fold more selective toward the N-domain. A high-resolution crystal structure of compound 16 in complex with the N-domain revealed the molecular basis for the observed selectivity.

Database of Mechanical Properties of Textile Composites

NASA Technical Reports Server (NTRS)

Delbrey, Jerry

1996-01-01

This report describes the approach followed to develop a database for mechanical properties of textile composites. The data in this database is assembled from NASA Advanced Composites Technology (ACT) programs and from data in the public domain. This database meets the data documentation requirements of MIL-HDBK-17, Section 8.1.2, which describes in detail the type and amount of information needed to completely document composite material properties. The database focuses on mechanical properties of textile composite. Properties are available for a range of parameters such as direction, fiber architecture, materials, environmental condition, and failure mode. The composite materials in the database contain innovative textile architectures such as the braided, woven, and knitted materials evaluated under the NASA ACT programs. In summary, the database contains results for approximately 3500 coupon level tests, for ten different fiber/resin combinations, and seven different textile architectures. It also includes a limited amount of prepreg tape composites data from ACT programs where side-by-side comparisons were made.

Extending the data dictionary for data/knowledge management

NASA Technical Reports Server (NTRS)

Hydrick, Cecile L.; Graves, Sara J.

1988-01-01

Current relational database technology provides the means for efficiently storing and retrieving large amounts of data. By combining techniques learned from the field of artificial intelligence with this technology, it is possible to expand the capabilities of such systems. This paper suggests using the expanded domain concept, an object-oriented organization, and the storing of knowledge rules within the relational database as a solution to the unique problems associated with CAD/CAM and engineering data.

Research on an expert system for database operation of simulation-emulation math models. Volume 1, Phase 1: Results

NASA Technical Reports Server (NTRS)

Kawamura, K.; Beale, G. O.; Schaffer, J. D.; Hsieh, B. J.; Padalkar, S.; Rodriguez-Moscoso, J. J.

1985-01-01

The results of the first phase of Research on an Expert System for Database Operation of Simulation/Emulation Math Models, is described. Techniques from artificial intelligence (AI) were to bear on task domains of interest to NASA Marshall Space Flight Center. One such domain is simulation of spacecraft attitude control systems. Two related software systems were developed to and delivered to NASA. One was a generic simulation model for spacecraft attitude control, written in FORTRAN. The second was an expert system which understands the usage of a class of spacecraft attitude control simulation software and can assist the user in running the software. This NASA Expert Simulation System (NESS), written in LISP, contains general knowledge about digital simulation, specific knowledge about the simulation software, and self knowledge.

Major accident prevention through applying safety knowledge management approach.

PubMed

Kalatpour, Omid

2016-01-01

Many scattered resources of knowledge are available to use for chemical accident prevention purposes. The common approach to management process safety, including using databases and referring to the available knowledge has some drawbacks. The main goal of this article was to devise a new emerged knowledge base (KB) for the chemical accident prevention domain. The scattered sources of safety knowledge were identified and scanned. Then, the collected knowledge was formalized through a computerized program. The Protégé software was used to formalize and represent the stored safety knowledge. The domain knowledge retrieved as well as data and information. This optimized approach improved safety and health knowledge management (KM) process and resolved some typical problems in the KM process. Upgrading the traditional resources of safety databases into the KBs can improve the interaction between the users and knowledge repository.

DBSecSys: A Database of Burkholderia mallei Secretion Systems

DTIC Science & Technology

2014-07-16

toxins and the lipases, as well as non-proteinaceous substrates, e.g., cyclic β- glucans and polysaccharides. 2* - Represents a Sec/Tat-dependent system...divided into three types: 1) the archetypal bacterial proteins exported into the periplasm via the Sec system; 2) trimeric proteins with a single beta ...barrel domain; and 3) pairs of proteins in which one partner carries the beta barrel domain and the other partner is the secreted protein. 6

Cry-Bt identifier: a biological database for PCR detection of Cry genes present in transgenic plants.

PubMed

Singh, Vinay Kumar; Ambwani, Sonu; Marla, Soma; Kumar, Anil

2009-10-23

We describe the development of a user friendly tool that would assist in the retrieval of information relating to Cry genes in transgenic crops. The tool also helps in detection of transformed Cry genes from Bacillus thuringiensis present in transgenic plants by providing suitable designed primers for PCR identification of these genes. The tool designed based on relational database model enables easy retrieval of information from the database with simple user queries. The tool also enables users to access related information about Cry genes present in various databases by interacting with different sources (nucleotide sequences, protein sequence, sequence comparison tools, published literature, conserved domains, evolutionary and structural data). http://insilicogenomics.in/Cry-btIdentifier/welcome.html.

The Classification of Protein Domains.

PubMed

Dawson, Natalie; Sillitoe, Ian; Marsden, Russell L; Orengo, Christine A

2017-01-01

The significant expansion in protein sequence and structure data that we are now witnessing brings with it a pressing need to bring order to the protein world. Such order enables us to gain insights into the evolution of proteins, their function and the extent to which the functional repertoire can vary across the three kingdoms of life. This has lead to the creation of a wide range of protein family classifications that aim to group proteins based upon their evolutionary relationships.In this chapter we discuss the approaches and methods that are frequently used in the classification of proteins, with a specific emphasis on the classification of protein domains. The construction of both domain sequence and domain structure databases is considered and we show how the use of domain family annotations to assign structural and functional information is enhancing our understanding of genomes.

Data Mining Research with the LSST

NASA Astrophysics Data System (ADS)

Borne, Kirk D.; Strauss, M. A.; Tyson, J. A.

2007-12-01

The LSST catalog database will exceed 10 petabytes, comprising several hundred attributes for 5 billion galaxies, 10 billion stars, and over 1 billion variable sources (optical variables, transients, or moving objects), extracted from over 20,000 square degrees of deep imaging in 5 passbands with thorough time domain coverage: 1000 visits over the 10-year LSST survey lifetime. The opportunities are enormous for novel scientific discoveries within this rich time-domain ultra-deep multi-band survey database. Data Mining, Machine Learning, and Knowledge Discovery research opportunities with the LSST are now under study, with a potential for new collaborations to develop to contribute to these investigations. We will describe features of the LSST science database that are amenable to scientific data mining, object classification, outlier identification, anomaly detection, image quality assurance, and survey science validation. We also give some illustrative examples of current scientific data mining research in astronomy, and point out where new research is needed. In particular, the data mining research community will need to address several issues in the coming years as we prepare for the LSST data deluge. The data mining research agenda includes: scalability (at petabytes scales) of existing machine learning and data mining algorithms; development of grid-enabled parallel data mining algorithms; designing a robust system for brokering classifications from the LSST event pipeline (which may produce 10,000 or more event alerts per night); multi-resolution methods for exploration of petascale databases; visual data mining algorithms for visual exploration of the data; indexing of multi-attribute multi-dimensional astronomical databases (beyond RA-Dec spatial indexing) for rapid querying of petabyte databases; and more. Finally, we will identify opportunities for synergistic collaboration between the data mining research group and the LSST Data Management and Science Collaboration teams.

Assignment of protein sequences to existing domain and family classification systems: Pfam and the PDB

PubMed Central

Dunbrack, Roland L.

2012-01-01

Motivation: Automating the assignment of existing domain and protein family classifications to new sets of sequences is an important task. Current methods often miss assignments because remote relationships fail to achieve statistical significance. Some assignments are not as long as the actual domain definitions because local alignment methods often cut alignments short. Long insertions in query sequences often erroneously result in two copies of the domain assigned to the query. Divergent repeat sequences in proteins are often missed. Results: We have developed a multilevel procedure to produce nearly complete assignments of protein families of an existing classification system to a large set of sequences. We apply this to the task of assigning Pfam domains to sequences and structures in the Protein Data Bank (PDB). We found that HHsearch alignments frequently scored more remotely related Pfams in Pfam clans higher than closely related Pfams, thus, leading to erroneous assignment at the Pfam family level. A greedy algorithm allowing for partial overlaps was, thus, applied first to sequence/HMM alignments, then HMM–HMM alignments and then structure alignments, taking care to join partial alignments split by large insertions into single-domain assignments. Additional assignment of repeat Pfams with weaker E-values was allowed after stronger assignments of the repeat HMM. Our database of assignments, presented in a database called PDBfam, contains Pfams for 99.4% of chains >50 residues. Availability: The Pfam assignment data in PDBfam are available at http://dunbrack2.fccc.edu/ProtCid/PDBfam, which can be searched by PDB codes and Pfam identifiers. They will be updated regularly. Contact: Roland.Dunbracks@fccc.edu PMID:22942020

Schistosomiais and Soil-Transmitted Helminth Control in Niger: Cost Effectiveness of School Based and Community Distributed Mass Drug Administration

PubMed Central

Leslie, Jacqueline; Garba, Amadou; Oliva, Elisa Bosque; Barkire, Arouna; Tinni, Amadou Aboubacar; Djibo, Ali; Mounkaila, Idrissa; Fenwick, Alan

2011-01-01

Background In 2004 Niger established a large scale schistosomiasis and soil-transmitted helminths control programme targeting children aged 5–14 years and adults. In two years 4.3 million treatments were delivered in 40 districts using school based and community distribution. Method and Findings Four districts were surveyed in 2006 to estimate the economic cost per district, per treatment and per schistosomiasis infection averted. The study compares the costs of treatment at start up and in a subsequent year, identifies the allocation of costs by activity, input and organisation, and assesses the cost of treatment. The cost of delivery provided by teachers is compared to cost of delivery by community distributers (CDD). The total economic cost of the programme including programmatic, national and local government costs and international support in four study districts, over two years, was US$ 456,718; an economic cost/treatment of $0.58. The full economic delivery cost of school based treatment in 2005/06 was $0.76, and for community distribution was $0.46. Including only the programme costs the figures are $0.47 and $0.41 respectively. Differences at sub-district are more marked. This is partly explained by the fact that a CDD treats 5.8 people for every one treated in school. The range in cost effectiveness for both direct and direct and indirect treatments is quantified and the need to develop and refine such estimates is emphasised. Conclusions The relative cost effectiveness of school and community delivery differs by country according to the composition of the population treated, the numbers targeted and treated at school and in the community, the cost and frequency of training teachers and CDDs. Options analysis of technical and implementation alternatives including a financial analysis should form part of the programme design process. PMID:22022622

Human exposure to PCDDs and their precursors from heron and tern eggs in the Yangtze River Delta indicate PCP origin.

PubMed

Zhou, Yihui; Yin, Ge; Asplund, Lillemor; Stewart, Kathryn; Rantakokko, Panu; Bignert, Anders; Ruokojärvi, Päivi; Kiviranta, Hannu; Qiu, Yanling; Ma, Zhijun; Bergman, Åke

2017-06-01

Polychlorinated dibenzo-p-dioxins (PCDDs) and polychlorinated dibenzofurans (PCDFs) are highly toxic to humans and wildlife. In the present study, PCDD/Fs were analyzed in the eggs of whiskered terns (Chlidonias hybrida), and genetically identified eggs from black-crowned night herons (Nycticorax nycticorax) sampled from two lakes in the Yangtze River Delta area, China. The median toxic equivalent (TEQ) of PCDD/Fs were 280 (range: 95-1500) and 400 (range: 220-1100) pg TEQ g -1 lw (WHO, 1998 for birds) in the eggs of black-crowned night heron and whiskered tern, respectively. Compared to known sources, concentrations of PCDDs relative to the sum of PCDD/Fs in bird eggs, demonstrated high abundance of octachlorodibenzo-p-dioxin (OCDD), 1,2,3,4,6,7,8-heptaCDD and 1,2,3,6,7,8-hexaCDD indicating pentachlorophenol (PCP), and/or sodium pentachlorophenolate (Na-PCP) as significant sources of the PCDD/Fs. The presence of polychlorinated diphenyl ethers (PCDEs), hydroxylated and methoxylated polychlorinated diphenyl ethers (OH- and MeO-PCDEs, known impurities in PCP products), corroborates this hypothesis. Further, significant correlations were found between the predominant congener CDE-206, 3'-OH-CDE-207, 2'-MeO-CDE-206 and OCDD, indicating a common origin. Eggs from the two lakes are sometimes used for human consumption. The WHO health-based tolerable intake of PCDD/Fs is exceeded if eggs from the two lakes are consumed regularly on a weekly basis, particularly for children. The TEQs extensively exceed maximum levels for PCDD/Fs in hen eggs and egg products according to EU legislation (2.5 pg TEQ g -1 lw). The results suggest immediate action should be taken to manage the contamination, and further studies evaluating the impacts of egg consumption from wild birds in China. Likewise, studies on dioxins and other POPs in common eggs need to be initiated around China. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Control of Viscous Fingering in Miscible Displacements in Porous Media with a Periodic Change of Injection Rate

NASA Astrophysics Data System (ADS)

Yuan, Q.; Zeng, F.; Knorr, K. D.; Imran, M.

2017-12-01

Context/PurposeThe viscous fingering (VF) is widely encountered in a series of miscible displacements such as CO2 sequestration and solvent-based enhanced oil recovery (EOR). Accurate prediction and effective control of its development are significant. Commercial simulators cannot capture VF because of large numerical diffusion. Moreover, previous measures for controlling VF using polymer are very expensive. In the present study, a periodic change of injection rate involving injection and extraction is used to control and reduce VF instabilities at zero cost. MethodsHighly accurate spectral method and fully implicit alternating direction implicit method are used to simulate VF with concentration-dependent diffusion (CDD) and velocity-induced dispersion (VID), although the consideration of CDD and VID may result in strong nonlinearity and stiff problem under unfavourable viscosity ratio. In-house code is developed. The VF is reduced by optimizing period and amplitude of injection rate. ResultsThe results show that the periodic change of injection rates can strongly affect VF and sweep efficiency. In particular, a period-stabilizing range is found in which the VF is reduced compared with widely used constant injection with the same amount of fluid injected. The frequent change of rate results in high sweep efficiency. The optimal injection scheme, when compared with constant injection, can improve sweep efficiency by 20-35%. InterpretationDispersion plays a key role in the mitigation of VF in periodic displacement rates. It enhances the uniform mixing of two fluids in injection stage in any period, while it can more effectively attenuate VF instabilities through the following extraction stage. Fast switch of injection and extraction can mitigate flow instability once it develops. ConclusionThis finding is very novel and significant as it is the first time to control VF instability in porous media without any additional cost. It shows great potential for EOR at zero cost.

Influence of process changes on PCDD/Fs produced in an iron ore sintering plant

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

Guerriero, E.; Bianchini, M.; Gigliucci, P.F.

2009-01-15

This study investigated the influence of different charge typologies and additives on the PCDD/Fs amount produced and on the congener profiles in an iron ore sintering plant. Many tests were carried out combining different typologies of charge (iron materials) and solid fuel ('coke breeze' or 'anthracite') with or without the use of urea. The PCDD/Fs produced ranged from 1.2 to 22.7 {mu} g I-TEQ/ton of agglomerate, whereas the PCDD/Fs released to the ambient air ranged from 0.10 to 1.92 ng I-TEQ/Nm{sup 3} because of cleaning in an electrostatic precipitator (ESP) and a Wetfine scrubber (WS). A more homogeneous charge withmore » a higher amount of fine particles charge appeared to produce a lower PCDD/Fs concentration due to a better combustion but this hypothesis needs further investigations on charges having different dimension particles. Only a synergitic action of urea and anthracite was able to reduce the high PCDD/Fs content due to the bad combustion of the more inhomogeneous charge with a lower amount of fine particles. The congener profile was a typical combustion process fingerprint because the PCDFs predominated, the highly chlorinated congeners (HeptaCDD and OctaCDD) prevailed in PCDDs, whereas in PCDFs the profile was more varied; 1,2,3,4,6,7,8-HeptaCDF was the main contributor to the total concentration while 2,3,4,7,8-PentaCDF was the main contributor to the I-TEQ concentration. Whereas all the parameters under scrutiny influenced strongly the amount of PCDD/Fs produced, they affected only slightly the fingerprint of PCDD/Fs. In all cases studied, the reduction obtained using urea, anthracite, or the more homogeneous charge with a higher amount of fine particles was slightly greater on the higher chlorinated congeners in respect to the lower ones.« less

Correlations of fish intake and plasma docosahexaenoic acid levels with each congener of PCDDs/PCDFs/dioxin-like PCBs in blood from the Japanese population.

PubMed

Kitayama, Atsushi; Arisawa, Kokichi; Uemura, Hirokazu; Hiyoshi, Mineyoshi; Takami, Hidenobu; Sawachika, Fusakazu; Yamaguchi, Miwa; Nakamoto, Mariko; Hasegawa, Manabu; Tanto, Masaharu; Shima, Masayuki; Sumiyoshi, Yoshio; Morinaga, Kenji; Kodama, Kazunori; Suzuki, Taka-Ichiro; Nagai, Masaki; Satoh, Hiroshi

2011-12-01

The purpose of the present study was to investigate the factors associated with blood levels of each congener of polychlorinated dibenzo-p-dioxins (PCDDs), polychlorinated dibenzofurans (PCDFs), and dioxin-like polychlorinated biphenyls (DL-PCBs) in the Japanese population. A cross-sectional study was performed on 1,656 subjects (755 men and 901 women) aged 15-73 years, who were living in 90 different areas of 30 prefectures in Japan. Blood levels of 29 PCDD, PCDF, and DL-PCB congeners were determined by high-resolution gas chromatography/mass spectrometry. In addition, a questionnaire survey on life style, including dietary habit, was carried out. The median total toxicity equivalent (TEQ) was 17 pgTEQ/g lipid. After adjustment for age, sex, body mass index, smoking habit, and consumption of other food groups, six PCDDs/PCDFs with 4-6 substituted chlorine atoms and 10 DL-PCBs, but not HeptaCDD/F or OctaCDD, showed significant positive correlations with the frequency of intake of fish and shellfish. Furthermore, significant positive relationships were also found between plasma levels of docosahexaenoic acid (DHA), a biomarker of fish intake, and 10 PCDDs/PCDFs with 4-6 chlorine atoms and 10 DL-PCBs. The partial correlation coefficients with plasma DHA were significantly higher for DL-PCBs than for PCDDs/PCDFs, and partial correlation coefficients for PCDDs/PCDFs significantly decreased with increasing number of chlorine atoms (Spearman r = -0.80, P = 0.001). Blood levels of PCDDs/PCDFs with 4-6 chlorine atoms and DL-PCBs were positively associated with fish intake in the Japanese population. These results may be explained by the higher degree of bioaccumulation of these congeners in fish and shellfish in the ecosystem, and the high consumption of fish among the Japanese population.

Extreme Precipitation in Poland in the Years 1951-2010

NASA Astrophysics Data System (ADS)

Malinowska, Miroslawa

2017-12-01

The characteristics of extreme precipitation, including the dominant trends, were analysed for eight stations located in different parts of Poland for the period 1951-2010. Five indices enabling the assessment of the intensity and frequency of both extremely dry and wet conditions were applied. The indices included the number of days with precipitation ≥10mm·d-1 (R10), maximum number of consecutive dry days (CDD), maximum 5-day precipitation total (R5d), simple daily intensity index (SDII), and the fraction of annual total precipitation due to events exceeding the 95th percentile calculated for the period 1961-1990. Annual trends were calculated using standard linear regression method, while the fit of the model was assessed with the F-test at the 95% confidence level. The analysed changes in extreme precipitation showed mixed patterns. A significant positive trend in the number of days with precipitation ≥10mm·d-1 (R10) was observed in central Poland, while a significant negative one, in south-eastern Poland. Based on the analysis of maximum 5-day precipitation totals (R5d), statistically significant positive trends in north-western, western and eastern parts of the country were detected, while the negative trends were found in the central and northeastern parts. Daily precipitation, expressed as single daily intensity index (SDII), increased over time in northern and central Poland. In southern Poland, the variation of SDII index showed non-significant negative tendencies. Finally, the fraction of annual total precipitation due to the events exceeding the 1961-1990 95th percentile increased at one station only, namely, in Warsaw. The indicator which refers to dry conditions, i.e. maximum number of consecutive dry days (CDD) displayed negative trends throughout the surveyed area, with the exception of Szczecin that is a representative of north-western Poland.

Computer aided identification of a Hevein-like antimicrobial peptide of bell pepper leaves for biotechnological use.

PubMed

Games, Patrícia Dias; daSilva, Elói Quintas Gonçalves; Barbosa, Meire de Oliveira; Almeida-Souza, Hebréia Oliveira; Fontes, Patrícia Pereira; deMagalhães, Marcos Jorge; Pereira, Paulo Roberto Gomes; Prates, Maura Vianna; Franco, Gloria Regina; Faria-Campos, Alessandra; Campos, Sérgio Vale Aguiar; Baracat-Pereira, Maria Cristina

2016-12-15

Antimicrobial peptides from plants present mechanisms of action that are different from those of conventional defense agents. They are under-explored but have a potential as commercial antimicrobials. Bell pepper leaves ('Magali R') are discarded after harvesting the fruit and are sources of bioactive peptides. This work reports the isolation by peptidomics tools, and the identification and partially characterization by computational tools of an antimicrobial peptide from bell pepper leaves, and evidences the usefulness of records and the in silico analysis for the study of plant peptides aiming biotechnological uses. Aqueous extracts from leaves were enriched in peptide by salt fractionation and ultrafiltration. An antimicrobial peptide was isolated by tandem chromatographic procedures. Mass spectrometry, automated peptide sequencing and bioinformatics tools were used alternately for identification and partial characterization of the Hevein-like peptide, named HEV-CANN. The computational tools that assisted to the identification of the peptide included BlastP, PSI-Blast, ClustalOmega, PeptideCutter, and ProtParam; conventional protein databases (DB) as Mascot, Protein-DB, GenBank-DB, RefSeq, Swiss-Prot, and UniProtKB; specific for peptides DB as Amper, APD2, CAMP, LAMPs, and PhytAMP; other tools included in ExPASy for Proteomics; The Bioactive Peptide Databases, and The Pepper Genome Database. The HEV-CANN sequence presented 40 amino acid residues, 4258.8 Da, theoretical pI-value of 8.78, and four disulfide bonds. It was stable, and it has inhibited the growth of phytopathogenic bacteria and a fungus. HEV-CANN presented a chitin-binding domain in their sequence. There was a high identity and a positive alignment of HEV-CANN sequence in various databases, but there was not a complete identity, suggesting that HEV-CANN may be produced by ribosomal synthesis, which is in accordance with its constitutive nature. Computational tools for proteomics and databases are not adjusted for short sequences, which hampered HEV-CANN identification. The adjustment of statistical tests in large databases for proteins is an alternative to promote the significant identification of peptides. The development of specific DB for plant antimicrobial peptides, with information about peptide sequences, functional genomic data, structural motifs and domains of molecules, functional domains, and peptide-biomolecule interactions are valuable and necessary.

Semantically Enabling Knowledge Representation of Metamorphic Petrology Data

NASA Astrophysics Data System (ADS)

West, P.; Fox, P. A.; Spear, F. S.; Adali, S.; Nguyen, C.; Hallett, B. W.; Horkley, L. K.

2012-12-01

More and more metamorphic petrology data is being collected around the world, and is now being organized together into different virtual data portals by means of virtual organizations. For example, there is the virtual data portal Petrological Database (PetDB, http://www.petdb.org) of the Ocean Floor that is organizing scientific information about geochemical data of ocean floor igneous and metamorphic rocks; and also The Metamorphic Petrology Database (MetPetDB, http://metpetdb.rpi.edu) that is being created by a global community of metamorphic petrologists in collaboration with software engineers and data managers at Rensselaer Polytechnic Institute. The current focus is to provide the ability for scientists and researchers to register their data and search the databases for information regarding sample collections. What we present here is the next step in evolution of the MetPetDB portal, utilizing semantically enabled features such as discovery, data casting, faceted search, knowledge representation, and linked data as well as organizing information about the community and collaboration within the virtual community itself. We take the information that is currently represented in a relational database and make it available through web services, SPARQL endpoints, semantic and triple-stores where inferencing is enabled. We will be leveraging research that has taken place in virtual observatories, such as the Virtual Solar Terrestrial Observatory (VSTO) and the Biological and Chemical Oceanography Data Management Office (BCO-DMO); vocabulary work done in various communities such as Observations and Measurements (ISO 19156), FOAF (Friend of a Friend), Bibo (Bibliography Ontology), and domain specific ontologies; enabling provenance traces of samples and subsamples using the different provenance ontologies; and providing the much needed linking of data from the various research organizations into a common, collaborative virtual observatory. In addition to better representing and presenting the actual data, we also look to organize and represent the knowledge information and expertise behind the data. Domain experts hold a lot of knowledge in their minds, in their presentations and publications, and elsewhere. Not only is this a technical issue, this is also a social issue in that we need to be able to encourage the domain experts to share their knowledge in a way that can be searched and queried over. With this additional focus in MetPetDB the site can be used more efficiently by other domain experts, but can also be utilized by non-specialists as well in order to educate people of the importance of the work being done as well as enable future domain experts.

Extension of the COG and arCOG databases by amino acid and nucleotide sequences

PubMed Central

Meereis, Florian; Kaufmann, Michael

2008-01-01

Background The current versions of the COG and arCOG databases, both excellent frameworks for studies in comparative and functional genomics, do not contain the nucleotide sequences corresponding to their protein or protein domain entries. Results Using sequence information obtained from GenBank flat files covering the completely sequenced genomes of the COG and arCOG databases, we constructed NUCOCOG (nucleotide sequences containing COG databases) as an extended version including all nucleotide sequences and in addition the amino acid sequences originally utilized to construct the current COG and arCOG databases. We make available three comprehensive single XML files containing the complete databases including all sequence information. In addition, we provide a web interface as a utility suitable to browse the NUCOCOG database for sequence retrieval. The database is accessible at . Conclusion NUCOCOG offers the possibility to analyze any sequence related property in the context of the COG and arCOG framework simply by using script languages such as PERL applied to a large but single XML document. PMID:19014535

SpirPro: A Spirulina proteome database and web-based tools for the analysis of protein-protein interactions at the metabolic level in Spirulina (Arthrospira) platensis C1.

PubMed

Senachak, Jittisak; Cheevadhanarak, Supapon; Hongsthong, Apiradee

2015-07-29

Spirulina (Arthrospira) platensis is the only cyanobacterium that in addition to being studied at the molecular level and subjected to gene manipulation, can also be mass cultivated in outdoor ponds for commercial use as a food supplement. Thus, encountering environmental changes, including temperature stresses, is common during the mass production of Spirulina. The use of cyanobacteria as an experimental platform, especially for photosynthetic gene manipulation in plants and bacteria, is becoming increasingly important. Understanding the mechanisms and protein-protein interaction networks that underlie low- and high-temperature responses is relevant to Spirulina mass production. To accomplish this goal, high-throughput techniques such as OMICs analyses are used. Thus, large datasets must be collected, managed and subjected to information extraction. Therefore, databases including (i) proteomic analysis and protein-protein interaction (PPI) data and (ii) domain/motif visualization tools are required for potential use in temperature response models for plant chloroplasts and photosynthetic bacteria. A web-based repository was developed including an embedded database, SpirPro, and tools for network visualization. Proteome data were analyzed integrated with protein-protein interactions and/or metabolic pathways from KEGG. The repository provides various information, ranging from raw data (2D-gel images) to associated results, such as data from interaction and/or pathway analyses. This integration allows in silico analyses of protein-protein interactions affected at the metabolic level and, particularly, analyses of interactions between and within the affected metabolic pathways under temperature stresses for comparative proteomic analysis. The developed tool, which is coded in HTML with CSS/JavaScript and depicted in Scalable Vector Graphics (SVG), is designed for interactive analysis and exploration of the constructed network. SpirPro is publicly available on the web at http://spirpro.sbi.kmutt.ac.th . SpirPro is an analysis platform containing an integrated proteome and PPI database that provides the most comprehensive data on this cyanobacterium at the systematic level. As an integrated database, SpirPro can be applied in various analyses, such as temperature stress response networking analysis in cyanobacterial models and interacting domain-domain analysis between proteins of interest.

Quality of clinical practice guidelines in delirium: a systematic appraisal.

PubMed

Bush, Shirley H; Marchington, Katie L; Agar, Meera; Davis, Daniel H J; Sikora, Lindsey; Tsang, Tammy W Y

2017-03-10

To determine the accessibility and currency of delirium guidelines, guideline summary papers and evaluation studies, and critically appraise guideline quality. Systematic literature search for formal guidelines (in English or French) with focus on delirium assessment and/or management in adults (≥18 years), guideline summary papers and evaluation studies.Full appraisal of delirium guidelines published between 2008 and 2013 and obtaining a 'Rigour of Development' domain screening score cut-off of >40% using the Appraisal of Guidelines for Research and Evaluation (AGREE II) instrument. Multiple bibliographic databases, guideline organisation databases, complemented by a grey literature search. 3327 database citations and 83 grey literature links were identified. A total of 118 retrieved delirium guidelines and related documents underwent full-text screening. A final 21 delirium guidelines (with 10 being >5 years old), 12 guideline summary papers and 3 evaluation studies were included. For 11 delirium guidelines published between 2008 and 2013, the screening AGREE II 'Rigour' scores ranged from 3% to 91%, with seven meeting the cut-off score of >40%. Overall, the highest rating AGREE II domains were 'Scope and Purpose' (mean 80.1%, range 64-100%) and 'Clarity and Presentation' (mean 76.7%, range 38-97%). The lowest rating domains were 'Applicability' (mean 48.7%, range 8-81%) and 'Editorial Independence' (mean 53%, range 2-90%). The three highest rating guidelines in the 'Applicability' domain incorporated monitoring criteria or audit and costing templates, and/or implementation strategies. Delirium guidelines are best sourced by a systematic grey literature search. Delirium guideline quality varied across all six AGREE II domains, demonstrating the importance of using a formal appraisal tool prior to guideline adaptation and implementation into clinical settings. Adding more knowledge translation resources to guidelines may improve their practical application and effective monitoring. More delirium guideline evaluation studies are needed to determine their effect on clinical practice. 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/.

Acquisition and analysis of a spectral and bidirectional database of urban materials over Toulouse (France)

NASA Astrophysics Data System (ADS)

Briottet, X.; Lachérade, S.; Pallotta, S.; Miesch, C.; Tanguy, B.; Le Men, H.

2006-05-01

This paper presents an experiment carried out in Toulouse in 2004. This campaign aims to create a specific library which will give us simultaneously information in three domains: a list of the main materials present in the city, the optical properties of each of them (spectral and directional) and their spatial variability in a given class. The spectral domain covers the entire optical domain from the visible to the Long Wave InfraRed range. Measurements have been carried out in the visible and near infrared spectral region (400-2500 nm) with an ASD spectroradiometer at a 20 cm resolution for outdoors measurements, and with a goniometer for laboratory ones at the same spatial resolution. A database of about 550 individual spectra has been created. These spectra could be divided into 4 classical urban classes like road (red asphalt, tar), pavement (red asphalt, tar), square (granite slab) and wall (brick, concrete). In addition to these "in situ" experiments, the bi-directional behaviours of urban material samples have been studied in laboratory with the Onera goniometer. Two material types have been distinguished: flat materials, which is isotropic, and textured materials, whose study is more complex. Whereas road and sidewalk materials are quite lambertian with a slight backscattering effect typical of rough surfaces, square materials like granite or concrete present a specular peak at large zenith angle. A specific study on tiles demonstrates their important anisotropic directional properties. In the infrared domain (3μm - 14μm), a SOC 400 spectroradiometer was used at a 1.27cm spatial resolution. A database of about 100 individual spectra has been created. These spectra could be divided into four classical urban classes like road (red asphalt, tar), pavement (red asphalt, tar), square (granite slab) and wall (bricks, painted walls). In each spectral domain, three variability types are considered: a physical variability which is intrinsic to the material, a contextual variability depending on the material use and a theoretical variability which is the one observed inside a chosen class.

Data warehousing in molecular biology.

PubMed

Schönbach, C; Kowalski-Saunders, P; Brusic, V

2000-05-01

In the business and healthcare sectors data warehousing has provided effective solutions for information usage and knowledge discovery from databases. However, data warehousing applications in the biological research and development (R&D) sector are lagging far behind. The fuzziness and complexity of biological data represent a major challenge in data warehousing for molecular biology. By combining experiences in other domains with our findings from building a model database, we have defined the requirements for data warehousing in molecular biology.

SIMAP—the database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage

PubMed Central

Arnold, Roland; Goldenberg, Florian; Mewes, Hans-Werner; Rattei, Thomas

2014-01-01

The Similarity Matrix of Proteins (SIMAP, http://mips.gsf.de/simap/) database has been designed to massively accelerate computationally expensive protein sequence analysis tasks in bioinformatics. It provides pre-calculated sequence similarities interconnecting the entire known protein sequence universe, complemented by pre-calculated protein features and domains, similarity clusters and functional annotations. SIMAP covers all major public protein databases as well as many consistently re-annotated metagenomes from different repositories. As of September 2013, SIMAP contains >163 million proteins corresponding to ∼70 million non-redundant sequences. SIMAP uses the sensitive FASTA search heuristics, the Smith–Waterman alignment algorithm, the InterPro database of protein domain models and the BLAST2GO functional annotation algorithm. SIMAP assists biologists by facilitating the interactive exploration of the protein sequence universe. Web-Service and DAS interfaces allow connecting SIMAP with any other bioinformatic tool and resource. All-against-all protein sequence similarity matrices of project-specific protein collections are generated on request. Recent improvements allow SIMAP to cover the rapidly growing sequenced protein sequence universe. New Web-Service interfaces enhance the connectivity of SIMAP. Novel tools for interactive extraction of protein similarity networks have been added. Open access to SIMAP is provided through the web portal; the portal also contains instructions and links for software access and flat file downloads. PMID:24165881

gPhoton: Time-tagged GALEX photon events analysis tools

NASA Astrophysics Data System (ADS)

Million, Chase C.; Fleming, S. W.; Shiao, B.; Loyd, P.; Seibert, M.; Smith, M.

2016-03-01

Written in Python, gPhoton calibrates and sky-projects the ~1.1 trillion ultraviolet photon events detected by the microchannel plates on the Galaxy Evolution Explorer Spacecraft (GALEX), archives these events in a publicly accessible database at the Mikulski Archive for Space Telescopes (MAST), and provides tools for working with the database to extract scientific results, particularly over short time domains. The software includes a re-implementation of core functionality of the GALEX mission calibration pipeline to produce photon list files from raw spacecraft data as well as a suite of command line tools to generate calibrated light curves, images, and movies from the MAST database.

Distributed databases for materials study of thermo-kinetic properties

NASA Astrophysics Data System (ADS)

Toher, Cormac

2015-03-01

High-throughput computational materials science provides researchers with the opportunity to rapidly generate large databases of materials properties. To rapidly add thermal properties to the AFLOWLIB consortium and Materials Project repositories, we have implemented an automated quasi-harmonic Debye model, the Automatic GIBBS Library (AGL). This enables us to screen thousands of materials for thermal conductivity, bulk modulus, thermal expansion and related properties. The search and sort functions of the online database can then be used to identify suitable materials for more in-depth study using more precise computational or experimental techniques. AFLOW-AGL source code is public domain and will soon be released within the GNU-GPL license.

Compressed domain ECG biometric with two-lead features

NASA Astrophysics Data System (ADS)

Lee, Wan-Jou; Chang, Wen-Whei

2016-07-01

This study presents a new method to combine ECG biometrics with data compression within a common JPEG2000 framework. We target the two-lead ECG configuration that is routinely used in long-term heart monitoring. Incorporation of compressed-domain biometric techniques enables faster person identification as it by-passes the full decompression. Experiments on public ECG databases demonstrate the validity of the proposed method for biometric identification with high accuracies on both healthy and diseased subjects.

Flight-testing and frequency-domain analysis for rotorcraft handling qualities

NASA Technical Reports Server (NTRS)

Ham, Johnnie A.; Gardner, Charles K.; Tischler, Mark B.

1995-01-01

A demonstration of frequency-domain flight-testing techniques and analysis was performed on a U.S. Army OH-58D helicopter in support of the OH-58D Airworthiness and Flight Characteristics Evaluation and of the Army's development and ongoing review of Aeronautical Design Standard 33C, Handling Qualities Requirements for Military Rotorcraft. Hover and forward flight (60 kn) tests were conducted in 1 flight hour by Army experimental test pilots. Further processing of the hover data generated a complete database of velocity, angular-rate, and acceleration-frequency responses to control inputs. A joint effort was then undertaken by the Airworthiness Qualification Test Dirtectorate and the U.S. Army Aeroflightdynamics Directorate to derive handling-quality information from the frequency-domain database using a variety of approaches. This report documents numerous results that have been obtained from the simple frequency-domain tests; in many areas, these results provide more insight into the aircraft dynmamics that affect handling qualities than do traditional flight tests. The handling-quality results include ADS-33C bandwidth and phase-delay calculations, vibration spectral determinations, transfer-function models to examine single-axis results, and a six-degree-of-freedom fully coupled state-space model. The ability of this model to accurately predict responses was verified using data from pulse inputs. This report also documents the frequency-sweep flight-test technique and data analysis used to support the tests.

Open Microphone Speech Understanding: Correct Discrimination Of In Domain Speech

NASA Technical Reports Server (NTRS)

Hieronymus, James; Aist, Greg; Dowding, John

2006-01-01

An ideal spoken dialogue system listens continually and determines which utterances were spoken to it, understands them and responds appropriately while ignoring the rest This paper outlines a simple method for achieving this goal which involves trading a slightly higher false rejection rate of in domain utterances for a higher correct rejection rate of Out of Domain (OOD) utterances. The system recognizes semantic entities specified by a unification grammar which is specialized by Explanation Based Learning (EBL). so that it only uses rules which are seen in the training data. The resulting grammar has probabilities assigned to each construct so that overgeneralizations are not a problem. The resulting system only recognizes utterances which reduce to a valid logical form which has meaning for the system and rejects the rest. A class N-gram grammar has been trained on the same training data. This system gives good recognition performance and offers good Out of Domain discrimination when combined with the semantic analysis. The resulting systems were tested on a Space Station Robot Dialogue Speech Database and a subset of the OGI conversational speech database. Both systems run in real time on a PC laptop and the present performance allows continuous listening with an acceptably low false acceptance rate. This type of open microphone system has been used in the Clarissa procedure reading and navigation spoken dialogue system which is being tested on the International Space Station.

Barriers related to prenatal care utilization among women

PubMed Central

Roozbeh, Nasibeh; Nahidi, Fatemeh; Hajiyan, Sepideh

2016-01-01

Objectives To investigate barriers related to prenatal care utilization among women. Methods Data was collected in both English and Persian databases. English databases included: the International Medical Sciences, Medline, Web of Science, Scopus, Google Scholar. The Persian databases included: the Iranmedex, the State Inpatient Databases (SID) with the use of related keywords, and on the basis of inclusion-exclusion criteria. The keywords included are barrier, prenatal care, women, access, and preventive factors. OR and AND were Boolean operators. After the study, articles were summarized, unrelated articles were rejected, and related articles were identified. Inclusion criteria were all published articles from 1990 to 2015, written in English and Persian languages. The titles and abstracts are related, and addressed all subjects about barriers related to prenatal care utilization. At the end, all duplicated articles were excluded. There were no restrictions for exclusion or inclusion of articles. Exclusion criteria were failure in reporting in studies, case studies, and lack of access to the full text. Results After searching various databases, 112 related articles were included. After reviewing articles’ titles, 67 unrelated articles and abstracts were rejected, 45 articles were evaluated, 20 of them were duplicated. Then, the qualities of 25 articles were analyzed. Therefore, 5 articles were excluded due to not mentioning the sample size, mismatches between method and data, or results. Total of 20 articles were selected for final analysis. Prenatal care utilization barrier can be divided into various domains such as individual barriers, financial barriers, organizational barriers, social, and cultural barriers. Conclusion To increase prenatal care coverage, it is necessary to pay attention to all domains, especially individual and financial barriers.

Allie: a database and a search service of abbreviations and long forms

PubMed Central

Yamamoto, Yasunori; Yamaguchi, Atsuko; Bono, Hidemasa; Takagi, Toshihisa

2011-01-01

Many abbreviations are used in the literature especially in the life sciences, and polysemous abbreviations appear frequently, making it difficult to read and understand scientific papers that are outside of a reader’s expertise. Thus, we have developed Allie, a database and a search service of abbreviations and their long forms (a.k.a. full forms or definitions). Allie searches for abbreviations and their corresponding long forms in a database that we have generated based on all titles and abstracts in MEDLINE. When a user query matches an abbreviation, Allie returns all potential long forms of the query along with their bibliographic data (i.e. title and publication year). In addition, for each candidate, co-occurring abbreviations and a research field in which it frequently appears in the MEDLINE data are displayed. This function helps users learn about the context in which an abbreviation appears. To deal with synonymous long forms, we use a dictionary called GENA that contains domain-specific terms such as gene, protein or disease names along with their synonymic information. Conceptually identical domain-specific terms are regarded as one term, and then conceptually identical abbreviation-long form pairs are grouped taking into account their appearance in MEDLINE. To keep up with new abbreviations that are continuously introduced, Allie has an automatic update system. In addition, the database of abbreviations and their long forms with their corresponding PubMed IDs is constructed and updated weekly. Database URL: The Allie service is available at http://allie.dbcls.jp/. PMID:21498548

The 2015 Nucleic Acids Research Database Issue and molecular biology database collection.

PubMed

Galperin, Michael Y; Rigden, Daniel J; Fernández-Suárez, Xosé M

2015-01-01

The 2015 Nucleic Acids Research Database Issue contains 172 papers that include descriptions of 56 new molecular biology databases, and updates on 115 databases whose descriptions have been previously published in NAR or other journals. Following the classification that has been introduced last year in order to simplify navigation of the entire issue, these articles are divided into eight subject categories. This year's highlights include RNAcentral, an international community portal to various databases on noncoding RNA; ValidatorDB, a validation database for protein structures and their ligands; SASBDB, a primary repository for small-angle scattering data of various macromolecular complexes; MoonProt, a database of 'moonlighting' proteins, and two new databases of protein-protein and other macromolecular complexes, ComPPI and the Complex Portal. This issue also includes an unusually high number of cancer-related databases and other databases dedicated to genomic basics of disease and potential drugs and drug targets. The size of NAR online Molecular Biology Database Collection, http://www.oxfordjournals.org/nar/database/a/, remained approximately the same, following the addition of 74 new resources and removal of 77 obsolete web sites. The entire Database Issue is freely available online on the Nucleic Acids Research web site (http://nar.oxfordjournals.org/). Published by Oxford University Press on behalf of Nucleic Acids Research 2014. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Specification, Design, and Analysis of Advanced HUMS Architectures

NASA Technical Reports Server (NTRS)

Mukkamala, Ravi

2004-01-01

During the two-year project period, we have worked on several aspects of domain-specific architectures for HUMS. In particular, we looked at using scenario-based approach for the design and designed a language for describing such architectures. The language is now being used in all aspects of our HUMS design. In particular, we have made contributions in the following areas. 1) We have employed scenarios in the development of HUMS in three main areas. They are: (a) To improve reusability by using scenarios as a library indexing tool and as a domain analysis tool; (b) To improve maintainability by recording design rationales from two perspectives - problem domain and solution domain; (c) To evaluate the software architecture. 2) We have defined a new architectural language called HADL or HUMS Architectural Definition Language. It is a customized version of xArch/xADL. It is based on XML and, hence, is easily portable from domain to domain, application to application, and machine to machine. Specifications written in HADL can be easily read and parsed using the currently available XML parsers. Thus, there is no need to develop a plethora of software to support HADL. 3) We have developed an automated design process that involves two main techniques: (a) Selection of solutions from a large space of designs; (b) Synthesis of designs. However, the automation process is not an absolute Artificial Intelligence (AI) approach though it uses a knowledge-based system that epitomizes a specific HUMS domain. The process uses a database of solutions as an aid to solve the problems rather than creating a new design in the literal sense. Since searching is adopted as the main technique, the challenges involved are: (a) To minimize the effort in searching the database where a very large number of possibilities exist; (b) To develop representations that could conveniently allow us to depict design knowledge evolved over many years; (c) To capture the required information that aid the automation process.

Life sciences domain analysis model

PubMed Central

Freimuth, Robert R; Freund, Elaine T; Schick, Lisa; Sharma, Mukesh K; Stafford, Grace A; Suzek, Baris E; Hernandez, Joyce; Hipp, Jason; Kelley, Jenny M; Rokicki, Konrad; Pan, Sue; Buckler, Andrew; Stokes, Todd H; Fernandez, Anna; Fore, Ian; Buetow, Kenneth H

2012-01-01

Objective Meaningful exchange of information is a fundamental challenge in collaborative biomedical research. To help address this, the authors developed the Life Sciences Domain Analysis Model (LS DAM), an information model that provides a framework for communication among domain experts and technical teams developing information systems to support biomedical research. The LS DAM is harmonized with the Biomedical Research Integrated Domain Group (BRIDG) model of protocol-driven clinical research. Together, these models can facilitate data exchange for translational research. Materials and methods The content of the LS DAM was driven by analysis of life sciences and translational research scenarios and the concepts in the model are derived from existing information models, reference models and data exchange formats. The model is represented in the Unified Modeling Language and uses ISO 21090 data types. Results The LS DAM v2.2.1 is comprised of 130 classes and covers several core areas including Experiment, Molecular Biology, Molecular Databases and Specimen. Nearly half of these classes originate from the BRIDG model, emphasizing the semantic harmonization between these models. Validation of the LS DAM against independently derived information models, research scenarios and reference databases supports its general applicability to represent life sciences research. Discussion The LS DAM provides unambiguous definitions for concepts required to describe life sciences research. The processes established to achieve consensus among domain experts will be applied in future iterations and may be broadly applicable to other standardization efforts. Conclusions The LS DAM provides common semantics for life sciences research. Through harmonization with BRIDG, it promotes interoperability in translational science. PMID:22744959

Public participation in genetic databases: crossing the boundaries between biobanks and forensic DNA databases through the principle of solidarity

PubMed Central

Machado, Helena; Silva, Susana

2015-01-01

The ethical aspects of biobanks and forensic DNA databases are often treated as separate issues. As a reflection of this, public participation, or the involvement of citizens in genetic databases, has been approached differently in the fields of forensics and medicine. This paper aims to cross the boundaries between medicine and forensics by exploring the flows between the ethical issues presented in the two domains and the subsequent conceptualisation of public trust and legitimisation. We propose to introduce the concept of ‘solidarity’, traditionally applied only to medical and research biobanks, into a consideration of public engagement in medicine and forensics. Inclusion of a solidarity-based framework, in both medical biobanks and forensic DNA databases, raises new questions that should be included in the ethical debate, in relation to both health services/medical research and activities associated with the criminal justice system. PMID:26139851

CELL5M: A geospatial database of agricultural indicators for Africa South of the Sahara.

PubMed

Koo, Jawoo; Cox, Cindy M; Bacou, Melanie; Azzarri, Carlo; Guo, Zhe; Wood-Sichra, Ulrike; Gong, Queenie; You, Liangzhi

2016-01-01

Recent progress in large-scale georeferenced data collection is widening opportunities for combining multi-disciplinary datasets from biophysical to socioeconomic domains, advancing our analytical and modeling capacity. Granular spatial datasets provide critical information necessary for decision makers to identify target areas, assess baseline conditions, prioritize investment options, set goals and targets and monitor impacts. However, key challenges in reconciling data across themes, scales and borders restrict our capacity to produce global and regional maps and time series. This paper provides overview, structure and coverage of CELL5M-an open-access database of geospatial indicators at 5 arc-minute grid resolution-and introduces a range of analytical applications and case-uses. CELL5M covers a wide set of agriculture-relevant domains for all countries in Africa South of the Sahara and supports our understanding of multi-dimensional spatial variability inherent in farming landscapes throughout the region.

BIND: the Biomolecular Interaction Network Database

PubMed Central

Bader, Gary D.; Betel, Doron; Hogue, Christopher W. V.

2003-01-01

The Biomolecular Interaction Network Database (BIND: http://bind.ca) archives biomolecular interaction, complex and pathway information. A web-based system is available to query, view and submit records. BIND continues to grow with the addition of individual submissions as well as interaction data from the PDB and a number of large-scale interaction and complex mapping experiments using yeast two hybrid, mass spectrometry, genetic interactions and phage display. We have developed a new graphical analysis tool that provides users with a view of the domain composition of proteins in interaction and complex records to help relate functional domains to protein interactions. An interaction network clustering tool has also been developed to help focus on regions of interest. Continued input from users has helped further mature the BIND data specification, which now includes the ability to store detailed information about genetic interactions. The BIND data specification is available as ASN.1 and XML DTD. PMID:12519993

3D THz hyperspectrum applied in security check-in

NASA Astrophysics Data System (ADS)

Damian, V.; Logofǎtu, P. C.; Vasile, T.

2016-12-01

We developed a measuring technology using a TDS-THz system to construct hyperspectral images of some objects, including hazardous materials. "T-rays" (the THz spectral domain of the light) have a growing importance in security and imagistic domain. Due to their property of penetrating through dielectric objects, and using non-ionizing radiations, the THz systems have become a standard for "hot-places" (airports, train stations etc.). The hyperspectral images are 3D images having 2D spatial dimension and one spectral dimension. In this way, we obtain simultaneously information about the form of the object and its molecular composition. For discriminating between substances, we must first build a database of spectra for hazardous and dangerous substances. We experiment our system on some items (among them a firecracker, a cigarette and a metal collar) and we tried to discriminate between them using the database of spectra.

[Family of ribosomal proteins S1 contains unique conservative domain].

PubMed

Deriusheva, E I; Machulin, A V; Selivanova, O M; Serdiuk, I N

2010-01-01

Different representatives of bacteria have different number of amino acid residues in the ribosomal proteins S1. This number varies from 111 (Spiroplasma kunkelii) to 863 a.a. (Treponema pallidum). Traditionally and for lack of this protein three-dimensional structure, its architecture is represented as repeating S1 domains. Number of these domains depends on the protein's length. Domain's quantity and its boundaries data are contained in the specialized databases, such as SMART, Pfam and PROSITE. However, for the same object these data may be very different. For search of domain's quantity and its boundaries, new approach, based on the analysis of dicted secondary structure (PsiPred), was used. This approach allowed us to reveal structural domains in amino acid sequences of S1 proteins and at that number varied from one to six. Alignment of S1 proteins, containing different domain's number, with the S1 RNAbinding domain of Escherichia coli PNPase elicited a fact that in family of ribosomal proteins SI one domain has maximal homology with S1 domain from PNPase. This conservative domain migrates along polypeptide chain and locates in proteins, containing different domain's number, according to specified pattern. In this domain as well in the S1 domain from PNPase, residues Phe-19, Phe-22, His-34, Asp-64 and Arg-68 are clustered on the surface and formed RNA binding site.

NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

PubMed Central

Pruitt, Kim D.; Tatusova, Tatiana; Maglott, Donna R.

2005-01-01

The National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) database (http://www.ncbi.nlm.nih.gov/RefSeq/) provides a non-redundant collection of sequences representing genomic data, transcripts and proteins. Although the goal is to provide a comprehensive dataset representing the complete sequence information for any given species, the database pragmatically includes sequence data that are currently publicly available in the archival databases. The database incorporates data from over 2400 organisms and includes over one million proteins representing significant taxonomic diversity spanning prokaryotes, eukaryotes and viruses. Nucleotide and protein sequences are explicitly linked, and the sequences are linked to other resources including the NCBI Map Viewer and Gene. Sequences are annotated to include coding regions, conserved domains, variation, references, names, database cross-references, and other features using a combined approach of collaboration and other input from the scientific community, automated annotation, propagation from GenBank and curation by NCBI staff. PMID:15608248

Fast Multivariate Search on Large Aviation Datasets

NASA Technical Reports Server (NTRS)

Bhaduri, Kanishka; Zhu, Qiang; Oza, Nikunj C.; Srivastava, Ashok N.

2010-01-01

Multivariate Time-Series (MTS) are ubiquitous, and are generated in areas as disparate as sensor recordings in aerospace systems, music and video streams, medical monitoring, and financial systems. Domain experts are often interested in searching for interesting multivariate patterns from these MTS databases which can contain up to several gigabytes of data. Surprisingly, research on MTS search is very limited. Most existing work only supports queries with the same length of data, or queries on a fixed set of variables. In this paper, we propose an efficient and flexible subsequence search framework for massive MTS databases, that, for the first time, enables querying on any subset of variables with arbitrary time delays between them. We propose two provably correct algorithms to solve this problem (1) an R-tree Based Search (RBS) which uses Minimum Bounding Rectangles (MBR) to organize the subsequences, and (2) a List Based Search (LBS) algorithm which uses sorted lists for indexing. We demonstrate the performance of these algorithms using two large MTS databases from the aviation domain, each containing several millions of observations Both these tests show that our algorithms have very high prune rates (>95%) thus needing actual

Metallopeptidases of Toxoplasma gondii: in silico identification and gene expression.

PubMed

Escotte-Binet, Sandie; Huguenin, Antoine; Aubert, Dominique; Martin, Anne-Pascaline; Kaltenbach, Matthieu; Florent, Isabelle; Villena, Isabelle

2018-01-01

Metallopeptidases are a family of proteins with domains that remain highly conserved throughout evolution. These hydrolases require divalent metal cation(s) to activate the water molecule in order to carry out their catalytic action on peptide bonds by nucleophilic attack. Metallopeptidases from parasitic protozoa, including Toxoplasma, are investigated because of their crucial role in parasite biology. In the present study, we screened the T. gondii database using PFAM motifs specific for metallopeptidases in association with the MEROPS peptidase Database (release 10.0). In all, 49 genes encoding proteins with metallopeptidase signatures were identified in the Toxoplasma genome. An Interpro Search enabled us to uncover their domain/motif organization, and orthologs with the highest similarity by BLAST were used for annotation. These 49 Toxoplasma metallopeptidases clustered into 15 families described in the MEROPS database. Experimental expression analysis of their genes in the tachyzoite stage revealed transcription for all genes studied. Further research on the role of these peptidases should increase our knowledge of basic Toxoplasma biology and provide opportunities to identify novel therapeutic targets. This type of study would also open a path towards the comparative biology of apicomplexans. © S. Escotte-Binet et al., published by EDP Sciences, 2018.

X-ray structure of a two-domain type laccase: a missing link in the evolution of multi-copper proteins.

PubMed

Komori, Hirofumi; Miyazaki, Kentaro; Higuchi, Yoshiki

2009-04-02

A multi-copper protein with two cupredoxin-like domains was identified from our in-house metagenomic database. The recombinant protein, mgLAC, contained four copper ions/subunits, oxidized various phenolic and non-phenolic substrates, and had spectroscopic properties similar to common laccases. X-ray structure analysis revealed a homotrimeric architecture for this enzyme, which resembles nitrite reductase (NIR). However, a difference in copper coordination was found at the domain interface. mgLAC contains a T2/T3 tri-nuclear copper cluster at this site, whereas a mononuclear T2 copper occupies this position in NIR. The trimer is thus an essential part of the architecture of two-domain multi-copper proteins, and mgLAC may be an evolutionary precursor of NIR.

Genomic analysis of bifunctional Class C-Class D β-lactamases in environmental bacteria.

PubMed

Silveira, Melise Chaves; Catanho, Marcos; Miranda, Antônio Basílio de

2018-01-01

β-lactamases, which are found in several bacterial species and environments, are the main cause of resistance to β-lactams in Gram-negative bacteria. In 2009, a protein (LRA-13) with two β-lactamase domains (one class C domain and one class D domain) was experimentally characterised, and an extended action spectrum against β-lactams consistent with two functional domains was found. Here, we present the results of searches in the non-redundant NCBI protein database that revealed the existence of a group of homologous bifunctional β-lactamases in the genomes of environmental bacteria. These findings suggest that bifunctional β-lactamases are widespread in nature; these findings also raise concern that bifunctional β-lactamases may be transferred to bacteria of clinical importance through lateral gene transfer mechanisms.

An approach to predict Sudden Cardiac Death (SCD) using time domain and bispectrum features from HRV signal.

PubMed

Houshyarifar, Vahid; Chehel Amirani, Mehdi

2016-08-12

In this paper we present a method to predict Sudden Cardiac Arrest (SCA) with higher order spectral (HOS) and linear (Time) features extracted from heart rate variability (HRV) signal. Predicting the occurrence of SCA is important in order to avoid the probability of Sudden Cardiac Death (SCD). This work is a challenge to predict five minutes before SCA onset. The method consists of four steps: pre-processing, feature extraction, feature reduction, and classification. In the first step, the QRS complexes are detected from the electrocardiogram (ECG) signal and then the HRV signal is extracted. In second step, bispectrum features of HRV signal and time-domain features are obtained. Six features are extracted from bispectrum and two features from time-domain. In the next step, these features are reduced to one feature by the linear discriminant analysis (LDA) technique. Finally, KNN and support vector machine-based classifiers are used to classify the HRV signals. We used two database named, MIT/BIH Sudden Cardiac Death (SCD) Database and Physiobank Normal Sinus Rhythm (NSR). In this work we achieved prediction of SCD occurrence for six minutes before the SCA with the accuracy over 91%.

Providing Data Quality Information for Remote Sensing Applications

NASA Astrophysics Data System (ADS)

Albrecht, F.; Blaschke, T.; Lang, S.; Abdulmutalib, H. M.; Szabó, G.; Barsi, Á.; Batini, C.; Bartsch, A.; Kugler, Zs.; Tiede, D.; Huang, G.

2018-04-01

The availability and accessibility of remote sensing (RS) data, cloud processing platforms and provided information products and services has increased the size and diversity of the RS user community. This development also generates a need for validation approaches to assess data quality. Validation approaches employ quality criteria in their assessment. Data Quality (DQ) dimensions as the basis for quality criteria have been deeply investigated in the database area and in the remote sensing domain. Several standards exist within the RS domain but a general classification - established for databases - has been adapted only recently. For an easier identification of research opportunities, a better understanding is required how quality criteria are employed in the RS lifecycle. Therefore, this research investigates how quality criteria support decisions that guide the RS lifecycle and how they relate to the measured DQ dimensions. Subsequently follows an overview of the relevant standards in the RS domain that is matched to the RS lifecycle. Conclusively, the required research needs are identified that would enable a complete understanding of the interrelationships between the RS lifecycle, the data sources and the DQ dimensions, an understanding that would be very valuable for designing validation approaches in RS.

The SH2 domain interaction landscape.

PubMed

Tinti, Michele; Kiemer, Lars; Costa, Stefano; Miller, Martin L; Sacco, Francesca; Olsen, Jesper V; Carducci, Martina; Paoluzi, Serena; Langone, Francesca; Workman, Christopher T; Blom, Nikolaj; Machida, Kazuya; Thompson, Christopher M; Schutkowski, Mike; Brunak, Søren; Mann, Matthias; Mayer, Bruce J; Castagnoli, Luisa; Cesareni, Gianni

2013-04-25

Members of the SH2 domain family modulate signal transduction by binding to short peptides containing phosphorylated tyrosines. Each domain displays a distinct preference for the sequence context of the phosphorylated residue. We have developed a high-density peptide chip technology that allows for probing of the affinity of most SH2 domains for a large fraction of the entire complement of tyrosine phosphopeptides in the human proteome. Using this technique, we have experimentally identified thousands of putative SH2-peptide interactions for more than 70 different SH2 domains. By integrating this rich data set with orthogonal context-specific information, we have assembled an SH2-mediated probabilistic interaction network, which we make available as a community resource in the PepspotDB database. A predicted dynamic interaction between the SH2 domains of the tyrosine phosphatase SHP2 and the phosphorylated tyrosine in the extracellular signal-regulated kinase activation loop was validated by experiments in living cells. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

Development of a Tsunami Scenario Database for Marmara Sea

NASA Astrophysics Data System (ADS)

Ozer Sozdinler, Ceren; Necmioglu, Ocal; Meral Ozel, Nurcan

2016-04-01

Due to the very short travel times in Marmara Sea, a Tsunami Early Warning System (TEWS) has to be strongly coupled with the earthquake early warning system and should be supported with a pre-computed tsunami scenario database to be queried in near real-time based on the initial earthquake parameters. To address this problem, 30 different composite earthquake scenarios with maximum credible Mw values based on 32 fault segments have been identified to produce a detailed scenario database for all possible earthquakes in the Marmara Sea with a tsunamigenic potential. The bathy/topo data of Marmara Sea was prepared using GEBCO and ASTER data, bathymetric measurements along Bosphorus, Istanbul and Dardanelle, Canakkale and the coastline digitized from satellite images. The coarser domain in 90m-grid size was divided into 11 sub-regions having 30m-grid size in order to increase the data resolution and precision of the calculation results. The analyses were performed in nested domains with numerical model NAMIDANCE using non-linear shallow water equations. In order to cover all the residential areas, industrial facilities and touristic locations, more than 1000 numerical gauge points were selected along the coasts of Marmara Sea, which are located at water depth of 5 to 10m in finer domain. The distributions of tsunami hydrodynamic parameters were investigated together with the change of water surface elevations, current velocities, momentum fluxes and other important parameters at the gauge points. This work is funded by the project MARsite - New Directions in Seismic Hazard assessment through Focused Earth Observation in the Marmara Supersite (FP7-ENV.2012 6.4-2, Grant 308417 - see NH2.3/GMPV7.4/SM7.7) and supported by SATREPS-MarDim Project (Earthquake and Tsunami Disaster Mitigation in the Marmara Region and Disaster Education in Turkey) and JICA (Japan International Cooperation Agency). The authors would like to acknowledge Ms. Basak Firat for her assistance in preparation of the database.

The uses of outcome measures within multidisciplinary early childhood intervention services: a systematic review.

PubMed

Calder, Samuel; Ward, Roslyn; Jones, Megan; Johnston, Jenelle; Claessen, Mary

2017-07-18

Purpose of the article: To review the use of outcome measures, across the domains of activity, participation, and environment, within multidisciplinary early childhood intervention services. A systematic literature search was undertaken that included four electronic databases: Medline, CINAHL, EMBASE, and the Cochrane Library and Cochrane Database of Systematic Review. Inclusion criteria were age 0-24 months, having or at risk of a developmental disability, in receipt of multidisciplinary early childhood intervention services, and included outcome measures across all domains of the International Classification of Functioning-Child & Youth (ICF-CY). Only peer-reviewed journal articles were considered. Eligible studies were coded using the Oxford Levels of Evidence. Methodological quality was assessed using the Physiotherapy Evidence Database (PEDro) Scale for randomised controlled trials and the QualSyst for non-randomised control trials. Of the total of 5764 records identified, 10 were considered to meet inclusion criteria. Fourteen outcome measures were identified, addressing the domains of activity, participation, and environment. Of these, eight have been recommended in the early intervention literature. While the methodological quality of the 10 studies varied, these papers make a contribution to the body of research that acknowledges the role of routine and enriched environments. Implications for Rehabilitation Core practice elements of multidisciplinary early childhood intervention services indicate it is necessary to select outcome measures framed within the International Classification of Functioning-Child & Youth to inform clinical decision-making for measuring intervention effectiveness across the domains of activity, participation and environment. Of the identified measures, three (Canadian Occupational Performance Measure, Pediatric Evaluation of Disability Inventory, and Goal Attainment Scaling) are well-established and identified in the literature as multidisciplinary outcome measures for children with developmental disability. The selection of an appropriate outcome measure depends on the age of the child, individual goals of the family, and the type of intervention. This requires the combination of measures as no one measure alone will capture all components of the International Classification of Functioning-Child & Youth.

[Bibliometric analysis of current glaucoma research based on Pubmed database].

PubMed

Huang, Wen-bin; Wang, Wei; Zhou, Min-wen; Chen, Shi-da; Zhang, Xiu-lan

2013-11-01

To survey the distribution pattern and subject domain knowledge of worldwide glaucoma research based on literatures in Pubmed database. Literatures on glaucoma published in 2007 to 2011 were identified in Pubmed database. The analytic items of an article include published year, country, language author, and journal. After core mesh terms had been characterized by BICOMS, the co-occurrence matrix was built. Cluster analysis was finished by SPSS 20.0. Then visualized network was drawn using ucinet 6.0. Totally 6427 literatures were included, the number of annual articles changed slightly between 2007 and 2011. The United States, England, Germany, Australia, and France together accounted for 77.63% of articles. There were 52 high-frequency subjects and hot topics were clustered into the following 10 categories: (1) Pathology of optic disc and nerve fibers and OCT application, (2) METHODS: of visual field (VF) and visual function examination, (3) Glaucoma drug medications, (4) Pathology and physiology of primary open angle glaucoma (POAG) including VF and intraocular pressure (IOP), (5) Glaucoma surgery, (6) Gene research related to POAG, (7) Glaucoma disease pathology and animal models, (8) Ocular hypertension (OHT) induced complications and corneal changes, (9) Etiology of congenital glaucoma and complications, (10) Etiology and epidemiology of glaucoma. The visualized domain knowledge mapping was successfully built. The pathology of optic disc and nerve fibers, medications, and surgery were well developed. Study on IOP and visual field was in the core domain, which have an important link to etiology, diagnosis, and therapy. The researches on glaucomatous gene, disease pathology model, congenital glaucoma, etiology and epidemiology were not developed well, which are of great promotion space. The distribution pattern and subject domain knowledge of worldwide glaucoma research in the recent five years were shown by using bibliometric analysis.Western developed countries play a leading role in the field of glaucoma research, the international influence of related research in China needs to be strengthened.

Geospatial Database for Strata Objects Based on Land Administration Domain Model (ladm)

NASA Astrophysics Data System (ADS)

Nasorudin, N. N.; Hassan, M. I.; Zulkifli, N. A.; Rahman, A. Abdul

2016-09-01

Recently in our country, the construction of buildings become more complex and it seems that strata objects database becomes more important in registering the real world as people now own and use multilevel of spaces. Furthermore, strata title was increasingly important and need to be well-managed. LADM is a standard model for land administration and it allows integrated 2D and 3D representation of spatial units. LADM also known as ISO 19152. The aim of this paper is to develop a strata objects database using LADM. This paper discusses the current 2D geospatial database and needs for 3D geospatial database in future. This paper also attempts to develop a strata objects database using a standard data model (LADM) and to analyze the developed strata objects database using LADM data model. The current cadastre system in Malaysia includes the strata title is discussed in this paper. The problems in the 2D geospatial database were listed and the needs for 3D geospatial database in future also is discussed. The processes to design a strata objects database are conceptual, logical and physical database design. The strata objects database will allow us to find the information on both non-spatial and spatial strata title information thus shows the location of the strata unit. This development of strata objects database may help to handle the strata title and information.

Proteins with an Euonymus lectin-like domain are ubiquitous in Embryophyta

PubMed Central

2009-01-01

Background Cloning of the Euonymus lectin led to the discovery of a novel domain that also occurs in some stress-induced plant proteins. The distribution and the diversity of proteins with an Euonymus lectin (EUL) domain were investigated using detailed analysis of sequences in publicly accessible genome and transcriptome databases. Results Comprehensive in silico analyses indicate that the recently identified Euonymus europaeus lectin domain represents a conserved structural unit of a novel family of putative carbohydrate-binding proteins, which will further be referred to as the Euonymus lectin (EUL) family. The EUL domain is widespread among plants. Analysis of retrieved sequences revealed that some sequences consist of a single EUL domain linked to an unrelated N-terminal domain whereas others comprise two in tandem arrayed EUL domains. A new classification system for these lectins is proposed based on the overall domain architecture. Evolutionary relationships among the sequences with EUL domains are discussed. Conclusion The identification of the EUL family provides the first evidence for the occurrence in terrestrial plants of a highly conserved plant specific domain. The widespread distribution of the EUL domain strikingly contrasts the more limited or even narrow distribution of most other lectin domains found in plants. The apparent omnipresence of the EUL domain is indicative for a universal role of this lectin domain in plants. Although there is unambiguous evidence that several EUL domains possess carbohydrate-binding activity further research is required to corroborate the carbohydrate-binding properties of different members of the EUL family. PMID:19930663

Visible and Thermal Imaging of Sea Ice and Open Water from Coast Guard Arctic Domain Awareness Flights

DTIC Science & Technology

2012-09-30

to better predict the seasonal evolution of the ice cover . APPROACH The Coast Guard Arctic Domain Awareness (ADA) flights based out of Kodiak...does not display a currently valid OMB control number. 1. REPORT DATE 2012 2. REPORT TYPE N/A 3. DATES COVERED - 4. TITLE AND SUBTITLE...satellite remote sensing data ( MODIS and SSMI) for flight planning before flights and during and after flights for inclusion in the SIZRS-DC database

[A security protocol for the exchange of personal medical data via Internet: monitoring treatment and drug effects].

PubMed

Viviani, R; Fischer, J; Spitzer, M; Freudenmann, R W

2004-04-01

We present a security protocol for the exchange of medical data via the Internet, based on the type/domain model. We discuss two applications of the protocol: in a system for the exchange of data for quality assurance, and in an on-line database of adverse reactions to drug use. We state that a type/domain security protocol can successfully comply with the complex requirements for data privacy and accessibility typical of such applications.

Domain Regeneration for Cross-Database Micro-Expression Recognition

NASA Astrophysics Data System (ADS)

Zong, Yuan; Zheng, Wenming; Huang, Xiaohua; Shi, Jingang; Cui, Zhen; Zhao, Guoying

2018-05-01

In this paper, we investigate the cross-database micro-expression recognition problem, where the training and testing samples are from two different micro-expression databases. Under this setting, the training and testing samples would have different feature distributions and hence the performance of most existing micro-expression recognition methods may decrease greatly. To solve this problem, we propose a simple yet effective method called Target Sample Re-Generator (TSRG) in this paper. By using TSRG, we are able to re-generate the samples from target micro-expression database and the re-generated target samples would share same or similar feature distributions with the original source samples. For this reason, we can then use the classifier learned based on the labeled source samples to accurately predict the micro-expression categories of the unlabeled target samples. To evaluate the performance of the proposed TSRG method, extensive cross-database micro-expression recognition experiments designed based on SMIC and CASME II databases are conducted. Compared with recent state-of-the-art cross-database emotion recognition methods, the proposed TSRG achieves more promising results.

MScanner: a classifier for retrieving Medline citations

PubMed Central

Poulter, Graham L; Rubin, Daniel L; Altman, Russ B; Seoighe, Cathal

2008-01-01

Background Keyword searching through PubMed and other systems is the standard means of retrieving information from Medline. However, ad-hoc retrieval systems do not meet all of the needs of databases that curate information from literature, or of text miners developing a corpus on a topic that has many terms indicative of relevance. Several databases have developed supervised learning methods that operate on a filtered subset of Medline, to classify Medline records so that fewer articles have to be manually reviewed for relevance. A few studies have considered generalisation of Medline classification to operate on the entire Medline database in a non-domain-specific manner, but existing applications lack speed, available implementations, or a means to measure performance in new domains. Results MScanner is an implementation of a Bayesian classifier that provides a simple web interface for submitting a corpus of relevant training examples in the form of PubMed IDs and returning results ranked by decreasing probability of relevance. For maximum speed it uses the Medical Subject Headings (MeSH) and journal of publication as a concise document representation, and takes roughly 90 seconds to return results against the 16 million records in Medline. The web interface provides interactive exploration of the results, and cross validated performance evaluation on the relevant input against a random subset of Medline. We describe the classifier implementation, cross validate it on three domain-specific topics, and compare its performance to that of an expert PubMed query for a complex topic. In cross validation on the three sample topics against 100,000 random articles, the classifier achieved excellent separation of relevant and irrelevant article score distributions, ROC areas between 0.97 and 0.99, and averaged precision between 0.69 and 0.92. Conclusion MScanner is an effective non-domain-specific classifier that operates on the entire Medline database, and is suited to retrieving topics for which many features may indicate relevance. Its web interface simplifies the task of classifying Medline citations, compared to building a pre-filter and classifier specific to the topic. The data sets and open source code used to obtain the results in this paper are available on-line and as supplementary material, and the web interface may be accessed at . PMID:18284683

Atomic interaction networks in the core of protein domains and their native folds.

PubMed

Soundararajan, Venkataramanan; Raman, Rahul; Raguram, S; Sasisekharan, V; Sasisekharan, Ram

2010-02-23

Vastly divergent sequences populate a majority of protein folds. In the quest to identify features that are conserved within protein domains belonging to the same fold, we set out to examine the entire protein universe on a fold-by-fold basis. We report that the atomic interaction network in the solvent-unexposed core of protein domains are fold-conserved, extraordinary sequence divergence notwithstanding. Further, we find that this feature, termed protein core atomic interaction network (or PCAIN) is significantly distinguishable across different folds, thus appearing to be "signature" of a domain's native fold. As part of this study, we computed the PCAINs for 8698 representative protein domains from families across the 1018 known protein folds to construct our seed database and an automated framework was developed for PCAIN-based characterization of the protein fold universe. A test set of randomly selected domains that are not in the seed database was classified with over 97% accuracy, independent of sequence divergence. As an application of this novel fold signature, a PCAIN-based scoring scheme was developed for comparative (homology-based) structure prediction, with 1-2 angstroms (mean 1.61A) C(alpha) RMSD generally observed between computed structures and reference crystal structures. Our results are consistent across the full spectrum of test domains including those from recent CASP experiments and most notably in the 'twilight' and 'midnight' zones wherein <30% and <10% target-template sequence identity prevails (mean twilight RMSD of 1.69A). We further demonstrate the utility of the PCAIN protocol to derive biological insight into protein structure-function relationships, by modeling the structure of the YopM effector novel E3 ligase (NEL) domain from plague-causative bacterium Yersinia Pestis and discussing its implications for host adaptive and innate immune modulation by the pathogen. Considering the several high-throughput, sequence-identity-independent applications demonstrated in this work, we suggest that the PCAIN is a fundamental fold feature that could be a valuable addition to the arsenal of protein modeling and analysis tools.

Atomic Interaction Networks in the Core of Protein Domains and Their Native Folds

PubMed Central

Soundararajan, Venkataramanan; Raman, Rahul; Raguram, S.; Sasisekharan, V.; Sasisekharan, Ram

2010-01-01

Vastly divergent sequences populate a majority of protein folds. In the quest to identify features that are conserved within protein domains belonging to the same fold, we set out to examine the entire protein universe on a fold-by-fold basis. We report that the atomic interaction network in the solvent-unexposed core of protein domains are fold-conserved, extraordinary sequence divergence notwithstanding. Further, we find that this feature, termed protein core atomic interaction network (or PCAIN) is significantly distinguishable across different folds, thus appearing to be “signature” of a domain's native fold. As part of this study, we computed the PCAINs for 8698 representative protein domains from families across the 1018 known protein folds to construct our seed database and an automated framework was developed for PCAIN-based characterization of the protein fold universe. A test set of randomly selected domains that are not in the seed database was classified with over 97% accuracy, independent of sequence divergence. As an application of this novel fold signature, a PCAIN-based scoring scheme was developed for comparative (homology-based) structure prediction, with 1–2 angstroms (mean 1.61A) Cα RMSD generally observed between computed structures and reference crystal structures. Our results are consistent across the full spectrum of test domains including those from recent CASP experiments and most notably in the ‘twilight’ and ‘midnight’ zones wherein <30% and <10% target-template sequence identity prevails (mean twilight RMSD of 1.69A). We further demonstrate the utility of the PCAIN protocol to derive biological insight into protein structure-function relationships, by modeling the structure of the YopM effector novel E3 ligase (NEL) domain from plague-causative bacterium Yersinia Pestis and discussing its implications for host adaptive and innate immune modulation by the pathogen. Considering the several high-throughput, sequence-identity-independent applications demonstrated in this work, we suggest that the PCAIN is a fundamental fold feature that could be a valuable addition to the arsenal of protein modeling and analysis tools. PMID:20186337

STCRDab: the structural T-cell receptor database

PubMed Central

de Oliveira, Saulo H P; Krawczyk, Konrad

2018-01-01

Abstract The Structural T–cell Receptor Database (STCRDab; http://opig.stats.ox.ac.uk/webapps/stcrdab) is an online resource that automatically collects and curates TCR structural data from the Protein Data Bank. For each entry, the database provides annotations, such as the α/β or γ/δ chain pairings, major histocompatibility complex details, and where available, antigen binding affinities. In addition, the orientation between the variable domains and the canonical forms of the complementarity-determining region loops are also provided. Users can select, view, and download individual or bulk sets of structures based on these criteria. Where available, STCRDab also finds antibody structures that are similar to TCRs, helping users explore the relationship between TCRs and antibodies. PMID:29087479

myChEMBL: a virtual machine implementation of open data and cheminformatics tools.

PubMed

Ochoa, Rodrigo; Davies, Mark; Papadatos, George; Atkinson, Francis; Overington, John P

2014-01-15

myChEMBL is a completely open platform, which combines public domain bioactivity data with open source database and cheminformatics technologies. myChEMBL consists of a Linux (Ubuntu) Virtual Machine featuring a PostgreSQL schema with the latest version of the ChEMBL database, as well as the latest RDKit cheminformatics libraries. In addition, a self-contained web interface is available, which can be modified and improved according to user specifications. The VM is available at: ftp://ftp.ebi.ac.uk/pub/databases/chembl/VM/myChEMBL/current. The web interface and web services code is available at: https://github.com/rochoa85/myChEMBL.

Using CLIPS in a distributed system: The Network Control Center (NCC) expert system

NASA Technical Reports Server (NTRS)

Wannemacher, Tom

1990-01-01

This paper describes an intelligent troubleshooting system for the Help Desk domain. It was developed on an IBM-compatible 80286 PC using Microsoft C and CLIPS and an AT&T 3B2 minicomputer using the UNIFY database and a combination of shell script, C programs and SQL queries. The two computers are linked by a lan. The functions of this system are to help non-technical NCC personnel handle trouble calls, to keep a log of problem calls with complete, concise information, and to keep a historical database of problems. The database helps identify hardware and software problem areas and provides a source of new rules for the troubleshooting knowledge base.

Structural genomics reveals EVE as a new ASCH/PUA-related domain

PubMed Central

Bertonati, Claudia; Punta, Marco; Fischer, Markus; Yachdav, Guy; Forouhar, Farhad; Zhou, Weihong; Kuzin, Alexander P.; Seetharaman, Jayaraman; Abashidze, Mariam; Ramelot, Theresa A.; Kennedy, Michael A.; Cort, John R.; Belachew, Adam; Hunt, John F.; Tong, Liang; Montelione, Gaetano T.; Rost, Burkhard

2014-01-01

Summary We report on several proteins recently solved by structural genomics consortia, in particular by the Northeast Structural Genomics consortium (NESG). The proteins considered in this study differ substantially in their sequences but they share a similar structural core, characterized by a pseudobarrel five-stranded beta sheet. This core corresponds to the PUA domain-like architecture in the SCOP database. By connecting sequence information with structural knowledge, we characterize a new subgroup of these proteins that we propose to be distinctly different from previously described PUA domain-like domains such as PUA proper or ASCH. We refer to these newly defined domains as EVE. Although EVE may have retained the ability of PUA domains to bind RNA, the available experimental and computational data suggests that both the details of its molecular function and its cellular function differ from those of other PUA domain-like domains. This study of EVE and its relatives illustrates how the combination of structure and genomics creates new insights by connecting a cornucopia of structures that map to the same evolutionary potential. Primary sequence information alone would have not been sufficient to reveal these evolutionary links. PMID:19191354

Structural Genomics Reveals EVE as a New ASCH/PUA-Related Domain

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

Bertonati, C.; Punta, M; Fischer, M

2008-01-01

We report on several proteins recently solved by structural genomics consortia, in particular by the Northeast Structural Genomics consortium (NESG). The proteins considered in this study differ substantially in their sequences but they share a similar structural core, characterized by a pseudobarrel five-stranded beta sheet. This core corresponds to the PUA domain-like architecture in the SCOP database. By connecting sequence information with structural knowledge, we characterize a new subgroup of these proteins that we propose to be distinctly different from previously described PUA domain-like domains such as PUA proper or ASCH. We refer to these newly defined domains as EVE.more » Although EVE may have retained the ability of PUA domains to bind RNA, the available experimental and computational data suggests that both the details of its molecular function and its cellular function differ from those of other PUA domain-like domains. This study of EVE and its relatives illustrates how the combination of structure and genomics creates new insights by connecting a cornucopia of structures that map to the same evolutionary potential. Primary sequence information alone would have not been sufficient to reveal these evolutionary links.« less

ClusterMine360: a database of microbial PKS/NRPS biosynthesis

PubMed Central

Conway, Kyle R.; Boddy, Christopher N.

2013-01-01

ClusterMine360 (http://www.clustermine360.ca/) is a database of microbial polyketide and non-ribosomal peptide gene clusters. It takes advantage of crowd-sourcing by allowing members of the community to make contributions while automation is used to help achieve high data consistency and quality. The database currently has >200 gene clusters from >185 compound families. It also features a unique sequence repository containing >10 000 polyketide synthase/non-ribosomal peptide synthetase domains. The sequences are filterable and downloadable as individual or multiple sequence FASTA files. We are confident that this database will be a useful resource for members of the polyketide synthases/non-ribosomal peptide synthetases research community, enabling them to keep up with the growing number of sequenced gene clusters and rapidly mine these clusters for functional information. PMID:23104377

The Human Transcript Database: A Catalogue of Full Length cDNA Inserts

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

Bouckk John; Michael McLeod; Kim Worley

1999-09-10

The BCM Search Launcher provided improved access to web-based sequence analysis services during the granting period and beyond. The Search Launcher web site grouped analysis procedures by function and provided default parameters that provided reasonable search results for most applications. For instance, most queries were automatically masked for repeat sequences prior to sequence database searches to avoid spurious matches. In addition to the web-based access and arrangements that were made using the functions easier, the BCM Search Launcher provided unique value-added applications like the BEAUTY sequence database search tool that combined information about protein domains and sequence database search resultsmore » to give an enhanced, more complete picture of the reliability and relative value of the information reported. This enhanced search tool made evaluating search results more straight-forward and consistent. Some of the favorite features of the web site are the sequence utilities and the batch client functionality that allows processing of multiple samples from the command line interface. One measure of the success of the BCM Search Launcher is the number of sites that have adopted the models first developed on the site. The graphic display on the BLAST search from the NCBI web site is one such outgrowth, as is the display of protein domain search results within BLAST search results, and the design of the Biology Workbench application. The logs of usage and comments from users confirm the great utility of this resource.« less

Conducting Privacy-Preserving Multivariable Propensity Score Analysis When Patient Covariate Information Is Stored in Separate Locations.

PubMed

Bohn, Justin; Eddings, Wesley; Schneeweiss, Sebastian

2017-03-15

Distributed networks of health-care data sources are increasingly being utilized to conduct pharmacoepidemiologic database studies. Such networks may contain data that are not physically pooled but instead are distributed horizontally (separate patients within each data source) or vertically (separate measures within each data source) in order to preserve patient privacy. While multivariable methods for the analysis of horizontally distributed data are frequently employed, few practical approaches have been put forth to deal with vertically distributed health-care databases. In this paper, we propose 2 propensity score-based approaches to vertically distributed data analysis and test their performance using 5 example studies. We found that these approaches produced point estimates close to what could be achieved without partitioning. We further found a performance benefit (i.e., lower mean squared error) for sequentially passing a propensity score through each data domain (called the "sequential approach") as compared with fitting separate domain-specific propensity scores (called the "parallel approach"). These results were validated in a small simulation study. This proof-of-concept study suggests a new multivariable analysis approach to vertically distributed health-care databases that is practical, preserves patient privacy, and warrants further investigation for use in clinical research applications that rely on health-care databases. © The Author 2017. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Towards communication-efficient quantum oblivious key distribution

NASA Astrophysics Data System (ADS)

Panduranga Rao, M. V.; Jakobi, M.

2013-01-01

Symmetrically private information retrieval, a fundamental problem in the field of secure multiparty computation, is defined as follows: A database D of N bits held by Bob is queried by a user Alice who is interested in the bit Db in such a way that (1) Alice learns Db and only Db and (2) Bob does not learn anything about Alice's choice b. While solutions to this problem in the classical domain rely largely on unproven computational complexity theoretic assumptions, it is also known that perfect solutions that guarantee both database and user privacy are impossible in the quantum domain. Jakobi [Phys. Rev. APLRAAN1050-294710.1103/PhysRevA.83.022301 83, 022301 (2011)] proposed a protocol for oblivious transfer using well-known quantum key device (QKD) techniques to establish an oblivious key to solve this problem. Their solution provided a good degree of database and user privacy (using physical principles like the impossibility of perfectly distinguishing nonorthogonal quantum states and the impossibility of superluminal communication) while being loss-resistant and implementable with commercial QKD devices (due to the use of the Scarani-Acin-Ribordy-Gisin 2004 protocol). However, their quantum oblivious key distribution (QOKD) protocol requires a communication complexity of O(NlogN). Since modern databases can be extremely large, it is important to reduce this communication as much as possible. In this paper, we first suggest a modification of their protocol wherein the number of qubits that need to be exchanged is reduced to O(N). A subsequent generalization reduces the quantum communication complexity even further in such a way that only a few hundred qubits are needed to be transferred even for very large databases.

Neuropsychological Performance Patterns of Adult ADHD Subtypes.

PubMed

LeRoy, Amy; Jacova, Claudia; Young, Caedy

2018-05-01

Neuropsychological performance patterns associated with adult ADHD subtypes are unknown. The aim of the current systematic review was to identify and synthesize available literature regarding neuropsychological performance associated with adult ADHD subtypes. Searches were completed using the databases PsycINFO and PubMed for studies published before March 2017 addressing adult ADHD subtypes and neuropsychological performance. Data characterizing the neuropsychological tests utilized in each study were obtained and sorted into eight domains. To summarize the results of all comparisons (ADHD subtype compared with control, or to each other), we counted the proportion of tests within each domain with significant group differences. We deemed four domains informative in differentiating ADHD subtypes from controls. Of these, memory was the only domain that held promise in distinguishing ADHD-Inattentive and ADHD-Combined. Limitations of the available literature are highlighted and recommendations for future research are provided.

Transcriptomics of the Bed Bug (Cimex lectularius)

PubMed Central

Rajarapu, Swapna P.; Jones, Susan C.; Mittapalli, Omprakash

2011-01-01

Background Bed bugs (Cimex lectularius) are blood-feeding insects poised to become one of the major pests in households throughout the United States. Resistance of C. lectularius to insecticides/pesticides is one factor thought to be involved in its sudden resurgence. Despite its high-impact status, scant knowledge exists at the genomic level for C. lectularius. Hence, we subjected the C. lectularius transcriptome to 454 pyrosequencing in order to identify potential genes involved in pesticide resistance. Methodology and Principal Findings Using 454 pyrosequencing, we obtained a total of 216,419 reads with 79,596,412 bp, which were assembled into 35,646 expressed sequence tags (3902 contigs and 31744 singletons). Nearly 85.9% of the C. lectularius sequences showed similarity to insect sequences, but 44.8% of the deduced proteins of C. lectularius did not show similarity with sequences in the GenBank non-redundant database. KEGG analysis revealed putative members of several detoxification pathways involved in pesticide resistance. Lamprin domains, Protein Kinase domains, Protein Tyrosine Kinase domains and cytochrome P450 domains were among the top Pfam domains predicted for the C. lectularius sequences. An initial assessment of putative defense genes, including a cytochrome P450 and a glutathione-S-transferase (GST), revealed high transcript levels for the cytochrome P450 (CYP9) in pesticide-exposed versus pesticide-susceptible C. lectularius populations. A significant number of single nucleotide polymorphisms (296) and microsatellite loci (370) were predicted in the C. lectularius sequences. Furthermore, 59 putative sequences of Wolbachia were retrieved from the database. Conclusions To our knowledge this is the first study to elucidate the genetic makeup of C. lectularius. This pyrosequencing effort provides clues to the identification of potential detoxification genes involved in pesticide resistance of C. lectularius and lays the foundation for future functional genomics studies. PMID:21283830

USDA food and nutrient databases provide the infrastructure for food and nutrition research, policy, and practice.

PubMed

Ahuja, Jaspreet K C; Moshfegh, Alanna J; Holden, Joanne M; Harris, Ellen

2013-02-01

The USDA food and nutrient databases provide the basic infrastructure for food and nutrition research, nutrition monitoring, policy, and dietary practice. They have had a long history that goes back to 1892 and are unique, as they are the only databases available in the public domain that perform these functions. There are 4 major food and nutrient databases released by the Beltsville Human Nutrition Research Center (BHNRC), part of the USDA's Agricultural Research Service. These include the USDA National Nutrient Database for Standard Reference, the Dietary Supplement Ingredient Database, the Food and Nutrient Database for Dietary Studies, and the USDA Food Patterns Equivalents Database. The users of the databases are diverse and include federal agencies, the food industry, health professionals, restaurants, software application developers, academia and research organizations, international organizations, and foreign governments, among others. Many of these users have partnered with BHNRC to leverage funds and/or scientific expertise to work toward common goals. The use of the databases has increased tremendously in the past few years, especially the breadth of uses. These new uses of the data are bound to increase with the increased availability of technology and public health emphasis on diet-related measures such as sodium and energy reduction. Hence, continued improvement of the databases is important, so that they can better address these challenges and provide reliable and accurate data.

Healthcare Databases in Thailand and Japan: Potential Sources for Health Technology Assessment Research.

PubMed

Saokaew, Surasak; Sugimoto, Takashi; Kamae, Isao; Pratoomsoot, Chayanin; Chaiyakunapruk, Nathorn

2015-01-01

Health technology assessment (HTA) has been continuously used for value-based healthcare decisions over the last decade. Healthcare databases represent an important source of information for HTA, which has seen a surge in use in Western countries. Although HTA agencies have been established in Asia-Pacific region, application and understanding of healthcare databases for HTA is rather limited. Thus, we reviewed existing databases to assess their potential for HTA in Thailand where HTA has been used officially and Japan where HTA is going to be officially introduced. Existing healthcare databases in Thailand and Japan were compiled and reviewed. Databases' characteristics e.g. name of database, host, scope/objective, time/sample size, design, data collection method, population/sample, and variables were described. Databases were assessed for its potential HTA use in terms of safety/efficacy/effectiveness, social/ethical, organization/professional, economic, and epidemiological domains. Request route for each database was also provided. Forty databases- 20 from Thailand and 20 from Japan-were included. These comprised of national censuses, surveys, registries, administrative data, and claimed databases. All databases were potentially used for epidemiological studies. In addition, data on mortality, morbidity, disability, adverse events, quality of life, service/technology utilization, length of stay, and economics were also found in some databases. However, access to patient-level data was limited since information about the databases was not available on public sources. Our findings have shown that existing databases provided valuable information for HTA research with limitation on accessibility. Mutual dialogue on healthcare database development and usage for HTA among Asia-Pacific region is needed.

The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes

PubMed Central

Rigden, Daniel J

2017-01-01

Abstract This year's Database Issue of Nucleic Acids Research contains 152 papers that include descriptions of 54 new databases and update papers on 98 databases, of which 16 have not been previously featured in NAR. As always, these databases cover a broad range of molecular biology subjects, including genome structure, gene expression and its regulation, proteins, protein domains, and protein–protein interactions. Following the recent trend, an increasing number of new and established databases deal with the issues of human health, from cancer-causing mutations to drugs and drug targets. In accordance with this trend, three recently compiled databases that have been selected by NAR reviewers and editors as ‘breakthrough’ contributions, denovo-db, the Monarch Initiative, and Open Targets, cover human de novo gene variants, disease-related phenotypes in model organisms, and a bioinformatics platform for therapeutic target identification and validation, respectively. We expect these databases to attract the attention of numerous researchers working in various areas of genetics and genomics. Looking back at the past 12 years, we present here the ‘golden set’ of databases that have consistently served as authoritative, comprehensive, and convenient data resources widely used by the entire community and offer some lessons on what makes a successful database. The Database Issue is freely available online at the https://academic.oup.com/nar web site. An updated version of the NAR Molecular Biology Database Collection is available at http://www.oxfordjournals.org/nar/database/a/. PMID:28053160

Current limitations of SNP data from the public domain for studies of complex disorders: a test for ten candidate genes for obesity and osteoporosis.

PubMed

Dvornyk, Volodymyr; Long, Ji-Rong; Xiong, Dong-Hai; Liu, Peng-Yuan; Zhao, Lan-Juan; Shen, Hui; Zhang, Yuan-Yuan; Liu, Yong-Jun; Rocha-Sanchez, Sonia; Xiao, Peng; Recker, Robert R; Deng, Hong-Wen

2004-02-25

Public SNP databases are frequently used to choose SNPs for candidate genes in the association and linkage studies of complex disorders. However, their utility for such studies of diseases with ethnic-dependent background has never been evaluated. To estimate the accuracy and completeness of SNP public databases, we analyzed the allele frequencies of 41 SNPs in 10 candidate genes for obesity and/or osteoporosis in a large American-Caucasian sample (1,873 individuals from 405 nuclear families) by PCR-invader assay. We compared our results with those from the databases and other published studies. Of the 41 SNPs, 8 were monomorphic in our sample. Twelve were reported for the first time for Caucasians and the other 29 SNPs in our sample essentially confirmed the respective allele frequencies for Caucasians in the databases and previous studies. The comparison of our data with other ethnic groups showed significant differentiation between the three major world ethnic groups at some SNPs (Caucasians and Africans differed at 3 of the 18 shared SNPs, and Caucasians and Asians differed at 13 of the 22 shared SNPs). This genetic differentiation may have an important implication for studying the well-known ethnic differences in the prevalence of obesity and osteoporosis, and complex disorders in general. A comparative analysis of the SNP data of the candidate genes obtained in the present study, as well as those retrieved from the public domain, suggests that the databases may currently have serious limitations for studying complex disorders with an ethnic-dependent background due to the incomplete and uneven representation of the candidate SNPs in the databases for the major ethnic groups. This conclusion attests to the imperative necessity of large-scale and accurate characterization of these SNPs in different ethnic groups.

Current limitations of SNP data from the public domain for studies of complex disorders: a test for ten candidate genes for obesity and osteoporosis

PubMed Central

Dvornyk, Volodymyr; Long, Ji-Rong; Xiong, Dong-Hai; Liu, Peng-Yuan; Zhao, Lan-Juan; Shen, Hui; Zhang, Yuan-Yuan; Liu, Yong-Jun; Rocha-Sanchez, Sonia; Xiao, Peng; Recker, Robert R; Deng, Hong-Wen

2004-01-01

Background Public SNP databases are frequently used to choose SNPs for candidate genes in the association and linkage studies of complex disorders. However, their utility for such studies of diseases with ethnic-dependent background has never been evaluated. Results To estimate the accuracy and completeness of SNP public databases, we analyzed the allele frequencies of 41 SNPs in 10 candidate genes for obesity and/or osteoporosis in a large American-Caucasian sample (1,873 individuals from 405 nuclear families) by PCR-invader assay. We compared our results with those from the databases and other published studies. Of the 41 SNPs, 8 were monomorphic in our sample. Twelve were reported for the first time for Caucasians and the other 29 SNPs in our sample essentially confirmed the respective allele frequencies for Caucasians in the databases and previous studies. The comparison of our data with other ethnic groups showed significant differentiation between the three major world ethnic groups at some SNPs (Caucasians and Africans differed at 3 of the 18 shared SNPs, and Caucasians and Asians differed at 13 of the 22 shared SNPs). This genetic differentiation may have an important implication for studying the well-known ethnic differences in the prevalence of obesity and osteoporosis, and complex disorders in general. Conclusion A comparative analysis of the SNP data of the candidate genes obtained in the present study, as well as those retrieved from the public domain, suggests that the databases may currently have serious limitations for studying complex disorders with an ethnic-dependent background due to the incomplete and uneven representation of the candidate SNPs in the databases for the major ethnic groups. This conclusion attests to the imperative necessity of large-scale and accurate characterization of these SNPs in different ethnic groups. PMID:15113403

Application of Wavelet Transform for PDZ Domain Classification

PubMed Central

Daqrouq, Khaled; Alhmouz, Rami; Balamesh, Ahmed; Memic, Adnan

2015-01-01

PDZ domains have been identified as part of an array of signaling proteins that are often unrelated, except for the well-conserved structural PDZ domain they contain. These domains have been linked to many disease processes including common Avian influenza, as well as very rare conditions such as Fraser and Usher syndromes. Historically, based on the interactions and the nature of bonds they form, PDZ domains have most often been classified into one of three classes (class I, class II and others - class III), that is directly dependent on their binding partner. In this study, we report on three unique feature extraction approaches based on the bigram and trigram occurrence and existence rearrangements within the domain's primary amino acid sequences in assisting PDZ domain classification. Wavelet packet transform (WPT) and Shannon entropy denoted by wavelet entropy (WE) feature extraction methods were proposed. Using 115 unique human and mouse PDZ domains, the existence rearrangement approach yielded a high recognition rate (78.34%), which outperformed our occurrence rearrangements based method. The recognition rate was (81.41%) with validation technique. The method reported for PDZ domain classification from primary sequences proved to be an encouraging approach for obtaining consistent classification results. We anticipate that by increasing the database size, we can further improve feature extraction and correct classification. PMID:25860375

[Genome-wide identification and expression analysis of the WRKY gene family in peach].

PubMed

Gu, Yan-bing; Ji, Zhi-rui; Chi, Fu-mei; Qiao, Zhuang; Xu, Cheng-nan; Zhang, Jun-xiang; Zhou, Zong-shan; Dong, Qing-long

2016-03-01

The WRKY transcription factors are one of the largest families of transcriptional regulators and play diverse regulatory roles in biotic and abiotic stresses, plant growth and development processes. In this study, the WRKY DNA-binding domain (Pfam Database number: PF03106) downloaded from Pfam protein families database was exploited to identify WRKY genes from the peach (Prunus persica 'Lovell') genome using HMMER 3.0. The obtained amino acid sequences were analyzed with DNAMAN 5.0, WebLogo 3, MEGA 5.1, MapInspect and MEME bioinformatics softwares. Totally 61 peach WRKY genes were found in the peach genome. Our phylogenetic analysis revealed that peach WRKY genes were classified into three Groups: Ⅰ, Ⅱ and Ⅲ. The WRKY N-terminal and C-terminal domains of Group Ⅰ (group I-N and group I-C) were monophyletic. The Group Ⅱ was sub-divided into five distinct clades (groupⅡ-a, Ⅱ-b, Ⅱ-c, Ⅱ-d and Ⅱ-e). Our domain analysis indicated that the WRKY regions contained a highly conserved heptapeptide stretch WRKYGQK at its N-terminus followed by a zinc-finger motif. The chromosome mapping analysis showed that peach WRKY genes were distributed with different densities over 8 chromosomes. The intron-exon structure analysis revealed that structures of the WRKY gene were highly conserved in the peach. The conserved motif analysis showed that the conserved motifs 1, 2 and 3, which specify the WRKY domain, were observed in all peach WRKY proteins, motif 5 as the unknown domain was observed in group Ⅱ-d, two WRKY domains were assigned to GroupⅠ. SqRT-PCR and qRT-PCR results indicated that 16 PpWRKY genes were expressed in roots, stems, leaves, flowers and fruits at various expression levels. Our analysis thus identified the PpWRKY gene families, and future functional studies are needed to reveal its specific roles.

High-throughput STR analysis for DNA database using direct PCR.

PubMed

Sim, Jeong Eun; Park, Su Jeong; Lee, Han Chul; Kim, Se-Yong; Kim, Jong Yeol; Lee, Seung Hwan

2013-07-01

Since the Korean criminal DNA database was launched in 2010, we have focused on establishing an automated DNA database profiling system that analyzes short tandem repeat loci in a high-throughput and cost-effective manner. We established a DNA database profiling system without DNA purification using a direct PCR buffer system. The quality of direct PCR procedures was compared with that of conventional PCR system under their respective optimized conditions. The results revealed not only perfect concordance but also an excellent PCR success rate, good electropherogram quality, and an optimal intra/inter-loci peak height ratio. In particular, the proportion of DNA extraction required due to direct PCR failure could be minimized to <3%. In conclusion, the newly developed direct PCR system can be adopted for automated DNA database profiling systems to replace or supplement conventional PCR system in a time- and cost-saving manner. © 2013 American Academy of Forensic Sciences Published 2013. This article is a U.S. Government work and is in the public domain in the U.S.A.

Constructing a Graph Database for Semantic Literature-Based Discovery.

PubMed

Hristovski, Dimitar; Kastrin, Andrej; Dinevski, Dejan; Rindflesch, Thomas C

2015-01-01

Literature-based discovery (LBD) generates discoveries, or hypotheses, by combining what is already known in the literature. Potential discoveries have the form of relations between biomedical concepts; for example, a drug may be determined to treat a disease other than the one for which it was intended. LBD views the knowledge in a domain as a network; a set of concepts along with the relations between them. As a starting point, we used SemMedDB, a database of semantic relations between biomedical concepts extracted with SemRep from Medline. SemMedDB is distributed as a MySQL relational database, which has some problems when dealing with network data. We transformed and uploaded SemMedDB into the Neo4j graph database, and implemented the basic LBD discovery algorithms with the Cypher query language. We conclude that storing the data needed for semantic LBD is more natural in a graph database. Also, implementing LBD discovery algorithms is conceptually simpler with a graph query language when compared with standard SQL.

Ontology to relational database transformation for web application development and maintenance

NASA Astrophysics Data System (ADS)

Mahmudi, Kamal; Inggriani Liem, M. M.; Akbar, Saiful

2018-03-01

Ontology is used as knowledge representation while database is used as facts recorder in a KMS (Knowledge Management System). In most applications, data are managed in a database system and updated through the application and then they are transformed to knowledge as needed. Once a domain conceptor defines the knowledge in the ontology, application and database can be generated from the ontology. Most existing frameworks generate application from its database. In this research, ontology is used for generating the application. As the data are updated through the application, a mechanism is designed to trigger an update to the ontology so that the application can be rebuilt based on the newest ontology. By this approach, a knowledge engineer has a full flexibility to renew the application based on the latest ontology without dependency to a software developer. In many cases, the concept needs to be updated when the data changed. The framework is built and tested in a spring java environment. A case study was conducted to proof the concepts.

GenBank.

PubMed

Benson, Dennis A; Karsch-Mizrachi, Ilene; Lipman, David J; Ostell, James; Wheeler, David L

2008-01-01

GenBank (R) is a comprehensive database that contains publicly available nucleotide sequences for more than 260 000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the web-based BankIt or standalone Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the European Molecular Biology Laboratory Nucleotide Sequence Database in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through NCBI's retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI Homepage: www.ncbi.nlm.nih.gov.

GenBank

PubMed Central

Benson, Dennis A.; Karsch-Mizrachi, Ilene; Lipman, David J.; Ostell, James; Wheeler, David L.

2008-01-01

GenBank (R) is a comprehensive database that contains publicly available nucleotide sequences for more than 260 000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the web-based BankIt or standalone Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the European Molecular Biology Laboratory Nucleotide Sequence Database in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through NCBI's retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI Homepage: www.ncbi.nlm.nih.gov PMID:18073190

Kinase Pathway Database: An Integrated Protein-Kinase and NLP-Based Protein-Interaction Resource

PubMed Central

Koike, Asako; Kobayashi, Yoshiyuki; Takagi, Toshihisa

2003-01-01

Protein kinases play a crucial role in the regulation of cellular functions. Various kinds of information about these molecules are important for understanding signaling pathways and organism characteristics. We have developed the Kinase Pathway Database, an integrated database involving major completely sequenced eukaryotes. It contains the classification of protein kinases and their functional conservation, ortholog tables among species, protein–protein, protein–gene, and protein–compound interaction data, domain information, and structural information. It also provides an automatic pathway graphic image interface. The protein, gene, and compound interactions are automatically extracted from abstracts for all genes and proteins by natural-language processing (NLP).The method of automatic extraction uses phrase patterns and the GENA protein, gene, and compound name dictionary, which was developed by our group. With this database, pathways are easily compared among species using data with more than 47,000 protein interactions and protein kinase ortholog tables. The database is available for querying and browsing at http://kinasedb.ontology.ims.u-tokyo.ac.jp/. PMID:12799355

How ISO/IEC 17799 can be used for base lining information assurance among entities using data mining for defense, homeland security, commercial, and other civilian/commercial domains

NASA Astrophysics Data System (ADS)

Perry, William G.

2006-04-01

One goal of database mining is to draw unique and valid perspectives from multiple data sources. Insights that are fashioned from closely-held data stores are likely to possess a high degree of reliability. The degree of information assurance comes into question, however, when external databases are accessed, combined and analyzed to form new perspectives. ISO/IEC 17799, Information technology-Security techniques-Code of practice for information security management, can be used to establish a higher level of information assurance among disparate entities using data mining in the defense, homeland security, commercial and other civilian/commercial domains. Organizations that meet ISO/IEC information security standards have identified and assessed risks, threats and vulnerabilities and have taken significant proactive steps to meet their unique security requirements. The ISO standards address twelve domains: risk assessment and treatment, security policy, organization of information security, asset management, human resources security, physical and environmental security, communications and operations management, access control, information systems acquisition, development and maintenance, information security incident management and business continuity management and compliance. Analysts can be relatively confident that if organizations are ISO 17799 compliant, a high degree of information assurance is likely to be a characteristic of the data sets being used. The reverse may be true. Extracting, fusing and drawing conclusions based upon databases with a low degree of information assurance may be wrought with all of the hazards that come from knowingly using bad data to make decisions. Using ISO/IEC 17799 as a baseline for information assurance can help mitigate these risks.

An Entropy Approach to Disclosure Risk Assessment: Lessons from Real Applications and Simulated Domains

PubMed Central

Airoldi, Edoardo M.; Bai, Xue; Malin, Bradley A.

2011-01-01

We live in an increasingly mobile world, which leads to the duplication of information across domains. Though organizations attempt to obscure the identities of their constituents when sharing information for worthwhile purposes, such as basic research, the uncoordinated nature of such environment can lead to privacy vulnerabilities. For instance, disparate healthcare providers can collect information on the same patient. Federal policy requires that such providers share “de-identified” sensitive data, such as biomedical (e.g., clinical and genomic) records. But at the same time, such providers can share identified information, devoid of sensitive biomedical data, for administrative functions. On a provider-by-provider basis, the biomedical and identified records appear unrelated, however, links can be established when multiple providers’ databases are studied jointly. The problem, known as trail disclosure, is a generalized phenomenon and occurs because an individual’s location access pattern can be matched across the shared databases. Due to technical and legal constraints, it is often difficult to coordinate between providers and thus it is critical to assess the disclosure risk in distributed environments, so that we can develop techniques to mitigate such risks. Research on privacy protection has so far focused on developing technologies to suppress or encrypt identifiers associated with sensitive information. There is growing body of work on the formal assessment of the disclosure risk of database entries in publicly shared databases, but a less attention has been paid to the distributed setting. In this research, we review the trail disclosure problem in several domains with known vulnerabilities and show that disclosure risk is influenced by the distribution of how people visit service providers. Based on empirical evidence, we propose an entropy metric for assessing such risk in shared databases prior to their release. This metric assesses risk by leveraging the statistical characteristics of a visit distribution, as opposed to person-level data. It is computationally efficient and superior to existing risk assessment methods, which rely on ad hoc assessment that are often computationally expensive and unreliable. We evaluate our approach on a range of location access patterns in simulated environments. Our results demonstrate the approach is effective at estimating trail disclosure risks and the amount of self-information contained in a distributed system is one of the main driving factors. PMID:21647242

Top-k similar graph matching using TraM in biological networks.

PubMed

Amin, Mohammad Shafkat; Finley, Russell L; Jamil, Hasan M

2012-01-01

Many emerging database applications entail sophisticated graph-based query manipulation, predominantly evident in large-scale scientific applications. To access the information embedded in graphs, efficient graph matching tools and algorithms have become of prime importance. Although the prohibitively expensive time complexity associated with exact subgraph isomorphism techniques has limited its efficacy in the application domain, approximate yet efficient graph matching techniques have received much attention due to their pragmatic applicability. Since public domain databases are noisy and incomplete in nature, inexact graph matching techniques have proven to be more promising in terms of inferring knowledge from numerous structural data repositories. In this paper, we propose a novel technique called TraM for approximate graph matching that off-loads a significant amount of its processing on to the database making the approach viable for large graphs. Moreover, the vector space embedding of the graphs and efficient filtration of the search space enables computation of approximate graph similarity at a throw-away cost. We annotate nodes of the query graphs by means of their global topological properties and compare them with neighborhood biased segments of the datagraph for proper matches. We have conducted experiments on several real data sets, and have demonstrated the effectiveness and efficiency of the proposed method

A Web application for the management of clinical workflow in image-guided and adaptive proton therapy for prostate cancer treatments.

PubMed

Yeung, Daniel; Boes, Peter; Ho, Meng Wei; Li, Zuofeng

2015-05-08

Image-guided radiotherapy (IGRT), based on radiopaque markers placed in the prostate gland, was used for proton therapy of prostate patients. Orthogonal X-rays and the IBA Digital Image Positioning System (DIPS) were used for setup correction prior to treatment and were repeated after treatment delivery. Following a rationale for margin estimates similar to that of van Herk,(1) the daily post-treatment DIPS data were analyzed to determine if an adaptive radiotherapy plan was necessary. A Web application using ASP.NET MVC5, Entity Framework, and an SQL database was designed to automate this process. The designed features included state-of-the-art Web technologies, a domain model closely matching the workflow, a database-supporting concurrency and data mining, access to the DIPS database, secured user access and roles management, and graphing and analysis tools. The Model-View-Controller (MVC) paradigm allowed clean domain logic, unit testing, and extensibility. Client-side technologies, such as jQuery, jQuery Plug-ins, and Ajax, were adopted to achieve a rich user environment and fast response. Data models included patients, staff, treatment fields and records, correction vectors, DIPS images, and association logics. Data entry, analysis, workflow logics, and notifications were implemented. The system effectively modeled the clinical workflow and IGRT process.

Wavelet domain textual coding of Ottoman script images

NASA Astrophysics Data System (ADS)

Gerek, Oemer N.; Cetin, Enis A.; Tewfik, Ahmed H.

1996-02-01

Image coding using wavelet transform, DCT, and similar transform techniques is well established. On the other hand, these coding methods neither take into account the special characteristics of the images in a database nor are they suitable for fast database search. In this paper, the digital archiving of Ottoman printings is considered. Ottoman documents are printed in Arabic letters. Witten et al. describes a scheme based on finding the characters in binary document images and encoding the positions of the repeated characters This method efficiently compresses document images and is suitable for database research, but it cannot be applied to Ottoman or Arabic documents as the concept of character is different in Ottoman or Arabic. Typically, one has to deal with compound structures consisting of a group of letters. Therefore, the matching criterion will be according to those compound structures. Furthermore, the text images are gray tone or color images for Ottoman scripts for the reasons that are described in the paper. In our method the compound structure matching is carried out in wavelet domain which reduces the search space and increases the compression ratio. In addition to the wavelet transformation which corresponds to the linear subband decomposition, we also used nonlinear subband decomposition. The filters in the nonlinear subband decomposition have the property of preserving edges in the low resolution subband image.

FLAPS (Fatigue Life Analysis Programs): Computer Programs to Predict Cyclic Life Using the Total Strain Version of Strainrange Partitioning and Other Life Prediction Methods. Users' Manual and Example Problems, Version 1.0

NASA Technical Reports Server (NTRS)

Arya, Vinod K.; Halford, Gary R. (Technical Monitor)

2003-01-01

This manual presents computer programs FLAPS for characterizing and predicting fatigue and creep-fatigue resistance of metallic materials in the high-temperature, long-life regime for isothermal and nonisothermal fatigue. The programs use the Total Strain version of Strainrange Partitioning (TS-SRP), and several other life prediction methods described in this manual. The user should be thoroughly familiar with the TS-SRP and these life prediction methods before attempting to use any of these programs. Improper understanding can lead to incorrect use of the method and erroneous life predictions. An extensive database has also been developed in a parallel effort. The database is probably the largest source of high-temperature, creep-fatigue test data available in the public domain and can be used with other life-prediction methods as well. This users' manual, software, and database are all in the public domain and can be obtained by contacting the author. The Compact Disk (CD) accompanying this manual contains an executable file for the FLAPS program, two datasets required for the example problems in the manual, and the creep-fatigue data in a format compatible with these programs.

JAIL: a structure-based interface library for macromolecules.

PubMed

Günther, Stefan; von Eichborn, Joachim; May, Patrick; Preissner, Robert

2009-01-01

The increasing number of solved macromolecules provides a solid number of 3D interfaces, if all types of molecular contacts are being considered. JAIL annotates three different kinds of macromolecular interfaces, those between interacting protein domains, interfaces of different protein chains and interfaces between proteins and nucleic acids. This results in a total number of about 184,000 database entries. All the interfaces can easily be identified by a detailed search form or by a hierarchical tree that describes the protein domain architectures classified by the SCOP database. Visual inspection of the interfaces is possible via an interactive protein viewer. Furthermore, large scale analyses are supported by an implemented sequential and by a structural clustering. Similar interfaces as well as non-redundant interfaces can be easily picked out. Additionally, the sequential conservation of binding sites was also included in the database and is retrievable via Jmol. A comprehensive download section allows the composition of representative data sets with user defined parameters. The huge data set in combination with various search options allow a comprehensive view on all interfaces between macromolecules included in the Protein Data Bank (PDB). The download of the data sets supports numerous further investigations in macromolecular recognition. JAIL is publicly available at http://bioinformatics.charite.de/jail.

MutationAligner: a resource of recurrent mutation hotspots in protein domains in cancer

PubMed Central

Gauthier, Nicholas Paul; Reznik, Ed; Gao, Jianjiong; Sumer, Selcuk Onur; Schultz, Nikolaus; Sander, Chris; Miller, Martin L.

2016-01-01

The MutationAligner web resource, available at http://www.mutationaligner.org, enables discovery and exploration of somatic mutation hotspots identified in protein domains in currently (mid-2015) more than 5000 cancer patient samples across 22 different tumor types. Using multiple sequence alignments of protein domains in the human genome, we extend the principle of recurrence analysis by aggregating mutations in homologous positions across sets of paralogous genes. Protein domain analysis enhances the statistical power to detect cancer-relevant mutations and links mutations to the specific biological functions encoded in domains. We illustrate how the MutationAligner database and interactive web tool can be used to explore, visualize and analyze mutation hotspots in protein domains across genes and tumor types. We believe that MutationAligner will be an important resource for the cancer research community by providing detailed clues for the functional importance of particular mutations, as well as for the design of functional genomics experiments and for decision support in precision medicine. MutationAligner is slated to be periodically updated to incorporate additional analyses and new data from cancer genomics projects. PMID:26590264

Cognitive impairment in COPD: a systematic review.

PubMed

Torres-Sánchez, Irene; Rodríguez-Alzueta, Elisabeth; Cabrera-Martos, Irene; López-Torres, Isabel; Moreno-Ramírez, Maria Paz; Valenza, Marie Carmen

2015-01-01

The objectives of this study were to characterize and clarify the relationships between the various cognitive domains affected in COPD patients and the disease itself, as well as to determine the prevalence of impairment in the various cognitive domains in such patients. To that end, we performed a systematic review using the following databases: PubMed, Scopus, and ScienceDirect. We included articles that provided information on cognitive impairment in COPD patients. The review of the findings of the articles showed a significant relationship between COPD and cognitive impairment. The most widely studied cognitive domains are memory and attention. Verbal memory and learning constitute the second most commonly impaired cognitive domain in patients with COPD. The prevalence of impairment in visuospatial memory and intermediate visual memory is 26.9% and 19.2%, respectively. We found that cognitive impairment is associated with the profile of COPD severity and its comorbidities. The articles reviewed demonstrated that there is considerable impairment of the cognitive domains memory and attention in patients with COPD. Future studies should address impairments in different cognitive domains according to the disease stage in patients with COPD.

A case Study of Applying Object-Relational Persistence in Astronomy Data Archiving

NASA Astrophysics Data System (ADS)

Yao, S. S.; Hiriart, R.; Barg, I.; Warner, P.; Gasson, D.

2005-12-01

The NOAO Science Archive (NSA) team is developing a comprehensive domain model to capture the science data in the archive. Java and an object model derived from the domain model weil address the application layer of the archive system. However, since RDBMS is the best proven technology for data management, the challenge is the paradigm mismatch between the object and the relational models. Transparent object-relational mapping (ORM) persistence is a successful solution to this challenge. In the data modeling and persistence implementation of NSA, we are using Hibernate, a well-accepted ORM tool, to bridge the object model in the business tier and the relational model in the database tier. Thus, the database is isolated from the Java application. The application queries directly on objects using a DBMS-independent object-oriented query API, which frees the application developers from the low level JDBC and SQL so that they can focus on the domain logic. We present the detailed design of the NSA R3 (Release 3) data model and object-relational persistence, including mapping, retrieving and caching. Persistence layer optimization and performance tuning will be analyzed. The system is being built on J2EE, so the integration of Hibernate into the EJB container and the transaction management are also explored.

Novel protein domains and repeats in Drosophila melanogaster: insights into structure, function, and evolution.

PubMed

Ponting, C P; Mott, R; Bork, P; Copley, R R

2001-12-01

Sequence database searching methods such as BLAST, are invaluable for predicting molecular function on the basis of sequence similarities among single regions of proteins. Searches of whole databases however, are not optimized to detect multiple homologous regions within a single polypeptide. Here we have used the prospero algorithm to perform self-comparisons of all predicted Drosophila melanogaster gene products. Predicted repeats, and their homologs from all species, were analyzed further to detect hitherto unappreciated evolutionary relationships. Results included the identification of novel tandem repeats in the human X-linked retinitis pigmentosa type-2 gene product, repeated segments in cystinosin, associated with a defect in cystine transport, and 'nested' homologous domains in dysferlin, whose gene is mutated in limb girdle muscular dystrophy. Novel signaling domain families were found that may regulate the microtubule-based cytoskeleton and ubiquitin-mediated proteolysis, respectively. Two families of glycosyl hydrolases were shown to contain internal repetitions that hint at their evolution via a piecemeal, modular approach. In addition, three examples of fruit fly genes were detected with tandem exons that appear to have arisen via internal duplication. These findings demonstrate how completely sequenced genomes can be exploited to further understand the relationships between molecular structure, function, and evolution.

MetaMapR: pathway independent metabolomic network analysis incorporating unknowns.

PubMed

Grapov, Dmitry; Wanichthanarak, Kwanjeera; Fiehn, Oliver

2015-08-15

Metabolic network mapping is a widely used approach for integration of metabolomic experimental results with biological domain knowledge. However, current approaches can be limited by biochemical domain or pathway knowledge which results in sparse disconnected graphs for real world metabolomic experiments. MetaMapR integrates enzymatic transformations with metabolite structural similarity, mass spectral similarity and empirical associations to generate richly connected metabolic networks. This open source, web-based or desktop software, written in the R programming language, leverages KEGG and PubChem databases to derive associations between metabolites even in cases where biochemical domain or molecular annotations are unknown. Network calculation is enhanced through an interface to the Chemical Translation System, which allows metabolite identifier translation between >200 common biochemical databases. Analysis results are presented as interactive visualizations or can be exported as high-quality graphics and numerical tables which can be imported into common network analysis and visualization tools. Freely available at http://dgrapov.github.io/MetaMapR/. Requires R and a modern web browser. Installation instructions, tutorials and application examples are available at http://dgrapov.github.io/MetaMapR/. ofiehn@ucdavis.edu. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

A computational model for predicting integrase catalytic domain of retrovirus.

PubMed

Wu, Sijia; Han, Jiuqiang; Zhang, Xinman; Zhong, Dexing; Liu, Ruiling

2017-06-21

Integrase catalytic domain (ICD) is an essential part in the retrovirus for integration reaction, which enables its newly synthesized DNA to be incorporated into the DNA of infected cells. Owing to the crucial role of ICD for the retroviral replication and the absence of an equivalent of integrase in host cells, it is comprehensible that ICD is a promising drug target for therapeutic intervention. However, annotated ICDs in UniProtKB database have still been insufficient for a good understanding of their statistical characteristics so far. Accordingly, it is of great importance to put forward a computational ICD model in this work to annotate these domains in the retroviruses. The proposed model then discovered 11,660 new putative ICDs after scanning sequences without ICD annotations. Subsequently in order to provide much confidence in ICD prediction, it was tested under different cross-validation methods, compared with other database search tools, and verified on independent datasets. Furthermore, an evolutionary analysis performed on the annotated ICDs of retroviruses revealed a tight connection between ICD and retroviral classification. All the datasets involved in this paper and the application software tool of this model can be available for free download at https://sourceforge.net/projects/icdtool/files/?source=navbar. Copyright © 2017 Elsevier Ltd. All rights reserved.

Properties and structure of a low-potential, penta-heme cytochrome c 552 from a thermophilic purple sulfur photosynthetic bacterium Thermochromatium tepidum.

PubMed

Chen, Jing-Hua; Yu, Long-Jiang; Boussac, Alain; Wang-Otomo, Zheng-Yu; Kuang, Tingyun; Shen, Jian-Ren

2018-04-24

The thermophilic purple sulfur bacterium Thermochromatium tepidum possesses four main water-soluble redox proteins involved in the electron transfer behavior. Crystal structures have been reported for three of them: a high potential iron-sulfur protein, cytochrome c', and one of two low-potential cytochrome c 552 (which is a flavocytochrome c) have been determined. In this study, we purified another low-potential cytochrome c 552 (LPC), determined its N-terminal amino acid sequence and the whole gene sequence, characterized it with absorption and electron paramagnetic spectroscopy, and solved its high-resolution crystal structure. This novel cytochrome was found to contain five c-type hemes. The overall fold of LPC consists of two distinct domains, one is the five heme-containing domain and the other one is an Ig-like domain. This provides a representative example for the structures of multiheme cytochromes containing an odd number of hemes, although the structures of multiheme cytochromes with an even number of hemes are frequently seen in the PDB database. Comparison of the sequence and structure of LPC with other proteins in the databases revealed several characteristic features which may be important for its functioning. Based on the results obtained, we discuss the possible intracellular function of this LPC in Tch. tepidum.

Automating document classification for the Immune Epitope Database

PubMed Central

Wang, Peng; Morgan, Alexander A; Zhang, Qing; Sette, Alessandro; Peters, Bjoern

2007-01-01

Background The Immune Epitope Database contains information on immune epitopes curated manually from the scientific literature. Like similar projects in other knowledge domains, significant effort is spent on identifying which articles are relevant for this purpose. Results We here report our experience in automating this process using Naïve Bayes classifiers trained on 20,910 abstracts classified by domain experts. Improvements on the basic classifier performance were made by a) utilizing information stored in PubMed beyond the abstract itself b) applying standard feature selection criteria and c) extracting domain specific feature patterns that e.g. identify peptides sequences. We have implemented the classifier into the curation process determining if abstracts are clearly relevant, clearly irrelevant, or if no certain classification can be made, in which case the abstracts are manually classified. Testing this classification scheme on an independent dataset, we achieve 95% sensitivity and specificity in the 51.1% of abstracts that were automatically classified. Conclusion By implementing text classification, we have sped up the reference selection process without sacrificing sensitivity or specificity of the human expert classification. This study provides both practical recommendations for users of text classification tools, as well as a large dataset which can serve as a benchmark for tool developers. PMID:17655769

INFOMAT: The international materials assessment and application centre's internet gateway

NASA Astrophysics Data System (ADS)

Branquinho, Carmen Lucia; Colodete, Leandro Tavares

2004-08-01

INFOMAT is an electronic directory structured to facilitate the search and retrieval of materials science and technology information sources. Linked to the homepage of the International Materials Assessment and Application Centre, INFOMAT presents descriptions of 392 proprietary databases with links to their host systems as well as direct links to over 180 public domain databases and over 2,400 web sites. Among the web sites are associations/unions, governmental and non-governmental institutions, industries, library holdings, market statistics, news services, on-line publications, standardization and intellectual property organizations, and universities/research groups.

Searching and Extracting Data from the EMBL-EBI Complex Portal.

PubMed

Meldal, Birgit H M; Orchard, Sandra

2018-01-01

The Complex Portal ( www.ebi.ac.uk/complexportal ) is an encyclopedia of macromolecular complexes. Complexes are assigned unique, stable IDs, are species specific, and list all participating members with links to an appropriate reference database (UniProtKB, ChEBI, RNAcentral). Each complex is annotated extensively with its functions, properties, structure, stoichiometry, tissue expression profile, and subcellular location. Links to domain-specific databases allow the user to access additional information and enable data searching and filtering. Complexes can be saved and downloaded in PSI-MI XML, MI-JSON, and tab-delimited formats.

Identification and human condition analysis based on the human voice analysis

NASA Astrophysics Data System (ADS)

Mieshkov, Oleksandr Yu.; Novikov, Oleksandr O.; Novikov, Vsevolod O.; Fainzilberg, Leonid S.; Kotyra, Andrzej; Smailova, Saule; Kozbekova, Ainur; Imanbek, Baglan

2017-08-01

The paper presents a two-stage biotechnical system for human condition analysis that is based on analysis of human voice signal. At the initial stage, the voice signal is pre-processed and its characteristics in time domain are determined. At the first stage, the developed system is capable of identifying the person in the database on the basis of the extracted characteristics. At the second stage, the model of a human voice is built on the basis of the real voice signals after clustering the whole database.

SORTEZ: a relational translator for NCBI's ASN.1 database.

PubMed

Hart, K W; Searls, D B; Overton, G C

1994-07-01

The National Center for Biotechnology Information (NCBI) has created a database collection that includes several protein and nucleic acid sequence databases, a biosequence-specific subset of MEDLINE, as well as value-added information such as links between similar sequences. Information in the NCBI database is modeled in Abstract Syntax Notation 1 (ASN.1) an Open Systems Interconnection protocol designed for the purpose of exchanging structured data between software applications rather than as a data model for database systems. While the NCBI database is distributed with an easy-to-use information retrieval system, ENTREZ, the ASN.1 data model currently lacks an ad hoc query language for general-purpose data access. For that reason, we have developed a software package, SORTEZ, that transforms the ASN.1 database (or other databases with nested data structures) to a relational data model and subsequently to a relational database management system (Sybase) where information can be accessed through the relational query language, SQL. Because the need to transform data from one data model and schema to another arises naturally in several important contexts, including efficient execution of specific applications, access to multiple databases and adaptation to database evolution this work also serves as a practical study of the issues involved in the various stages of database transformation. We show that transformation from the ASN.1 data model to a relational data model can be largely automated, but that schema transformation and data conversion require considerable domain expertise and would greatly benefit from additional support tools.

Ultra-Structure database design methodology for managing systems biology data and analyses

PubMed Central

Maier, Christopher W; Long, Jeffrey G; Hemminger, Bradley M; Giddings, Morgan C

2009-01-01

Background Modern, high-throughput biological experiments generate copious, heterogeneous, interconnected data sets. Research is dynamic, with frequently changing protocols, techniques, instruments, and file formats. Because of these factors, systems designed to manage and integrate modern biological data sets often end up as large, unwieldy databases that become difficult to maintain or evolve. The novel rule-based approach of the Ultra-Structure design methodology presents a potential solution to this problem. By representing both data and processes as formal rules within a database, an Ultra-Structure system constitutes a flexible framework that enables users to explicitly store domain knowledge in both a machine- and human-readable form. End users themselves can change the system's capabilities without programmer intervention, simply by altering database contents; no computer code or schemas need be modified. This provides flexibility in adapting to change, and allows integration of disparate, heterogenous data sets within a small core set of database tables, facilitating joint analysis and visualization without becoming unwieldy. Here, we examine the application of Ultra-Structure to our ongoing research program for the integration of large proteomic and genomic data sets (proteogenomic mapping). Results We transitioned our proteogenomic mapping information system from a traditional entity-relationship design to one based on Ultra-Structure. Our system integrates tandem mass spectrum data, genomic annotation sets, and spectrum/peptide mappings, all within a small, general framework implemented within a standard relational database system. General software procedures driven by user-modifiable rules can perform tasks such as logical deduction and location-based computations. The system is not tied specifically to proteogenomic research, but is rather designed to accommodate virtually any kind of biological research. Conclusion We find Ultra-Structure offers substantial benefits for biological information systems, the largest being the integration of diverse information sources into a common framework. This facilitates systems biology research by integrating data from disparate high-throughput techniques. It also enables us to readily incorporate new data types, sources, and domain knowledge with no change to the database structure or associated computer code. Ultra-Structure may be a significant step towards solving the hard problem of data management and integration in the systems biology era. PMID:19691849

Gene and protein nomenclature in public databases

PubMed Central

Fundel, Katrin; Zimmer, Ralf

2006-01-01

Background Frequently, several alternative names are in use for biological objects such as genes and proteins. Applications like manual literature search, automated text-mining, named entity identification, gene/protein annotation, and linking of knowledge from different information sources require the knowledge of all used names referring to a given gene or protein. Various organism-specific or general public databases aim at organizing knowledge about genes and proteins. These databases can be used for deriving gene and protein name dictionaries. So far, little is known about the differences between databases in terms of size, ambiguities and overlap. Results We compiled five gene and protein name dictionaries for each of the five model organisms (yeast, fly, mouse, rat, and human) from different organism-specific and general public databases. We analyzed the degree of ambiguity of gene and protein names within and between dictionaries, to a lexicon of common English words and domain-related non-gene terms, and we compared different data sources in terms of size of extracted dictionaries and overlap of synonyms between those. The study shows that the number of genes/proteins and synonyms covered in individual databases varies significantly for a given organism, and that the degree of ambiguity of synonyms varies significantly between different organisms. Furthermore, it shows that, despite considerable efforts of co-curation, the overlap of synonyms in different data sources is rather moderate and that the degree of ambiguity of gene names with common English words and domain-related non-gene terms varies depending on the considered organism. Conclusion In conclusion, these results indicate that the combination of data contained in different databases allows the generation of gene and protein name dictionaries that contain significantly more used names than dictionaries obtained from individual data sources. Furthermore, curation of combined dictionaries considerably increases size and decreases ambiguity. The entries of the curated synonym dictionary are available for manual querying, editing, and PubMed- or Google-search via the ProThesaurus-wiki. For automated querying via custom software, we offer a web service and an exemplary client application. PMID:16899134

Healthcare Databases in Thailand and Japan: Potential Sources for Health Technology Assessment Research

PubMed Central

Saokaew, Surasak; Sugimoto, Takashi; Kamae, Isao; Pratoomsoot, Chayanin; Chaiyakunapruk, Nathorn

2015-01-01

Background Health technology assessment (HTA) has been continuously used for value-based healthcare decisions over the last decade. Healthcare databases represent an important source of information for HTA, which has seen a surge in use in Western countries. Although HTA agencies have been established in Asia-Pacific region, application and understanding of healthcare databases for HTA is rather limited. Thus, we reviewed existing databases to assess their potential for HTA in Thailand where HTA has been used officially and Japan where HTA is going to be officially introduced. Method Existing healthcare databases in Thailand and Japan were compiled and reviewed. Databases’ characteristics e.g. name of database, host, scope/objective, time/sample size, design, data collection method, population/sample, and variables were described. Databases were assessed for its potential HTA use in terms of safety/efficacy/effectiveness, social/ethical, organization/professional, economic, and epidemiological domains. Request route for each database was also provided. Results Forty databases– 20 from Thailand and 20 from Japan—were included. These comprised of national censuses, surveys, registries, administrative data, and claimed databases. All databases were potentially used for epidemiological studies. In addition, data on mortality, morbidity, disability, adverse events, quality of life, service/technology utilization, length of stay, and economics were also found in some databases. However, access to patient-level data was limited since information about the databases was not available on public sources. Conclusion Our findings have shown that existing databases provided valuable information for HTA research with limitation on accessibility. Mutual dialogue on healthcare database development and usage for HTA among Asia-Pacific region is needed. PMID:26560127

The GED4GEM project: development of a Global Exposure Database for the Global Earthquake Model initiative

USGS Publications Warehouse

Gamba, P.; Cavalca, D.; Jaiswal, K.S.; Huyck, C.; Crowley, H.

2012-01-01

In order to quantify earthquake risk of any selected region or a country of the world within the Global Earthquake Model (GEM) framework (www.globalquakemodel.org/), a systematic compilation of building inventory and population exposure is indispensable. Through the consortium of leading institutions and by engaging the domain-experts from multiple countries, the GED4GEM project has been working towards the development of a first comprehensive publicly available Global Exposure Database (GED). This geospatial exposure database will eventually facilitate global earthquake risk and loss estimation through GEM’s OpenQuake platform. This paper provides an overview of the GED concepts, aims, datasets, and inference methodology, as well as the current implementation scheme, status and way forward.

Disgust sensitivity is primarily associated with purity-based moral judgments.

PubMed

Wagemans, Fieke M A; Brandt, Mark J; Zeelenberg, Marcel

2018-03-01

Individual differences in disgust sensitivity are associated with a range of judgments and attitudes related to the moral domain. Some perspectives suggest that the association between disgust sensitivity and moral judgments will be equally strong across all moral domains (i.e., purity, authority, loyalty, care, fairness, and liberty). Other perspectives predict that disgust sensitivity is primarily associated with judgments of specific moral domains (e.g., primarily purity). However, no study has systematically tested if disgust sensitivity is associated with moral judgments of the purity domain specifically, more generally to moral judgments of the binding moral domains, or to moral judgments of all of the moral domains equally. Across 5 studies (total N = 1,104), we find consistent evidence for the notion that disgust sensitivity relates more strongly to moral condemnation of purity-based transgressions (meta-analytic r = .40) than to moral condemnation of transgressions of any of the other domains (range meta-analytic rs: .07-.27). Our findings are in line with predictions from Moral Foundations Theory, which predicts that personality characteristics like disgust sensitivity make people more sensitive to a certain set of moral issues. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Working Group Reports: Working Group 1 - Software Systems Design and Implementation for Environmental Modeling

EPA Science Inventory

The purpose of the Interagency Steering Committee on Multimedia Environmental Modeling (ISCMEM) is to foster the exchange of information about environmental modeling tools, modeling frameworks, and environmental monitoring databases that are all in the public domain. It is compos...

BTKbase, mutation database for X-linked agammaglobulinemia (XLA).

PubMed Central

Vihinen, M; Brandau, O; Brandén, L J; Kwan, S P; Lappalainen, I; Lester, T; Noordzij, J G; Ochs, H D; Ollila, J; Pienaar, S M; Riikonen, P; Saha, B K; Smith, C I

1998-01-01

X-linked agammaglobulinemia (XLA) is an immunodeficiency caused by mutations in the gene coding for Bruton's agammaglobulinemia tyrosine kinase (BTK). A database (BTKbase) of BTK mutations has been compiled and the recent update lists 463 mutation entries from 406 unrelated families showing 303 unique molecular events. In addition to mutations, the database also lists variants or polymorphisms. Each patient is given a unique patient identity number (PIN). Information is included regarding the phenotype including symptoms. Mutations in all the five domains of BTK have been noticed to cause the disease, the most common event being missense mutations. The mutations appear almost uniformly throughout the molecule and frequently affect CpG sites that code for arginine residues. The putative structural implications of all the missense mutations are given in the database. The improved version of the registry having a number of new features is available at http://www. helsinki.fi/science/signal/btkbase.html PMID:9399844

Drill hole data for coal beds in the Powder River Basin, Montana and Wyoming

USGS Publications Warehouse

Haacke, Jon E.; Scott, David C.

2013-01-01

This report by the U.S. Geological Survey (USGS) of the Powder River Basin (PRB) of Montana and Wyoming is part of the U.S. Coal Resources and Reserves Assessment Project. Essential to that project was the creation of a comprehensive drill hole database that was used for coal bed correlation and for coal resource and reserve assessments in the PRB. This drill hole database was assembled using data from the USGS National Coal Resources Data System, several other Federal and State agencies, and selected mining companies. Additionally, USGS personnel manually entered lithologic picks into the database from geophysical logs of coalbed methane, oil, and gas wells. Of the 29,928 drill holes processed, records of 21,393 are in the public domain and are included in this report. The database contains location information, lithology, and coal bed names for each drill hole.

GenBank

PubMed Central

Benson, Dennis A.; Karsch-Mizrachi, Ilene; Lipman, David J.; Ostell, James; Wheeler, David L.

2007-01-01

GenBank (R) is a comprehensive database that contains publicly available nucleotide sequences for more than 240 000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the web-based BankIt or standalone Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the EMBL Data Library in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through NCBI's retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI Homepage (). PMID:17202161

ExPASy: SIB bioinformatics resource portal.

PubMed

Artimo, Panu; Jonnalagedda, Manohar; Arnold, Konstantin; Baratin, Delphine; Csardi, Gabor; de Castro, Edouard; Duvaud, Séverine; Flegel, Volker; Fortier, Arnaud; Gasteiger, Elisabeth; Grosdidier, Aurélien; Hernandez, Céline; Ioannidis, Vassilios; Kuznetsov, Dmitry; Liechti, Robin; Moretti, Sébastien; Mostaguir, Khaled; Redaschi, Nicole; Rossier, Grégoire; Xenarios, Ioannis; Stockinger, Heinz

2012-07-01

ExPASy (http://www.expasy.org) has worldwide reputation as one of the main bioinformatics resources for proteomics. It has now evolved, becoming an extensible and integrative portal accessing many scientific resources, databases and software tools in different areas of life sciences. Scientists can henceforth access seamlessly a wide range of resources in many different domains, such as proteomics, genomics, phylogeny/evolution, systems biology, population genetics, transcriptomics, etc. The individual resources (databases, web-based and downloadable software tools) are hosted in a 'decentralized' way by different groups of the SIB Swiss Institute of Bioinformatics and partner institutions. Specifically, a single web portal provides a common entry point to a wide range of resources developed and operated by different SIB groups and external institutions. The portal features a search function across 'selected' resources. Additionally, the availability and usage of resources are monitored. The portal is aimed for both expert users and people who are not familiar with a specific domain in life sciences. The new web interface provides, in particular, visual guidance for newcomers to ExPASy.

Direct Numerical Simulation of Pebble Bed Flows: Database Development and Investigation of Low-Frequency Temporal Instabilities

DOE PAGES

Fick, Lambert H.; Merzari, Elia; Hassan, Yassin A.

2017-02-20

Computational analyses of fluid flow through packed pebble bed domains using the Reynolds-averaged NavierStokes framework have had limited success in the past. Because of a lack of high-fidelity experimental or computational data, optimization of Reynolds-averaged closure models for these geometries has not been extensively developed. In the present study, direct numerical simulation was employed to develop a high-fidelity database that can be used for optimizing Reynolds-averaged closure models for pebble bed flows. A face-centered cubic domain with periodic boundaries was used. Flow was simulated at a Reynolds number of 9308 and cross-verified by using available quasi-DNS data. During the simulations,more » low-frequency instability modes were observed that affected the stationary solution. Furthermore, these instabilities were investigated by using the method of proper orthogonal decomposition, and a correlation was found between the time-dependent asymmetry of the averaged velocity profile data and the behavior of the highest energy eigenmodes.« less

Meta4: a web application for sharing and annotating metagenomic gene predictions using web services.

PubMed

Richardson, Emily J; Escalettes, Franck; Fotheringham, Ian; Wallace, Robert J; Watson, Mick

2013-01-01

Whole-genome shotgun metagenomics experiments produce DNA sequence data from entire ecosystems, and provide a huge amount of novel information. Gene discovery projects require up-to-date information about sequence homology and domain structure for millions of predicted proteins to be presented in a simple, easy-to-use system. There is a lack of simple, open, flexible tools that allow the rapid sharing of metagenomics datasets with collaborators in a format they can easily interrogate. We present Meta4, a flexible and extensible web application that can be used to share and annotate metagenomic gene predictions. Proteins and predicted domains are stored in a simple relational database, with a dynamic front-end which displays the results in an internet browser. Web services are used to provide up-to-date information about the proteins from homology searches against public databases. Information about Meta4 can be found on the project website, code is available on Github, a cloud image is available, and an example implementation can be seen at.

EUROPA2: Plan Database Services for Planning and Scheduling Applications

NASA Technical Reports Server (NTRS)

Bedrax-Weiss, Tania; Frank, Jeremy; Jonsson, Ari; McGann, Conor

2004-01-01

NASA missions require solving a wide variety of planning and scheduling problems with temporal constraints; simple resources such as robotic arms, communications antennae and cameras; complex replenishable resources such as memory, power and fuel; and complex constraints on geometry, heat and lighting angles. Planners and schedulers that solve these problems are used in ground tools as well as onboard systems. The diversity of planning problems and applications of planners and schedulers precludes a one-size fits all solution. However, many of the underlying technologies are common across planning domains and applications. We describe CAPR, a formalism for planning that is general enough to cover a wide variety of planning and scheduling domains of interest to NASA. We then describe EUROPA(sub 2), a software framework implementing CAPR. EUROPA(sub 2) provides efficient, customizable Plan Database Services that enable the integration of CAPR into a wide variety of applications. We describe the design of EUROPA(sub 2) from the perspective of both modeling, customization and application integration to different classes of NASA missions.

Direct Numerical Simulation of Pebble Bed Flows: Database Development and Investigation of Low-Frequency Temporal Instabilities

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

Fick, Lambert H.; Merzari, Elia; Hassan, Yassin A.

Computational analyses of fluid flow through packed pebble bed domains using the Reynolds-averaged NavierStokes framework have had limited success in the past. Because of a lack of high-fidelity experimental or computational data, optimization of Reynolds-averaged closure models for these geometries has not been extensively developed. In the present study, direct numerical simulation was employed to develop a high-fidelity database that can be used for optimizing Reynolds-averaged closure models for pebble bed flows. A face-centered cubic domain with periodic boundaries was used. Flow was simulated at a Reynolds number of 9308 and cross-verified by using available quasi-DNS data. During the simulations,more » low-frequency instability modes were observed that affected the stationary solution. Furthermore, these instabilities were investigated by using the method of proper orthogonal decomposition, and a correlation was found between the time-dependent asymmetry of the averaged velocity profile data and the behavior of the highest energy eigenmodes.« less

It's all about gains: Risk preferences in problem gambling.

PubMed

Ring, Patrick; Probst, Catharina C; Neyse, Levent; Wolff, Stephan; Kaernbach, Christian; van Eimeren, Thilo; Camerer, Colin F; Schmidt, Ulrich

2018-06-07

Problem gambling is a serious socioeconomic problem involving high individual and social costs. In this article, we study risk preferences of problem gamblers including their risk attitudes in the gain and loss domains, their weighting of probabilities, and their degree of loss aversion. Our findings indicate that problem gamblers are systematically more risk taking and less sensitive toward changes in probabilities in the gain domain only. Neither their risk attitudes in the loss domain nor their degree of loss aversion are significantly different from the controls. Additional evidence for a similar degree of sensitivity toward negative outcomes is gained from skin conductance data-a psychophysiological marker for emotional arousal-in a threat-of-shock task. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

The Thiamin Pyrophosphate-Motif

NASA Technical Reports Server (NTRS)

Dominiak, P.; Ciszak, E.

2003-01-01

Using databases the authors have identified a common thiamin pyrophosphate (TPP)-motif in the family of functionally diverse TPP-dependent enzymes. This common motif consists of multimeric organization of subunits and two catalytic centers. Each catalytic center (PP:PYR) is formed at the interface of the PP-domain binding the magnesium ion, pyrophosphate and amhopyrimidine ring of TPP, and the PYR-domain binding the aminopyrimidine ring of that cofactor. A pair of these catalytic centers constitutes the catalytic core (PP:PYR)(sub 2) within these enzymes. Analysis of the structural elements of this catalytic core reveals novel definition of the common amino acid sequences, which are GXPhiX(sub 4)(G)PhiXXGQ and GDGX(sub 25-30)NN in the PP-domain, and the EX(sub 4)(G)PhiXXGPhi in the PYR-domain, where Phi corresponds to a hydrophobic amino acid. This TPP-motif provides a novel tool for annotation of TPP-dependent enzymes useful in advancing functional proteomics.

CONNJUR Workflow Builder: A software integration environment for spectral reconstruction

PubMed Central

Fenwick, Matthew; Weatherby, Gerard; Vyas, Jay; Sesanker, Colbert; Martyn, Timothy O.; Ellis, Heidi J.C.; Gryk, Michael R.

2015-01-01

CONNJUR Workflow Builder (WB) is an open-source software integration environment that leverages existing spectral reconstruction tools to create a synergistic, coherent platform for converting biomolecular NMR data from the time domain to the frequency domain. WB provides data integration of primary data and metadata using a relational database, and includes a library of pre-built workflows for processing time domain data. WB simplifies maximum entropy reconstruction, facilitating the processing of non-uniformly sampled time domain data. As will be shown in the paper, the unique features of WB provide it with novel abilities to enhance the quality, accuracy, and fidelity of the spectral reconstruction process. WB also provides features which promote collaboration, education, parameterization, and non-uniform data sets along with processing integrated with the Rowland NMR Toolkit (RNMRTK) and NMRPipe software packages. WB is available free of charge in perpetuity, dual-licensed under the MIT and GPL open source licenses. PMID:26066803

A feature dictionary supporting a multi-domain medical knowledge base.

PubMed

Naeymi-Rad, F

1989-01-01

Because different terminology is used by physicians of different specialties in different locations to refer to the same feature (signs, symptoms, test results), it is essential that our knowledge development tools provide a means to access a common pool of terms. This paper discusses the design of an online medical dictionary that provides a solution to this problem for developers of multi-domain knowledge bases for MEDAS (Medical Emergency Decision Assistance System). Our Feature Dictionary supports phrase equivalents for features, feature interactions, feature classifications, and translations to the binary features generated by the expert during knowledge creation. It is also used in the conversion of a domain knowledge to the database used by the MEDAS inference diagnostic sessions. The Feature Dictionary also provides capabilities for complex queries across multiple domains using the supported relations. The Feature Dictionary supports three methods for feature representation: (1) for binary features, (2) for continuous valued features, and (3) for derived features.

CONNJUR Workflow Builder: a software integration environment for spectral reconstruction.

PubMed

Fenwick, Matthew; Weatherby, Gerard; Vyas, Jay; Sesanker, Colbert; Martyn, Timothy O; Ellis, Heidi J C; Gryk, Michael R

2015-07-01

CONNJUR Workflow Builder (WB) is an open-source software integration environment that leverages existing spectral reconstruction tools to create a synergistic, coherent platform for converting biomolecular NMR data from the time domain to the frequency domain. WB provides data integration of primary data and metadata using a relational database, and includes a library of pre-built workflows for processing time domain data. WB simplifies maximum entropy reconstruction, facilitating the processing of non-uniformly sampled time domain data. As will be shown in the paper, the unique features of WB provide it with novel abilities to enhance the quality, accuracy, and fidelity of the spectral reconstruction process. WB also provides features which promote collaboration, education, parameterization, and non-uniform data sets along with processing integrated with the Rowland NMR Toolkit (RNMRTK) and NMRPipe software packages. WB is available free of charge in perpetuity, dual-licensed under the MIT and GPL open source licenses.

Domain identification moderates the effect of positive stereotypes on Chinese American women's math performance.

PubMed

Saad, Carmel S; Meyer, Oanh L; Dhindsa, Manveen; Zane, Nolan

2015-01-01

We examined whether an individual difference factor, math domain identification, moderated performance following positive stereotype activation. We hypothesized that positive stereotype activation would improve performance for those more math identified (compared to a control condition), but would hinder performance for those less math identified. We examined 116 Chinese American women (mean age = 19 years). Participants were assigned to the positive stereotype activation condition or to the control condition before completing a math test. Positive stereotype activation led more math identified participants to perform significantly better than the control condition, whereas it led less math identified participants to perform significantly worse than the control condition. Domain identification moderates the effect of positive stereotype activation. Educators should consider how testing situations are constructed, especially when test takers do not identify highly with the domain. (PsycINFO Database Record (c) 2015 APA, all rights reserved).

Graph Databases for Large-Scale Healthcare Systems: A Framework for Efficient Data Management and Data Services

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

Park, Yubin; Shankar, Mallikarjun; Park, Byung H.

Designing a database system for both efficient data management and data services has been one of the enduring challenges in the healthcare domain. In many healthcare systems, data services and data management are often viewed as two orthogonal tasks; data services refer to retrieval and analytic queries such as search, joins, statistical data extraction, and simple data mining algorithms, while data management refers to building error-tolerant and non-redundant database systems. The gap between service and management has resulted in rigid database systems and schemas that do not support effective analytics. We compose a rich graph structure from an abstracted healthcaremore » RDBMS to illustrate how we can fill this gap in practice. We show how a healthcare graph can be automatically constructed from a normalized relational database using the proposed 3NF Equivalent Graph (3EG) transformation.We discuss a set of real world graph queries such as finding self-referrals, shared providers, and collaborative filtering, and evaluate their performance over a relational database and its 3EG-transformed graph. Experimental results show that the graph representation serves as multiple de-normalized tables, thus reducing complexity in a database and enhancing data accessibility of users. Based on this finding, we propose an ensemble framework of databases for healthcare applications.« less

Rosette Assay: Highly Customizable Dot-Blot for SH2 Domain Screening.

PubMed

Ng, Khong Y; Machida, Kazuya

2017-01-01

With a growing number of high-throughput studies, structural analyses, and availability of protein-protein interaction databases, it is now possible to apply web-based prediction tools to SH2 domain-interactions. However, in silico prediction is not always reliable and requires experimental validation. Rosette assay is a dot blot-based reverse-phase assay developed for the assessment of binding between SH2 domains and their ligands. It is conveniently customizable, allowing for low- to high-throughput analysis of interactions between various numbers of SH2 domains and their ligands, e.g., short peptides, purified proteins, and cell lysates. The binding assay is performed in a 96-well plate (MBA or MWA apparatus) in which a sample spotted membrane is incubated with up to 96 labeled SH2 domains. Bound domains are detected and quantified using a chemiluminescence or near-infrared fluorescence (IR) imaging system. In this chapter, we describe a practical protocol for rosette assay to assess interactions between synthesized tyrosine phosphorylated peptides and a library of GST-tagged SH2 domains. Since the methodology is not confined to assessment of SH2-pTyr interactions, rosette assay can be broadly utilized for ligand and drug screening using different protein interaction domains or antibodies.

Sharing chemical structures with peer-reviewed publications. Are we there yet?

EPA Science Inventory

In the domain of chemistry one of the greatest benefits to publishing research is that data are shared. Unfortunately, the vast majority of chemical structure data remain locked up in document form, primarily as PDF files. Despite the explosive growth of online chemical databases...

Toward designing for trust in database automation

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

Duez, P. P.; Jamieson, G. A.

Appropriate reliance on system automation is imperative for safe and productive work, especially in safety-critical systems. It is unsafe to rely on automation beyond its designed use; conversely, it can be both unproductive and unsafe to manually perform tasks that are better relegated to automated tools. Operator trust in automated tools mediates reliance, and trust appears to affect how operators use technology. As automated agents become more complex, the question of trust in automation is increasingly important. In order to achieve proper use of automation, we must engender an appropriate degree of trust that is sensitive to changes in operatingmore » functions and context. In this paper, we present research concerning trust in automation in the domain of automated tools for relational databases. Lee and See have provided models of trust in automation. One model developed by Lee and See identifies three key categories of information about the automation that lie along a continuum of attributional abstraction. Purpose-, process-and performance-related information serve, both individually and through inferences between them, to describe automation in such a way as to engender r properly-calibrated trust. Thus, one can look at information from different levels of attributional abstraction as a general requirements analysis for information key to appropriate trust in automation. The model of information necessary to engender appropriate trust in automation [1] is a general one. Although it describes categories of information, it does not provide insight on how to determine the specific information elements required for a given automated tool. We have applied the Abstraction Hierarchy (AH) to this problem in the domain of relational databases. The AH serves as a formal description of the automation at several levels of abstraction, ranging from a very abstract purpose-oriented description to a more concrete description of the resources involved in the automated process. The connection between an AH for an automated tool and a list of information elements at the three levels of attributional abstraction is then direct, providing a method for satisfying information requirements for appropriate trust in automation. In this paper, we will present our method for developing specific information requirements for an automated tool, based on a formal analysis of that tool and the models presented by Lee and See. We will show an example of the application of the AH to automation, in the domain of relational database automation, and the resulting set of specific information elements for appropriate trust in the automated tool. Finally, we will comment on the applicability of this approach to the domain of nuclear plant instrumentation. (authors)« less

Distribution and cluster analysis of predicted intrinsically disordered protein Pfam domains

PubMed Central

Williams, Robert W; Xue, Bin; Uversky, Vladimir N; Dunker, A Keith

2013-01-01

The Pfam database groups regions of proteins by how well hidden Markov models (HMMs) can be trained to recognize similarities among them. Conservation pressure is probably in play here. The Pfam seed training set includes sequence and structure information, being drawn largely from the PDB. A long standing hypothesis among intrinsically disordered protein (IDP) investigators has held that conservation pressures are also at play in the evolution of different kinds of intrinsic disorder, but we find that predicted intrinsic disorder (PID) is not always conserved across Pfam domains. Here we analyze distributions and clusters of PID regions in 193024 members of the version 23.0 Pfam seed database. To include the maximum information available for proteins that remain unfolded in solution, we employ the 10 linearly independent Kidera factors1–3 for the amino acids, combined with PONDR4 predictions of disorder tendency, to transform the sequences of these Pfam members into an 11 column matrix where the number of rows is the length of each Pfam region. Cluster analyses of the set of all regions, including those that are folded, show 6 groupings of domains. Cluster analyses of domains with mean VSL2b scores greater than 0.5 (half predicted disorder or more) show at least 3 separated groups. It is hypothesized that grouping sets into shorter sequences with more uniform length will reveal more information about intrinsic disorder and lead to more finely structured and perhaps more accurate predictions. HMMs could be trained to include this information. PMID:28516017

A general structure-property relationship to predict the enthalpy of vaporisation at ambient temperatures.

PubMed

Oberg, T

2007-01-01

The vapour pressure is the most important property of an anthropogenic organic compound in determining its partitioning between the atmosphere and the other environmental media. The enthalpy of vaporisation quantifies the temperature dependence of the vapour pressure and its value around 298 K is needed for environmental modelling. The enthalpy of vaporisation can be determined by different experimental methods, but estimation methods are needed to extend the current database and several approaches are available from the literature. However, these methods have limitations, such as a need for other experimental results as input data, a limited applicability domain, a lack of domain definition, and a lack of predictive validation. Here we have attempted to develop a quantitative structure-property relationship (QSPR) that has general applicability and is thoroughly validated. Enthalpies of vaporisation at 298 K were collected from the literature for 1835 pure compounds. The three-dimensional (3D) structures were optimised and each compound was described by a set of computationally derived descriptors. The compounds were randomly assigned into a calibration set and a prediction set. Partial least squares regression (PLSR) was used to estimate a low-dimensional QSPR model with 12 latent variables. The predictive performance of this model, within the domain of application, was estimated at n=560, q2Ext=0.968 and s=0.028 (log transformed values). The QSPR model was subsequently applied to a database of 100,000+ structures, after a similar 3D optimisation and descriptor generation. Reliable predictions can be reported for compounds within the previously defined applicability domain.

The WRKY transcription factor family in Brachypodium distachyon.

PubMed

Tripathi, Prateek; Rabara, Roel C; Langum, Tanner J; Boken, Ashley K; Rushton, Deena L; Boomsma, Darius D; Rinerson, Charles I; Rabara, Jennifer; Reese, R Neil; Chen, Xianfeng; Rohila, Jai S; Rushton, Paul J

2012-06-22

A complete assembled genome sequence of wheat is not yet available. Therefore, model plant systems for wheat are very valuable. Brachypodium distachyon (Brachypodium) is such a system. The WRKY family of transcription factors is one of the most important families of plant transcriptional regulators with members regulating important agronomic traits. Studies of WRKY transcription factors in Brachypodium and wheat therefore promise to lead to new strategies for wheat improvement. We have identified and manually curated the WRKY transcription factor family from Brachypodium using a pipeline designed to identify all potential WRKY genes. 86 WRKY transcription factors were found, a total higher than all other current databases. We therefore propose that our numbering system (BdWRKY1-BdWRKY86) becomes the standard nomenclature. In the JGI v1.0 assembly of Brachypodium with the MIPS/JGI v1.0 annotation, nine of the transcription factors have no gene model and eleven gene models are probably incorrectly predicted. In total, twenty WRKY transcription factors (23.3%) do not appear to have accurate gene models. To facilitate use of our data, we have produced The Database of Brachypodium distachyon WRKY Transcription Factors. Each WRKY transcription factor has a gene page that includes predicted protein domains from MEME analyses. These conserved protein domains reflect possible input and output domains in signaling. The database also contains a BLAST search function where a large dataset of WRKY transcription factors, published genes, and an extensive set of wheat ESTs can be searched. We also produced a phylogram containing the WRKY transcription factor families from Brachypodium, rice, Arabidopsis, soybean, and Physcomitrella patens, together with published WRKY transcription factors from wheat. This phylogenetic tree provides evidence for orthologues, co-orthologues, and paralogues of Brachypodium WRKY transcription factors. The description of the WRKY transcription factor family in Brachypodium that we report here provides a framework for functional genomics studies in an important model system. Our database is a resource for both Brachypodium and wheat studies and ultimately projects aimed at improving wheat through manipulation of WRKY transcription factors.

The WRKY transcription factor family in Brachypodium distachyon

PubMed Central

2012-01-01

Background A complete assembled genome sequence of wheat is not yet available. Therefore, model plant systems for wheat are very valuable. Brachypodium distachyon (Brachypodium) is such a system. The WRKY family of transcription factors is one of the most important families of plant transcriptional regulators with members regulating important agronomic traits. Studies of WRKY transcription factors in Brachypodium and wheat therefore promise to lead to new strategies for wheat improvement. Results We have identified and manually curated the WRKY transcription factor family from Brachypodium using a pipeline designed to identify all potential WRKY genes. 86 WRKY transcription factors were found, a total higher than all other current databases. We therefore propose that our numbering system (BdWRKY1-BdWRKY86) becomes the standard nomenclature. In the JGI v1.0 assembly of Brachypodium with the MIPS/JGI v1.0 annotation, nine of the transcription factors have no gene model and eleven gene models are probably incorrectly predicted. In total, twenty WRKY transcription factors (23.3%) do not appear to have accurate gene models. To facilitate use of our data, we have produced The Database of Brachypodium distachyon WRKY Transcription Factors. Each WRKY transcription factor has a gene page that includes predicted protein domains from MEME analyses. These conserved protein domains reflect possible input and output domains in signaling. The database also contains a BLAST search function where a large dataset of WRKY transcription factors, published genes, and an extensive set of wheat ESTs can be searched. We also produced a phylogram containing the WRKY transcription factor families from Brachypodium, rice, Arabidopsis, soybean, and Physcomitrella patens, together with published WRKY transcription factors from wheat. This phylogenetic tree provides evidence for orthologues, co-orthologues, and paralogues of Brachypodium WRKY transcription factors. Conclusions The description of the WRKY transcription factor family in Brachypodium that we report here provides a framework for functional genomics studies in an important model system. Our database is a resource for both Brachypodium and wheat studies and ultimately projects aimed at improving wheat through manipulation of WRKY transcription factors. PMID:22726208

Pentachlorophenol from an old henhouse as a dioxin source in eggs and related human exposure.

PubMed

Piskorska-Pliszczynska, Jadwiga; Strucinski, Pawel; Mikolajczyk, Szczepan; Maszewski, Sebastian; Rachubik, Jaroslaw; Pajurek, Marek

2016-01-01

High levels of polychlorinated dibenzo-p-dioxins (PCDDs) and polychlorinated dibenzofurans (PCDFs) were detected in free-range eggs, and these levels reached a concentration of 29.84 ± 7.45 pg of WHO-TEQ/g of fat. This value exceeded the EU maximum permitted level of 2.5 pg of WHO-TEQ/g of fat for PCDD/F congeners by twelve-fold. A chemical analysis (HRGC-HRMS) revealed elevated amounts of OCDD, OCDF, HxCDD, HpCDD and HpCDF. During the investigation, samples of feed, soil, wall scrapings, wooden ceiling of the henhouse and tissues from laying hens were examined for dioxin contents (30 samples altogether). The long and complicated investigation found that the source of dioxins in the poultry farm was pentachlorophenol-treated wood, which was used as structural components in the 40-year-old farm building adapted to a henhouse. The wooden building material contained PCDD/Fs at a concentration of 3922.60 ± 560.93 pg of WHO-TEQ/g and 11.0 ± 2.8 μg/kg of PCP. The potential risk associated with dioxin intake was characterized by comparing the theoretically calculated weekly and monthly intakes with the toxicological reference values (TRVs), namely the Tolerable Weekly Intake (TWI) and Provisional Tolerable Monthly Intake (PTMI) values of 14 pg of WHO-TEQ/kg of bw and 70 pg of WHO-TEQ/kg of bw, respectively. The intake of dioxins estimated for high egg consumers (approximately 5-6 eggs/week) exceeded the TWI and PTMI values, which may pose a risk of delayed adverse health effects. The estimated dose of PCDD/Fs and DL-PCBs for children consuming 5 eggs per week exceeded the TWI by as much as 450% because of their nearly 5-fold-lower body weight. Although the dioxin intake estimated for the average consumption of eggs in the general population did not exceed any of the TRVs applied (58.7% TWI and 51.1% PTMI), such a situation should be considered unacceptable from a public health perspective because eggs are not the only source of these contaminants. Copyright © 2015 Elsevier Ltd. All rights reserved.

ENSO modulation of seasonal rainfall and extremes in Indonesia

NASA Astrophysics Data System (ADS)

Supari; Tangang, Fredolin; Salimun, Ester; Aldrian, Edvin; Sopaheluwakan, Ardhasena; Juneng, Liew

2017-12-01

This paper provides a detailed description of how ENSO events affect seasonal and extreme precipitation over Indonesia. Daily precipitation data from 97 stations across Indonesia covering the period from 1981 to 2012 were used to investigate the effects of El Niño and La Niña on extreme precipitation characteristics including intensity, frequency and duration, as defined based on a subset of the Expert Team on Climate Change Detection and Indices (ETCCDI). Although anomalous signals in these three indices were consistent with those of total rainfall, anomalies in the duration of extremes [i.e., consecutive dry days (CDD) and consecutive wet days (CWD)] were much more robust. El Niño impacts were particularly prominent during June-July-August (JJA) and September-October-November (SON), when anomalously dry conditions were experienced throughout the country. However, from SON, a wet anomaly appeared over northern Sumatra, later expanding eastward during December-January-February (DJF) and March-April-May (MAM), creating contrasting conditions of wet in the west and dry in the east. We attribute this apparent eastward expansion of a wet anomaly during El Niño progression to the equatorial convergence of two anti-cyclonic circulations, one residing north of the equator and the other south of the equator. These anti-cyclonic circulations strengthen and weaken according to seasonal changes and their coupling with regional seas, hence shaping moisture transport and convergence. During La Niña events, the eastward expansion of an opposite (i.e., dry) anomaly was also present but less prominent than that of El Niño. We attribute this to differences in regional ocean—atmosphere coupling, which result in the contrasting seasonal evolution of the two corresponding anomalous cyclonic circulations and in turn suggests the strong nonlinearity of El Niño and La Niña responses over the Maritime Continent. Based on the seasonal behaviour of anomalous CDD and CWD, we propose five sub-divisions of the Indonesian region for both El Niño and La Niña.

Emission characteristic of polychlorinated dibenzo-p-dioxins and polychlorinated dibenzofurans (PCDD/Fs) from medical waste incinerators (MWIs) in China in 2016: A comparison between higher emission levels of MWIs and lower emission levels of MWIs.

PubMed

Li, Jiafu; Lv, Zhiwei; Du, Lei; Li, Xiaonan; Hu, Xuepeng; Wang, Chong; Niu, Zhiguang; Zhang, Ying

2017-02-01

Emission characteristic of polychlorinated dibenzo-p-dioxins and polychlorinated dibenzofurans (PCDD/Fs) from 12 medical waste incinerators (MWIs) which have a total yearly capacity of 523 440 ton medical waste and accounted for 8.1% of total yearly capacity of 246 MWIs in China were studied. The congeners profile, emissions and toxic equivalent concentrations (TEQ) indicators of PCDD/Fs in stack gas from two groups of MWIs were researched, and the possible formation mechanisms of PCDD/Fs from MWIs were preliminarily discussed. The results of present study were summarized as follows. (1) The total concentrations and TEQ of PCDD/Fs in stack gas from MWIs were 0.516-122.803 ng Nm -3 and 0.031-3.463 ng I-TEQ Nm -3 , respectively. (2) 1,2,3,4,6,7,8-H7CDF, O8CDD, O8CDF and 1,2,3,4,6,7,8-H7CDD were the indicatory PCDD/Fs of MWI source, which could be used to apportion the sources of PCDD/Fs in environmental medium in China. (3) The emission factors of PCDD/Fs from MWIs ranged from 32.7 to 4900.0 ng I-TEQ ton -1 with a mean of 1923.6 ng I-TEQ ton -1 . (4) The gas emissions of PCDD/Fs from researched 12 MWIs and all of MWIs in China in 2016 were 37.742 and 465.951 mg I-TEQ year -1 , respectively. (5) 1,2,3,7,8,9-H6CDF and 1,2,3,4,7,8-H6CDF were effective TEQ indicators for the real-time monitoring of the PCDD/Fs emission. (6) The congeners profile and factor composition of PCDD/Fs in stack gas from two groups of MWIs were researched based on positive matrix factorization (PMF) model, and the possible formation mechanisms of PCDD/Fs from MWIs were preliminarily discussed. Copyright © 2016 Elsevier Ltd. All rights reserved.

SU-E-J-116: Uncertainties Associated with Dose Summation of High-Dose Rate Brachytherapy and Intensity Modulated Radiotherapy for Gynecological Cases

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

Kauweloa, K; Bergamo, A; Gutierrez, A

Purpose: Determining the cumulative dose distribution (CDD) for gynecological patients treated with both high-dose rate (HDR) brachytherapy and intensity-modulated radiotherapy (IMRT) is challenging. The purpose of this work is to study the uncertainty of performing this with a structure-guided deformable (SGD) approach in Velocity. Methods: For SGD, the Hounsfield units inside specified contours are overridden to set uniform values. Deformable image registration (DIR) is the run on these process images, which forces the DIR to focus on these contour boundaries. 18 gynecological cancer patients were used in this study. The original bladder and rectum planning contours for these patients weremore » used to drive the SGD. A second set of contours were made of the bladder by the same person with the intent of carefully making them completely consistent with each other. This second set was utilized to evaluate the spatial accuracy of the SGD. The determined spatial accuracy was then multiplied by the local dose gradient to determine a dose uncertainty associated with the SGD dose warping. The normal tissue complication probability (NTCP) was then calculated for each dose volume histogram (DVH) that included four different probabilistic uncertainties associated with the spatial errors (e.g., 68.3% and 95.4%). Results: The NTCPs for each DVH (e.g., NTCP-−95.4%, NTCP-−68.3%, NTCP-68.3%, NTCP-95.4%) differed amongst patients. All patients had an NTCP-−95.4% close to 0%, while NTCP-95.4% ranged from 0.67% to 100%. Nine patients had an NTCP-−95.4% less than 50% while the remaining nine patients had NTCP-95.4% greater than 50%. Conclusion: The uncertainty associated with this CDD technique renders a large NTCP uncertainty. Thus, it is currently not practical for clinical use. The two ways to improve this would be to use more precise contours to drive the SGD and to use a more accurate DIR algorithm.« less

A future Outlook: Web based Simulation of Hydrodynamic models

NASA Astrophysics Data System (ADS)

Islam, A. S.; Piasecki, M.

2003-12-01

Despite recent advances to present simulation results as 3D graphs or animation contours, the modeling user community still faces some shortcomings when trying to move around and analyze data. Typical problems include the lack of common platforms with standard vocabulary to exchange simulation results from different numerical models, insufficient descriptions about data (metadata), lack of robust search and retrieval tools for data, and difficulties to reuse simulation domain knowledge. This research demonstrates how to create a shared simulation domain in the WWW and run a number of models through multi-user interfaces. Firstly, meta-datasets have been developed to describe hydrodynamic model data based on geographic metadata standard (ISO 19115) that has been extended to satisfy the need of the hydrodynamic modeling community. The Extended Markup Language (XML) is used to publish this metadata by the Resource Description Framework (RDF). Specific domain ontology for Web Based Simulation (WBS) has been developed to explicitly define vocabulary for the knowledge based simulation system. Subsequently, this knowledge based system is converted into an object model using Meta Object Family (MOF). The knowledge based system acts as a Meta model for the object oriented system, which aids in reusing the domain knowledge. Specific simulation software has been developed based on the object oriented model. Finally, all model data is stored in an object relational database. Database back-ends help store, retrieve and query information efficiently. This research uses open source software and technology such as Java Servlet and JSP, Apache web server, Tomcat Servlet Engine, PostgresSQL databases, Protégé ontology editor, RDQL and RQL for querying RDF in semantic level, Jena Java API for RDF. Also, we use international standards such as the ISO 19115 metadata standard, and specifications such as XML, RDF, OWL, XMI, and UML. The final web based simulation product is deployed as Web Archive (WAR) files which is platform and OS independent and can be used by Windows, UNIX, or Linux. Keywords: Apache, ISO 19115, Java Servlet, Jena, JSP, Metadata, MOF, Linux, Ontology, OWL, PostgresSQL, Protégé, RDF, RDQL, RQL, Tomcat, UML, UNIX, Windows, WAR, XML

The CompTox Chemistry Dashboard: a community data resource for environmental chemistry.

PubMed

Williams, Antony J; Grulke, Christopher M; Edwards, Jeff; McEachran, Andrew D; Mansouri, Kamel; Baker, Nancy C; Patlewicz, Grace; Shah, Imran; Wambaugh, John F; Judson, Richard S; Richard, Ann M

2017-11-28

Despite an abundance of online databases providing access to chemical data, there is increasing demand for high-quality, structure-curated, open data to meet the various needs of the environmental sciences and computational toxicology communities. The U.S. Environmental Protection Agency's (EPA) web-based CompTox Chemistry Dashboard is addressing these needs by integrating diverse types of relevant domain data through a cheminformatics layer, built upon a database of curated substances linked to chemical structures. These data include physicochemical, environmental fate and transport, exposure, usage, in vivo toxicity, and in vitro bioassay data, surfaced through an integration hub with link-outs to additional EPA data and public domain online resources. Batch searching allows for direct chemical identifier (ID) mapping and downloading of multiple data streams in several different formats. This facilitates fast access to available structure, property, toxicity, and bioassay data for collections of chemicals (hundreds to thousands at a time). Advanced search capabilities are available to support, for example, non-targeted analysis and identification of chemicals using mass spectrometry. The contents of the chemistry database, presently containing ~ 760,000 substances, are available as public domain data for download. The chemistry content underpinning the Dashboard has been aggregated over the past 15 years by both manual and auto-curation techniques within EPA's DSSTox project. DSSTox chemical content is subject to strict quality controls to enforce consistency among chemical substance-structure identifiers, as well as list curation review to ensure accurate linkages of DSSTox substances to chemical lists and associated data. The Dashboard, publicly launched in April 2016, has expanded considerably in content and user traffic over the past year. It is continuously evolving with the growth of DSSTox into high-interest or data-rich domains of interest to EPA, such as chemicals on the Toxic Substances Control Act listing, while providing the user community with a flexible and dynamic web-based platform for integration, processing, visualization and delivery of data and resources. The Dashboard provides support for a broad array of research and regulatory programs across the worldwide community of toxicologists and environmental scientists.

Executive Functions in Children with Specific Language Impairment: A Meta-Analysis

ERIC Educational Resources Information Center

Pauls, Laura J.; Archibald, Lisa M. D.

2016-01-01

Purpose: Mounting evidence demonstrates deficits in children with specific language impairment (SLI) beyond the linguistic domain. Using meta-analysis, this study examined differences in children with and without SLI on tasks measuring inhibition and cognitive flexibility. Method: Databases were searched for articles comparing children (4-14…

20180318 - Sharing chemical structures with peer-reviewed publications. Are we there yet? (ACS Spring)

EPA Science Inventory

In the domain of chemistry one of the greatest benefits to publishing research is that data are shared. Unfortunately, the vast majority of chemical structure data remain locked up in document form, primarily as PDF files. Despite the explosive growth of online chemical databases...

Computer-Based Mapping for Curriculum Development.

ERIC Educational Resources Information Center

Allen, Brockenbrough S.; And Others

This article describes the results of a three-month experiment in the use of computer-based semantic networks for curriculum development. A team of doctoral and master's degree students developed a 1200-item computer database representing a tentative "domain of competency" for a proposed MA degree in Workforce Education and Lifelong…

Identification of food and beverage spoilage yeasts from DNA sequence analyses

USDA-ARS?s Scientific Manuscript database

Detection, identification, and classification of yeasts has undergone a major transformation in the last decade and a half following application of gene sequence analyses and genome comparisons. Development of a database (barcode) of easily determined DNA sequences from domains 1 and 2 (D1/D2) of th...

Statistical Learning in Specific Language Impairment: A Meta-Analysis

ERIC Educational Resources Information Center

Lammertink, Imme; Boersma, Paul; Wijnen, Frank; Rispens, Judith

2017-01-01

Purpose: The current meta-analysis provides a quantitative overview of published and unpublished studies on statistical learning in the auditory verbal domain in people with and without specific language impairment (SLI). The database used for the meta-analysis is accessible online and open to updates (Community-Augmented Meta-Analysis), which…

Multi-Disciplinary Learning through a Database Development Project

ERIC Educational Resources Information Center

Ng, Vincent; Lau, Chloe; Shum, Pearl

2012-01-01

Recently, there are many good examples of how multi-disciplinary learning can support students to learn collaboratively and not solely focus on a single professional sector. During the Fall 2011 and Spring 2012 semesters, we have attempted to gather students studying different professional domains together. Students from the Department of…