Ruffling of Metalloporphyrins Bound to IsdG And IsdI, Two Heme Degrading Enzymes in Staphylococcus Aureus

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

Lee, W.C.; Reniere, M.L.; Skaar, E.P.

2009-05-19

IsdG and IsdI are paralogous proteins that are intracellular components of a complex heme uptake system in Staphylococcus aureus. IsdG and IsdI were shown previously to reductively degrade hemin. Crystal structures of the apoproteins show that these proteins belong to a newly identified heme degradation family distinct from canonical eukaryotic and prokaryotic heme oxygenases. Here we report the crystal structures of an inactive N7A variant of IsdG in complex with Fe{sup 3+}-protoporphyrin IX (IsdG-hemin) and of IsdI in complex with cobalt protoporphyrin IX (IsdI-CoPPIX) to 1.8 {angstrom} or better resolution. These structures show that the metalloporphyrins are buried into similarmore » deep clefts such that the propionic acids form salt bridges to two Arg residues. His{sup 77} (IsdG) or His{sup 76} (IsdI), a critical residue required for activity, is coordinated to the Fe{sup 3+} or Co{sup 3+} atoms, respectively. The bound porphyrin rings form extensive steric interactions in the binding cleft such that the rings are highly distorted from the plane. This distortion is best described as ruffled and places the {beta}- and {delta}-meso carbons proximal to the distal oxygen-binding site. In the IsdG-hemin structure, Fe{sup 3+} is pentacoordinate, and the distal side is occluded by the side chain of Ile{sup 55}. However, in the structure of IsdI-CoPPIX, the distal side of the CoPPIX accommodates a chloride ion in a cavity formed through a conformational change in Ile{sup 55}. The chloride ion participates in a hydrogen bond to the side chain amide of Asn{sup 6}. Together the structures suggest a reaction mechanism in which a reactive peroxide intermediate proceeds with nucleophilic oxidation at the {beta}- or {delta}-meso carbon of the hemin.« less

Hemoglobin binding and catalytic heme extraction by IsdB near iron transporter domains.

PubMed

Bowden, Catherine F M; Verstraete, Meghan M; Eltis, Lindsay D; Murphy, Michael E P

2014-04-15

The Isd (iron-regulated surface determinant) system is a multiprotein transporter that allows bacterium Staphylococcus aureus to take up iron from hemoglobin (Hb) during human infection. In this system, IsdB is a cell wall-anchored surface protein that contains two near iron transporter (NEAT) domains, one of which binds heme. IsdB rapidly extracts heme from Hb and transfers it to IsdA for relay into the bacterial cell. Using a series of recombinant IsdB constructs that included at least one NEAT domain, we demonstrated that both domains are required to bind Hb with high affinity (KD = 0.42 ± 0.05 μM) and to extract heme from Hb. Moreover, IsdB extracted heme only from oxidized metHb, although it also bound oxyHb and the Hb-CO complex. In a reconstituted model of the biological heme relay pathway, IsdB catalyzed the transfer of heme from metHb to IsdA with a Km for metHb of 0.75 ± 0.07 μN and a kcat of 0.22 ± 0.01 s(-1). The latter is consistent with the transfer of heme from metHb to IsdB being the rate-limiting step. With both NEAT domains and the linker region present in a single contiguous polypeptide, high-affinity Hb binding was achieved, rapid heme uptake was observed, and multiple turnovers of heme extraction from metHb and transfer to IsdA were conducted, representing all known Hb-heme uptake functions of the full-length IsdB protein.

Is It Time to Say Farewell to the ISDS System?

PubMed Central

Lencucha, Raphael

2017-01-01

Investor-state dispute settlement (ISDS) continues to plague health-oriented government regulation. This is particularly reflected in recent challenges to tobacco control measures through bilateral investment agreements. There are numerous reform proposals circulating within the public health community. However, I suggest that perhaps it is time for the community to explore a stronger position on ISDS. I draw from mounting evidence on the problematic uses of the ISDS to explore the proposition that ISDS is no longer justified. I tackle the normative question of should the ISDS system persist and point out that the ISDS system is not justifiable from a development perspective and because of its nefarious use, is of no added value to a system that could rely on domestic courts. PMID:28812817

Rescuing the Rescuer: On the Protein Complex between the Human Mitochondrial Acyl Carrier Protein and ISD11.

PubMed

Herrera, María Georgina; Pignataro, María Florencia; Noguera, Martín Ezequiel; Cruz, Karen Magalí; Santos, Javier

2018-05-16

Iron-sulfur clusters are essential cofactors in many biochemical processes. ISD11, one of the subunits of the protein complex that carries out the cluster assembly in mitochondria, is necessary for cysteine desulfurase NFS1 stability and function. Several authors have recently provided evidence showing that ISD11 interacts with the acyl carrier protein (ACP). We carried out the coexpression of human mitochondrial ACP and ISD11 in E. coli. This work shows that ACP and ISD11 form a soluble, structured, and stable complex able to bind to the human NFS1 subunit modulating its activity. Results suggest that ACP plays a key-role in ISD11 folding and stability in vitro. These findings offer the opportunity to study the mechanism of interaction between ISD11 and NFS1.

A Model for the Redesign of Training Materials for the Nuclear Power Industry.

ERIC Educational Resources Information Center

Gredler, Margaret Bell

1986-01-01

Presents consultant/staff model for training program redesign and discusses activities involved: interpretation of Instructional System Design (ISD) model concepts into plans in trainer's content area and sequenced sets of content-appropriate verbs for objectives; presenting training sessions on design issues; and holding individual conference…

Improved Spatial Differencing Scheme for 2-D DOA Estimation of Coherent Signals with Uniform Rectangular Arrays.

PubMed

Shi, Junpeng; Hu, Guoping; Sun, Fenggang; Zong, Binfeng; Wang, Xin

2017-08-24

This paper proposes an improved spatial differencing (ISD) scheme for two-dimensional direction of arrival (2-D DOA) estimation of coherent signals with uniform rectangular arrays (URAs). We first divide the URA into a number of row rectangular subarrays. Then, by extracting all the data information of each subarray, we only perform difference-operation on the auto-correlations, while the cross-correlations are kept unchanged. Using the reconstructed submatrices, both the forward only ISD (FO-ISD) and forward backward ISD (FB-ISD) methods are developed under the proposed scheme. Compared with the existing spatial smoothing techniques, the proposed scheme can use more data information of the sample covariance matrix and also suppress the effect of additive noise more effectively. Simulation results show that both FO-ISD and FB-ISD can improve the estimation performance largely as compared to the others, in white or colored noise conditions.

Improved Spatial Differencing Scheme for 2-D DOA Estimation of Coherent Signals with Uniform Rectangular Arrays

PubMed Central

Hu, Guoping; Zong, Binfeng; Wang, Xin

2017-01-01

This paper proposes an improved spatial differencing (ISD) scheme for two-dimensional direction of arrival (2-D DOA) estimation of coherent signals with uniform rectangular arrays (URAs). We first divide the URA into a number of row rectangular subarrays. Then, by extracting all the data information of each subarray, we only perform difference-operation on the auto-correlations, while the cross-correlations are kept unchanged. Using the reconstructed submatrices, both the forward only ISD (FO-ISD) and forward backward ISD (FB-ISD) methods are developed under the proposed scheme. Compared with the existing spatial smoothing techniques, the proposed scheme can use more data information of the sample covariance matrix and also suppress the effect of additive noise more effectively. Simulation results show that both FO-ISD and FB-ISD can improve the estimation performance largely as compared to the others, in white or colored noise conditions. PMID:28837115

Staphylococcus lugdunensis IsdG Liberates Iron from Host Heme▿

PubMed Central

Haley, Kathryn P.; Janson, Eric M.; Heilbronner, Simon; Foster, Timothy J.; Skaar, Eric P.

2011-01-01

Staphylococcus lugdunensis is often found as part of the normal flora of human skin but has the potential to cause serious infections even in healthy individuals. It remains unclear what factors enable S. lugdunensis to transition from a skin commensal to an invasive pathogen. Analysis of the complete genome reveals a putative iron-regulated surface determinant (Isd) system encoded within S. lugdunensis. In other bacteria, the Isd system permits the utilization of host heme as a source of nutrient iron to facilitate bacterial growth during infection. In this study, we establish that S. lugdunensis expresses an iron-regulated IsdG-family heme oxygenase that binds and degrades heme. Heme degradation by IsdG results in the release of free iron and the production of the chromophore staphylobilin. IsdG-mediated heme catabolism enables the use of heme as a sole source of iron, establishing IsdG as a pathophysiologically relevant heme oxygenase in S. lugdunensis. Together these findings offer insight into how S. lugdunensis fulfills its nutritional requirements while invading host tissues and establish the S. lugdunensis Isd system as being involved in heme-iron utilization. PMID:21764939

Facial Anthropometric Norms among Kosovo - Albanian Adults.

PubMed

Staka, Gloria; Asllani-Hoxha, Flurije; Bimbashi, Venera

2017-09-01

The development of an anthropometric craniofacial database is a necessary multidisciplinary proposal. The aim of this study was to establish facial anthropometric norms and to investigate into sexual dimorphism in facial variables among Kosovo Albanian adults. The sample included 204 students of Dental School, Faculty of Medicine, University of Pristina. Using direct anthropometry, a series of 8 standard facial measurements was taken on each subject with digital caliper with an accuracy of 0.01 mm (Boss, Hamburg-Germany). The normative data and percentile rankings were calculated. Gender differences in facial variables were analyzed using t- test for independent samples (p<0.05). The index of sexual dimorphism (ISD) and percentage of sexual dimorphism were calculated for each facial measurement. ormative data for all facial anthropometric measurements in males were higher than in females. Male average norms compared with the female average norms differed significantly from each other (p>0.05).The highest index of sexual dimorphism (ISD) was found for the lower facial height 1.120, for which the highest percentage of sexual dimorphism, 12.01%., was also found. The lowest ISD was found for intercanthal width, 1.022, accompanied with the lowest percentage of sexual dimorphism, 2.23%. The obtained results have established the facial anthropometric norms among Kosovo Albanian adults. Sexual dimorphism has been confirmed for each facial measurement.

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

McKinney, M.J.; Jenkins, S.

Project JEM (Jarvis Enhancement of Males) is a pre-college program directed toward stimulating disadvantaged, talented African American males in grades four, five, and six to attend college and major in mathematics, science, computer science, or related technical areas needed by the US Department of Energy. Twenty young African American male students were recruited from Gladewater Independent School District (ISD), Longview ISD, Hawkins ISD, Tyler ISD, Winona ISD and big Sandy ISD. Students enrolled in the program range from ages 10 to 13 and are in grades four, five and six. Student participants in the 1997 Project JEM Program attended Saturdaymore » Academy sessions and a four week intensive, summer residential program. The information here provides a synopsis of the activities which were conducted through each program component.« less

Students as Library Detectives and Books as Clues: An Application of ISD in K-12 Schools

ERIC Educational Resources Information Center

Moore, Kimberly J.; Knowlton, Dave S.

2006-01-01

Instructional Systems Design (ISD) is the systematic development of instructional strategies that are grounded in both learning and instructional theory. ISD is usually overlooked as a useful methodology in K-12 schools. ISD is extremely expensive in terms of the time required to develop instruction, and it often seems more appropriate as an…

Improving Cardiac Surgical Site Infection Reporting and Prevention By Using Registry Data for Case Ascertainment.

PubMed

Nayar, Vaidehi; Kennedy, Andrea; Pappas, Janine; Atchley, Krista D; Field, Cynthia; Smathers, Sarah; Teszner, Eva E; Sammons, Julia S; Coffin, Susan E; Gerber, Jeffrey S; Spray, Thomas L; Steven, James M; Bell, Louis M; Forrer, Joan; Gonzalez, Fernando; Chi, Albert; Nieczpiel, William J; Martin, John N; Gaynor, J William

2016-01-01

The use of administrative data for surgical site infection (SSI) surveillance leads to inaccurate reporting of SSI rates [1]. A quality improvement (QI) initiative was conducted linking clinical registry and administrative databases to improve reporting and reduce the incidence of SSI [2]. At our institution, The Society of Thoracic Surgeons Congenital Heart Surgery Database (STS-CHSD) and infection surveillance database (ISD) were linked to the enterprise data warehouse containing electronic health record (EHR) billing data. A data visualization tool was created to (1) use the STS-CHSD for case ascertainment, (2) resolve discrepancies between the databases, and (3) assess impact of QI initiatives, including wound alert reports, bedside reviews, prevention bundles, and billing coder education. Over the 24-month study period, 1,715 surgical cases were ascertained according to the STS-CHSD clinical criteria, with 23 SSIs identified through the STS-CHSD, 20 SSIs identified through the ISD, and 32 SSIs identified through the billing database. The rolling 12-month STS-CHSD SSI rate decreased from 2.73% (21 of 769 as of January 2013) to 1.11% (9 of 813 as of December 2014). Thirty reporting discrepancies were reviewed to ensure accuracy. Workflow changes facilitated communication and improved adjudication of suspected SSIs. Billing coder education increased coding accuracy and narrowed variation between the 3 SSI sources. The data visualization tool demonstrated temporal relationships between QI initiatives and SSI rate reductions. Linkage of registry and infection control surveillance data with the EHR improves SSI surveillance. The visualization tool and workflow changes facilitated communication, SSI adjudication, and assessment of the QI initiatives. Implementation of these initiatives was associated with decreased SSI rates. Copyright © 2016 The Society of Thoracic Surgeons. Published by Elsevier Inc. All rights reserved.

Association of imaging abnormalities of the subcallosal septal area with Alzheimer's disease and mild cognitive impairment.

PubMed

Gan, C L; O'Sullivan, M J; Metzler-Baddeley, C; Halpin, S

2017-11-01

To evaluate the use the distance between the adjacent septal nuclei as a surrogate marker of septal area atrophy seen in Alzheimer's disease (AD). Interseptal distance (ISD) was measured, blind to clinical details, in 250 patients who underwent computed tomography (CT) of the brain at University Hospital of Wales. Clinical details including memory problem history were retrieved. An ISD cut-off value that discriminated those with and without memory symptoms was sought. ISD measurements were also made in 20 AD patients. To test both the method and the defined cut-off, measurements were then made in an independent cohort of 21 mild cognitive impairment (MCI) patients and 45 age-matched healthy controls, in a randomised and blinded fashion. ISD measurement was achieved in all patients. In 28 patients with memory symptoms, the mean ISD was 5.9 mm compared with 2.3 mm in those without overt symptoms (p=0.001). The optimum ISD cut-off value was 4 mm (sensitivity 85.7% and specificity 85.8%). All AD patients had an ISD of >4 mm (mean ISD= 6.1 mm). The mean ISD for MCI patients was 3.84 mm compared with 2.18 mm in age-matched healthy controls (p=0.001). Using a 4 mm cut-off correctly categorised 10 mild cognitive impairment patients (47.6%) and 38 healthy controls (84.4%). ISD is a simple and reliable surrogate measurement for septal area atrophy, applicable to CT and magnetic resonance imaging (MRI). It can be used to help select patients for further investigation. Copyright © 2017 The Royal College of Radiologists. Published by Elsevier Ltd. All rights reserved.

lean-ISD.

ERIC Educational Resources Information Center

Wallace, Guy W.

2001-01-01

Explains lean instructional systems design/development (ISD) as it relates to curriculum architecture design, based on Japan's lean production system. Discusses performance-based systems; ISD models; processes for organizational training and development; curriculum architecture to support job performance; and modular curriculum development. (LRW)

[Mechanisms of retroviral immunosuppressive domain-induced immune modulation].

PubMed

Blinov, V M; Krasnov, G S; Shargunov, A V; Shurdov, M A; Zverev, V V

2013-01-01

Immunosuppressive domains (ISD) of viral envelope glycoproteins provide highly pathogenic phenotypes of various retroviruses. ISD interaction with immune cells leads to an inhibition of a response. In the 1980s it was shown that the fragment of ISD comprising of 17 amino acids (named CKS-17) is carrying out such immune modulation. However the underlying mechanisms were not known. The years of thorough research allowed to identify the regulation of Ras-Raf-MEK-MAPK and PI3K-AKT-mTOR cellular pathways as a result of ISD interaction with immune cells. By the way, this leads to decrease of secretion of stimulatory cytokines (e.g., IL-12) and increase of inhibitory, anti-inflammatory ones (e.g., IL-10). One of the receptor tyrosine kinases inducing signal in these pathways acts as the primary target of ISD while other key regulators--cAMP and diacylglycerol (DAG), act as secondary messengers of signal transduction. Immunosuppressive-like domains can be found not only in retroviruses; the presence of ISD within Ebola viral envelope glycoproteins caused extremely hard clinical course of virus-induced hemorrhagic fever. A number of retroviral-origin fragments encoding ISD can be found in the human genome. These regions are expressed in the placenta within genes of syncytins providing a tolerance of mother's immune system to an embryo. The present review is devoted to molecular aspects of retroviral ISD-induced modulation of host immune system.

Naturally occurring IgG antibody levels to the Staphylococcus aureus protein IsdB in humans

PubMed Central

Zorman, Julie K; Esser, Mark; Raedler, Michael; Kreiswirth, Barry N; Ala'aldeen, Dlawer AA; Kartsonis, Nicholas; Smugar, Steven S; Anderson, Annaliesa S; McNeely, Tessie; Arduino, Jean Marie

2013-01-01

Staphylococcus aureus is a well-recognized, clinically important cause of nosocomial infections, and as such, a vaccine to prevent S. aureus infections would be an important achievement. A Phase IIB/III study of V710, a vaccine containing iron-regulated surface determinant B (IsdB), demonstrated significant sero-conversion rates in cardiovascular surgery patients following a single pre-surgery immunization. However, the vaccine was not efficacious in preventing bacteremia or deep sternal wound infection post-surgery, thus raising the possibility that IsdB might not be available for immune recognition during infection. The purpose of the work described herein was to evaluate and quantify the naturally occurring anti-IsdB levels at baseline and over time during infection, to understand whether IsdB is expressed during a S. aureus infection in hospitalized non-vaccinated patients. We evaluated baseline and follow-up titers in 3 populations: (1) healthy subjects, (2) hospitalized patients with non-S. aureus infections, and (3) hospitalized patients with S. aureus infections. Baseline anti-IsdB levels generally overlapped between the 3 groups, but were highly variable within each group. In healthy subjects, baseline and follow-up levels were highly correlated (Spearman's rho = 0.93), and the geometric mean fold-rise (GMFR) in anti-IsdB levels between study entry and last value was 0.9-fold (95% confidence interval (CI): 0.8 to 1.0 ; p = 0.09), showing no trend over time. The convalescent GMFR in anti-IsdB levels from baseline was 1.7-fold (95% CI: 1.3 to 2.2, p = 0.0008) during S. aureus infection, significantly different from the 1.0-fold GMFR (95% CI: 0.9–1.2, p = 0.60) in non-S. aureus infection, p = 0.005. Additionally, S. aureus isolates (51) obtained from the hospitalized patient group expressed the IsdB protein in vitro. Collectively, these data suggest that IsdB expression levels rise substantially following infection with S. aureus, but not with other pathogens, and IsdB is likely well-conserved across S. aureus strains. PMID:23778314

Naturally occurring IgG antibody levels to the Staphylococcus aureus protein IsdB in humans.

PubMed

Zorman, Julie K; Esser, Mark; Raedler, Michael; Kreiswirth, Barry N; Ala'Aldeen, Dlawer A A; Kartsonis, Nicholas; Smugar, Steven S; Anderson, Annaliesa S; McNeely, Tessie; Arduino, Jean Marie

2013-09-01

Staphylococcus aureus is a well-recognized, clinically important cause of nosocomial infections, and as such, a vaccine to prevent S. aureus infections would be an important achievement. A Phase IIB/III study of V710, a vaccine containing iron-regulated surface determinant B (IsdB), demonstrated significant sero-conversion rates in cardiovascular surgery patients following a single pre-surgery immunization. However, the vaccine was not efficacious in preventing bacteremia or deep sternal wound infection post-surgery, thus raising the possibility that IsdB might not be available for immune recognition during infection. The purpose of the work described herein was to evaluate and quantify the naturally occurring anti-IsdB levels at baseline and over time during infection, to understand whether IsdB is expressed during a S. aureus infection in hospitalized non-vaccinated patients. We evaluated baseline and follow-up titers in 3 populations: (1) healthy subjects, (2) hospitalized patients with non-S. aureus infections, and (3) hospitalized patients with S. aureus infections. Baseline anti-IsdB levels generally overlapped between the 3 groups, but were highly variable within each group. In healthy subjects, baseline and follow-up levels were highly correlated (Spearman's rho = 0.93), and the geometric mean fold-rise (GMFR) in anti-IsdB levels between study entry and last value was 0.9-fold (95% confidence interval (CI): 0.8 to 1.0 ; p = 0.09), showing no trend over time. The convalescent GMFR in anti-IsdB levels from baseline was 1.7-fold (95% CI: 1.3 to 2.2, p = 0.0008) during S. aureus infection, significantly different from the 1.0-fold GMFR (95% CI: 0.9-1.2, p = 0.60) in non-S. aureus infection, p = 0.005. Additionally, S. aureus isolates (51) obtained from the hospitalized patient group expressed the IsdB protein in vitro. Collectively, these data suggest that IsdB expression levels rise substantially following infection with S. aureus, but not with other pathogens, and IsdB is likely well-conserved across S. aureus strains.

Pulsed laser deposition of YBCO films on ISD MgO buffered metal tapes

NASA Astrophysics Data System (ADS)

Ma, B.; Li, M.; Koritala, R. E.; Fisher, B. L.; Markowitz, A. R.; Erck, R. A.; Baurceanu, R.; Dorris, S. E.; Miller, D. J.; Balachandran, U.

2003-04-01

Biaxially textured magnesium oxide (MgO) films deposited by inclined-substrate deposition (ISD) are desirable for rapid production of high-quality template layers for YBCO-coated conductors. High-quality YBCO films were grown on ISD MgO buffered metallic substrates by pulsed laser deposition (PLD). Columnar grains with a roof-tile surface structure were observed in the ISD MgO films. X-ray pole figure analysis revealed that the (002) planes of the ISD MgO films are tilted at an angle from the substrate normal. A small full-width at half maximum (FWHM) of approx9° was observed in the phi-scan for ISD MgO films deposited at an inclination angle of 55°. In-plane texture in the ISD MgO films developed in the first approx0.5 mum from the substrate surface, and then stabilized with further increases in film thickness. Yttria-stabilized zirconia and ceria buffer layers were deposited on the ISD MgO grown on metallic substrates prior to the deposition of YBCO by PLD. YBCO films with the c-axis parallel to the substrate normal have a unique orientation relationship with the ISD MgO films. An orientation relationship of YBCOlangle100rangleparallelMgOlangle111rangle and YBCOlangle010rangleparallelMgOlangle110rangle was measured by x-ray pole figure analyses and confirmed by transmission electron microscopy. A Tc of 91 K with a sharp transition and transport Jc of 5.5 × 105 A cm-2 at 77 K in self-field were measured on a YBCO film that was 0.46 mum thick, 4 mm wide and 10 mm long.

Development of an In-Situ Decommissioning Sensor Network Test Bed for Structural Condition Monitoring - 12156

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

Zeigler, Kristine E.; Ferguson, Blythe A.

2012-07-01

The Savannah River National Laboratory (SRNL) has established an In Situ Decommissioning (ISD) Sensor Network Test Bed, a unique, small scale, configurable environment, for the assessment of prospective sensors on actual ISD system material, at minimal cost. The Department of Energy (DOE) is presently implementing permanent entombment of contaminated, large nuclear structures via ISD. The ISD end state consists of a grout-filled concrete civil structure within the concrete frame of the original building. Validation of ISD system performance models and verification of actual system conditions can be achieved through the development a system of sensors to monitor the materials andmore » condition of the structure. The ISD Sensor Network Test Bed has been designed and deployed to addresses the DOE-Environmental Management Technology Need to develop a remote monitoring system to determine and verify ISD system performance. Commercial off-the-shelf sensors have been installed on concrete blocks taken from walls of the P Reactor Building at the Savannah River Site. Deployment of this low-cost structural monitoring system provides hands-on experience with sensor networks. The initial sensor system consists of groutable thermistors for temperature and moisture monitoring, strain gauges for crack growth monitoring, tilt-meters for settlement monitoring, and a communication system for data collection. Baseline data and lessons learned from system design and installation and initial field testing will be utilized for future ISD sensor network development and deployment. The Sensor Network Test Bed at SRNL uses COTS sensors on concrete blocks from the outer wall of the P Reactor Building to measure conditions expected to occur in ISD structures. Knowledge and lessons learned gained from installation, testing, and monitoring of the equipment will be applied to sensor installation in a meso-scale test bed at FIU and in future ISD structures. The initial data collected from the sensors installed on the P Reactor Building blocks define the baseline materials condition of the P Reactor ISD external concrete structure. Continued monitoring of the blocks will enable evaluation of the effects of aging on the P Reactor ISD structure. The collected data will support validation of the material degradation model and assessment of the condition of the ISD structure over time. The following are recommendations for continued development of the ISD Sensor Network Test Bed: - Establish a long-term monitoring program using the concrete blocks with existing sensor and/or additional sensors for trending the concrete materials and structural condition; - Continue development of a stand-alone test bed sensor system that is self-powered and provides wireless transmission of data to a user-accessible dashboard; - Develop and implement periodic NDE/DE characterization of the concrete blocks to provide verification and validation for the measurements obtained through the sensor system and concrete degradation model(s). (authors)« less

MALDI In-Source Decay of Protein: The Mechanism of c-Ion Formation

PubMed Central

Takayama, Mitsuo

2016-01-01

The in-source decay (ISD) phenomenon, the fragmentation at an N–Cα bond of a peptide backbone that occurs within several tens of nanoseconds in the ion-source in matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS), is discussed from the standpoints of the discovery and early publications dealing with MALDI-ISD, the formation of c-ions in energy-sudden desorption/ionization methods, the formation of radical species in a MALDI, model construction for ISD, and matrix materials that are suitable for use in MALDI-ISD. The formation of c-ions derived from peptides and proteins in MALDI-ISD can be rationalized by a mechanism involving intermolecular hydrogen transfer, denoted as the “Takayama’s model” by De Pauw’s group (Anal. Chem. 79: 8678–8685, 2007). It should be emphasized that the model for MALDI-ISD was constructed on the basis of X-ray crystallography and scanning probe microscopy (SPM) analyses of matrix crystals, as well as the use of isotopically-labelled peptides. PMID:27162707

Multi-Virulence-Locus Sequence Typing of Staphylococcus lugdunensis Generates Results Consistent with a Clonal Population Structure and Is Reliable for Epidemiological Typing

PubMed Central

Didi, Jennifer; Lemée, Ludovic; Gibert, Laure; Pons, Jean-Louis

2014-01-01

Staphylococcus lugdunensis is an emergent virulent coagulase-negative staphylococcus responsible for severe infections similar to those caused by Staphylococcus aureus. To understand its potentially pathogenic capacity and have further detailed knowledge of the molecular traits of this organism, 93 isolates from various geographic origins were analyzed by multi-virulence-locus sequence typing (MVLST), targeting seven known or putative virulence-associated loci (atlLR2, atlLR3, hlb, isdJ, SLUG_09050, SLUG_16930, and vwbl). The polymorphisms of the putative virulence-associated loci were moderate and comparable to those of the housekeeping genes analyzed by multilocus sequence typing (MLST). However, the MVLST scheme generated 43 virulence types (VTs) compared to 20 sequence types (STs) based on MLST, indicating that MVLST was significantly more discriminating (Simpson's index [D], 0.943). No hypervirulent lineage or cluster specific to carriage strains was defined. The results of multilocus sequence analysis of known and putative virulence-associated loci are consistent with a clonal population structure for S. lugdunensis, suggesting a coevolution of these genes with housekeeping genes. Indeed, the nonsynonymous to synonymous evolutionary substitutions (dN/dS) ratio, the Tajima's D test, and Single-likelihood ancestor counting (SLAC) analysis suggest that all virulence-associated loci were under negative selection, even atlLR2 (AtlL protein) and SLUG_16930 (FbpA homologue), for which the dN/dS ratios were higher. In addition, this analysis of virulence-associated loci allowed us to propose a trilocus sequence typing scheme based on the intragenic regions of atlLR3, isdJ, and SLUG_16930, which is more discriminant than MLST for studying short-term epidemiology and further characterizing the lineages of the rare but highly pathogenic S. lugdunensis. PMID:25078912

Structural Couple Therapy in the Treatment of Inhibited Sexual Drive.

ERIC Educational Resources Information Center

Fish, Linda Stone; And Others

1994-01-01

Examined structural couple therapy approach to treatment of inhibited sexual desire (ISD). Results from clinical sample of 19 couples with ISD suggest that structural couple therapy approach to ISD is effective in reducing symptoms of sexual disorder and in increasing couple satisfaction. (Author/NB)

General Systems Theory and Instructional Systems Design.

ERIC Educational Resources Information Center

Salisbury, David F.

1990-01-01

Describes basic concepts in the field of general systems theory (GST) and identifies commonalities that exist between GST and instructional systems design (ISD). Models and diagrams that depict system elements in ISD are presented, and two matrices that show how GST has been used in ISD literature are included. (11 references) (LRW)

Designing for the ISD Life Cycle.

ERIC Educational Resources Information Center

Wallace, Guy W.; Hybert, Peter R.; Smith, Kelly R.; Blecke, Brian D.

2002-01-01

Outlines the recent criticisms of traditional ISD (Instructional Systems Design) and discusses the implications that impact the life cycle costs of T&D (Training and Development) projects and their ROI (Return On Investment) potential. Describes a modified approach to ISD which mimics the modular approach of systems engineering design.…

Refractory heartburn: comparison of intercellular space diameter in documented GERD vs. functional heartburn.

PubMed

Vela, Marcelo F; Craft, Brandon M; Sharma, Neeraj; Freeman, Janice; Hazen-Martin, Debra

2011-05-01

Refractory heartburn despite acid suppression may be explained by ongoing gastroesophageal reflux disease (GERD) or functional heartburn (FH), i.e., symptoms without evidence of GERD. Impedance-pH monitoring (impedance-pH) detects acid and nonacid reflux and is useful for evaluating acid-suppressed, refractory patients. Intercellular space diameter (ISD) of esophageal epithelium measured by transmission electron microscopy (TEM) is a marker of epithelial damage present in both erosive and nonerosive reflux disease. ISD has not been used to study refractory heartburn or FH. Our aim was to compare ISD in healthy controls and refractory heartburn patients with GERD and FH. In refractory heartburn patients (heartburn more than twice/week for at least 2 months despite proton pump inhibitor (PPI) b.i.d.), erosive esophagitis and/or abnormal impedance-pH (increased acid exposure or positive symptom index) defined GERD; normal esophagogastroduodenoscopy (EGD)/impedance-pH defined FH. Asymptomatic, healthy controls had normal EGD and pH-metry. Mean ISD in each subject, determined by blinded TEM of esophageal biopsies, was the average of 100 measurements (10 measurements in each of 10 micrographs). In all, 11 healthy controls, 11 FH, and 15 GERD patients were studied. Mean ISD was significantly higher in GERD compared with controls (0.87 vs. 0.32 μm, P=0.003) and FH (0.87 vs. 0.42 μm, P=0.012). Mean ISD was similar in FH and controls (0.42 vs. 0.32 μm, P=0.1). The proportion of patients with abnormal ISD was significantly higher for GERD compared with FH (60 vs. 9%, P=0.014). ISD is increased in refractory heartburn patients with GERD but not those with FH. Our findings suggest that measurement of ISD by TEM might be a useful tool to distinguish GERD from FH in patients with refractory heartburn.

Use of isosorbide dinitrate for the symptomatic treatment of patients with Chagas' disease achalasia. A double-blind, crossover trial.

PubMed

Ferreira-Filho, L P; Patto, R J; Troncon, L E; Oliveira, R B

1991-01-01

1. A randomized, double-blind, placebo-controlled trial was carried out to determine the efficacy of isosorbide dinitrate (ISD) on dysphagia in patients with Chagasic achalasia. 2. Twenty-three patients with Chagas' disease and dysphagia entered the study and 20 (87%) completed the two 7-day treatment periods. Subjects were given either 5 mg ISD (12 patients) or placebo (11 patients) by the sublingual route for the first 7 days. On the 8th day, patients crossed over and began another 7-day period during which they received the opposite, identical-appearing tablets. 3. Scores attributed by uninformed investigators for the frequency and severity of dysphagia were significantly lower (P less than 0.05) following ISD treatment than after the placebo period or for the pretreatment condition. A significantly higher degree of improvement of dysphagia was experienced by the patients during ISD treatment than during the placebo period. Fourteen patients experienced meal-related headaches during ISD, but not placebo treatment. The extent of improvement in general well-being due to ISD was the same when the drug was given in the first or second test period. 4. Our results indicate that ISD, 5 mg by the sublingual route, is effective in alleviating dysphagia in patients with Chagasic achalasia but its usefulness is limited by the high rate of headache as a side effect.

Instructional System Development (ISD) in the Armed Services: Methodology and Application. Final Report, August 25, 1977 through March 19, 1979.

ERIC Educational Resources Information Center

Vineberg, Robert; Joyner, John N.

Instructional System Development (ISD) methodologies and practices were examined in the Army, Navy, Marine Corps, and Air Force, each of which prescribes the ISD system involving rigorous derivation of training requirements from job requirements, selection of instructional strategies to maximize training efficiency, and revision of instruction…

User-Centered Innovation: A Model for "Early Usability Testing."

ERIC Educational Resources Information Center

Sugar, William A.; Boling, Elizabeth

The goal of this study is to show how some concepts and techniques from disciplines outside Instructional Systems Development (ISD) have the potential to extend and enhance the traditional view of ISD practice when they are employed very early in the ISD process. The concepts and techniques employed were user-centered in design and usability, and…

Circumferential urinary sphincter surface electromyography: A novel diagnostic method for intrinsic sphincter deficiency.

PubMed

Heesakkers, John; Gerretsen, Reza; Izeta, Ander; Sievert, Karl-Dietrich; Farag, Fawzy

2016-02-01

The diagnosis of intrinsic sphincter deficiency (ISD) in patients with stress urinary incontinence (SUI) is not well established. We explored the possibility of applying a new tool: minimally invasive circumferential sphincter surface electromyography (CSS-EMG) to assess the muscular integrity of the urethral sphincter in patients with SUI/ISD. CSS-EMG of the urethral sphincter and urodynamic studies were performed in 44 women with SUI. A urethral pressure profile (UPP) was measured in four directions. Maximal urethral closure pressure (MUCP) <40 cm/H2 O or the presence of SUI without urethral hypermobility was used to define ISD. Twenty-one patients had urodynamic SUI, 23 had no SUI and 12 patients had ISD. The mean average rectified value (ARV) of the motor unit action potential (MUAP), an indicator of the strength of urethral rhabdosphincter, was estimated. ARV measured in the 12 o'clock quadrant during maximal contraction was the only CSS-EMG parameter that had significant predictive value for ISD. With an increase in the 12 o'clock ARV value, the likelihood of ISD decreases (Odds Ratio 0.36 95% confidence interval 0.67-0.92). In the ROC curve with ARV measured in the 12 o'clock quadrant during maximal contraction, the explained area was 0.794 (P = 0.02); implying that ARV measured at the 12 o'clock quadrant during maximal contraction was able to predict ISD significantly. Myogenic changes of the urethral sphincter that contribute to ISD can be assessed with CSS-EMG. This new concept for assessing the functionality of the female urethral sphincter may assist with better understanding of the pathophysiology, the diagnosis and the treatment of SUI. © 2014 Wiley Periodicals, Inc.

Intermittent self-dilatation for urethral stricture disease in males: A systematic review and meta-analysis.

PubMed

Ivaz, Stella L; Veeratterapillay, Rajan; Jackson, Matthew J; Harding, Christopher K; Dorkin, Trevor J; Andrich, Daniela E; Mundy, Anthony R

2016-09-01

Intermittent self-dilatation (ISD) may be recommended to reduce the risk of recurrent urethral stricture. Level one evidence to support the use of this intervention is lacking. Determine the clinical and cost-effectiveness of ISD for the management of urethral stricture disease in males. The strategy developed for the Cochrane Incontinence Review Group as a whole (last searched May 7, 2014). Randomised trials where one arm was a programme of ISD for urethral stricture. At least two independent review authors carried out trial assessment, selection, and data abstraction. Data from six trials that were pooled and collectively rated very low quality per the GRADE approach, indicated that recurrent urethral stricture was less likely in men who performed ISD than those who did not (RR 0.70, 95% CI 0.48-1.00). Two trials compared programmes of ISD but the data were not combined and neither were sufficiently robust to draw firm conclusions. Three trials compared devices for performing ISD, results from one of which were too uncertain to determine the effects of a low friction hydrophilic catheter versus a polyvinyl chloride catheter on risk of recurrent urethral stricture (RR 0.32, 95% CI 0.07 to 1.40); another did not find evidence of a difference between 1% triamcinolone gel for lubricating the ISD catheter versus water-based gel on risk of recurrent urethral stricture (RR 0.68, 95% CI 0.35 to 1.32). No trials gave cost-effectiveness or validated PRO data. ISD may decrease the risk of recurrent urethral stricture. A well-designed RCT is required to determine whether that benefit alone is sufficient to make this intervention worthwhile and in whom. Neurourol. Urodynam. 35:759-763, 2016. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

5-Nitrosalicylic Acid as a Novel Matrix for In-Source Decay in Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry

PubMed Central

Asakawa, Daiki

2013-01-01

The matrix-assisted laser desorption/ionization in-source decay (MALDI-ISD) of peptides and glycans was studied using an oxidizing chemical, 5-nitrosalicylic acid (5-NSA) as the matrix. The use of 5-NSA for the MALDI-ISD of peptides and glycans promoted fragmentation pathways involving “hydrogen-deficient” radical precursors. Hydrogen abstraction from peptides resulted in the production of a “hydrogen-deficient” peptide radical that contained a radical site on the amide nitrogen in the peptide backbone with subsequent radical-induced cleavage at the Cα–C bonds. Cleavage at the Cα–C bond leads to the production of an a•/x fragment pair and the radical a• ions then undergo further hydrogen abstraction to form a ions after Cα–C bond cleavage. Since the Pro residue does not contain a nitrogen-centered radical site, Cα–C bond cleavage does not occur at this site. Alternatively, the specific cleavage of CO−N bonds leads to a b•/y fragment pair at Xxx−Pro which occurs via hydrogen abstraction from the Cα−H in the Pro residue. In contrast, “hydrogen-deficient” glycan radicals were generated by hydrogen abstraction from hydroxyl groups in glycans. Both glycosidic and cross-ring cleavages occurred as the result of the degradation of “hydrogen-deficient” glycan radicals. Cross-ring cleavage ions are potentially useful in linkage analysis, one of the most critical steps in the characterization of glycans. Moreover, isobaric glycans could be distinguished by structure specific ISD ions, and the molar ratio of glycan isomers in a mixture can be estimated from their fragment ions abundance ratios. MALDI-ISD with 5-NSA could be a useful method for the sequencing of peptides including the location of post-translational modifications, identification and semi-quantitative analysis of mixtures of glycan isomers. PMID:24860709

Strategic self-regulation, decision-making and emotion processing in poly-substance abusers in their first year of abstinence.

PubMed

Verdejo-García, Antonio; Rivas-Pérez, Cristina; Vilar-López, Raquel; Pérez-García, Miguel

2007-01-12

Individuals with substance dependence (ISD) frequently show signs of impaired emotion processing, self-regulation and decision-making, even after prolonged abstinence from drug use and partial recovery of other neuropsychological functions. These impairments have been associated with alterations in the orbitofrontal cortex (OFC) in lesion and imaging studies. The aim of this study was to examine the performance of a group of ISD, who had been abstinent for at least 4 months, on a series of emotional perception, self-regulation and decision-making tests sensitive to OFC dysfunction. Thirty ISD (poly-substance abusers in their first year of abstinence) and 35 healthy comparison (HC) participants were in the study. We administered the Ekman Faces Test (EFT), the Revised Strategy Application Test (R-SAT) and the Iowa Gambling Task (IGT) to both ISD and HC. Results showed that the ISD presented significant deficits in the recognition of facial emotional expressions and decision-making as measured by the EFT and the IGT. The ISD also showed poorer strategy awareness, impaired self-regulation and higher impulsivity on the R-SAT. We found significant correlations between the different measures linked to OFC functioning. We did not find significant correlations between length of abstinence and performance on these tests. These results suggest that the evaluation of emotion, self-regulation and decision-making contributes greatly to the characterization of the persistent deficits exhibited by ISD during prolonged abstinence.

Competing for Iron: Duplication and Amplification of the isd Locus in Staphylococcus lugdunensis HKU09-01 Provides a Competitive Advantage to Overcome Nutritional Limitation

PubMed Central

Heilbronner, Simon; Brozyna, Jeremy R.; Heinrichs, David E.; Skaar, Eric P.; Peschel, Andreas; Foster, Timothy J.

2016-01-01

Staphylococcus lugdunensis is a coagulase negative bacterial pathogen that is particularly associated with severe cases of infectious endocarditis. Unique amongst the coagulase-negative staphylococci, S. lugdunensis harbors an iron regulated surface determinant locus (isd). This locus facilitates the acquisition of heme as a source of nutrient iron during infection and allows iron limitation caused by “nutritional immunity” to be overcome. The isd locus is duplicated in S. lugdunensis HKU09-01 and we show here that the duplication is intrinsically unstable and undergoes accordion-like amplification and segregation leading to extensive isd copy number variation. Amplification of the locus increased the level of expression of Isd proteins and improved binding of hemoglobin to the cell surface of S. lugdunensis. Furthermore, Isd overexpression provided an advantage when strains were competing for a limited amount of hemoglobin as the sole source of iron. Gene duplications and amplifications (GDA) are events of fundamental importance for bacterial evolution and are frequently associated with antibiotic resistance in many species. As such, GDAs are regarded as evolutionary adaptions to novel selective pressures in hostile environments pointing towards a special importance of isd for S. lugdunensis. For the first time we show an example of a GDA that involves a virulence factor of a Gram-positive pathogen and link the GDA directly to a competitive advantage when the bacteria were struggling with selective pressures mimicking “nutritional immunity”. PMID:27575058

Competing for Iron: Duplication and Amplification of the isd Locus in Staphylococcus lugdunensis HKU09-01 Provides a Competitive Advantage to Overcome Nutritional Limitation.

PubMed

Heilbronner, Simon; Monk, Ian R; Brozyna, Jeremy R; Heinrichs, David E; Skaar, Eric P; Peschel, Andreas; Foster, Timothy J

2016-08-01

Staphylococcus lugdunensis is a coagulase negative bacterial pathogen that is particularly associated with severe cases of infectious endocarditis. Unique amongst the coagulase-negative staphylococci, S. lugdunensis harbors an iron regulated surface determinant locus (isd). This locus facilitates the acquisition of heme as a source of nutrient iron during infection and allows iron limitation caused by "nutritional immunity" to be overcome. The isd locus is duplicated in S. lugdunensis HKU09-01 and we show here that the duplication is intrinsically unstable and undergoes accordion-like amplification and segregation leading to extensive isd copy number variation. Amplification of the locus increased the level of expression of Isd proteins and improved binding of hemoglobin to the cell surface of S. lugdunensis. Furthermore, Isd overexpression provided an advantage when strains were competing for a limited amount of hemoglobin as the sole source of iron. Gene duplications and amplifications (GDA) are events of fundamental importance for bacterial evolution and are frequently associated with antibiotic resistance in many species. As such, GDAs are regarded as evolutionary adaptions to novel selective pressures in hostile environments pointing towards a special importance of isd for S. lugdunensis. For the first time we show an example of a GDA that involves a virulence factor of a Gram-positive pathogen and link the GDA directly to a competitive advantage when the bacteria were struggling with selective pressures mimicking "nutritional immunity".

Development of coated conductors by inclined substrate deposition

NASA Astrophysics Data System (ADS)

Balachandran, U.; Ma, B.; Li, M.; Fisher, B. L.; Koritala, R. E.; Miller, D. J.; Dorris, S. E.

2003-10-01

Inclined substrate deposition (ISD) offers the potential for rapid production of high-quality biaxially textured buffer layers suitable for YBa 2Cu 3O 7- δ (YBCO)-coated conductors. We have grown biaxially textured magnesium oxide (MgO) films on Hastelloy C276 (HC) substrates by ISD at deposition rates of 20-100 Å/s. Scanning electron microscopy of the ISD MgO films showed columnar grain structures with a roof-tile-shaped surface. X-ray pole figure analysis revealed that the c-axis of the ISD MgO films is titled at an angle ≈32° from the substrate normal. A small full-width at half maximum of ≈9° was observed for the φ-scan of MgO films. YBCO films were grown on ISD MgO buffered HC substrates by pulsed laser deposition and were determined to be biaxially aligned with the c-axis parallel to the substrate normal. The orientation relationship between the ISD template and the top YBCO film was investigated by X-ray pole figure analysis and transmission electron microscopy. A transport critical current density of Jc=5.5×10 5 A/cm 2 at 77 K in self-field was measured on a YBCO film that was 0.46-μm thick, 4-mm wide, 10-mm long.

The effectiveness of istradefylline for the treatment of gait deficits and sleepiness in patients with Parkinson's disease.

PubMed

Matsuura, Keita; Kajikawa, Hiroyuki; Tabei, Ken-Ichi; Satoh, Masayuki; Kida, Hirotaka; Nakamura, Naoko; Tomimoto, Hidekazu

2018-01-01

Istradefylline is useful in treating the wearing-off state in Parkinson's disease (PD). We investigated the effectiveness of istradefylline (ISD) in improving arousal, sleep, and gait deficits in patients with PD. We examined 14 patients with PD treated with ISD. We assessed the patients using the Unified Parkinson's Disease Rating Scale, Parkinson's Disease Questionnaire, Timed Up-and-Go test (TUG), Freezing of Gait Questionnaire (FOG-Q), Epworth Sleepiness Scale (ESS), and Parkinson's Disease Sleep Scale (PDSS) before and 1 month after ISD use. ESS scores were significantly lower 1 month after the start of ISD treatment (6.79±6.50) than before the intervention (8.14±6.15, Wilcoxon signed-rank test, p=0.0033). PDSS scores were not significantly different 1 month after beginning the treatment (112±23mm) when compared to those before the intervention (110±27mm, Wilcoxon signed-rank test, p=0.40). TUG scores were not changed after 1 month of ISD use (14.9±8.3s) when compared to those before the intervention (21.3±30.0s, Wilcoxon signed-rank test, p=0.59). Although these measures were not significantly affected by ISD treatment, some patients remarkably improved after the treatment. FOG-Q scores were significantly lower 1 month after the beginning of treatment (9.79±7.16) than those before the intervention (12.14±5.82, Wilcoxon signed-rank test, p=0.030). ISD may improve daytime sleepiness and FOG in patients with PD. Copyright © 2017 Elsevier B.V. All rights reserved.

Immunosuppressive Drug Discontinuation in Noninfectious Uveitis From Real-Life Clinical Practice: A Survival Analysis.

PubMed

Abásolo, Lydia; Rosales, Zulema; Díaz-Valle, David; Gómez-Gómez, Alejandro; Peña-Blanco, Rayma C; Prieto-García, Ángela; Benítez-Del-Castillo, José Manuel; Pato, Esperanza; García-Feijoo, Julián; Fernández-Gutiérrez, Benjamín; Rodriguez-Rodriguez, Luis

2016-09-01

To assess in uveitis patients the rate of immunosuppressive drug (ISD) discontinuation in real-life clinical practice, comparing this rate among ISDs. Longitudinal retrospective cohort study. We included uveitis patients attending a tertiary eye referral center from Madrid (Spain) between 1989 and 2015, prescribed any ISDs (cyclosporine, methotrexate, azathioprine, anti-TNF drugs, or others). Our main outcome was discontinuation of all ISDs owing to clinical efficacy, inefficacy, adverse drug reaction (ADR), and other medical causes. Discontinuation rates (DRs) per 100 patient-years were estimated. Variables associated with specific-cause discontinuations were analyzed using Cox bivariate and multivariate models. We analyzed 110 patients with 263 treatment courses and 665.2 patient-years of observation. Cyclosporine (66.4%), methotrexate (47.3%), azathioprine (30.9%), and anti-TNFs (30.9%) were the most frequently used ISDs. Treatment was suspended in 136 cases (mostly owing to clinical efficacy [38.2%], inefficacy [26.5%], and ADRs [22.8%]). All-cause DR with 95% confidence interval was 20.4 [17.3-24.2]. Retention rates at 1 and 10 years were 74% and 16%, respectively. In the multivariate analysis, combined treatment exhibited higher DRs owing to clinical efficacy than other ISDs in monotherapy. Conversely, nonbiologic combination therapy with azathioprine exhibited the highest DR owing to ADRs. Clinical efficacy was the most frequent cause for ISD discontinuation, followed by inefficacy and ADRs. DR owing to efficacy was higher for combination therapy. Furthermore, nonbiologic combination therapy with azathioprine was associated with a higher DR owing to ADRs. Copyright © 2016 Elsevier Inc. All rights reserved.

Multi-virulence-locus sequence typing of Staphylococcus lugdunensis generates results consistent with a clonal population structure and is reliable for epidemiological typing.

PubMed

Didi, Jennifer; Lemée, Ludovic; Gibert, Laure; Pons, Jean-Louis; Pestel-Caron, Martine

2014-10-01

Staphylococcus lugdunensis is an emergent virulent coagulase-negative staphylococcus responsible for severe infections similar to those caused by Staphylococcus aureus. To understand its potentially pathogenic capacity and have further detailed knowledge of the molecular traits of this organism, 93 isolates from various geographic origins were analyzed by multi-virulence-locus sequence typing (MVLST), targeting seven known or putative virulence-associated loci (atlLR2, atlLR3, hlb, isdJ, SLUG_09050, SLUG_16930, and vwbl). The polymorphisms of the putative virulence-associated loci were moderate and comparable to those of the housekeeping genes analyzed by multilocus sequence typing (MLST). However, the MVLST scheme generated 43 virulence types (VTs) compared to 20 sequence types (STs) based on MLST, indicating that MVLST was significantly more discriminating (Simpson's index [D], 0.943). No hypervirulent lineage or cluster specific to carriage strains was defined. The results of multilocus sequence analysis of known and putative virulence-associated loci are consistent with a clonal population structure for S. lugdunensis, suggesting a coevolution of these genes with housekeeping genes. Indeed, the nonsynonymous to synonymous evolutionary substitutions (dN/dS) ratio, the Tajima's D test, and Single-likelihood ancestor counting (SLAC) analysis suggest that all virulence-associated loci were under negative selection, even atlLR2 (AtlL protein) and SLUG_16930 (FbpA homologue), for which the dN/dS ratios were higher. In addition, this analysis of virulence-associated loci allowed us to propose a trilocus sequence typing scheme based on the intragenic regions of atlLR3, isdJ, and SLUG_16930, which is more discriminant than MLST for studying short-term epidemiology and further characterizing the lineages of the rare but highly pathogenic S. lugdunensis. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Four Levels of Moral Conflict in ISD

NASA Astrophysics Data System (ADS)

Vartiainen, Tero

This study introduces a literature-based classification of moral conflicts in information systems development (ISD). The classification describes what moral conflicts an IS professional confronts in ISD as a whole and includes intentional, functional, managerial, and societal levels. The internal structure of moral conflicts is exemplified by means of a philosophical and a business ethics theory. The limitations of the study are considered and practical implications for the teaching of computer ethics are discussed.

Differential expression of cysteine desulfurases in soybean

PubMed Central

2011-01-01

Background Iron-sulfur [Fe-S] clusters are prosthetic groups required to sustain fundamental life processes including electron transfer, metabolic reactions, sensing, signaling, gene regulation and stabilization of protein structures. In plants, the biogenesis of Fe-S protein is compartmentalized and adapted to specific needs of the cell. Many environmental factors affect plant development and limit productivity and geographical distribution. The impact of these limiting factors is particularly relevant for major crops, such as soybean, which has worldwide economic importance. Results Here we analyze the transcriptional profile of the soybean cysteine desulfurases NFS1, NFS2 and ISD11 genes, involved in the biogenesis of [Fe-S] clusters, by quantitative RT-PCR. NFS1, ISD11 and NFS2 encoding two mitochondrial and one plastid located proteins, respectively, are duplicated and showed distinct transcript levels considering tissue and stress response. NFS1 and ISD11 are highly expressed in roots, whereas NFS2 showed no differential expression in tissues. Cold-treated plants showed a decrease in NFS2 and ISD11 transcript levels in roots, and an increased expression of NFS1 and ISD11 genes in leaves. Plants treated with salicylic acid exhibited increased NFS1 transcript levels in roots but lower levels in leaves. In silico analysis of promoter regions indicated the presence of different cis-elements in cysteine desulfurase genes, in good agreement with differential expression of each locus. Our data also showed that increasing of transcript levels of mitochondrial genes, NFS1/ISD11, are associated with higher activities of aldehyde oxidase and xanthine dehydrogenase, two cytosolic Fe-S proteins. Conclusions Our results suggest a relationship between gene expression pattern, biochemical effects, and transcription factor binding sites in promoter regions of cysteine desulfurase genes. Moreover, data show proportionality between NFS1 and ISD11 genes expression. PMID:22099069

Comparing influence of intermittent subglottic secretions drainage with/without closed suction systems on the incidence of ventilator associated pneumonia.

PubMed

Juneja, Deven; Javeri, Yash; Singh, Omender; Nasa, Prashant; Pandey, Rameshwar; Uniyal, Bhupesh

2011-07-01

Intermittent subglottic drainage (ISD) of secretions is recommended for prevention of ventilator-associated pneumonia (VAP) as it reduces microaspiration from the area around the cuff. Poor suction techniques can contribute to VAP, hence closed suction system (CSS) may have theoretical benefit in VAP prevention. Combination of these two techniques may provide added advantage. To study the influence of ISD with/without CSS on the incidence of VAP. Data from 311 patients requiring mechanical ventilation (MV) for more than 72 hours were collected retrospectively. They were divided into four groups as follows: group A, no intervention; group B, only CSS; group C, only ISD; and group D, ISD with CSS. These groups were compared with respect to incidence of VAP, duration of MV, length of ICU and hospital stay and ICU mortality. Patients in the four groups were comparable with respect to age, sex ratio and admission Acute Physiology and Chronic Health Evaluation (APACHE) II scores. Incidence of VAP per 1000 ventilator days in groups A, B, C, and D were 25, 23.9, 15.7 and 14.3, respectively (P=0.04). There was no significant difference in the duration of MV (P=0.33), length of ICU (P=0.55) and hospital stay (P=0.36) and ICU mortality (P=0.9) among the four groups. ISD of secretions reduces the incidence of VAP. CSS alone or in combination with ISD has no significant effect on VAP incidence. Hence, ISD may be recommended for VAP prevention, but indications other than VAP prevention should determine the type of the suction system.

Haploidentical transplant for myelodysplastic syndrome: registry-based comparison with identical sibling transplant.

PubMed

Wang, Y; Wang, H-X; Lai, Y-R; Sun, Z-M; Wu, D-P; Jiang, M; Liu, D-H; Xu, K-L; Liu, Q-F; Liu, L; Wang, J-B; Gao, F; Ou-Yang, J; Gao, S-J; Xu, L-P; Huang, X-J

2016-10-01

Encouraging results from a small sample of patients with myelodysplastic syndrome (MDS) undergoing haploidentical donor (HID) hematopoietic stem cell transplantation (HSCT) must be extended. Furthermore, an algorithm derived from a comparison of the outcomes of HID and identical-sibling donor (ISD) HSCT must be established. Therefore, the outcomes of 454 MDS patients who underwent HSCT from HIDs (n=226) or ISDs (n=228) between 2003 and 2013 that were reported to the Chinese Bone Marrow Transplantation Registry were analyzed. Among the 3/6 HID (n=136), 4-5/6 HID (n=90) and ISD patient groups, the 4-year adjusted cumulative incidences of non-relapse mortality were 34, 29 and 16%, respectively (overall P=0.004), and of relapse were 6, 7 and 10%, respectively (overall P=0.36). The 4-year adjusted probabilities of overall survival were 58, 63 and 73%, respectively (overall P=0.07), and of relapse-free-survival were 58, 63 and 71%, respectively (overall P=0.14); pairwise comparison showed that the difference was only statistically significant in the 3/6 HID vs ISD pair. The data suggest that ISDs remain the best donor source for MDS patients while HIDs (perhaps 4-5/6 HID in particular) could be a valid alternative when an ISD is not available; human leukocyte antigen disparity had no effect on survival among the HID patients.

Why Can't We Bet on ISD Outcomes: ISD ``Form'' as a Predictor of Success

NASA Astrophysics Data System (ADS)

Newman, Mike; Pan, Shan L.; Pan, Gary

The record of failure to deliver large-scale information systems (IS) in a timely fashion that offer value to major commercial and public organizations is legendary. Just looking to critical success factors such as top management support and user involvement in order to understand how to deliver better systems can at best be a partial solution. We seem to overlook an obvious area in our organizations: what can we learn from our information system development (ISD) historical patterns? In order to develop this idea we draw on parallels in sport where current performance and behaviour are believed to be closely linked to historical precedents, or “form”. In that domain, historical patterns are a fallible but valuable predictor of success. Our thesis is that past negative patterns in ISD will tend to repeat themselves without radical intervention. Put another way, failure begets failure. After examining the game of football as an allegory for ISD, we look briefly at two organizations that have experienced a pattern of failure in the IS area in the past but have transformed the way they build IS, moving from negative patterns to successful ones. This chapter ends with suggestions for managers charged with developing new IS as to how they might use their understanding of ISD “form” to improve their chances of success.

PREFACE: 8th International Symposium of the Digital Earth (ISDE8)

NASA Astrophysics Data System (ADS)

2014-02-01

Proceedings of the 8th International Symposium of Digital Earth (8th ISDE) 2013 Kuching, Sarawak, Malaysia, 26th-29th August, 2013 Conference logo This proceedings consists of the peer-reviewed papers from 8th International Symposium for Digital Earth (ISDE) held in Kuching, Sarawak, Malaysia during 26th-29th August, 2013. The 8th ISDE was a successful event in the Symposium Series of the International Society of Digital Earth, that was previously held in China (1999), Canada (2001), Czech Republic (2003), Japan (2005), the United States (2007), China (2009), and Australia (2011). The 8th ISDE, with the theme 'Transforming Knowledge into Sustainable Practice' aims to enable digital earth scientists, experts and professionals related to the field of geospatial science and technology to provide a brand new opportunity to share their ideas and insights on how we share knowledge and act together globally. In addition, the ISDE symposium series has been providing a venue for researchers and industry practitioners to discuss new ideas, collaborate to solve complex solutions to various complex problems, and importantly, pave new ways in digital earth environment. This 8th ISDE included 20 technical sessions, workshops and student sessions in various areas of digital earth; ranging from digital earth vision & innovation; earth observation technologies; ICT technologies (including spatial data infrastructures); empowering the community and engaging society; applications and innovation of digital earth for environmental applications such as hazard, pollution, flood, air quality, disaster and health, biodiversity, sustainability, forestry, early warning and emergency management, national security, natural resource management and agriculture; mining, energy and resources development; transformation towards sustainable low carbon society; digital city and green cities: towards urban sustainability; and managing water environment for sustainable development. The success of the 8th ISDE was due to commitments of many: authors, keynote speakers, session chairs, the organising committee, technical and scientific committee, student volunteers from Universiti Teknologi Malaysia (UTM) and Universiti Malaysia Sarawak (UNIMAS), and many others of various roles. We acknowledged all sponsors to 8th ISDE, namely Sarawak Convention Bureau, Malaysia Convention & Exhibition Bureau, and ESRI. We also thanked all exhibitors and contributors of the 8th ISDE: TSKAY Technologies Sdn Bhd, Coordinates-India, Taylor & Francis-Singapore, Beijing Space Eye-China, RS&GIS Consultancy, CRCSI-Australia, Jurupro Sdn Bhd, Inst of Remote Sensing and Digital Earth (RADI)-China, Department of Survey and Mapping Malaysia, SPECIM, Satellite Imaging (M) Sdn Bhd, IPASA-UTM, Sustainable Research Alliance-UTM, Sarawak Forest Department, International Society of Digital Earth-China, INSTeG-UTM, and UNIMAS. August 2013 Mazlan Hashim Samsudin Ahmad Yin Chai Wang Details of the organisation and committees are available in the PDF

The current role of direct vision internal urethrotomy and self-catheterization for anterior urethral strictures

PubMed Central

Dubey, Deepak

2011-01-01

Introduction: Direct visual internal urethrotomy (DVIU) followed by intermittent self-dilatation (ISD) is the most commonly performed intervention for urethral stricture disease. The objective of this paper is to outline the current scientific evidence supporting this approach for its use in the management of anterior urethral strictures. Materials and Methods: A Pubmed database search was performed with the words “internal urethrotomy” and “internal urethrotomy” self-catheterization. All papers dealing with this subject were scrutinized. Cross-references from the retrieved articles were also viewed. Only English language articles were included in the analyses. Studies were analyzed to identify predictors for success for DVIU. Results: Initial studies showed excellent outcomes with DVIU with success rates ranging from 50% to 85%. However, these studies reported only short-term results. Recent studies with longer followup have shown a poor success rate ranging from 6% to 28%. Stricture length and degree of fibrosis (luminal narrowing) were found to be predictors of response. Repeated urethrotomies were associated with poor results. Studies involving intermittent self-catheterization following DVIU have shown no role in short-term ISD with one study reporting beneficial effects if continued for more than a year. A significant number of studies have shown long-term complications with SC and high dropout rates. Conclusions: DVIU is associated with poor long-term cure rates. It remains as a treatment of first choice for bulbar urethral strictures <1 cm with minimal spongiofibrosis. There is no role for repeated urethrotomy as outcomes are uniformly poor. ISD, when used for more than a year on a weekly or biweekly basis may delay the onset of stricture recurrence. PMID:22022065

Influence of sound source location on the behavior and physiology of the precedence effect in cats.

PubMed

Dent, Micheal L; Tollin, Daniel J; Yin, Tom C T

2009-08-01

Psychophysical experiments on the precedence effect (PE) in cats have shown that they localize pairs of auditory stimuli presented from different locations in space based on the spatial position of the stimuli and the interstimulus delay (ISD) between the stimuli in a manner similar to humans. Cats exhibit localization dominance for pairs of transient stimuli with |ISDs| from approximately 0.4 to 10 ms, summing localization for |ISDs| < 0.4 ms and breakdown of fusion for |ISDs| > 10 ms, which is the approximate echo threshold. The neural correlates to the PE have been described in both anesthetized and unanesthetized animals at many levels from auditory nerve to cortex. Single-unit recordings from the inferior colliculus (IC) and auditory cortex of cats demonstrate that neurons respond to both lead and lag sounds at ISDs above behavioral echo thresholds, but the response to the lag is reduced at shorter ISDs, consistent with localization dominance. Here the influence of the relative locations of the leading and lagging sources on the PE was measured behaviorally in a psychophysical task and physiologically in the IC of awake behaving cats. At all configurations of lead-lag stimulus locations, the cats behaviorally exhibited summing localization, localization dominance, and breakdown of fusion. Recordings from the IC of awake behaving cats show neural responses paralleling behavioral measurements. Both behavioral and physiological results suggest systematically shorter echo thresholds when stimuli are further apart in space.

Influence of Sound Source Location on the Behavior and Physiology of the Precedence Effect in Cats

PubMed Central

Dent, Micheal L.; Tollin, Daniel J.; Yin, Tom C. T.

2009-01-01

Psychophysical experiments on the precedence effect (PE) in cats have shown that they localize pairs of auditory stimuli presented from different locations in space based on the spatial position of the stimuli and the interstimulus delay (ISD) between the stimuli in a manner similar to humans. Cats exhibit localization dominance for pairs of transient stimuli with |ISDs| from ∼0.4 to 10 ms, summing localization for |ISDs| < 0.4 ms and breakdown of fusion for |ISDs| > 10 ms, which is the approximate echo threshold. The neural correlates to the PE have been described in both anesthetized and unanesthetized animals at many levels from auditory nerve to cortex. Single-unit recordings from the inferior colliculus (IC) and auditory cortex of cats demonstrate that neurons respond to both lead and lag sounds at ISDs above behavioral echo thresholds, but the response to the lag is reduced at shorter ISDs, consistent with localization dominance. Here the influence of the relative locations of the leading and lagging sources on the PE was measured behaviorally in a psychophysical task and physiologically in the IC of awake behaving cats. At all configurations of lead-lag stimulus locations, the cats behaviorally exhibited summing localization, localization dominance, and breakdown of fusion. Recordings from the IC of awake behaving cats show neural responses paralleling behavioral measurements. Both behavioral and physiological results suggest systematically shorter echo thresholds when stimuli are further apart in space. PMID:19439668

A Novel Staphylococcus aureus Vaccine: Iron Surface Determinant B Induces Rapid Antibody Responses in Rhesus Macaques and Specific Increased Survival in a Murine S. aureus Sepsis Model

PubMed Central

Kuklin, Nelly A.; Clark, Desmond J.; Secore, Susan; Cook, James; Cope, Leslie D.; McNeely, Tessie; Noble, Liliane; Brown, Martha J.; Zorman, Julie K.; Wang, Xin Min; Pancari, Gregory; Fan, Hongxia; Isett, Kevin; Burgess, Bruce; Bryan, Janine; Brownlow, Michelle; George, Hugh; Meinz, Maria; Liddell, Mary E.; Kelly, Rosemarie; Schultz, Loren; Montgomery, Donna; Onishi, Janet; Losada, Maria; Martin, Melissa; Ebert, Timothy; Tan, Charles Y.; Schofield, Timothy L.; Nagy, Eszter; Meineke, Andreas; Joyce, Joseph G.; Kurtz, Myra B.; Caulfield, Michael J.; Jansen, Kathrin U.; McClements, William; Anderson, Annaliesa S.

2006-01-01

Staphylococcus aureus is a major cause of nosocomial infections worldwide, and the rate of resistance to clinically relevant antibiotics, such as methicillin, is increasing; furthermore, there has been an increase in the number of methicillin-resistant S. aureus community-acquired infections. Effective treatment and prevention strategies are urgently needed. We investigated the potential of the S. aureus surface protein iron surface determinant B (IsdB) as a prophylactic vaccine against S. aureus infection. IsdB is an iron-sequestering protein that is conserved in diverse S. aureus clinical isolates, both methicillin resistant and methicillin sensitive, and it is expressed on the surface of all isolates tested. The vaccine was highly immunogenic in mice when it was formulated with amorphous aluminum hydroxyphosphate sulfate adjuvant, and the resulting antibody responses were associated with reproducible and significant protection in animal models of infection. The specificity of the protective immune responses in mice was demonstrated by using an S. aureus strain deficient for IsdB and HarA, a protein with a high level of identity to IsdB. We also demonstrated that IsdB is highly immunogenic in rhesus macaques, inducing a more-than-fivefold increase in antibody titers after a single immunization. Based on the data presented here, IsdB has excellent prospects for use as a vaccine against S. aureus disease in humans. PMID:16552052

A novel Staphylococcus aureus vaccine: iron surface determinant B induces rapid antibody responses in rhesus macaques and specific increased survival in a murine S. aureus sepsis model.

PubMed

Kuklin, Nelly A; Clark, Desmond J; Secore, Susan; Cook, James; Cope, Leslie D; McNeely, Tessie; Noble, Liliane; Brown, Martha J; Zorman, Julie K; Wang, Xin Min; Pancari, Gregory; Fan, Hongxia; Isett, Kevin; Burgess, Bruce; Bryan, Janine; Brownlow, Michelle; George, Hugh; Meinz, Maria; Liddell, Mary E; Kelly, Rosemarie; Schultz, Loren; Montgomery, Donna; Onishi, Janet; Losada, Maria; Martin, Melissa; Ebert, Timothy; Tan, Charles Y; Schofield, Timothy L; Nagy, Eszter; Meineke, Andreas; Joyce, Joseph G; Kurtz, Myra B; Caulfield, Michael J; Jansen, Kathrin U; McClements, William; Anderson, Annaliesa S

2006-04-01

Staphylococcus aureus is a major cause of nosocomial infections worldwide, and the rate of resistance to clinically relevant antibiotics, such as methicillin, is increasing; furthermore, there has been an increase in the number of methicillin-resistant S. aureus community-acquired infections. Effective treatment and prevention strategies are urgently needed. We investigated the potential of the S. aureus surface protein iron surface determinant B (IsdB) as a prophylactic vaccine against S. aureus infection. IsdB is an iron-sequestering protein that is conserved in diverse S. aureus clinical isolates, both methicillin resistant and methicillin sensitive, and it is expressed on the surface of all isolates tested. The vaccine was highly immunogenic in mice when it was formulated with amorphous aluminum hydroxyphosphate sulfate adjuvant, and the resulting antibody responses were associated with reproducible and significant protection in animal models of infection. The specificity of the protective immune responses in mice was demonstrated by using an S. aureus strain deficient for IsdB and HarA, a protein with a high level of identity to IsdB. We also demonstrated that IsdB is highly immunogenic in rhesus macaques, inducing a more-than-fivefold increase in antibody titers after a single immunization. Based on the data presented here, IsdB has excellent prospects for use as a vaccine against S. aureus disease in humans.

The computational complexity of elliptic curve integer sub-decomposition (ISD) method

NASA Astrophysics Data System (ADS)

Ajeena, Ruma Kareem K.; Kamarulhaili, Hailiza

2014-07-01

The idea of the GLV method of Gallant, Lambert and Vanstone (Crypto 2001) is considered a foundation stone to build a new procedure to compute the elliptic curve scalar multiplication. This procedure, that is integer sub-decomposition (ISD), will compute any multiple kP of elliptic curve point P which has a large prime order n with two low-degrees endomorphisms ψ1 and ψ2 of elliptic curve E over prime field Fp. The sub-decomposition of values k1 and k2, not bounded by ±C√n , gives us new integers k11, k12, k21 and k22 which are bounded by ±C√n and can be computed through solving the closest vector problem in lattice. The percentage of a successful computation for the scalar multiplication increases by ISD method, which improved the computational efficiency in comparison with the general method for computing scalar multiplication in elliptic curves over the prime fields. This paper will present the mechanism of ISD method and will shed light mainly on the computation complexity of the ISD approach that will be determined by computing the cost of operations. These operations include elliptic curve operations and finite field operations.

Generic Drugs - Decreasing Costs and Room for Increased Number of Kidney Transplantations.

PubMed

Spasovski, Goce

2015-01-01

Kidney transplantation is the best treatment option in comparison to dialysis, although patients are obliged to receive life-long medical treatment with immunosuppressive drugs (ISDs) for prevention of the graft rejection. Such immunosuppressive treatment may be costly and associated with multiple adverse effects. Since costs are viewed as one of the major constraints for the increasing number of transplantation, the use of generic ISDs may decrease the overall cost of transplantation and raise the possibility for its further development. An ideal ISD should have the security margin between toxic and therapeutic dose, and prevent development of acute or chronic rejection of the transplanted kidney. This is particularly important for drugs with a "narrow therapeutical index" (NTI), where small differences in dose or concentration lead to dose and concentration-dependent, serious therapeutic failures and/or adverse drug reactions. The NTI generic drug is approved if within 90%-112% of the area under the curve of the original product the pharmacokinetics fulfills the strict criteria of pharmaceutical equivalence and bioequivalence. Every generic has to be proven to be bioequivalent to the innovator product, and not to other generic products because of the possible generic "drift". Thus, the generic ISDs may be economically attractive, but theoretically, they may pose a risk to transplant patients. Such risks may be reduced if a long-term clinical studies showing cost-effectiveness of generic ISDs in de novo and prevalent transplant patients for every new generic ISD are performed. In conclusion, the increased number of solid organ transplantation goes in line with the increased health care expenditure for ISDs. The generic immunosuppressants could be a possible solution if safely substituted for innovator products or other generic drug of choice. The substantial cost reduction needs to be redirected into organ donation initiatives so that more patients can benefit from the further increase in transplantation.

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

Kertzscher, G; Beddar, S

Purpose: To study the promising potential of inorganic scintillator detectors (ISDs) and investigate various unwanted luminescence properties which may compromise their accuracy. Methods: The ISDs were comprised of a ruby crystal coupled to a polymethyl methacrylate (PMMA) fiber-optic cable and a charged coupled device camera. A new type of ISD was manufactured and included a long-pass filter that was sandwiched between the crystal and the fiber-optic cable. The purpose of the filter was to suppress the Cerenkov and fluorescence background light induced in the PMMA (the stem signal) from striking the ruby crystal, generating unwanted ruby excitation. A variety ofmore » experiments were performed to characterize the ruby based ISDs. The relative contribution of the induced ruby signal and the stem signal were quantified while exposing the detector and a bare fiber-optic cable to a high dose rate (HDR) brachytherapy (BT) source, respectively. The unwanted ruby excitation was quantified while irradiating the fiber-optic cable with the detector volume shielded. Other experiments addressed time-dependent luminescence properties and a comparison to other commonly used organic scintillator detectors (BCF-12, BCF-60). Results: When the BT source dwelled 0.5 cm away from the fiber-optic cable, the unwanted ruby excitation amounted to >5% of the total signal if the source-distance from the scintillator was >7 cm. However, the unwanted excitation was suppressed to <1% if the ISD incorporated an optic filter. The stem signal was suppressed with a 20 nm band-pass filter and was <3% as long as the source-distance was <7 cm. The ruby based ISDs generated signal up to 20(40) times that of BCF-12(BCF-60). Conclusion: The study presents solutions to unwanted luminescence properties of ruby based ISDs for HDR BT. An optic filter should be sandwiched between the scintillator volume and the fiber-optic cable to prevent the stem signal to excite the ruby crystal.« less

JAK3 as an Emerging Target for Topical Treatment of Inflammatory Skin Diseases.

PubMed

Alves de Medeiros, Ana Karina; Speeckaert, Reinhart; Desmet, Eline; Van Gele, Mireille; De Schepper, Sofie; Lambert, Jo

2016-01-01

The recent interest and elucidation of the JAK/STAT signaling pathway created new targets for the treatment of inflammatory skin diseases (ISDs). JAK inhibitors in oral and topical formulations have shown beneficial results in psoriasis and alopecia areata. Patients suffering from other ISDs might also benefit from JAK inhibition. Given the development of specific JAK inhibitors, the expression patterns of JAKs in different ISDs needs to be clarified. We aimed to analyze the expression of JAK/STAT family members in a set of prevalent ISDs: psoriasis, lichen planus (LP), cutaneous lupus erythematosus (CLE), atopic dermatitis (AD), pyoderma gangrenosum (PG) and alopecia areata (AA) versus healthy controls for (p)JAK1, (p)JAK2, (p)JAK3, (p)TYK2, pSTAT1, pSTAT2 and pSTAT3. The epidermis carried in all ISDs, except for CLE, a strong JAK3 signature. The dermal infiltrate showed a more diverse expression pattern. JAK1, JAK2 and JAK3 were significantly overexpressed in PG and AD suggesting the need for pan-JAK inhibitors. In contrast, psoriasis and LP showed only JAK1 and JAK3 upregulation, while AA and CLE were characterized by a single dermal JAK signal (pJAK3 and pJAK1, respectively). This indicates that the latter diseases may benefit from more targeted JAK inhibitors. Our in vitro keratinocyte psoriasis model displayed reversal of the psoriatic JAK profile following tofacitinib treatment. This direct interaction with keratinocytes may decrease the need for deep skin penetration of topical JAK inhibitors in order to exert its effects on dermal immune cells. In conclusion, these results point to the important contribution of the JAK/STAT pathway in several ISDs. Considering the epidermal JAK3 expression levels, great interest should go to the investigation of topical JAK3 inhibitors as therapeutic option of ISDs.

Ruby-based inorganic scintillation detectors for 192Ir brachytherapy

NASA Astrophysics Data System (ADS)

Kertzscher, Gustavo; Beddar, Sam

2016-11-01

We tested the potential of ruby inorganic scintillation detectors (ISDs) for use in brachytherapy and investigated various unwanted luminescence properties that may compromise their accuracy. The ISDs were composed of a ruby crystal coupled to a poly(methyl methacrylate) fiber-optic cable and a charge-coupled device camera. The ISD also included a long-pass filter that was sandwiched between the ruby crystal and the fiber-optic cable. The long-pass filter prevented the Cerenkov and fluorescence background light (stem signal) induced in the fiber-optic cable from striking the ruby crystal, which generates unwanted photoluminescence rather than the desired radioluminescence. The relative contributions of the radioluminescence signal and the stem signal were quantified by exposing the ruby detectors to a high-dose-rate brachytherapy source. The photoluminescence signal was quantified by irradiating the fiber-optic cable with the detector volume shielded. Other experiments addressed time-dependent luminescence properties and compared the ISDs to commonly used organic scintillator detectors (BCF-12, BCF-60). When the brachytherapy source dwelled 0.5 cm away from the fiber-optic cable, the unwanted photoluminescence was reduced from  >5% to  <1% of the total signal as long as the ISD incorporated the long-pass filter. The stem signal was suppressed with a band-pass filter and was  <3% as long as the source distance from the scintillator was  <7 cm. Some ruby crystals exhibited time-dependent luminescence properties that altered the ruby signal by  >5% within 10 s from the onset of irradiation and after the source had retracted. The ruby-based ISDs generated signals of up to 20 times that of BCF-12-based detectors. The study presents solutions to unwanted luminescence properties of ruby-based ISDs for high-dose-rate brachytherapy. An optic filter should be sandwiched between the ruby crystal and the fiber-optic cable to suppress the photoluminescence. Furthermore, we recommend avoiding ruby crystals that exhibit significant time-dependent luminescence.

Ruby-based inorganic scintillation detectors for 192Ir brachytherapy

PubMed Central

Kertzscher, Gustavo; Beddar, Sam

2016-01-01

We tested the potential of ruby inorganic scintillation detectors (ISDs) for use in brachytherapy and investigated various unwanted luminescence properties that may compromise their accuracy. The ISDs were composed of a ruby crystal coupled to a poly(methyl methacrylate) fiber-optic cable and a charge-coupled device camera. The ISD also included a long-pass filter that was sandwiched between the ruby crystal and the fiber-optic cable. The long-pass filter prevented the Cerenkov and fluorescence background light (stem signal) induced in the fiber-optic cable from striking the ruby crystal, which generates unwanted photoluminescence rather than the desired radioluminescence. The relative contributions of the radioluminescence signal and the stem signal were quantified by exposing the ruby detectors to a high-dose-rate brachytherapy source. The photoluminescence signal was quantified by irradiating the fiber-optic cable with the detector volume shielded. Other experiments addressed time-dependent luminescence properties and compared the ISDs to commonly used organic scintillator detectors (BCF-12, BCF-60). When the brachytherapy source dwelled 0.5 cm away from the fiber-optic cable, the unwanted photoluminescence was reduced from > 5% to < 1% of the total signal as long as the ISD incorporated the long-pass filter. The stem signal was suppressed with a band-pass filter and was < 3% as long as the source distance from the scintillator was < 7 cm. Some ruby crystals exhibited time-dependent luminescence properties that altered the ruby signal by > 5% within 10 s from the onset of irradiation and after the source had retracted. The ruby-based ISDs generated signals of up to 20 times that of BCF-12-based detectors. The study presents solutions to unwanted luminescence properties of ruby-based ISDs for high-dose-rate brachytherapy. An optic filter should be sandwiched between the ruby crystal and the fiber-optic cable to suppress the photoluminescence. Furthermore, we recommend avoiding ruby crystals that exhibit significant time-dependent luminescence. PMID:27740947

Ruby-based inorganic scintillation detectors for 192Ir brachytherapy.

PubMed

Kertzscher, Gustavo; Beddar, Sam

2016-11-07

We tested the potential of ruby inorganic scintillation detectors (ISDs) for use in brachytherapy and investigated various unwanted luminescence properties that may compromise their accuracy. The ISDs were composed of a ruby crystal coupled to a poly(methyl methacrylate) fiber-optic cable and a charge-coupled device camera. The ISD also included a long-pass filter that was sandwiched between the ruby crystal and the fiber-optic cable. The long-pass filter prevented the Cerenkov and fluorescence background light (stem signal) induced in the fiber-optic cable from striking the ruby crystal, which generates unwanted photoluminescence rather than the desired radioluminescence. The relative contributions of the radioluminescence signal and the stem signal were quantified by exposing the ruby detectors to a high-dose-rate brachytherapy source. The photoluminescence signal was quantified by irradiating the fiber-optic cable with the detector volume shielded. Other experiments addressed time-dependent luminescence properties and compared the ISDs to commonly used organic scintillator detectors (BCF-12, BCF-60). When the brachytherapy source dwelled 0.5 cm away from the fiber-optic cable, the unwanted photoluminescence was reduced from  >5% to  <1% of the total signal as long as the ISD incorporated the long-pass filter. The stem signal was suppressed with a band-pass filter and was  <3% as long as the source distance from the scintillator was  <7 cm. Some ruby crystals exhibited time-dependent luminescence properties that altered the ruby signal by  >5% within 10 s from the onset of irradiation and after the source had retracted. The ruby-based ISDs generated signals of up to 20 times that of BCF-12-based detectors. The study presents solutions to unwanted luminescence properties of ruby-based ISDs for high-dose-rate brachytherapy. An optic filter should be sandwiched between the ruby crystal and the fiber-optic cable to suppress the photoluminescence. Furthermore, we recommend avoiding ruby crystals that exhibit significant time-dependent luminescence.

Dilated intercellular space diameter as marker of reflux-related mucosal injury in children with chronic cough and gastro-oesophageal reflux disease.

PubMed

Borrelli, O; Mancini, V; Thapar, N; Ribolsi, M; Emerenziani, S; de'Angelis, G; Bizzarri, B; Lindley, K J; Cicala, M

2014-04-01

The diagnostic corroboration of the relationship between gastro-oesophageal reflux disease (GERD) and chronic cough remains challenging. To compare oesophageal mucosal intercellular space diameter (ISD) in children with GERD, children with gastro-oesophageal reflux (GER)-related cough (GrC) and a control group, and to explore the relationship between baseline impedance levels and dilated ISD in children with GER-related cough. Forty children with GERD, 15 children with GrC and 12 controls prospectively underwent oesophagogastroduodenoscopy (EGD) with oesophageal biopsies taken 2-3 cm above squamocolumnar junction. ISD were quantified using transmission electron microscopy. Impedance-pH monitoring with evaluation of baseline impedance in the most distal impedance channel was performed in both patient groups. A significant difference in mean ISD values was found between GrC patients (0.9 ± 0.2 μm) and controls (0.5 ± 0.2 μm, P < 0.001), whereas there was no difference between GrC and GERD group (1 ± 0.3 μm, NS). No difference was found in the mean ISD between GrC children with or without pathological oesophageal acid exposure time (1 ± 0.3 vs. 0.9 ± 0.2 μm), and there was no correlation between ISD and any reflux parameter. Finally, there was no correlation between ISD and distal baseline impedance values (r:-0.35; NS). In children with reflux-related cough, dilated intercellular space diameter appears to be an objective and useful marker of oesophageal mucosal injury regardless of acid exposure, and its evaluation should be considered for those patients where the diagnosis is uncertain. In children with reflux-related cough, baseline impedance levels have no role in identifying reflux-induced oesophageal mucosal ultrastructural changes. © 2014 John Wiley & Sons Ltd.

Can improvised somatic dance reduce acute pain for young people in hospital?

PubMed

Dowler, Lisa

2016-11-08

Aim This study explores the effects of improvised somatic dance (ISD) on children and young people experiencing acute pain following orthopaedic or cardiac surgery, or post-acquired brain injury. Methods The study involved 25 children and young people and adopted a mixed methods approach. This included a descriptive qualitative approach to help the participants and witnesses verbalise their experience of ISD, and pain scores were assessed before and after ISD using validated pain assessment tools. Data were analysed using descriptive statistical analysis. Findings A total of 92% of participants experienced a reduction in pain, with 80% experiencing a >50% reduction. There was an improved sense of well-being for all. Conclusion Although not a replacement for pharmacological treatments, a multidimensional, child-centred and inclusive approach with ISD can be a useful complementary, non-pharmacological method of pain management in children and young people.

Deduction of initial strategy distributions of agents in mix-game models

NASA Astrophysics Data System (ADS)

Gou, Chengling

2006-11-01

This paper reports the effort of deducing the initial strategy distributions (ISDs) of agents in mix-game models that is used to predict a real financial time series generated from a target financial market. Using mix-games to predict Shanghai Index, we find that the time series of prediction accurate rates is sensitive to the ISDs of agents in group 2 who play a minority game, but less sensitive to the ISDs of agents in group 1 who play a majority game. And agents in group 2 tend to cluster in full strategy space (FSS) if the real financial time series has obvious tendency (upward or downward), otherwise they tend to scatter in FSS. We also find that the ISDs and the number of agents in group 1 influence the level of prediction accurate rates. Finally, this paper gives suggestion about further research.

Standardized pelvic floor exercises improve stress urinary incontinence in women with intrinsic sphincter deficiency.

PubMed

Lehmann, Corinne; Zipponi, Ingrid; Baumann, Marc U; Radlinger, Lorenz; Mueller, Michael D; Kuhn, Annette

2016-08-01

Pelvic floor rehabilitation is the conservative therapy of choice for women with stress urinary incontinence (SUI). The success rate of surgical procedures in SUI patients with intrinsic sphincter deficiency (ISD) is low. The aim of this study was to analyse the effect of a standardized physiotherapy on patients with SUI and normotonic urethra and ISD. In this study, 64 patients with ISD and 69 patients with normotonic urethra were enrolled. Maximum urethral pressure (MUCP) >20 cm H2 O was considered as normotonic urethral pressure. Before and after physiotherapy MUCP was measured and cough testing was performed. Additionally, patient reported outcome was assessed using the King's Health Questionnaire (KHQ). For statistical analyses Excel 2010 (Microsoft Inc; Redmond, Washington) and SPSS 20 (SPSS Inc; Chicago, Illinois) for Windows were used. Power calculation was based on the primary endpoint incontinence impact and general health. For power calculation, GraphPad Statmate version 2.00 for Windows was used. Sixty-four patients with ISD and 69 patients with normotonic urethra were included in the study. In SUI patients with normotonic and hypotonic urethra KHQ-scores regarding the primary endpoins "general health" and "incontinence impact" significantly improved following standardized physiotherapy. In both groups MUCP increased after physiotherapy. In SUI patients with ISD standardized physiotherapy resulted in a decreased incidence of a positive cough test. Standardized physiotherapy should be offered to patients with SUI and ISD. Long-term results are subject to future studies. Neurourol. Urodynam. 35:711-716, 2016. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Revealing Ligand Binding Sites and Quantifying Subunit Variants of Noncovalent Protein Complexes in a Single Native Top-Down FTICR MS Experiment

NASA Astrophysics Data System (ADS)

Li, Huilin; Wongkongkathep, Piriya; Van Orden, Steve L.; Ogorzalek Loo, Rachel R.; Loo, Joseph A.

2014-12-01

"Native" mass spectrometry (MS) has been proven to be increasingly useful for structural biology studies of macromolecular assemblies. Using horse liver alcohol dehydrogenase (hADH) and yeast alcohol dehydrogenase (yADH) as examples, we demonstrate that rich information can be obtained in a single native top-down MS experiment using Fourier transform ion cyclotron mass spectrometry (FTICR MS). Beyond measuring the molecular weights of the protein complexes, isotopic mass resolution was achieved for yeast ADH tetramer (147 kDa) with an average resolving power of 412,700 at m/z 5466 in absorption mode, and the mass reflects that each subunit binds to two zinc atoms. The N-terminal 89 amino acid residues were sequenced in a top-down electron capture dissociation (ECD) experiment, along with the identifications of the zinc binding site at Cys46 and a point mutation (V58T). With the combination of various activation/dissociation techniques, including ECD, in-source dissociation (ISD), collisionally activated dissociation (CAD), and infrared multiphoton dissociation (IRMPD), 40% of the yADH sequence was derived directly from the native tetramer complex. For hADH, native top-down ECD-MS shows that both E and S subunits are present in the hADH sample, with a relative ratio of 4:1. Native top-down ISD of the hADH dimer shows that each subunit (E and S chains) binds not only to two zinc atoms, but also the NAD/NADH ligand, with a higher NAD/NADH binding preference for the S chain relative to the E chain. In total, 32% sequence coverage was achieved for both E and S chains.

Autonomous Driver Based on an Intelligent System of Decision-Making.

PubMed

Czubenko, Michał; Kowalczuk, Zdzisław; Ordys, Andrew

The paper presents and discusses a system ( xDriver ) which uses an Intelligent System of Decision-making (ISD) for the task of car driving. The principal subject is the implementation, simulation and testing of the ISD system described earlier in our publications (Kowalczuk and Czubenko in artificial intelligence and soft computing lecture notes in computer science, lecture notes in artificial intelligence, Springer, Berlin, 2010, 2010, In Int J Appl Math Comput Sci 21(4):621-635, 2011, In Pomiary Autom Robot 2(17):60-5, 2013) for the task of autonomous driving. The design of the whole ISD system is a result of a thorough modelling of human psychology based on an extensive literature study. Concepts somehow similar to the ISD system can be found in the literature (Muhlestein in Cognit Comput 5(1):99-105, 2012; Wiggins in Cognit Comput 4(3):306-319, 2012), but there are no reports of a system which would model the human psychology for the purpose of autonomously driving a car. The paper describes assumptions for simulation, the set of needs and reactions (characterizing the ISD system), the road model and the vehicle model, as well as presents some results of simulation. It proves that the xDriver system may behave on the road as a very inexperienced driver.

Flexible Xxx–Asp/Asn and Gly–Xxx Residues of Equine Cytochrome c in Matrix-Assisted Laser Desorption/Ionization In-Source Decay Mass Spectrometry

PubMed Central

Takayama, Mitsuo

2012-01-01

The backbone flexibility of a protein has been studied from the standpoint of the susceptibility of amino acid residues to in-source decay (ISD) in matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS). Residues more susceptible to MALDI-ISD, namely Xxx–Asp/Asn and Gly–Xxx, were identified from the discontinuous intense peak of c′-ions originating from specific cleavage at N–Cα bonds of the backbone of equine cytochrome c. The identity of the residues susceptible to ISD was consistent with the known flexible backbone amides as estimated by hydrogen/deuterium exchange (HDX) experiments. The identity of these flexible amino acid residues (Asp, Asn, and Gly) is consistent with the fact that these residues are preferred in flexible secondary structure free from intramolecular hydrogen-bonded structures such as α-helix and β-sheet. The MALDI-ISD spectrum of equine cytochrome c gave not only intense N-terminal side c′-ions originating from N–Cα bond cleavage at Xxx–Asp/Asn and Gly–Xxx residues, but also C-terminal side complement z′-ions originating from the same cleavage sites. The present study implies that MALDI-ISD can give information about backbone flexibility of proteins, comparable with the protection factors estimated by HDX. PMID:24349908

Flexible xxx-asp/asn and gly-xxx residues of equine cytochrome C in matrix-assisted laser desorption/ionization in-source decay mass spectrometry.

PubMed

Takayama, Mitsuo

2012-01-01

The backbone flexibility of a protein has been studied from the standpoint of the susceptibility of amino acid residues to in-source decay (ISD) in matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS). Residues more susceptible to MALDI-ISD, namely Xxx-Asp/Asn and Gly-Xxx, were identified from the discontinuous intense peak of c'-ions originating from specific cleavage at N-Cα bonds of the backbone of equine cytochrome c. The identity of the residues susceptible to ISD was consistent with the known flexible backbone amides as estimated by hydrogen/deuterium exchange (HDX) experiments. The identity of these flexible amino acid residues (Asp, Asn, and Gly) is consistent with the fact that these residues are preferred in flexible secondary structure free from intramolecular hydrogen-bonded structures such as α-helix and β-sheet. The MALDI-ISD spectrum of equine cytochrome c gave not only intense N-terminal side c'-ions originating from N-Cα bond cleavage at Xxx-Asp/Asn and Gly-Xxx residues, but also C-terminal side complement z'-ions originating from the same cleavage sites. The present study implies that MALDI-ISD can give information about backbone flexibility of proteins, comparable with the protection factors estimated by HDX.

Effectiveness of midurethral slings in intrinsic sphincteric-related stress urinary incontinence.

PubMed

Lim, Yik N; Dwyer, Peter L

2009-10-01

Previous literature has shown that urodynamic evidence of intrinsic sphincter deficiency (ISD) decreases the surgical success of traditional antistress incontinence surgeries. The aim of this review is to assess recent evidence on the effectiveness of the increasingly popular midurethral slings (MUS) in women with ISD and stress urinary incontinence. Using the ISD definition of maximum urethral closure pressure of 20 cm H2O or less and/or abdominal/valsalva leak point pressure of 60 cm H2O or less, current literature would suggest that the effectiveness of retropubic MUS is reduced but remained acceptable in women with stress urinary incontinence and ISD. There are conflicting data on whether coexisting poor urethral mobility could further compromise surgical success. Of note, there is now emerging evidence to suggest that transobturator tapes are associated with much higher failure rates in this setting and retropubic MUS should be used instead. Currently, there is too little data on the new single-incision mini-slings for any recommendation of use in women with stress incontinence with good or poor intrinsic urethral function. MUS is an effective treatment for stress urinary incontinence. However, when urodynamic evidence of ISD is present, the retropubic approach may be preferable to the transobturator approach.

Is it ethical to prescribe generic immunosuppressive drugs to renal transplant patients?

PubMed

Allard, Julie; Fortin, Marie-Chantal

2014-01-01

This review was conducted to determine the ethical acceptability of prescribing generic immunosuppressive drugs to renal transplant patients. The literature search was conducted using Pubmed and Google Scholar. The use of generic immunosuppressive drugs (ISDs) in transplantation is a controversial topic. There is a consensus among transplant societies that clinical data is lacking and that caution should be exercised. The reluctance to use generic ISDs in organ transplantation is partly related to the fact that most are "critical dose drugs", and that either low dosing or overdosing could have serious adverse consequences for both patients and society (i.e., the loss of scarce organs). In this paper, we examine the various ethical issues involved such as distributive justice, physician duties, risks versus benefits, conflict of interest, informed consent, and logistical and economic issues. Our analysis was limited by the paucity of clinical data on generic ISDs and the absence of health economics studies to quantify the benefits of prescribing generic ISDs. Our study led us to conclude that it would be ethical to prescribe generic ISDs provided certain conditions were met. These include regulatory safeguards to minimize the risks of substitution; education of patients; and further clinical and health economics studies to better inform clinicians, patients and society of the risks and costs related to drug substitution.

Stardust Interstellar Preliminary Examination X: Impact Speeds and Directions of Interstellar Grains on the Stardust Dust Collector

NASA Technical Reports Server (NTRS)

Sterken, Veerle J.; Westphal, Andrew J.; Altobelli, Nicolas; Grun, Eberhard; Hillier, Jon K.; Postberg, Frank; Allen, Carlton; Stroud, Rhonda M.; Sandford, S. A.; Zolensky, Michael E.

2014-01-01

On the basis of an interstellar dust model compatible with Ulysses and Galileo observations, we calculate and predict the trajectories of interstellar dust (ISD) in the solar system and the distribution of the impact speeds, directions, and flux of ISD particles on the Stardust Interstellar Dust Collector during the two collection periods of the mission. We find that the expected impact velocities are generally low (less than 10 km per second) for particles with the ratio of the solar radiation pressure force to the solar gravitational force beta greater than 1, and that some of the particles will impact on the cometary side of the collector. If we assume astronomical silicates for particle material and a density of 2 grams per cubic centimeter, and use the Ulysses measurements and the ISD trajectory simulations, we conclude that the total number of (detectable) captured ISD particles may be on the order of 50. In companion papers in this volume, we report the discovery of three interstellar dust candidates in the Stardust aerogel tiles. The impact directions and speeds of these candidates are consistent with those calculated from our ISD propagation model, within the uncertainties of the model and of the observations.

Extending the Instructional Systems Development Methodology.

ERIC Educational Resources Information Center

O'Neill, Colin E.

1993-01-01

Describes ways that components of Information Engineering (IE) methodology can be used by training system developers to extend Instructional Systems Development (ISD) methodology. Aspects of IE that are useful in ISD are described, including requirements determination, group facilitation, integrated automated tool support, and prototyping.…

Predicting Nitrogen Transport From Individual Sewage Disposal Systems for a Proposed Development in Adams County, Colorado

NASA Astrophysics Data System (ADS)

Heatwole, K. K.; McCray, J.; Lowe, K.

2005-12-01

Individual sewage disposal systems (ISDS) have demonstrated the capability to be an effective method of treatment for domestic wastewater. They also are advantageous from a water resources standpoint because there is little water leaving the local hydrologic system. However, if unfavorable settings exist, ISDS can have a detrimental effect on local water-quality. This presentation will focus on assessing the potential impacts of a large housing development to area water quality. The residential development plans to utilize ISDS to accommodate all domestic wastewater generated within the development. The area of interest is located just west of Brighton, Colorado, on the northwestern margin of the Denver Basin. Efforts of this research will focus on impacts of ISDS to local groundwater and surface water systems. The Arapahoe Aquifer, which exists at relatively shallow depths in the area of proposed development, is suspected to be vulnerable to contamination from ISDS. Additionally, the local water quality of the Arapahoe Aquifer was not well known at the start of the study. As a result, nitrate was selected as a fo-cus water quality parameter because it is easily produced through nitrification of septic tank effluent and because of the previous agricultural practices that could be another potential source of nitrate. Several different predictive tools were used to attempt to predict the potential impacts of ISDS to water quality in the Arapahoe Aquifer. The objectives of these tools were to 1) assess the vulnerability of the Arapahoe Aquifer to ni-trate contamination, 2) predict the nitrate load to the aquifer, and 3) determine the sensitivity of different parameter inputs and the overall prediction uncertainty. These predictive tools began with very simple mass-loading calcula-tions and progressed to more complex, vadose-zone numerical contaminant transport modeling.

Structure of human Fe-S assembly subcomplex reveals unexpected cysteine desulfurase architecture and acyl-ACP-ISD11 interactions.

PubMed

Cory, Seth A; Van Vranken, Jonathan G; Brignole, Edward J; Patra, Shachin; Winge, Dennis R; Drennan, Catherine L; Rutter, Jared; Barondeau, David P

2017-07-03

In eukaryotes, sulfur is mobilized for incorporation into multiple biosynthetic pathways by a cysteine desulfurase complex that consists of a catalytic subunit (NFS1), LYR protein (ISD11), and acyl carrier protein (ACP). This NFS1-ISD11-ACP (SDA) complex forms the core of the iron-sulfur (Fe-S) assembly complex and associates with assembly proteins ISCU2, frataxin (FXN), and ferredoxin to synthesize Fe-S clusters. Here we present crystallographic and electron microscopic structures of the SDA complex coupled to enzyme kinetic and cell-based studies to provide structure-function properties of a mitochondrial cysteine desulfurase. Unlike prokaryotic cysteine desulfurases, the SDA structure adopts an unexpected architecture in which a pair of ISD11 subunits form the dimeric core of the SDA complex, which clarifies the critical role of ISD11 in eukaryotic assemblies. The different quaternary structure results in an incompletely formed substrate channel and solvent-exposed pyridoxal 5'-phosphate cofactor and provides a rationale for the allosteric activator function of FXN in eukaryotic systems. The structure also reveals the 4'-phosphopantetheine-conjugated acyl-group of ACP occupies the hydrophobic core of ISD11, explaining the basis of ACP stabilization. The unexpected architecture for the SDA complex provides a framework for understanding interactions with acceptor proteins for sulfur-containing biosynthetic pathways, elucidating mechanistic details of eukaryotic Fe-S cluster biosynthesis, and clarifying how defects in Fe-S cluster assembly lead to diseases such as Friedreich's ataxia. Moreover, our results support a lock-and-key model in which LYR proteins associate with acyl-ACP as a mechanism for fatty acid biosynthesis to coordinate the expression, Fe-S cofactor maturation, and activity of the respiratory complexes.

Design for Effective Staff Development.

ERIC Educational Resources Information Center

Seagren, Alan T.

This paper presents a model for designing an effective staff development program. The rationale, philosophy, and instructional design utilized in the instructional Staff Development (ISD) program provides the basis for the design presented. The ISD program was conceptualized, developed, pilot tested, and field tested as a cooperative research…

What Should Instructional Designers Know about General Systems Theory?

ERIC Educational Resources Information Center

Salisbury, David F.

1989-01-01

Describes basic concepts in the field of general systems theory (GST) and explains the relationship between instructional systems design (ISD) and GST. Benefits of integrating GST into the curriculum of ISD graduate programs are discussed, and a short bibliography on GST is included. (LRW)

Behavior Analysis in Distance Education: A Systems Approach.

ERIC Educational Resources Information Center

Coldeway, Dan O.

1987-01-01

Describes a model of instructional theory relevant to individualized distance education that is based on Keller's Personalized System of Instruction (PSI), behavior analysis, and the instructional systems development model (ISD). Systems theory is emphasized, and ISD and behavior analysis are discussed as cybernetic processes. (LRW)

Structure and functional dynamics of the mitochondrial Fe/S cluster synthesis complex.

PubMed

Boniecki, Michal T; Freibert, Sven A; Mühlenhoff, Ulrich; Lill, Roland; Cygler, Miroslaw

2017-11-03

Iron-sulfur (Fe/S) clusters are essential protein cofactors crucial for many cellular functions including DNA maintenance, protein translation, and energy conversion. De novo Fe/S cluster synthesis occurs on the mitochondrial scaffold protein ISCU and requires cysteine desulfurase NFS1, ferredoxin, frataxin, and the small factors ISD11 and ACP (acyl carrier protein). Both the mechanism of Fe/S cluster synthesis and function of ISD11-ACP are poorly understood. Here, we present crystal structures of three different NFS1-ISD11-ACP complexes with and without ISCU, and we use SAXS analyses to define the 3D architecture of the complete mitochondrial Fe/S cluster biosynthetic complex. Our structural and biochemical studies provide mechanistic insights into Fe/S cluster synthesis at the catalytic center defined by the active-site Cys of NFS1 and conserved Cys, Asp, and His residues of ISCU. We assign specific regulatory rather than catalytic roles to ISD11-ACP that link Fe/S cluster synthesis with mitochondrial lipid synthesis and cellular energy status.

Integrated service delivery networks for seniors: early perceptions of family physicians.

PubMed

Milette, Linda; Hébert, Réjean; Veil, Anne

2005-08-01

To document the early perceptions of family physicians regarding integrated service delivery (ISD) networks a few weeks before and 6 months after establishing these networks and to identify obstacles to using case managers. Cross-sectional survey with two questionnaires mailed 6 months apart. Three regional municipalities (one urban and two rural) in the Eastern Townships of Quebec. All family physicians in the three areas (n = 267). A total of 124 physicians (of 206 eligible; 60% response rate) answered the first questionnaire, and 104 of these the second (86% response rate). The first questionnaire asked what family physicians thought about ISD networks and the emerging case management function, and whether they were interested in participating in ISD networks. The second measured physicians' participation in ISD networks, asked whether their perceptions of case management had changed, and identified obstacles to using case managers. Nearly all (98%) respondents to the preimplementation questionnaire believed that family physicians will increasingly have to belong to ISD networks. Very few (8.2%), however, felt involved or consulted in decisions about developing and implementing these networks. More than one quarter (27%) did not know that an ISD network for older people would be established in their area, and 84.3% did not feel sufficiently informed to be involved. Most family physicians (85.7%) said they were interested in using case managers. Six months after implementation, 70.2% of physicians knew that case managers were available; 35.6% had used a case manager. During implementation, physicians' opinions about case management were slightly less positive than they had been. The three main obstacles to using case managers were forgetting to use them (69.1%), the habit of using social workers instead (63.6%), and not knowing how to contact them (59.4%). Physicians are interested in participating in ISD networks and working with case managers. They must be better informed, however, about the availability of case managers, how they can reach case managers, case managers' precise role, and the advantages to themselves and their patients of using these services.

Integrated service delivery networks for seniors

PubMed Central

Milette, Linda; Hébert, Réjean; Veil, Anne

2005-01-01

OBJECTIVE To document the early perceptions of family physicians regarding integrated service delivery (ISD) networks a few weeks before and 6 months after establishing these networks and to identify obstacles to using case managers. DESIGN Cross-sectional survey with two questionnaires mailed 6 months apart. SETTING Three regional municipalities (one urban and two rural) in the Eastern Townships of Quebec. PARTICIPANTS All family physicians in the three areas (n = 267). A total of 124 physicians (of 206 eligible; 60% response rate) answered the first questionnaire, and 104 of these the second (86% response rate). MAIN OUTCOME MEASURES The first questionnaire asked what family physicians thought about ISD networks and the emerging case management function, and whether they were interested in participating in ISD networks. The second measured physicians’ participation in ISD networks, asked whether their perceptions of case management had changed, and identified obstacles to using case managers. RESULTS Nearly all (98%) respondents to the preimplementation questionnaire believed that family physicians will increasingly have to belong to ISD networks. Very few (8.2%), however, felt involved or consulted in decisions about developing and implementing these networks. More than one quarter (27%) did not know that an ISD network for older people would be established in their area, and 84.3% did not feel sufficiently informed to be involved. Most family physicians (85.7%) said they were interested in using case managers. Six months after implementation, 70.2% of physicians knew that case managers were available; 35.6% had used a case manager. During implementation, physicians’ opinions about case management were slightly less positive than they had been. The three main obstacles to using case managers were forgetting to use them (69.1%), the habit of using social workers instead (63.6%), and not knowing how to contact them (59.4%). CONCLUSION Physicians are interested in participating in ISD networks and working with case managers. They must be better informed, however, about the availability of case managers, how they can reach case managers, case managers’ precise role, and the advantages to themselves and their patients of using these services. PMID:16926947

The birth canal: correlation between the pubic arch angle, the interspinous diameter, and the obstetrical conjugate: a computed tomography biometric study in reproductive age women.

PubMed

Perlman, Sharon; Raviv-Zilka, Lisa; Levinsky, Denis; Gidron, Ayelet; Achiron, Reuven; Gilboa, Yinon; Kivilevitch, Zvi

2018-04-22

Assessment of pelvic configuration is an important factor in the prediction of a successful vaginal birth. However, manual evaluation of the pelvis is practically a vanishing art, and imaging techniques are not available as a real-time bed-side tool. Unlike the obstetrical conjugate diameter (OC) and inter spinous diameter (ISD), the pubic arch angle (PAA) can be easily measured by transperineal ultrasound. Three-dimensional computed tomography bone reconstructions were used to measure the three main birth canal diameters, evaluate the correlation between them, and establish the normal reference range for the inlet, mid-, and pelvic outlet. Measurements of the PAA, obstetric conjugate (OC), and ISD were performed offline using three-dimensional post processing reconstruction in bone algorithm application of the pelvis on examinations performed for suspected renal colic in nonpregnant reproductive age woman. The mean of two measurements was used for statistical analysis which included reproducibility of measurements, regression curve estimation between PAA, OC, and ISD, and calculation of the respective reference range centiles for each PAA degree. Two hundred ninety-eight women comprised the study group. The mean ± SD of the PAA, ISD, and OC were 104.9° (±7.4), 103.8 mm (±7.3), and 129.9 mm (±8.3), respectively. The intra- and interobserver agreement defined by the intraclass correlation coefficient (ICC) was excellent for all parameters (range 0.905-0.993). A significant positive correlation was found between PAA and ISD and between PAA and OCD (Pearson's correlation = 0.373 (p < .001), and 0.163 (p = .022), respectively). The best regression formula was found with quadratic regression for inter spinous diameter (ISD): 34.122778 + (0.962182*PAA - 0.002830*PAA 2 ), and linear regression for obstetric conjugate (OC): 110.638397 + 0.183156*PAA. Modeled mean, SD, and reference centiles of the ISD and OCD were calculated using the above regression models as function of the PAA. We report significant correlation between the three pelvic landmarks with greatest impact on the prediction of a successful vaginal delivery: the PAA which is easily measured sonographically and the ISD and OC which are not measurable by ultrasound. This correlation may serve as a basis for future studies to assess its utility and prognostic value for a safe vaginal delivery.

A practitioner-driven research agenda for syndromic surveillance

DOE PAGES

Hopkins, Richard S.; Gunn, Julia; Berezowski, John; ...

2017-05-02

The objective here is to obtain feedback and seek future directions for an ISDS initiative to establish and update research questions in Informatics, Analytics,Communications, and Systems Research with the greatest perceived impact for improving surveillance practice.Introduction Over the past fifteen years, syndromic surveillance (SyS) has evolved from a set of ad hoc methods used mostly in post-disaster settings, then expanded with broad support and development because of bioterrorism concerns, and subsequently evolved to a mature technology that runs continuously to detect and monitor a wide range of health issues. Continued enhancements needed to meet the challenges of novel health threatsmore » with increasingly complex information sources will require technical advances focused on day-to-day public health needs.Since its formation in 2005, the International Society for Disease Surveillance (ISDS) has sought to clarify and coordinate global priorities in surveillance research. As part of a practitioner-driven initiative to identify current research priorities in SyS, ISDS polled its members about capabilities needed by SyS practitioners that could be improved as a result of research efforts. A taskforce of the ISDS Research Committee, consisting of national and global subject matter experts (SMEs) in SyS and ISDS professional staff, carried out the project. This panel will discuss the results and the preferred means to determine and communicate priorities in the future.« less

Integrated specialty service readiness in health reform: connections in haemophilia comprehensive care.

PubMed

Pritchard, A M; Page, D

2008-05-01

The World Health Organization (WHO) has identified primary healthcare reform as a global priority whereby innovative practice changes are directed at improving health. This transformation to health reform in haemophilia service requires clarification of comprehensive care to reflect the WHO definition of health and key elements of primary healthcare reform. While comprehensive care supports effective healthcare delivery, comprehensive care must also be regarded beyond immediate patient management to reflect the broader system purpose in the care continuum with institutions, community agencies and government. Furthermore, health reform may be facilitated through integrated service delivery (ISD). ISD in specialty haemophilia care has the potential to reduce repetition of assessments, enhance care plan communication between providers and families, provide 24-h access to care, improve information availability regarding care quality and outcomes, consolidate access for multiple healthcare encounters and facilitate family self-efficacy and autonomy [1]. Three core aspects of ISD have been distinguished: clinical integration, information management and technology and vertical integration in local communities [2]. Selected examples taken from Canadian haemophilia comprehensive care illustrate how practice innovations are bridged with a broader system level approach and may support initiatives in other contexts. These innovations are thought to indicate readiness regarding ISD. Reflecting on the existing capacity of haemophilia comprehensive care teams will assist providers to connect and direct their existing strengths towards ISD and health reform.

A practitioner-driven research agenda for syndromic surveillance

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

Hopkins, Richard S.; Gunn, Julia; Berezowski, John

The objective here is to obtain feedback and seek future directions for an ISDS initiative to establish and update research questions in Informatics, Analytics,Communications, and Systems Research with the greatest perceived impact for improving surveillance practice.Introduction Over the past fifteen years, syndromic surveillance (SyS) has evolved from a set of ad hoc methods used mostly in post-disaster settings, then expanded with broad support and development because of bioterrorism concerns, and subsequently evolved to a mature technology that runs continuously to detect and monitor a wide range of health issues. Continued enhancements needed to meet the challenges of novel health threatsmore » with increasingly complex information sources will require technical advances focused on day-to-day public health needs.Since its formation in 2005, the International Society for Disease Surveillance (ISDS) has sought to clarify and coordinate global priorities in surveillance research. As part of a practitioner-driven initiative to identify current research priorities in SyS, ISDS polled its members about capabilities needed by SyS practitioners that could be improved as a result of research efforts. A taskforce of the ISDS Research Committee, consisting of national and global subject matter experts (SMEs) in SyS and ISDS professional staff, carried out the project. This panel will discuss the results and the preferred means to determine and communicate priorities in the future.« less

Improved design of dynamic vibration absorber by using the inerter and its application in vehicle suspension

NASA Astrophysics Data System (ADS)

Shen, Yujie; Chen, Long; Yang, Xiaofeng; Shi, Dehua; Yang, Jun

2016-01-01

Inerter is a recently proposed mechanical element with two terminals. The novelty of this paper is to present the improved design which aims to add traditional dynamic vibration absorber to the vehicle body by using the inerter. Based on this background, a new vehicle suspension structure called ISD suspension, including the inerter, spring and damper has been created. A dual-mass vibration model including the ISD suspension is considered in this study. Parameters are obtained by using the genetic optimizing algorithm. The frequency-domain simulation confirms that the ISD suspension can effectively improve the damping performance of the suspension system, especially at the offset frequency of the vehicle body, which is consistent with the feature of the dynamic vibration absorber added to the vehicle body mass. At last, a prototype ball screw inerter has been designed and the bench test of a quarter-car model has been undertaken. Under the conditions of the random road input, the vehicle ride comfort evaluation of body acceleration RMS value decreases by 4% at most, the suspension deflection RMS value decreases by 16% at most, the tire dynamic load RMS value decreases by 6% at most. Power spectral density results also indicate that the ISD suspension has superior damping performance than passive suspension which proves that the proposed ISD suspension is deemed effective.

Integrating Cognitive Task Analysis into Instructional Systems Development.

ERIC Educational Resources Information Center

Ryder, Joan M.; Redding, Richard E.

1993-01-01

Discussion of instructional systems development (ISD) focuses on recent developments in cognitive task analysis and describes the Integrated Task Analysis Model, a framework for integrating cognitive and behavioral task analysis methods within the ISD model. Three components of expertise are analyzed: skills, knowledge, and mental models. (96…

Developing Instructional Technology Products Using Effective Project Management Practices

ERIC Educational Resources Information Center

Allen, Stephanie; Hardin, Paul C.

2008-01-01

Delivering a successful instructional technology (IT) product depends on more than just having an extremely creative instructional solution or following an instructional systems design (ISD) model. Proper planning, direction, and execution of the project are require, as well. We present a model of management that encompasses the ISD process. Five…

Reconceiving ISD: Three Perspectives on Rapid Prototyping as a Paradigm Shift.

ERIC Educational Resources Information Center

Rathbun, Gail A.; And Others

Confronting recent design challenges, instructional designers have latched onto adaptive procedural techniques from outside the Instructional Systems Design (ISD) field. This discussion of rapid prototyping (RP) examines the perspectives of: (1) the prototype as the designer"s cognitive tool; (2) the designer as co-inquirer; and (3) the…

Investigating Reliabilities of Intraindividual Variability Indicators

ERIC Educational Resources Information Center

Wang, Lijuan; Grimm, Kevin J.

2012-01-01

Reliabilities of the two most widely used intraindividual variability indicators, "ISD[superscript 2]" and "ISD", are derived analytically. Both are functions of the sizes of the first and second moments of true intraindividual variability, the size of the measurement error variance, and the number of assessments within a burst. For comparison,…

The New ISD: Applying Cognitive Strategies to Instructional Design.

ERIC Educational Resources Information Center

Clark, Ruth Colvin

2002-01-01

Discusses cognitive models of instruction that can help develop new models of Instructional Systems Design (ISD) that include cognitive task analysis to identify mental models; constructive assumptions of learning; working memory and long-term memory; retrieval of new knowledge and skills from long-term memory; and support of metacognitive skills.…

Group Performance in Information Systems Project Groups: An Empirical Study

ERIC Educational Resources Information Center

Bahli, Bouchaib; Buyukkurt, Meral Demirbag

2005-01-01

The importance of teamwork in Information Systems Development (ISD) practice and education has been acknowledged but not studied extensively to date. This paper tests a model of how groups participating in ISD projects perform and examines the relationships between some antecedents of this performance based on group research theory well…

Visibility into the Work: TQM Work Process Analysis with HPT and ISD.

ERIC Educational Resources Information Center

Beagles, Charles A.; Griffin, Steven L.

2003-01-01

Discusses the use of total quality management (TQM), work process flow diagrams, and ISD (instructional systems development) tools with HPT (human performance technology) to address performance gaps in the Veterans Benefits Administration (VBA). Describes performance goals, which were to improve accuracy and reduce backlog of claim files. (LRW)

A Symbiosis between Instructional Systems Design and Project Management

ERIC Educational Resources Information Center

Pan, Cheng-Chang

2012-01-01

This study is intended to explore a complementary relationship between instructional systems design (ISD) and project management in an attempt to build a plausible case for integrating project management as a distinct course in the core of the graduate instructional systems design programs. It is argued that ISD and project management should form…

A Standard Procedure for Conducting Cognitive Task Analysis.

ERIC Educational Resources Information Center

Redding, Richard E.

Traditional methods for task analysis have been largely based on the Instructional Systems Development (ISD) model, which is widely used throughout industry and the military. The first part of this document gives an overview of cognitive task analysis, which is conducted within the first phase of ISD. The following steps of cognitive task analysis…

Putting College and Career Readiness at the Forefront of District Priorities in Dallas

ERIC Educational Resources Information Center

Hall, Shane

2013-01-01

Dallas Independent School District's (ISD) efforts to develop a system of college readiness indicators began in 2008, when they received a Bill & Melinda Gates Foundation grant under the foundation's College-Ready Education initiative. With this grant, Dallas ISD's Performance Management and Analytics department developed a college readiness…

Examining the Dynamics of Managing Information Systems Development Projects: A Control Loss Perspective

ERIC Educational Resources Information Center

Narayanaswamy, Ravi

2009-01-01

The failure rate of information systems development (ISD) projects continues to pose a big challenge for organizations. The success rate of ISD projects is less then forty percent. Factors such as disagreements and miscommunications among project manager and team members, poor monitoring and intermediary problems contribute to project failure.…

California Integrated Service Delivery Evaluation Report. Phase I

ERIC Educational Resources Information Center

Moore, Richard W.; Rossy, Gerard; Roberts, William; Chapman, Kenneth; Sanchez, Urte; Hanley, Chris

2010-01-01

This study is a formative evaluation of the OneStop Career Center Integrated Service Delivery (ISD) Model within the California Workforce System. The study was sponsored by the California Workforce Investment Board. The study completed four in-depth case studies of California OneStops to describe how they implemented the ISD model which brings…

A Narrative Inquiry into the Influence of Coaching Methodology on Three Specific Teacher Knowledge Communities

ERIC Educational Resources Information Center

Martindell, Peter Timothy

2012-01-01

This narrative inquiry studied the influences of coaching methodology, critical incidents, and critical relationships on three specific teacher knowledge communities--the Portfolio Group, the Houston ISD literacy coach network, and the Imperial ISD Secondary English Language Arts helping teacher workgroup. This inquiry is situated within the…

E-Resources Management: How We Positioned Our Organization to Implement an Electronic Resources Management System

ERIC Educational Resources Information Center

White, Marilyn; Sanders, Susan

2009-01-01

The Information Services Division (ISD) of the National Institute of Standards and Technology (NIST) positioned itself to successfully implement an electronic resources management system. This article highlights the ISD's unique ability to "team" across the organization to realize a common goal, develop leadership qualities in support of…

General Systems Theory and Instructional Design.

ERIC Educational Resources Information Center

Salisbury, David F.

The use of general systems theory in the field of instructional systems design (ISD) is explored in this paper. Drawing on work by Young, the writings of 12 representative ISD writers and researchers were surveyed to determine the use of 60 general systems theory concepts by the individual authors. The average number of concepts used by these…

Respiratory chain supercomplexes associate with the cysteine desulfurase complex of the iron–sulfur cluster assembly machinery

PubMed Central

Böttinger, Lena; Mårtensson, Christoph U.; Song, Jiyao; Zufall, Nicole; Wiedemann, Nils; Becker, Thomas

2018-01-01

Mitochondria are the powerhouses of eukaryotic cells. The activity of the respiratory chain complexes generates a proton gradient across the inner membrane, which is used by the F1FO-ATP synthase to produce ATP for cellular metabolism. In baker’s yeast, Saccharomyces cerevisiae, the cytochrome bc1 complex (complex III) and cytochrome c oxidase (complex IV) associate in respiratory chain supercomplexes. Iron–sulfur clusters (ISC) form reactive centers of respiratory chain complexes. The assembly of ISC occurs in the mitochondrial matrix and is essential for cell viability. The cysteine desulfurase Nfs1 provides sulfur for ISC assembly and forms with partner proteins the ISC-biogenesis desulfurase complex (ISD complex). Here, we report an unexpected interaction of the active ISD complex with the cytochrome bc1 complex and cytochrome c oxidase. The individual deletion of complex III or complex IV blocks the association of the ISD complex with respiratory chain components. We conclude that the ISD complex binds selectively to respiratory chain supercomplexes. We propose that this molecular link contributes to coordination of iron–sulfur cluster formation with respiratory activity. PMID:29386296

Considerations in the modern management of stress urinary incontinence resulting from intrinsic sphincter deficiency.

PubMed

Hillary, Christopher James; Osman, Nadir; Chapple, Christopher

2015-09-01

Intrinsic sphincter deficiency (ISD) is a common cause of stress urinary incontinence and is associated with more severe symptoms, often being associated with failed previous surgery. Due to the impaired sphincteric function, alternative surgical approaches are often required. The purpose of this review is to appraise the contemporary literature on the diagnosis and management of ISD. A PubMed search was performed to identify articles published between 1990 and 2014 using the following terms: ISD, stress urinary incontinence and type III stress urinary incontinence. Publications were screened for relevance, and full manuscripts were retrieved. Most studies base the diagnosis of ISD upon urodynamic appearances using recognized criteria (Valsalva leak point pressure <60 cm H2O or a maximum urethral closure pressure <20 cm H2O) in addition to clinical features. A range of non-surgical and surgical treatment options are available for the patient. Pubovaginal slings are more effective than retropubic colposuspensions with outcomes comparable to those reported with midurethral slings. The artificial urinary sphincter provides long-term cure rates; however, it is associated with specific morbidity including device erosion, mechanical failure and revision. The benefits of bulking agents, however, are not sustained beyond 1 year. There are few randomized controlled trials that compare accepted treatments specifically for patients with ISD. The lack of standardization in the definition and diagnostic criteria used limits inter-study comparisons. An assessment of urethral pressure profile when combined with the clinical features may help predict outcomes of surgical intervention.

A Synergy between the Technological Process and a Methodology for Web Design: Implications for Technological Problem Solving and Design

ERIC Educational Resources Information Center

Jakovljevic, Maria; Ankiewicz, Piet; De swardt, Estelle; Gross, Elna

2004-01-01

Traditional instructional methodology in the Information System Design (ISD) environment lacks explicit strategies for promoting the cognitive skills of prospective system designers. This contributes to the fragmented knowledge and low motivational and creative involvement of learners in system design tasks. In addition, present ISD methodologies,…

The Applicability of the ISD 4-Factor Model of Job Analysis in Identifying Task Training Priority in Nine Technical Military Occupational Specialties.

ERIC Educational Resources Information Center

Siebold, Guy L.

Research was conducted to assess the applicability of the Instructional Systems Development (ISD) job analysis procedures to nine technical aviation maintenance military occupational specialties (MOS). Job analysis questionnaires were developed for each of the nine aviation maintenance MOS's. Research teams administered the questionnaires to…

Impact of Function, Experience, and Training of School District Police on School Climate

ERIC Educational Resources Information Center

Denham, Magdalena

2013-01-01

Purpose: The purpose of this quantitative study was to investigate the impact that function, experience, and training of Independent School District School Resource Officers (ISD SROs) have on school climate. The participants were ISD SROs (n = 172) and teachers (n = 162) located in middle and high schools in Texas. Method: The Role of Law…

With Little Research out There It's a Matter of Learning What Works in Teaching Students with Deafness and Autism

ERIC Educational Resources Information Center

Bradley, Lee Ann; Krakowski, Brandi; Thiessen, Ann

2008-01-01

The development of language and literacy is the foundation for all other learning. This statement is the guiding philosophy at the Iowa School for the Deaf (ISD). Teachers at ISD believe that intensive, highly structured early intervention and education work best to support cognitive and communication development in their students. However, little…

Professional Organizations and Publications in ISD&T Recommended to New Professionals by Faculty Members

ERIC Educational Resources Information Center

Kim, Minjeong; Lee, Youngmin

2006-01-01

New members in the field of instructional systems design and technology (ISD&T), including new students in this field, can find lists of publications and organizations available for them to read and to join. However, they may also wish to know which of these publications and organizations are recommended by established professionals. The field of…

The NTeQ ISD Model: A Tech-Driven Model for Digital Natives (DNs)

ERIC Educational Resources Information Center

Williams, C.; Anekwe, J. U.

2017-01-01

Integrating Technology for enquiry (NTeQ) instructional development model (ISD), is believed to be a technology-driven model. The authors x-rayed the ten-step model to reaffirm the ICT knowledge demand of the learner and the educator; hence computer-based activities at various stages of the model are core elements. The model also is conscious of…

Effect of gap detection threshold on consistency of speech in children with speech sound disorder.

PubMed

Sayyahi, Fateme; Soleymani, Zahra; Akbari, Mohammad; Bijankhan, Mahmood; Dolatshahi, Behrooz

2017-02-01

The present study examined the relationship between gap detection threshold and speech error consistency in children with speech sound disorder. The participants were children five to six years of age who were categorized into three groups of typical speech, consistent speech disorder (CSD) and inconsistent speech disorder (ISD).The phonetic gap detection threshold test was used for this study, which is a valid test comprised six syllables with inter-stimulus intervals between 20-300ms. The participants were asked to listen to the recorded stimuli three times and indicate whether they heard one or two sounds. There was no significant difference between the typical and CSD groups (p=0.55), but there were significant differences in performance between the ISD and CSD groups and the ISD and typical groups (p=0.00). The ISD group discriminated between speech sounds at a higher threshold. Children with inconsistent speech errors could not distinguish speech sounds during time-limited phonetic discrimination. It is suggested that inconsistency in speech is a representation of inconsistency in auditory perception, which causes by high gap detection threshold. Copyright © 2016 Elsevier Ltd. All rights reserved.

Influence of secondary structure on in-source decay of protein in matrix-assisted laser desorption/ionization mass spectrometry.

PubMed

Takayama, Mitsuo; Osaka, Issey; Sakakura, Motoshi

2012-01-01

The susceptibility of the N-Cα bond of the peptide backbone to specific cleavage by in-source decay (ISD) in matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) was studied from the standpoint of the secondary structure of three proteins. A naphthalene derivative, 5-amino-1-naphtol (5,1-ANL), was used as the matrix. The resulting c'-ions, which originate from the cleavage at N-Cα bonds in flexible secondary structures such as turn and bend, and are free from intra-molecular hydrogen-bonded α-helix structure, gave relatively intense peaks. Furthermore, ISD spectra of the proteins showed that the N-Cα bonds of specific amino acid residues, namely Gly-Xxx, Xxx-Asp, and Xxx-Asn, were more susceptible to MALDI-ISD than other amino acid residues. This is in agreement with the observation that Gly, Asp and Asn residues usually located in turns, rather than α-helix. The results obtained indicate that protein molecules embedded into the matrix crystal in the MALDI experiments maintain their secondary structures as determined by X-ray crystallography, and that MALDI-ISD has the capability for providing information concerning the secondary structure of protein.

Properties of an interspinous fixation device (ISD) in lumbar fusion constructs: a biomechanical study.

PubMed

Techy, Fernando; Mageswaran, Prasath; Colbrunn, Robb W; Bonner, Tara F; McLain, Robert F

2013-05-01

Segmental fixation improves fusion rates and promotes patient mobility by controlling instability after lumbar surgery. Efforts to obtain stability using less invasive techniques have lead to the advent of new implants and constructs. A new interspinous fixation device (ISD) has been introduced as a minimally invasive method of stabilizing two adjacent interspinous processes by augmenting an interbody cage in transforaminal interbody fusion. The ISD is intended to replace the standard pedicle screw instrumentation used for posterior fixation. The purpose of this study is to compare the rigidity of these implant systems when supplementing an interbody cage as used in transforaminal lumbar interbody fusion. An in vitro human cadaveric biomechanical study. Seven human cadaver spines (T12 to the sacrum) were mounted in a custom-designed testing apparatus, for biomechanical testing using a multiaxial robotic system. A comparison of segmental stiffness was carried out among five conditions: intact spine control; interbody spacer (IBS), alone; interbody cage with ISD; IBS, ISD, and unilateral pedicle screws (unilat); and IBS, with bilateral pedicle screws (bilat). An industrial robot (KUKA, GmbH, Augsburg, Germany) applied a pure moment (±5 Nm) in flexion-extension (FE), lateral bending (LB), and axial rotation (AR) through an anchor to the T12 vertebral body. The relative vertebral motion was captured using an optoelectronic camera system (Optotrak; Northern Digital, Inc., Waterloo, Ontario, Canada). The load sensor and the camera were synchronized. Maximum rotation was measured at each level and compared with the intact control. Implant constructs were compared with the control and with each other. A statistical analysis was performed using analysis of variance. A comparison between the intact spine and the IBS group showed no significant difference in the range of motion (ROM) in FE, LB, or AR for the operated level, L3-L4. After implantation of the ISD to augment the IBS, there was a significant decrease in the ROM of 74% in FE (p<.001) but no significant change in the ROM in LB and AR. The unilat construct significantly reduced the ROM by 77% compared with FE control (p<.001) and by 55% (p=.002) and 42% (p=.04) in LB and AR, respectively, compared with control. The bilat construct reduced the ROM in FE by 77% (p<.001), LB by 77% (p=.001), and AR by 65% (p=.001) when compared with the control spine. There was no statistically significant difference in the ROM in FE among the stand-alone ISD, unilat, and bilat constructs. However, in both LB and AR, the unilat and the bilat constructs were significantly stiffer (reduction in the ROM) than the ISD and the IBS combination. The ISD stability in LB and AR was not different from the intact control with no instrumentation at all. There was no statistical difference between the stability of the unilat and the bilat constructs in any direction. However, LB and AR in the unilat group produced a mean rotation of 3.83°±3.30° and 2.33°±1.33°, respectively, compared with the bilat construct that limited motion to 1.96°±1.46° and 1.39°±0.73°. There was a trend suggesting that the bilat construct was the most rigid construct. In FE, the ISD can provide lumbar stability comparable with Bilat instrumentation. It provides minimal rigidity in LB and AR when used alone to stabilize the segment after an IBS placement. The unilat and the more typical bilat screw constructs were shown to provide similar levels of stability in all directions after an IBS placement, though the bilat construct showed a trend toward improved stiffness overall. Copyright © 2013 Elsevier Inc. All rights reserved.

Combining Project Management Methods: A Case Study of Dlstributed Work Practices

NASA Astrophysics Data System (ADS)

Backlund, Per; Lundell, Björn

The increasing complexity of information systems development (ISD) projects call for improved project management practices. This, together with an endeavour to improve the success rate of ISD projects (Lyytinen and Robey 1999; Cooke-Davies 2002; White and Fortune 2002), has served as drivers for various efforts in process improvement such as the introduction of new development methods (Fitzgerald 1997; Iivari and Maansaari 1998).

Prediction of posterior ligamentous complex injury in thoracolumbar fractures using non-MRI imaging techniques.

PubMed

Rajasekaran, Shanmuganathan; Maheswaran, Anupama; Aiyer, Siddharth N; Kanna, Rishi; Dumpa, Srikanth Reddy; Shetty, Ajoy Prasad

2016-06-01

We aimed to formulate a radiological index based on plain radiographs and computer tomography (CT) to reliably detect posterior ligamentous complex (PLC) injury without need for MRI. Sixty out of 148 consecutive thoracolumbar fractures with doubtful PLC were assessed with MRI, CT and radiographs. PLC injury was assessed with the following radiological parameters: superior-inferior end plate angle (SIEA), vertebral body height (BH), local kyphosis (LK), inter-spinous distance (ISD) and inter-pedicular distance (IPD) and correlated with MRI findings of PLC injury. Statistical analysis was performed to identify the predictive values for the parameters to identify PLC damage. MRI identified PLC injury in 25/60 cases. The ISD and LK were found to be significant predictors of PLC injury. On radiographs the mean LK with PLC damage was 25.86° compared to 21.02° with an intact PLC (p = 0.006). The ISD difference was 6.70 mm in cases with PLC damage compared to 2.86 mm with an intact PLC (p = 0.011). In CT images, the mean LK with PLC damage was 22.96° compared to 18.44° with an intact PLC ( p = 0.019). The ISD difference was 3.10 mm with PLC damage compared to 1.62 mm without PLC damage (p = 0.005). On plain radiographs the presence of LK greater than 20 °(CI 64-95) and ISD difference greater than 2 mm (CI 70-97) can predict PLC injury. These guidelines may be utilised in the emergency room especially when the associated cost, availability and time delay in performing MRI are a concern.

An Accelerated Release Study to Evaluate Long-Acting Contraceptive Levonorgestrel-Containing in Situ Forming Depot Systems

PubMed Central

Janagam, Dileep R.; Wang, Lizhu; Ananthula, Suryatheja; Johnson, James R.; Lowe, Tao L.

2016-01-01

Biodegradable polymer-based injectable in situ forming depot (ISD) systems that solidify in the body to form a solid or semisolid reservoir are becoming increasingly attractive as an injectable dosage form for sustained (months to years) parenteral drug delivery. Evaluation of long-term drug release from the ISD systems during the formulation development is laborious and costly. An accelerated release method that can effectively correlate the months to years of long-term release in a short time such as days or weeks is economically needed. However, no such accelerated ISD system release method has been reported in the literature to date. The objective of the current study was to develop a short-term accelerated in vitro release method for contraceptive levonorgestrel (LNG)-containing ISD systems to screen formulations for more than 3-month contraception after a single subcutaneous injection. The LNG-containing ISD formulations were prepared by using biodegradable poly(lactide-co-glycolide) and polylactic acid polymer and solvent mixtures containing N-methyl-2-pyrrolidone and benzyl benzoate or triethyl citrate. Drug release studies were performed under real-time (long-term) conditions (PBS, pH 7.4, 37 °C) and four accelerated (short-term) conditions: (A) PBS, pH 7.4, 50 °C; (B) 25% ethanol in PBS, pH 7.4, 50 °C; (C) 25% ethanol in PBS, 2% Tween 20, pH 7.4, 50 °C; and (D) 25% ethanol in PBS, 2% Tween 20, pH 9, 50 °C. The LNG release profile, including the release mechanism under the accelerated condition D within two weeks, correlated (r2 ≥ 0.98) well with that under real-time conditions at four months. PMID:27598191

A Pilot Randomized Controlled Trial of Novel Dressing and Securement Techniques in 101 Pediatric Patients.

PubMed

Kleidon, Tricia M; Ullman, Amanda J; Gibson, Victoria; Chaseling, Brett; Schoutrop, Jason; Mihala, Gabor; Rickard, Claire M

2017-11-01

To evaluate feasibility of an efficacy trial comparing peripherally inserted central catheter (PICC) dressing and securement techniques to prevent complications and failure. This pilot, 3-armed, randomized controlled trial was undertaken at Royal Children's Hospital and Lady Cilento Children's Hospital, Brisbane, Australia, between April 2014 and September 2015. Pediatric participants (N = 101; age range, 0-18 y) were assigned to standard care (bordered polyurethane [BPU] dressing, sutureless securement device), tissue adhesive (TA) (plus BPU dressing), or integrated securement dressings (ISDs). Average PICC dwell time was 8.1 days (range, 0.2-27.7 d). Primary outcome was trial feasibility including PICC failure. Secondary outcomes were PICC complications, dressing performance, and parent and staff satisfaction. Protocol feasibility was established. PICC failure was 6% (2/32) with standard care, 6% (2/31) with ISD, and 3% (1/32) with TA. PICC complications were 16% across all groups. TA provided immediate postoperative hemostasis, prolonging the first dressing change until 5.5 days compared with 3.5 days and 2.5 days with standard care and ISD respectively. Bleeding was the most common reason for first dressing change: standard care (n = 18; 75%), ISD (n = 11; 69%), TA (n = 4; 27%). Parental satisfaction (median 9.7/10; P = .006) and staff feedback (9.2/10; P = .002) were most positive for ISD. This research suggests safety and acceptability of different securement dressings compared with standard care; securement dressings may also reduce dressing changes after insertion. Further research is required to confirm clinically cost-effective methods to prevent PICC failure. Copyright © 2017 SIR. Published by Elsevier Inc. All rights reserved.

Physiological and Psychophysical Modeling of the Precedence Effect

PubMed Central

Xia, Jing; Brughera, Andrew; Colburn, H. Steven

2010-01-01

Many past studies of sound localization explored the precedence effect (PE), in which a pair of brief, temporally close sounds from different directions is perceived as coming from a location near that of the first-arriving sound. Here, a computational model of low-frequency inferior colliculus (IC) neurons accounts for both physiological and psychophysical responses to PE click stimuli. In the model, IC neurons have physiologically plausible inputs, receiving excitation from the ipsilateral medial superior olive (MSO) and long-lasting inhibition from both ipsilateral and contralateral MSOs, relayed through the dorsal nucleus of the lateral lemniscus. In this model, physiological suppression of the lagging response depends on the inter-stimulus delay (ISD) between the lead and lag as well as their relative locations. Psychophysical predictions are generated from a population of model neurons. At all ISDs, predicted lead localization is good. At short ISDs, the estimated location of the lag is near that of the lead, consistent with subjects perceiving both lead and lag from the lead location. As ISD increases, the estimated lag location moves closer to the true lag location, consistent with listeners’ perception of two sounds from separate locations. Together, these simulations suggest that location-dependent suppression in IC neurons can explain the behavioral phenomenon known as the precedence effect. PMID:20358242

Access of Hydrogen-Radicals to the Peptide-Backbone as a Measure for Estimating the Flexibility of Proteins Using Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry

PubMed Central

Takayama, Mitsuo; Nagoshi, Keishiro; Iimuro, Ryunosuke; Inatomi, Kazuma

2014-01-01

A factor for estimating the flexibility of proteins is described that uses a cleavage method of “in-source decay (ISD)” coupled with matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS). The MALDI-ISD spectra of bovine serum albumin (BSA), myoglobin and thioredoxin show discontinuous intense ion peaks originating from one-side preferential cleavage at the N-Cα bond of Xxx-Asp, Xxx-Asn, Xxx-Cys and Gly-Xxx residues. Consistent with these observations, Asp, Asn and Gly residues are also identified by other flexibility measures such as B-factor, turn preference, protection and fluorescence decay factors, while Asp, Asn, Cys and Gly residues are identified by turn preference factor based on X-ray crystallography. The results suggest that protein molecules embedded in/on MALDI matrix crystals partly maintain α-helix and that the reason some of the residues are more susceptible to ISD (Asp, Asn, Cys and Gly) and others less so (Ile and Val) is because of accessibility of the peptide backbone to hydrogen-radicals from matrix molecules. The hydrogen-radical accessibility in MALDI-ISD could therefore be adopted as a factor for measuring protein flexibility. PMID:24828203

A simple graphical method for measuring inherent safety.

PubMed

Gupta, J P; Edwards, David W

2003-11-14

Inherently safer design (ISD) concepts have been with us for over two decades since their elaboration by Kletz [Chem. Ind. 9 (1978) 124]. Interest has really taken off globally since the early nineties after several major mishaps occurred during the eighties (Bhopal, Mexico city, Piper-alfa, Philips Petroleum, to name a few). Academic and industrial research personnel have been actively involved into devising inherently safer ways of production. The regulatory bodies have also shown deep interest since ISD makes the production safer and hence their tasks easier. Research funding has also been forthcoming for new developments as well as for demonstration projects.A natural question that arises is as to how to measure ISD characteristics of a process? Several researchers have worked on this [Trans. IChemE, Process Safety Environ. Protect. B 71 (4) (1993) 252; Inherent safety in process plant design, Ph.D. Thesis, VTT Publication Number 384, Helsinki University of Technology, Espoo, Finland, 1999; Proceedings of the Mary Kay O'Connor Process Safety Center Symposium, 2001, p. 509]. Many of the proposed methods are very elegant, yet too involved for easy adoption by the industry which is scared of yet another safety analysis regime. In a recent survey [Trans. IChemE, Process Safety Environ. Prog. B 80 (2002) 115], companies desired a rather simple method to measure ISD. Simplification is also an important characteristic of ISD. It is therefore desirable to have a simple ISD measurement procedure. The ISD measurement procedure proposed in this paper can be used to differentiate between two or more processes for the same end product. The salient steps are: Consider each of the important parameters affecting the safety (e.g., temperature, pressure, toxicity, flammability, etc.) and the range of possible values these parameters can have for all the process routes under consideration for an end product. Plot these values for each step in each process route and compare. No addition of values for disparate hazards (temperature, pressure, inventory, toxicity, flammability, etc.) is being suggested to derive an overall ISD index value since that conceals the effects of different parameters. Further, addition of numbers with different units ( degrees C for temperature, atm/bar for pressure, t for inventory, etc.) is inappropriate in scientific sense. The proposed approach has a major advantage of expanding consideration in future to incorporate economic, regulatory, pollution control and worker health aspects, as well as factors such as the experience one has or 'the comfort level' one feels with each of the processes under consideration. Additionally, it would also guide the designers and decision makers into affecting specific changes in the processes to reduce the unsafe features. We demonstrate our simple approach by using the example of six routes to make methyl methacrylate as documented by Edwards and Lawrence [Trans. IChemE, Process Safety Environ. Protect. B 71 (4) (1993) 252; Quantifying inherent safety of chemical process routes, Ph.D. Thesis, Loughborough University, Loughborough, UK, 1996] and show that the decision could well have been different if addition of disparate hazards had not been done.

An Evaluation of the Application of ISD to P-3 Pilot Training.

DTIC Science & Technology

1980-06-01

THESIS AN EVALUATION OF THE APPLICATION OF ISD TO P-3 PILOT TRAINING by William Allen. Snider June 1980 Thesis Advisor: J. K. Arima Approved for...also from quasi-governmental agencies such as RAND and HUMRRO, saw great potential in the use of techniques such as modelling to increase the precision...scores. The preceding discussion suggests that organizational climate , as well as experience, is strongly related to pilot performance on NATOPS

Previous ISD Program Review.

DTIC Science & Technology

1981-03-01

report. The detail required for such a review would be unwieldy and would comsume inordinate amounts of time. The result of the document review will...attempts have been made at writing specific behavioral objectives (SBOs). These, however, have proven to be inadequate in that they are not stated in... behavioral terms (e.g., "will understand," "will have a knowledge of," etc.). C. Development of CRO/CRTs? In nearly all cases, ISD teams are just

A Monte Carlo Simulation Study of the Reliability of Intraindividual Variability

PubMed Central

Estabrook, Ryne; Grimm, Kevin J.; Bowles, Ryan P.

2012-01-01

Recent research has seen intraindividual variability (IIV) become a useful technique to incorporate trial-to-trial variability into many types of psychological studies. IIV as measured by individual standard deviations (ISDs) has shown unique prediction to several types of positive and negative outcomes (Ram, Rabbit, Stollery, & Nesselroade, 2005). One unanswered question regarding measuring intraindividual variability is its reliability and the conditions under which optimal reliability is achieved. Monte Carlo simulation studies were conducted to determine the reliability of the ISD compared to the intraindividual mean. The results indicate that ISDs generally have poor reliability and are sensitive to insufficient measurement occasions, poor test reliability, and unfavorable amounts and distributions of variability in the population. Secondary analysis of psychological data shows that use of individual standard deviations in unfavorable conditions leads to a marked reduction in statistical power, although careful adherence to underlying statistical assumptions allows their use as a basic research tool. PMID:22268793

Improving patient safety by instructional systems design

PubMed Central

Battles, J B

2006-01-01

Education and training are important elements in patient safety, both as a potential contributing factor to risks and hazards of healthcare associated injury or harm and as an intervention to be used in eliminating or preventing such harm. All too often we have relied on training as the only interventions for patient safety without examining other alternatives or realizing that, in some cases, the training systems themselves are part of the problem. One way to ensure safety by design is to apply established design principles to education and training. Instructional systems design (ISD) is a systematic method of development of education and training programs for improved learner performance. The ISD process involves five integrated steps: analysis, development, design, implementation, and evaluation (ADDIE). The application of ISD using the ADDIE approach can eliminate or prevent education and training from being a contributing factor of health associated injury or harm, and can also be effective in preventing injury or harm. PMID:17142604

Facilitating Learning in SPI through Co-design

NASA Astrophysics Data System (ADS)

Seigerroth, Ulf; Lind, Mikael

Information system development (ISD) is not a stable discipline. On the contrary, ISD must constantly cope with rapidly changing and diversifying technologies, application domains, and organizational contexts [14]. ISD is a complex and a multi dimensional phenomenon [5, 15]. As a consequence of this. Software Process Improvement (SPI) can also be regarded as a complex and multi dimensional phenomenon [16]. Problems that are accentuated in relation to SPI are: SPI is in its current shape a quite young discipline [15], there is a sparse amount of SPI-theories that can guide SPI initiatives [19], SPI-initiatives often focus on the system development (SD)-process, methods and tools which is a narrow focus that leave out important aspects such as business orientation [6], organization and social factors [4, 5] and the learning process [19]. Arguments have therefore been raised that there is a need for both researchers and practitioners to better understand SD-organisations and their practice [5].

Meeting the home-care needs of disabled older persons living in the community: does integrated services delivery make a difference?

PubMed Central

2011-01-01

Background The PRISMA Model is an innovative coordination-type integrated-service-delivery (ISD) network designed to manage and better match resources to the complex and evolving needs of elders. The goal of this study was to examine the impact of this ISD network on unmet needs among disabled older persons living in the community. Methods Using data from the PRISMA study, we compared unmet needs of elders living in the community in areas with or without an ISD network. Disabilities and unmet needs were assessed with the Functional Autonomy Measurement System (SMAF). We used growth-curve analysis to examine changes in unmet needs over time and the variables associated with initial status and change. Sociodemographic characteristics, level of disability, self-perceived health status, cognitive functioning, level of empowerment, and the hours of care received were investigated as covariates. Lastly, we report the prevalence of needs and unmet needs for 29 activities in both areas at the end of the study. Results On average, participants were 83 years old; 62% were women. They had a moderate level of disability and mild cognitive problems. On average, they received 2.07 hours/day (SD = 1.08) of disability-related care, mostly provided by family. The findings from growth-curve analysis suggest that elders living in the area where ISD was implemented and those with higher levels of disability experience better fulfillment of their needs over time. Besides the area, being a woman, living alone, having a higher level of disability, more cognitive impairments, and a lower level of empowerment were linked to initial unmet needs (r2 = 0.25; p < 0.001). At the end of the study, 35% (95% CI: 31% to 40%) of elders with needs living in the ISD area had at least one unmet need, compared to 67% (95% CI: 62% to 71%) in the other area. In general, unmet needs were highest for bathing, grooming, urinary incontinence, walking outside, seeing, hearing, preparing meals, and taking medications. Conclusions In spite of more than 30 years of home-care services in the province of Quebec, disabled older adults living in the community still have unmet needs. ISD networks such as the PRISMA Model, however, appear to offer an effective response to the long-term-care needs of the elderly. PMID:22029878

Meeting the home-care needs of disabled older persons living in the community: does integrated services delivery make a difference?

PubMed

Dubuc, Nicole; Dubois, Marie-France; Raîche, Michel; Gueye, N'Deye Rokhaya; Hébert, Réjean

2011-10-26

The PRISMA Model is an innovative coordination-type integrated-service-delivery (ISD) network designed to manage and better match resources to the complex and evolving needs of elders. The goal of this study was to examine the impact of this ISD network on unmet needs among disabled older persons living in the community. Using data from the PRISMA study, we compared unmet needs of elders living in the community in areas with or without an ISD network. Disabilities and unmet needs were assessed with the Functional Autonomy Measurement System (SMAF). We used growth-curve analysis to examine changes in unmet needs over time and the variables associated with initial status and change. Sociodemographic characteristics, level of disability, self-perceived health status, cognitive functioning, level of empowerment, and the hours of care received were investigated as covariates. Lastly, we report the prevalence of needs and unmet needs for 29 activities in both areas at the end of the study. On average, participants were 83 years old; 62% were women. They had a moderate level of disability and mild cognitive problems. On average, they received 2.07 hours/day (SD = 1.08) of disability-related care, mostly provided by family. The findings from growth-curve analysis suggest that elders living in the area where ISD was implemented and those with higher levels of disability experience better fulfillment of their needs over time. Besides the area, being a woman, living alone, having a higher level of disability, more cognitive impairments, and a lower level of empowerment were linked to initial unmet needs (r2 = 0.25; p < 0.001). At the end of the study, 35% (95% CI: 31% to 40%) of elders with needs living in the ISD area had at least one unmet need, compared to 67% (95% CI: 62% to 71%) in the other area. In general, unmet needs were highest for bathing, grooming, urinary incontinence, walking outside, seeing, hearing, preparing meals, and taking medications. In spite of more than 30 years of home-care services in the province of Quebec, disabled older adults living in the community still have unmet needs. ISD networks such as the PRISMA Model, however, appear to offer an effective response to the long-term-care needs of the elderly.

Quantitative proteomic view on secreted, cell surface-associated, and cytoplasmic proteins of the methicillin-resistant human pathogen Staphylococcus aureus under iron-limited conditions.

PubMed

Hempel, Kristina; Herbst, Florian-Alexander; Moche, Martin; Hecker, Michael; Becher, Dörte

2011-04-01

Staphylococcus aureus is capable of colonizing and infecting humans by its arsenal of surface-exposed and secreted proteins. Iron-limited conditions in mammalian body fluids serve as a major environmental signal to bacteria to express virulence determinants. Here we present a comprehensive, gel-free, and GeLC-MS/MS-based quantitative proteome profiling of S. aureus under this infection-relevant situation. (14)N(15)N metabolic labeling and three complementing approaches were combined for relative quantitative analyses of surface-associated proteins. The surface-exposed and secreted proteome profiling approaches comprise trypsin shaving, biotinylation, and precipitation of the supernatant. By analysis of the outer subproteomic and cytoplasmic protein fraction, 1210 proteins could be identified including 221 surface-associated proteins. Thus, access was enabled to 70% of the predicted cell wall-associated proteins, 80% of the predicted sortase substrates, two/thirds of lipoproteins and more than 50% of secreted and cytoplasmic proteins. For iron-deficiency, 158 surface-associated proteins were quantified. Twenty-nine proteins were found in altered amounts showing particularly surface-exposed proteins strongly induced, such as the iron-regulated surface determinant proteins IsdA, IsdB, IsdC and IsdD as well as lipid-anchored iron compound-binding proteins. The work presents a crucial subject for understanding S. aureus pathophysiology by the use of methods that allow quantitative surface proteome profiling.

Differential Function of Lip Residues in the Mechanism and Biology of an Anthrax Hemophore

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

Ekworomadu, MarCia T.; Poor, Catherine B.; Owens, Cedric P.

To replicate in mammalian hosts, bacterial pathogens must acquire iron. The majority of iron is coordinated to the protoporphyrin ring of heme, which is further bound to hemoglobin. Pathogenic bacteria utilize secreted hemophores to acquire heme from heme sources such as hemoglobin. Bacillus anthracis, the causative agent of anthrax disease, secretes two hemophores, IsdX1 and IsdX2, to acquire heme from host hemoglobin and enhance bacterial replication in iron-starved environments. Both proteins contain NEAr-iron Transporter (NEAT) domains, a conserved protein module that functions in heme acquisition in Gram-positive pathogens. Here, we report the structure of IsdX1, the first of a Gram-positivemore » hemophore, with and without bound heme. Overall, IsdX1 forms an immunoglobin-like fold that contains, similar to other NEAT proteins, a 3{sub 10}-helix near the heme-binding site. Because the mechanistic function of this helix in NEAT proteins is not yet defined, we focused on the contribution of this region to hemophore and NEAT protein activity, both biochemically and biologically in cultured cells. Site-directed mutagenesis of amino acids in and adjacent to the helix identified residues important for heme and hemoglobin association, with some mutations affecting both properties and other mutations affecting only heme stabilization. IsdX1 with mutations that reduced the ability to associate with hemoglobin and bind heme failed to restore the growth of a hemophore-deficient strain of B. anthracis on hemoglobin as the sole iron source. These data indicate that not only is the 3{sub 10}-helix important for NEAT protein biology, but also that the processes of hemoglobin and heme binding can be both separate as well as coupled, the latter function being necessary for maximal heme-scavenging activity. These studies enhance our understanding of NEAT domain and hemophore function and set the stage for structure-based inhibitor design to block NEAT domain interaction with upstream ligands.« less

High-definition computed tomography for coronary artery stent imaging: a phantom study.

PubMed

Yang, Wen Jie; Chen, Ke Min; Pang, Li Fang; Guo, Ying; Li, Jian Ying; Zhang, Huang; Pan, Zi Lai

2012-01-01

To assess the performance of a high-definition CT (HDCT) for imaging small caliber coronary stents (≤ 3 mm) by comparing different scan modes of a conventional 64-row standard-definition CT (SDCT). A cardiac phantom with twelve stents (2.5 mm and 3.0 mm in diameter) was scanned by HDCT and SDCT. The scan modes were retrospective electrocardiography (ECG)-gated helical and prospective ECG-triggered axial with tube voltages of 120 kVp and 100 kVp, respectively. The inner stent diameters (ISD) and the in-stent attenuation value (AV(in-stent)) and the in-vessel extra-stent attenuation value (AV(in-vessel)) were measured by two observers. The artificial lumen narrowing (ALN = [ISD - ISD(measured)]/ISD) and artificial attenuation increase between in-stent and in-vessel (AAI = AV(in-stent) - AV(in-vessel)) were calculated. All data was analyzed by intraclass correlation and ANOVA-test. The correlation coefficient of ISD, AV(in-vessel) and AV(in-stent) between the two observers was good. The ALNs of HDCT were statistically lower than that of SDCT (30 ± 5.7% versus 35 ± 5.4%, p < 0.05). HDCT had statistically lower AAI values than SDCT (15.7 ± 81.4 HU versus 71.4 ± 90.5 HU, p < 0.05). The prospective axial dataset demonstrated smaller ALN than the retrospective helical dataset on both HDCT and SDCT (p < 0.05). Additionally, there were no differences in ALN between the 120 kVp and 100 kVp tube voltages on HDCT (p = 0.05). High-definition CT helps improve measurement accuracy for imaging coronary stents compared to SDCT. HDCT with 100 kVp and the prospective ECG-triggered axial technique, with a lower radiation dose than 120 kVp application, may be advantageous in evaluating coronary stents with smaller calibers (≤ 3 mm).

Predicting Gene-Disease Associations Using Multiple Species Data

DTIC Science & Technology

2011-10-20

CCF-0916309) to ISD. ISD also acknowledges support from the Moncrief Grand Challenge Award. 1Fixing C − = 1, log10 C + was varied in the range 1, 2... William P Schiemann, Ste- fan N Constantinescu, Lily Huang, Roya Khosravi-Far, Hanno Steen, Muneesh Tewari, Saghi Ghaffari, Gerard C Blobe, Chi V...Austin The University of Texas at Austin 101 East 27th Street Austin, TX 78712 -1539 REPORT DOCUMENTATION PAGE b. ABSTRACT UU c . THIS PAGE UU 2. REPORT

The Invasive Species Forecasting System: A Space-Based Decision Support Infrastructure for Managing Biological Invasions

NASA Astrophysics Data System (ADS)

Most, N. N.; Kendig, D.; Wichman, K.; Pollack, N.; Ilagan, A.; Morisette, J. T.; Pedelty, J. A.; Tilmes, C.; Smith, J. A.; Pfister, R.; Schnase, J. L.; Stohgren, T. J.; Crosier, C.; Graham, J.; Newman, G.; Kalkhan, M. A.; Reich, R.

2004-12-01

The spread of invasive species is one of the most daunting environmental, economic, and human-health problems facing the United States and the World today. It is one of several grand challenge environmental problems being addressed by NASA's Science Mission Directorate through a national application partnership with the US Geological Survey. NASA and USGS are working together to develop a National Invasive Species Forecasting System (ISFS) for the management and control of invasive species on Department of Interior and adjacent lands. As part of this effort, we are using NASA's EOS Clearing House (ECHO) framework to create an Invasive Species Data Service (ISDS). The ISDS will be a networked service that integrates a suite of NASA remote sensing data providers with the ecological field data resources of the National Biological Information Infrastructure (NBII). Aggregated ISDS data will feed directly into ISFS analysis routines to produce landscape-scale predictive maps of species distributions. ISDS and the ECHO framework thus provide an efficient interface between existing NASA data systems and decision support systems that are the province of federal agencies and other national organizations. The effort significantly broadens the use of NASA data in managing the Nation's invasive species threat. In this talk, we will describe the NASA/USGS invasive species partnership, provide an overview of the Invasive Species Forecasting System, and show how we are using ECHO technologies as the middle-ware framework for a comprehensive Invasive Species Data Service.

Constraints on the Interstellar Dust Flux Based on Stardust at Home Search Results

NASA Technical Reports Server (NTRS)

Zolensky, Michael E.; Westphal, J.; Allen, C.; Anderson, D.; Bajt, S.; Bechtel, H. A.; Borg, J.; Brenker, F.; Bridges, J.; Brownlee, D. E.;

ISD3: a particokinetic model for predicting the combined effects of particle sedimentation, diffusion and dissolution on cellular dosimetry for in vitro systems

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

Thomas, Dennis G.; Smith, Jordan N.; Thrall, Brian D.

The development of particokinetic models describing the delivery of insoluble or poorly soluble nanoparticles to cells in liquid cell culture systems has improved the basis for dose-response analysis, hazard ranking from high-throughput systems, and now allows for translation of exposures across in vitro and in vivo test systems. Complimentary particokinetic models that address processes controlling delivery of both particles and released ions to cells, and the influence of particle size changes from dissolution on particle delivery for cell-culture systems would help advance our understanding of the role of particles ion dosimetry on cellular toxicology. We developed ISD3, an extension ofmore » our previously published model for insoluble particles, by deriving a specific formulation of the Population Balance Equation for soluble particles. ISD3 describes the time, concentration and particle size dependent dissolution of particles, their delivery to cells, and the delivery and uptake of ions to cells in in vitro liquid test systems. The model is modular, and can be adapted by application of any empirical model of dissolution, alternative approaches to calculating sedimentation rates, and cellular uptake or treatment of boundary conditions. We apply the model to calculate the particle and ion dosimetry of nanosilver and silver ions in vitro after calibration of two empirical models, one for particle dissolution and one for ion uptake. The results demonstrate utility and accuracy of the ISD3 framework for dosimetry in these systems. Total media ion concentration, particle concentration and total cell-associated silver time-courses were well described by the model, across 2 concentrations of 20 and 110 nm particles. ISD3 was calibrated to dissolution data for 20 nm particles as a function of serum protein concentration, but successfully described the media and cell dosimetry time-course for both particles at all concentrations and time points. We also report the finding that protein content in media has effects both on the initial rate of dissolution and the resulting near-steady state ion concentration in solution.« less

Non-thermal Processes in the Formation of Mercury's Tenuous Exosphere

NASA Astrophysics Data System (ADS)

Schaible, M. J.; Bennett, C.; Jones, B. M.; Orlando, T. M.

2017-12-01

Recent observations from the MESSENGER spacecraft orbiting Mercury have established that a quasi-trapped population of ions and electrons with 1-10 keV energy exists at a distance of about 1.5 RM (RM is Mercury's radius) around much of the planet. Recent observations from the Fast Imaging Plasma Spectrometer (FIPS), taken < 400 km from the surface, have shown a plasma cusp with energetic heavy ions (i.e. Na+ and O+ groups). The sources of these ions are not clear. A newly developed global kinetic transport model suggests that electron-stimulated desorption (ESD), and possibly light ion stimulated desorption (ISD), can directly yield ions that can be transported and dynamically accelerated to the plasma cusp regions observed by FIPS. Neutrals desorbed from the surface by ESD, ISD, photon-stimulated desorption (PSD) and meteorite impact may also be photoionized and transported/injected into the cusp region. Though the relative importance of these mechanisms in the formation of Mercury's tenuous atmosphere and the subsequent effects on the exosphere/magnetosphere dynamics are not known, it is likely that all of these contribute significantly. The goals of this work are to measure desorption cross-sections and ejection velocities for Na+, O+, and water group ions under relevant electron and ion bombardment energies. This program utilizes state-of-the art surface science capabilities to probe the role of ESD and ISD as a source of ions and neutrals present in the exosphere of Mercury. The experimental chamber is equipped with a dosing system, a cryogenic cooled temperature controlled sample holder, as well as pulsed ion and electron sources. The ESD and ISD ion yields and velocity measurements are obtained directly by sampling with a time-of-flight mass spectrometer. The measured ESD ion yields from adsorbate covered Mercury surface analogs such as the sulfur bearing minerals MgS, Na2S and K2S are low. Additionally, ISD experiments using incident protons also yielded low ion signals. These results implicate PSD and neutral desorption as dominant processes. The information obtained from these experiments can be directly incorporated into model simulations for comparison with data recently obtained by the FIPS instrument.

Long-term effect of presurgical nasoalveolar molding on growth of maxillary arch in unilateral cleft lip and palate: randomized controlled trial.

PubMed

Shetty, V; Agrawal, R K; Sailer, H F

2017-08-01

The objective of this study was to investigate the long-term effect of presurgical nasoalveolar molding (PNAM) on growth of the maxillary arch through early childhood until 6 years of age in complete unilateral cleft lip and palate (UCLP) patients presenting for PNAM at different ages. Complete UCLP patients who were treated at our centre were divided into two groups. The study group underwent PNAM and was further subdivided into three subgroups (PNAM initiated within 1 month, between 1 and 6 months, and between 6 and 12 months of age in subgroup I, II, and III, respectively). The control group did not undergo PNAM and was further subdivided into three subgroups. Patients were evaluated at T1 (first visit), T2 (before cheiloplasty), and T3 (at 6 years). Between T1and T2, the intersegment distance (ISD) reduced significantly in the study group but increased in the control group, whereas the intercanine width (ICW) in both the study and control groups did not show significant change. Between T2 and T3, ISD and ICW were reduced significantly in the control group due to arch collapse, whereas in the study group, ISD reduced slightly with ICW remaining almost similar to noncleft norms. We conclude that reduced ISD following PNAM improves arch symmetry and stability, and thus may prevent arch collapse in the long term. Copyright © 2017 International Association of Oral and Maxillofacial Surgeons. Published by Elsevier Ltd. All rights reserved.

A heteronuclear zero quantum coherence Nz-exchange experiment that resolves resonance overlap and its application to measure the rates of heme binding to the IsdC protein.

PubMed

Robson, Scott A; Peterson, Robert; Bouchard, Louis-S; Villareal, Valerie A; Clubb, Robert T

2010-07-21

Chemical exchange phenomena in NMR spectra can be quantitatively interpreted to measure the rates of ligand binding, as well as conformational and chemical rearrangements. In macromolecules, processes that occur slowly on the chemical shift time scale are frequently studied using 2D heteronuclear ZZ or N(z)-exchange spectroscopy. However, to successfully apply this method, peaks arising from each exchanging species must have unique chemical shifts in both dimensions, a condition that is often not satisfied in protein-ligand binding equilibria for (15)N nuclei. To overcome the problem of (15)N chemical shift degeneracy we developed a heteronuclear zero-quantum (and double-quantum) coherence N(z)-exchange experiment that resolves (15)N chemical shift degeneracy in the indirect dimension. We demonstrate the utility of this new experiment by measuring the heme binding kinetics of the IsdC protein from Staphylococcus aureus. Because of peak overlap, we could not reliably analyze binding kinetics using conventional methods. However, our new experiment resulted in six well-resolved systems that yielded interpretable data. We measured a relatively slow k(off) rate of heme from IsdC (<10 s(-1)), which we interpret as necessary so heme loaded IsdC has time to encounter downstream binding partners to which it passes the heme. The utility of using this new exchange experiment can be easily expanded to (13)C nuclei. We expect our heteronuclear zero-quantum coherence N(z)-exchange experiment will expand the usefulness of exchange spectroscopy to slow chemical exchange events that involve ligand binding.

Initial Spore Density Has an Influence on Ochratoxin A Content in Aspergillus ochraceus CGMCC 3.4412 in PDB and Its Interaction with Seeds.

PubMed

Li, Caiyan; Song, Yanmin; Xiong, Lu; Huang, Kunlun; Liang, Zhihong

2017-04-21

The morphology and secondary metabolism of Aspergillus spp. are associated with initial spore density (ISD). Fatty acids (FA) are involved in the biosynthesis of aflatoxins (AF) through Aspergillus quorum sensing (QS). Here, we studied how ochratoxin A (OTA) was regulated by spore density in Aspergillus ochraceus CGMCC 3.4412. The results contribute to understanding the role of spore density in morphogenesis, OTA biosynthesis, and host-pathogen interactions. When A. ochraceus was grown in Potato Dextrose Broth (PDB) media at different spore densities (from 10¹ to 10⁶ spores/mL), more OTA was produced when ISD were increased, but a higher level of ISD inhibited OTA biosynthesis. Seed infection studies showed that peanuts ( Arachis hypogaea ) and soybeans ( Glycine max ) with high FA content were more susceptible to OTA production when infected by A. ochraceus and reactive oxygen species (ROS)-induced OTA biosynthesis. These results suggested that FA was vital for OTA biosynthesis, and that oxidative stress was closely related to OTA biosynthesis in A. ochraceus .

Constraining the Origin of Impact Craters on Al Foils from the Stardust Interstellar Dust Collector

NASA Technical Reports Server (NTRS)

Stroud, Rhonda M.; Achilles, Cheri; Allen, Carlton; Ansari, Asna; Bajt, Sasa; Bassim, Nabil; Bastien, Ron S.; Bechtel, H. A.; Borg, Janet; Brenker, Frank E.;

Expedition_55_Education_Interview_with_Aransas_County_ISD_and_Port_Aransas_ISD_2018_117_1450_645746

NASA Image and Video Library

2018-04-27

SPACE STATION CREW MEMBERS DISCUSS LIFE IN SPACE WITH TEXAS STUDENTS----- Aboard the International Space Station, Expedition 55 Flight Engineers Drew Feustel and Scott Tingle of NASA discussed life and research on the orbital laboratory during an in-flight educational event April 27 with students from the Aransas County Independent School District and the Port Aransas County Independent School District in Aransas Pass, Texas. Feustel is in the second month of a six-month mission on the station, while Tingle is scheduled to return to Earth June 3 to complete his half-year in space.

The Socialization of Virtual Teams: Implications for ISD

NASA Astrophysics Data System (ADS)

Mullally, Brenda; Stapleton, Larry

Studies show that Information Systems Development (ISD) projects do not fulfil stakeholder expectations of completion time, quality and budget. (2005) study shows that development is more about social interaction and mutual understanding than following a prescribed method. Systems development is a social process where interactions help to make sense of the reality within which the system is developed (Hirschheirn et al., 1991). Research concentrates on methodology when in fact method may not be the primary problem. Authors have called for further research to investigate the true nature of the current systems development environment in real organisational situations (Fitzgerald, 2000).

Frataxin Directly Stimulates Mitochondrial Cysteine Desulfurase by Exposing Substrate-binding Sites, and a Mutant Fe-S Cluster Scaffold Protein with Frataxin-bypassing Ability Acts Similarly*♦

PubMed Central

Pandey, Alok; Gordon, Donna M.; Pain, Jayashree; Stemmler, Timothy L.; Dancis, Andrew; Pain, Debkumar

2013-01-01

For iron-sulfur (Fe-S) cluster synthesis in mitochondria, the sulfur is derived from the amino acid cysteine by the cysteine desulfurase activity of Nfs1. The enzyme binds the substrate cysteine in the pyridoxal phosphate-containing site, and a persulfide is formed on the active site cysteine in a manner depending on the accessory protein Isd11. The persulfide is then transferred to the scaffold Isu, where it combines with iron to form the Fe-S cluster intermediate. Frataxin is implicated in the process, although it is unclear where and how, and deficiency causes Friedreich ataxia. Using purified proteins and isolated mitochondria, we show here that the yeast frataxin homolog (Yfh1) directly and specifically stimulates cysteine binding to Nfs1 by exposing substrate-binding sites. This novel function of frataxin does not require iron, Isu1, or Isd11. Once bound to Nfs1, the substrate cysteine is the source of the Nfs1 persulfide, but this step is independent of frataxin and strictly dependent on Isd11. Recently, a point mutation in Isu1 was found to bypass many frataxin functions. The data presented here show that the Isu1 suppressor mimics the frataxin effects on Nfs1, explaining the bypassing activity. We propose a regulatory mechanism for the Nfs1 persulfide-forming activity. Specifically, at least two separate conformational changes must occur in the enzyme for optimum activity as follows: one is mediated by frataxin interaction that exposes the “buried” substrate-binding sites, and the other is mediated by Isd11 interaction that brings the bound substrate cysteine and the active site cysteine in proximity for persulfide formation. PMID:24217246

Alternative end-joining catalyzes robust IgH locus deletions and translocations in the combined absence of ligase 4 and Ku70.

PubMed

Boboila, Cristian; Jankovic, Mila; Yan, Catherine T; Wang, Jing H; Wesemann, Duane R; Zhang, Tingting; Fazeli, Alex; Feldman, Lauren; Nussenzweig, Andre; Nussenzweig, Michel; Alt, Frederick W

2010-02-16

Class switch recombination (CSR) in B lymphocytes is initiated by introduction of multiple DNA double-strand breaks (DSBs) into switch (S) regions that flank immunoglobulin heavy chain (IgH) constant region exons. CSR is completed by joining a DSB in the donor S mu to a DSB in a downstream acceptor S region (e.g., S gamma1) by end-joining. In normal cells, many CSR junctions are mediated by classical nonhomologous end-joining (C-NHEJ), which employs the Ku70/80 complex for DSB recognition and XRCC4/DNA ligase 4 for ligation. Alternative end-joining (A-EJ) mediates CSR, at reduced levels, in the absence of C-NHEJ, even in combined absence of Ku70 and ligase 4, demonstrating an A-EJ pathway totally distinct from C-NHEJ. Multiple DSBs are introduced into S mu during CSR, with some being rejoined or joined to each other to generate internal switch deletions (ISDs). In addition, S-region DSBs can be joined to other chromosomes to generate translocations, the level of which is increased by absence of a single C-NHEJ component (e.g., XRCC4). We asked whether ISD and S-region translocations occur in the complete absence of C-NHEJ (e.g., in Ku70/ligase 4 double-deficient B cells). We found, unexpectedly, that B-cell activation for CSR generates substantial ISD in both S mu and S gamma1 and that ISD in both is greatly increased by the absence of C-NHEJ. IgH chromosomal translocations to the c-myc oncogene also are augmented in the combined absence of Ku70 and ligase 4. We discuss the implications of these findings for A-EJ in normal and abnormal DSB repair.

High-definition computed tomography for coronary artery stents imaging compared with standard-definition 64-row multidectector computed tomography: an initial in vivo study.

PubMed

Yang, Wen Jie; Zhang, Huan; Xiao, Hua; Li, Jian Ying; Liu, Yan; Pan, Zi Lai; Chen, Ke Min

2012-01-01

The evaluation of coronary stents by computed tomography (CT) remains difficult. We assessed the imaging performance of a high-definition CT scanner (HDCT) by comparing with a conventional 64-row standard-definition CT (SDCT). One hundred thirty-eight consecutive stented patients underwent coronary CT angiography, among whom 66 patients were examined by HDCT, and 72 patients by SDCT (LightSpeed VCT XT; GE Healthcare, Waukesha, Wis). The image quality score, the inner stent diameter (ISD), and the radiation dose were analyzed. All data were statistically tested by SPSS 13.0 software (SPSS Inc, Chicago, Ill). In 72 patients examined using SDCT, 135 stents were detected; in 66 patients examined using HDCT, 119 stents were detected. The image quality score on HDCT was significantly better than that on SDCT (1.4 [SD, 0.7] vs 1.9 [SD, 0.8]). The ISD on HDCT was significantly higher than that on SDCT (1.8 [SD, 0.5] vs 1.6 [SD, 0.4]). There was no significant difference of either image quality score or ISD between the HDCT and SDCT groups in stents with 2.5-mm diameter. Images on HDCT showed significantly better image quality score and larger ISD than images on SDCT in 2.75-, 3-, and 3.5-mm stents. For patients examined by retrospective electrocardiogram-gated technique, the radiation dose on HDCT was significantly lower than that on SDCT (11.3 [SD, 2.9] vs 15.1 [SD, 3.8] mSv). High-definition CT scanner offered improved image quality and measurement accuracy for imaging coronary stents compared with conventional SDCT, providing higher spatial resolution and lower dose for evaluating coronary stents with 2.75- to 3.5-mm diameter.

Negative ion MALDI-TOF MS, ISD and PSD of neutral underivatized oligosaccharides without anionic dopant strategies, using 2,5-DHAP as a matrix.

PubMed

Jovanović, Marko; Peter-Katalinić, Jasna

2016-02-01

Oligosaccharides represent complex class of analytes for mass spectrometric analysis due to the high variety of structural isomers concerning glycosidic linkages and possible branching. A systematic study of the negative ion mode matrix-assisted laser desorption/ionization (MALDI) mass spectrometry of various neutral oligosaccharides under selection of an appropriate matrix, like 2,5-dihydroxyacetophenone (2,5-DHAP) is reported here, without commonly used anion dopant strategies. Nevertheless, we were able to generate relevant in-source decay (ISD) cross-ring fragment ions, typically obtained in the negative ion mode. Data observed indicate that the intrinsic property of the terminal non-reduced aldose is crucial for this behavior. A systematic study of the post source decay (PSD) of molecular, pseudomolecular and ISD cross-ring cleavage precursor ions is reported here. A direct comparison of the positive and negative ion mode MALDI MS1 and PSD behavior of neutral oligosaccharides could also be performed under the use of the same matrix preparation, because 2,5-DHAP is fully compatible with positive ion mode acquisition. We found that PSD spectra of deprotonated neutral oligosaccharides obtained in the negative ion mode are richer, because they contained both glycosidic and cross-ring fragment ions. However, we also found that cross-ring fragment ions are readily produced in the positive ion mode when potassiated precursor ions were selected. In addition, we show evidence that non-anionic dopants and specific instrumental parameters can also significantly influence the ISD fragmentation. Taken together, our results should increase our understanding of oligosaccharide behavior in the negative ion mode as well as increase our knowledge regarding many aspects of in-source MALDI chemistry. Copyright © 2016 John Wiley & Sons, Ltd.

Frataxin directly stimulates mitochondrial cysteine desulfurase by exposing substrate-binding sites, and a mutant Fe-S cluster scaffold protein with frataxin-bypassing ability acts similarly.

PubMed

Pandey, Alok; Gordon, Donna M; Pain, Jayashree; Stemmler, Timothy L; Dancis, Andrew; Pain, Debkumar

2013-12-27

For iron-sulfur (Fe-S) cluster synthesis in mitochondria, the sulfur is derived from the amino acid cysteine by the cysteine desulfurase activity of Nfs1. The enzyme binds the substrate cysteine in the pyridoxal phosphate-containing site, and a persulfide is formed on the active site cysteine in a manner depending on the accessory protein Isd11. The persulfide is then transferred to the scaffold Isu, where it combines with iron to form the Fe-S cluster intermediate. Frataxin is implicated in the process, although it is unclear where and how, and deficiency causes Friedreich ataxia. Using purified proteins and isolated mitochondria, we show here that the yeast frataxin homolog (Yfh1) directly and specifically stimulates cysteine binding to Nfs1 by exposing substrate-binding sites. This novel function of frataxin does not require iron, Isu1, or Isd11. Once bound to Nfs1, the substrate cysteine is the source of the Nfs1 persulfide, but this step is independent of frataxin and strictly dependent on Isd11. Recently, a point mutation in Isu1 was found to bypass many frataxin functions. The data presented here show that the Isu1 suppressor mimics the frataxin effects on Nfs1, explaining the bypassing activity. We propose a regulatory mechanism for the Nfs1 persulfide-forming activity. Specifically, at least two separate conformational changes must occur in the enzyme for optimum activity as follows: one is mediated by frataxin interaction that exposes the "buried" substrate-binding sites, and the other is mediated by Isd11 interaction that brings the bound substrate cysteine and the active site cysteine in proximity for persulfide formation.

Staphylococcus aureus Growth using Human Hemoglobin as an Iron Source

PubMed Central

Pishchany, Gleb; Haley, Kathryn P.; Skaar, Eric P.

2013-01-01

S. aureus is a pathogenic bacterium that requires iron to carry out vital metabolic functions and cause disease. The most abundant reservoir of iron inside the human host is heme, which is the cofactor of hemoglobin. To acquire iron from hemoglobin, S. aureus utilizes an elaborate system known as the iron-regulated surface determinant (Isd) system1. Components of the Isd system first bind host hemoglobin, then extract and import heme, and finally liberate iron from heme in the bacterial cytoplasm2,3. This pathway has been dissected through numerous in vitro studies4-9. Further, the contribution of the Isd system to infection has been repeatedly demonstrated in mouse models8,10-14. Establishing the contribution of the Isd system to hemoglobin-derived iron acquisition and growth has proven to be more challenging. Growth assays using hemoglobin as a sole iron source are complicated by the instability of commercially available hemoglobin, contaminating free iron in the growth medium, and toxicity associated with iron chelators. Here we present a method that overcomes these limitations. High quality hemoglobin is prepared from fresh blood and is stored in liquid nitrogen. Purified hemoglobin is supplemented into iron-deplete medium mimicking the iron-poor environment encountered by pathogens inside the vertebrate host. By starving S. aureus of free iron and supplementing with a minimally manipulated form of hemoglobin we induce growth in a manner that is entirely dependent on the ability to bind hemoglobin, extract heme, pass heme through the bacterial cell envelope and degrade heme in the cytoplasm. This assay will be useful for researchers seeking to elucidate the mechanisms of hemoglobin-/heme-derived iron acquisition in S. aureus and possibly other bacterial pathogens. PMID:23426144

Top-down and middle-down approach by fraction collection enrichment using off-line capillary electrophoresis - mass spectrometry coupling: Application to monoclonal antibody Fc/2 charge variants.

PubMed

Biacchi, Michael; Said, Nassur; Beck, Alain; Leize-Wagner, Emmanuelle; François, Yannis-Nicolas

2017-05-19

The characterization of complex protein mixtures represents one of the biggest challenge in many research fields such as biological or biopharmaceutical sciences. Out of all categories, monoclonal antibodies (mAbs) and related products drawn the most interest due to their strong therapeutic potency and specificity. Because of their intrinsic complexity due to a large number of micro-heterogeneities, there is a crucial need for analytical methods to provide comprehensive in-depth characterization of these proteins. In this work, we developed a methodology using CE-UV/MALDI-MS to perform top-down or middle-down characterization after fraction collection enrichment applied to intact protein and mAbs samples. The performance of the method was evaluated with the rapid separation of three intact protein mixture. Good robustness of CZE separation and quality of MALDI-MS spectra and MALDI-ISD spectra of each protein confirms the usefulness of sample enrichment to obtain adequate quantity of deposed protein for top-down analysis and the proof of principle of the method. In a second step, the method was applied to the middle-down characterization of Fc/2 cetuximab variants. Identification of around 9% sequence coverage of Fc/2 cetuximab fragments allows to conclude on the feasibility of the strategy for middle-down characterization of Fc/2 cetuximab variants using CE-UV/MALDI-MS. Moreover, MALDI-ISD fragmentation of Fc/2 cetuximab variants confirm separation phenomenon based on the formation of Fc/2 dimers with and without C-terminal truncation. Copyright © 2017 Elsevier B.V. All rights reserved.

Synthesis of amino acids in earth orbit: proposal

NASA Astrophysics Data System (ADS)

Kobayashi, Kensei; Kaneko, Takeo; Kouchi, Akira; Hashimoto, Hirofumi; Saito, Takeshi; Yamashita, Masamichi

1999-01-01

Organic compounds in comets are of interest since they could be the sources of the terrestrial biosphere. They are supposed to be formed in an interstellar dust (ISD) environment. We performed laboratory simulation of the formation of bioorganic compounds in ISD environments: Amino acid precursors were detected in the products after ice mixture of CO (or CH4, CH3OH), NH3 and H2O. The present results should be confirmed in actual space conditions, such as in an exposed facility of JEM. We are designing an apparatus of such exobiology experiments in earth orbit (EEEO). Basic designs proposed for EEEO, remaining problems, and expected outcome will be discussed.

iSDS: a self-configurable software-defined storage system for enterprise

NASA Astrophysics Data System (ADS)

Chen, Wen-Shyen Eric; Huang, Chun-Fang; Huang, Ming-Jen

2018-01-01

Storage is one of the most important aspects of IT infrastructure for various enterprises. But, enterprises are interested in more than just data storage; they are interested in such things as more reliable data protection, higher performance and reduced resource consumption. Traditional enterprise-grade storage satisfies these requirements at high cost. It is because traditional enterprise-grade storage is usually designed and constructed by customised field-programmable gate array to achieve high-end functionality. However, in this ever-changing environment, enterprises request storage with more flexible deployment and at lower cost. Moreover, the rise of new application fields, such as social media, big data, video streaming service etc., makes operational tasks for administrators more complex. In this article, a new storage system called intelligent software-defined storage (iSDS), based on software-defined storage, is described. More specifically, this approach advocates using software to replace features provided by traditional customised chips. To alleviate the management burden, it also advocates applying machine learning to automatically configure storage to meet dynamic requirements of workloads running on storage. This article focuses on the analysis feature of iSDS cluster by detailing its architecture and design.

Variation in practice: an analysis of Scottish Surgical Profiles ENT data.

PubMed

Yeo, J C L; Ah-See, K W; Mackenzie, K

2013-02-01

Variation in otolaryngology intervention rates is reported in the Scottish Surgical Profiles Project. Tonsillectomy is one of the selected key indicator procedures. The variation in practice was discussed nationally at the Scottish Otolaryngology Society summer meetings in 2009 and 2010. NHS Grampian had a significantly higher tonsillectomy rate compared with other Scottish NHS boards. To determine the accuracy of NHS Grampian data reported by the Information Service Division (ISD) and to record the appropriateness of listing of patients for tonsillectomy with reference to the Scottish Intercollegiate Guidelines Network (SIGN). Retrospective review of case notes and surgical records of patients who had undergone tonsillectomy between March 2007 and March 2008 in NHS Grampian. Between March 2007 and March 2008, 509 tonsillectomy cases were performed in NHS Grampian. This corresponded to the data received from ISD. 87% of tonsillectomies performed were compliant with SIGN guidelines. The Scottish otolaryngology clinicians have found the reporting of the intervention rates stimulating and challenging. Discussion of the surgical profile project regularly at national specialty meetings resulted in a preliminary detailed targeted audit of those who were persistent outliers for tonsillectomy. This refuted the presumed reasons for this variation, namely inaccurate figures from ISD and inappropriate listings by clinicians.

Microanalysis of Hypervelocity Impact Residues of Possible Interstellar Origin

NASA Technical Reports Server (NTRS)

Stroud, Rhonda M.; Achilles, Cheri; Allen, Carlton; Anasari, Asna; Bajt, Sasa; Bassim, Nabil; Bastien, Ron S.; Bechtel, H. A.; Borg, Janet; Brenker, Frank E.;

Review of field studies of aircraft noise-induced sleep disturbance.

PubMed

Michaud, David S; Fidell, Sanford; Pearsons, Karl; Campbell, Kenneth C; Keith, Stephen E

2007-01-01

Aircraft noise-induced sleep disturbance (AN-ISD) is potentially among the more serious effects of aircraft noise on people. This literature review of recent field studies of AN-ISD finds that reliable generalization of findings to population-level effects is complicated by individual differences among subjects, methodological and analytic differences among studies, and predictive relationships that account for only a small fraction of the variance in the relationship between noise exposure and sleep disturbance. It is nonetheless apparent in the studied circumstances of residential exposure that sleep disturbance effects of nighttime aircraft noise intrusions are not dramatic on a per-event basis, and that linkages between outdoor aircraft noise exposure and sleep disturbance are tenuous. It is also apparent that AN-ISD occurs more often during later than earlier parts of the night; that indoor sound levels are more closely associated with sleep disturbance than outdoor measures; and that spontaneous awakenings, or awakenings attributable to nonaircraft indoor noises, occur more often than awakenings attributed to aircraft noise. Predictions of sleep disturbance due to aircraft noise should not be based on over-simplifications of the findings of the reviewed studies, and these reports should be treated with caution in developing regulatory policy for aircraft noise.

Managing many patients with a urethral stricture: a cost-benefit analysis of treatment options.

PubMed

Ogbonna, B C

1998-05-01

To report a management method in a community where there are many patients with urethral stricture and where the short-term goal of providing some treatment to most may override the sometimes conflicting long-term aim of minimizing recurrence rates. Over a 3-year period, using optical urethrotomy in 76 patients followed by intermittent self-dilatation (ISD) in 29, urethroplasty in 28 and dilatation in three, 92 of 134 patients with a urethral stricture were treated and the outcome compared. The overall recurrence rate was 22%; a combination of urethrotomy plus ISD had a recurrence rate of 17% and gave a mean duration of follow-up without recurrence similar to that after urethroplasty. ISD significantly increased both the time before recurrence and the duration of follow-up without recurrence after urethrotomy. In addition to providing lasting treatment to many patients, urethrotomy was also 10 times cheaper, 10 times faster to perform and offered the surgeon better protection from infection with human immunodeficiency virus than did urethroplasty. Because wrongly selecting urethrotomy (resulting in a failed procedure) wastes valuable operating time and resources, the pre-operative recognition of strictures unsuitable for urethrotomy and their treatment by urethroplasty is important for overall efficiency.

Effectiveness of combined chloroquine and primaquine treatment in 14 days versus intermittent single dose regimen, in an open, non-randomized, clinical trial, to eliminate Plasmodium vivax in southern Mexico.

PubMed

Gonzalez-Ceron, Lilia; Rodriguez, Mario H; Sandoval, Marco A; Santillan, Frida; Galindo-Virgen, Sonia; Betanzos, Angel F; Rosales, Angel F; Palomeque, Olga L

2015-10-30

In Mexico, combined chloroquine (CQ) and primaquine (PQ) treatment has been used since the late 1950s to treat Plasmodium vivax infections. Although malaria transmission has declined, current treatment strategies must be evaluated to advance towards malaria elimination. The clinical and parasitological outcome of treating symptomatic P. vivax with the 14-day (T14) treatment or intermittent single dose (ISD) regimen was evaluated in southern Mexico between February 2008 and September 2010. Patients over 12 months old with P. vivax mono-infection and asexual parasitaemia ≥500 parasites/µl were treated under supervision. After diagnosis (day 0), treatment began immediately. T14 patients received CQ for 3 days (10, 10 and 5 mg/kg) and PQ daily for 14 days (0.25 mg/kg), while ISD patients received a single dose of CQ (10 mg/kg) and PQ (0.75 mg/kg) on days 0, 30, 60, 180, 210, and 240. Follow-up was done by observing clinical and laboratory (by microscopy, serology and PCR) outcome, considering two endpoints: primary blood infection clearance and clinical response at ~28 days, and the incidence of recurrent blood infection during 12 months. Parasite genotypes of primary/recurrent blood infections were analysed. During the first 28 days, no differences in parasite clearance or clinical outcome were observed between T14 (86 patients) and ISD (67 patients). On day 3, 95 % of patients in both groups showed no blood parasites, and no recurrences were detected on days 7-28. Contrarily, the therapeutic effectiveness (absence of recurrent parasitaemia) was distinct for T14 versus ISD at 12 months: 83.7 versus 50 %, respectively (p = 0.000). Symptomatic and asymptomatic infections were recorded on days 31-352. Some parasite recurrences were detected by PCR and/or serological testing. T14 was effective for opportune elimination of the primary blood infection and preventing relapse episodes. The first single dose of CQ-PQ eliminated primary blood infection as efficiently as the initial three-dose scheme of T14, but the ISD regimen should be abandoned. A single combined dose administered to symptomatic patients in remote areas while awaiting parasitological diagnosis may contribute to halting P. vivax transmission. Alternatives for meeting the challenge of T14 supervision are discussed. NIH-USA, ClinicalTrial.gov Identifier: NCT02394197.

ISD3: a particokinetic model for predicting the combined effects of particle sedimentation, diffusion and dissolution on cellular dosimetry for in vitro systems.

PubMed

Thomas, Dennis G; Smith, Jordan N; Thrall, Brian D; Baer, Donald R; Jolley, Hadley; Munusamy, Prabhakaran; Kodali, Vamsi; Demokritou, Philip; Cohen, Joel; Teeguarden, Justin G

2018-01-25

The development of particokinetic models describing the delivery of insoluble or poorly soluble nanoparticles to cells in liquid cell culture systems has improved the basis for dose-response analysis, hazard ranking from high-throughput systems, and now allows for translation of exposures across in vitro and in vivo test systems. Complimentary particokinetic models that address processes controlling delivery of both particles and released ions to cells, and the influence of particle size changes from dissolution on particle delivery for cell-culture systems would help advance our understanding of the role of particles and ion dosimetry on cellular toxicology. We developed ISD3, an extension of our previously published model for insoluble particles, by deriving a specific formulation of the Population Balance Equation for soluble particles. ISD3 describes the time, concentration and particle size dependent dissolution of particles, their delivery to cells, and the delivery and uptake of ions to cells in in vitro liquid test systems. We applied the model to calculate the particle and ion dosimetry of nanosilver and silver ions in vitro after calibration of two empirical models, one for particle dissolution and one for ion uptake. Total media ion concentration, particle concentration and total cell-associated silver time-courses were well described by the model, across 2 concentrations of 20 and 110 nm particles. ISD3 was calibrated to dissolution data for 20 nm particles as a function of serum protein concentration, but successfully described the media and cell dosimetry time-course for both particles at all concentrations and time points. We also report the finding that protein content in media affects the initial rate of dissolution and the resulting near-steady state ion concentration in solution for the systems we have studied. By combining experiments and modeling, we were able to quantify the influence of proteins on silver particle solubility, determine the relative amounts of silver ions and particles in exposed cells, and demonstrate the influence of particle size changes resulting from dissolution on particle delivery to cells in culture. ISD3 is modular and can be adapted to new applications by replacing descriptions of dissolution, sedimentation and boundary conditions with those appropriate for particles other than silver.

MIPS: a database for genomes and protein sequences.

PubMed Central

Mewes, H W; Heumann, K; Kaps, A; Mayer, K; Pfeiffer, F; Stocker, S; Frishman, D

1999-01-01

The Munich Information Center for Protein Sequences (MIPS-GSF), Martinsried near Munich, Germany, develops and maintains genome oriented databases. It is commonplace that the amount of sequence data available increases rapidly, but not the capacity of qualified manual annotation at the sequence databases. Therefore, our strategy aims to cope with the data stream by the comprehensive application of analysis tools to sequences of complete genomes, the systematic classification of protein sequences and the active support of sequence analysis and functional genomics projects. This report describes the systematic and up-to-date analysis of genomes (PEDANT), a comprehensive database of the yeast genome (MYGD), a database reflecting the progress in sequencing the Arabidopsis thaliana genome (MATD), the database of assembled, annotated human EST clusters (MEST), and the collection of protein sequence data within the framework of the PIR-International Protein Sequence Database (described elsewhere in this volume). MIPS provides access through its WWW server (http://www.mips.biochem.mpg.de) to a spectrum of generic databases, including the above mentioned as well as a database of protein families (PROTFAM), the MITOP database, and the all-against-all FASTA database. PMID:9847138

Performance of the image statistics decoder in conjunction with the Goldstone-VLA array

NASA Technical Reports Server (NTRS)

Wang, H. C.; Pitt, G. H., III

1989-01-01

During Voyager's Neptune encounter, the National Radio Astronomy Observatory's Very Large Array (VLA) will be arrayed with Goldstone antennas to receive the transmitted telemetry data from the spacecraft. The telemetry signal from the VLA will drop out periodically, resulting in a periodic drop in the received signal-to-noise ratio (SNR). The Image Statistics Decoder (ISD), which assumes a correlation between pixels, can improve the bit error rate (BER) for images during these dropout periods. Simulation results have shown that the ISD, in conjunction with the Goldstone-VLA array can provide a 3-dB gain for uncompressed images at a BER of 5.0 x 10(exp -3).

The precedence effect and its buildup and breakdown in ferrets and humans

PubMed Central

Tolnai, Sandra; Litovsky, Ruth Y.; King, Andrew J.

2014-01-01

Although many studies have examined the precedence effect (PE), few have tested whether it shows a buildup and breakdown in nonhuman animals comparable to that seen in humans. These processes are thought to reflect the ability of the auditory system to adjust to a listener's acoustic environment, and their mechanisms are still poorly understood. In this study, ferrets were trained on a two-alternative forced-choice task to discriminate the azimuthal direction of brief sounds. In one experiment, pairs of noise bursts were presented from two loudspeakers at different interstimulus delays (ISDs). Results showed that localization performance changed as a function of ISD in a manner consistent with the PE being operative. A second experiment investigated buildup and breakdown of the PE by measuring the ability of ferrets to discriminate the direction of a click pair following presentation of a conditioning train. Human listeners were also tested using this paradigm. In both species, performance was better when the test clicks and conditioning train had the same ISD but deteriorated following a switch in the direction of the leading and lagging sounds between the conditioning train and test clicks. These results suggest that ferrets, like humans, experience a buildup and breakdown of the PE. PMID:24606278

Browse diversity and iron loading in captive sumatran rhinoceroses (Dicerorhinus sumatrensis): a comparison of sanctuary and zoological populations.

PubMed

Candra, Dedi; Radcliffe, Robin W; Andriansyah; Khan, Mohammad; Tsu, I-Hsien; Paglia, Donald E

2012-09-01

Iron storage disease (ISD) is now recognized as a serious clinical disorder acquired by two species of browsing rhinoceroses, the African black (Diceros bicornis) and the Asian Sumatran (Dicerorhinus sumatrensis) rhinoceroses, when displaced from their natural habitats. The most complete knowledge of ISD comes from studies of the black rhinoceros, but the Asian species is also at risk. Sumatran rhinoceroses housed in traditional zoological settings outside of range countries have suffered significant morbidity and mortality potentially related to ISD induced by diet and/or other confinement conditions. With so few animals in captivity, very little information exists on iron loading in the Sumatran rhinoceros. To better characterize the problem, we retrospectively compared captive management conditions of Sumatran rhinoceroses housed under traditional zoological care with those in two native sanctuary environments. In general, zoo rhinoceroses are offered a paucity of plants and browse species compared with their sanctuary and wild counterparts managed in native rainforest habitats. Iron analyte levels and limited histopathologic observations in these populations suggest variable tendencies to overload iron, dependent upon differences in managed diet and individual food preferences. More detailed investigation of these markedly dissimilar ex situ populations is warranted to better understand the role of nutrition and other conditions affecting iron loading in browser rhinoceroses.

A new modal-based approach for modelling the bump foil structure in the simultaneous solution of foil-air bearing rotor dynamic problems

NASA Astrophysics Data System (ADS)

Bin Hassan, M. F.; Bonello, P.

2017-05-01

Recently-proposed techniques for the simultaneous solution of foil-air bearing (FAB) rotor dynamic problems have been limited to a simple bump foil model in which the individual bumps were modelled as independent spring-damper (ISD) subsystems. The present paper addresses this limitation by introducing a modal model of the bump foil structure into the simultaneous solution scheme. The dynamics of the corrugated bump foil structure are first studied using the finite element (FE) technique. This study is experimentally validated using a purpose-made corrugated foil structure. Based on the findings of this study, it is proposed that the dynamics of the full foil structure, including bump interaction and foil inertia, can be represented by a modal model comprising a limited number of modes. This full foil structure modal model (FFSMM) is then adapted into the rotordynamic FAB problem solution scheme, instead of the ISD model. Preliminary results using the FFSMM under static and unbalance excitation conditions are proven to be reliable by comparison against the corresponding ISD foil model results and by cross-correlating different methods for computing the deflection of the full foil structure. The rotor-bearing model is also validated against experimental and theoretical results in the literature.

Deadly outbreak of iron storage disease (ISD) in Italian birds of the family Turdidae.

PubMed

Pavone, Silvia; Salamida, Sonia; Pecorelli, Ivan; Rossi, Elisabetta; Manuali, Elisabetta

2014-09-01

A widespread deadly outbreak occurred in captive birds belonging to the family Turdidae in Italy. The present study was performed on 46 dead birds coming from 3 small decoy-bird breeders in central Italy. Only Turdus pilaris, Turdus iliacus, Turdus philomelos and Turdus merula were affected. No other species of bird held by these breeders died. A change of diet before the hunting season was reported from all breeders. Full necropsy of the animals and histological investigations of representative tissue samples were performed. Microscopical examination showed marked iron deposits in liver samples. Bacteriological investigations and molecular analysis to exclude bacterial and viral diseases were carried out. Contamination of food pellet samples by mycotoxins and analysis to detect heavy metal contaminants in food pellet samples were considered. An interesting result was the high iron content found in food pellets. It was higher than that considered suitable for birds, especially for species susceptible to development iron storage disease (ISD). Taken together, the results suggested an outbreak of ISD caused by the high iron content of food given to the birds before the hunting season. The high mortality recorded only in species belonging to the family Turdidae suggests a genetic predisposition in the affected birds.

Field Evaluation in Four NEEMO Divers of a Prototype In-suit Doppler Ultrasound Bubble Detector

NASA Technical Reports Server (NTRS)

Acock, K. E.; Gernhardt, M. L.; Conkin, J.; Powell, M. R.

2004-01-01

It is desirable to know if astronauts produce venous gas emboli (VGE) as a result of their exposure to 4.3 psia during space walks. The current prototype in-suit Doppler (ISD) ultrasound bubble detector provides an objective assessment of decompression stress by monitoring for VGE. The NOAA Aquarius habitat and NASA Extreme Environment Mission Operations (NEEMO) series of dives provided an opportunity to assess the ability of the prototype ISDs to record venous blood flow and possibly detect VGE in the pulmonary artery. From July 16 to 29,2003, four aquanauts (two males and two females) donned the ISD for a 4 hr automated recording session, following excursion dives (up to 6hrs and 29 MSW below storage depth) from air saturation at 17 MSW. Doppler recordings for 32 excursion dives were collected. The recordings consisted of approximately 150 digital wave files. Each wave file contained 24 sec of recording for each min. A 1 - 4 Doppler Quality Score (DQS) was assigned to each wave file in 17 of the 32 records evaluated to date. A DQS of 1 indicates a poor flow signal and a score of 4 indicates an optimum signal. Only 23% of all wave files had DQSs considered adequate to detect low grade VGE (Spencer I-II). The distribution of DQS in 2,356 wave files is as follows: DQS 1-56%, DQS 2-21%, DQS 3-18% and DQS 4-5%. Six of the 17 records had false positive VGE (Spencer I-IV) detected in one or more wave files per dive record. The false positive VGE recordings are attributable to air entrainment associated with drinking (verified by control tests), and this observation is important as astronauts drink water during space walks. The current ISD design provides quality recordings only over a narrow range of chest anatomy.

Is there an association between local health department organizational and administrative factors and childhood immunization coverage rates?

PubMed

Ransom, James; Schaff, Katherine; Kan, Lilly

2012-01-01

Vaccines are valuable, cost-effective tools for preventing disease and improving community health. Despite the importance and ubiquity of vaccinations, childhood immunization coverage rates vary widely by geography, race, and ethnicity. These differences have been documented for nearly two decades, but their sources are poorly understood. Between 2005 and 2008, immunization staff of the National Association of County & City Health Officials (NACCHO) visited 17 local health department (LHD) immunization programs in 10 states to assess their immunization service delivery (ISD) practices and their impact on community childhood immunization coverage rates. To qualitatively characterize LHD immunization programs and specific organizational factors underlying ISD performance challenges and successes related to community childhood immunization coverage rates. Case studies were conducted in a convenience sample of 17 geographically and demographically diverse LHDs, predicated on each LHD's childhood immunization coverage rates per data from the National Immunization Survey and/or Kindergarten Retrospective Survey. NACCHO staff selected LHDs with high (> or = 80% up to date [UTD]), moderate (> or = 75% UTD but < 80% UTD), and low (< 75% UTD) coverage rates. All immunization staff members interviewed (n = 112) were included in focus group interviews at each LHD per a standard semi-structured interview script developed by NACCHO staff. Supporting documents from each LHD immunization program were also collected for inclusion in the analysis. Content and thematic analyses of interview transcripts and supporting documents were conducted. Two thematic dimensions and six key factors emerged from the data. The dimensions of the themes were success and challenge elements. The organizational factors that were associated with success and/or challenges with regard to improving childhood immunization coverage rates included 1) leadership: organizational leadership and management related to aligning ISD with other child-focused services within the LHD; 2) resources: organizational efforts focused on aligning federal and state ISD financing with local ISD needs; 3) politics: political advocacy and partnering with local community stakeholders, including local political entities and boards of health to better organize ISD; 4) community engagement/coalitions and partnerships: partnerships, coalitions, and community engagement to support local immunization-related decision-making and prioritization; 5) credibility: agency credibility and its ability to influence community attitudes and perspectives on the health department's value in terms of child health; and 6) cultural competency of LHD staff: LHD staff members' perceptions and understandings of its community's cultural, economic, and demographic attributes shaped their responses to and understandings of the community and how they interacted with it in terms of service delivery. Public health researchers are in a nascent stage of understanding how health department organizational factors may contribute to specific community health outcomes, such as childhood immunization coverage rates. An implicit challenge to LHD immunization programs is to implement strategies that lead to equitable and high vaccination coverage among children, despite shrinking resources and community demographic differences. Community-specific attributes (e.g., poverty, lack of health insurance, or geographic isolation) affect childhood immunization coverage rates, but internal LHD aspects such as leadership and organizational culture also likely have a significant impact.

Ground-Water Quality and Potential Effects of Individual Sewage Disposal System Effluent on Ground-Water Quality in Park County, Colorado, 2001-2004

USGS Publications Warehouse

Miller, Lisa D.; Ortiz, Roderick F.

2007-01-01

In 2000, the U.S. Geological Survey, in cooperation with Park County, Colorado, began a study to evaluate ground-water quality in the various aquifers in Park County that supply water to domestic wells. The focus of this study was to identify and describe the principal natural and human factors that affect ground-water quality. In addition, the potential effects of individual sewage disposal system (ISDS) effluent on ground-water quality were evaluated. Ground-water samples were collected from domestic water-supply wells from July 2001 through October 2004 in the alluvial, crystalline-rock, sedimentary-rock, and volcanic-rock aquifers to assess general ground-water quality and effects of ISDS's on ground-water quality throughout Park County. Samples were analyzed for physical properties, major ions, nutrients, bacteria, and boron; and selected samples also were analyzed for dissolved organic carbon, human-related (wastewater) compounds, trace elements, radionuclides, and age-dating constituents (tritium and chlorofluorocarbons). Drinking-water quality is adequate for domestic use throughout Park County with a few exceptions. Only about 3 percent of wells had concentrations of fluoride, nitrate, and (or) uranium that exceeded U.S. Environmental Protection Agency national, primary drinking-water standards. These primary drinking-water standards were exceeded only in wells completed in the crystalline-rock aquifers in eastern Park County. Escherichia coli bacteria were detected in one well near Guffey, and total coliform bacteria were detected in about 11 percent of wells sampled throughout the county. The highest total coliform concentrations were measured southeast of the city of Jefferson and west of Tarryall Reservoir. Secondary drinking-water standards were exceeded more frequently. About 19 percent of wells had concentrations of one or more constituents (pH, chloride, fluoride, sulfate, and dissolved solids) that exceeded secondary drinking-water standards. Currently (2004), there is no federally enforced drinking-water standard for radon in public water-supply systems, but proposed regulations suggest a maximum contaminant level of 300 picocuries per liter (pCi/L) and an alternative maximum contaminant level of 4,000 pCi/L contingent on other mitigating remedial activities to reduce radon levels in indoor air. Radon concentrations in about 91 percent of ground-water samples were greater than or equal to 300 pCi/L, and about 25 percent had radon concentrations greater than or equal to 4,000 pCi/L. Generally, the highest radon concentrations were measured in samples collected from wells completed in the crystalline-rock aquifers. Analyses of ground-water-quality data indicate that recharge from ISDS effluent has affected some local ground-water systems in Park County. Because roughly 90 percent of domestic water used is assumed to be recharged by ISDS's, detections of human-related (wastewater) compounds in ground water in Park County are not surprising; however, concentrations of constituents associated with ISDS effluent generally are low (concentrations near the laboratory reporting levels). Thirty-eight different organic wastewater compounds were detected in 46 percent of ground-water samples, and the number of compounds detected per sample ranged from 1 to 17 compounds. Samples collected from wells with detections of wastewater compounds also had significantly higher (p-value < 0.05) chloride and boron concentrations than samples from wells with no detections of wastewater compounds. ISDS density (average subdivision lot size used to estimate ISDS density) was related to ground-water quality in Park County. Chloride and boron concentrations were significantly higher in ground-water samples collected from wells located in areas that had average subdivision lot sizes of less than 1 acre than in areas that had average subdivision lot sizes greater than or equal to 1 acre. For wells completed in the crystalline-

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

Tiered Human Integrated Sequence Search Databases for Shotgun Proteomics.

PubMed

Deutsch, Eric W; Sun, Zhi; Campbell, David S; Binz, Pierre-Alain; Farrah, Terry; Shteynberg, David; Mendoza, Luis; Omenn, Gilbert S; Moritz, Robert L

2016-11-04

The results of analysis of shotgun proteomics mass spectrometry data can be greatly affected by the selection of the reference protein sequence database against which the spectra are matched. For many species there are multiple sources from which somewhat different sequence sets can be obtained. This can lead to confusion about which database is best in which circumstances-a problem especially acute in human sample analysis. All sequence databases are genome-based, with sequences for the predicted gene and their protein translation products compiled. Our goal is to create a set of primary sequence databases that comprise the union of sequences from many of the different available sources and make the result easily available to the community. We have compiled a set of four sequence databases of varying sizes, from a small database consisting of only the ∼20,000 primary isoforms plus contaminants to a very large database that includes almost all nonredundant protein sequences from several sources. This set of tiered, increasingly complete human protein sequence databases suitable for mass spectrometry proteomics sequence database searching is called the Tiered Human Integrated Search Proteome set. In order to evaluate the utility of these databases, we have analyzed two different data sets, one from the HeLa cell line and the other from normal human liver tissue, with each of the four tiers of database complexity. The result is that approximately 0.8%, 1.1%, and 1.5% additional peptides can be identified for Tiers 2, 3, and 4, respectively, as compared with the Tier 1 database, at substantially increasing computational cost. This increase in computational cost may be worth bearing if the identification of sequence variants or the discovery of sequences that are not present in the reviewed knowledge base entries is an important goal of the study. We find that it is useful to search a data set against a simpler database, and then check the uniqueness of the discovered peptides against a more complex database. We have set up an automated system that downloads all the source databases on the first of each month and automatically generates a new set of search databases and makes them available for download at http://www.peptideatlas.org/thisp/ .

Tiered Human Integrated Sequence Search Databases for Shotgun Proteomics

PubMed Central

Deutsch, Eric W.; Sun, Zhi; Campbell, David S.; Binz, Pierre-Alain; Farrah, Terry; Shteynberg, David; Mendoza, Luis; Omenn, Gilbert S.; Moritz, Robert L.

2016-01-01

The results of analysis of shotgun proteomics mass spectrometry data can be greatly affected by the selection of the reference protein sequence database against which the spectra are matched. For many species there are multiple sources from which somewhat different sequence sets can be obtained. This can lead to confusion about which database is best in which circumstances – a problem especially acute in human sample analysis. All sequence databases are genome-based, with sequences for the predicted gene and their protein translation products compiled. Our goal is to create a set of primary sequence databases that comprise the union of sequences from many of the different available sources and make the result easily available to the community. We have compiled a set of four sequence databases of varying sizes, from a small database consisting of only the ~20,000 primary isoforms plus contaminants to a very large database that includes almost all non-redundant protein sequences from several sources. This set of tiered, increasingly complete human protein sequence databases suitable for mass spectrometry proteomics sequence database searching is called the Tiered Human Integrated Search Proteome set. In order to evaluate the utility of these databases, we have analyzed two different data sets, one from the HeLa cell line and the other from normal human liver tissue, with each of the four tiers of database complexity. The result is that approximately 0.8%, 1.1%, and 1.5% additional peptides can be identified for Tiers 2, 3, and 4, respectively, as compared with the Tier 1 database, at substantially increasing computational cost. This increase in computational cost may be worth bearing if the identification of sequence variants or the discovery of sequences that are not present in the reviewed knowledge base entries is an important goal of the study. We find that it is useful to search a data set against a simpler database, and then check the uniqueness of the discovered peptides against a more complex database. We have set up an automated system that downloads all the source databases on the first of each month and automatically generates a new set of search databases and makes them available for download at http://www.peptideatlas.org/thisp/. PMID:27577934

System, method and apparatus for generating phrases from a database

NASA Technical Reports Server (NTRS)

McGreevy, Michael W. (Inventor)

2004-01-01

A phrase generation is a method of generating sequences of terms, such as phrases, that may occur within a database of subsets containing sequences of terms, such as text. A database is provided and a relational model of the database is created. A query is then input. The query includes a term or a sequence of terms or multiple individual terms or multiple sequences of terms or combinations thereof. Next, several sequences of terms that are contextually related to the query are assembled from contextual relations in the model of the database. The sequences of terms are then sorted and output. Phrase generation can also be an iterative process used to produce sequences of terms from a relational model of a database.

Neurophysiological correlates of word processing deficits in isolated reading and isolated spelling disorders.

PubMed

Bakos, Sarolta; Landerl, Karin; Bartling, Jürgen; Schulte-Körne, Gerd; Moll, Kristina

2018-03-01

In consistent orthographies, isolated reading disorders (iRD) and isolated spelling disorders (iSD) are nearly as common as combined reading-spelling disorders (cRSD). However, the exact nature of the underlying word processing deficits in isolated versus combined literacy deficits are not well understood yet. We applied a phonological lexical decision task (including words, pseudohomophones, legal and illegal pseudowords) during ERP recording to investigate the neurophysiological correlates of lexical and sublexical word-processing in children with iRD, iSD and cRSD compared to typically developing (TD) 9-year-olds. TD children showed enhanced early sensitivity (N170) for word material and for the violation of orthographic rules compared to the other groups. Lexical orthographic effects (higher LPC amplitude for words than for pseudohomophones) were the same in the TD and iRD groups, although processing took longer in children with iRD. In the iSD and cRSD groups, lexical orthographic effects were evident and stable over time only for correctly spelled words. Orthographic representations were intact in iRD children, but word processing took longer compared to TD. Children with spelling disorders had partly missing orthographic representations. Our study is the first to specify the underlying neurophysiology of word processing deficits associated with isolated literacy deficits. Copyright © 2017 International Federation of Clinical Neurophysiology. Published by Elsevier B.V. All rights reserved.

A web-based genomic sequence database for the Streptomycetaceae: a tool for systematics and genome mining

USDA-ARS?s Scientific Manuscript database

The ARS Microbial Genome Sequence Database (http://199.133.98.43), a web-based database server, was established utilizing the BIGSdb (Bacterial Isolate Genomics Sequence Database) software package, developed at Oxford University, as a tool to manage multi-locus sequence data for the family Streptomy...

The EMBL nucleotide sequence database

PubMed Central

Stoesser, Guenter; Baker, Wendy; van den Broek, Alexandra; Camon, Evelyn; Garcia-Pastor, Maria; Kanz, Carola; Kulikova, Tamara; Lombard, Vincent; Lopez, Rodrigo; Parkinson, Helen; Redaschi, Nicole; Sterk, Peter; Stoehr, Peter; Tuli, Mary Ann

2001-01-01

The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl/) is maintained at the European Bioinformatics Institute (EBI) in an international collaboration with the DNA Data Bank of Japan (DDBJ) and GenBank at the NCBI (USA). Data is exchanged amongst the collaborating databases on a daily basis. The major contributors to the EMBL database are individual authors and genome project groups. Webin is the preferred web-based submission system for individual submitters, whilst automatic procedures allow incorporation of sequence data from large-scale genome sequencing centres and from the European Patent Office (EPO). Database releases are produced quarterly. Network services allow free access to the most up-to-date data collection via ftp, email and World Wide Web interfaces. EBI’s Sequence Retrieval System (SRS), a network browser for databanks in molecular biology, integrates and links the main nucleotide and protein databases plus many specialized databases. For sequence similarity searching a variety of tools (e.g. Blitz, Fasta, BLAST) are available which allow external users to compare their own sequences against the latest data in the EMBL Nucleotide Sequence Database and SWISS-PROT. PMID:11125039

ESTuber db: an online database for Tuber borchii EST sequences.

PubMed

Lazzari, Barbara; Caprera, Andrea; Cosentino, Cristian; Stella, Alessandra; Milanesi, Luciano; Viotti, Angelo

2007-03-08

The ESTuber database (http://www.itb.cnr.it/estuber) includes 3,271 Tuber borchii expressed sequence tags (EST). The dataset consists of 2,389 sequences from an in-house prepared cDNA library from truffle vegetative hyphae, and 882 sequences downloaded from GenBank and representing four libraries from white truffle mycelia and ascocarps at different developmental stages. An automated pipeline was prepared to process EST sequences using public software integrated by in-house developed Perl scripts. Data were collected in a MySQL database, which can be queried via a php-based web interface. Sequences included in the ESTuber db were clustered and annotated against three databases: the GenBank nr database, the UniProtKB database and a third in-house prepared database of fungi genomic sequences. An algorithm was implemented to infer statistical classification among Gene Ontology categories from the ontology occurrences deduced from the annotation procedure against the UniProtKB database. Ontologies were also deduced from the annotation of more than 130,000 EST sequences from five filamentous fungi, for intra-species comparison purposes. Further analyses were performed on the ESTuber db dataset, including tandem repeats search and comparison of the putative protein dataset inferred from the EST sequences to the PROSITE database for protein patterns identification. All the analyses were performed both on the complete sequence dataset and on the contig consensus sequences generated by the EST assembly procedure. The resulting web site is a resource of data and links related to truffle expressed genes. The Sequence Report and Contig Report pages are the web interface core structures which, together with the Text search utility and the Blast utility, allow easy access to the data stored in the database.

Compressing DNA sequence databases with coil.

PubMed

White, W Timothy J; Hendy, Michael D

2008-05-20

Publicly available DNA sequence databases such as GenBank are large, and are growing at an exponential rate. The sheer volume of data being dealt with presents serious storage and data communications problems. Currently, sequence data is usually kept in large "flat files," which are then compressed using standard Lempel-Ziv (gzip) compression - an approach which rarely achieves good compression ratios. While much research has been done on compressing individual DNA sequences, surprisingly little has focused on the compression of entire databases of such sequences. In this study we introduce the sequence database compression software coil. We have designed and implemented a portable software package, coil, for compressing and decompressing DNA sequence databases based on the idea of edit-tree coding. coil is geared towards achieving high compression ratios at the expense of execution time and memory usage during compression - the compression time represents a "one-off investment" whose cost is quickly amortised if the resulting compressed file is transmitted many times. Decompression requires little memory and is extremely fast. We demonstrate a 5% improvement in compression ratio over state-of-the-art general-purpose compression tools for a large GenBank database file containing Expressed Sequence Tag (EST) data. Finally, coil can efficiently encode incremental additions to a sequence database. coil presents a compelling alternative to conventional compression of flat files for the storage and distribution of DNA sequence databases having a narrow distribution of sequence lengths, such as EST data. Increasing compression levels for databases having a wide distribution of sequence lengths is a direction for future work.

Compressing DNA sequence databases with coil

PubMed Central

White, W Timothy J; Hendy, Michael D

2008-01-01

Background Publicly available DNA sequence databases such as GenBank are large, and are growing at an exponential rate. The sheer volume of data being dealt with presents serious storage and data communications problems. Currently, sequence data is usually kept in large "flat files," which are then compressed using standard Lempel-Ziv (gzip) compression – an approach which rarely achieves good compression ratios. While much research has been done on compressing individual DNA sequences, surprisingly little has focused on the compression of entire databases of such sequences. In this study we introduce the sequence database compression software coil. Results We have designed and implemented a portable software package, coil, for compressing and decompressing DNA sequence databases based on the idea of edit-tree coding. coil is geared towards achieving high compression ratios at the expense of execution time and memory usage during compression – the compression time represents a "one-off investment" whose cost is quickly amortised if the resulting compressed file is transmitted many times. Decompression requires little memory and is extremely fast. We demonstrate a 5% improvement in compression ratio over state-of-the-art general-purpose compression tools for a large GenBank database file containing Expressed Sequence Tag (EST) data. Finally, coil can efficiently encode incremental additions to a sequence database. Conclusion coil presents a compelling alternative to conventional compression of flat files for the storage and distribution of DNA sequence databases having a narrow distribution of sequence lengths, such as EST data. Increasing compression levels for databases having a wide distribution of sequence lengths is a direction for future work. PMID:18489794

MIPS: a database for protein sequences, homology data and yeast genome information.

PubMed Central

Mewes, H W; Albermann, K; Heumann, K; Liebl, S; Pfeiffer, F

1997-01-01

The MIPS group (Martinsried Institute for Protein Sequences) at the Max-Planck-Institute for Biochemistry, Martinsried near Munich, Germany, collects, processes and distributes protein sequence data within the framework of the tripartite association of the PIR-International Protein Sequence Database (,). MIPS contributes nearly 50% of the data input to the PIR-International Protein Sequence Database. The database is distributed on CD-ROM together with PATCHX, an exhaustive supplement of unique, unverified protein sequences from external sources compiled by MIPS. Through its WWW server (http://www.mips.biochem.mpg.de/ ) MIPS permits internet access to sequence databases, homology data and to yeast genome information. (i) Sequence similarity results from the FASTA program () are stored in the FASTA database for all proteins from PIR-International and PATCHX. The database is dynamically maintained and permits instant access to FASTA results. (ii) Starting with FASTA database queries, proteins have been classified into families and superfamilies (PROT-FAM). (iii) The HPT (hashed position tree) data structure () developed at MIPS is a new approach for rapid sequence and pattern searching. (iv) MIPS provides access to the sequence and annotation of the complete yeast genome (), the functional classification of yeast genes (FunCat) and its graphical display, the 'Genome Browser' (). A CD-ROM based on the JAVA programming language providing dynamic interactive access to the yeast genome and the related protein sequences has been compiled and is available on request. PMID:9016498

Possible cometary bioorganic compounds as sources of planetary biospheres

NASA Astrophysics Data System (ADS)

Kobayashi, K.; Takano, Y.; Kaneko, T.; Hashimoto, H.; Saito, T.

Complex organi c compound s were discovered in the coma of Comet Halley [1], whi c h suggested that they w er e p ossibl e sources of the terr estria l biosp here. It has not been confirmed, however, that bioorganic compounds like amino acids were contained in comet ary nuclei. It has been hypothe sized that cometary organic compounds wer e formed in interstellar dust particles (ISDs) [2]. A great nu mber of experiments have been done s imulat i ng the condition o ISDf environments. Amino acids were reported to form in simulated ISD environments by proton irradiation [3] and by UV irradiation [4] of simulat ed ISD ice mantles. Here w e discuss nature of bioorganic compounds formed in simul a t e d ISD environments, and compare wit h those f ormed in simulated primitive planet ary atmospheres. A gas mixt ure of carbon monoxi d e, ammonia and water was irradiated wit h high - energy protons, gamma rays or UV light. All of hydrolysates o f the products gave a wide variety of a ino acids, t ogethe r with uracil a d cytosine. When amn mixture of methanol, ammonia and w at e r (1:1:2.8) was irradiated wit h gamma rays or UV light at 77K, 293K or 353K, am ino acids were also detect e d in each hydrolysates: The G-value ( energy yield) of glycine (the most abundant amino acids in the products) was ca. 0.01, which was independent from the temp eratur e or the phase (s olid, liquid or gas). These results s ugg est that amino acid precursors can be formed in ISD environments quite effe c t i vely even if the materials were frozen in low temperature. If comets can bring sufficient kinds and amount of bioorganic co mpou nds to planets, planetary biospheres can be generated, regardless of the comp osit ion of planet ary atmospheres. It will be quite interesting to find and analyze cometary organics left in planets and satellites such as the moon, as wel l as in cometary bodies. [1] J. Kissel and F. R. Kreuger, Natur e, 326, 755 (1987). [2] J. M. Greenberg and A. Li, Adv. Space Res., 19, 981 (1997). [3] K. Kobayashi, et al., Adv. Space Res ., 16, 21 (1995); T. Kasam atsu, et al., Bull. Chem . Soc. Jpn., 70, 1021 (1997). [4] R. Briggs , et al., Origins Life Evol. Biosphere, 22, 287 (1992); K. Kobayas hi, et al., Adv. Space Res., 23, 401 (1999 ) ; M. P. Bern stein, et al., Nature, 416, 401 (2002); G. M. M unoz Caro, et al., Nature, 416, 403 (2002).

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

FARME DB: a functional antibiotic resistance element database

PubMed Central

Wallace, James C.; Port, Jesse A.; Smith, Marissa N.; Faustman, Elaine M.

2017-01-01

Antibiotic resistance (AR) is a major global public health threat but few resources exist that catalog AR genes outside of a clinical context. Current AR sequence databases are assembled almost exclusively from genomic sequences derived from clinical bacterial isolates and thus do not include many microbial sequences derived from environmental samples that confer resistance in functional metagenomic studies. These environmental metagenomic sequences often show little or no similarity to AR sequences from clinical isolates using standard classification criteria. In addition, existing AR databases provide no information about flanking sequences containing regulatory or mobile genetic elements. To help address this issue, we created an annotated database of DNA and protein sequences derived exclusively from environmental metagenomic sequences showing AR in laboratory experiments. Our Functional Antibiotic Resistant Metagenomic Element (FARME) database is a compilation of publically available DNA sequences and predicted protein sequences conferring AR as well as regulatory elements, mobile genetic elements and predicted proteins flanking antibiotic resistant genes. FARME is the first database to focus on functional metagenomic AR gene elements and provides a resource to better understand AR in the 99% of bacteria which cannot be cultured and the relationship between environmental AR sequences and antibiotic resistant genes derived from cultured isolates. Database URL: http://staff.washington.edu/jwallace/farme PMID:28077567

Brassica ASTRA: an integrated database for Brassica genomic research.

PubMed

Love, Christopher G; Robinson, Andrew J; Lim, Geraldine A C; Hopkins, Clare J; Batley, Jacqueline; Barker, Gary; Spangenberg, German C; Edwards, David

2005-01-01

Brassica ASTRA is a public database for genomic information on Brassica species. The database incorporates expressed sequences with Swiss-Prot and GenBank comparative sequence annotation as well as secondary Gene Ontology (GO) annotation derived from the comparison with Arabidopsis TAIR GO annotations. Simple sequence repeat molecular markers are identified within resident sequences and mapped onto the closely related Arabidopsis genome sequence. Bacterial artificial chromosome (BAC) end sequences derived from the Multinational Brassica Genome Project are also mapped onto the Arabidopsis genome sequence enabling users to identify candidate Brassica BACs corresponding to syntenic regions of Arabidopsis. This information is maintained in a MySQL database with a web interface providing the primary means of interrogation. The database is accessible at http://hornbill.cspp.latrobe.edu.au.

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

Overlap and diversity in antimicrobial peptide databases: compiling a non-redundant set of sequences.

PubMed

Aguilera-Mendoza, Longendri; Marrero-Ponce, Yovani; Tellez-Ibarra, Roberto; Llorente-Quesada, Monica T; Salgado, Jesús; Barigye, Stephen J; Liu, Jun

2015-08-01

The large variety of antimicrobial peptide (AMP) databases developed to date are characterized by a substantial overlap of data and similarity of sequences. Our goals are to analyze the levels of redundancy for all available AMP databases and use this information to build a new non-redundant sequence database. For this purpose, a new software tool is introduced. A comparative study of 25 AMP databases reveals the overlap and diversity among them and the internal diversity within each database. The overlap analysis shows that only one database (Peptaibol) contains exclusive data, not present in any other, whereas all sequences in the LAMP_Patent database are included in CAMP_Patent. However, the majority of databases have their own set of unique sequences, as well as some overlap with other databases. The complete set of non-duplicate sequences comprises 16 990 cases, which is almost half of the total number of reported peptides. On the other hand, the diversity analysis identifies the most and least diverse databases and proves that all databases exhibit some level of redundancy. Finally, we present a new parallel-free software, named Dover Analyzer, developed to compute the overlap and diversity between any number of databases and compile a set of non-redundant sequences. These results are useful for selecting or building a suitable representative set of AMPs, according to specific needs. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Database-independent Protein Sequencing (DiPS) Enables Full-length de Novo Protein and Antibody Sequence Determination.

PubMed

Savidor, Alon; Barzilay, Rotem; Elinger, Dalia; Yarden, Yosef; Lindzen, Moshit; Gabashvili, Alexandra; Adiv Tal, Ophir; Levin, Yishai

2017-06-01

Traditional "bottom-up" proteomic approaches use proteolytic digestion, LC-MS/MS, and database searching to elucidate peptide identities and their parent proteins. Protein sequences absent from the database cannot be identified, and even if present in the database, complete sequence coverage is rarely achieved even for the most abundant proteins in the sample. Thus, sequencing of unknown proteins such as antibodies or constituents of metaproteomes remains a challenging problem. To date, there is no available method for full-length protein sequencing, independent of a reference database, in high throughput. Here, we present Database-independent Protein Sequencing, a method for unambiguous, rapid, database-independent, full-length protein sequencing. The method is a novel combination of non-enzymatic, semi-random cleavage of the protein, LC-MS/MS analysis, peptide de novo sequencing, extraction of peptide tags, and their assembly into a consensus sequence using an algorithm named "Peptide Tag Assembler." As proof-of-concept, the method was applied to samples of three known proteins representing three size classes and to a previously un-sequenced, clinically relevant monoclonal antibody. Excluding leucine/isoleucine and glutamic acid/deamidated glutamine ambiguities, end-to-end full-length de novo sequencing was achieved with 99-100% accuracy for all benchmarking proteins and the antibody light chain. Accuracy of the sequenced antibody heavy chain, including the entire variable region, was also 100%, but there was a 23-residue gap in the constant region sequence. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

THGS: a web-based database of Transmembrane Helices in Genome Sequences

PubMed Central

Fernando, S. A.; Selvarani, P.; Das, Soma; Kumar, Ch. Kiran; Mondal, Sukanta; Ramakumar, S.; Sekar, K.

2004-01-01

Transmembrane Helices in Genome Sequences (THGS) is an interactive web-based database, developed to search the transmembrane helices in the user-interested gene sequences available in the Genome Database (GDB). The proposed database has provision to search sequence motifs in transmembrane and globular proteins. In addition, the motif can be searched in the other sequence databases (Swiss-Prot and PIR) or in the macromolecular structure database, Protein Data Bank (PDB). Further, the 3D structure of the corresponding queried motif, if it is available in the solved protein structures deposited in the Protein Data Bank, can also be visualized using the widely used graphics package RASMOL. All the sequence databases used in the present work are updated frequently and hence the results produced are up to date. The database THGS is freely available via the world wide web and can be accessed at http://pranag.physics.iisc.ernet.in/thgs/ or http://144.16.71.10/thgs/. PMID:14681375

MIPS: a database for protein sequences and complete genomes.

PubMed Central

Mewes, H W; Hani, J; Pfeiffer, F; Frishman, D

1998-01-01

The MIPS group [Munich Information Center for Protein Sequences of the German National Center for Environment and Health (GSF)] at the Max-Planck-Institute for Biochemistry, Martinsried near Munich, Germany, is involved in a number of data collection activities, including a comprehensive database of the yeast genome, a database reflecting the progress in sequencing the Arabidopsis thaliana genome, the systematic analysis of other small genomes and the collection of protein sequence data within the framework of the PIR-International Protein Sequence Database (described elsewhere in this volume). Through its WWW server (http://www.mips.biochem.mpg.de ) MIPS provides access to a variety of generic databases, including a database of protein families as well as automatically generated data by the systematic application of sequence analysis algorithms. The yeast genome sequence and its related information was also compiled on CD-ROM to provide dynamic interactive access to the 16 chromosomes of the first eukaryotic genome unraveled. PMID:9399795

The LANL hemorrhagic fever virus database, a new platform for analyzing biothreat viruses.

PubMed

Kuiken, Carla; Thurmond, Jim; Dimitrijevic, Mira; Yoon, Hyejin

2012-01-01

Hemorrhagic fever viruses (HFVs) are a diverse set of over 80 viral species, found in 10 different genera comprising five different families: arena-, bunya-, flavi-, filo- and togaviridae. All these viruses are highly variable and evolve rapidly, making them elusive targets for the immune system and for vaccine and drug design. About 55,000 HFV sequences exist in the public domain today. A central website that provides annotated sequences and analysis tools will be helpful to HFV researchers worldwide. The HFV sequence database collects and stores sequence data and provides a user-friendly search interface and a large number of sequence analysis tools, following the model of the highly regarded and widely used Los Alamos HIV database [Kuiken, C., B. Korber, and R.W. Shafer, HIV sequence databases. AIDS Rev, 2003. 5: p. 52-61]. The database uses an algorithm that aligns each sequence to a species-wide reference sequence. The NCBI RefSeq database [Sayers et al. (2011) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 39, D38-D51.] is used for this; if a reference sequence is not available, a Blast search finds the best candidate. Using this method, sequences in each genus can be retrieved pre-aligned. The HFV website can be accessed via http://hfv.lanl.gov.

Combined electrical transport and capacitance spectroscopy of a MoS2-LiNbO3 field effect transistor

NASA Astrophysics Data System (ADS)

Michailow, Wladislaw; Schülein, Florian J. R.; Möller, Benjamin; Preciado, Edwin; Nguyen, Ariana E.; von Son, Gretel; Mann, John; Hörner, Andreas L.; Wixforth, Achim; Bartels, Ludwig; Krenner, Hubert J.

2017-01-01

We have measured both the current-voltage ( ISD - VGS ) and capacitance-voltage (C- VGS ) characteristics of a MoS2-LiNbO3 field effect transistor. From the measured capacitance, we calculate the electron surface density and show that its gate voltage dependence follows the theoretical prediction resulting from the two-dimensional free electron model. This model allows us to fit the measured ISD - VGS characteristics over the entire range of VGS . Combining this experimental result with the measured current-voltage characteristics, we determine the field effect mobility as a function of gate voltage. We show that for our device, this improved combined approach yields significantly smaller values (more than a factor of 4) of the electron mobility than the conventional analysis of the current-voltage characteristics only.

Comparison of Effectiveness between Tension-Free Vaginal Tape (TVT) and Trans-Obturator Tape (TOT) in Patients with Stress Urinary Incontinence and Intrinsic Sphincter Deficiency

PubMed Central

Kim, Hyeong Gon; Park, Hyoung Keun; Paick, Sung Hyun; Choi, Woo Suk

2016-01-01

Background The aim of this study was to compare the two types of mid-urethral slings for stress urinary incontinence (SUI) with intrinsic sphincter deficiency (ISD). Methods This retrospective study included patients who underwent tension-free vaginal tape (TVT) procedure or transobturator tape (TOT) procedure by a single surgeon for SUI with ISD, defined as Valsalva leak point pressure (VLPP) < 60 cmH2O in a urodynamic study. Cases of neurogenic bladder, previous SUI surgery, and concomitant cystocele repair were excluded. The primary outcome was treatment success at 12 months, defined by self-reported absence of symptoms, no leakage episodes recorded, and no retreatment. Results Among the 157 women who were included in the final analysis, 105 patients received TVT and 52 patients received TOT. Age, underlying diseases, Stamey grade, cystocele grade, and presence of urge incontinence were not significantly different between the two groups. Urodynamic parameters including maximal urethral closing pressure, detrusor overactivity, VLPP, urethral hypermobility (Q-tip ≥ 30°), were also comparable between the two groups. Success rate was significantly higher in the TVT group than in the TOT group (95.2% vs. 82.7%, p = 0.009). On multivariate analysis, only TOT surgery (OR = 3.922, 95%CI = 1.223–12.582, p = 0.022) was a risk factor for failure following surgical treatment. Conclusion TVT is more effective than TOT in treatment of female SUI with ISD. PMID:27228092

Comparison of Effectiveness between Tension-Free Vaginal Tape (TVT) and Trans-Obturator Tape (TOT) in Patients with Stress Urinary Incontinence and Intrinsic Sphincter Deficiency.

PubMed

Kim, Hyeong Gon; Park, Hyoung Keun; Paick, Sung Hyun; Choi, Woo Suk

2016-01-01

The aim of this study was to compare the two types of mid-urethral slings for stress urinary incontinence (SUI) with intrinsic sphincter deficiency (ISD). This retrospective study included patients who underwent tension-free vaginal tape (TVT) procedure or transobturator tape (TOT) procedure by a single surgeon for SUI with ISD, defined as Valsalva leak point pressure (VLPP) < 60 cmH2O in a urodynamic study. Cases of neurogenic bladder, previous SUI surgery, and concomitant cystocele repair were excluded. The primary outcome was treatment success at 12 months, defined by self-reported absence of symptoms, no leakage episodes recorded, and no retreatment. Among the 157 women who were included in the final analysis, 105 patients received TVT and 52 patients received TOT. Age, underlying diseases, Stamey grade, cystocele grade, and presence of urge incontinence were not significantly different between the two groups. Urodynamic parameters including maximal urethral closing pressure, detrusor overactivity, VLPP, urethral hypermobility (Q-tip ≥ 30°), were also comparable between the two groups. Success rate was significantly higher in the TVT group than in the TOT group (95.2% vs. 82.7%, p = 0.009). On multivariate analysis, only TOT surgery (OR = 3.922, 95%CI = 1.223-12.582, p = 0.022) was a risk factor for failure following surgical treatment. TVT is more effective than TOT in treatment of female SUI with ISD.

Intraindividual variability in vigilance performance: does degrading visual stimuli mimic age-related "neural noise"?

PubMed

MacDonald, Stuart W S; Hultsch, David F; Bunce, David

2006-07-01

Intraindividual performance variability, or inconsistency, has been shown to predict neurological status, physiological functioning, and age differences and declines in cognition. However, potential moderating factors of inconsistency are not well understood. The present investigation examined whether inconsistency in vigilance response latencies varied as a function of time-on-task and task demands by degrading visual stimuli in three separate conditions (10%, 20%, and 30%). Participants were 24 younger women aged 21 to 30 years (M = 24.04, SD = 2.51) and 23 older women aged 61 to 83 years (M = 68.70, SD = 6.38). A measure of within-person inconsistency, the intraindividual standard deviation (ISD), was computed for each individual across reaction time (RT) trials (3 blocks of 45 event trials) for each condition of the vigilance task. Greater inconsistency was observed with increasing stimulus degradation and age, even after controlling for group differences in mean RTs and physical condition. Further, older adults were more inconsistent than younger adults for similar degradation conditions, with ISD scores for younger adults in the 30% condition approximating estimates observed for older adults in the 10% condition. Finally, a measure of perceptual sensitivity shared increasing negative associations with ISDs, with this association further modulated as a function of age but to a lesser degree by degradation condition. Results support current hypotheses suggesting that inconsistency serves as a marker of neurological integrity and are discussed in terms of potential underlying mechanisms.

Gas-phase fragmentation of peptides by MALDI in-source decay with limited amide hydrogen (1H/2H) scrambling.

PubMed

Bache, Nicolai; Rand, Kasper D; Roepstorff, Peter; Jørgensen, Thomas J D

2008-08-15

To achieve a fundamental understanding of the function of proteins and protein complexes at the molecular level, it is crucial to obtain a detailed knowledge about their dynamic and structural properties. The kinetics of backbone amide hydrogen exchange is intimately linked to the structural dynamics of the protein, and in recent years, the monitoring of the isotopic exchange of these hydrogens by mass spectrometry has become a recognized method. At present, the resolution of this method is, however, limited and single-residue resolution is typically only obtained for a few residues in a protein. It would therefore be desirable if gas-phase fragmentation could be used to localize incorporated deuterons as this would ultimately lead to single-residue resolution. A central obstacle for this approach is, however, the occurrence of intramolecular migration of amide hydrogens upon activation of the gaseous protein (i.e., hydrogen scrambling). Here we investigate the occurrence of scrambling in selectively labeled peptides upon fragmentation by matrix-assisted laser desorption/ionization in-source decay (MALDI ISD). We have utilized peptides with a unique regioselective deuterium incorporation that allows us to accurately determine the extent of scrambling upon fragmentation. Our results show that the level of scrambling upon MALDI ISD is so low that the solution deuteration pattern is readily apparent in the gas-phase fragment ions. These results suggest that MALDI ISD may prove useful for hydrogen exchange studies of purified peptides and small proteins.

High-definition computed tomography for coronary artery stents imaging: Initial evaluation of the optimal reconstruction algorithm.

PubMed

Cui, Xiaoming; Li, Tao; Li, Xin; Zhou, Weihua

2015-05-01

The aim of this study was to evaluate the in vivo performance of four image reconstruction algorithms in a high-definition CT (HDCT) scanner with improved spatial resolution for the evaluation of coronary artery stents and intrastent lumina. Thirty-nine consecutive patients with a total of 71 implanted coronary stents underwent coronary CT angiography (CCTA) on a HDCT (Discovery CT 750 HD; GE Healthcare) with the high-resolution scanning mode. Four different reconstruction algorithms (HD-stand, HD-detail; HD-stand-plus; HD-detail-plus) were applied to reconstruct the stented coronary arteries. Image quality for stent characterization was assessed. Image noise and intrastent luminal diameter were measured. The relationship between the measurement of inner stent diameter (ISD) and the true stent diameter (TSD) and stent type were analysed. The stent-dedicated kernel (HD-detail) offered the highest percentage (53.5%) of good image quality for stent characterization and the highest ratio (68.0±8.4%) of visible stent lumen/true stent lumen for luminal diameter measurement at the expense of an increased overall image noise. The Pearson correlation coefficient between the ISD and TSD measurement and spearman correlation coefficient between the ISD measurement and stent type were 0.83 and 0.48, respectively. Compared with standard reconstruction algorithms, high-definition CT imaging technique with dedicated high-resolution reconstruction algorithm provides more accurate stent characterization and intrastent luminal diameter measurement. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Sequencing artifacts in the type A influenza database and attempts to correct them

USDA-ARS?s Scientific Manuscript database

Currently over 300,000 Type A influenza gene sequences representing over 50,000 strains are available in publicly available databases. However, the quality of the sequences submitted are determined by the contributor and many sequence errors are present in the databases, which can affect the result...

A Reference Viral Database (RVDB) To Enhance Bioinformatics Analysis of High-Throughput Sequencing for Novel Virus Detection

PubMed Central

Goodacre, Norman; Aljanahi, Aisha; Nandakumar, Subhiksha; Mikailov, Mike

2018-01-01

ABSTRACT Detection of distantly related viruses by high-throughput sequencing (HTS) is bioinformatically challenging because of the lack of a public database containing all viral sequences, without abundant nonviral sequences, which can extend runtime and obscure viral hits. Our reference viral database (RVDB) includes all viral, virus-related, and virus-like nucleotide sequences (excluding bacterial viruses), regardless of length, and with overall reduced cellular sequences. Semantic selection criteria (SEM-I) were used to select viral sequences from GenBank, resulting in a first-generation viral database (VDB). This database was manually and computationally reviewed, resulting in refined, semantic selection criteria (SEM-R), which were applied to a new download of updated GenBank sequences to create a second-generation VDB. Viral entries in the latter were clustered at 98% by CD-HIT-EST to reduce redundancy while retaining high viral sequence diversity. The viral identity of the clustered representative sequences (creps) was confirmed by BLAST searches in NCBI databases and HMMER searches in PFAM and DFAM databases. The resulting RVDB contained a broad representation of viral families, sequence diversity, and a reduced cellular content; it includes full-length and partial sequences and endogenous nonretroviral elements, endogenous retroviruses, and retrotransposons. Testing of RVDBv10.2, with an in-house HTS transcriptomic data set indicated a significantly faster run for virus detection than interrogating the entirety of the NCBI nonredundant nucleotide database, which contains all viral sequences but also nonviral sequences. RVDB is publically available for facilitating HTS analysis, particularly for novel virus detection. It is meant to be updated on a regular basis to include new viral sequences added to GenBank. IMPORTANCE To facilitate bioinformatics analysis of high-throughput sequencing (HTS) data for the detection of both known and novel viruses, we have developed a new reference viral database (RVDB) that provides a broad representation of different virus species from eukaryotes by including all viral, virus-like, and virus-related sequences (excluding bacteriophages), regardless of their size. In particular, RVDB contains endogenous nonretroviral elements, endogenous retroviruses, and retrotransposons. Sequences were clustered to reduce redundancy while retaining high viral sequence diversity. A particularly useful feature of RVDB is the reduction of cellular sequences, which can enhance the run efficiency of large transcriptomic and genomic data analysis and increase the specificity of virus detection. PMID:29564396

A Reference Viral Database (RVDB) To Enhance Bioinformatics Analysis of High-Throughput Sequencing for Novel Virus Detection.

PubMed

Goodacre, Norman; Aljanahi, Aisha; Nandakumar, Subhiksha; Mikailov, Mike; Khan, Arifa S

2018-01-01

Detection of distantly related viruses by high-throughput sequencing (HTS) is bioinformatically challenging because of the lack of a public database containing all viral sequences, without abundant nonviral sequences, which can extend runtime and obscure viral hits. Our reference viral database (RVDB) includes all viral, virus-related, and virus-like nucleotide sequences (excluding bacterial viruses), regardless of length, and with overall reduced cellular sequences. Semantic selection criteria (SEM-I) were used to select viral sequences from GenBank, resulting in a first-generation viral database (VDB). This database was manually and computationally reviewed, resulting in refined, semantic selection criteria (SEM-R), which were applied to a new download of updated GenBank sequences to create a second-generation VDB. Viral entries in the latter were clustered at 98% by CD-HIT-EST to reduce redundancy while retaining high viral sequence diversity. The viral identity of the clustered representative sequences (creps) was confirmed by BLAST searches in NCBI databases and HMMER searches in PFAM and DFAM databases. The resulting RVDB contained a broad representation of viral families, sequence diversity, and a reduced cellular content; it includes full-length and partial sequences and endogenous nonretroviral elements, endogenous retroviruses, and retrotransposons. Testing of RVDBv10.2, with an in-house HTS transcriptomic data set indicated a significantly faster run for virus detection than interrogating the entirety of the NCBI nonredundant nucleotide database, which contains all viral sequences but also nonviral sequences. RVDB is publically available for facilitating HTS analysis, particularly for novel virus detection. It is meant to be updated on a regular basis to include new viral sequences added to GenBank. IMPORTANCE To facilitate bioinformatics analysis of high-throughput sequencing (HTS) data for the detection of both known and novel viruses, we have developed a new reference viral database (RVDB) that provides a broad representation of different virus species from eukaryotes by including all viral, virus-like, and virus-related sequences (excluding bacteriophages), regardless of their size. In particular, RVDB contains endogenous nonretroviral elements, endogenous retroviruses, and retrotransposons. Sequences were clustered to reduce redundancy while retaining high viral sequence diversity. A particularly useful feature of RVDB is the reduction of cellular sequences, which can enhance the run efficiency of large transcriptomic and genomic data analysis and increase the specificity of virus detection.

The Histone Database: an integrated resource for histones and histone fold-containing proteins

PubMed Central

Mariño-Ramírez, Leonardo; Levine, Kevin M.; Morales, Mario; Zhang, Suiyuan; Moreland, R. Travis; Baxevanis, Andreas D.; Landsman, David

2011-01-01

Eukaryotic chromatin is composed of DNA and protein components—core histones—that act to compactly pack the DNA into nucleosomes, the fundamental building blocks of chromatin. These nucleosomes are connected to adjacent nucleosomes by linker histones. Nucleosomes are highly dynamic and, through various core histone post-translational modifications and incorporation of diverse histone variants, can serve as epigenetic marks to control processes such as gene expression and recombination. The Histone Sequence Database is a curated collection of sequences and structures of histones and non-histone proteins containing histone folds, assembled from major public databases. Here, we report a substantial increase in the number of sequences and taxonomic coverage for histone and histone fold-containing proteins available in the database. Additionally, the database now contains an expanded dataset that includes archaeal histone sequences. The database also provides comprehensive multiple sequence alignments for each of the four core histones (H2A, H2B, H3 and H4), the linker histones (H1/H5) and the archaeal histones. The database also includes current information on solved histone fold-containing structures. The Histone Sequence Database is an inclusive resource for the analysis of chromatin structure and function focused on histones and histone fold-containing proteins. Database URL: The Histone Sequence Database is freely available and can be accessed at http://research.nhgri.nih.gov/histones/. PMID:22025671

The MAR databases: development and implementation of databases specific for marine metagenomics

PubMed Central

Klemetsen, Terje; Raknes, Inge A; Fu, Juan; Agafonov, Alexander; Balasundaram, Sudhagar V; Tartari, Giacomo; Robertsen, Espen

2018-01-01

Abstract We introduce the marine databases; MarRef, MarDB and MarCat (https://mmp.sfb.uit.no/databases/), which are publicly available resources that promote marine research and innovation. These data resources, which have been implemented in the Marine Metagenomics Portal (MMP) (https://mmp.sfb.uit.no/), are collections of richly annotated and manually curated contextual (metadata) and sequence databases representing three tiers of accuracy. While MarRef is a database for completely sequenced marine prokaryotic genomes, which represent a marine prokaryote reference genome database, MarDB includes all incomplete sequenced prokaryotic genomes regardless level of completeness. The last database, MarCat, represents a gene (protein) catalog of uncultivable (and cultivable) marine genes and proteins derived from marine metagenomics samples. The first versions of MarRef and MarDB contain 612 and 3726 records, respectively. Each record is built up of 106 metadata fields including attributes for sampling, sequencing, assembly and annotation in addition to the organism and taxonomic information. Currently, MarCat contains 1227 records with 55 metadata fields. Ontologies and controlled vocabularies are used in the contextual databases to enhance consistency. The user-friendly web interface lets the visitors browse, filter and search in the contextual databases and perform BLAST searches against the corresponding sequence databases. All contextual and sequence databases are freely accessible and downloadable from https://s1.sfb.uit.no/public/mar/. PMID:29106641

Using SQL Databases for Sequence Similarity Searching and Analysis.

PubMed

Pearson, William R; Mackey, Aaron J

2017-09-13

Relational databases can integrate diverse types of information and manage large sets of similarity search results, greatly simplifying genome-scale analyses. By focusing on taxonomic subsets of sequences, relational databases can reduce the size and redundancy of sequence libraries and improve the statistical significance of homologs. In addition, by loading similarity search results into a relational database, it becomes possible to explore and summarize the relationships between all of the proteins in an organism and those in other biological kingdoms. This unit describes how to use relational databases to improve the efficiency of sequence similarity searching and demonstrates various large-scale genomic analyses of homology-related data. It also describes the installation and use of a simple protein sequence database, seqdb_demo, which is used as a basis for the other protocols. The unit also introduces search_demo, a database that stores sequence similarity search results. The search_demo database is then used to explore the evolutionary relationships between E. coli proteins and proteins in other organisms in a large-scale comparative genomic analysis. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

Mass spectrometry-based protein identification by integrating de novo sequencing with database searching.

PubMed

Wang, Penghao; Wilson, Susan R

2013-01-01

Mass spectrometry-based protein identification is a very challenging task. The main identification approaches include de novo sequencing and database searching. Both approaches have shortcomings, so an integrative approach has been developed. The integrative approach firstly infers partial peptide sequences, known as tags, directly from tandem spectra through de novo sequencing, and then puts these sequences into a database search to see if a close peptide match can be found. However the current implementation of this integrative approach has several limitations. Firstly, simplistic de novo sequencing is applied and only very short sequence tags are used. Secondly, most integrative methods apply an algorithm similar to BLAST to search for exact sequence matches and do not accommodate sequence errors well. Thirdly, by applying these methods the integrated de novo sequencing makes a limited contribution to the scoring model which is still largely based on database searching. We have developed a new integrative protein identification method which can integrate de novo sequencing more efficiently into database searching. Evaluated on large real datasets, our method outperforms popular identification methods.

Using relational databases for improved sequence similarity searching and large-scale genomic analyses.

PubMed

Mackey, Aaron J; Pearson, William R

2004-10-01

Relational databases are designed to integrate diverse types of information and manage large sets of search results, greatly simplifying genome-scale analyses. Relational databases are essential for management and analysis of large-scale sequence analyses, and can also be used to improve the statistical significance of similarity searches by focusing on subsets of sequence libraries most likely to contain homologs. This unit describes using relational databases to improve the efficiency of sequence similarity searching and to demonstrate various large-scale genomic analyses of homology-related data. This unit describes the installation and use of a simple protein sequence database, seqdb_demo, which is used as a basis for the other protocols. These include basic use of the database to generate a novel sequence library subset, how to extend and use seqdb_demo for the storage of sequence similarity search results and making use of various kinds of stored search results to address aspects of comparative genomic analysis.

Organizing, exploring, and analyzing antibody sequence data: the case for relational-database managers.

PubMed

Owens, John

2009-01-01

Technological advances in the acquisition of DNA and protein sequence information and the resulting onrush of data can quickly overwhelm the scientist unprepared for the volume of information that must be evaluated and carefully dissected to discover its significance. Few laboratories have the luxury of dedicated personnel to organize, analyze, or consistently record a mix of arriving sequence data. A methodology based on a modern relational-database manager is presented that is both a natural storage vessel for antibody sequence information and a conduit for organizing and exploring sequence data and accompanying annotation text. The expertise necessary to implement such a plan is equal to that required by electronic word processors or spreadsheet applications. Antibody sequence projects maintained as independent databases are selectively unified by the relational-database manager into larger database families that contribute to local analyses, reports, interactive HTML pages, or exported to facilities dedicated to sophisticated sequence analysis techniques. Database files are transposable among current versions of Microsoft, Macintosh, and UNIX operating systems.

The LANL hemorrhagic fever virus database, a new platform for analyzing biothreat viruses

PubMed Central

Kuiken, Carla; Thurmond, Jim; Dimitrijevic, Mira; Yoon, Hyejin

2012-01-01

Hemorrhagic fever viruses (HFVs) are a diverse set of over 80 viral species, found in 10 different genera comprising five different families: arena-, bunya-, flavi-, filo- and togaviridae. All these viruses are highly variable and evolve rapidly, making them elusive targets for the immune system and for vaccine and drug design. About 55 000 HFV sequences exist in the public domain today. A central website that provides annotated sequences and analysis tools will be helpful to HFV researchers worldwide. The HFV sequence database collects and stores sequence data and provides a user-friendly search interface and a large number of sequence analysis tools, following the model of the highly regarded and widely used Los Alamos HIV database [Kuiken, C., B. Korber, and R.W. Shafer, HIV sequence databases. AIDS Rev, 2003. 5: p. 52–61]. The database uses an algorithm that aligns each sequence to a species-wide reference sequence. The NCBI RefSeq database [Sayers et al. (2011) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 39, D38–D51.] is used for this; if a reference sequence is not available, a Blast search finds the best candidate. Using this method, sequences in each genus can be retrieved pre-aligned. The HFV website can be accessed via http://hfv.lanl.gov. PMID:22064861

Sequencing artifacts in the type A influenza databases and attempts to correct them.

PubMed

Suarez, David L; Chester, Nikki; Hatfield, Jason

2014-07-01

There are over 276 000 influenza gene sequences in public databases, with the quality of the sequences determined by the contributor. As part of a high school class project, influenza sequences with possible errors were identified in the public databases based on the size of the gene being longer than expected, with the hypothesis that these sequences would have an error. Students contacted sequence submitters alerting them of the possible sequence issue(s) and requested they the suspect sequence(s) be correct as appropriate. Type A influenza viruses were screened, and gene segments longer than the accepted size were identified for further analysis. Attention was placed on sequences with additional nucleotides upstream or downstream of the highly conserved non-coding ends of the viral segments. A total of 1081 sequences were identified that met this criterion. Three types of errors were commonly observed: non-influenza primer sequence wasn't removed from the sequence; PCR product was cloned and plasmid sequence was included in the sequence; and Taq polymerase added an adenine at the end of the PCR product. Internal insertions of nucleotide sequence were also commonly observed, but in many cases it was unclear if the sequence was correct or actually contained an error. A total of 215 sequences, or 22.8% of the suspect sequences, were corrected in the public databases in the first year of the student project. Unfortunately 138 additional sequences with possible errors were added to the databases in the second year. Additional awareness of the need for data integrity of sequences submitted to public databases is needed to fully reap the benefits of these large data sets. © 2014 The Authors. Influenza and Other Respiratory Viruses Published by John Wiley & Sons Ltd.

Nucleotide Sequence Database Comparison for Routine Dermatophyte Identification by Internal Transcribed Spacer 2 Genetic Region DNA Barcoding.

PubMed

Normand, A C; Packeu, A; Cassagne, C; Hendrickx, M; Ranque, S; Piarroux, R

2018-05-01

Conventional dermatophyte identification is based on morphological features. However, recent studies have proposed to use the nucleotide sequences of the rRNA internal transcribed spacer (ITS) region as an identification barcode of all fungi, including dermatophytes. Several nucleotide databases are available to compare sequences and thus identify isolates; however, these databases often contain mislabeled sequences that impair sequence-based identification. We evaluated five of these databases on a clinical isolate panel. We selected 292 clinical dermatophyte strains that were prospectively subjected to an ITS2 nucleotide sequence analysis. Sequences were analyzed against the databases, and the results were compared to clusters obtained via DNA alignment of sequence segments. The DNA tree served as the identification standard throughout the study. According to the ITS2 sequence identification, the majority of strains (255/292) belonged to the genus Trichophyton , mainly T. rubrum complex ( n = 184), T. interdigitale ( n = 40), T. tonsurans ( n = 26), and T. benhamiae ( n = 5). Other genera included Microsporum (e.g., M. canis [ n = 21], M. audouinii [ n = 10], Nannizzia gypsea [ n = 3], and Epidermophyton [ n = 3]). Species-level identification of T. rubrum complex isolates was an issue. Overall, ITS DNA sequencing is a reliable tool to identify dermatophyte species given that a comprehensive and correctly labeled database is consulted. Since many inaccurate identification results exist in the DNA databases used for this study, reference databases must be verified frequently and amended in line with the current revisions of fungal taxonomy. Before describing a new species or adding a new DNA reference to the available databases, its position in the phylogenetic tree must be verified. Copyright © 2018 American Society for Microbiology.

MIPS: a database for genomes and protein sequences

PubMed Central

Mewes, H. W.; Frishman, D.; Güldener, U.; Mannhaupt, G.; Mayer, K.; Mokrejs, M.; Morgenstern, B.; Münsterkötter, M.; Rudd, S.; Weil, B.

2002-01-01

The Munich Information Center for Protein Sequences (MIPS-GSF, Neuherberg, Germany) continues to provide genome-related information in a systematic way. MIPS supports both national and European sequencing and functional analysis projects, develops and maintains automatically generated and manually annotated genome-specific databases, develops systematic classification schemes for the functional annotation of protein sequences, and provides tools for the comprehensive analysis of protein sequences. This report updates the information on the yeast genome (CYGD), the Neurospora crassa genome (MNCDB), the databases for the comprehensive set of genomes (PEDANT genomes), the database of annotated human EST clusters (HIB), the database of complete cDNAs from the DHGP (German Human Genome Project), as well as the project specific databases for the GABI (Genome Analysis in Plants) and HNB (Helmholtz–Netzwerk Bioinformatik) networks. The Arabidospsis thaliana database (MATDB), the database of mitochondrial proteins (MITOP) and our contribution to the PIR International Protein Sequence Database have been described elsewhere [Schoof et al. (2002) Nucleic Acids Res., 30, 91–93; Scharfe et al. (2000) Nucleic Acids Res., 28, 155–158; Barker et al. (2001) Nucleic Acids Res., 29, 29–32]. All databases described, the protein analysis tools provided and the detailed descriptions of our projects can be accessed through the MIPS World Wide Web server (http://mips.gsf.de). PMID:11752246

MIPS: a database for genomes and protein sequences.

PubMed

Mewes, H W; Frishman, D; Güldener, U; Mannhaupt, G; Mayer, K; Mokrejs, M; Morgenstern, B; Münsterkötter, M; Rudd, S; Weil, B

2002-01-01

The Munich Information Center for Protein Sequences (MIPS-GSF, Neuherberg, Germany) continues to provide genome-related information in a systematic way. MIPS supports both national and European sequencing and functional analysis projects, develops and maintains automatically generated and manually annotated genome-specific databases, develops systematic classification schemes for the functional annotation of protein sequences, and provides tools for the comprehensive analysis of protein sequences. This report updates the information on the yeast genome (CYGD), the Neurospora crassa genome (MNCDB), the databases for the comprehensive set of genomes (PEDANT genomes), the database of annotated human EST clusters (HIB), the database of complete cDNAs from the DHGP (German Human Genome Project), as well as the project specific databases for the GABI (Genome Analysis in Plants) and HNB (Helmholtz-Netzwerk Bioinformatik) networks. The Arabidospsis thaliana database (MATDB), the database of mitochondrial proteins (MITOP) and our contribution to the PIR International Protein Sequence Database have been described elsewhere [Schoof et al. (2002) Nucleic Acids Res., 30, 91-93; Scharfe et al. (2000) Nucleic Acids Res., 28, 155-158; Barker et al. (2001) Nucleic Acids Res., 29, 29-32]. All databases described, the protein analysis tools provided and the detailed descriptions of our projects can be accessed through the MIPS World Wide Web server (http://mips.gsf.de).

The VirusBanker database uses a Java program to allow flexible searching through Bunyaviridae sequences.

PubMed

Fourment, Mathieu; Gibbs, Mark J

2008-02-05

Viruses of the Bunyaviridae have segmented negative-stranded RNA genomes and several of them cause significant disease. Many partial sequences have been obtained from the segments so that GenBank searches give complex results. Sequence databases usually use HTML pages to mediate remote sorting, but this approach can be limiting and may discourage a user from exploring a database. The VirusBanker database contains Bunyaviridae sequences and alignments and is presented as two spreadsheets generated by a Java program that interacts with a MySQL database on a server. Sequences are displayed in rows and may be sorted using information that is displayed in columns and includes data relating to the segment, gene, protein, species, strain, sequence length, terminal sequence and date and country of isolation. Bunyaviridae sequences and alignments may be downloaded from the second spreadsheet with titles defined by the user from the columns, or viewed when passed directly to the sequence editor, Jalview. VirusBanker allows large datasets of aligned nucleotide and protein sequences from the Bunyaviridae to be compiled and winnowed rapidly using criteria that are formulated heuristically.

A public HTLV-1 molecular epidemiology database for sequence management and data mining.

PubMed

Araujo, Thessika Hialla Almeida; Souza-Brito, Leandro Inacio; Libin, Pieter; Deforche, Koen; Edwards, Dustin; de Albuquerque-Junior, Antonio Eduardo; Vandamme, Anne-Mieke; Galvao-Castro, Bernardo; Alcantara, Luiz Carlos Junior

2012-01-01

It is estimated that 15 to 20 million people are infected with the human T-cell lymphotropic virus type 1 (HTLV-1). At present, there are more than 2,000 unique HTLV-1 isolate sequences published. A central database to aggregate sequence information from a range of epidemiological aspects including HTLV-1 infections, pathogenesis, origins, and evolutionary dynamics would be useful to scientists and physicians worldwide. Described here, we have developed a database that collects and annotates sequence data and can be accessed through a user-friendly search interface. The HTLV-1 Molecular Epidemiology Database website is available at http://htlv1db.bahia.fiocruz.br/. All data was obtained from publications available at GenBank or through contact with the authors. The database was developed using Apache Webserver 2.1.6 and SGBD MySQL. The webpage interfaces were developed in HTML and sever-side scripting written in PHP. The HTLV-1 Molecular Epidemiology Database is hosted on the Gonçalo Moniz/FIOCRUZ Research Center server. There are currently 2,457 registered sequences with 2,024 (82.37%) of those sequences representing unique isolates. Of these sequences, 803 (39.67%) contain information about clinical status (TSP/HAM, 17.19%; ATL, 7.41%; asymptomatic, 12.89%; other diseases, 2.17%; and no information, 60.32%). Further, 7.26% of sequences contain information on patient gender while 5.23% of sequences provide the age of the patient. The HTLV-1 Molecular Epidemiology Database retrieves and stores annotated HTLV-1 proviral sequences from clinical, epidemiological, and geographical studies. The collected sequences and related information are now accessible on a publically available and user-friendly website. This open-access database will support clinical research and vaccine development related to viral genotype.

Corruption of genomic databases with anomalous sequence.

PubMed

Lamperti, E D; Kittelberger, J M; Smith, T F; Villa-Komaroff, L

1992-06-11

We describe evidence that DNA sequences from vectors used for cloning and sequencing have been incorporated accidentally into eukaryotic entries in the GenBank database. These incorporations were not restricted to one type of vector or to a single mechanism. Many minor instances may have been the result of simple editing errors, but some entries contained large blocks of vector sequence that had been incorporated by contamination or other accidents during cloning. Some cases involved unusual rearrangements and areas of vector distant from the normal insertion sites. Matches to vector were found in 0.23% of 20,000 sequences analyzed in GenBank Release 63. Although the possibility of anomalous sequence incorporation has been recognized since the inception of GenBank and should be easy to avoid, recent evidence suggests that this problem is increasing more quickly than the database itself. The presence of anomalous sequence may have serious consequences for the interpretation and use of database entries, and will have an impact on issues of database management. The incorporated vector fragments described here may also be useful for a crude estimate of the fidelity of sequence information in the database. In alignments with well-defined ends, the matching sequences showed 96.8% identity to vector; when poorer matches with arbitrary limits were included, the aggregate identity to vector sequence was 94.8%.

The MAR databases: development and implementation of databases specific for marine metagenomics.

PubMed

Klemetsen, Terje; Raknes, Inge A; Fu, Juan; Agafonov, Alexander; Balasundaram, Sudhagar V; Tartari, Giacomo; Robertsen, Espen; Willassen, Nils P

2018-01-04

We introduce the marine databases; MarRef, MarDB and MarCat (https://mmp.sfb.uit.no/databases/), which are publicly available resources that promote marine research and innovation. These data resources, which have been implemented in the Marine Metagenomics Portal (MMP) (https://mmp.sfb.uit.no/), are collections of richly annotated and manually curated contextual (metadata) and sequence databases representing three tiers of accuracy. While MarRef is a database for completely sequenced marine prokaryotic genomes, which represent a marine prokaryote reference genome database, MarDB includes all incomplete sequenced prokaryotic genomes regardless level of completeness. The last database, MarCat, represents a gene (protein) catalog of uncultivable (and cultivable) marine genes and proteins derived from marine metagenomics samples. The first versions of MarRef and MarDB contain 612 and 3726 records, respectively. Each record is built up of 106 metadata fields including attributes for sampling, sequencing, assembly and annotation in addition to the organism and taxonomic information. Currently, MarCat contains 1227 records with 55 metadata fields. Ontologies and controlled vocabularies are used in the contextual databases to enhance consistency. The user-friendly web interface lets the visitors browse, filter and search in the contextual databases and perform BLAST searches against the corresponding sequence databases. All contextual and sequence databases are freely accessible and downloadable from https://s1.sfb.uit.no/public/mar/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Breathe Easy at Home

PubMed Central

Rosofsky, Anna; Reid, Margaret; Sandel, Megan; Zielenbach, Molly; Murphy, Johnna; Scammell, Madeleine K.

2016-01-01

The Breathe Easy at Home Program enables clinicians to refer asthmatic patients to Boston Inspectional Services Department (ISD) if they suspect housing conditions trigger symptoms. The authors conducted one-on-one interviews with clinicians (n = 10) who referred patients, and focus groups with inspectors from the ISD (n = 9) and a variety of stakeholders (n = 13), to gain insight into program function and implementation. Clinician interviews revealed inconsistencies in enrollment approaches, dissatisfaction with the web-based system, and patient follow-up difficulties. Inspectors identified barriers to working effectively with residents and landlords, and the stakeholder focus group highlighted successes of an unusual institutional collaboration. Interviews and focus groups identified strong and personal rapport between clinicians, inspectors, and patients as key to program retention, and that participating families required additional support throughout the process. Despite recommendations for improvement in program implementation, clinicians, inspectors, and stakeholders felt that the program overall improved both the home environment and asthma outcomes. PMID:28462348

Frail elderly patients. New model for integrated service delivery.

PubMed Central

Hébert, Rejean; Durand, Pierre J.; Dubuc, Nicole; Tourigny, André

2003-01-01

PROBLEM BEING ADDRESSED: Given the complex needs of frail older people and the multiplicity of care providers and services, care for this clientele lacks continuity. OBJECTIVE OF PROGRAM: Integrated service delivery (ISD) systems have been developed to improve continuity and increase the efficacy and efficiency of services. PROGRAM DESCRIPTION: The Program of Research to Integrate Services for the Maintenance of Autonomy (PRISMA) is an innovative ISD model based on coordination. It includes coordination between decision makers and managers of different organizations and services; a single entry point; a case-management process; individualized service plans; a single assessment instrument based on clients' functional autonomy, coupled with a case-mix classification system; and a computerized clinical chart for communicating between institutions and professionals for client monitoring. CONCLUSION: Preliminary results on the efficacy of this model showed a decreased incidence of functional decline, a decreased burden for caregivers, and a smaller proportion of older people wishing to enter institutions. PMID:12943358

"Children at risk": development, implementation, and effectiveness of a school-based violence intervention and prevention program.

PubMed

Walker, Sharon L; Smith, Donald J

2009-01-01

Violence impacts the lives of children on a daily basis. In their communities, they witness drive-by shootings, drug deals, and violence in their schools while many endure abuse, neglect, and violent behavior in their homes. Because the traumatizing impact of such exposure disrupts a child's ability to concentrate and learn, the Dallas Independent School District (ISD) sought content expertise to develop a training vehicle for school district professionals. The program aimed to raise the awareness of educators to problems related to domestic violence and the myriad of circumstances at home and in the community that lead to exposure to violence. Approximately 15,000 faculty and staff of Dallas ISD were educated in the identification, intervention, and prevention of exposure to violence. Referrals and inquiries related to abuse have increased (approximately 70%) while the city of Dallas has witnessed a drop in the number of domestic violence and child abuse offenses.

MIPS: analysis and annotation of proteins from whole genomes

PubMed Central

Mewes, H. W.; Amid, C.; Arnold, R.; Frishman, D.; Güldener, U.; Mannhaupt, G.; Münsterkötter, M.; Pagel, P.; Strack, N.; Stümpflen, V.; Warfsmann, J.; Ruepp, A.

2004-01-01

The Munich Information Center for Protein Sequences (MIPS-GSF), Neuherberg, Germany, provides protein sequence-related information based on whole-genome analysis. The main focus of the work is directed toward the systematic organization of sequence-related attributes as gathered by a variety of algorithms, primary information from experimental data together with information compiled from the scientific literature. MIPS maintains automatically generated and manually annotated genome-specific databases, develops systematic classification schemes for the functional annotation of protein sequences and provides tools for the comprehensive analysis of protein sequences. This report updates the information on the yeast genome (CYGD), the Neurospora crassa genome (MNCDB), the database of complete cDNAs (German Human Genome Project, NGFN), the database of mammalian protein–protein interactions (MPPI), the database of FASTA homologies (SIMAP), and the interface for the fast retrieval of protein-associated information (QUIPOS). The Arabidopsis thaliana database, the rice database, the plant EST databases (MATDB, MOsDB, SPUTNIK), as well as the databases for the comprehensive set of genomes (PEDANT genomes) are described elsewhere in the 2003 and 2004 NAR database issues, respectively. All databases described, and the detailed descriptions of our projects can be accessed through the MIPS web server (http://mips.gsf.de). PMID:14681354

MIPS: analysis and annotation of proteins from whole genomes.

PubMed

Mewes, H W; Amid, C; Arnold, R; Frishman, D; Güldener, U; Mannhaupt, G; Münsterkötter, M; Pagel, P; Strack, N; Stümpflen, V; Warfsmann, J; Ruepp, A

2004-01-01

The Munich Information Center for Protein Sequences (MIPS-GSF), Neuherberg, Germany, provides protein sequence-related information based on whole-genome analysis. The main focus of the work is directed toward the systematic organization of sequence-related attributes as gathered by a variety of algorithms, primary information from experimental data together with information compiled from the scientific literature. MIPS maintains automatically generated and manually annotated genome-specific databases, develops systematic classification schemes for the functional annotation of protein sequences and provides tools for the comprehensive analysis of protein sequences. This report updates the information on the yeast genome (CYGD), the Neurospora crassa genome (MNCDB), the database of complete cDNAs (German Human Genome Project, NGFN), the database of mammalian protein-protein interactions (MPPI), the database of FASTA homologies (SIMAP), and the interface for the fast retrieval of protein-associated information (QUIPOS). The Arabidopsis thaliana database, the rice database, the plant EST databases (MATDB, MOsDB, SPUTNIK), as well as the databases for the comprehensive set of genomes (PEDANT genomes) are described elsewhere in the 2003 and 2004 NAR database issues, respectively. All databases described, and the detailed descriptions of our projects can be accessed through the MIPS web server (http://mips.gsf.de).

AgdbNet – antigen sequence database software for bacterial typing

PubMed Central

Jolley, Keith A; Maiden, Martin CJ

2006-01-01

Background Bacterial typing schemes based on the sequences of genes encoding surface antigens require databases that provide a uniform, curated, and widely accepted nomenclature of the variants identified. Due to the differences in typing schemes, imposed by the diversity of genes targeted, creating these databases has typically required the writing of one-off code to link the database to a web interface. Here we describe agdbNet, widely applicable web database software that facilitates simultaneous BLAST querying of multiple loci using either nucleotide or peptide sequences. Results Databases are described by XML files that are parsed by a Perl CGI script. Each database can have any number of loci, which may be defined by nucleotide and/or peptide sequences. The software is currently in use on at least five public databases for the typing of Neisseria meningitidis, Campylobacter jejuni and Streptococcus equi and can be set up to query internal isolate tables or suitably-configured external isolate databases, such as those used for multilocus sequence typing. The style of the resulting website can be fully configured by modifying stylesheets and through the use of customised header and footer files that surround the output of the script. Conclusion The software provides a rapid means of setting up customised Internet antigen sequence databases. The flexible configuration options enable typing schemes with differing requirements to be accommodated. PMID:16790057

Undergraduate courses for enhancing design ability in naval architecture

NASA Astrophysics Data System (ADS)

Lee, Kyu-Yeul; Ku, Namkug; Cha, Ju-Hwan

2013-09-01

Contemporary lectures in undergraduate engineering courses typically focus on teaching major technical knowledge-based theories in a limited time. Therefore, most lectures do not allow the students to gain understanding of how the theories are applied, especially in Naval Architecture and Ocean Engineering departments. Shipyards require students to acquire practical ship design skills in undergraduate courses. To meet this requirement, two lectures are organized by the authors; namely, "Planning Procedure of Naval Architecture & Ocean Engineering" (PNAOE) and "Innovative Ship Design" (ISD). The concept of project-based and collaborative learning is applied in these two lectures. In the PNAOE lecture, sophomores receive instruction in the designing and building of model ships, and the students' work is evaluated in a model ship contest. This curriculum enables students to understand the concepts of ship design and production. In the ISD lecture, seniors learn how to develop their creative ideas about ship design and communicate with members of group. They are encouraged to cooperate with others and understand the ship design process. In the capstone design course, students receive guidance to facilitate understanding of how the knowledge from their sophomore or junior classes, such as fluid mechanics, statics, and dynamics, can be applied to practical ship design. Students are also encouraged to compete in the ship design contest organized by the Society of Naval Architects of Korea. Moreover, the effectiveness of project-based and collaborative learning for enhancing interest in the shipbuilding Industry and understanding the ship design process is demonstrated by citing the PNAOE and ISD lectures as examples.

Induced sputum deposition improves diagnostic yields of pulmonary alveolar proteinosis: A clinicopathological and methodological study of 17 cases.

PubMed

Huang, Ziling; Yi, Xianghua; Luo, Benfang; Zhu, Jian; Wu, Yunjin; Jiang, Wenxia; Chu, Haiqing; Yang, Zhongmin; Li, Shuai; Zhu, Hailong; Zhang, Suxia; Zhang, Lanjing; Zeng, Yu

2016-01-01

Pulmonary alveolar proteinosis (PAP) is a rare diffuse lung disease characterized by the accumulation of intra-alveolar lipoprotein-like surfactants. Lung core biopsy and bronchoalveolar lavage (BAL) fluid are currently the two major sources of sampling for diagnosis. In the present study, we assessed the value of induced sputum in diagnosing PAP by transmission electron microscopy and examined the PAP 2-year death rate in Asians. Transmission electron microscopy was performed on the samples from 17 patients with PAP, 13 patients with inflammatory lung diseases, and 13 healthy adults. The PAP patients were followed up for 3-156 months, and inflammatory lung diseases patients or healthy adults for 12-36 months. The ultrastructural features including diagnostic lamellar bodies of induced sputum deposition (ISD) samples were similar to that of the BAL fluid sediment. However, the rates of lamellar bodies were 73.7% in the ISD group, significantly higher than the spontaneous sputum deposition (SSD) group (42.1%, P < .0487) and similar to the BAL sediment (76.2%) and the lung biopsy (54.5%) groups. The overall 2-year death rate of our PAP patients was 17.6% (3/17), not statistically different from the healthy adults and patients with inflammatory diseases (0/13, P = .237 for both). ISD may be the preferred non-invasive sampling method for diagnosing PAP by electronic microscopy because of the higher diagnostic yield than SSD. The diagnostic yields of this noninvasive method were similar to that of lung core biopsy and BAL.

Comparison of thermal and microwave paleointensity estimates in specimens that violate Thellier's laws

NASA Astrophysics Data System (ADS)

Grappone, J. M., Jr.; Biggin, A. J.; Barrett, T. J.; Hill, M. J.

2017-12-01

Deep in the Earth, thermodynamic behavior drives the geodynamo and creates the Earth's magnetic field. Determining how the strength of the field, its paleointensity (PI), varies with time, is vital to our understanding of Earth's evolution. Thellier-style paleointensity experiments assume the presence of non-interacting, single domain (SD) magnetic particles, which follow Thellier's laws. Most natural rocks however, contain larger, multi-domain (MD) or interacting single domain (ISD) particles that often violate these laws and cause experiments to fail. Even for samples that pass reliability criteria designed to minimize the impact of MD or ISD grains, different PI techniques can give systematically different estimates, implying violation of Thellier's laws. Our goal is to identify any disparities in PI results that may be explainable by protocol-specific MD and ISD behavior and determine optimum methods to maximize accuracy. Volcanic samples from the Hawai'ian SOH1 borehole previously produced method-dependent PI estimates. Previous studies showed consistently lower PI values when using a microwave (MW) system and the perpendicular method than using the original thermal Thellier-Thellier (OT) technique. However, the data were ambiguous regarding the cause of the discrepancy. The diverging estimates appeared to be either the result of using OT instead of the perpendicular method or the result of using MW protocols instead of thermal protocols. Comparison experiments were conducted using the thermal perpendicular method and microwave OT technique to bridge the gap. Preliminary data generally show that the perpendicular method gives lower estimates than OT for comparable Hlab values. MW estimates are also generally lower than thermal estimates using the same protocol.

BioWarehouse: a bioinformatics database warehouse toolkit

PubMed Central

Lee, Thomas J; Pouliot, Yannick; Wagner, Valerie; Gupta, Priyanka; Stringer-Calvert, David WJ; Tenenbaum, Jessica D; Karp, Peter D

2006-01-01

Background This article addresses the problem of interoperation of heterogeneous bioinformatics databases. Results We introduce BioWarehouse, an open source toolkit for constructing bioinformatics database warehouses using the MySQL and Oracle relational database managers. BioWarehouse integrates its component databases into a common representational framework within a single database management system, thus enabling multi-database queries using the Structured Query Language (SQL) but also facilitating a variety of database integration tasks such as comparative analysis and data mining. BioWarehouse currently supports the integration of a pathway-centric set of databases including ENZYME, KEGG, and BioCyc, and in addition the UniProt, GenBank, NCBI Taxonomy, and CMR databases, and the Gene Ontology. Loader tools, written in the C and JAVA languages, parse and load these databases into a relational database schema. The loaders also apply a degree of semantic normalization to their respective source data, decreasing semantic heterogeneity. The schema supports the following bioinformatics datatypes: chemical compounds, biochemical reactions, metabolic pathways, proteins, genes, nucleic acid sequences, features on protein and nucleic-acid sequences, organisms, organism taxonomies, and controlled vocabularies. As an application example, we applied BioWarehouse to determine the fraction of biochemically characterized enzyme activities for which no sequences exist in the public sequence databases. The answer is that no sequence exists for 36% of enzyme activities for which EC numbers have been assigned. These gaps in sequence data significantly limit the accuracy of genome annotation and metabolic pathway prediction, and are a barrier for metabolic engineering. Complex queries of this type provide examples of the value of the data warehousing approach to bioinformatics research. Conclusion BioWarehouse embodies significant progress on the database integration problem for bioinformatics. PMID:16556315

BioWarehouse: a bioinformatics database warehouse toolkit.

PubMed

Lee, Thomas J; Pouliot, Yannick; Wagner, Valerie; Gupta, Priyanka; Stringer-Calvert, David W J; Tenenbaum, Jessica D; Karp, Peter D

2006-03-23

This article addresses the problem of interoperation of heterogeneous bioinformatics databases. We introduce BioWarehouse, an open source toolkit for constructing bioinformatics database warehouses using the MySQL and Oracle relational database managers. BioWarehouse integrates its component databases into a common representational framework within a single database management system, thus enabling multi-database queries using the Structured Query Language (SQL) but also facilitating a variety of database integration tasks such as comparative analysis and data mining. BioWarehouse currently supports the integration of a pathway-centric set of databases including ENZYME, KEGG, and BioCyc, and in addition the UniProt, GenBank, NCBI Taxonomy, and CMR databases, and the Gene Ontology. Loader tools, written in the C and JAVA languages, parse and load these databases into a relational database schema. The loaders also apply a degree of semantic normalization to their respective source data, decreasing semantic heterogeneity. The schema supports the following bioinformatics datatypes: chemical compounds, biochemical reactions, metabolic pathways, proteins, genes, nucleic acid sequences, features on protein and nucleic-acid sequences, organisms, organism taxonomies, and controlled vocabularies. As an application example, we applied BioWarehouse to determine the fraction of biochemically characterized enzyme activities for which no sequences exist in the public sequence databases. The answer is that no sequence exists for 36% of enzyme activities for which EC numbers have been assigned. These gaps in sequence data significantly limit the accuracy of genome annotation and metabolic pathway prediction, and are a barrier for metabolic engineering. Complex queries of this type provide examples of the value of the data warehousing approach to bioinformatics research. BioWarehouse embodies significant progress on the database integration problem for bioinformatics.

Plying Your Craft: Instructional Development and the Use of Heuristics.

ERIC Educational Resources Information Center

Noel, Kent L.; Hewlett, Brent

1981-01-01

Examines an instructional systems design (ISD) model used by Bell Laboratories as an illustration of how heuristics can be brought to bear upon the design and development of instructional materials. Ten references are listed. (Author/MER)

The VirusBanker database uses a Java program to allow flexible searching through Bunyaviridae sequences

PubMed Central

Fourment, Mathieu; Gibbs, Mark J

2008-01-01

Background Viruses of the Bunyaviridae have segmented negative-stranded RNA genomes and several of them cause significant disease. Many partial sequences have been obtained from the segments so that GenBank searches give complex results. Sequence databases usually use HTML pages to mediate remote sorting, but this approach can be limiting and may discourage a user from exploring a database. Results The VirusBanker database contains Bunyaviridae sequences and alignments and is presented as two spreadsheets generated by a Java program that interacts with a MySQL database on a server. Sequences are displayed in rows and may be sorted using information that is displayed in columns and includes data relating to the segment, gene, protein, species, strain, sequence length, terminal sequence and date and country of isolation. Bunyaviridae sequences and alignments may be downloaded from the second spreadsheet with titles defined by the user from the columns, or viewed when passed directly to the sequence editor, Jalview. Conclusion VirusBanker allows large datasets of aligned nucleotide and protein sequences from the Bunyaviridae to be compiled and winnowed rapidly using criteria that are formulated heuristically. PMID:18251994

Comet: an open-source MS/MS sequence database search tool.

PubMed

Eng, Jimmy K; Jahan, Tahmina A; Hoopmann, Michael R

2013-01-01

Proteomics research routinely involves identifying peptides and proteins via MS/MS sequence database search. Thus the database search engine is an integral tool in many proteomics research groups. Here, we introduce the Comet search engine to the existing landscape of commercial and open-source database search tools. Comet is open source, freely available, and based on one of the original sequence database search tools that has been widely used for many years. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Aptamer Database

PubMed Central

Lee, Jennifer F.; Hesselberth, Jay R.; Meyers, Lauren Ancel; Ellington, Andrew D.

2004-01-01

The aptamer database is designed to contain comprehensive sequence information on aptamers and unnatural ribozymes that have been generated by in vitro selection methods. Such data are not normally collected in ‘natural’ sequence databases, such as GenBank. Besides serving as a storehouse of sequences that may have diagnostic or therapeutic utility, the database serves as a valuable resource for theoretical biologists who describe and explore fitness landscapes. The database is updated monthly and is publicly available at http://aptamer.icmb.utexas.edu/. PMID:14681367

JICST Factual Database JICST DNA Database

NASA Astrophysics Data System (ADS)

Shirokizawa, Yoshiko; Abe, Atsushi

Japan Information Center of Science and Technology (JICST) has started the on-line service of DNA database in October 1988. This database is composed of EMBL Nucleotide Sequence Library and Genetic Sequence Data Bank. The authors outline the database system, data items and search commands. Examples of retrieval session are presented.

NCBI-compliant genome submissions: tips and tricks to save time and money.

PubMed

Pirovano, Walter; Boetzer, Marten; Derks, Martijn F L; Smit, Sandra

2017-03-01

Genome sequences nowadays play a central role in molecular biology and bioinformatics. These sequences are shared with the scientific community through sequence databases. The sequence repositories of the International Nucleotide Sequence Database Collaboration (INSDC, comprising GenBank, ENA and DDBJ) are the largest in the world. Preparing an annotated sequence in such a way that it will be accepted by the database is challenging because many validation criteria apply. In our opinion, it is an undesirable situation that researchers who want to submit their sequence need either a lot of experience or help from partners to get the job done. To save valuable time and money, we list a number of recommendations for people who want to submit an annotated genome to a sequence database, as well as for tool developers, who could help to ease the process. © The Author 2015. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

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.

Greenville ISD. Integrated Lesson Plans.

ERIC Educational Resources Information Center

East Texas State Univ., Commerce. Educational Development and Training Center.

This packet contains nine lesson plans for integrated academic and vocational education courses. Lesson plans for the following courses are included: industrial technology, automotive technology, English, mathematical applications, science, home economics, and mathematics. Some of the topics covered are as follows: mechanical drawing, automobile…

ISPI's Value Proposition: Two Examples.

ERIC Educational Resources Information Center

Swinney, John

2003-01-01

Describes two experiences that illustrate the value of the International Society for Performance Improvement (ISPI). Highlights include measuring organizational results; identifying opportunities to improve performance; training as part of the solution; the role of ISD (instructional systems design); HPT (human performance technology) issues; and…

SW#db: GPU-Accelerated Exact Sequence Similarity Database Search.

PubMed

Korpar, Matija; Šošić, Martin; Blažeka, Dino; Šikić, Mile

2015-01-01

In recent years we have witnessed a growth in sequencing yield, the number of samples sequenced, and as a result-the growth of publicly maintained sequence databases. The increase of data present all around has put high requirements on protein similarity search algorithms with two ever-opposite goals: how to keep the running times acceptable while maintaining a high-enough level of sensitivity. The most time consuming step of similarity search are the local alignments between query and database sequences. This step is usually performed using exact local alignment algorithms such as Smith-Waterman. Due to its quadratic time complexity, alignments of a query to the whole database are usually too slow. Therefore, the majority of the protein similarity search methods prior to doing the exact local alignment apply heuristics to reduce the number of possible candidate sequences in the database. However, there is still a need for the alignment of a query sequence to a reduced database. In this paper we present the SW#db tool and a library for fast exact similarity search. Although its running times, as a standalone tool, are comparable to the running times of BLAST, it is primarily intended to be used for exact local alignment phase in which the database of sequences has already been reduced. It uses both GPU and CPU parallelization and was 4-5 times faster than SSEARCH, 6-25 times faster than CUDASW++ and more than 20 times faster than SSW at the time of writing, using multiple queries on Swiss-prot and Uniref90 databases.

The annotation-enriched non-redundant patent sequence databases.

PubMed

Li, Weizhong; Kondratowicz, Bartosz; McWilliam, Hamish; Nauche, Stephane; Lopez, Rodrigo

2013-01-01

The EMBL-European Bioinformatics Institute (EMBL-EBI) offers public access to patent sequence data, providing a valuable service to the intellectual property and scientific communities. The non-redundant (NR) patent sequence databases comprise two-level nucleotide and protein sequence clusters (NRNL1, NRNL2, NRPL1 and NRPL2) based on sequence identity (level-1) and patent family (level-2). Annotation from the source entries in these databases is merged and enhanced with additional information from the patent literature and biological context. Corrections in patent publication numbers, kind-codes and patent equivalents significantly improve the data quality. Data are available through various user interfaces including web browser, downloads via FTP, SRS, Dbfetch and EBI-Search. Sequence similarity/homology searches against the databases are available using BLAST, FASTA and PSI-Search. In this article, we describe the data collection and annotation and also outline major changes and improvements introduced since 2009. Apart from data growth, these changes include additional annotation for singleton clusters, the identifier versioning for tracking entry change and the entry mappings between the two-level databases. Database URL: http://www.ebi.ac.uk/patentdata/nr/

The Annotation-enriched non-redundant patent sequence databases

PubMed Central

Li, Weizhong; Kondratowicz, Bartosz; McWilliam, Hamish; Nauche, Stephane; Lopez, Rodrigo

2013-01-01

The EMBL-European Bioinformatics Institute (EMBL-EBI) offers public access to patent sequence data, providing a valuable service to the intellectual property and scientific communities. The non-redundant (NR) patent sequence databases comprise two-level nucleotide and protein sequence clusters (NRNL1, NRNL2, NRPL1 and NRPL2) based on sequence identity (level-1) and patent family (level-2). Annotation from the source entries in these databases is merged and enhanced with additional information from the patent literature and biological context. Corrections in patent publication numbers, kind-codes and patent equivalents significantly improve the data quality. Data are available through various user interfaces including web browser, downloads via FTP, SRS, Dbfetch and EBI-Search. Sequence similarity/homology searches against the databases are available using BLAST, FASTA and PSI-Search. In this article, we describe the data collection and annotation and also outline major changes and improvements introduced since 2009. Apart from data growth, these changes include additional annotation for singleton clusters, the identifier versioning for tracking entry change and the entry mappings between the two-level databases. Database URL: http://www.ebi.ac.uk/patentdata/nr/ PMID:23396323

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.

Specialized microbial databases for inductive exploration of microbial genome sequences

PubMed Central

Fang, Gang; Ho, Christine; Qiu, Yaowu; Cubas, Virginie; Yu, Zhou; Cabau, Cédric; Cheung, Frankie; Moszer, Ivan; Danchin, Antoine

2005-01-01

Background The enormous amount of genome sequence data asks for user-oriented databases to manage sequences and annotations. Queries must include search tools permitting function identification through exploration of related objects. Methods The GenoList package for collecting and mining microbial genome databases has been rewritten using MySQL as the database management system. Functions that were not available in MySQL, such as nested subquery, have been implemented. Results Inductive reasoning in the study of genomes starts from "islands of knowledge", centered around genes with some known background. With this concept of "neighborhood" in mind, a modified version of the GenoList structure has been used for organizing sequence data from prokaryotic genomes of particular interest in China. GenoChore , a set of 17 specialized end-user-oriented microbial databases (including one instance of Microsporidia, Encephalitozoon cuniculi, a member of Eukarya) has been made publicly available. These databases allow the user to browse genome sequence and annotation data using standard queries. In addition they provide a weekly update of searches against the world-wide protein sequences data libraries, allowing one to monitor annotation updates on genes of interest. Finally, they allow users to search for patterns in DNA or protein sequences, taking into account a clustering of genes into formal operons, as well as providing extra facilities to query sequences using predefined sequence patterns. Conclusion This growing set of specialized microbial databases organize data created by the first Chinese bacterial genome programs (ThermaList, Thermoanaerobacter tencongensis, LeptoList, with two different genomes of Leptospira interrogans and SepiList, Staphylococcus epidermidis) associated to related organisms for comparison. PMID:15698474

The use of sequence-based SSR mining for the development of a vast collection of microsatellites in Aquilegia Formosa

Treesearch

Brandon Schlautman; Vera Pfeiffer; Juan Zalapa; Johanne Brunet

2014-01-01

Numerous microsatellite markers were developed for Aquilegia formosafrom sequences deposited within the Expressed Sequence Tag (EST), Genomic Survey Sequence (GSS), and Nucleotide databases in NCBI. Microsatellites (SSRs) were identified and primers were designed for 9 SSR containing sequences in the Nucleotide database, 3803 sequences in the EST...

Reference System of DNA and Protein Sequences on CD-ROM

NASA Astrophysics Data System (ADS)

Nasu, Hisanori; Ito, Toshiaki

DNASIS-DBREF31 is a database for DNA and Protein sequences in the form of optical Compact Disk (CD) ROM, developed and commercialized by Hitachi Software Engineering Co., Ltd. Both nucleic acid base sequences and protein amino acid sequences can be retrieved from a single CD-ROM. Existing database is offered in the form of on-line service, floppy disks, or magnetic tape, all of which have some problems or other, such as usability or storage capacity. DNASIS-DBREF31 newly adopt a CD-ROM as a database device to realize a mass storage and personal use of the database.

Transterm—extended search facilities and improved integration with other databases

PubMed Central

Jacobs, Grant H.; Stockwell, Peter A.; Tate, Warren P.; Brown, Chris M.

2006-01-01

Transterm has now been publicly available for >10 years. Major changes have been made since its last description in this database issue in 2002. The current database provides data for key regions of mRNA sequences, a curated database of mRNA motifs and tools to allow users to investigate their own motifs or mRNA sequences. The key mRNA regions database is derived computationally from Genbank. It contains 3′ and 5′ flanking regions, the initiation and termination signal context and coding sequence for annotated CDS features from Genbank and RefSeq. The database is non-redundant, enabling summary files and statistics to be prepared for each species. Advances include providing extended search facilities, the database may now be searched by BLAST in addition to regular expressions (patterns) allowing users to search for motifs such as known miRNA sequences, and the inclusion of RefSeq data. The database contains >40 motifs or structural patterns important for translational control. In this release, patterns from UTRsite and Rfam are also incorporated with cross-referencing. Users may search their sequence data with Transterm or user-defined patterns. The system is accessible at . PMID:16381889

Insulin-sensitising drugs versus the combined oral contraceptive pill for hirsutism, acne and risk of diabetes, cardiovascular disease, and endometrial cancer in polycystic ovary syndrome.

PubMed

Costello, M; Shrestha, B; Eden, J; Sjoblom, P; Johnson, N

2007-01-24

Insulin-sensitizing drugs (ISDs) have recently been advocated as possibly a safer and more effective long-term treatment than the oral contraceptive pill (OCP) in women with polycystic ovary syndrome (PCOS). It is important to directly compare the efficacy and safety of ISDs versus OCPs in the long-term treatment of women with PCOS. To assess the effectiveness and safety of ISDs versus the OCP (alone or in combination) in improving clinical, hormonal, and metabolic features of PCOS. We searched the Cochrane Menstrual Disorders and Subfertility Group Trials Register (September 2005), Cochrane Central Register of Controlled Trials (CENTRAL (Ovid), third quarter 2005), MEDLINE (1966 to September 2005), CINAHL (1982 to September 2005), and EMBASE (1988 to September 2005). References of the identified articles were handsearched, and pharmaceutical companies and experts in the field were also contacted for additional relevant studies. Randomised controlled trials which compared ISDs versus the OCP (alone or in combination). Performed independently by two review authors. Six trials were included for analysis, four of which compared metformin versus OCP (104 participants) and two of which compared OCP combined with metformin versus OCP alone (70 participants). Limited data demonstrated no evidence of difference in effect between metformin and the OCP on hirsutism and acne. There was either insufficient or no data on the relative efficacy of metformin or the OCP (alone or in combination) for preventing the development of diabetes, cardiovascular disease, or endometrial cancer. Metformin was less effective than the OCP in improving menstrual pattern (Peto odds ratio (OR) 0.08, 95% CI 0.01 to 0.45). Metformin resulted in a higher incidence of gastrointestinal (Peto OR 7.75, 95% CI 1.32 to 45.71), and a lower incidence of non-gastrointestinal (Peto OR 0.11, 95% CI 0.03 to 0.39), severe adverse effects requiring stopping of medication. Metformin was less effective in reducing serum androgen levels (total testosterone: weighted mean difference (WMD) 0.54, 95% CI 0.22 to 0.86; free androgen index: WMD 3.69, 95% CI 2.56 to 4.83). Metformin was more effective than the OCP in reducing fasting insulin (WMD -3.46, 95% CI -5.39 to -1.52) and not increasing triglyceride (WMD -0.48, 95% -0.86 to -0.09) levels, but there was insufficient evidence regarding comparative effects on reducing fasting glucose or cholesterol levels. Up to 12-months treatment with the OCP is associated with an improvement in menstrual pattern and serum androgen levels compared with metformin; but metformin treatment results in a reduction in fasting insulin and lower triglyceride levels than with the OCP. Side-effect profiles differ between the two drugs. There is either extremely limited or no data on important clinical outcomes such as the development of diabetes, cardiovascular disease, or endometrial cancer. There are no data comparing ISDs other than metformin (that is rosiglitazone, pioglitazone, and D-chiro-inositol) versus OCPs (alone or in combination).

PhytoREF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy.

PubMed

Decelle, Johan; Romac, Sarah; Stern, Rowena F; Bendif, El Mahdi; Zingone, Adriana; Audic, Stéphane; Guiry, Michael D; Guillou, Laure; Tessier, Désiré; Le Gall, Florence; Gourvil, Priscillia; Dos Santos, Adriana L; Probert, Ian; Vaulot, Daniel; de Vargas, Colomban; Christen, Richard

2015-11-01

Photosynthetic eukaryotes have a critical role as the main producers in most ecosystems of the biosphere. The ongoing environmental metabarcoding revolution opens the perspective for holistic ecosystems biological studies of these organisms, in particular the unicellular microalgae that often lack distinctive morphological characters and have complex life cycles. To interpret environmental sequences, metabarcoding necessarily relies on taxonomically curated databases containing reference sequences of the targeted gene (or barcode) from identified organisms. To date, no such reference framework exists for photosynthetic eukaryotes. In this study, we built the PhytoREF database that contains 6490 plastidial 16S rDNA reference sequences that originate from a large diversity of eukaryotes representing all known major photosynthetic lineages. We compiled 3333 amplicon sequences available from public databases and 879 sequences extracted from plastidial genomes, and generated 411 novel sequences from cultured marine microalgal strains belonging to different eukaryotic lineages. A total of 1867 environmental Sanger 16S rDNA sequences were also included in the database. Stringent quality filtering and a phylogeny-based taxonomic classification were applied for each 16S rDNA sequence. The database mainly focuses on marine microalgae, but sequences from land plants (representing half of the PhytoREF sequences) and freshwater taxa were also included to broaden the applicability of PhytoREF to different aquatic and terrestrial habitats. PhytoREF, accessible via a web interface (http://phytoref.fr), is a new resource in molecular ecology to foster the discovery, assessment and monitoring of the diversity of photosynthetic eukaryotes using high-throughput sequencing. © 2015 John Wiley & Sons Ltd.

The Evolution of Instructional Design Principles for Intelligent Computer-Assisted Instruction.

ERIC Educational Resources Information Center

Dede, Christopher; Swigger, Kathleen

1988-01-01

Discusses and compares the design and development of computer assisted instruction (CAI) and intelligent computer assisted instruction (ICAI). Topics discussed include instructional systems design (ISD), artificial intelligence, authoring languages, intelligent tutoring systems (ITS), qualitative models, and emerging issues in instructional…

Procedures for Trade and Industrial Program Development.

ERIC Educational Resources Information Center

Campbell, Clifton P.

The instructional systems development (ISD) approach for the development and accomplishment of vocational training programs provides a methodology for gathering and analyzing job information, developing instructional materials in a variety of media, conducting instruction, and evaluating and improving the effectiveness of training programs. This…

Austin ISD. Integrated Lesson Plans.

ERIC Educational Resources Information Center

East Texas State Univ., Commerce. Educational Development and Training Center.

This packet contains 14 lesson plans for integrated academic and vocational education courses. Lesson plans for the following courses are included: integrated physics and principles of technology; algebra and principles of technology; principles of technology, language arts, and economics; physics and industrial electronics; physics and…

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

Cognitive inconsistency in bipolar patients is determined by increased intra-individual variability in initial phase of task performance.

PubMed

Krukow, Paweł; Szaniawska, Ola; Harciarek, Michał; Plechawska-Wójcik, Małgorzata; Jonak, Kamil

2017-03-01

Bipolar patients show high intra-individual variability during cognitive processing. However, it is not known whether there are a specific fluctuations of variability contributing to the overall high cognitive inconsistency. The objective was to compare dynamic profiles of patients and healthy controls to identify hypothetical differences and their associations with overall variability and processing speed. Changes of reaction times iSD during processing speed test performance over time was measured by dividing the iSD for whole task into four consecutive parts. Motor speed and cognitive effort were controlled. Patients with BD exhibited significantly lower results regarding processing speed and higher intra-individual variability comparing with HC. The profile of intra-individual variability changes over time of performance was significantly different in BD versus HC groups: F(3, 207)=8.60, p<0.0001, η p 2 =0.11. iSD of BD patients in the initial phase of performance was three times higher than in the last. There was no significant differences between four intervals in HC group. Inter-group difference in the initial part of the profiles was significant also after controlling for several cognitive and clinical variables. Applied computer version of Cognitive Speed Test was relatively new and, thus, replication studies are needed. Effect seen in the present study is driven mainly by the BD type I. Patients with BD exhibits problems with setting a stimulus-response association in starting phase of cognitive processing. This deficit may negatively interfere with the other cognitive functions, decreasing level of psychosocial functioning, therefore should be explored in future studies. Copyright © 2017 Elsevier B.V. All rights reserved.

Top-down MALDI-in-source decay-FTICR mass spectrometry of isotopically resolved proteins.

PubMed

Nicolardi, Simone; Switzar, Linda; Deelder, André M; Palmblad, Magnus; van der Burgt, Yuri E M

2015-03-17

An accurate mass measurement of a known protein provides information on potential amino acid deletions and post-translational modifications. Although this field is dominated by strategies based on electrospray ionization, mass spectrometry (MS) methods using matrix-assisted laser desorption/ionization (MALDI) have the advantage of yielding predominantly singly charged precursor ions, thus avoiding peak overlap from different charge states of multiple species. Such MALDI-MS methods require mass measurement at ultrahigh resolution, which is provided by Fourier transform ion cyclotron resonance (FTICR) mass analyzers. Recently, using a MALDI-FTICR-MS platform equipped with a 15 T magnet, we reported on the mass analysis of intact human serum peptides and small proteins with isotopic resolution up to ∼15 kDa and identified new proteoforms from an accurate measurement of mass distances. In the current study, we have used this FTICR system after an upgrade with a novel dynamically harmonized ICR cell, i.e., ParaCell, for mapping isotopically resolved intact proteins up to about 17 kDa and performed top-down MALDI in-source decay (ISD) analysis. Standard proteins myoglobin (m/z-value 16,950) and ribonuclease B (m/z-value 14,900) were measured with resolving powers of 62,000 and 61,000, respectively. Furthermore, it will be shown that (singly charged) MALDI-ISD fragment ions can be measured at isotopic resolution up to m/z-value 12,000 (e.g., resolving power 39,000 at m/z-value 12,000) providing more reliable identifications. Moreover, examples are presented of pseudo-MS(3) experiments on ISD fragment ions from RNase B by collisional-induced dissociation (CID).

Characterization of singly and multiply PEGylated insulin isomers by reversed-phase ultra-performance liquid chromatography interfaced with ion mobility mass spectrometry.

PubMed

Gerislioglu, Selim; Adams, Scott R; Wesdemiotis, Chrys

2018-04-03

Conjugation of poly(ethylene glycol) (PEG) to protein drugs (PEGylation) is increasingly utilized in the biotherapeutics field because it improves significantly the drugs' circulatory half-life, solubility, and shelf-life. The activity of a PEGylated drug depends on the number, size, and location of the attached PEG chain(s). This study introduces a 2D separation approach, including reversed-phase ultra-performance liquid chromatography (RP-UPLC) and ion mobility mass spectrometry (IM-MS), in order to determine the structural properties of the conjugates, as demonstrated for a PEGylated insulin sample that was prepared by random amine PEGylation. The UPLC dimension allowed separation based on polarity. Electrospray ionization (ESI) of the eluates followed by in-source dissociation (ISD) truncated the PEG chains and created insulin fragments that provided site-specific information based on whether they contained a marker at the potential conjugation sites. Separation of the latter fragments by size and charge in the orthogonal IM dimension (pseudo-4D UPLC-ISD-IM-MS approach) enabled clear detection and identification of the positional isomers formed upon PEGylation. The results showed a highly heterogeneous mixture of singly and multiply conjugated isomers plus unconjugated material. PEGylation was observed on all three possible attachment sites (ε-NH 2 of LysB29, A- and B-chain N-termini). Each PEGylation site was validated by analysis of the same product after disulfide bond cleavage, so that the PEGylated A- and B- chain could be individually characterized with the same pseudo-4D UPLC-ISD-IM-MS method. Copyright © 2018 Elsevier B.V. All rights reserved.

Multi-center Performance Evaluations of Tacrolimus and Cyclosporine Electrochemiluminescence Immunoassays in the Asia-Pacific Region

PubMed Central

Qin, Xuzhen; Rui, Jianzhong; Xia, Yong; Mu, Hong; Song, Sang Hoon; Raja Aziddin, Raja Elina; Miles, Gabrielle; Sun, Yuli

2018-01-01

Background The immunosuppressant drugs (ISDs), tacrolimus and cyclosporine, are vital for solid organ transplant patients to prevent rejection. However, toxicity is a concern, and absorption is highly variable across patients; therefore, ISD levels need to be precisely monitored. In the Asia-Pacific (APAC) region, tacrolimus and cyclosporine concentrations are typically measured using immunoassays. The objective of this study was to assess the analytical performance of Roche Elecsystacrolimus and cyclosporinee electrochemiluminescence immunoassays (ECLIAs). Methods This evaluation was performed in seven centers across China, South Korea, and Malaysia. Imprecision (repeatability and reproducibility), assay accuracy, and lot-to-lot reagent variability were tested. The Elecsys ECLIAs were compared with commercially available immunoassays (Architect, Dimension, and Viva-E systems) using whole blood samples from patients with various transplant types (kidney, liver, heart, and bone marrow). Results Coefficients of variation for repeatability and reproducibility were ≤5.4% and ≤12.4%, respectively, for the tacrolimus ECLIA, and ≤5.1% and ≤7.3%, respectively, for the cyclosporine ECLIA. Method comparisons of the tacrolimus ECLIA with Architect, Dimension, and Viva-E systems yielded slope values of 1.01, 1.14, and 0.897, respectively. The cyclosporine ECLIA showed even closer agreements with the Architect, Dimension, and Viva-E systems (slope values of 1.04, 1.04, and 1.09, respectively). No major differences were observed among the different transplant types. Conclusions The tacrolimus and cyclosporine ECLIAs demonstrated excellent precision and close agreement with other immunoassays tested. These results show that both assays are suitable for ISD monitoring in an APAC population across a range of different transplant types. PMID:29214751

Pelvimetry in nulliparous and primiparous women using 3 Tesla magnetic resonance imaging.

PubMed

Hampel, Franziska; Hallscheidt, Peter; Sohn, Christof; Schlehe, Bettina; Brocker, Kerstin A

2018-02-21

To perform pelvimetry in nulliparous and primiparous women using 3 Tesla magnetic resonance imaging (3T MRI). Twenty-five nulliparous volunteers and 25 primiparous women underwent pelvic 3T MRI within one week after vaginal childbirth in a prospective clinical single-center trial. The pelvimetric parameters interspinous distance (ISD), intertuberous distance (ITD), sagittal outlet (SO), obstetric conjugate (OC), and coccygeal curved length (CCL) were adapted from anthropometric measurements as well as from sonographic and computed tomography-based pelvimetry performed on high-resolution T2-weighted images. We compared the results of the two study groups to one another, recent literature and postpartum-diagnosed levator ani muscle (LAM) injuries. The mean values for primipara/nullipara were ISD 107 ± 8.3/105 ± 8.4 mm, ITD 119.8 ± 10.2/118.4 ± 13.1 mm, OC 129.4 ± 10/130.8 ± 6.9 mm, SO 114.3 ± 7.8/112.5 ± 8.9 mm, and CCL 37.3 ± 7.4/39 ± 8 mm. Significant differences (P < 0.05) were found between the results for OC, SO, and CCL (primipara) and ISD, ITD and OC (nullipara) and the values in the literature. No significant difference in pelvimetric values was found between the groups. A significant correlation was found between the pelvimetric parameters and five types of LAM injuries. Two-dimensional 3T MRI combines high-resolution images with objective pelvimetric measurements applicable in a postpartum setting. Our results provide a good foundation for further MRI-based studies evaluating the bony pelvis and its relation to LAM injuries during vaginal childbirth. © 2018 Wiley Periodicals, Inc.

Specific Cα-C Bond Cleavage of β-Carbon-Centered Radical Peptides Produced by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry

NASA Astrophysics Data System (ADS)

Nagoshi, Keishiro; Yamakoshi, Mariko; Sakamoto, Kenya; Takayama, Mitsuo

2018-04-01

Radical-driven dissociation (RDD) of hydrogen-deficient peptide ions [M - H + H]·+ has been examined using matrix-assisted laser dissociation/ionization in-source decay mass spectrometry (MALDI-ISD MS) with the hydrogen-abstracting matrices 4-nitro-1-naphthol (4,1-NNL) and 5-nitrosalicylic acid (5-NSA). The preferential fragment ions observed in the ISD spectra include N-terminal [a] + ions and C-terminal [x]+, [y + 2]+, and [w]+ ions which imply that β-carbon (Cβ)-centered radical peptide ions [M - Hβ + H]·+ are predominantly produced in MALDI conditions. RDD reactions from the peptide ions [M - Hβ + H]·+ successfully explains the fact that both [a]+ and [x]+ ions arising from cleavage at the Cα-C bond of the backbone of Gly-Xxx residues are missing from the ISD spectra. Furthermore, the formation of [a]+ ions originating from the cleavage of Cα-C bond of deuterated Ala(d3)-Xxx residues indicates that the [a]+ ions are produced from the peptide ions [M - Hβ + H]·+ generated by deuteron-abstraction from Ala(d3) residues. It is suggested that from the standpoint of hydrogen abstraction via direct interactions between the nitro group of matrix and hydrogen of peptides, the generation of the peptide radical ions [M - Hβ + H]·+ is more favorable than that of the α-carbon (Cα)-centered radical ions [M - Hα + H]·+ and the amide nitrogen-centered radical ions [M - HN + H]·+, while ab initio calculations indicate that the formation of [M - Hα + H]·+ is energetically most favorable. [Figure not available: see fulltext.

A re-adjustable sling for female recurrent stress incontinence and sphincteric deficiency: Outcomes and complications in 125 patients using the Remeex sling system.

PubMed

Errando, Carlos; Rodriguez-Escovar, Fernando; Gutierrez, Cristina; Baez, Carlos; Araño, Pedro; Villavicencio, Humberto

2010-11-01

To evaluate the outcomes, complications, and quality of life of patients after a Remeex re-adjustable sling for recurrent stress urinary incontinence (SUI) and intrinsic sphincteric deficiency (ISD) indications. One hundred twenty-five patients with SUI were prospectively evaluated following a re-adjustable sling in a single tertiary academic Center. Patients were classified by Q-tip, urodynamic and clinical criteria into ISD (70) and recurrent SUI (55). All patients underwent a re-adjustable sling placement. Outcome measures included pad-test, urodynamics, and the King's Health Questionnaire. After a mean follow-up of 38 months (26-72), 109 patients (87%) are cured of SUI based on pad-test, clinical, and urodynamic criteria. Sixteen patients (13%) remain incontinent. Nine of those (7%) are satisfied to the point that they decline re-adjustment of the sling, and seven (6%) are on the waiting list for re-adjustment. Nineteen patients show urge incontinence (9 with previous urodynamic mixed incontinence, 10 (8%) with de novo detrusor overactivity). Twenty-one patients benefited from a re-adjustment of the sling during the follow-up. The tension was increased in 17 cases (continent at discharge) due to recurrence of SUI, and reduced in 4 due to obstruction. The Varitensor was removed in 1 case due to infection. No other complications were seen. The Remeex re-adjustable sling system provides a good cure rate for recurrent SUI and ISD with a low complication rate. The ability to increase or decrease sling tension allowed us to achieve cure in patients who were not initially dry, and to relieve obstruction in every case attempted. © 2010 Wiley-Liss, Inc.

Phase IIa Study of the Immunogenicity and Safety of the Novel Staphylococcus aureus Vaccine V710 in Adults with End-Stage Renal Disease Receiving Hemodialysis

PubMed Central

Moustafa, Moustafa; Aronoff, George R.; Chandran, Chandra; Hartzel, Jonathan S.; Smugar, Steven S.; Galphin, Claude M.; Mailloux, Lionel U.; Brown, Elizabeth; DiNubile, Mark J.; Kartsonis, Nicholas A.

2012-01-01

Bacteremia is the second leading cause of death in patients with end-stage renal disease who are on hemodialysis. A vaccine eliciting long-term immune responses against Staphylococcus aureus in patients on chronic hemodialysis may reduce the incidence of bacteremia and its complications in these patients. V710 is a vaccine containing iron surface determinant B (IsdB), a highly conserved S. aureus surface protein, which has been shown to be immunogenic in healthy subjects. In this blinded phase II immunogenicity study, 206 chronic hemodialysis patients between the ages of 18 and 80 years old were randomized to receive 60 μg V710 (with or without adjuvant), 90 μg V710 (with adjuvant), or a placebo in various combinations on days 1, 28, and 180. All 201 vaccinated patients were to be followed through day 360. The primary hypothesis was that at least 1 of the 3 groups receiving 2 V710 doses on days 1 and 28 would have a ≥2.5 geometric mean fold rise (GMFR) in anti-IsdB IgG titers over the baseline 28 days after the second vaccination (day 56). At day 56, all three groups receiving 2 doses of V710 achieved a ≥2.5 GMFR in anti-IsdB antibodies compared to the baseline (P values of <0.001 for all 3 groups), satisfying the primary immunogenicity hypothesis. None of the 33 reported serious adverse experiences were considered vaccine related by the investigators. V710 induced sustained antibody responses for at least 1 year postvaccination in patients on chronic hemodialysis. PMID:22837094

RECOVIR Software for Identifying Viruses

NASA Technical Reports Server (NTRS)

Chakravarty, Sugoto; Fox, George E.; Zhu, Dianhui

2013-01-01

Most single-stranded RNA (ssRNA) viruses mutate rapidly to generate a large number of strains with highly divergent capsid sequences. Determining the capsid residues or nucleotides that uniquely characterize these strains is critical in understanding the strain diversity of these viruses. RECOVIR (an acronym for "recognize viruses") software predicts the strains of some ssRNA viruses from their limited sequence data. Novel phylogenetic-tree-based databases of protein or nucleic acid residues that uniquely characterize these virus strains are created. Strains of input virus sequences (partial or complete) are predicted through residue-wise comparisons with the databases. RECOVIR uses unique characterizing residues to identify automatically strains of partial or complete capsid sequences of picorna and caliciviruses, two of the most highly diverse ssRNA virus families. Partition-wise comparisons of the database residues with the corresponding residues of more than 300 complete and partial sequences of these viruses resulted in correct strain identification for all of these sequences. This study shows the feasibility of creating databases of hitherto unknown residues uniquely characterizing the capsid sequences of two of the most highly divergent ssRNA virus families. These databases enable automated strain identification from partial or complete capsid sequences of these human and animal pathogens.

Extended Edited Synoptic Cloud Reports from Ships and Land Stations Over the Globe, 1952-2009 (NDP-026C)

DOE Data Explorer

Hahn, C. J. [University of Arizona; Warren, S. G. [University of Washington; Eastman, R.

1999-08-01

This database contains surface synoptic weather reports for the entire globe, gathered from various available data sets. The reports were processed, edited, and rewritten to provide a single dataset of individual observations of clouds, spanning the 57 years 1952-2008 for ship data and the 39 years 1971-2009 for land station data. In addition to the cloud portion of the synoptic report, each edited report also includes the associated pressure, present weather, wind, air temperature, and dew point (and sea surface temperature over oceans). This data set is called the "Extended Edited Cloud Report Archive" (EECRA). The EECRA is based solely on visual cloud observations from weather stations, reported in the WMO synoptic code (WMO, 1974). Reports must contain cloud-type information to be included in the archive. Past data sources include those from the Fleet Numerical Oceanographic Center (FNOC, 1971-1976) and the National Centers for Environmental Prediction (NCEP, 1977-1996). This update uses data from a new source, the 'Integrated Surface Database' (ISD, 1997-2009; Smith et al., 2011). Our past analyses of the EECRA identified a subset of 5388 weather stations that were determined to produce reliable day and night observations of cloud amount and type. The update contains observations only from this subset of stations. Details concerning processing, previous problems, contents, and comments are available in the archive's original documentation . The EECRA contains about 81 million cloud observations from ships and 380 million from land stations. The data files have been compressed using unix. Unix/linux users can "uncompress" or "gunzip" the files after downloading. If you're interested in the NDP-026C database, then you'll also want to explore its related data products, NDP-026D and NDP-026E.

O-GLYCBASE Version 3.0: a revised database of O-glycosylated proteins.

PubMed Central

Hansen, J E; Lund, O; Nilsson, J; Rapacki, K; Brunak, S

1998-01-01

O-GLYCBASE is a revised database of information on glycoproteins and their O-linked glycosylation sites. Entries are compiled and revised from the literature, and from the sequence databases. Entries include information about species, sequence, glycosylation sites and glycan type and is fully cross-referenced. Compared to version 2.0 the number of entries has increased by 20%. Sequence logos displaying the acceptor specificity patterns for the GalNAc, mannose and GlcNAc transferases are shown. The O-GLYCBASE database is available through the WWW at http://www.cbs.dtu. dk/databases/OGLYCBASE/ PMID:9399880

Emerging Technologies, ISD, and Learning Environments: Critical Perspectives.

ERIC Educational Resources Information Center

Hannafin, Michael J.

1992-01-01

Reviews the evolution of instructional systems design and computer-based learning environments, focusing on the effects of technological advances. Classification of learning environments is discussed in the context of the dimensions of scope (macrolevel or microlevel), user activity (generative or mathemagenic), educational activity (goal-directed…

Instructional System Development.

ERIC Educational Resources Information Center

Department of the Air Force, Washington, DC.

The manual presents a technology of instructional design and a model for developing and conducting efficient and cost effective Air Force instructional systems. Chapter 1 provides an overview of Instructional System Development (ISD). Chapters 2-6 each focus on a step of the process: analysis of system requirements; definition of…

Socorro ISD. Integrated Lesson Plans.

ERIC Educational Resources Information Center

East Texas State Univ., Commerce. Educational Development and Training Center.

This packet contains 29 lesson plans for integrated academic and vocational education courses. Lesson plans for the following courses are included: algebra, health occupations education, English, biology, laboratory mathematics, and health care sciences. Some of the topics covered are as follows: statistics, vital signs, graphing, ethics, special…

Mansfield ISD. Integrated Lesson Plans.

ERIC Educational Resources Information Center

East Texas State Univ., Commerce. Educational Development and Training Center.

This packet contains 27 lesson plans for integrated academic and vocational education courses. Lesson plans for the following courses are included: horticulture, algebra, physical science, general mechanical repair, foods and nutrition, home economics, and microcomputer applications. Some of the topics covered are as follows: seed germination,…

Learning Objects: A User-Centered Design Process

ERIC Educational Resources Information Center

Branon, Rovy F., III

2011-01-01

Design research systematically creates or improves processes, products, and programs through an iterative progression connecting practice and theory (Reinking, 2008; van den Akker, 2006). Developing a new instructional systems design (ISD) processes through design research is necessary when new technologies emerge that challenge existing practices…

Are neurocognitive speed and inconsistency similarly affected in type 2 diabetes?

PubMed

Whitehead, Bonnie P; Dixon, Roger A; Hultsch, David F; MacDonald, Stuart W S

2011-07-01

Type 2 diabetes (T2D) is a disease of aging with indirect but detectable and cumulative neurological implications. We systematically tested whether neurocognitive speed (mean rate) or inconsistency (intraindividual variability) was the more sensitive clinical marker of T2D. Three of four research questions used a cross-sectional wave of the Victoria Longitudinal Study (VLS) divided into T2D (age 55-81 years) and control (age = 53-91 years) groups. The fourth question addressed relative two-wave longitudinal changes. Each of four speeded tasks produced intraindividual mean rate (IM) and intraindividual standard deviation (ISD) scores. First, the T2D group performed more slowly than the controls. Second, this deficit extended to inconsistency, but less uniformly. Third, based on logistic regression analyses, IM was the more effective predictor of T2D status. Fourth, we observed similar longitudinal change patterns for IM and ISD. Results are linked to the theoretical location of T2D on an adjusted neural vulnerability continuum.

Are Neurocognitive Speed and Inconsistency Similarly Affected in Type 2 Diabetes?

PubMed Central

Whitehead, Bonnie P.; Dixon, Roger A.; Hultsch, David F.; MacDonald, Stuart W.S.

2011-01-01

Type 2 diabetes (T2D) is a disease of aging with indirect but detectable and cumulative neurological implications. We systematically tested whether neurocognitive speed (mean rate) or inconsistency (intraindividual variability) was the more sensitive clinical marker of T2D. Three of four research questions used a cross-sectional wave of the Victoria Longitudinal Study (VLS) divided into T2D (age 55-81 years) and control (age = 53-91 years) groups. The fourth question addressed relative two-wave longitudinal changes. Each of four speeded tasks produced intraindividual mean rate (IM) and intraindividual standard deviation (ISD) scores. First, the T2D group performed more slowly than the controls. Second, this deficit extended to inconsistency, but less uniformly. Third, based on logistic regression analyses, IM was the more effective predictor of T2D status. Fourth, we observed similar longitudinal change patterns for IM and ISD. Results are linked to the theoretical location of T2D on an adjusted neural vulnerability continuum. PMID:21416426

Breathe Easy at Home: A Qualitative Evaluation of a Pediatric Asthma Intervention.

PubMed

Rosofsky, Anna; Reid, Margaret; Sandel, Megan; Zielenbach, Molly; Murphy, Johnna; Scammell, Madeleine K

2016-01-01

The Breathe Easy at Home Program enables clinicians to refer asthmatic patients to Boston Inspectional Services Department (ISD) if they suspect housing conditions trigger symptoms. The authors conducted one-on-one interviews with clinicians ( n = 10) who referred patients, and focus groups with inspectors from the ISD ( n = 9) and a variety of stakeholders ( n = 13), to gain insight into program function and implementation. Clinician interviews revealed inconsistencies in enrollment approaches, dissatisfaction with the web-based system, and patient follow-up difficulties. Inspectors identified barriers to working effectively with residents and landlords, and the stakeholder focus group highlighted successes of an unusual institutional collaboration. Interviews and focus groups identified strong and personal rapport between clinicians, inspectors, and patients as key to program retention, and that participating families required additional support throughout the process. Despite recommendations for improvement in program implementation, clinicians, inspectors, and stakeholders felt that the program overall improved both the home environment and asthma outcomes.

MEGGASENSE - The Metagenome/Genome Annotated Sequence Natural Language Search Engine: A Platform for 
the Construction of Sequence Data Warehouses.

PubMed

Gacesa, Ranko; Zucko, Jurica; Petursdottir, Solveig K; Gudmundsdottir, Elisabet Eik; Fridjonsson, Olafur H; Diminic, Janko; Long, Paul F; Cullum, John; Hranueli, Daslav; Hreggvidsson, Gudmundur O; Starcevic, Antonio

2017-06-01

The MEGGASENSE platform constructs relational databases of DNA or protein sequences. The default functional analysis uses 14 106 hidden Markov model (HMM) profiles based on sequences in the KEGG database. The Solr search engine allows sophisticated queries and a BLAST search function is also incorporated. These standard capabilities were used to generate the SCATT database from the predicted proteome of Streptomyces cattleya . The implementation of a specialised metagenome database (AMYLOMICS) for bioprospecting of carbohydrate-modifying enzymes is described. In addition to standard assembly of reads, a novel 'functional' assembly was developed, in which screening of reads with the HMM profiles occurs before the assembly. The AMYLOMICS database incorporates additional HMM profiles for carbohydrate-modifying enzymes and it is illustrated how the combination of HMM and BLAST analyses helps identify interesting genes. A variety of different proteome and metagenome databases have been generated by MEGGASENSE.

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/

Protein sequence annotation in the genome era: the annotation concept of SWISS-PROT+TREMBL.

PubMed

Apweiler, R; Gateau, A; Contrino, S; Martin, M J; Junker, V; O'Donovan, C; Lang, F; Mitaritonna, N; Kappus, S; Bairoch, A

1997-01-01

SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotation, a minimal level of redundancy and high level of integration with other databases. Ongoing genome sequencing projects have dramatically increased the number of protein sequences to be incorporated into SWISS-PROT. Since we do not want to dilute the quality standards of SWISS-PROT by incorporating sequences without proper sequence analysis and annotation, we cannot speed up the incorporation of new incoming data indefinitely. However, as we also want to make the sequences available as fast as possible, we introduced TREMBL (TRanslation of EMBL nucleotide sequence database), a supplement to SWISS-PROT. TREMBL consists of computer-annotated entries in SWISS-PROT format derived from the translation of all coding sequences (CDS) in the EMBL nucleotide sequence database, except for CDS already included in SWISS-PROT. While TREMBL is already of immense value, its computer-generated annotation does not match the quality of SWISS-PROTs. The main difference is in the protein functional information attached to sequences. With this in mind, we are dedicating substantial effort to develop and apply computer methods to enhance the functional information attached to TREMBL entries.

A 5.8S nuclear ribosomal RNA gene sequence database: applications to ecology and evolution

NASA Technical Reports Server (NTRS)

Cullings, K. W.; Vogler, D. R.

1998-01-01

We complied a 5.8S nuclear ribosomal gene sequence database for animals, plants, and fungi using both newly generated and GenBank sequences. We demonstrate the utility of this database as an internal check to determine whether the target organism and not a contaminant has been sequenced, as a diagnostic tool for ecologists and evolutionary biologists to determine the placement of asexual fungi within larger taxonomic groups, and as a tool to help identify fungi that form ectomycorrhizae.

E-MSD: an integrated data resource for bioinformatics.

PubMed

Velankar, S; McNeil, P; Mittard-Runte, V; Suarez, A; Barrell, D; Apweiler, R; Henrick, K

2005-01-01

The Macromolecular Structure Database (MSD) group (http://www.ebi.ac.uk/msd/) continues to enhance the quality and consistency of macromolecular structure data in the worldwide Protein Data Bank (wwPDB) and to work towards the integration of various bioinformatics data resources. One of the major obstacles to the improved integration of structural databases such as MSD and sequence databases like UniProt is the absence of up to date and well-maintained mapping between corresponding entries. We have worked closely with the UniProt group at the EBI to clean up the taxonomy and sequence cross-reference information in the MSD and UniProt databases. This information is vital for the reliable integration of the sequence family databases such as Pfam and Interpro with the structure-oriented databases of SCOP and CATH. This information has been made available to the eFamily group (http://www.efamily.org.uk/) and now forms the basis of the regular interchange of information between the member databases (MSD, UniProt, Pfam, Interpro, SCOP and CATH). This exchange of annotation information has enriched the structural information in the MSD database with annotation from wider sequence-oriented resources. This work was carried out under the 'Structure Integration with Function, Taxonomy and Sequences (SIFTS)' initiative (http://www.ebi.ac.uk/msd-srv/docs/sifts) in the MSD group.

MagnaportheDB: a federated solution for integrating physical and genetic map data with BAC end derived sequences for the rice blast fungus Magnaporthe grisea.

PubMed

Martin, Stanton L; Blackmon, Barbara P; Rajagopalan, Ravi; Houfek, Thomas D; Sceeles, Robert G; Denn, Sheila O; Mitchell, Thomas K; Brown, Douglas E; Wing, Rod A; Dean, Ralph A

2002-01-01

We have created a federated database for genome studies of Magnaporthe grisea, the causal agent of rice blast disease, by integrating end sequence data from BAC clones, genetic marker data and BAC contig assembly data. A library of 9216 BAC clones providing >25-fold coverage of the entire genome was end sequenced and fingerprinted by HindIII digestion. The Image/FPC software package was then used to generate an assembly of 188 contigs covering >95% of the genome. The database contains the results of this assembly integrated with hybridization data of genetic markers to the BAC library. AceDB was used for the core database engine and a MySQL relational database, populated with numerical representations of BAC clones within FPC contigs, was used to create appropriately scaled images. The database is being used to facilitate sequencing efforts. The database also allows researchers mapping known genes or other sequences of interest, rapid and easy access to the fundamental organization of the M.grisea genome. This database, MagnaportheDB, can be accessed on the web at http://www.cals.ncsu.edu/fungal_genomics/mgdatabase/int.htm.

A two-step database search method improves sensitivity in peptide sequence matches for metaproteomics and proteogenomics studies.

PubMed

Jagtap, Pratik; Goslinga, Jill; Kooren, Joel A; McGowan, Thomas; Wroblewski, Matthew S; Seymour, Sean L; Griffin, Timothy J

2013-04-01

Large databases (>10(6) sequences) used in metaproteomic and proteogenomic studies present challenges in matching peptide sequences to MS/MS data using database-search programs. Most notably, strict filtering to avoid false-positive matches leads to more false negatives, thus constraining the number of peptide matches. To address this challenge, we developed a two-step method wherein matches derived from a primary search against a large database were used to create a smaller subset database. The second search was performed against a target-decoy version of this subset database merged with a host database. High confidence peptide sequence matches were then used to infer protein identities. Applying our two-step method for both metaproteomic and proteogenomic analysis resulted in twice the number of high confidence peptide sequence matches in each case, as compared to the conventional one-step method. The two-step method captured almost all of the same peptides matched by the one-step method, with a majority of the additional matches being false negatives from the one-step method. Furthermore, the two-step method improved results regardless of the database search program used. Our results show that our two-step method maximizes the peptide matching sensitivity for applications requiring large databases, especially valuable for proteogenomics and metaproteomics studies. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structator: fast index-based search for RNA sequence-structure patterns

PubMed Central

2011-01-01

Background The secondary structure of RNA molecules is intimately related to their function and often more conserved than the sequence. Hence, the important task of searching databases for RNAs requires to match sequence-structure patterns. Unfortunately, current tools for this task have, in the best case, a running time that is only linear in the size of sequence databases. Furthermore, established index data structures for fast sequence matching, like suffix trees or arrays, cannot benefit from the complementarity constraints introduced by the secondary structure of RNAs. Results We present a novel method and readily applicable software for time efficient matching of RNA sequence-structure patterns in sequence databases. Our approach is based on affix arrays, a recently introduced index data structure, preprocessed from the target database. Affix arrays support bidirectional pattern search, which is required for efficiently handling the structural constraints of the pattern. Structural patterns like stem-loops can be matched inside out, such that the loop region is matched first and then the pairing bases on the boundaries are matched consecutively. This allows to exploit base pairing information for search space reduction and leads to an expected running time that is sublinear in the size of the sequence database. The incorporation of a new chaining approach in the search of RNA sequence-structure patterns enables the description of molecules folding into complex secondary structures with multiple ordered patterns. The chaining approach removes spurious matches from the set of intermediate results, in particular of patterns with little specificity. In benchmark experiments on the Rfam database, our method runs up to two orders of magnitude faster than previous methods. Conclusions The presented method's sublinear expected running time makes it well suited for RNA sequence-structure pattern matching in large sequence databases. RNA molecules containing several stem-loop substructures can be described by multiple sequence-structure patterns and their matches are efficiently handled by a novel chaining method. Beyond our algorithmic contributions, we provide with Structator a complete and robust open-source software solution for index-based search of RNA sequence-structure patterns. The Structator software is available at http://www.zbh.uni-hamburg.de/Structator. PMID:21619640

Fastidious Gram-Negatives: Identification by the Vitek 2 Neisseria-Haemophilus Card and by Partial 16S rRNA Gene Sequencing Analysis.

PubMed

Sönksen, Ute Wolff; Christensen, Jens Jørgen; Nielsen, Lisbeth; Hesselbjerg, Annemarie; Hansen, Dennis Schrøder; Bruun, Brita

2010-12-31

Taxonomy and identification of fastidious Gram negatives are evolving and challenging. We compared identifications achieved with the Vitek 2 Neisseria-Haemophilus (NH) card and partial 16S rRNA gene sequence (526 bp stretch) analysis with identifications obtained with extensive phenotypic characterization using 100 fastidious Gram negative bacteria. Seventy-five strains represented 21 of the 26 taxa included in the Vitek 2 NH database and 25 strains represented related species not included in the database. Of the 100 strains, 31 were the type strains of the species. Vitek 2 NH identification results: 48 of 75 database strains were correctly identified, 11 strains gave `low discrimination´, seven strains were unidentified, and nine strains were misidentified. Identification of 25 non-database strains resulted in 14 strains incorrectly identified as belonging to species in the database. Partial 16S rRNA gene sequence analysis results: For 76 strains phenotypic and sequencing identifications were identical, for 23 strains the sequencing identifications were either probable or possible, and for one strain only the genus was confirmed. Thus, the Vitek 2 NH system identifies most of the commonly occurring species included in the database. Some strains of rarely occurring species and strains of non-database species closely related to database species cause problems. Partial 16S rRNA gene sequence analysis performs well, but does not always suffice, additional phenotypical characterization being useful for final identification.

Fastidious Gram-Negatives: Identification by the Vitek 2 Neisseria-Haemophilus Card and by Partial 16S rRNA Gene Sequencing Analysis

PubMed Central

Sönksen, Ute Wolff; Christensen, Jens Jørgen; Nielsen, Lisbeth; Hesselbjerg, Annemarie; Hansen, Dennis Schrøder; Bruun, Brita

2010-01-01

Taxonomy and identification of fastidious Gram negatives are evolving and challenging. We compared identifications achieved with the Vitek 2 Neisseria-Haemophilus (NH) card and partial 16S rRNA gene sequence (526 bp stretch) analysis with identifications obtained with extensive phenotypic characterization using 100 fastidious Gram negative bacteria. Seventy-five strains represented 21 of the 26 taxa included in the Vitek 2 NH database and 25 strains represented related species not included in the database. Of the 100 strains, 31 were the type strains of the species. Vitek 2 NH identification results: 48 of 75 database strains were correctly identified, 11 strains gave `low discrimination´, seven strains were unidentified, and nine strains were misidentified. Identification of 25 non-database strains resulted in 14 strains incorrectly identified as belonging to species in the database. Partial 16S rRNA gene sequence analysis results: For 76 strains phenotypic and sequencing identifications were identical, for 23 strains the sequencing identifications were either probable or possible, and for one strain only the genus was confirmed. Thus, the Vitek 2 NH system identifies most of the commonly occurring species included in the database. Some strains of rarely occurring species and strains of non-database species closely related to database species cause problems. Partial 16S rRNA gene sequence analysis performs well, but does not always suffice, additional phenotypical characterization being useful for final identification. PMID:21347215

SinEx DB: a database for single exon coding sequences in mammalian genomes.

PubMed

Jorquera, Roddy; Ortiz, Rodrigo; Ossandon, F; Cárdenas, Juan Pablo; Sepúlveda, Rene; González, Carolina; Holmes, David S

2016-01-01

Eukaryotic genes are typically interrupted by intragenic, noncoding sequences termed introns. However, some genes lack introns in their coding sequence (CDS) and are generally known as 'single exon genes' (SEGs). In this work, a SEG is defined as a nuclear, protein-coding gene that lacks introns in its CDS. Whereas, many public databases of Eukaryotic multi-exon genes are available, there are only two specialized databases for SEGs. The present work addresses the need for a more extensive and diverse database by creating SinEx DB, a publicly available, searchable database of predicted SEGs from 10 completely sequenced mammalian genomes including human. SinEx DB houses the DNA and protein sequence information of these SEGs and includes their functional predictions (KOG) and the relative distribution of these functions within species. The information is stored in a relational database built with My SQL Server 5.1.33 and the complete dataset of SEG sequences and their functional predictions are available for downloading. SinEx DB can be interrogated by: (i) a browsable phylogenetic schema, (ii) carrying out BLAST searches to the in-house SinEx DB of SEGs and (iii) via an advanced search mode in which the database can be searched by key words and any combination of searches by species and predicted functions. SinEx DB provides a rich source of information for advancing our understanding of the evolution and function of SEGs.Database URL: www.sinex.cl. © The Author(s) 2016. Published by Oxford University Press.

muBLASTP: database-indexed protein sequence search on multicore CPUs.

PubMed

Zhang, Jing; Misra, Sanchit; Wang, Hao; Feng, Wu-Chun

2016-11-04

The Basic Local Alignment Search Tool (BLAST) is a fundamental program in the life sciences that searches databases for sequences that are most similar to a query sequence. Currently, the BLAST algorithm utilizes a query-indexed approach. Although many approaches suggest that sequence search with a database index can achieve much higher throughput (e.g., BLAT, SSAHA, and CAFE), they cannot deliver the same level of sensitivity as the query-indexed BLAST, i.e., NCBI BLAST, or they can only support nucleotide sequence search, e.g., MegaBLAST. Due to different challenges and characteristics between query indexing and database indexing, the existing techniques for query-indexed search cannot be used into database indexed search. muBLASTP, a novel database-indexed BLAST for protein sequence search, delivers identical hits returned to NCBI BLAST. On Intel Haswell multicore CPUs, for a single query, the single-threaded muBLASTP achieves up to a 4.41-fold speedup for alignment stages, and up to a 1.75-fold end-to-end speedup over single-threaded NCBI BLAST. For a batch of queries, the multithreaded muBLASTP achieves up to a 5.7-fold speedups for alignment stages, and up to a 4.56-fold end-to-end speedup over multithreaded NCBI BLAST. With a newly designed index structure for protein database and associated optimizations in BLASTP algorithm, we re-factored BLASTP algorithm for modern multicore processors that achieves much higher throughput with acceptable memory footprint for the database index.

BLAST and FASTA similarity searching for multiple sequence alignment.

PubMed

Pearson, William R

2014-01-01

BLAST, FASTA, and other similarity searching programs seek to identify homologous proteins and DNA sequences based on excess sequence similarity. If two sequences share much more similarity than expected by chance, the simplest explanation for the excess similarity is common ancestry-homology. The most effective similarity searches compare protein sequences, rather than DNA sequences, for sequences that encode proteins, and use expectation values, rather than percent identity, to infer homology. The BLAST and FASTA packages of sequence comparison programs provide programs for comparing protein and DNA sequences to protein databases (the most sensitive searches). Protein and translated-DNA comparisons to protein databases routinely allow evolutionary look back times from 1 to 2 billion years; DNA:DNA searches are 5-10-fold less sensitive. BLAST and FASTA can be run on popular web sites, but can also be downloaded and installed on local computers. With local installation, target databases can be customized for the sequence data being characterized. With today's very large protein databases, search sensitivity can also be improved by searching smaller comprehensive databases, for example, a complete protein set from an evolutionarily neighboring model organism. By default, BLAST and FASTA use scoring strategies target for distant evolutionary relationships; for comparisons involving short domains or queries, or searches that seek relatively close homologs (e.g. mouse-human), shallower scoring matrices will be more effective. Both BLAST and FASTA provide very accurate statistical estimates, which can be used to reliably identify protein sequences that diverged more than 2 billion years ago.

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

Tandem mass spectrometry for the detection of plant pathogenic fungi and the effects of database composition on protein inferences.

PubMed

Padliya, Neerav D; Garrett, Wesley M; Campbell, Kimberly B; Tabb, David L; Cooper, Bret

2007-11-01

LC-MS/MS has demonstrated potential for detecting plant pathogens. Unlike PCR or ELISA, LC-MS/MS does not require pathogen-specific reagents for the detection of pathogen-specific proteins and peptides. However, the MS/MS approach we and others have explored does require a protein sequence reference database and database-search software to interpret tandem mass spectra. To evaluate the limitations of database composition on pathogen identification, we analyzed proteins from cultured Ustilago maydis, Phytophthora sojae, Fusarium graminearum, and Rhizoctonia solani by LC-MS/MS. When the search database did not contain sequences for a target pathogen, or contained sequences to related pathogens, target pathogen spectra were reliably matched to protein sequences from nontarget organisms, giving an illusion that proteins from nontarget organisms were identified. Our analysis demonstrates that when database-search software is used as part of the identification process, a paradox exists whereby additional sequences needed to detect a wide variety of possible organisms may lead to more cross-species protein matches and misidentification of pathogens.

Coping with Uncertainty in an Agile Systems Development Course

ERIC Educational Resources Information Center

Taipalus, Toni; Seppänen, Ville; Pirhonen, Maritta

2018-01-01

Uncertain and ambiguous environments are commonplace in information systems development (ISD) projects, and while different Agile frameworks welcome changes in organizational, technical, and business environments, the incurred uncertainty is known to negatively affect the development process and the quality of the final product. The effects of…

Hot Topics in School Public Relations.

ERIC Educational Resources Information Center

Lange, Lois, Ed.; Young, Jay, Ed.

This document examines the public relations activities occurring in K-12 and intermediate school districts, needs for other activities, and how Michigan School Public Relations Association (MSPRA) can assist. Written surveys were mailed to 394 K-12 and Intermediate School District (ISD) superintendents. Analysis showed that very few school…

DoOP: Databases of Orthologous Promoters, collections of clusters of orthologous upstream sequences from chordates and plants

PubMed Central

Barta, Endre; Sebestyén, Endre; Pálfy, Tamás B.; Tóth, Gábor; Ortutay, Csaba P.; Patthy, László

2005-01-01

DoOP (http://doop.abc.hu/) is a database of eukaryotic promoter sequences (upstream regions) aiming to facilitate the recognition of regulatory sites conserved between species. The annotated first exons of human and Arabidopsis thaliana genes were used as queries in BLAST searches to collect the most closely related orthologous first exon sequences from Chordata and Viridiplantae species. Up to 3000 bp DNA segments upstream from these first exons constitute the clusters in the chordate and plant sections of the Database of Orthologous Promoters. Release 1.0 of DoOP contains 21 061 chordate clusters from 284 different species and 7548 plant clusters from 269 different species. The database can be used to find and retrieve promoter sequences of a given gene from various species and it is also suitable to see the most trivial conserved sequence blocks in the orthologous upstream regions. Users can search DoOP with either sequence or text (annotation) to find promoter clusters of various genes. In addition to the sequence data, the positions of the conserved sequence blocks derived from multiple alignments, the positions of repetitive elements and the positions of transcription start sites known from the Eukaryotic Promoter Database (EPD) can be viewed graphically. PMID:15608291

DoOP: Databases of Orthologous Promoters, collections of clusters of orthologous upstream sequences from chordates and plants.

PubMed

Barta, Endre; Sebestyén, Endre; Pálfy, Tamás B; Tóth, Gábor; Ortutay, Csaba P; Patthy, László

2005-01-01

DoOP (http://doop.abc.hu/) is a database of eukaryotic promoter sequences (upstream regions) aiming to facilitate the recognition of regulatory sites conserved between species. The annotated first exons of human and Arabidopsis thaliana genes were used as queries in BLAST searches to collect the most closely related orthologous first exon sequences from Chordata and Viridiplantae species. Up to 3000 bp DNA segments upstream from these first exons constitute the clusters in the chordate and plant sections of the Database of Orthologous Promoters. Release 1.0 of DoOP contains 21,061 chordate clusters from 284 different species and 7548 plant clusters from 269 different species. The database can be used to find and retrieve promoter sequences of a given gene from various species and it is also suitable to see the most trivial conserved sequence blocks in the orthologous upstream regions. Users can search DoOP with either sequence or text (annotation) to find promoter clusters of various genes. In addition to the sequence data, the positions of the conserved sequence blocks derived from multiple alignments, the positions of repetitive elements and the positions of transcription start sites known from the Eukaryotic Promoter Database (EPD) can be viewed graphically.

Non-redundant patent sequence databases with value-added annotations at two levels

PubMed Central

Li, Weizhong; McWilliam, Hamish; de la Torre, Ana Richart; Grodowski, Adam; Benediktovich, Irina; Goujon, Mickael; Nauche, Stephane; Lopez, Rodrigo

2010-01-01

The European Bioinformatics Institute (EMBL-EBI) provides public access to patent data, including abstracts, chemical compounds and sequences. Sequences can appear multiple times due to the filing of the same invention with multiple patent offices, or the use of the same sequence by different inventors in different contexts. Information relating to the source invention may be incomplete, and biological information available in patent documents elsewhere may not be reflected in the annotation of the sequence. Search and analysis of these data have become increasingly challenging for both the scientific and intellectual-property communities. Here, we report a collection of non-redundant patent sequence databases, which cover the EMBL-Bank nucleotides patent class and the patent protein databases and contain value-added annotations from patent documents. The databases were created at two levels by the use of sequence MD5 checksums. Sequences within a level-1 cluster are 100% identical over their whole length. Level-2 clusters were defined by sub-grouping level-1 clusters based on patent family information. Value-added annotations, such as publication number corrections, earliest publication dates and feature collations, significantly enhance the quality of the data, allowing for better tracking and cross-referencing. The databases are available format: http://www.ebi.ac.uk/patentdata/nr/. PMID:19884134

Non-redundant patent sequence databases with value-added annotations at two levels.

PubMed

Li, Weizhong; McWilliam, Hamish; de la Torre, Ana Richart; Grodowski, Adam; Benediktovich, Irina; Goujon, Mickael; Nauche, Stephane; Lopez, Rodrigo

2010-01-01

The European Bioinformatics Institute (EMBL-EBI) provides public access to patent data, including abstracts, chemical compounds and sequences. Sequences can appear multiple times due to the filing of the same invention with multiple patent offices, or the use of the same sequence by different inventors in different contexts. Information relating to the source invention may be incomplete, and biological information available in patent documents elsewhere may not be reflected in the annotation of the sequence. Search and analysis of these data have become increasingly challenging for both the scientific and intellectual-property communities. Here, we report a collection of non-redundant patent sequence databases, which cover the EMBL-Bank nucleotides patent class and the patent protein databases and contain value-added annotations from patent documents. The databases were created at two levels by the use of sequence MD5 checksums. Sequences within a level-1 cluster are 100% identical over their whole length. Level-2 clusters were defined by sub-grouping level-1 clusters based on patent family information. Value-added annotations, such as publication number corrections, earliest publication dates and feature collations, significantly enhance the quality of the data, allowing for better tracking and cross-referencing. The databases are available format: http://www.ebi.ac.uk/patentdata/nr/.

The Universal Protein Resource (UniProt): an expanding universe of protein information.

PubMed

Wu, Cathy H; Apweiler, Rolf; Bairoch, Amos; Natale, Darren A; Barker, Winona C; Boeckmann, Brigitte; Ferro, Serenella; Gasteiger, Elisabeth; Huang, Hongzhan; Lopez, Rodrigo; Magrane, Michele; Martin, Maria J; Mazumder, Raja; O'Donovan, Claire; Redaschi, Nicole; Suzek, Baris

2006-01-01

The Universal Protein Resource (UniProt) provides a central resource on protein sequences and functional annotation with three database components, each addressing a key need in protein bioinformatics. The UniProt Knowledgebase (UniProtKB), comprising the manually annotated UniProtKB/Swiss-Prot section and the automatically annotated UniProtKB/TrEMBL section, is the preeminent storehouse of protein annotation. The extensive cross-references, functional and feature annotations and literature-based evidence attribution enable scientists to analyse proteins and query across databases. The UniProt Reference Clusters (UniRef) speed similarity searches via sequence space compression by merging sequences that are 100% (UniRef100), 90% (UniRef90) or 50% (UniRef50) identical. Finally, the UniProt Archive (UniParc) stores all publicly available protein sequences, containing the history of sequence data with links to the source databases. UniProt databases continue to grow in size and in availability of information. Recent and upcoming changes to database contents, formats, controlled vocabularies and services are described. New download availability includes all major releases of UniProtKB, sequence collections by taxonomic division and complete proteomes. A bibliography mapping service has been added, and an ID mapping service will be available soon. UniProt databases can be accessed online at http://www.uniprot.org or downloaded at ftp://ftp.uniprot.org/pub/databases/.

BIOPEP database and other programs for processing bioactive peptide sequences.

PubMed

Minkiewicz, Piotr; Dziuba, Jerzy; Iwaniak, Anna; Dziuba, Marta; Darewicz, Małgorzata

2008-01-01

This review presents the potential for application of computational tools in peptide science based on a sample BIOPEP database and program as well as other programs and databases available via the World Wide Web. The BIOPEP application contains a database of biologically active peptide sequences and a program enabling construction of profiles of the potential biological activity of protein fragments, calculation of quantitative descriptors as measures of the value of proteins as potential precursors of bioactive peptides, and prediction of bonds susceptible to hydrolysis by endopeptidases in a protein chain. Other bioactive and allergenic peptide sequence databases are also presented. Programs enabling the construction of binary and multiple alignments between peptide sequences, the construction of sequence motifs attributed to a given type of bioactivity, searching for potential precursors of bioactive peptides, and the prediction of sites susceptible to proteolytic cleavage in protein chains are available via the Internet as are other approaches concerning secondary structure prediction and calculation of physicochemical features based on amino acid sequence. Programs for prediction of allergenic and toxic properties have also been developed. This review explores the possibilities of cooperation between various programs.

GenBank.

PubMed

Benson, Dennis A; Karsch-Mizrachi, Ilene; Lipman, David J; Ostell, James; Sayers, Eric W

2010-01-01

GenBank is a comprehensive database that contains publicly available nucleotide sequences for more than 300,000 organisms named at the genus level or lower, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole genome shotgun (WGS) and environmental sampling 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 the NCBI Entrez retrieval system, 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 bi-monthly 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

Benson, Dennis A; Karsch-Mizrachi, Ilene; Lipman, David J; Ostell, James; Sayers, Eric W

2009-01-01

GenBank is a comprehensive database that contains publicly available nucleotide sequences for more than 300,000 organisms named at the genus level or lower, 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(R) 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 the National Center for Biotechnology Information (NCBI) Entrez retrieval system, 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.

The Porcelain Crab Transcriptome and PCAD, the Porcelain Crab Microarray and Sequence Database

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

Tagmount, Abderrahmane; Wang, Mei; Lindquist, Erika

2010-01-27

Background: With the emergence of a completed genome sequence of the freshwater crustacean Daphnia pulex, construction of genomic-scale sequence databases for additional crustacean sequences are important for comparative genomics and annotation. Porcelain crabs, genus Petrolisthes, have been powerful crustacean models for environmental and evolutionary physiology with respect to thermal adaptation and understanding responses of marine organisms to climate change. Here, we present a large-scale EST sequencing and cDNA microarray database project for the porcelain crab Petrolisthes cinctipes. Methodology/Principal Findings: A set of ~;;30K unique sequences (UniSeqs) representing ~;;19K clusters were generated from ~;;98K high quality ESTs from a set ofmore » tissue specific non-normalized and mixed-tissue normalized cDNA libraries from the porcelain crab Petrolisthes cinctipes. Homology for each UniSeq was assessed using BLAST, InterProScan, GO and KEGG database searches. Approximately 66percent of the UniSeqs had homology in at least one of the databases. All EST and UniSeq sequences along with annotation results and coordinated cDNA microarray datasets have been made publicly accessible at the Porcelain Crab Array Database (PCAD), a feature-enriched version of the Stanford and Longhorn Array Databases.Conclusions/Significance: The EST project presented here represents the third largest sequencing effort for any crustacean, and the largest effort for any crab species. Our assembly and clustering results suggest that our porcelain crab EST data set is equally diverse to the much larger EST set generated in the Daphnia pulex genome sequencing project, and thus will be an important resource to the Daphnia research community. Our homology results support the pancrustacea hypothesis and suggest that Malacostraca may be ancestral to Branchiopoda and Hexapoda. Our results also suggest that our cDNA microarrays cover as much of the transcriptome as can reasonably be captured in EST library sequencing approaches, and thus represent a rich resource for studies of environmental genomics.« less

A comprehensive aligned nifH gene database: a multipurpose tool for studies of nitrogen-fixing bacteria.

PubMed

Gaby, John Christian; Buckley, Daniel H

2014-01-01

We describe a nitrogenase gene sequence database that facilitates analysis of the evolution and ecology of nitrogen-fixing organisms. The database contains 32 954 aligned nitrogenase nifH sequences linked to phylogenetic trees and associated sequence metadata. The database includes 185 linked multigene entries including full-length nifH, nifD, nifK and 16S ribosomal RNA (rRNA) gene sequences. Evolutionary analyses enabled by the multigene entries support an ancient horizontal transfer of nitrogenase genes between Archaea and Bacteria and provide evidence that nifH has a different history of horizontal gene transfer from the nifDK enzyme core. Further analyses show that lineages in nitrogenase cluster I and cluster III have different rates of substitution within nifD, suggesting that nifD is under different selection pressure in these two lineages. Finally, we find that that the genetic divergence of nifH and 16S rRNA genes does not correlate well at sequence dissimilarity values used commonly to define microbial species, as stains having <3% sequence dissimilarity in their 16S rRNA genes can have up to 23% dissimilarity in nifH. The nifH database has a number of uses including phylogenetic and evolutionary analyses, the design and assessment of primers/probes and the evaluation of nitrogenase sequence diversity. Database URL: http://www.css.cornell.edu/faculty/buckley/nifh.htm.

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

A comprehensive aligned nifH gene database: a multipurpose tool for studies of nitrogen-fixing bacteria

PubMed Central

Gaby, John Christian; Buckley, Daniel H.

2014-01-01

We describe a nitrogenase gene sequence database that facilitates analysis of the evolution and ecology of nitrogen-fixing organisms. The database contains 32 954 aligned nitrogenase nifH sequences linked to phylogenetic trees and associated sequence metadata. The database includes 185 linked multigene entries including full-length nifH, nifD, nifK and 16S ribosomal RNA (rRNA) gene sequences. Evolutionary analyses enabled by the multigene entries support an ancient horizontal transfer of nitrogenase genes between Archaea and Bacteria and provide evidence that nifH has a different history of horizontal gene transfer from the nifDK enzyme core. Further analyses show that lineages in nitrogenase cluster I and cluster III have different rates of substitution within nifD, suggesting that nifD is under different selection pressure in these two lineages. Finally, we find that that the genetic divergence of nifH and 16S rRNA genes does not correlate well at sequence dissimilarity values used commonly to define microbial species, as stains having <3% sequence dissimilarity in their 16S rRNA genes can have up to 23% dissimilarity in nifH. The nifH database has a number of uses including phylogenetic and evolutionary analyses, the design and assessment of primers/probes and the evaluation of nitrogenase sequence diversity. Database URL: http://www.css.cornell.edu/faculty/buckley/nifh.htm PMID:24501396

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.

A meta-analysis of bacterial diversity in the feces of cattle

USDA-ARS?s Scientific Manuscript database

In this study, we conducted a meta-analysis on 16S rRNA gene sequences of bovine fecal origin that are publicly available in the RDP database. A total of 13663 sequences including 603 isolate sequences were identified in the RDP database (Release 11, Update 1), where 13447 sequences were assigned t...

PineElm_SSRdb: a microsatellite marker database identified from genomic, chloroplast, mitochondrial and EST sequences of pineapple (Ananas comosus (L.) Merrill).

PubMed

Chaudhary, Sakshi; Mishra, Bharat Kumar; Vivek, Thiruvettai; Magadum, Santoshkumar; Yasin, Jeshima Khan

2016-01-01

Simple Sequence Repeats or microsatellites are resourceful molecular genetic markers. There are only few reports of SSR identification and development in pineapple. Complete genome sequence of pineapple available in the public domain can be used to develop numerous novel SSRs. Therefore, an attempt was made to identify SSRs from genomic, chloroplast, mitochondrial and EST sequences of pineapple which will help in deciphering genetic makeup of its germplasm resources. A total of 359511 SSRs were identified in pineapple (356385 from genome sequence, 45 from chloroplast sequence, 249 in mitochondrial sequence and 2832 from EST sequences). The list of EST-SSR markers and their details are available in the database. PineElm_SSRdb is an open source database available for non-commercial academic purpose at http://app.bioelm.com/ with a mapping tool which can develop circular maps of selected marker set. This database will be of immense use to breeders, researchers and graduates working on Ananas spp. and to others working on cross-species transferability of markers, investigating diversity, mapping and DNA fingerprinting.

PlantCAZyme: a database for plant carbohydrate-active enzymes

PubMed Central

Ekstrom, Alexander; Taujale, Rahil; McGinn, Nathan; Yin, Yanbin

2014-01-01

PlantCAZyme is a database built upon dbCAN (database for automated carbohydrate active enzyme annotation), aiming to provide pre-computed sequence and annotation data of carbohydrate active enzymes (CAZymes) to plant carbohydrate and bioenergy research communities. The current version contains data of 43 790 CAZymes of 159 protein families from 35 plants (including angiosperms, gymnosperms, lycophyte and bryophyte mosses) and chlorophyte algae with fully sequenced genomes. Useful features of the database include: (i) a BLAST server and a HMMER server that allow users to search against our pre-computed sequence data for annotation purpose, (ii) a download page to allow batch downloading data of a specific CAZyme family or species and (iii) protein browse pages to provide an easy access to the most comprehensive sequence and annotation data. Database URL: http://cys.bios.niu.edu/plantcazyme/ PMID:25125445

RNAcentral: an international database of ncRNA sequences

DOE PAGES

Williams, Kelly Porter

2014-10-28

The field of non-coding RNA biology has been hampered by the lack of availability of a comprehensive, up-to-date collection of accessioned RNA sequences. Here we present the first release of RNAcentral, a database that collates and integrates information from an international consortium of established RNA sequence databases. The initial release contains over 8.1 million sequences, including representatives of all major functional classes. A web portal (http://rnacentral.org) provides free access to data, search functionality, cross-references, source code and an integrated genome browser for selected species.

An Integrated Molecular Database on Indian Insects.

PubMed

Pratheepa, Maria; Venkatesan, Thiruvengadam; Gracy, Gandhi; Jalali, Sushil Kumar; Rangheswaran, Rajagopal; Antony, Jomin Cruz; Rai, Anil

2018-01-01

MOlecular Database on Indian Insects (MODII) is an online database linking several databases like Insect Pest Info, Insect Barcode Information System (IBIn), Insect Whole Genome sequence, Other Genomic Resources of National Bureau of Agricultural Insect Resources (NBAIR), Whole Genome sequencing of Honey bee viruses, Insecticide resistance gene database and Genomic tools. This database was developed with a holistic approach for collecting information about phenomic and genomic information of agriculturally important insects. This insect resource database is available online for free at http://cib.res.in. http://cib.res.in/.

IFLA General Conference, 1986. Collections and Services Division. Section: Serial Publications. Papers.

ERIC Educational Resources Information Center

International Federation of Library Associations and Institutions, The Hague (Netherlands).

Papers on serial publications presented at the 1986 International Federation of Library Associations (IFLA) conference include: (1) "Scenario for Microcomputer-Based Serials Cataloging from ISDS (International Serials Data System) Records--New Horizons for Serial Librarianship in the Developing Countries by the Availability of Adequate…

Atascocita Springs Elementary School

ERIC Educational Resources Information Center

Nigaglioni, Irene; Yocham, Deborah

2011-01-01

With the significant amount of time invested in researching the best techniques for delivering instruction to their students, Humble ISD is always on the forefront of education. Taking the recommendations of their active and vocal community groups, the district embarked in the design of the 26th elementary school, Atascocita Springs Elementary…

Training in Japan: The Use of Instructional Systems Design.

ERIC Educational Resources Information Center

Taguchi, Mina; Keller, John M.

This study investigated the kinds of training conducted in Japanese companies and the degree to which instructional systems design (ISD) is implemented. A random sample of 12 Japanese companies in the banking, automobile manufacturing, electrical machinery, wholesale stores, insurance and securities, and transportation industries were surveyed; a…

Job Aid Manuals for Phase II--DESIGN of the Instructional Systems Development Model.

ERIC Educational Resources Information Center

Schulz, Russel E.; Farrell, Jean R.

Designed to supplement the descriptive authoring flowcharts presented in a companion volume, this manual includes specific guidance, examples, and other information referred to in the flowcharts for the implementation of the second phase of the Instructional Systems Development Model (ISD). The introductory section includes definitions;…

Job Aid Manuals for Phase I--ANALYZE of the Instructional Systems Development Model.

ERIC Educational Resources Information Center

Schulz, Russel E.; Farrell, Jean R.

Designed to supplement the descriptive authoring flowcharts in a companion volume, this manual includes specific guidance, examples, and other information referred to in the flowcharts for the implementation of the first phase of the Instructional Systems Development Model (ISD). The introductory section includes definitions; descriptions of…

The Leadership Gap: Preparing Leaders for Urban Schools

ERIC Educational Resources Information Center

Lee, Omaira Z.

2010-01-01

The purpose of this mixed-methods, purposive case study was to investigate the impact of participation in the Metropolitan ISD Principal Coaching Initiative (MPCI) on leadership practice. The MPCI is a district-wide executive leadership capacity building strategy, which combines the District's standards-based leadership curriculum with a…

Magic Spells. MicroSIFT Courseware Evaluation.

ERIC Educational Resources Information Center

Northwest Regional Educational Lab., Portland, OR.

THE FOLLOWING IS THE FULL TEXT OF THIS DOCUMENT (Except for the Evaluation Summary Table): VERSION: Copyright 1981. PRODUCER: Advanced Learning Technology, Inc., 4370 Alpine Road, Portola Valley, CA 94025. EVALUATION COMPLETED: January, 1983 by the Oakland ISD, Pontiac, Michigan. COST: $45.00. ABILITY LEVEL: Grades 1 to 8. SUBJECT: Language Arts.…

ISD Model Building: From Tabula Rasa to Apple Peel

ERIC Educational Resources Information Center

Ruark, Benjamin E.

2008-01-01

An evidence-based practice (EBP) model is proposed to replace the more-art-than-science "rope bridge" currently spanning the defining space of a training need and the designing space of a training curriculum. The rope bridge analogy symbolizes a way to address perceived deficiencies and research gaps in the…

Rapid Prototyping: An Alternative Instructional Design Strategy.

ERIC Educational Resources Information Center

Tripp, Steven D.; Bichelmeyer, Barbara

1990-01-01

Discusses the nature of instructional design and describes rapid prototyping as a feasible model for instructional system design (ISD). The use of prototyping in software engineering is described, similarities between software design and instructional design are discussed, and an example is given which uses rapid prototyping in designing a…

Spelling Strategy. MicroSIFT Courseware Evaluation.

ERIC Educational Resources Information Center

Northwest Regional Educational Lab., Portland, OR.

THE FOLLOWING IS THE FULL TEXT OF THIS DOCUMENT (Except for the Evaluation Summary Table): VERSION: Copyright 1981. PRODUCER: Behavioral Engineering, 230 Mt. Hermon Road, Suite 207, Scotts Valley, CA 95066. EVALUATION COMPLETED: January, 1983 at the Oakland ISD in Pontiac, Michigan. COST: $45.00. ABILITY LEVEL: Grades 2 to 8. SUBJECT: Language…

Developing Distance Education Content Using the TAPPA Process

ERIC Educational Resources Information Center

Moore, Robert L.

2016-01-01

The proliferation of distance education has occurred alongside the emerging technologies of the Web 2.0 and Web 3.0 environments, changing the way instructors approach, design, and deliver their instructional materials. In the past, instructional design (ID) practitioners relied on instruction system design (ISD) models that focused primarily on…

Speed Reader. MicroSIFT Courseware Evaluation.

ERIC Educational Resources Information Center

Northwest Regional Educational Lab., Portland, OR.

THE FOLLOWING IS THE FULL TEXT OF THIS DOCUMENT (Except for the Evaluation Summary Table): VERSION: Copyright 1981. PRODUCER: Davidson and Associates, 6069 Groveoak Place #12, Rancho Palos Verdes, CA 90274. EVALUATION COMPLETED: January, 1983 by the Oakland ISD of Pontiac, Michigan. COST: $70.00. ABILITY LEVEL: Secondary. SUBJECT: Reading. MEDIUM…

ELL to Go

ERIC Educational Resources Information Center

Demski, Jennifer

2011-01-01

Township High School District 214 in Arlington Heights, Illinois, and Comal Independent School District (ISD) in New Braunfels, Texas, are pioneers in the incorporation of mobile devices such as the iPad and iPod Touch in the English language learner (ELL) classroom. Though it's too soon to collect significant quantitative data regarding the…

Defining the "D" in ISD. Part 1: Task-General Instructional Methods.

ERIC Educational Resources Information Center

Clark, Ruth Colvin

1986-01-01

The first of two articles designed to provide guidelines for the instructional development phase of instructional systems development focuses on general instructional methods supporting all instructional tasks. Teaching methods that support selective attention, processing in working memory, and connecting in long-term memory are described and…

Job Aid Manuals for Phase III--DEVELOP of the Instructional Systems Development Model.

ERIC Educational Resources Information Center

Schulz, Russel E.; Farrell, Jean R.

Designed to supplement the descriptive authoring flowcharts presented in a companion volume, this manual includes specific guidance, examples, and other information referred to in the flowcharts for the implementation of the third phase of the Instructional Systems Development Model (ISD). The introductory section includes definitions;…

Overcoming Species Boundaries in Peptide Identification with Bayesian Information Criterion-driven Error-tolerant Peptide Search (BICEPS)*

PubMed Central

Renard, Bernhard Y.; Xu, Buote; Kirchner, Marc; Zickmann, Franziska; Winter, Dominic; Korten, Simone; Brattig, Norbert W.; Tzur, Amit; Hamprecht, Fred A.; Steen, Hanno

2012-01-01

Currently, the reliable identification of peptides and proteins is only feasible when thoroughly annotated sequence databases are available. Although sequencing capacities continue to grow, many organisms remain without reliable, fully annotated reference genomes required for proteomic analyses. Standard database search algorithms fail to identify peptides that are not exactly contained in a protein database. De novo searches are generally hindered by their restricted reliability, and current error-tolerant search strategies are limited by global, heuristic tradeoffs between database and spectral information. We propose a Bayesian information criterion-driven error-tolerant peptide search (BICEPS) and offer an open source implementation based on this statistical criterion to automatically balance the information of each single spectrum and the database, while limiting the run time. We show that BICEPS performs as well as current database search algorithms when such algorithms are applied to sequenced organisms, whereas BICEPS only uses a remotely related organism database. For instance, we use a chicken instead of a human database corresponding to an evolutionary distance of more than 300 million years (International Chicken Genome Sequencing Consortium (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432, 695–716). We demonstrate the successful application to cross-species proteomics with a 33% increase in the number of identified proteins for a filarial nematode sample of Litomosoides sigmodontis. PMID:22493179

E-MSD: an integrated data resource for bioinformatics

PubMed Central

Velankar, S.; McNeil, P.; Mittard-Runte, V.; Suarez, A.; Barrell, D.; Apweiler, R.; Henrick, K.

2005-01-01

The Macromolecular Structure Database (MSD) group (http://www.ebi.ac.uk/msd/) continues to enhance the quality and consistency of macromolecular structure data in the worldwide Protein Data Bank (wwPDB) and to work towards the integration of various bioinformatics data resources. One of the major obstacles to the improved integration of structural databases such as MSD and sequence databases like UniProt is the absence of up to date and well-maintained mapping between corresponding entries. We have worked closely with the UniProt group at the EBI to clean up the taxonomy and sequence cross-reference information in the MSD and UniProt databases. This information is vital for the reliable integration of the sequence family databases such as Pfam and Interpro with the structure-oriented databases of SCOP and CATH. This information has been made available to the eFamily group (http://www.efamily.org.uk/) and now forms the basis of the regular interchange of information between the member databases (MSD, UniProt, Pfam, Interpro, SCOP and CATH). This exchange of annotation information has enriched the structural information in the MSD database with annotation from wider sequence-oriented resources. This work was carried out under the ‘Structure Integration with Function, Taxonomy and Sequences (SIFTS)’ initiative (http://www.ebi.ac.uk/msd-srv/docs/sifts) in the MSD group. PMID:15608192

MAGIC database and interfaces: an integrated package for gene discovery and expression.

PubMed

Cordonnier-Pratt, Marie-Michèle; Liang, Chun; Wang, Haiming; Kolychev, Dmitri S; Sun, Feng; Freeman, Robert; Sullivan, Robert; Pratt, Lee H

2004-01-01

The rapidly increasing rate at which biological data is being produced requires a corresponding growth in relational databases and associated tools that can help laboratories contend with that data. With this need in mind, we describe here a Modular Approach to a Genomic, Integrated and Comprehensive (MAGIC) Database. This Oracle 9i database derives from an initial focus in our laboratory on gene discovery via production and analysis of expressed sequence tags (ESTs), and subsequently on gene expression as assessed by both EST clustering and microarrays. The MAGIC Gene Discovery portion of the database focuses on information derived from DNA sequences and on its biological relevance. In addition to MAGIC SEQ-LIMS, which is designed to support activities in the laboratory, it contains several additional subschemas. The latter include MAGIC Admin for database administration, MAGIC Sequence for sequence processing as well as sequence and clone attributes, MAGIC Cluster for the results of EST clustering, MAGIC Polymorphism in support of microsatellite and single-nucleotide-polymorphism discovery, and MAGIC Annotation for electronic annotation by BLAST and BLAT. The MAGIC Microarray portion is a MIAME-compliant database with two components at present. These are MAGIC Array-LIMS, which makes possible remote entry of all information into the database, and MAGIC Array Analysis, which provides data mining and visualization. Because all aspects of interaction with the MAGIC Database are via a web browser, it is ideally suited not only for individual research laboratories but also for core facilities that serve clients at any distance.

Stardust Interstellar Preliminary Examination

NASA Astrophysics Data System (ADS)

Westphal, A.; Stardust Interstellar Preliminary Examation Team: http://www. ssl. berkeley. edu/~westphal/ISPE/

2011-12-01

A. J. Westphal, C. Allen, A. Ansari, S. Bajt, R. S. Bastien, H. A. Bechtel, J. Borg, F. E. Brenker, J. Bridges, D. E. Brownlee, M. Burchell, M. Burghammer, A. L. Butterworth, A. M. Davis, P. Cloetens, C. Floss, G. Flynn, D. Frank, Z. Gainsforth, E. Grün, P. R. Heck, J. K. Hillier, P. Hoppe, G. Huss, J. Huth, B. Hvide, A. Kearsley, A. J. King, B. Lai, J. Leitner, L. Lemelle, H. Leroux, R. Lettieri, W. Marchant, L. R. Nittler, R. Ogliore, F. Postberg, M. C. Price, S. A. Sandford, J.-A. Sans Tresseras, T. Schoonjans, S. Schmitz, G. Silversmit, A. Simionovici, V. A. Solé, R. Srama, T. Stephan, V. Sterken, J. Stodolna, R. M. Stroud, S. Sutton, M. Trieloff, P. Tsou, A. Tsuchiyama, T. Tyliszczak, B. Vekemans, L. Vincze, D. Zevin, M. E. Zolensky, >29,000 Stardust@home dusters ISPE author affiliations are at http://www.ssl.berkeley.edu/~westphal/ISPE/. In 2000 and 2002, a ~0.1m2 array of aerogel tiles and alumi-num foils onboard the Stardust spacecraft was exposed to the interstellar dust (ISD) stream for an integrated time of 200 days. The exposure took place in interplanetary space, beyond the orbit of Mars, and thus was free of the ubiquitous orbital debris in low-earth orbit that precludes effective searches for interstellar dust there. Despite the long exposure of the Stardust collector, <<100 ISD particles are expected to have been captured. The particles are thought to be ~1μm or less in size, and the total ISD collection is probably <10-6 by mass of the collection of cometary dust parti-cles captured in the Stardust cometary dust collector from the coma of the Jupiter-family comet Wild 2. Thus, although the first solid sample from the local interstellar medium is clearly of high interest, the diminutive size of the particles and the low numbers of particles present daunting challenges. Nevertheless, six recent developments have made a Preliminary Examination (PE) of this sample practical: (1) rapid automated digital optical scanning microscopy for three-dimensional imaging of the aerogel collector; (2) rapid automated digital scanning electron microscopy for imaging of the aluminum foils; (3) an effective, massively-distributed search by citizen scientists through the Internet; (4) extraction and sample preparation tech-niques for μm-sized particles in aerogel; (5) advances in capabili-ties of synchrotron infrared and X-ray microprobes that enable non-destructive analyses of sub-μm particles in situ in aerogel; and (6) the development of focused-ion beam (FIB) milling tech-niques for sample preparation. The Stardust Interstellar PE consists of six related projects: the identification of tracks through automated scanning microscopy and distributed searching by volunteers (Stardust@home); the extraction of tracks from aerogel in "picokeystones"; the analysis of tracks using synchrotron microprobes; the identifica-tion and analysis of impacts in aluminum foils; laboratory investigations of ISD analogs using an electrostatic dust accelerator; and modeling of ISD propagation in the heliosphere. To date we have identified four impacts in the aerogel collector and one on the foils of probable interstellar origin. We will report on our analyses and implications for the solid component of the local interstellar medium.

Metagenomic Taxonomy-Guided Database-Searching Strategy for Improving Metaproteomic Analysis.

PubMed

Xiao, Jinqiu; Tanca, Alessandro; Jia, Ben; Yang, Runqing; Wang, Bo; Zhang, Yu; Li, Jing

2018-04-06

Metaproteomics provides a direct measure of the functional information by investigating all proteins expressed by a microbiota. However, due to the complexity and heterogeneity of microbial communities, it is very hard to construct a sequence database suitable for a metaproteomic study. Using a public database, researchers might not be able to identify proteins from poorly characterized microbial species, while a sequencing-based metagenomic database may not provide adequate coverage for all potentially expressed protein sequences. To address this challenge, we propose a metagenomic taxonomy-guided database-search strategy (MT), in which a merged database is employed, consisting of both taxonomy-guided reference protein sequences from public databases and proteins from metagenome assembly. By applying our MT strategy to a mock microbial mixture, about two times as many peptides were detected as with the metagenomic database only. According to the evaluation of the reliability of taxonomic attribution, the rate of misassignments was comparable to that obtained using an a priori matched database. We also evaluated the MT strategy with a human gut microbial sample, and we found 1.7 times as many peptides as using a standard metagenomic database. In conclusion, our MT strategy allows the construction of databases able to provide high sensitivity and precision in peptide identification in metaproteomic studies, enabling the detection of proteins from poorly characterized species within the microbiota.

Contamination of sequence databases with adaptor sequences

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

Yoshikawa, Takeo; Sanders, A.R.; Detera-Wadleigh, S.D.

Because of the exponential increase in the amount of DNA sequences being added to the public databases on a daily basis, it has become imperative to identify sources of contamination rapidly. Previously, contaminations of sequence databases have been reported to alert the scientific community to the problem. These contaminations can be divided into two categories. The first category comprises host sequences that have been difficult for submitters to manage or control. Examples include anomalous sequences derived from Escherichia coli, which are inserted into the chromosomes (and plasmids) of the bacterial hosts. Insertion sequences are highly mobile and are capable ofmore » transposing themselves into plasmids during cloning manipulation. Another example of the first category is the infection with yeast genomic DNA or with bacterial DNA of some commercially available cDNA libraries from Clontech. The second category of database contamination is due to the inadvertent inclusion of nonhost sequences. This category includes incorporation of cloning-vector sequences and multicloning sites in the database submission. M13-derived artifacts have been common, since M13-based vectors have been widely used for subcloning DNA fragments. Recognizing this problem, the National Center for Biotechnology Information (NCBI) started to screen, in April 1994, all sequences directly submitted to GenBank, against a set of vector data retrieved from GenBank by use of key-word searches, such as {open_quotes}vector.{close_quotes} In this report, we present evidence for another sequence artifact that is widespread but that, to our knowledge, has not yet been reported. 11 refs., 1 tab.« less

ESTree db: a Tool for Peach Functional Genomics

PubMed Central

Lazzari, Barbara; Caprera, Andrea; Vecchietti, Alberto; Stella, Alessandra; Milanesi, Luciano; Pozzi, Carlo

2005-01-01

Background The ESTree db represents a collection of Prunus persica expressed sequenced tags (ESTs) and is intended as a resource for peach functional genomics. A total of 6,155 successful EST sequences were obtained from four in-house prepared cDNA libraries from Prunus persica mesocarps at different developmental stages. Another 12,475 peach EST sequences were downloaded from public databases and added to the ESTree db. An automated pipeline was prepared to process EST sequences using public software integrated by in-house developed Perl scripts and data were collected in a MySQL database. A php-based web interface was developed to query the database. Results The ESTree db version as of April 2005 encompasses 18,630 sequences representing eight libraries. Contig assembly was performed with CAP3. Putative single nucleotide polymorphism (SNP) detection was performed with the AutoSNP program and a search engine was implemented to retrieve results. All the sequences and all the contig consensus sequences were annotated both with blastx against the GenBank nr db and with GOblet against the viridiplantae section of the Gene Ontology db. Links to NiceZyme (Expasy) and to the KEGG metabolic pathways were provided. A local BLAST utility is available. A text search utility allows querying and browsing the database. Statistics were provided on Gene Ontology occurrences to assign sequences to Gene Ontology categories. Conclusion The resulting database is a comprehensive resource of data and links related to peach EST sequences. The Sequence Report and Contig Report pages work as the web interface core structures, giving quick access to data related to each sequence/contig. PMID:16351742

ESTree db: a tool for peach functional genomics.

PubMed

Lazzari, Barbara; Caprera, Andrea; Vecchietti, Alberto; Stella, Alessandra; Milanesi, Luciano; Pozzi, Carlo

2005-12-01

The ESTree db http://www.itb.cnr.it/estree/ represents a collection of Prunus persica expressed sequenced tags (ESTs) and is intended as a resource for peach functional genomics. A total of 6,155 successful EST sequences were obtained from four in-house prepared cDNA libraries from Prunus persica mesocarps at different developmental stages. Another 12,475 peach EST sequences were downloaded from public databases and added to the ESTree db. An automated pipeline was prepared to process EST sequences using public software integrated by in-house developed Perl scripts and data were collected in a MySQL database. A php-based web interface was developed to query the database. The ESTree db version as of April 2005 encompasses 18,630 sequences representing eight libraries. Contig assembly was performed with CAP3. Putative single nucleotide polymorphism (SNP) detection was performed with the AutoSNP program and a search engine was implemented to retrieve results. All the sequences and all the contig consensus sequences were annotated both with blastx against the GenBank nr db and with GOblet against the viridiplantae section of the Gene Ontology db. Links to NiceZyme (Expasy) and to the KEGG metabolic pathways were provided. A local BLAST utility is available. A text search utility allows querying and browsing the database. Statistics were provided on Gene Ontology occurrences to assign sequences to Gene Ontology categories. The resulting database is a comprehensive resource of data and links related to peach EST sequences. The Sequence Report and Contig Report pages work as the web interface core structures, giving quick access to data related to each sequence/contig.

Unlimited Thirst for Genome Sequencing, Data Interpretation, and Database Usage in Genomic Era: The Road towards Fast-Track Crop Plant Improvement

PubMed Central

Govindaraj, Mahalingam

2015-01-01

The number of sequenced crop genomes and associated genomic resources is growing rapidly with the advent of inexpensive next generation sequencing methods. Databases have become an integral part of all aspects of science research, including basic and applied plant and animal sciences. The importance of databases keeps increasing as the volume of datasets from direct and indirect genomics, as well as other omics approaches, keeps expanding in recent years. The databases and associated web portals provide at a minimum a uniform set of tools and automated analysis across a wide range of crop plant genomes. This paper reviews some basic terms and considerations in dealing with crop plant databases utilization in advancing genomic era. The utilization of databases for variation analysis with other comparative genomics tools, and data interpretation platforms are well described. The major focus of this review is to provide knowledge on platforms and databases for genome-based investigations of agriculturally important crop plants. The utilization of these databases in applied crop improvement program is still being achieved widely; otherwise, the end for sequencing is not far away. PMID:25874133

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

ORFer--retrieval of protein sequences and open reading frames from GenBank and storage into relational databases or text files.

PubMed

Büssow, Konrad; Hoffmann, Steve; Sievert, Volker

2002-12-19

Functional genomics involves the parallel experimentation with large sets of proteins. This requires management of large sets of open reading frames as a prerequisite of the cloning and recombinant expression of these proteins. A Java program was developed for retrieval of protein and nucleic acid sequences and annotations from NCBI GenBank, using the XML sequence format. Annotations retrieved by ORFer include sequence name, organism and also the completeness of the sequence. The program has a graphical user interface, although it can be used in a non-interactive mode. For protein sequences, the program also extracts the open reading frame sequence, if available, and checks its correct translation. ORFer accepts user input in the form of single or lists of GenBank GI identifiers or accession numbers. It can be used to extract complete sets of open reading frames and protein sequences from any kind of GenBank sequence entry, including complete genomes or chromosomes. Sequences are either stored with their features in a relational database or can be exported as text files in Fasta or tabulator delimited format. The ORFer program is freely available at http://www.proteinstrukturfabrik.de/orfer. The ORFer program allows for fast retrieval of DNA sequences, protein sequences and their open reading frames and sequence annotations from GenBank. Furthermore, storage of sequences and features in a relational database is supported. Such a database can supplement a laboratory information system (LIMS) with appropriate sequence information.

Partial DNA sequencing of Douglas-fir cDNAs used in RFLP mapping

Treesearch

K.D. Jermstad; D.L. Bassoni; C.S. Kinlaw; D.B. Neale

1998-01-01

DNA sequences from 87 Douglas-fir (Pseudotsuga menziesii [Mirb.] Franco) cDNA RFLP probes were determined. Sequences were submitted to the GenBank dbEST database and searched for similarity against nucleotide and protein databases using the BLASTn and BLASTx programs. Twenty-one sequences (24%) were assigned putative functions; 18 of which...

Application of cytochrome b DNA sequences for the authentication of endangered snake species.

PubMed

Wong, Ka-Lok; Wang, Jun; But, Paul Pui-Hay; Shaw, Pang-Chui

2004-01-06

In order to enforce the conservation program and curbing the illegal trading and consumption of endangered snake species, the value of cytochrome b sequence in the authentication of snake species was evaluated. As an illustration, DNA was extracted, selected cytochrome b DNA sequences amplified and sequenced from six snakes commonly consumed in Hong Kong. Cataloging with sequences available in public, a cytochrome b database containing 90 species of snakes was constructed. In this database, sequence homology between snakes ranged from 70.68 to 95.11%. On the other hand, intraspecific variation of three tested snakes was 0-0.98%. Using the database, we were able to determine the identity of six meat samples confiscated by the Agriculture, Fisheries and Conservation Department, HKSAR.

The Importance of Biological Databases in Biological Discovery.

PubMed

Baxevanis, Andreas D; Bateman, Alex

2015-06-19

Biological databases play a central role in bioinformatics. They offer scientists the opportunity to access a wide variety of biologically relevant data, including the genomic sequences of an increasingly broad range of organisms. This unit provides a brief overview of major sequence databases and portals, such as GenBank, the UCSC Genome Browser, and Ensembl. Model organism databases, including WormBase, The Arabidopsis Information Resource (TAIR), and those made available through the Mouse Genome Informatics (MGI) resource, are also covered. Non-sequence-centric databases, such as Online Mendelian Inheritance in Man (OMIM), the Protein Data Bank (PDB), MetaCyc, and the Kyoto Encyclopedia of Genes and Genomes (KEGG), are also discussed. Copyright © 2015 John Wiley & Sons, Inc.

A Bayesian taxonomic classification method for 16S rRNA gene sequences with improved species-level accuracy.

PubMed

Gao, Xiang; Lin, Huaiying; Revanna, Kashi; Dong, Qunfeng

2017-05-10

Species-level classification for 16S rRNA gene sequences remains a serious challenge for microbiome researchers, because existing taxonomic classification tools for 16S rRNA gene sequences either do not provide species-level classification, or their classification results are unreliable. The unreliable results are due to the limitations in the existing methods which either lack solid probabilistic-based criteria to evaluate the confidence of their taxonomic assignments, or use nucleotide k-mer frequency as the proxy for sequence similarity measurement. We have developed a method that shows significantly improved species-level classification results over existing methods. Our method calculates true sequence similarity between query sequences and database hits using pairwise sequence alignment. Taxonomic classifications are assigned from the species to the phylum levels based on the lowest common ancestors of multiple database hits for each query sequence, and further classification reliabilities are evaluated by bootstrap confidence scores. The novelty of our method is that the contribution of each database hit to the taxonomic assignment of the query sequence is weighted by a Bayesian posterior probability based upon the degree of sequence similarity of the database hit to the query sequence. Our method does not need any training datasets specific for different taxonomic groups. Instead only a reference database is required for aligning to the query sequences, making our method easily applicable for different regions of the 16S rRNA gene or other phylogenetic marker genes. Reliable species-level classification for 16S rRNA or other phylogenetic marker genes is critical for microbiome research. Our software shows significantly higher classification accuracy than the existing tools and we provide probabilistic-based confidence scores to evaluate the reliability of our taxonomic classification assignments based on multiple database matches to query sequences. Despite its higher computational costs, our method is still suitable for analyzing large-scale microbiome datasets for practical purposes. Furthermore, our method can be applied for taxonomic classification of any phylogenetic marker gene sequences. Our software, called BLCA, is freely available at https://github.com/qunfengdong/BLCA .

PSSRdb: a relational database of polymorphic simple sequence repeats extracted from prokaryotic genomes.

PubMed

Kumar, Pankaj; Chaitanya, Pasumarthy S; Nagarajaram, Hampapathalu A

2011-01-01

PSSRdb (Polymorphic Simple Sequence Repeats database) (http://www.cdfd.org.in/PSSRdb/) is a relational database of polymorphic simple sequence repeats (PSSRs) extracted from 85 different species of prokaryotes. Simple sequence repeats (SSRs) are the tandem repeats of nucleotide motifs of the sizes 1-6 bp and are highly polymorphic. SSR mutations in and around coding regions affect transcription and translation of genes. Such changes underpin phase variations and antigenic variations seen in some bacteria. Although SSR-mediated phase variation and antigenic variations have been well-studied in some bacteria there seems a lot of other species of prokaryotes yet to be investigated for SSR mediated adaptive and other evolutionary advantages. As a part of our on-going studies on SSR polymorphism in prokaryotes we compared the genome sequences of various strains and isolates available for 85 different species of prokaryotes and extracted a number of SSRs showing length variations and created a relational database called PSSRdb. This database gives useful information such as location of PSSRs in genomes, length variation across genomes, the regions harboring PSSRs, etc. The information provided in this database is very useful for further research and analysis of SSRs in prokaryotes.

PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification.

PubMed

Thomas, Paul D; Kejariwal, Anish; Campbell, Michael J; Mi, Huaiyu; Diemer, Karen; Guo, Nan; Ladunga, Istvan; Ulitsky-Lazareva, Betty; Muruganujan, Anushya; Rabkin, Steven; Vandergriff, Jody A; Doremieux, Olivier

2003-01-01

The PANTHER database was designed for high-throughput analysis of protein sequences. One of the key features is a simplified ontology of protein function, which allows browsing of the database by biological functions. Biologist curators have associated the ontology terms with groups of protein sequences rather than individual sequences. Statistical models (Hidden Markov Models, or HMMs) are built from each of these groups. The advantage of this approach is that new sequences can be automatically classified as they become available. To ensure accurate functional classification, HMMs are constructed not only for families, but also for functionally distinct subfamilies. Multiple sequence alignments and phylogenetic trees, including curator-assigned information, are available for each family. The current version of the PANTHER database includes training sequences from all organisms in the GenBank non-redundant protein database, and the HMMs have been used to classify gene products across the entire genomes of human, and Drosophila melanogaster. The ontology terms and protein families and subfamilies, as well as Drosophila gene c;assifications, can be browsed and searched for free. Due to outstanding contractual obligations, access to human gene classifications and to protein family trees and multiple sequence alignments will temporarily require a nominal registration fee. PANTHER is publicly available on the web at http://panther.celera.com.

Version VI of the ESTree db: an improved tool for peach transcriptome analysis

PubMed Central

Lazzari, Barbara; Caprera, Andrea; Vecchietti, Alberto; Merelli, Ivan; Barale, Francesca; Milanesi, Luciano; Stella, Alessandra; Pozzi, Carlo

2008-01-01

Background The ESTree database (db) is a collection of Prunus persica and Prunus dulcis EST sequences that in its current version encompasses 75,404 sequences from 3 almond and 19 peach libraries. Nine peach genotypes and four peach tissues are represented, from four fruit developmental stages. The aim of this work was to implement the already existing ESTree db by adding new sequences and analysis programs. Particular care was given to the implementation of the web interface, that allows querying each of the database features. Results A Perl modular pipeline is the backbone of sequence analysis in the ESTree db project. Outputs obtained during the pipeline steps are automatically arrayed into the fields of a MySQL database. Apart from standard clustering and annotation analyses, version VI of the ESTree db encompasses new tools for tandem repeat identification, annotation against genomic Rosaceae sequences, and positioning on the database of oligomer sequences that were used in a peach microarray study. Furthermore, known protein patterns and motifs were identified by comparison to PROSITE. Based on data retrieved from sequence annotation against the UniProtKB database, a script was prepared to track positions of homologous hits on the GO tree and build statistics on the ontologies distribution in GO functional categories. EST mapping data were also integrated in the database. The PHP-based web interface was upgraded and extended. The aim of the authors was to enable querying the database according to all the biological aspects that can be investigated from the analysis of data available in the ESTree db. This is achieved by allowing multiple searches on logical subsets of sequences that represent different biological situations or features. Conclusions The version VI of ESTree db offers a broad overview on peach gene expression. Sequence analyses results contained in the database, extensively linked to external related resources, represent a large amount of information that can be queried via the tools offered in the web interface. Flexibility and modularity of the ESTree analysis pipeline and of the web interface allowed the authors to set up similar structures for different datasets, with limited manual intervention. PMID:18387211

Suitability of partial 16S ribosomal RNA gene sequence analysis for the identification of dangerous bacterial pathogens.

PubMed

Ruppitsch, W; Stöger, A; Indra, A; Grif, K; Schabereiter-Gurtner, C; Hirschl, A; Allerberger, F

2007-03-01

In a bioterrorism event a rapid tool is needed to identify relevant dangerous bacteria. The aim of the study was to assess the usefulness of partial 16S rRNA gene sequence analysis and the suitability of diverse databases for identifying dangerous bacterial pathogens. For rapid identification purposes a 500-bp fragment of the 16S rRNA gene of 28 isolates comprising Bacillus anthracis, Brucella melitensis, Burkholderia mallei, Burkholderia pseudomallei, Francisella tularensis, Yersinia pestis, and eight genus-related and unrelated control strains was amplified and sequenced. The obtained sequence data were submitted to three public and two commercial sequence databases for species identification. The most frequent reason for incorrect identification was the lack of the respective 16S rRNA gene sequences in the database. Sequence analysis of a 500-bp 16S rDNA fragment allows the rapid identification of dangerous bacterial species. However, for discrimination of closely related species sequencing of the entire 16S rRNA gene, additional sequencing of the 23S rRNA gene or sequencing of the 16S-23S rRNA intergenic spacer is essential. This work provides comprehensive information on the suitability of partial 16S rDNA analysis and diverse databases for rapid and accurate identification of dangerous bacterial pathogens.

ANCAC: amino acid, nucleotide, and codon analysis of COGs--a tool for sequence bias analysis in microbial orthologs.

PubMed

Meiler, Arno; Klinger, Claudia; Kaufmann, Michael

2012-09-08

The COG database is the most popular collection of orthologous proteins from many different completely sequenced microbial genomes. Per definition, a cluster of orthologous groups (COG) within this database exclusively contains proteins that most likely achieve the same cellular function. Recently, the COG database was extended by assigning to every protein both the corresponding amino acid and its encoding nucleotide sequence resulting in the NUCOCOG database. This extended version of the COG database is a valuable resource connecting sequence features with the functionality of the respective proteins. Here we present ANCAC, a web tool and MySQL database for the analysis of amino acid, nucleotide, and codon frequencies in COGs on the basis of freely definable phylogenetic patterns. We demonstrate the usefulness of ANCAC by analyzing amino acid frequencies, codon usage, and GC-content in a species- or function-specific context. With respect to amino acids we, at least in part, confirm the cognate bias hypothesis by using ANCAC's NUCOCOG dataset as the largest one available for that purpose thus far. Using the NUCOCOG datasets, ANCAC connects taxonomic, amino acid, and nucleotide sequence information with the functional classification via COGs and provides a GUI for flexible mining for sequence-bias. Thereby, to our knowledge, it is the only tool for the analysis of sequence composition in the light of physiological roles and phylogenetic context without requirement of substantial programming-skills.

ANCAC: amino acid, nucleotide, and codon analysis of COGs – a tool for sequence bias analysis in microbial orthologs

PubMed Central

2012-01-01

Background The COG database is the most popular collection of orthologous proteins from many different completely sequenced microbial genomes. Per definition, a cluster of orthologous groups (COG) within this database exclusively contains proteins that most likely achieve the same cellular function. Recently, the COG database was extended by assigning to every protein both the corresponding amino acid and its encoding nucleotide sequence resulting in the NUCOCOG database. This extended version of the COG database is a valuable resource connecting sequence features with the functionality of the respective proteins. Results Here we present ANCAC, a web tool and MySQL database for the analysis of amino acid, nucleotide, and codon frequencies in COGs on the basis of freely definable phylogenetic patterns. We demonstrate the usefulness of ANCAC by analyzing amino acid frequencies, codon usage, and GC-content in a species- or function-specific context. With respect to amino acids we, at least in part, confirm the cognate bias hypothesis by using ANCAC’s NUCOCOG dataset as the largest one available for that purpose thus far. Conclusions Using the NUCOCOG datasets, ANCAC connects taxonomic, amino acid, and nucleotide sequence information with the functional classification via COGs and provides a GUI for flexible mining for sequence-bias. Thereby, to our knowledge, it is the only tool for the analysis of sequence composition in the light of physiological roles and phylogenetic context without requirement of substantial programming-skills. PMID:22958836

Entomopathogen ID: a curated sequence resource for entomopathogenic fungi

USDA-ARS?s Scientific Manuscript database

We report the development of a publicly accessible, curated database of Hypocrealean entomopathogenic fungi sequence data. The goal is to provide a platform for users to easily access sequence data from reference strains. The database can be used to accurately identify unknown entomopathogenic fungi...

Patome: a database server for biological sequence annotation and analysis in issued patents and published patent applications.

PubMed

Lee, Byungwook; Kim, Taehyung; Kim, Seon-Kyu; Lee, Kwang H; Lee, Doheon

2007-01-01

With the advent of automated and high-throughput techniques, the number of patent applications containing biological sequences has been increasing rapidly. However, they have attracted relatively little attention compared to other sequence resources. We have built a database server called Patome, which contains biological sequence data disclosed in patents and published applications, as well as their analysis information. The analysis is divided into two steps. The first is an annotation step in which the disclosed sequences were annotated with RefSeq database. The second is an association step where the sequences were linked to Entrez Gene, OMIM and GO databases, and their results were saved as a gene-patent table. From the analysis, we found that 55% of human genes were associated with patenting. The gene-patent table can be used to identify whether a particular gene or disease is related to patenting. Patome is available at http://www.patome.org/; the information is updated bimonthly.

Patome: a database server for biological sequence annotation and analysis in issued patents and published patent applications

PubMed Central

Lee, Byungwook; Kim, Taehyung; Kim, Seon-Kyu; Lee, Kwang H.; Lee, Doheon

2007-01-01

With the advent of automated and high-throughput techniques, the number of patent applications containing biological sequences has been increasing rapidly. However, they have attracted relatively little attention compared to other sequence resources. We have built a database server called Patome, which contains biological sequence data disclosed in patents and published applications, as well as their analysis information. The analysis is divided into two steps. The first is an annotation step in which the disclosed sequences were annotated with RefSeq database. The second is an association step where the sequences were linked to Entrez Gene, OMIM and GO databases, and their results were saved as a gene–patent table. From the analysis, we found that 55% of human genes were associated with patenting. The gene–patent table can be used to identify whether a particular gene or disease is related to patenting. Patome is available at ; the information is updated bimonthly. PMID:17085479

GOBASE—a database of mitochondrial and chloroplast information

PubMed Central

O'Brien, Emmet A.; Badidi, Elarbi; Barbasiewicz, Ania; deSousa, Cristina; Lang, B. Franz; Burger, Gertraud

2003-01-01

GOBASE is a relational database containing integrated sequence, RNA secondary structure and biochemical and taxonomic information about organelles. GOBASE release 6 (summer 2002) contains over 130 000 mitochondrial sequences, an increase of 37% over the previous release, and more than 30 000 chloroplast sequences in a new auxiliary database. To handle this flood of new data, we have designed and implemented GOpop, a Java system for population and verification of the database. We have also implemented a more powerful and flexible user interface using the PHP programming language. http://megasun.bch.umontreal.ca/gobase/gobase.html. PMID:12519975

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

LISTA, LISTA-HOP and LISTA-HON: a comprehensive compilation of protein encoding sequences and its associated homology databases from the yeast Saccharomyces.

PubMed Central

Dölz, R; Mossé, M O; Slonimski, P P; Bairoch, A; Linder, P

1996-01-01

We continued our effort to make a comprehensive database (LISTA) for the yeast Saccharomyces cerevisiae. As in previous editions the genetic names are consistently associated to each sequence with a known and confirmed ORF. If necessary, synonyms are given in the case of allelic duplicated sequences. Although the first publication of a sequence gives-according to our rules-the genetic name of a gene, in some instances more commonly used names are given to avoid nomenclature problems and the use of ancient designations which are no longer used. In these cases the old designation is given as synonym. Thus sequences can be found either by the name or by synonyms given in LISTA. Each entry contains the genetic name, the mnemonic from the EMBL data bank, the codon bias, reference of the publication of the sequence, Chromosomal location as far as known, SWISSPROT and EMBL accession numbers. New entries will also contain the name from the systematic sequencing efforts. Since the release of LISTA4.1 we update the database continuously. To obtain more information on the included sequences, each entry has been screened against non-redundant nucleotide and protein data bank collections resulting in LISTA-HON and LISTA-HOP. This release includes reports from full Smith and Watermann peptide-level searches against a non-redundant protein sequence database. The LISTA data base can be linked to the associated data sets or to nucleotide and protein banks by the Sequence Retrieval System (SRS). The database is available by FTP and on World Wide Web. PMID:8594599

RNAcentral: A comprehensive database of non-coding RNA sequences

DOE PAGES

Williams, Kelly Porter; Lau, Britney Yan

2016-10-28

RNAcentral is a database of non-coding RNA (ncRNA) sequences that aggregates data from specialised ncRNA resources and provides a single entry point for accessing ncRNA sequences of all ncRNA types from all organisms. Since its launch in 2014, RNAcentral has integrated twelve new resources, taking the total number of collaborating database to 22, and began importing new types of data, such as modified nucleotides from MODOMICS and PDB. We created new species-specific identifiers that refer to unique RNA sequences within a context of single species. Furthermore, the website has been subject to continuous improvements focusing on text and sequence similaritymore » searches as well as genome browsing functionality.« less

RNAcentral: A comprehensive database of non-coding RNA sequences

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

Williams, Kelly Porter; Lau, Britney Yan

RNAcentral is a database of non-coding RNA (ncRNA) sequences that aggregates data from specialised ncRNA resources and provides a single entry point for accessing ncRNA sequences of all ncRNA types from all organisms. Since its launch in 2014, RNAcentral has integrated twelve new resources, taking the total number of collaborating database to 22, and began importing new types of data, such as modified nucleotides from MODOMICS and PDB. We created new species-specific identifiers that refer to unique RNA sequences within a context of single species. Furthermore, the website has been subject to continuous improvements focusing on text and sequence similaritymore » searches as well as genome browsing functionality.« less

Development and applications of the EntomopathogenID MLSA database for use in agricultural systems

USDA-ARS?s Scientific Manuscript database

The current study reports the development and application of a publicly accessible, curated database of Hypocrealean entomopathogenic fungi sequence data. The goal was to provide a platform for users to easily access sequence data from reference strains. The database can be used to accurately identi...

Supervised Learning for Detection of Duplicates in Genomic Sequence Databases.

PubMed

Chen, Qingyu; Zobel, Justin; Zhang, Xiuzhen; Verspoor, Karin

2016-01-01

First identified as an issue in 1996, duplication in biological databases introduces redundancy and even leads to inconsistency when contradictory information appears. The amount of data makes purely manual de-duplication impractical, and existing automatic systems cannot detect duplicates as precisely as can experts. Supervised learning has the potential to address such problems by building automatic systems that learn from expert curation to detect duplicates precisely and efficiently. While machine learning is a mature approach in other duplicate detection contexts, it has seen only preliminary application in genomic sequence databases. We developed and evaluated a supervised duplicate detection method based on an expert curated dataset of duplicates, containing over one million pairs across five organisms derived from genomic sequence databases. We selected 22 features to represent distinct attributes of the database records, and developed a binary model and a multi-class model. Both models achieve promising performance; under cross-validation, the binary model had over 90% accuracy in each of the five organisms, while the multi-class model maintains high accuracy and is more robust in generalisation. We performed an ablation study to quantify the impact of different sequence record features, finding that features derived from meta-data, sequence identity, and alignment quality impact performance most strongly. The study demonstrates machine learning can be an effective additional tool for de-duplication of genomic sequence databases. All Data are available as described in the supplementary material.

Ebbie: automated analysis and storage of small RNA cloning data using a dynamic web server

PubMed Central

Ebhardt, H Alexander; Wiese, Kay C; Unrau, Peter J

2006-01-01

Background DNA sequencing is used ubiquitously: from deciphering genomes[1] to determining the primary sequence of small RNAs (smRNAs) [2-5]. The cloning of smRNAs is currently the most conventional method to determine the actual sequence of these important regulators of gene expression. Typical smRNA cloning projects involve the sequencing of hundreds to thousands of smRNA clones that are delimited at their 5' and 3' ends by fixed sequence regions. These primers result from the biochemical protocol used to isolate and convert the smRNA into clonable PCR products. Recently we completed a smRNA cloning project involving tobacco plants, where analysis was required for ~700 smRNA sequences[6]. Finding no easily accessible research tool to enter and analyze smRNA sequences we developed Ebbie to assist us with our study. Results Ebbie is a semi-automated smRNA cloning data processing algorithm, which initially searches for any substring within a DNA sequencing text file, which is flanked by two constant strings. The substring, also termed smRNA or insert, is stored in a MySQL and BlastN database. These inserts are then compared using BlastN to locally installed databases allowing the rapid comparison of the insert to both the growing smRNA database and to other static sequence databases. Our laboratory used Ebbie to analyze scores of DNA sequencing data originating from an smRNA cloning project[6]. Through its built-in instant analysis of all inserts using BlastN, we were able to quickly identify 33 groups of smRNAs from ~700 database entries. This clustering allowed the easy identification of novel and highly expressed clusters of smRNAs. Ebbie is available under GNU GPL and currently implemented on Conclusion Ebbie was designed for medium sized smRNA cloning projects with about 1,000 database entries [6-8].Ebbie can be used for any type of sequence analysis where two constant primer regions flank a sequence of interest. The reliable storage of inserts, and their annotation in a MySQL database, BlastN[9] comparison of new inserts to dynamic and static databases make it a powerful new tool in any laboratory using DNA sequencing. Ebbie also prevents manual mistakes during the excision process and speeds up annotation and data-entry. Once the server is installed locally, its access can be restricted to protect sensitive new DNA sequencing data. Ebbie was primarily designed for smRNA cloning projects, but can be applied to a variety of RNA and DNA cloning projects[2,3,10,11]. PMID:16584563

Mitochondrial DNA control region sequences from Nairobi (Kenya): inferring phylogenetic parameters for the establishment of a forensic database.

PubMed

Brandstätter, Anita; Peterson, Christine T; Irwin, Jodi A; Mpoke, Solomon; Koech, Davy K; Parson, Walther; Parsons, Thomas J

2004-10-01

Large forensic mtDNA databases which adhere to strict guidelines for generation and maintenance, are not available for many populations outside of the United States and western Europe. We have established a high quality mtDNA control region sequence database for urban Nairobi as both a reference database for forensic investigations, and as a tool to examine the genetic variation of Kenyan sequences in the context of known African variation. The Nairobi sequences exhibited high variation and a low random match probability, indicating utility for forensic testing. Haplogroup identification and frequencies were compared with those reported from other published studies on African, or African-origin populations from Mozambique, Sierra Leone, and the United States, and suggest significant differences in the mtDNA compositions of the various populations. The quality of the sequence data in our study was investigated and supported using phylogenetic measures. Our data demonstrate the diversity and distinctiveness of African populations, and underline the importance of establishing additional forensic mtDNA databases of indigenous African populations.

mESAdb: microRNA Expression and Sequence Analysis Database

PubMed Central

Kaya, Koray D.; Karakülah, Gökhan; Yakıcıer, Cengiz M.; Acar, Aybar C.; Konu, Özlen

2011-01-01

microRNA expression and sequence analysis database (http://konulab.fen.bilkent.edu.tr/mirna/) (mESAdb) is a regularly updated database for the multivariate analysis of sequences and expression of microRNAs from multiple taxa. mESAdb is modular and has a user interface implemented in PHP and JavaScript and coupled with statistical analysis and visualization packages written for the R language. The database primarily comprises mature microRNA sequences and their target data, along with selected human, mouse and zebrafish expression data sets. mESAdb analysis modules allow (i) mining of microRNA expression data sets for subsets of microRNAs selected manually or by motif; (ii) pair-wise multivariate analysis of expression data sets within and between taxa; and (iii) association of microRNA subsets with annotation databases, HUGE Navigator, KEGG and GO. The use of existing and customized R packages facilitates future addition of data sets and analysis tools. Furthermore, the ability to upload and analyze user-specified data sets makes mESAdb an interactive and expandable analysis tool for microRNA sequence and expression data. PMID:21177657

mESAdb: microRNA expression and sequence analysis database.

PubMed

Kaya, Koray D; Karakülah, Gökhan; Yakicier, Cengiz M; Acar, Aybar C; Konu, Ozlen

2011-01-01

microRNA expression and sequence analysis database (http://konulab.fen.bilkent.edu.tr/mirna/) (mESAdb) is a regularly updated database for the multivariate analysis of sequences and expression of microRNAs from multiple taxa. mESAdb is modular and has a user interface implemented in PHP and JavaScript and coupled with statistical analysis and visualization packages written for the R language. The database primarily comprises mature microRNA sequences and their target data, along with selected human, mouse and zebrafish expression data sets. mESAdb analysis modules allow (i) mining of microRNA expression data sets for subsets of microRNAs selected manually or by motif; (ii) pair-wise multivariate analysis of expression data sets within and between taxa; and (iii) association of microRNA subsets with annotation databases, HUGE Navigator, KEGG and GO. The use of existing and customized R packages facilitates future addition of data sets and analysis tools. Furthermore, the ability to upload and analyze user-specified data sets makes mESAdb an interactive and expandable analysis tool for microRNA sequence and expression data.

BrEPS 2.0: Optimization of sequence pattern prediction for enzyme annotation.

PubMed

Dudek, Christian-Alexander; Dannheim, Henning; Schomburg, Dietmar

2017-01-01

The prediction of gene functions is crucial for a large number of different life science areas. Faster high throughput sequencing techniques generate more and larger datasets. The manual annotation by classical wet-lab experiments is not suitable for these large amounts of data. We showed earlier that the automatic sequence pattern-based BrEPS protocol, based on manually curated sequences, can be used for the prediction of enzymatic functions of genes. The growing sequence databases provide the opportunity for more reliable patterns, but are also a challenge for the implementation of automatic protocols. We reimplemented and optimized the BrEPS pattern generation to be applicable for larger datasets in an acceptable timescale. Primary improvement of the new BrEPS protocol is the enhanced data selection step. Manually curated annotations from Swiss-Prot are used as reliable source for function prediction of enzymes observed on protein level. The pool of sequences is extended by highly similar sequences from TrEMBL and SwissProt. This allows us to restrict the selection of Swiss-Prot entries, without losing the diversity of sequences needed to generate significant patterns. Additionally, a supporting pattern type was introduced by extending the patterns at semi-conserved positions with highly similar amino acids. Extended patterns have an increased complexity, increasing the chance to match more sequences, without losing the essential structural information of the pattern. To enhance the usability of the database, we introduced enzyme function prediction based on consensus EC numbers and IUBMB enzyme nomenclature. BrEPS is part of the Braunschweig Enzyme Database (BRENDA) and is available on a completely redesigned website and as download. The database can be downloaded and used with the BrEPScmd command line tool for large scale sequence analysis. The BrEPS website and downloads for the database creation tool, command line tool and database are freely accessible at http://breps.tu-bs.de.

BrEPS 2.0: Optimization of sequence pattern prediction for enzyme annotation

PubMed Central

Schomburg, Dietmar

2017-01-01

The prediction of gene functions is crucial for a large number of different life science areas. Faster high throughput sequencing techniques generate more and larger datasets. The manual annotation by classical wet-lab experiments is not suitable for these large amounts of data. We showed earlier that the automatic sequence pattern-based BrEPS protocol, based on manually curated sequences, can be used for the prediction of enzymatic functions of genes. The growing sequence databases provide the opportunity for more reliable patterns, but are also a challenge for the implementation of automatic protocols. We reimplemented and optimized the BrEPS pattern generation to be applicable for larger datasets in an acceptable timescale. Primary improvement of the new BrEPS protocol is the enhanced data selection step. Manually curated annotations from Swiss-Prot are used as reliable source for function prediction of enzymes observed on protein level. The pool of sequences is extended by highly similar sequences from TrEMBL and SwissProt. This allows us to restrict the selection of Swiss-Prot entries, without losing the diversity of sequences needed to generate significant patterns. Additionally, a supporting pattern type was introduced by extending the patterns at semi-conserved positions with highly similar amino acids. Extended patterns have an increased complexity, increasing the chance to match more sequences, without losing the essential structural information of the pattern. To enhance the usability of the database, we introduced enzyme function prediction based on consensus EC numbers and IUBMB enzyme nomenclature. BrEPS is part of the Braunschweig Enzyme Database (BRENDA) and is available on a completely redesigned website and as download. The database can be downloaded and used with the BrEPScmd command line tool for large scale sequence analysis. The BrEPS website and downloads for the database creation tool, command line tool and database are freely accessible at http://breps.tu-bs.de. PMID:28750104

It Takes a Village to Design a Course: Embedding a Librarian in Course Design

ERIC Educational Resources Information Center

Mudd, Alex; Summey, Terri; Upson, Matt

2015-01-01

Often associated with online learning, instructional design is a process utilized in efficiently designing training and instruction to help ensure effectiveness. Typically, the instructional systems design (ISD) process uses a team-based approach, consisting of an instructor, a facilitator, a designer and a subject matter expert. Although library…

Interservice Procedures for Instructional Systems Development: Executive Summary and Model.

ERIC Educational Resources Information Center

Branson, Robert K.

The document is the last of a five-part series focusing in minute detail on the processes involved in the formulation of an instructional systems development (ISD) program for military interservice training that will adequately train individuals to do a particular job and which can also be applied to any interservice curriculum development…

ISD Designed Medical Specialist Training.

ERIC Educational Resources Information Center

Rock, Samuel K., Jr.; Chagalis, George P.

The Basic Medical Specialist course has one of the largest enrollments of the U.S. Army's Academy of Health Sciences; 11,000 soldiers were trained in this course in 1977 and 1978. Training encompasses both emergency first aid (for field medics) and basic nursing skills. A task force working to improve Army training developed this course, in…

MVP and Instructional Systems Design in Online Courses

ERIC Educational Resources Information Center

Franklin, Jennifer L.

2017-01-01

This chapter is based on three premises. The first premise is that the use of instructional systems design (ISD) methods is important in online as well as traditional classroom settings. A second premise is that improving the motivational design of instruction brings benefits to teachers and learners alike. The third premise, specific to this…

Army Job Training Development and Testing Practices Compared to the Instructional Systems Development Model.

ERIC Educational Resources Information Center

Oxford-Carpenter, Rebecca L.; And Others

This paper presents an evaluation of Army job training development and testing practices, with a focus on Advanced Individual Testing. Information comes from intensive interviews with school instructors and from observations in the schools. Results indicate that some aspects of the Instructional Systems Development (ISD) model have been…

Supporting Solo at the District Level

ERIC Educational Resources Information Center

Woodard, Mary

2011-01-01

School librarians in the Mesquite Independent School District (ISD) have been operating solo on their campuses since the 1970s. Campus clerical assistance in the school libraries was a luxury that they couldn't afford. Since the district's vision was of a teaching librarian, a Library Processing Department was established in 1972. As years passed,…

School Resource Officers for Bullying Interventions: A Mixed-Methods Analysis

ERIC Educational Resources Information Center

Robles-Pina, Rebecca A.; Denham, Magdalena A.

2012-01-01

The number of school police officers, School Resource Officers (SROs), is increasing on school campuses to assist in preventing school violence, and in particular bullying. This mixed-methods study was conducted to compare the knowledge and perceptions of SROs (N = 184) hired by independent school districts (ISD SROs) and those contracted from law…

Spectrally Shaped DP-16QAM Super-Channel Transmission with Multi-Channel Digital Back-Propagation

PubMed Central

Maher, Robert; Xu, Tianhua; Galdino, Lidia; Sato, Masaki; Alvarado, Alex; Shi, Kai; Savory, Seb J.; Thomsen, Benn C.; Killey, Robert I.; Bayvel, Polina

2015-01-01

The achievable transmission capacity of conventional optical fibre communication systems is limited by nonlinear distortions due to the Kerr effect and the difficulty in modulating the optical field to effectively use the available fibre bandwidth. In order to achieve a high information spectral density (ISD), while simultaneously maintaining transmission reach, multi-channel fibre nonlinearity compensation and spectrally efficient data encoding must be utilised. In this work, we use a single coherent super-receiver to simultaneously receive a DP-16QAM super-channel, consisting of seven spectrally shaped 10GBd sub-carriers spaced at the Nyquist frequency. Effective nonlinearity mitigation is achieved using multi-channel digital back-propagation (MC-DBP) and this technique is combined with an optimised forward error correction implementation to demonstrate a record gain in transmission reach of 85%; increasing the maximum transmission distance from 3190 km to 5890 km, with an ISD of 6.60 b/s/Hz. In addition, this report outlines for the first time, the sensitivity of MC-DBP gain to linear transmission line impairments and defines a trade-off between performance and complexity. PMID:25645457

Fate of individual sewage disposal system wastewater within regolith in mountainous terrain

NASA Astrophysics Data System (ADS)

Dano, Kathleen; Poeter, Eileen; Thyne, Geoff

2008-06-01

In order to improve understanding of the fate of septic tank or individual sewage disposal system (ISDS) effluent in regolith overlying fractured-rock aquifers, effluent from an ISDS in such a setting was tracked via geophysical, hydrological, and geochemical methods. Under typical precipitation conditions, the effluent entered the fractured bedrock within 5 m of the boundary of the constructed infiltration area. During a period of unusually high spring recharge, the plume migrated between 50 and 100 m within the regolith before infiltrating the fractured bedrock. The chemical signature of the effluent is similar to that required to account for the decline in water quality, suggesting a causative relationship (as estimated from mass-balance models of the surface-water chemistry near the mouth of the basin). The elevated salt content of the effluent during periods of high natural recharge to the infiltration area correlates with elevated salt concentrations in surface and groundwater at the basin scale, suggesting that some of the effluent salt load may be stored in the unsaturated zone during dry periods and flushed during periods of elevated natural recharge.

Long-Distance Rescue and Slow Extinction Dynamics Govern Multiscale Metapopulations.

PubMed

Huth, Géraldine; Haegeman, Bart; Pitard, Estelle; Munoz, François

2015-10-01

Rare long-distance dispersal is known to be critical for species dynamics, but how the interplay between short- and long-distance colonization influences regional persistence in a fragmented habitat remains poorly understood. We propose a metapopulation model that combines local colonization within habitat islands and long-distance colonization between islands. We study how regional occupancy dynamics are affected by the multiscale colonization process. We find that the island size distribution (ISD) is a key driver of the long-term occupancy dynamics. When the ISD is heterogeneous-that is, when the size of islands is variable-we show that extinction dynamics become very slow. We demonstrate that this behavior is unrelated to the well-known extinction debt near the critical extinction threshold. Hence, this finding questions the equivalence between extinction debt and critical transitions in the context of metapopulation collapse. Furthermore, we show that long-distance colonization can rescue small islands from extinction and sustain a steady regional occupancy. These results provide novel theoretical and practical insights into extinction dynamics and persistence in fragmented habitats and are thus relevant for the design of conservation strategies.

Assessing outcome after a modified vaginal wall sling for stress incontinence with intrinsic sphincter deficiency.

PubMed

Costantini, Elisabetta; Mearini, Luigi; Mearini, Ettore; Pajoncini, Cinzia; Guercini, Federico; Bini, Vittorio; Porena, Massimo

2005-01-01

Forty women with stress incontinence, intrinsic sphincter deficiency (ISD), associated or not with urethral hypermobility, a Valsalva leak point pressure (VLLP)<60 cmH(2)0 and a maximum urethral closure pressure<30 cmH(2)0 underwent in situ vaginal wall sling. The main modification to the technique was the use of two small Marlex meshes placed at the lateral edges of the sling. Outcome was assessed by pad use, surgical results and patients' satisfaction. Data of 39/40 patients were analyzed after a minimum follow-up of 1 year. After surgery 30/39 patients were completely dry (no pads), stress incontinence disappeared in 22/39, and 30/39 patients were satisfied with outcome. Reasons for dissatisfaction included recurrence of stress incontinence in three, infections in one and urge incontinence in five. Overall results are good given this category of patients. The vaginal wall sling can be recommended for patients with ISD because the results are promising, it corrects urethral hypermobility and, in our experience, it does not cause obstruction if correctly performed.

a Study of the Impact of Insolation on Remote Sensing-Based Landcover and Landuse Data Extraction

NASA Astrophysics Data System (ADS)

Becek, K.; Borkowski, A.; Mekik, Ç.

2016-06-01

We examined the dependency of the pixel reflectance of hyperspectral imaging spectrometer data (HISD) on a normalized total insolation index (NTII). The NTII was estimated using a light detection and ranging (LiDAR)-derived digital surface model (DSM). The NTII and the pixel reflectance were dependent, to various degrees, on the band considered, and on the properties of the objects. The findings could be used to improve land cover (LC)/land use (LU) classification, using indices constructed from the spectral bands of imaging spectrometer data (ISD). To study this possibility, we investigated the normalized difference vegetation index (NDVI) at various NTII levels. The results also suggest that the dependency of the pixel reflectance and NTII could be used to mitigate the shadows in ISD. This project was carried out using data provided by the Hyperspectral Image Analysis Group and the NSF-funded Centre for Airborne Laser Mapping (NCALM), University of Houston, for the purpose of organizing the 2013 Data Fusion Contest (IEEE 2014). This contest was organized by the IEEE GRSS Data Fusion Technical Committee.

Architectural Principles for Orchestration of Cross-Organizational Service Delivery: Case Studies from the Netherlands

NASA Astrophysics Data System (ADS)

van Veenstra, Anne Fleur; Janssen, Marijn

One of the main challenges for e-government is to create coherent services for citizens and businesses. Realizing Integrated Service Delivery (ISD) requires government agencies to collaborate across their organizational boundaries. The coordination of processes across multiple organizations to realize ISD is called orchestration. One way of achieving orchestration is to formalize processes using architecture. In this chapter we identify architectural principles for orchestration by looking at three case studies of cross-organizational service delivery chain formation in the Netherlands. In total, six generic principles were formulated and subsequently validated in two workshops with experts. These principles are: (i) build an intelligent front office, (ii) give processes a clear starting point and end, (iii) build a central workflow application keeping track of the process, (iv) differentiate between simple and complex processes, (v) ensure that the decision-making responsibility and the overview of the process are not performed by the same process role, and (vi) create a central point where risk profiles are maintained. Further research should focus on how organizations can adapt these principles to their own situation.

Germline-encoded neutralization of a Staphylococcus aureus virulence factor by the human antibody repertoire.

PubMed

Yeung, Yik Andy; Foletti, Davide; Deng, Xiaodi; Abdiche, Yasmina; Strop, Pavel; Glanville, Jacob; Pitts, Steven; Lindquist, Kevin; Sundar, Purnima D; Sirota, Marina; Hasa-Moreno, Adela; Pham, Amber; Melton Witt, Jody; Ni, Irene; Pons, Jaume; Shelton, David; Rajpal, Arvind; Chaparro-Riggers, Javier

2016-11-18

Staphylococcus aureus is both an important pathogen and a human commensal. To explore this ambivalent relationship between host and microbe, we analysed the memory humoral response against IsdB, a protein involved in iron acquisition, in four healthy donors. Here we show that in all donors a heavily biased use of two immunoglobulin heavy chain germlines generated high affinity (pM) antibodies that neutralize the two IsdB NEAT domains, IGHV4-39 for NEAT1 and IGHV1-69 for NEAT2. In contrast to the typical antibody/antigen interactions, the binding is primarily driven by the germline-encoded hydrophobic CDRH-2 motifs of IGHV1-69 and IGHV4-39, with a binding mechanism nearly identical for each antibody derived from different donors. Our results suggest that IGHV1-69 and IGHV4-39, while part of the adaptive immune system, may have evolved under selection pressure to encode a binding motif innately capable of recognizing and neutralizing a structurally conserved protein domain involved in pathogen iron acquisition.

JRC GMO-Amplicons: a collection of nucleic acid sequences related to genetically modified organisms

PubMed Central

Petrillo, Mauro; Angers-Loustau, Alexandre; Henriksson, Peter; Bonfini, Laura; Patak, Alex; Kreysa, Joachim

2015-01-01

The DNA target sequence is the key element in designing detection methods for genetically modified organisms (GMOs). Unfortunately this information is frequently lacking, especially for unauthorized GMOs. In addition, patent sequences are generally poorly annotated, buried in complex and extensive documentation and hard to link to the corresponding GM event. Here, we present the JRC GMO-Amplicons, a database of amplicons collected by screening public nucleotide sequence databanks by in silico determination of PCR amplification with reference methods for GMO analysis. The European Union Reference Laboratory for Genetically Modified Food and Feed (EU-RL GMFF) provides these methods in the GMOMETHODS database to support enforcement of EU legislation and GM food/feed control. The JRC GMO-Amplicons database is composed of more than 240 000 amplicons, which can be easily accessed and screened through a web interface. To our knowledge, this is the first attempt at pooling and collecting publicly available sequences related to GMOs in food and feed. The JRC GMO-Amplicons supports control laboratories in the design and assessment of GMO methods, providing inter-alia in silico prediction of primers specificity and GM targets coverage. The new tool can assist the laboratories in the analysis of complex issues, such as the detection and identification of unauthorized GMOs. Notably, the JRC GMO-Amplicons database allows the retrieval and characterization of GMO-related sequences included in patents documentation. Finally, it can help annotating poorly described GM sequences and identifying new relevant GMO-related sequences in public databases. The JRC GMO-Amplicons is freely accessible through a web-based portal that is hosted on the EU-RL GMFF website. Database URL: http://gmo-crl.jrc.ec.europa.eu/jrcgmoamplicons/ PMID:26424080

JRC GMO-Amplicons: a collection of nucleic acid sequences related to genetically modified organisms.

PubMed

Petrillo, Mauro; Angers-Loustau, Alexandre; Henriksson, Peter; Bonfini, Laura; Patak, Alex; Kreysa, Joachim

2015-01-01

The DNA target sequence is the key element in designing detection methods for genetically modified organisms (GMOs). Unfortunately this information is frequently lacking, especially for unauthorized GMOs. In addition, patent sequences are generally poorly annotated, buried in complex and extensive documentation and hard to link to the corresponding GM event. Here, we present the JRC GMO-Amplicons, a database of amplicons collected by screening public nucleotide sequence databanks by in silico determination of PCR amplification with reference methods for GMO analysis. The European Union Reference Laboratory for Genetically Modified Food and Feed (EU-RL GMFF) provides these methods in the GMOMETHODS database to support enforcement of EU legislation and GM food/feed control. The JRC GMO-Amplicons database is composed of more than 240 000 amplicons, which can be easily accessed and screened through a web interface. To our knowledge, this is the first attempt at pooling and collecting publicly available sequences related to GMOs in food and feed. The JRC GMO-Amplicons supports control laboratories in the design and assessment of GMO methods, providing inter-alia in silico prediction of primers specificity and GM targets coverage. The new tool can assist the laboratories in the analysis of complex issues, such as the detection and identification of unauthorized GMOs. Notably, the JRC GMO-Amplicons database allows the retrieval and characterization of GMO-related sequences included in patents documentation. Finally, it can help annotating poorly described GM sequences and identifying new relevant GMO-related sequences in public databases. The JRC GMO-Amplicons is freely accessible through a web-based portal that is hosted on the EU-RL GMFF website. Database URL: http://gmo-crl.jrc.ec.europa.eu/jrcgmoamplicons/. © The Author(s) 2015. Published by Oxford University Press.

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.

iMETHYL: an integrative database of human DNA methylation, gene expression, and genomic variation.

PubMed

Komaki, Shohei; Shiwa, Yuh; Furukawa, Ryohei; Hachiya, Tsuyoshi; Ohmomo, Hideki; Otomo, Ryo; Satoh, Mamoru; Hitomi, Jiro; Sobue, Kenji; Sasaki, Makoto; Shimizu, Atsushi

2018-01-01

We launched an integrative multi-omics database, iMETHYL (http://imethyl.iwate-megabank.org). iMETHYL provides whole-DNA methylation (~24 million autosomal CpG sites), whole-genome (~9 million single-nucleotide variants), and whole-transcriptome (>14 000 genes) data for CD4 + T-lymphocytes, monocytes, and neutrophils collected from approximately 100 subjects. These data were obtained from whole-genome bisulfite sequencing, whole-genome sequencing, and whole-transcriptome sequencing, making iMETHYL a comprehensive database.

Evaluation of the authenticity of a highly novel environmental sequence from boreal forest soil using ribosomal RNA secondary structure modeling

Treesearch

D.J. Glass; N. Takebayashi; L. Olson; D.L. Taylor

2013-01-01

The number of sequences from both formally described taxa and uncultured environmental DNA deposited in the International Nucleotide Sequence Databases has increased substantially over the last two decades. Although the majority of these sequences represent authentic gene copies, there is evidence of DNA artifacts in these databases as well. These include lab artifacts...

REFGEN and TREENAMER: Automated Sequence Data Handling for Phylogenetic Analysis in the Genomic Era

PubMed Central

Leonard, Guy; Stevens, Jamie R.; Richards, Thomas A.

2009-01-01

The phylogenetic analysis of nucleotide sequences and increasingly that of amino acid sequences is used to address a number of biological questions. Access to extensive datasets, including numerous genome projects, means that standard phylogenetic analyses can include many hundreds of sequences. Unfortunately, most phylogenetic analysis programs do not tolerate the sequence naming conventions of genome databases. Managing large numbers of sequences and standardizing sequence labels for use in phylogenetic analysis programs can be a time consuming and laborious task. Here we report the availability of an online resource for the management of gene sequences recovered from public access genome databases such as GenBank. These web utilities include the facility for renaming every sequence in a FASTA alignment file, with each sequence label derived from a user-defined combination of the species name and/or database accession number. This facility enables the user to keep track of the branching order of the sequences/taxa during multiple tree calculations and re-optimisations. Post phylogenetic analysis, these webpages can then be used to rename every label in the subsequent tree files (with a user-defined combination of species name and/or database accession number). Together these programs drastically reduce the time required for managing sequence alignments and labelling phylogenetic figures. Additional features of our platform include the automatic removal of identical accession numbers (recorded in the report file) and generation of species and accession number lists for use in supplementary materials or figure legends. PMID:19812722

PASS2: an automated database of protein alignments organised as structural superfamilies.

PubMed

Bhaduri, Anirban; Pugalenthi, Ganesan; Sowdhamini, Ramanathan

2004-04-02

The functional selection and three-dimensional structural constraints of proteins in nature often relates to the retention of significant sequence similarity between proteins of similar fold and function despite poor sequence identity. Organization of structure-based sequence alignments for distantly related proteins, provides a map of the conserved and critical regions of the protein universe that is useful for the analysis of folding principles, for the evolutionary unification of protein families and for maximizing the information return from experimental structure determination. The Protein Alignment organised as Structural Superfamily (PASS2) database represents continuously updated, structural alignments for evolutionary related, sequentially distant proteins. An automated and updated version of PASS2 is, in direct correspondence with SCOP 1.63, consisting of sequences having identity below 40% among themselves. Protein domains have been grouped into 628 multi-member superfamilies and 566 single member superfamilies. Structure-based sequence alignments for the superfamilies have been obtained using COMPARER, while initial equivalencies have been derived from a preliminary superposition using LSQMAN or STAMP 4.0. The final sequence alignments have been annotated for structural features using JOY4.0. The database is supplemented with sequence relatives belonging to different genomes, conserved spatially interacting and structural motifs, probabilistic hidden markov models of superfamilies based on the alignments and useful links to other databases. Probabilistic models and sensitive position specific profiles obtained from reliable superfamily alignments aid annotation of remote homologues and are useful tools in structural and functional genomics. PASS2 presents the phylogeny of its members both based on sequence and structural dissimilarities. Clustering of members allows us to understand diversification of the family members. The search engine has been improved for simpler browsing of the database. The database resolves alignments among the structural domains consisting of evolutionarily diverged set of sequences. Availability of reliable sequence alignments of distantly related proteins despite poor sequence identity and single-member superfamilies permit better sampling of structures in libraries for fold recognition of new sequences and for the understanding of protein structure-function relationships of individual superfamilies. PASS2 is accessible at http://www.ncbs.res.in/~faculty/mini/campass/pass2.html

Using the TIGR gene index databases for biological discovery.

PubMed

Lee, Yuandan; Quackenbush, John

2003-11-01

The TIGR Gene Index web pages provide access to analyses of ESTs and gene sequences for nearly 60 species, as well as a number of resources derived from these. Each species-specific database is presented using a common format with a homepage. A variety of methods exist that allow users to search each species-specific database. Methods implemented currently include nucleotide or protein sequence queries using WU-BLAST, text-based searches using various sequence identifiers, searches by gene, tissue and library name, and searches using functional classes through Gene Ontology assignments. This protocol provides guidance for using the Gene Index Databases to extract information.

Ariadne: a database search engine for identification and chemical analysis of RNA using tandem mass spectrometry data.

PubMed

Nakayama, Hiroshi; Akiyama, Misaki; Taoka, Masato; Yamauchi, Yoshio; Nobe, Yuko; Ishikawa, Hideaki; Takahashi, Nobuhiro; Isobe, Toshiaki

2009-04-01

We present here a method to correlate tandem mass spectra of sample RNA nucleolytic fragments with an RNA nucleotide sequence in a DNA/RNA sequence database, thereby allowing tandem mass spectrometry (MS/MS)-based identification of RNA in biological samples. Ariadne, a unique web-based database search engine, identifies RNA by two probability-based evaluation steps of MS/MS data. In the first step, the software evaluates the matches between the masses of product ions generated by MS/MS of an RNase digest of sample RNA and those calculated from a candidate nucleotide sequence in a DNA/RNA sequence database, which then predicts the nucleotide sequences of these RNase fragments. In the second step, the candidate sequences are mapped for all RNA entries in the database, and each entry is scored for a function of occurrences of the candidate sequences to identify a particular RNA. Ariadne can also predict post-transcriptional modifications of RNA, such as methylation of nucleotide bases and/or ribose, by estimating mass shifts from the theoretical mass values. The method was validated with MS/MS data of RNase T1 digests of in vitro transcripts. It was applied successfully to identify an unknown RNA component in a tRNA mixture and to analyze post-transcriptional modification in yeast tRNA(Phe-1).

Novel primers for complete mitochondrial cytochrome b genesequencing in mammals

USGS Publications Warehouse

Naidu, Ashwin; Fitak, Robert R.; Munguia-Vega, Adrian; Culver, Melanie

2011-01-01

Sequence-based species identification relies on the extent and integrity of sequence data available in online databases such as GenBank. When identifying species from a sample of unknown origin, partial DNA sequences obtained from the sample are aligned against existing sequences in databases. When the sequence from the matching species is not present in the database, high-scoring alignments with closely related sequences might produce unreliable results on species identity. For species identification in mammals, the cytochrome b (cyt b) gene has been identified to be highly informative; thus, large amounts of reference sequence data from the cyt b gene are much needed. To enhance availability of cyt b gene sequence data on a large number of mammalian species in GenBank and other such publicly accessible online databases, we identified a primer pair for complete cyt b gene sequencing in mammals. Using this primer pair, we successfully PCR amplified and sequenced the complete cyt b gene from 40 of 44 mammalian species representing 10 orders of mammals. We submitted 40 complete, correctly annotated, cyt b protein coding sequences to GenBank. To our knowledge, this is the first single primer pair to amplify the complete cyt b gene in a broad range of mammalian species. This primer pair can be used for the addition of new cyt b gene sequences and to enhance data available on species represented in GenBank. The availability of novel and complete gene sequences as high-quality reference data can improve the reliability of sequence-based species identification.

Equivalent Indels – Ambiguous Functional Classes and Redundancy in Databases

PubMed Central

Assmus, Jens; Kleffe, Jürgen; Schmitt, Armin O.; Brockmann, Gudrun A.

2013-01-01

There is considerable interest in studying sequenced variations. However, while the positions of substitutions are uniquely identifiable by sequence alignment, the location of insertions and deletions still poses problems. Each insertion and deletion causes a change of sequence. Yet, due to low complexity or repetitive sequence structures, the same indel can sometimes be annotated in different ways. Two indels which differ in allele sequence and position can be one and the same, i.e. the alternative sequence of the whole chromosome is identical in both cases and, therefore, the two deletions are biologically equivalent. In such a case, it is impossible to identify the exact position of an indel merely based on sequence alignment. Thus, variation entries in a mutation database are not necessarily uniquely defined. We prove the existence of a contiguous region around an indel in which all deletions of the same length are biologically identical. Databases often show only one of several possible locations for a given variation. Furthermore, different data base entries can represent equivalent variation events. We identified 1,045,590 such problematic entries of insertions and deletions out of 5,860,408 indel entries in the current human database of Ensembl. Equivalent indels are found in sequence regions of different functions like exons, introns or 5' and 3' UTRs. One and the same variation can be assigned to several different functional classifications of which only one is correct. We implemented an algorithm that determines for each indel database entry its complete set of equivalent indels which is uniquely characterized by the indel itself and a given interval of the reference sequence. PMID:23658777

SALAD database: a motif-based database of protein annotations for plant comparative genomics

PubMed Central

Mihara, Motohiro; Itoh, Takeshi; Izawa, Takeshi

2010-01-01

Proteins often have several motifs with distinct evolutionary histories. Proteins with similar motifs have similar biochemical properties and thus related biological functions. We constructed a unique comparative genomics database termed the SALAD database (http://salad.dna.affrc.go.jp/salad/) from plant-genome-based proteome data sets. We extracted evolutionarily conserved motifs by MEME software from 209 529 protein-sequence annotation groups selected by BLASTP from the proteome data sets of 10 species: rice, sorghum, Arabidopsis thaliana, grape, a lycophyte, a moss, 3 algae, and yeast. Similarity clustering of each protein group was performed by pairwise scoring of the motif patterns of the sequences. The SALAD database provides a user-friendly graphical viewer that displays a motif pattern diagram linked to the resulting bootstrapped dendrogram for each protein group. Amino-acid-sequence-based and nucleotide-sequence-based phylogenetic trees for motif combination alignment, a logo comparison diagram for each clade in the tree, and a Pfam-domain pattern diagram are also available. We also developed a viewer named ‘SALAD on ARRAYs’ to view arbitrary microarray data sets of paralogous genes linked to the same dendrogram in a window. The SALAD database is a powerful tool for comparing protein sequences and can provide valuable hints for biological analysis. PMID:19854933

Assembly: a resource for assembled genomes at NCBI

PubMed Central

Kitts, Paul A.; Church, Deanna M.; Thibaud-Nissen, Françoise; Choi, Jinna; Hem, Vichet; Sapojnikov, Victor; Smith, Robert G.; Tatusova, Tatiana; Xiang, Charlie; Zherikov, Andrey; DiCuccio, Michael; Murphy, Terence D.; Pruitt, Kim D.; Kimchi, Avi

2016-01-01

The NCBI Assembly database (www.ncbi.nlm.nih.gov/assembly/) provides stable accessioning and data tracking for genome assembly data. The model underlying the database can accommodate a range of assembly structures, including sets of unordered contig or scaffold sequences, bacterial genomes consisting of a single complete chromosome, or complex structures such as a human genome with modeled allelic variation. The database provides an assembly accession and version to unambiguously identify the set of sequences that make up a particular version of an assembly, and tracks changes to updated genome assemblies. The Assembly database reports metadata such as assembly names, simple statistical reports of the assembly (number of contigs and scaffolds, contiguity metrics such as contig N50, total sequence length and total gap length) as well as the assembly update history. The Assembly database also tracks the relationship between an assembly submitted to the International Nucleotide Sequence Database Consortium (INSDC) and the assembly represented in the NCBI RefSeq project. Users can find assemblies of interest by querying the Assembly Resource directly or by browsing available assemblies for a particular organism. Links in the Assembly Resource allow users to easily download sequence and annotations for current versions of genome assemblies from the NCBI genomes FTP site. PMID:26578580

SALAD database: a motif-based database of protein annotations for plant comparative genomics.

PubMed

Mihara, Motohiro; Itoh, Takeshi; Izawa, Takeshi

2010-01-01

Proteins often have several motifs with distinct evolutionary histories. Proteins with similar motifs have similar biochemical properties and thus related biological functions. We constructed a unique comparative genomics database termed the SALAD database (http://salad.dna.affrc.go.jp/salad/) from plant-genome-based proteome data sets. We extracted evolutionarily conserved motifs by MEME software from 209,529 protein-sequence annotation groups selected by BLASTP from the proteome data sets of 10 species: rice, sorghum, Arabidopsis thaliana, grape, a lycophyte, a moss, 3 algae, and yeast. Similarity clustering of each protein group was performed by pairwise scoring of the motif patterns of the sequences. The SALAD database provides a user-friendly graphical viewer that displays a motif pattern diagram linked to the resulting bootstrapped dendrogram for each protein group. Amino-acid-sequence-based and nucleotide-sequence-based phylogenetic trees for motif combination alignment, a logo comparison diagram for each clade in the tree, and a Pfam-domain pattern diagram are also available. We also developed a viewer named 'SALAD on ARRAYs' to view arbitrary microarray data sets of paralogous genes linked to the same dendrogram in a window. The SALAD database is a powerful tool for comparing protein sequences and can provide valuable hints for biological analysis.

Architecture of the Human Mitochondrial Iron-Sulfur Cluster Assembly Machinery.

PubMed

Gakh, Oleksandr; Ranatunga, Wasantha; Smith, Douglas Y; Ahlgren, Eva-Christina; Al-Karadaghi, Salam; Thompson, James R; Isaya, Grazia

2016-09-30

Fe-S clusters, essential cofactors needed for the activity of many different enzymes, are assembled by conserved protein machineries inside bacteria and mitochondria. As the architecture of the human machinery remains undefined, we co-expressed in Escherichia coli the following four proteins involved in the initial step of Fe-S cluster synthesis: FXN 42-210 (iron donor); [NFS1]·[ISD11] (sulfur donor); and ISCU (scaffold upon which new clusters are assembled). We purified a stable, active complex consisting of all four proteins with 1:1:1:1 stoichiometry. Using negative staining transmission EM and single particle analysis, we obtained a three-dimensional model of the complex with ∼14 Å resolution. Molecular dynamics flexible fitting of protein structures docked into the EM map of the model revealed a [FXN 42-210 ] 24 ·[NFS1] 24 ·[ISD11] 24 ·[ISCU] 24 complex, consistent with the measured 1:1:1:1 stoichiometry of its four components. The complex structure fulfills distance constraints obtained from chemical cross-linking of the complex at multiple recurring interfaces, involving hydrogen bonds, salt bridges, or hydrophobic interactions between conserved residues. The complex consists of a central roughly cubic [FXN 42-210 ] 24 ·[ISCU] 24 sub-complex with one symmetric ISCU trimer bound on top of one symmetric FXN 42-210 trimer at each of its eight vertices. Binding of 12 [NFS1] 2 ·[ISD11] 2 sub-complexes to the surface results in a globular macromolecule with a diameter of ∼15 nm and creates 24 Fe-S cluster assembly centers. The organization of each center recapitulates a previously proposed conserved mechanism for sulfur donation from NFS1 to ISCU and reveals, for the first time, a path for iron donation from FXN 42-210 to ISCU. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Architecture of the Human Mitochondrial Iron-Sulfur Cluster Assembly Machinery*

PubMed Central

Gakh, Oleksandr; Ranatunga, Wasantha; Smith, Douglas Y.; Ahlgren, Eva-Christina; Al-Karadaghi, Salam; Thompson, James R.; Isaya, Grazia

2016-01-01

Fe-S clusters, essential cofactors needed for the activity of many different enzymes, are assembled by conserved protein machineries inside bacteria and mitochondria. As the architecture of the human machinery remains undefined, we co-expressed in Escherichia coli the following four proteins involved in the initial step of Fe-S cluster synthesis: FXN42–210 (iron donor); [NFS1]·[ISD11] (sulfur donor); and ISCU (scaffold upon which new clusters are assembled). We purified a stable, active complex consisting of all four proteins with 1:1:1:1 stoichiometry. Using negative staining transmission EM and single particle analysis, we obtained a three-dimensional model of the complex with ∼14 Å resolution. Molecular dynamics flexible fitting of protein structures docked into the EM map of the model revealed a [FXN42–210]24·[NFS1]24·[ISD11]24·[ISCU]24 complex, consistent with the measured 1:1:1:1 stoichiometry of its four components. The complex structure fulfills distance constraints obtained from chemical cross-linking of the complex at multiple recurring interfaces, involving hydrogen bonds, salt bridges, or hydrophobic interactions between conserved residues. The complex consists of a central roughly cubic [FXN42–210]24·[ISCU]24 sub-complex with one symmetric ISCU trimer bound on top of one symmetric FXN42–210 trimer at each of its eight vertices. Binding of 12 [NFS1]2·[ISD11]2 sub-complexes to the surface results in a globular macromolecule with a diameter of ∼15 nm and creates 24 Fe-S cluster assembly centers. The organization of each center recapitulates a previously proposed conserved mechanism for sulfur donation from NFS1 to ISCU and reveals, for the first time, a path for iron donation from FXN42–210 to ISCU. PMID:27519411

Matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. A comparison of fragmentation patterns of linear dextran obtained by in-source decay, post-source decay and collision-induced dissociation and the stability of linear and cyclic glucans studied by in-source decay.

PubMed

Bashir, Sajid; Giannakopulos, Anastassios E; Derrick, Peter J; Critchley, Peter; Bottrill, Andrew; Padley, Henry J

2004-01-01

In the first part of this study fragmentation patterns from a range of dextran oligomers (containing 4-20 anhydroglucose units) were compared in three different methods of analysis coupled with matrix-assisted laser desorption/ionisation (MALDI) mass spectrometry. Collision-induced-dissociation (CID), prompt in-source decay (ISD) and post-source decay (PSD) all caused cleavage of the glycosidic bonds. Both CID and to a lesser extent ISD caused further cleavage of pyranose rings of the individual sugar residues. There was very little cleavage of pyranose rings detected in the PSD spectrum. Derivatisation of the reducing end-groups of the oligodextrans with 1-phenyl-3-methyl-5-pyrazolone (PMP) restricted cleavage in the MALDI mass spectrometer to the non-reducing end, and further it enabled the saccharides to be separated by HPLC so that a single chain length could be examined as a standard. Maltoheptaose was also used as a standard. In the second part of the study prompt ISD-MALDI mass spectrometry was used to compare the fragmentation of three oligoglucans, dextran, maltodextrin and gamma cyclodextrin, that have different linkages and different secondary structure. The results showed that the degree of fragmentation correlated with the degree of freedom in the saccharide chains in solution determined by NMR. Dextran the most random conformation was fragmented most whereas there was little evidence of any fragments, not even glycosidic bond breakage from cyclodextrin, even when the laser power was increased considerably. The fragmentation pattern of maltodextrin was intermediate. The patterns of fragmentation produced by MALDI mass spectrometry, particularly where standards are available to calibrate the spectrum and the energy of the laser is controlled, can be used to predict the type of linkage present.

Different utilization of intensive care services (ICSs) for patients dying of hemorrhagic and ischemic stroke, a hospital-based survey.

PubMed

Wang, Vinchi; Hsieh, Chieh-Chao; Huang, Yen-Ling; Chen, Chia-Ping; Hsieh, Yi-Ting; Chao, Tzu-Hao

2018-02-01

The intensive care service (ICS) saves lives and rescues the neurological function of stroke patients. We wondered the different utilization of ICS for patients with ischemic and hemorrhagic stroke, especially those who died within 30 days after stroke.Sixty-seven patients died during 2011 to 2015 due to acute stroke (42 due to intracranial hemorrhage [ICH]; 25 due to cerebral infarct [CI]). The durations of hospital stay (hospital staying days [HSDs]) and ICS staying days (ISDs) and codes of the do-not-resuscitate (DNR) were surveyed among these medical records. Statistics included chi-square and descriptive analyses.In this study, CI patients had a longer HSD (mean 14.3 days), as compared with ICH patients (mean 8.3 days); however, the ICH patients had a higher percentage of early entry within the first 24 hours of admission into ICS than CI group (95.1% vs 60.0%, P = .003). A higher rate of CI patients died in holidays or weekends than those with ICH (44.0% vs 21.4%, P = .051). DNR, requested mainly from direct descendants (children or grandchildren), was coded in all 25 CI patients (100.0%) and 38 ICH patients (90.5%). More cases with early DNR coded within 24 hours after admission occurred in ICH group (47%, 12% in CI patients, P = .003). None of the stroke patient had living wills. Withhold of endotracheal intubation (ETI) occurred among CI patients, more than for ICH patients (76.0% vs 18.4%, P < .005).In conclusion, CI patients longer HSD, ISD, higher mortality within holidays or weekends, and higher ETI withhold; but less percentage of ICS utilization expressed by a lower ISD/HSD ratio. This ICS utilization is a key issue of medical quality for stroke care.

Feasibility Study of NMR Based Serum Metabolomic Profiling to Animal Health Monitoring: A Case Study on Iron Storage Disease in Captive Sumatran Rhinoceros (Dicerorhinus sumatrensis).

PubMed

Watanabe, Miki; Roth, Terri L; Bauer, Stuart J; Lane, Adam; Romick-Rosendale, Lindsey E

2016-01-01

A variety of wildlife species maintained in captivity are susceptible to iron storage disease (ISD), or hemochromatosis, a disease resulting from the deposition of excess iron into insoluble iron clusters in soft tissue. Sumatran rhinoceros (Dicerorhinus sumatrensis) is one of the rhinoceros species that has evolutionarily adapted to a low-iron diet and is susceptible to iron overload. Hemosiderosis is reported at necropsy in many African black and Sumatran rhinoceroses but only a small number of animals reportedly die from hemochromatosis. The underlying cause and reasons for differences in susceptibility to hemochromatosis within the taxon remains unclear. Although serum ferritin concentrations have been useful in monitoring the progression of ISD in many species, there is some question regarding their value in diagnosing hemochromatosis in the Sumatran rhino. To investigate the metabolic changes during the development of hemochromatosis and possibly increase our understanding of its progression and individual susceptibility differences, the serum metabolome from a Sumatran rhinoceros was investigated by nuclear magnetic resonance (NMR)-based metabolomics. The study involved samples from female rhinoceros at the Cincinnati Zoo (n = 3), including two animals that died from liver failure caused by ISD, and the Sungai Dusun Rhinoceros Conservation Centre in Peninsular Malaysia (n = 4). Principal component analysis was performed to visually and statistically compare the metabolic profiles of the healthy animals. The results indicated that significant differences were present between the animals at the zoo and the animals in the conservation center. A comparison of the 43 serum metabolomes of three zoo rhinoceros showed two distinct groupings, healthy (n = 30) and unhealthy (n = 13). A total of eighteen altered metabolites were identified in healthy versus unhealthy samples. Results strongly suggest that NMR-based metabolomics is a valuable tool for animal health monitoring and may provide insight into the progression of this and other insidious diseases.

Does hemipelvis structure and position influence acetabulum orientation?

PubMed

Musielak, Bartosz; Jóźwiak, Marek; Rychlik, Michał; Chen, Brian Po-Jung; Idzior, Maciej; Grzegorzewski, Andrzej

2016-03-16

Although acetabulum orientation is well established anatomically and radiographically, its relation to the innominate bone has rarely been addressed. If explored, it could open the discussion on patomechanisms of such complex disorders as femoroacetabular impingement (FAI). We therefore evaluated the influence of pelvic bone position and structure on acetabular spatial orientation. We describe this relation and its clinical implications. This retrospective study was based on computed tomography scanning of three-dimensional models of 31 consecutive male pelvises (62 acetabulums). All measurements were based on CT spatial reconstruction with the use of highly specialized software (Rhinoceros). Relations between acetabular orientation (inclination, tilt, anteversion angles) and pelvic structure were evaluated. The following parameters were evaluated to assess the pelvic structure: iliac opening angle, iliac tilt angle, interspinous distance (ISD), intertuberous distance (ITD), height of the pelvis (HP), and the ISD/ITD/HP ratio. The linear and nonlinear dependence of the acetabular angles and hemipelvic measurements were examined with Pearson's product - moment correlation and Spearman's rank correlation coefficient. Correlations different from 0 with p < 0.05 were considered statistically significant. Comparison of the axis position with pelvis structure with orientation in the horizontal plane revealed a significant positive correlation between the acetabular anteversion angle and the iliac opening angle (p = 0.041 and 0.008, respectively). In the frontal plane, there was a positive correlation between the acetabular inclination angle and the iliac tilt angle (p = 0.025 and 0.014, respectively) and the acetabular inclination angle and the ISD/ITD/HP ratio (both p = 0.048). There is a significant correlation of the hemipelvic structure and acetabular orientation under anatomic conditions, especially in the frontal and horizontal planes. In the anteroposterior view, the more tilted-down innominate bone causes a more caudally oriented acetabulum axis, whereas in the horizontal view this relation is reversed. This study may serve as a basis for the discussion on the role of the pelvis in common disorders of the hip.

Taxonomic evaluation of unidentified Streptomyces isolates in the ARS Culture Collection (NRRL) using multi-locus sequence analysis

USDA-ARS?s Scientific Manuscript database

The ARS Culture Collection (NRRL) currently contains 7569 strains within the family Streptomycetaceae but 4368 of them have not been characterized to the species level. A gene sequence database using the Bacterial Isolate Genomic Sequence Database package (BIGSdb) (Jolley & Maiden, 2010) is availabl...

The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple Saccharomyces cerevisiae strains at the Saccharomyces Genome Database

PubMed Central

Engel, Stacia R.; Cherry, J. Michael

2013-01-01

The first completed eukaryotic genome sequence was that of the yeast Saccharomyces cerevisiae, and the Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) is the original model organism database. SGD remains the authoritative community resource for the S. cerevisiae reference genome sequence and its annotation, and continues to provide comprehensive biological information correlated with S. cerevisiae genes and their products. A diverse set of yeast strains have been sequenced to explore commercial and laboratory applications, and a brief history of those strains is provided. The publication of these new genomes has motivated the creation of new tools, and SGD will annotate and provide comparative analyses of these sequences, correlating changes with variations in strain phenotypes and protein function. We are entering a new era at SGD, as we incorporate these new sequences and make them accessible to the scientific community, all in an effort to continue in our mission of educating researchers and facilitating discovery. Database URL: http://www.yeastgenome.org/ PMID:23487186

probeBase—an online resource for rRNA-targeted oligonucleotide probes and primers: new features 2016

PubMed Central

Greuter, Daniel; Loy, Alexander; Horn, Matthias; Rattei, Thomas

2016-01-01

probeBase http://www.probebase.net is a manually maintained and curated database of rRNA-targeted oligonucleotide probes and primers. Contextual information and multiple options for evaluating in silico hybridization performance against the most recent rRNA sequence databases are provided for each oligonucleotide entry, which makes probeBase an important and frequently used resource for microbiology research and diagnostics. Here we present a major update of probeBase, which was last featured in the NAR Database Issue 2007. This update describes a complete remodeling of the database architecture and environment to accommodate computationally efficient access. Improved search functions, sequence match tools and data output now extend the opportunities for finding suitable hierarchical probe sets that target an organism or taxon at different taxonomic levels. To facilitate the identification of complementary probe sets for organisms represented by short rRNA sequence reads generated by amplicon sequencing or metagenomic analysis with next generation sequencing technologies such as Illumina and IonTorrent, we introduce a novel tool that recovers surrogate near full-length rRNA sequences for short query sequences and finds matching oligonucleotides in probeBase. PMID:26586809

Large-Scale Concatenation cDNA Sequencing

PubMed Central

Yu, Wei; Andersson, Björn; Worley, Kim C.; Muzny, Donna M.; Ding, Yan; Liu, Wen; Ricafrente, Jennifer Y.; Wentland, Meredith A.; Lennon, Greg; Gibbs, Richard A.

1997-01-01

A total of 100 kb of DNA derived from 69 individual human brain cDNA clones of 0.7–2.0 kb were sequenced by concatenated cDNA sequencing (CCS), whereby multiple individual DNA fragments are sequenced simultaneously in a single shotgun library. The method yielded accurate sequences and a similar efficiency compared with other shotgun libraries constructed from single DNA fragments (>20 kb). Computer analyses were carried out on 65 cDNA clone sequences and their corresponding end sequences to examine both nucleic acid and amino acid sequence similarities in the databases. Thirty-seven clones revealed no DNA database matches, 12 clones generated exact matches (≥98% identity), and 16 clones generated nonexact matches (57%–97% identity) to either known human or other species genes. Of those 28 matched clones, 8 had corresponding end sequences that failed to identify similarities. In a protein similarity search, 27 clone sequences displayed significant matches, whereas only 20 of the end sequences had matches to known protein sequences. Our data indicate that full-length cDNA insert sequences provide significantly more nucleic acid and protein sequence similarity matches than expressed sequence tags (ESTs) for database searching. [All 65 cDNA clone sequences described in this paper have been submitted to the GenBank data library under accession nos. U79240–U79304.] PMID:9110174

[Integrated DNA barcoding database for identifying Chinese animal medicine].

PubMed

Shi, Lin-Chun; Yao, Hui; Xie, Li-Fang; Zhu, Ying-Jie; Song, Jing-Yuan; Zhang, Hui; Chen, Shi-Lin

2014-06-01

In order to construct an integrated DNA barcoding database for identifying Chinese animal medicine, the authors and their cooperators have completed a lot of researches for identifying Chinese animal medicines using DNA barcoding technology. Sequences from GenBank have been analyzed simultaneously. Three different methods, BLAST, barcoding gap and Tree building, have been used to confirm the reliabilities of barcode records in the database. The integrated DNA barcoding database for identifying Chinese animal medicine has been constructed using three different parts: specimen, sequence and literature information. This database contained about 800 animal medicines and the adulterants and closely related species. Unknown specimens can be identified by pasting their sequence record into the window on the ID page of species identification system for traditional Chinese medicine (www. tcmbarcode. cn). The integrated DNA barcoding database for identifying Chinese animal medicine is significantly important for animal species identification, rare and endangered species conservation and sustainable utilization of animal resources.

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

LISTA, LISTA-HOP and LISTA-HON: a comprehensive compilation of protein encoding sequences and its associated homology databases from the yeast Saccharomyces.

PubMed Central

Dölz, R; Mossé, M O; Slonimski, P P; Bairoch, A; Linder, P

1994-01-01

We continued our effort to make a comprehensive database (LISTA) for the yeast Saccharomyces cerevisiae. In this database each sequence has been attributed a single genetic name. In the case of duplicated sequences a simple method has been applied to distinguish between sequences of one and the same gene from non-allelic sequences of duplicated genes. If necessary, synonyms are given in the case of allelic duplicated sequences. Thus sequences can be found either by the name or by synonyms given in LISTA. Each entry contains the genetic name, the mnemonic from the EMBL data bank, the codon bias, reference of the publication of the sequence, Chromosomal location as far as known, Swissprot and EMBL accession numbers. To obtain more information on the included sequences, each entry has been screened against non-redundant nucleotide and protein data bank collections resulting in LISTA-HON and LISTA-HOP. The LISTA data base can be linked to the associated data sets or to nucleotide and protein banks by the Sequence Retrieval System (SRS). PMID:7937046

Gene Unprediction with Spurio: A tool to identify spurious protein sequences.

PubMed

Höps, Wolfram; Jeffryes, Matt; Bateman, Alex

2018-01-01

We now have access to the sequences of tens of millions of proteins. These protein sequences are essential for modern molecular biology and computational biology. The vast majority of protein sequences are derived from gene prediction tools and have no experimental supporting evidence for their translation.  Despite the increasing accuracy of gene prediction tools there likely exists a large number of spurious protein predictions in the sequence databases.  We have developed the Spurio tool to help identify spurious protein predictions in prokaryotes.  Spurio searches the query protein sequence against a prokaryotic nucleotide database using tblastn and identifies homologous sequences. The tblastn matches are used to score the query sequence's likelihood of being a spurious protein prediction using a Gaussian process model. The most informative feature is the appearance of stop codons within the presumed translation of homologous DNA sequences. Benchmarking shows that the Spurio tool is able to distinguish spurious from true proteins. However, transposon proteins are prone to be predicted as spurious because of the frequency of degraded homologs found in the DNA sequence databases. Our initial experiments suggest that less than 1% of the proteins in the UniProtKB sequence database are likely to be spurious and that Spurio is able to identify over 60 times more spurious proteins than the AntiFam resource. The Spurio software and source code is available under an MIT license at the following URL: https://bitbucket.org/bateman-group/spurio.

Differentially Private Frequent Sequence Mining via Sampling-based Candidate Pruning

PubMed Central

Xu, Shengzhi; Cheng, Xiang; Li, Zhengyi; Xiong, Li

2016-01-01

In this paper, we study the problem of mining frequent sequences under the rigorous differential privacy model. We explore the possibility of designing a differentially private frequent sequence mining (FSM) algorithm which can achieve both high data utility and a high degree of privacy. We found, in differentially private FSM, the amount of required noise is proportionate to the number of candidate sequences. If we could effectively reduce the number of unpromising candidate sequences, the utility and privacy tradeoff can be significantly improved. To this end, by leveraging a sampling-based candidate pruning technique, we propose a novel differentially private FSM algorithm, which is referred to as PFS2. The core of our algorithm is to utilize sample databases to further prune the candidate sequences generated based on the downward closure property. In particular, we use the noisy local support of candidate sequences in the sample databases to estimate which sequences are potentially frequent. To improve the accuracy of such private estimations, a sequence shrinking method is proposed to enforce the length constraint on the sample databases. Moreover, to decrease the probability of misestimating frequent sequences as infrequent, a threshold relaxation method is proposed to relax the user-specified threshold for the sample databases. Through formal privacy analysis, we show that our PFS2 algorithm is ε-differentially private. Extensive experiments on real datasets illustrate that our PFS2 algorithm can privately find frequent sequences with high accuracy. PMID:26973430

A comprehensive and scalable database search system for metaproteomics.

PubMed

Chatterjee, Sandip; Stupp, Gregory S; Park, Sung Kyu Robin; Ducom, Jean-Christophe; Yates, John R; Su, Andrew I; Wolan, Dennis W

2016-08-16

Mass spectrometry-based shotgun proteomics experiments rely on accurate matching of experimental spectra against a database of protein sequences. Existing computational analysis methods are limited in the size of their sequence databases, which severely restricts the proteomic sequencing depth and functional analysis of highly complex samples. The growing amount of public high-throughput sequencing data will only exacerbate this problem. We designed a broadly applicable metaproteomic analysis method (ComPIL) that addresses protein database size limitations. Our approach to overcome this significant limitation in metaproteomics was to design a scalable set of sequence databases assembled for optimal library querying speeds. ComPIL was integrated with a modified version of the search engine ProLuCID (termed "Blazmass") to permit rapid matching of experimental spectra. Proof-of-principle analysis of human HEK293 lysate with a ComPIL database derived from high-quality genomic libraries was able to detect nearly all of the same peptides as a search with a human database (~500x fewer peptides in the database), with a small reduction in sensitivity. We were also able to detect proteins from the adenovirus used to immortalize these cells. We applied our method to a set of healthy human gut microbiome proteomic samples and showed a substantial increase in the number of identified peptides and proteins compared to previous metaproteomic analyses, while retaining a high degree of protein identification accuracy and allowing for a more in-depth characterization of the functional landscape of the samples. The combination of ComPIL with Blazmass allows proteomic searches to be performed with database sizes much larger than previously possible. These large database searches can be applied to complex meta-samples with unknown composition or proteomic samples where unexpected proteins may be identified. The protein database, proteomic search engine, and the proteomic data files for the 5 microbiome samples characterized and discussed herein are open source and available for use and additional analysis.

Navigating through the Jungle of Allergens: Features and Applications of Allergen Databases.

PubMed

Radauer, Christian

2017-01-01

The increasing number of available data on allergenic proteins demanded the establishment of structured, freely accessible allergen databases. In this review article, features and applications of 6 of the most widely used allergen databases are discussed. The WHO/IUIS Allergen Nomenclature Database is the official resource of allergen designations. Allergome is the most comprehensive collection of data on allergens and allergen sources. AllergenOnline is aimed at providing a peer-reviewed database of allergen sequences for prediction of allergenicity of proteins, such as those planned to be inserted into genetically modified crops. The Structural Database of Allergenic Proteins (SDAP) provides a database of allergen sequences, structures, and epitopes linked to bioinformatics tools for sequence analysis and comparison. The Immune Epitope Database (IEDB) is the largest repository of T-cell, B-cell, and major histocompatibility complex protein epitopes including epitopes of allergens. AllFam classifies allergens into families of evolutionarily related proteins using definitions from the Pfam protein family database. These databases contain mostly overlapping data, but also show differences in terms of their targeted users, the criteria for including allergens, data shown for each allergen, and the availability of bioinformatics tools. © 2017 S. Karger AG, Basel.

Internet-accessible DNA sequence database for identifying fusaria from human and animal infections.

PubMed

O'Donnell, Kerry; Sutton, Deanna A; Rinaldi, Michael G; Sarver, Brice A J; Balajee, S Arunmozhi; Schroers, Hans-Josef; Summerbell, Richard C; Robert, Vincent A R G; Crous, Pedro W; Zhang, Ning; Aoki, Takayuki; Jung, Kyongyong; Park, Jongsun; Lee, Yong-Hwan; Kang, Seogchan; Park, Bongsoo; Geiser, David M

2010-10-01

Because less than one-third of clinically relevant fusaria can be accurately identified to species level using phenotypic data (i.e., morphological species recognition), we constructed a three-locus DNA sequence database to facilitate molecular identification of the 69 Fusarium species associated with human or animal mycoses encountered in clinical microbiology laboratories. The database comprises partial sequences from three nuclear genes: translation elongation factor 1α (EF-1α), the largest subunit of RNA polymerase (RPB1), and the second largest subunit of RNA polymerase (RPB2). These three gene fragments can be amplified by PCR and sequenced using primers that are conserved across the phylogenetic breadth of Fusarium. Phylogenetic analyses of the combined data set reveal that, with the exception of two monotypic lineages, all clinically relevant fusaria are nested in one of eight variously sized and strongly supported species complexes. The monophyletic lineages have been named informally to facilitate communication of an isolate's clade membership and genetic diversity. To identify isolates to the species included within the database, partial DNA sequence data from one or more of the three genes can be used as a BLAST query against the database which is Web accessible at FUSARIUM-ID (http://isolate.fusariumdb.org) and the Centraalbureau voor Schimmelcultures (CBS-KNAW) Fungal Biodiversity Center (http://www.cbs.knaw.nl/fusarium). Alternatively, isolates can be identified via phylogenetic analysis by adding sequences of unknowns to the DNA sequence alignment, which can be downloaded from the two aforementioned websites. The utility of this database should increase significantly as members of the clinical microbiology community deposit in internationally accessible culture collections (e.g., CBS-KNAW or the Fusarium Research Center) cultures of novel mycosis-associated fusaria, along with associated, corrected sequence chromatograms and data, so that the sequence results can be verified and isolates are made available for future study.

PrionHome: a database of prions and other sequences relevant to prion phenomena.

PubMed

Harbi, Djamel; Parthiban, Marimuthu; Gendoo, Deena M A; Ehsani, Sepehr; Kumar, Manish; Schmitt-Ulms, Gerold; Sowdhamini, Ramanathan; Harrison, Paul M

2012-01-01

Prions are units of propagation of an altered state of a protein or proteins; prions can propagate from organism to organism, through cooption of other protein copies. Prions contain no necessary nucleic acids, and are important both as both pathogenic agents, and as a potential force in epigenetic phenomena. The original prions were derived from a misfolded form of the mammalian Prion Protein PrP. Infection by these prions causes neurodegenerative diseases. Other prions cause non-Mendelian inheritance in budding yeast, and sometimes act as diseases of yeast. We report the bioinformatic construction of the PrionHome, a database of >2000 prion-related sequences. The data was collated from various public and private resources and filtered for redundancy. The data was then processed according to a transparent classification system of prionogenic sequences (i.e., sequences that can make prions), prionoids (i.e., proteins that propagate like prions between individual cells), and other prion-related phenomena. There are eight PrionHome classifications for sequences. The first four classifications are derived from experimental observations: prionogenic sequences, prionoids, other prion-related phenomena, and prion interactors. The second four classifications are derived from sequence analysis: orthologs, paralogs, pseudogenes, and candidate-prionogenic sequences. Database entries list: supporting information for PrionHome classifications, prion-determinant areas (where relevant), and disordered and compositionally-biased regions. Also included are literature references for the PrionHome classifications, transcripts and genomic coordinates, and structural data (including comparative models made for the PrionHome from manually curated alignments). We provide database usage examples for both vertebrate and fungal prion contexts. Using the database data, we have performed a detailed analysis of the compositional biases in known budding-yeast prionogenic sequences, showing that the only abundant bias pattern is for asparagine bias with subsidiary serine bias. We anticipate that this database will be a useful experimental aid and reference resource. It is freely available at: http://libaio.biol.mcgill.ca/prion.

PrionHome: A Database of Prions and Other Sequences Relevant to Prion Phenomena

PubMed Central

Harbi, Djamel; Parthiban, Marimuthu; Gendoo, Deena M. A.; Ehsani, Sepehr; Kumar, Manish; Schmitt-Ulms, Gerold; Sowdhamini, Ramanathan; Harrison, Paul M.

2012-01-01

Prions are units of propagation of an altered state of a protein or proteins; prions can propagate from organism to organism, through cooption of other protein copies. Prions contain no necessary nucleic acids, and are important both as both pathogenic agents, and as a potential force in epigenetic phenomena. The original prions were derived from a misfolded form of the mammalian Prion Protein PrP. Infection by these prions causes neurodegenerative diseases. Other prions cause non-Mendelian inheritance in budding yeast, and sometimes act as diseases of yeast. We report the bioinformatic construction of the PrionHome, a database of >2000 prion-related sequences. The data was collated from various public and private resources and filtered for redundancy. The data was then processed according to a transparent classification system of prionogenic sequences (i.e., sequences that can make prions), prionoids (i.e., proteins that propagate like prions between individual cells), and other prion-related phenomena. There are eight PrionHome classifications for sequences. The first four classifications are derived from experimental observations: prionogenic sequences, prionoids, other prion-related phenomena, and prion interactors. The second four classifications are derived from sequence analysis: orthologs, paralogs, pseudogenes, and candidate-prionogenic sequences. Database entries list: supporting information for PrionHome classifications, prion-determinant areas (where relevant), and disordered and compositionally-biased regions. Also included are literature references for the PrionHome classifications, transcripts and genomic coordinates, and structural data (including comparative models made for the PrionHome from manually curated alignments). We provide database usage examples for both vertebrate and fungal prion contexts. Using the database data, we have performed a detailed analysis of the compositional biases in known budding-yeast prionogenic sequences, showing that the only abundant bias pattern is for asparagine bias with subsidiary serine bias. We anticipate that this database will be a useful experimental aid and reference resource. It is freely available at: http://libaio.biol.mcgill.ca/prion. PMID:22363733

PROFESS: a PROtein Function, Evolution, Structure and Sequence database

PubMed Central

Triplet, Thomas; Shortridge, Matthew D.; Griep, Mark A.; Stark, Jaime L.; Powers, Robert; Revesz, Peter

2010-01-01

The proliferation of biological databases and the easy access enabled by the Internet is having a beneficial impact on biological sciences and transforming the way research is conducted. There are ∼1100 molecular biology databases dispersed throughout the Internet. To assist in the functional, structural and evolutionary analysis of the abundant number of novel proteins continually identified from whole-genome sequencing, we introduce the PROFESS (PROtein Function, Evolution, Structure and Sequence) database. Our database is designed to be versatile and expandable and will not confine analysis to a pre-existing set of data relationships. A fundamental component of this approach is the development of an intuitive query system that incorporates a variety of similarity functions capable of generating data relationships not conceived during the creation of the database. The utility of PROFESS is demonstrated by the analysis of the structural drift of homologous proteins and the identification of potential pancreatic cancer therapeutic targets based on the observation of protein–protein interaction networks. Database URL: http://cse.unl.edu/∼profess/ PMID:20624718

Faster sequence homology searches by clustering subsequences.

PubMed

Suzuki, Shuji; Kakuta, Masanori; Ishida, Takashi; Akiyama, Yutaka

2015-04-15

Sequence homology searches are used in various fields. New sequencing technologies produce huge amounts of sequence data, which continuously increase the size of sequence databases. As a result, homology searches require large amounts of computational time, especially for metagenomic analysis. We developed a fast homology search method based on database subsequence clustering, and implemented it as GHOSTZ. This method clusters similar subsequences from a database to perform an efficient seed search and ungapped extension by reducing alignment candidates based on triangle inequality. The database subsequence clustering technique achieved an ∼2-fold increase in speed without a large decrease in search sensitivity. When we measured with metagenomic data, GHOSTZ is ∼2.2-2.8 times faster than RAPSearch and is ∼185-261 times faster than BLASTX. The source code is freely available for download at http://www.bi.cs.titech.ac.jp/ghostz/ akiyama@cs.titech.ac.jp Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

GenBank.

PubMed

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 (www.ncbi.nlm.nih.gov).

GenBank.

PubMed

Benson, Dennis A; Karsch-Mizrachi, Ilene; Lipman, David J; Ostell, James; Wheeler, David L

2005-01-01

GenBank is a comprehensive database that contains publicly available DNA sequences for more than 165,000 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 the UK and the DNA Data Bank of Japan helps to ensure 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, go to the NCBI Homepage at http://www.ncbi.nlm.nih.gov.

GenBank.

PubMed

Benson, Dennis A; Karsch-Mizrachi, Ilene; Lipman, David J; Ostell, James; Wheeler, David L

2006-01-01

GenBank (R) is a comprehensive database that contains publicly available DNA sequences for more than 205 000 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, go to the NCBI Homepage at www.ncbi.nlm.nih.gov.

LOVD: easy creation of a locus-specific sequence variation database using an "LSDB-in-a-box" approach.

PubMed

Fokkema, Ivo F A C; den Dunnen, Johan T; Taschner, Peter E M

2005-08-01

The completion of the human genome project has initiated, as well as provided the basis for, the collection and study of all sequence variation between individuals. Direct access to up-to-date information on sequence variation is currently provided most efficiently through web-based, gene-centered, locus-specific databases (LSDBs). We have developed the Leiden Open (source) Variation Database (LOVD) software approaching the "LSDB-in-a-Box" idea for the easy creation and maintenance of a fully web-based gene sequence variation database. LOVD is platform-independent and uses PHP and MySQL open source software only. The basic gene-centered and modular design of the database follows the recommendations of the Human Genome Variation Society (HGVS) and focuses on the collection and display of DNA sequence variations. With minimal effort, the LOVD platform is extendable with clinical data. The open set-up should both facilitate and promote functional extension with scripts written by the community. The LOVD software is freely available from the Leiden Muscular Dystrophy pages (www.DMD.nl/LOVD/). To promote the use of LOVD, we currently offer curators the possibility to set up an LSDB on our Leiden server. (c) 2005 Wiley-Liss, Inc.

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

HadISD: a quality-controlled global synoptic report database for selected variables at long-term stations from 1973-2011

NASA Astrophysics Data System (ADS)

Dunn, R. J. H.; Willett, K. M.; Thorne, P. W.; Woolley, E. V.; Durre, I.; Dai, A.; Parker, D. E.; Vose, R. S.

2012-10-01

This paper describes the creation of HadISD: an automatically quality-controlled synoptic resolution dataset of temperature, dewpoint temperature, sea-level pressure, wind speed, wind direction and cloud cover from global weather stations for 1973-2011. The full dataset consists of over 6000 stations, with 3427 long-term stations deemed to have sufficient sampling and quality for climate applications requiring sub-daily resolution. As with other surface datasets, coverage is heavily skewed towards Northern Hemisphere mid-latitudes. The dataset is constructed from a large pre-existing ASCII flatfile data bank that represents over a decade of substantial effort at data retrieval, reformatting and provision. These raw data have had varying levels of quality control applied to them by individual data providers. The work proceeded in several steps: merging stations with multiple reporting identifiers; reformatting to netCDF; quality control; and then filtering to form a final dataset. Particular attention has been paid to maintaining true extreme values where possible within an automated, objective process. Detailed validation has been performed on a subset of global stations and also on UK data using known extreme events to help finalise the QC tests. Further validation was performed on a selection of extreme events world-wide (Hurricane Katrina in 2005, the cold snap in Alaska in 1989 and heat waves in SE Australia in 2009). Some very initial analyses are performed to illustrate some of the types of problems to which the final data could be applied. Although the filtering has removed the poorest station records, no attempt has been made to homogenise the data thus far, due to the complexity of retaining the true distribution of high-resolution data when applying adjustments. Hence non-climatic, time-varying errors may still exist in many of the individual station records and care is needed in inferring long-term trends from these data. This dataset will allow the study of high frequency variations of temperature, pressure and humidity on a global basis over the last four decades. Both individual extremes and the overall population of extreme events could be investigated in detail to allow for comparison with past and projected climate. A version-control system has been constructed for this dataset to allow for the clear documentation of any updates and corrections in the future.

gEVE: a genome-based endogenous viral element database provides comprehensive viral protein-coding sequences in mammalian genomes.

PubMed

Nakagawa, So; Takahashi, Mahoko Ueda

2016-01-01

In mammals, approximately 10% of genome sequences correspond to endogenous viral elements (EVEs), which are derived from ancient viral infections of germ cells. Although most EVEs have been inactivated, some open reading frames (ORFs) of EVEs obtained functions in the hosts. However, EVE ORFs usually remain unannotated in the genomes, and no databases are available for EVE ORFs. To investigate the function and evolution of EVEs in mammalian genomes, we developed EVE ORF databases for 20 genomes of 19 mammalian species. A total of 736,771 non-overlapping EVE ORFs were identified and archived in a database named gEVE (http://geve.med.u-tokai.ac.jp). The gEVE database provides nucleotide and amino acid sequences, genomic loci and functional annotations of EVE ORFs for all 20 genomes. In analyzing RNA-seq data with the gEVE database, we successfully identified the expressed EVE genes, suggesting that the gEVE database facilitates studies of the genomic analyses of various mammalian species.Database URL: http://geve.med.u-tokai.ac.jp. © The Author(s) 2016. Published by Oxford University Press.

gEVE: a genome-based endogenous viral element database provides comprehensive viral protein-coding sequences in mammalian genomes

PubMed Central

Nakagawa, So; Takahashi, Mahoko Ueda

2016-01-01

In mammals, approximately 10% of genome sequences correspond to endogenous viral elements (EVEs), which are derived from ancient viral infections of germ cells. Although most EVEs have been inactivated, some open reading frames (ORFs) of EVEs obtained functions in the hosts. However, EVE ORFs usually remain unannotated in the genomes, and no databases are available for EVE ORFs. To investigate the function and evolution of EVEs in mammalian genomes, we developed EVE ORF databases for 20 genomes of 19 mammalian species. A total of 736,771 non-overlapping EVE ORFs were identified and archived in a database named gEVE (http://geve.med.u-tokai.ac.jp). The gEVE database provides nucleotide and amino acid sequences, genomic loci and functional annotations of EVE ORFs for all 20 genomes. In analyzing RNA-seq data with the gEVE database, we successfully identified the expressed EVE genes, suggesting that the gEVE database facilitates studies of the genomic analyses of various mammalian species. Database URL: http://geve.med.u-tokai.ac.jp PMID:27242033

Tandem Mass Spectrum Sequencing: An Alternative to Database Search Engines in Shotgun Proteomics.

PubMed

Muth, Thilo; Rapp, Erdmann; Berven, Frode S; Barsnes, Harald; Vaudel, Marc

2016-01-01

Protein identification via database searches has become the gold standard in mass spectrometry based shotgun proteomics. However, as the quality of tandem mass spectra improves, direct mass spectrum sequencing gains interest as a database-independent alternative. In this chapter, the general principle of this so-called de novo sequencing is introduced along with pitfalls and challenges of the technique. The main tools available are presented with a focus on user friendly open source software which can be directly applied in everyday proteomic workflows.

SH-2F LAMPS Instructional Systems Development: Phase II. Final Report.

ERIC Educational Resources Information Center

Gibbons, Andrew S.; Hymes, Jonah P.

This project was one of four aircrew training development projects in a continuing study of the methodology, effectiveness, and resource requirements of the Instructional Systems Development (ISD) process. This report covers the Phase II activities of a two-phase project for the development of aircrew training for SH-2F anti-submarine warfare…

Linking Strategic Planning and Management Control.

DTIC Science & Technology

1984-03-01

contribution it intends to make to its shareholders, employees, customers, and communities . Corporate strategy defines the businesses in which a...identifies six factors to consider regarding strategy implementation. How to communicate the 42 .................... . -.......... . corporate goals is...D. Irwin, Inc., 1975. Anthony, R. N., and Welsch, G. A., Fundamentals of Management Accounting, Richard D. Irwin, Inc., 1974. Argenti , J., Corporate

Instructional Staff Development. Component 5: Pupil Centered Inquiry.

ERIC Educational Resources Information Center

Lux, John E.; Wright, Delivee L.

This trainer's manual for the fifth of six components of the Instructional Staff Development (ISD) program is designed to prepare teachers to develop a model for use in Pupil Centered Inquiry teaching (PCI). This component is said to build on the teacher's knowledge, skills, and attitudes gained in the first four components; the entire program is…

Assessing Earth and Environmental Science Enrollment Trends in Texas Public High Schools

ERIC Educational Resources Information Center

Sanders, Joan G.

2012-01-01

Scope and Method of Study: This study assesses the status of Earth and environmental sciences education in Texas Public High Schools by analyzing enrollment proportions of 11th and 12th grade students in 607 Independent School Districts (ISD) for the 2010-2011 academic school year using a quantitative, non-experimental alpha research design. This…

Social Ecology and Worksite Training and Development: Introducing the Social in Instructional System Design

ERIC Educational Resources Information Center

Weinstein, Marc G.; Shuck, Brad

2011-01-01

Human resource development (HRD) is recognized as an interdisciplinary field covering the breadth of behavioral and social sciences. However, since its inception, instructional systems design (ISD), a methodology widely used in the HRD field, has been based on a narrow range of behavioral science. Grounded in general system's theory, the ISD…

Transformational Leaders Wanted: Dallas Independent School District's Aspiring Principals Program

ERIC Educational Resources Information Center

Parvin, Jennifer Lee

2012-01-01

The purpose of this research was to explore and describe the development, implementation, and impact of the Dallas Independent School District's (ISD) Aspiring Principals Program. This study of principal preparation has relevance as a K-16 issue for two primary reasons. First, K-12 schools are focused on graduating students who are college and…

Instructional Design Models and Research on Teacher Thinking: Toward a New Conceptual Model for Research and Development.

ERIC Educational Resources Information Center

Moallem, Mahnaz

Instructional designers believe that it is important to expose pre-service and in-service teachers to Instructional Systems Design (ISD) procedures and products so teachers can utilize them. Educational literature, however, reveals few attempts to relate instructional design theory and methods to teaching practice. This paper proposes a new…

Software Independent Verification and Validation (SIV&V) Simplified

DTIC Science & Technology

2006-12-01

Configuration Item I/O Input/Output I2V2 Independent Integrated Verification and Validation IBM International Business Machines ICD Interface...IPT Integrated Product Team IRS Interface Requirements Specification ISD Integrated System Diagram ITD Integrated Test Description ITP ...programming languages such as COBOL (Common Business Oriented Language) (Codasyl committee 1960), and FORTRAN (FORmula TRANslator) ( IBM 1952) (Robat 11

Course of Study for General Office Clerk. Grades Eleven and Twelve.

ERIC Educational Resources Information Center

Denovchek, Josephine H.; Saunders, Gretchen L.

Designed to meet the needs of the community of Warren, Ohio, for competent office clerks, this course of study is presented as a sample that illustrates a format based on the instructional systems development (ISD) process. As a course of study for preparing students for entry-level employment as clerk-typists, file clerks, billing clerks, payroll…

The Friends of Northside ISD Libraries Sets Sail

ERIC Educational Resources Information Center

Hultgren, Joyce

2009-01-01

The Director of Library and Textbook services for the Northside Independent School District (NISD) Jana Knezek, had long wanted to create a Friends group and she realized how beneficial it would be to have an organization in place that could serve as an advocate for school library issues. Jana temporarily put aside that desire and participated in…

High Technology Product Training for Sales Representatives of Spectrum Healthcare Solutions and International Business Machines Corporation.

ERIC Educational Resources Information Center

Crystal, Enid

This report describes an application of the Instructional Systems Design (ISD) process to a product knowledge training project for Spectrum Healthcare Solutions, Inc., including the steps and substeps in the phases of analysis, design, development, implementation, and evaluation. The training project was designed to address the need for increased…

916 ISD Summer Assessment Team Facilitator for Transition of Students from Agency to Public School Programs.

ERIC Educational Resources Information Center

Johns, Antoinette; And Others

The presentation reviews the evolution of a summer special education assessment team. The interdisciplinary team grew from a due process specialist and occupational therapist to include a speech clinician. Their roles changed from processing students for special education to facilitating the transition of students and their families from private…

The Strategic Impact Model: An Integrative Approach to Performance Improvement and Instructional Systems Design

ERIC Educational Resources Information Center

Molenda, Michael; Pershing, James A.

2004-01-01

Training in business settings and instruction in academic settings have never taken place in a vacuum, but in earlier times many instructional technology professionals behaved as though they did. Models of instructional systems design (ISD) placed training and instruction at the center of the universe ignoring the impact of the external…

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

TFBSshape: a motif database for DNA shape features of transcription factor binding sites.

PubMed

Yang, Lin; Zhou, Tianyin; Dror, Iris; Mathelier, Anthony; Wasserman, Wyeth W; Gordân, Raluca; Rohs, Remo

2014-01-01

Transcription factor binding sites (TFBSs) are most commonly characterized by the nucleotide preferences at each position of the DNA target. Whereas these sequence motifs are quite accurate descriptions of DNA binding specificities of transcription factors (TFs), proteins recognize DNA as a three-dimensional object. DNA structural features refine the description of TF binding specificities and provide mechanistic insights into protein-DNA recognition. Existing motif databases contain extensive nucleotide sequences identified in binding experiments based on their selection by a TF. To utilize DNA shape information when analysing the DNA binding specificities of TFs, we developed a new tool, the TFBSshape database (available at http://rohslab.cmb.usc.edu/TFBSshape/), for calculating DNA structural features from nucleotide sequences provided by motif databases. The TFBSshape database can be used to generate heat maps and quantitative data for DNA structural features (i.e., minor groove width, roll, propeller twist and helix twist) for 739 TF datasets from 23 different species derived from the motif databases JASPAR and UniPROBE. As demonstrated for the basic helix-loop-helix and homeodomain TF families, our TFBSshape database can be used to compare, qualitatively and quantitatively, the DNA binding specificities of closely related TFs and, thus, uncover differential DNA binding specificities that are not apparent from nucleotide sequence alone.

TFBSshape: a motif database for DNA shape features of transcription factor binding sites

PubMed Central

Yang, Lin; Zhou, Tianyin; Dror, Iris; Mathelier, Anthony; Wasserman, Wyeth W.; Gordân, Raluca; Rohs, Remo

2014-01-01

Transcription factor binding sites (TFBSs) are most commonly characterized by the nucleotide preferences at each position of the DNA target. Whereas these sequence motifs are quite accurate descriptions of DNA binding specificities of transcription factors (TFs), proteins recognize DNA as a three-dimensional object. DNA structural features refine the description of TF binding specificities and provide mechanistic insights into protein–DNA recognition. Existing motif databases contain extensive nucleotide sequences identified in binding experiments based on their selection by a TF. To utilize DNA shape information when analysing the DNA binding specificities of TFs, we developed a new tool, the TFBSshape database (available at http://rohslab.cmb.usc.edu/TFBSshape/), for calculating DNA structural features from nucleotide sequences provided by motif databases. The TFBSshape database can be used to generate heat maps and quantitative data for DNA structural features (i.e., minor groove width, roll, propeller twist and helix twist) for 739 TF datasets from 23 different species derived from the motif databases JASPAR and UniPROBE. As demonstrated for the basic helix-loop-helix and homeodomain TF families, our TFBSshape database can be used to compare, qualitatively and quantitatively, the DNA binding specificities of closely related TFs and, thus, uncover differential DNA binding specificities that are not apparent from nucleotide sequence alone. PMID:24214955

CUDASW++: optimizing Smith-Waterman sequence database searches for CUDA-enabled graphics processing units

PubMed Central

Liu, Yongchao; Maskell, Douglas L; Schmidt, Bertil

2009-01-01

Background The Smith-Waterman algorithm is one of the most widely used tools for searching biological sequence databases due to its high sensitivity. Unfortunately, the Smith-Waterman algorithm is computationally demanding, which is further compounded by the exponential growth of sequence databases. The recent emergence of many-core architectures, and their associated programming interfaces, provides an opportunity to accelerate sequence database searches using commonly available and inexpensive hardware. Findings Our CUDASW++ implementation (benchmarked on a single-GPU NVIDIA GeForce GTX 280 graphics card and a dual-GPU GeForce GTX 295 graphics card) provides a significant performance improvement compared to other publicly available implementations, such as SWPS3, CBESW, SW-CUDA, and NCBI-BLAST. CUDASW++ supports query sequences of length up to 59K and for query sequences ranging in length from 144 to 5,478 in Swiss-Prot release 56.6, the single-GPU version achieves an average performance of 9.509 GCUPS with a lowest performance of 9.039 GCUPS and a highest performance of 9.660 GCUPS, and the dual-GPU version achieves an average performance of 14.484 GCUPS with a lowest performance of 10.660 GCUPS and a highest performance of 16.087 GCUPS. Conclusion CUDASW++ is publicly available open-source software. It provides a significant performance improvement for Smith-Waterman-based protein sequence database searches by fully exploiting the compute capability of commonly used CUDA-enabled low-cost GPUs. PMID:19416548

Tachyon search speeds up retrieval of similar sequences by several orders of magnitude.

PubMed

Tan, Joshua; Kuchibhatla, Durga; Sirota, Fernanda L; Sherman, Westley A; Gattermayer, Tobias; Kwoh, Chia Yee; Eisenhaber, Frank; Schneider, Georg; Maurer-Stroh, Sebastian

2012-06-15

The usage of current sequence search tools becomes increasingly slower as databases of protein sequences continue to grow exponentially. Tachyon, a new algorithm that identifies closely related protein sequences ~200 times faster than standard BLAST, circumvents this limitation with a reduced database and oligopeptide matching heuristic. The tool is publicly accessible as a webserver at http://tachyon.bii.a-star.edu.sg and can also be accessed programmatically through SOAP.

Responding to a Zoonotic Emergency with Multi-omics Research: Pentatrichomonas hominis Hydrogenosomal Protein Characterization with Use of RNA Sequencing and Proteomics.

PubMed

Fang, Yi-Kai; Chien, Kun-Yi; Huang, Kuo-Yang; Cheng, Wei-Hung; Ku, Fu-Mann; Lin, Rose; Chen, Ting-Wen; Huang, Po-Jung; Chiu, Cheng-Hsun; Tang, Petrus

2016-11-01

Pentatrichomonas hominis is an anaerobic flagellated protist that colonizes the large intestine of a number of mammals, including cats, dogs, nonhuman primates, and humans. The wide host range of this organism is alarming and suggests a rising zoonotic emergency. However, knowledge on in-depth biology of this protist is still limited. Similar to the human pathogen, Trichomonas vaginalis, P. hominis possesses hydrogenosomes instead of mitochondria. Studies in T. vaginalis indicated that hydrogenosome is essential for cell survival and associated with numerous pivotal biological functions, including drug resistance. To further decipher the biology of this important organelle, we undertook proteomic research in P. hominis hydrogenosomes. Lacking a decoded P. hominis genome, we utilized an RNA sequencing (RNA-seq) data set generated from P. hominis axenic culture as the reference for proteome analysis. Using this in-house reference data set and mass spectrometry (MS), we identified 442 putative hydrogenosomal proteins. Interestingly, the composition of the P. hominis hydrogenosomal proteins is very similar to that of T. vaginalis, but proteins such as Hmp36, Pam16, Pam18, and Isd11 are absent based on both MS and the RNA-seq. Our data underscore that P. hominis expresses different homologs of multiple gene families from T. vaginalis. To the best of our knowledge, we present here the first hydrogenosome proteome in a protist other than T. vaginalis that offers crucial new scholarship for global health, therapeutics, diagnostics, and veterinary medicine research. In addition, the research strategy used here using RNA sequencing and proteomics might inform future multi-omics research in other understudied organisms without decoded genomes.

Viral Genome DataBase: storing and analyzing genes and proteins from complete viral genomes.

PubMed

Hiscock, D; Upton, C

2000-05-01

The Viral Genome DataBase (VGDB) contains detailed information of the genes and predicted protein sequences from 15 completely sequenced genomes of large (&100 kb) viruses (2847 genes). The data that is stored includes DNA sequence, protein sequence, GenBank and user-entered notes, molecular weight (MW), isoelectric point (pI), amino acid content, A + T%, nucleotide frequency, dinucleotide frequency and codon use. The VGDB is a mySQL database with a user-friendly JAVA GUI. Results of queries can be easily sorted by any of the individual parameters. The software and additional figures and information are available at http://athena.bioc.uvic.ca/genomes/index.html .

REDIdb: the RNA editing database.

PubMed

Picardi, Ernesto; Regina, Teresa Maria Rosaria; Brennicke, Axel; Quagliariello, Carla

2007-01-01

The RNA Editing Database (REDIdb) is an interactive, web-based database created and designed with the aim to allocate RNA editing events such as substitutions, insertions and deletions occurring in a wide range of organisms. The database contains both fully and partially sequenced DNA molecules for which editing information is available either by experimental inspection (in vitro) or by computational detection (in silico). Each record of REDIdb is organized in a specific flat-file containing a description of the main characteristics of the entry, a feature table with the editing events and related details and a sequence zone with both the genomic sequence and the corresponding edited transcript. REDIdb is a relational database in which the browsing and identification of editing sites has been simplified by means of two facilities to either graphically display genomic or cDNA sequences or to show the corresponding alignment. In both cases, all editing sites are highlighted in colour and their relative positions are detailed by mousing over. New editing positions can be directly submitted to REDIdb after a user-specific registration to obtain authorized secure access. This first version of REDIdb database stores 9964 editing events and can be freely queried at http://biologia.unical.it/py_script/search.html.

UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions.

PubMed

Robasky, Kimberly; Bulyk, Martha L

2011-01-01

The Universal PBM Resource for Oligonucleotide-Binding Evaluation (UniPROBE) database is a centralized repository of information on the DNA-binding preferences of proteins as determined by universal protein-binding microarray (PBM) technology. Each entry for a protein (or protein complex) in UniPROBE provides the quantitative preferences for all possible nucleotide sequence variants ('words') of length k ('k-mers'), as well as position weight matrix (PWM) and graphical sequence logo representations of the k-mer data. In this update, we describe >130% expansion of the database content, incorporation of a protein BLAST (blastp) tool for finding protein sequence matches in UniPROBE, the introduction of UniPROBE accession numbers and additional database enhancements. The UniPROBE database is available at http://uniprobe.org.

Next-generation sequencing can reveal in vitro-generated PCR crossover products: some artifactual sequences correspond to HLA alleles in the IMGT/HLA database.

PubMed

Holcomb, C L; Rastrou, M; Williams, T C; Goodridge, D; Lazaro, A M; Tilanus, M; Erlich, H A

2014-01-01

The high-resolution human leukocyte antigen (HLA) genotyping assay that we developed using 454 sequencing and Conexio software uses generic polymerase chain reaction (PCR) primers for DRB exon 2. Occasionally, we observed low abundance DRB amplicon sequences that resulted from in vitro PCR 'crossing over' between DRB1 and DRB3/4/5. These hybrid sequences, revealed by the clonal sequencing property of the 454 system, were generally observed at a read depth of 5%-10% of the true alleles. They usually contained at least one mismatch with the IMGT/HLA database, and consequently, were easily recognizable and did not cause a problem for HLA genotyping. Sometimes, however, these artifactual sequences matched a rare allele and the automatic genotype assignment was incorrect. These observations raised two issues: (1) could PCR conditions be modified to reduce such artifacts? and (2) could some of the rare alleles listed in the IMGT/HLA database be artifacts rather than true alleles? Because PCR crossing over occurs during late cycles of PCR, we compared DRB genotypes resulting from 28 and (our standard) 35 cycles of PCR. For all 21 cell line DNAs amplified for 35 cycles, crossover products were detected. In 33% of the cases, these hybrid sequences corresponded to named alleles. With amplification for only 28 cycles, these artifactual sequences were not detectable. To investigate whether some rare alleles in the IMGT/HLA database might be due to PCR artifacts, we analyzed four samples obtained from the investigators who submitted the sequences. In three cases, the sequences were generated from true alleles. In one case, our 454 sequencing revealed an error in the previously submitted sequence. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

CLAST: CUDA implemented large-scale alignment search tool.

PubMed

Yano, Masahiro; Mori, Hiroshi; Akiyama, Yutaka; Yamada, Takuji; Kurokawa, Ken

2014-12-11

Metagenomics is a powerful methodology to study microbial communities, but it is highly dependent on nucleotide sequence similarity searching against sequence databases. Metagenomic analyses with next-generation sequencing technologies produce enormous numbers of reads from microbial communities, and many reads are derived from microbes whose genomes have not yet been sequenced, limiting the usefulness of existing sequence similarity search tools. Therefore, there is a clear need for a sequence similarity search tool that can rapidly detect weak similarity in large datasets. We developed a tool, which we named CLAST (CUDA implemented large-scale alignment search tool), that enables analyses of millions of reads and thousands of reference genome sequences, and runs on NVIDIA Fermi architecture graphics processing units. CLAST has four main advantages over existing alignment tools. First, CLAST was capable of identifying sequence similarities ~80.8 times faster than BLAST and 9.6 times faster than BLAT. Second, CLAST executes global alignment as the default (local alignment is also an option), enabling CLAST to assign reads to taxonomic and functional groups based on evolutionarily distant nucleotide sequences with high accuracy. Third, CLAST does not need a preprocessed sequence database like Burrows-Wheeler Transform-based tools, and this enables CLAST to incorporate large, frequently updated sequence databases. Fourth, CLAST requires <2 GB of main memory, making it possible to run CLAST on a standard desktop computer or server node. CLAST achieved very high speed (similar to the Burrows-Wheeler Transform-based Bowtie 2 for long reads) and sensitivity (equal to BLAST, BLAT, and FR-HIT) without the need for extensive database preprocessing or a specialized computing platform. Our results demonstrate that CLAST has the potential to be one of the most powerful and realistic approaches to analyze the massive amount of sequence data from next-generation sequencing technologies.

The Yak genome database: an integrative database for studying yak biology and high-altitude adaption

PubMed Central

2012-01-01

Background The yak (Bos grunniens) is a long-haired bovine that lives at high altitudes and is an important source of milk, meat, fiber and fuel. The recent sequencing, assembly and annotation of its genome are expected to further our understanding of the means by which it has adapted to life at high altitudes and its ecologically important traits. Description The Yak Genome Database (YGD) is an internet-based resource that provides access to genomic sequence data and predicted functional information concerning the genes and proteins of Bos grunniens. The curated data stored in the YGD includes genome sequences, predicted genes and associated annotations, non-coding RNA sequences, transposable elements, single nucleotide variants, and three-way whole-genome alignments between human, cattle and yak. YGD offers useful searching and data mining tools, including the ability to search for genes by name or using function keywords as well as GBrowse genome browsers and/or BLAST servers, which can be used to visualize genome regions and identify similar sequences. Sequence data from the YGD can also be downloaded to perform local searches. Conclusions A new yak genome database (YGD) has been developed to facilitate studies on high-altitude adaption and bovine genomics. The database will be continuously updated to incorporate new information such as transcriptome data and population resequencing data. The YGD can be accessed at http://me.lzu.edu.cn/yak. PMID:23134687

SS-Wrapper: a package of wrapper applications for similarity searches on Linux clusters.

PubMed

Wang, Chunlin; Lefkowitz, Elliot J

2004-10-28

Large-scale sequence comparison is a powerful tool for biological inference in modern molecular biology. Comparing new sequences to those in annotated databases is a useful source of functional and structural information about these sequences. Using software such as the basic local alignment search tool (BLAST) or HMMPFAM to identify statistically significant matches between newly sequenced segments of genetic material and those in databases is an important task for most molecular biologists. Searching algorithms are intrinsically slow and data-intensive, especially in light of the rapid growth of biological sequence databases due to the emergence of high throughput DNA sequencing techniques. Thus, traditional bioinformatics tools are impractical on PCs and even on dedicated UNIX servers. To take advantage of larger databases and more reliable methods, high performance computation becomes necessary. We describe the implementation of SS-Wrapper (Similarity Search Wrapper), a package of wrapper applications that can parallelize similarity search applications on a Linux cluster. Our wrapper utilizes a query segmentation-search (QS-search) approach to parallelize sequence database search applications. It takes into consideration load balancing between each node on the cluster to maximize resource usage. QS-search is designed to wrap many different search tools, such as BLAST and HMMPFAM using the same interface. This implementation does not alter the original program, so newly obtained programs and program updates should be accommodated easily. Benchmark experiments using QS-search to optimize BLAST and HMMPFAM showed that QS-search accelerated the performance of these programs almost linearly in proportion to the number of CPUs used. We have also implemented a wrapper that utilizes a database segmentation approach (DS-BLAST) that provides a complementary solution for BLAST searches when the database is too large to fit into the memory of a single node. Used together, QS-search and DS-BLAST provide a flexible solution to adapt sequential similarity searching applications in high performance computing environments. Their ease of use and their ability to wrap a variety of database search programs provide an analytical architecture to assist both the seasoned bioinformaticist and the wet-bench biologist.

SS-Wrapper: a package of wrapper applications for similarity searches on Linux clusters

PubMed Central

Wang, Chunlin; Lefkowitz, Elliot J

2004-01-01

Background Large-scale sequence comparison is a powerful tool for biological inference in modern molecular biology. Comparing new sequences to those in annotated databases is a useful source of functional and structural information about these sequences. Using software such as the basic local alignment search tool (BLAST) or HMMPFAM to identify statistically significant matches between newly sequenced segments of genetic material and those in databases is an important task for most molecular biologists. Searching algorithms are intrinsically slow and data-intensive, especially in light of the rapid growth of biological sequence databases due to the emergence of high throughput DNA sequencing techniques. Thus, traditional bioinformatics tools are impractical on PCs and even on dedicated UNIX servers. To take advantage of larger databases and more reliable methods, high performance computation becomes necessary. Results We describe the implementation of SS-Wrapper (Similarity Search Wrapper), a package of wrapper applications that can parallelize similarity search applications on a Linux cluster. Our wrapper utilizes a query segmentation-search (QS-search) approach to parallelize sequence database search applications. It takes into consideration load balancing between each node on the cluster to maximize resource usage. QS-search is designed to wrap many different search tools, such as BLAST and HMMPFAM using the same interface. This implementation does not alter the original program, so newly obtained programs and program updates should be accommodated easily. Benchmark experiments using QS-search to optimize BLAST and HMMPFAM showed that QS-search accelerated the performance of these programs almost linearly in proportion to the number of CPUs used. We have also implemented a wrapper that utilizes a database segmentation approach (DS-BLAST) that provides a complementary solution for BLAST searches when the database is too large to fit into the memory of a single node. Conclusions Used together, QS-search and DS-BLAST provide a flexible solution to adapt sequential similarity searching applications in high performance computing environments. Their ease of use and their ability to wrap a variety of database search programs provide an analytical architecture to assist both the seasoned bioinformaticist and the wet-bench biologist. PMID:15511296

MUBII-TB-DB: a database of mutations associated with antibiotic resistance in Mycobacterium tuberculosis.

PubMed

Flandrois, Jean-Pierre; Lina, Gérard; Dumitrescu, Oana

2014-04-14

Tuberculosis is an infectious bacterial disease caused by Mycobacterium tuberculosis. It remains a major health threat, killing over one million people every year worldwide. An early antibiotic therapy is the basis of the treatment, and the emergence and spread of multidrug and extensively drug-resistant mutant strains raise significant challenges. As these bacteria grow very slowly, drug resistance mutations are currently detected using molecular biology techniques. Resistance mutations are identified by sequencing the resistance-linked genes followed by a comparison with the literature data. The only online database is the TB Drug Resistance Mutation database (TBDReaM database); however, it requires mutation detection before use, and its interrogation is complex due to its loose syntax and grammar. The MUBII-TB-DB database is a simple, highly structured text-based database that contains a set of Mycobacterium tuberculosis mutations (DNA and proteins) occurring at seven loci: rpoB, pncA, katG; mabA(fabG1)-inhA, gyrA, gyrB, and rrs. Resistance mutation data were extracted after the systematic review of MEDLINE referenced publications before March 2013. MUBII analyzes the query sequence obtained by PCR-sequencing using two parallel strategies: i) a BLAST search against a set of previously reconstructed mutated sequences and ii) the alignment of the query sequences (DNA and its protein translation) with the wild-type sequences. The post-treatment includes the extraction of the aligned sequences together with their descriptors (position and nature of mutations). The whole procedure is performed using the internet. The results are graphs (alignments) and text (description of the mutation, therapeutic significance). The system is quick and easy to use, even for technicians without bioinformatics training. MUBII-TB-DB is a structured database of the mutations occurring at seven loci of major therapeutic value in tuberculosis management. Moreover, the system provides interpretation of the mutations in biological and therapeutic terms and can evolve by the addition of newly described mutations. Its goal is to provide easy and comprehensive access through a client-server model over the Web to an up-to-date database of mutations that lead to the resistance of M. tuberculosis to antibiotics.

A curated gluten protein sequence database to support development of proteomics methods for determination of gluten in gluten-free foods.

PubMed

Bromilow, Sophie; Gethings, Lee A; Buckley, Mike; Bromley, Mike; Shewry, Peter R; Langridge, James I; Clare Mills, E N

2017-06-23

The unique physiochemical properties of wheat gluten enable a diverse range of food products to be manufactured. However, gluten triggers coeliac disease, a condition which is treated using a gluten-free diet. Analytical methods are required to confirm if foods are gluten-free, but current immunoassay-based methods can unreliable and proteomic methods offer an alternative but require comprehensive and well annotated sequence databases which are lacking for gluten. A manually a curated database (GluPro V1.0) of gluten proteins, comprising 630 discrete unique full length protein sequences has been compiled. It is representative of the different types of gliadin and glutenin components found in gluten. An in silico comparison of their coeliac toxicity was undertaken by analysing the distribution of coeliac toxic motifs. This demonstrated that whilst the α-gliadin proteins contained more toxic motifs, these were distributed across all gluten protein sub-types. Comparison of annotations observed using a discovery proteomics dataset acquired using ion mobility MS/MS showed that more reliable identifications were obtained using the GluPro V1.0 database compared to the complete reviewed Viridiplantae database. This highlights the value of a curated sequence database specifically designed to support the proteomic workflows and the development of methods to detect and quantify gluten. We have constructed the first manually curated open-source wheat gluten protein sequence database (GluPro V1.0) in a FASTA format to support the application of proteomic methods for gluten protein detection and quantification. We have also analysed the manually verified sequences to give the first comprehensive overview of the distribution of sequences able to elicit a reaction in coeliac disease, the prevalent form of gluten intolerance. Provision of this database will improve the reliability of gluten protein identification by proteomic analysis, and aid the development of targeted mass spectrometry methods in line with Codex Alimentarius Commission requirements for foods designed to meet the needs of gluten intolerant individuals. Copyright © 2017. Published by Elsevier B.V.

Hmrbase: a database of hormones and their receptors

PubMed Central

Rashid, Mamoon; Singla, Deepak; Sharma, Arun; Kumar, Manish; Raghava, Gajendra PS

2009-01-01

Background Hormones are signaling molecules that play vital roles in various life processes, like growth and differentiation, physiology, and reproduction. These molecules are mostly secreted by endocrine glands, and transported to target organs through the bloodstream. Deficient, or excessive, levels of hormones are associated with several diseases such as cancer, osteoporosis, diabetes etc. Thus, it is important to collect and compile information about hormones and their receptors. Description This manuscript describes a database called Hmrbase which has been developed for managing information about hormones and their receptors. It is a highly curated database for which information has been collected from the literature and the public databases. The current version of Hmrbase contains comprehensive information about ~2000 hormones, e.g., about their function, source organism, receptors, mature sequences, structures etc. Hmrbase also contains information about ~3000 hormone receptors, in terms of amino acid sequences, subcellular localizations, ligands, and post-translational modifications etc. One of the major features of this database is that it provides data about ~4100 hormone-receptor pairs. A number of online tools have been integrated into the database, to provide the facilities like keyword search, structure-based search, mapping of a given peptide(s) on the hormone/receptor sequence, sequence similarity search. This database also provides a number of external links to other resources/databases in order to help in the retrieving of further related information. Conclusion Owing to the high impact of endocrine research in the biomedical sciences, the Hmrbase could become a leading data portal for researchers. The salient features of Hmrbase are hormone-receptor pair-related information, mapping of peptide stretches on the protein sequences of hormones and receptors, Pfam domain annotations, categorical browsing options, online data submission, DrugPedia linkage etc. Hmrbase is available online for public from . PMID:19589147

T3SEdb: data warehousing of virulence effectors secreted by the bacterial Type III Secretion System.

PubMed

Tay, Daniel Ming Ming; Govindarajan, Kunde Ramamoorthy; Khan, Asif M; Ong, Terenze Yao Rui; Samad, Hanif M; Soh, Wei Wei; Tong, Minyan; Zhang, Fan; Tan, Tin Wee

2010-10-15

Effectors of Type III Secretion System (T3SS) play a pivotal role in establishing and maintaining pathogenicity in the host and therefore the identification of these effectors is important in understanding virulence. However, the effectors display high level of sequence diversity, therefore making the identification a difficult process. There is a need to collate and annotate existing effector sequences in public databases to enable systematic analyses of these sequences for development of models for screening and selection of putative novel effectors from bacterial genomes that can be validated by a smaller number of key experiments. Herein, we present T3SEdb http://effectors.bic.nus.edu.sg/T3SEdb, a specialized database of annotated T3SS effector (T3SE) sequences containing 1089 records from 46 bacterial species compiled from the literature and public protein databases. Procedures have been defined for i) comprehensive annotation of experimental status of effectors, ii) submission and curation review of records by users of the database, and iii) the regular update of T3SEdb existing and new records. Keyword fielded and sequence searches (BLAST, regular expression) are supported for both experimentally verified and hypothetical T3SEs. More than 171 clusters of T3SEs were detected based on sequence identity comparisons (intra-cluster difference up to ~60%). Owing to this high level of sequence diversity of T3SEs, the T3SEdb provides a large number of experimentally known effector sequences with wide species representation for creation of effector predictors. We created a reliable effector prediction tool, integrated into the database, to demonstrate the application of the database for such endeavours. T3SEdb is the first specialised database reported for T3SS effectors, enriched with manual annotations that facilitated systematic construction of a reliable prediction model for identification of novel effectors. The T3SEdb represents a platform for inclusion of additional annotations of metadata for future developments of sophisticated effector prediction models for screening and selection of putative novel effectors from bacterial genomes/proteomes that can be validated by a small number of key experiments.

VKCDB: voltage-gated K+ channel database updated and upgraded.

PubMed

Gallin, Warren J; Boutet, Patrick A

2011-01-01

The Voltage-gated K(+) Channel DataBase (VKCDB) (http://vkcdb.biology.ualberta.ca) makes a comprehensive set of sequence data readily available for phylogenetic and comparative analysis. The current update contains 2063 entries for full-length or nearly full-length unique channel sequences from Bacteria (477), Archaea (18) and Eukaryotes (1568), an increase from 346 solely eukaryotic entries in the original release. In addition to protein sequences for channels, corresponding nucleotide sequences of the open reading frames corresponding to the amino acid sequences are now available and can be extracted in parallel with sets of protein sequences. Channels are categorized into subfamilies by phylogenetic analysis and by using hidden Markov model analyses. Although the raw database contains a number of fragmentary, duplicated, obsolete and non-channel sequences that were collected in early steps of data collection, the web interface will only return entries that have been validated as likely K(+) channels. The retrieval function of the web interface allows retrieval of entries that contain a substantial fraction of the core structural elements of VKCs, fragmentary entries, or both. The full database can be downloaded as either a MySQL dump or as an XML dump from the web site. We have now implemented automated updates at quarterly intervals.

The SUPERFAMILY database in 2004: additions and improvements.

PubMed

Madera, Martin; Vogel, Christine; Kummerfeld, Sarah K; Chothia, Cyrus; Gough, Julian

2004-01-01

The SUPERFAMILY database provides structural assignments to protein sequences and a framework for analysis of the results. At the core of the database is a library of profile Hidden Markov Models that represent all proteins of known structure. The library is based on the SCOP classification of proteins: each model corresponds to a SCOP domain and aims to represent an entire superfamily. We have applied the library to predicted proteins from all completely sequenced genomes (currently 154), the Swiss-Prot and TrEMBL databases and other sequence collections. Close to 60% of all proteins have at least one match, and one half of all residues are covered by assignments. All models and full results are available for download and online browsing at http://supfam.org. Users can study the distribution of their superfamily of interest across all completely sequenced genomes, investigate with which other superfamilies it combines and retrieve proteins in which it occurs. Alternatively, concentrating on a particular genome as a whole, it is possible first, to find out its superfamily composition, and secondly, to compare it with that of other genomes to detect superfamilies that are over- or under-represented. In addition, the webserver provides the following standard services: sequence search; keyword search for genomes, superfamilies and sequence identifiers; and multiple alignment of genomic, PDB and custom sequences.

Molecular Identification and Databases in Fusarium

USDA-ARS?s Scientific Manuscript database

DNA sequence-based methods for identifying pathogenic and mycotoxigenic Fusarium isolates have become the gold standard worldwide. Moreover, fusarial DNA sequence data are increasing rapidly in several web-accessible databases for comparative purposes. Unfortunately, the use of Basic Alignment Sea...

MerCat: a versatile k-mer counter and diversity estimator for database-independent property analysis obtained from metagenomic and/or metatranscriptomic sequencing data

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

White, Richard A.; Panyala, Ajay R.; Glass, Kevin A.

MerCat is a parallel, highly scalable and modular property software package for robust analysis of features in next-generation sequencing data. MerCat inputs include assembled contigs and raw sequence reads from any platform resulting in feature abundance counts tables. MerCat allows for direct analysis of data properties without reference sequence database dependency commonly used by search tools such as BLAST and/or DIAMOND for compositional analysis of whole community shotgun sequencing (e.g. metagenomes and metatranscriptomes).

Glycan fragment database: a database of PDB-based glycan 3D structures.

PubMed

Jo, Sunhwan; Im, Wonpil

2013-01-01

The glycan fragment database (GFDB), freely available at http://www.glycanstructure.org, is a database of the glycosidic torsion angles derived from the glycan structures in the Protein Data Bank (PDB). Analogous to protein structure, the structure of an oligosaccharide chain in a glycoprotein, referred to as a glycan, can be characterized by the torsion angles of glycosidic linkages between relatively rigid carbohydrate monomeric units. Knowledge of accessible conformations of biologically relevant glycans is essential in understanding their biological roles. The GFDB provides an intuitive glycan sequence search tool that allows the user to search complex glycan structures. After a glycan search is complete, each glycosidic torsion angle distribution is displayed in terms of the exact match and the fragment match. The exact match results are from the PDB entries that contain the glycan sequence identical to the query sequence. The fragment match results are from the entries with the glycan sequence whose substructure (fragment) or entire sequence is matched to the query sequence, such that the fragment results implicitly include the influences from the nearby carbohydrate residues. In addition, clustering analysis based on the torsion angle distribution can be performed to obtain the representative structures among the searched glycan structures.

Winnowing sequences from a database search.

PubMed

Berman, P; Zhang, Z; Wolf, Y I; Koonin, E V; Miller, W

2000-01-01

In database searches for sequence similarity, matches to a distinct sequence region (e.g., protein domain) are frequently obscured by numerous matches to another region of the same sequence. In order to cope with this problem, algorithms are developed to discard redundant matches. One model for this problem begins with a list of intervals, each with an associated score; each interval gives the range of positions in the query sequence that align to a database sequence, and the score is that of the alignment. If interval I is contained in interval J, and I's score is less than J's, then I is said to be dominated by J. The problem is then to identify each interval that is dominated by at least K other intervals, where K is a given level of "tolerable redundancy." An algorithm is developed to solve the problem in O(N log N) time and O(N*) space, where N is the number of intervals and N* is a precisely defined value that never exceeds N and is frequently much smaller. This criterion for discarding database hits has been implemented in the Blast program, as illustrated herein with examples. Several variations and extensions of this approach are also described.

The Comprehensive Phytopathogen Genomics Resource: a web-based resource for data-mining plant pathogen genomes.

PubMed

Hamilton, John P; Neeno-Eckwall, Eric C; Adhikari, Bishwo N; Perna, Nicole T; Tisserat, Ned; Leach, Jan E; Lévesque, C André; Buell, C Robin

2011-01-01

The Comprehensive Phytopathogen Genomics Resource (CPGR) provides a web-based portal for plant pathologists and diagnosticians to view the genome and trancriptome sequence status of 806 bacterial, fungal, oomycete, nematode, viral and viroid plant pathogens. Tools are available to search and analyze annotated genome sequences of 74 bacterial, fungal and oomycete pathogens. Oomycete and fungal genomes are obtained directly from GenBank, whereas bacterial genome sequences are downloaded from the A Systematic Annotation Package (ASAP) database that provides curation of genomes using comparative approaches. Curated lists of bacterial genes relevant to pathogenicity and avirulence are also provided. The Plant Pathogen Transcript Assemblies Database provides annotated assemblies of the transcribed regions of 82 eukaryotic genomes from publicly available single pass Expressed Sequence Tags. Data-mining tools are provided along with tools to create candidate diagnostic markers, an emerging use for genomic sequence data in plant pathology. The Plant Pathogen Ribosomal DNA (rDNA) database is a resource for pathogens that lack genome or transcriptome data sets and contains 131 755 rDNA sequences from GenBank for 17 613 species identified as plant pathogens and related genera. Database URL: http://cpgr.plantbiology.msu.edu.

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.

Complementary DNA sequencing and identification of mRNAs from the venomous gland of Agkistrodon piscivorus leucostoma.

PubMed

Jia, Ying; Cantu, Bruno A; Sánchez, Elda E; Pérez, John C

2008-06-15

To advance our knowledge on the snake venom composition and transcripts expressed in venom gland at the molecular level, we constructed a cDNA library from the venom gland of Agkistrodon piscivorus leucostoma for the generation of expressed sequence tags (ESTs) database. From the randomly sequenced 2112 independent clones, we have obtained ESTs for 1309 (62%) cDNAs, which showed significant deduced amino acid sequence similarity (scores >80) to previously characterized proteins in National Center for Biotechnology Information (NCBI) database. Ribosomal proteins make up 47 clones (2%) and the remaining 756 (36%) cDNAs represent either unknown identity or show BLASTX sequence identity scores of <80 with known GenBank accessions. The most highly expressed gene encoding phospholipase A(2) (PLA(2)) accounting for 35% of A. p. leucostoma venom gland cDNAs was identified and further confirmed by crude venom applied to sodium dodecyl sulfate/polyacrylamide gel electrophoresis (SDS-PAGE) electrophoresis and protein sequencing. A total of 180 representative genes were obtained from the sequence assemblies and deposited to EST database. Clones showing sequence identity to disintegrins, thrombin-like enzymes, hemorrhagic toxins, fibrinogen clotting inhibitors and plasminogen activators were also identified in our EST database. These data can be used to develop a research program that will help us identify genes encoding proteins that are of medical importance or proteins involved in the mechanisms of the toxin venom.

HIV Sequence Compendium 2015

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

Foley, Brian Thomas; Leitner, Thomas Kenneth; Apetrei, Cristian

This compendium is an annual printed summary of the data contained in the HIV sequence database. We try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2015. Hence, though it is published in 2015 and called the 2015 Compendium, its contents correspond to the 2014 curated alignments on our website. The number of sequences in the HIV database ismore » still increasing. In total, at the end of 2014, there were 624,121 sequences in the HIV Sequence Database, an increase of 7% since the previous year. This is the first year that the number of new sequences added to the database has decreased compared to the previous year. The number of near complete genomes (>7000 nucleotides) increased to 5834 by end of 2014. However, as in previous years, the compendium alignments contain only a fraction of these. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/ content/sequence/NEWALIGN/align.html As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.« less

A combined strategy involving Sanger and 454 pyrosequencing increases genomic resources to aid in the management of reproduction, disease control and genetic selection in the turbot (Scophthalmus maximus).

PubMed

Ribas, Laia; Pardo, Belén G; Fernández, Carlos; Alvarez-Diós, José Antonio; Gómez-Tato, Antonio; Quiroga, María Isabel; Planas, Josep V; Sitjà-Bobadilla, Ariadna; Martínez, Paulino; Piferrer, Francesc

2013-03-15

Genomic resources for plant and animal species that are under exploitation primarily for human consumption are increasingly important, among other things, for understanding physiological processes and for establishing adequate genetic selection programs. Current available techniques for high-throughput sequencing have been implemented in a number of species, including fish, to obtain a proper description of the transcriptome. The objective of this study was to generate a comprehensive transcriptomic database in turbot, a highly priced farmed fish species in Europe, with potential expansion to other areas of the world, for which there are unsolved production bottlenecks, to understand better reproductive- and immune-related functions. This information is essential to implement marker assisted selection programs useful for the turbot industry. Expressed sequence tags were generated by Sanger sequencing of cDNA libraries from different immune-related tissues after several parasitic challenges. The resulting database ("Turbot 2 database") was enlarged with sequences generated from a 454 sequencing run of brain-hypophysis-gonadal axis-derived RNA obtained from turbot at different development stages. The assembly of Sanger and 454 sequences generated 52,427 consensus sequences ("Turbot 3 database"), of which 23,661 were successfully annotated. A total of 1,410 sequences were confirmed to be related to reproduction and key genes involved in sex differentiation and maturation were identified for the first time in turbot (AR, AMH, SRY-related genes, CYP19A, ZPGs, STAR FSHR, etc.). Similarly, 2,241 sequences were related to the immune system and several novel key immune genes were identified (BCL, TRAF, NCK, CD28 and TOLLIP, among others). The number of genes of many relevant reproduction- and immune-related pathways present in the database was 50-90% of the total gene count of each pathway. In addition, 1,237 microsatellites and 7,362 single nucleotide polymorphisms (SNPs) were also compiled. Further, 2,976 putative natural antisense transcripts (NATs) including microRNAs were also identified. The combined sequencing strategies employed here significantly increased the turbot genomic resources available, including 34,400 novel sequences. The generated database contains a larger number of genes relevant for reproduction- and immune-associated studies, with an excellent coverage of most genes present in many relevant physiological pathways. This database also allowed the identification of many microsatellites and SNP markers that will be very useful for population and genome screening and a valuable aid in marker assisted selection programs.

The DNA Data Bank of Japan launches a new resource, the DDBJ Omics Archive of functional genomics experiments.

PubMed

Kodama, Yuichi; Mashima, Jun; Kaminuma, Eli; Gojobori, Takashi; Ogasawara, Osamu; Takagi, Toshihisa; Okubo, Kousaku; Nakamura, Yasukazu

2012-01-01

The DNA Data Bank of Japan (DDBJ; http://www.ddbj.nig.ac.jp) maintains and provides archival, retrieval and analytical resources for biological information. The central DDBJ resource consists of public, open-access nucleotide sequence databases including raw sequence reads, assembly information and functional annotation. Database content is exchanged with EBI and NCBI within the framework of the International Nucleotide Sequence Database Collaboration (INSDC). In 2011, DDBJ launched two new resources: the 'DDBJ Omics Archive' (DOR; http://trace.ddbj.nig.ac.jp/dor) and BioProject (http://trace.ddbj.nig.ac.jp/bioproject). DOR is an archival database of functional genomics data generated by microarray and highly parallel new generation sequencers. Data are exchanged between the ArrayExpress at EBI and DOR in the common MAGE-TAB format. BioProject provides an organizational framework to access metadata about research projects and the data from the projects that are deposited into different databases. In this article, we describe major changes and improvements introduced to the DDBJ services, and the launch of two new resources: DOR and BioProject.

PlantTFDB: a comprehensive plant transcription factor database

PubMed Central

Guo, An-Yuan; Chen, Xin; Gao, Ge; Zhang, He; Zhu, Qi-Hui; Liu, Xiao-Chuan; Zhong, Ying-Fu; Gu, Xiaocheng; He, Kun; Luo, Jingchu

2008-01-01

Transcription factors (TFs) play key roles in controlling gene expression. Systematic identification and annotation of TFs, followed by construction of TF databases may serve as useful resources for studying the function and evolution of transcription factors. We developed a comprehensive plant transcription factor database PlantTFDB (http://planttfdb.cbi.pku.edu.cn), which contains 26 402 TFs predicted from 22 species, including five model organisms with available whole genome sequence and 17 plants with available EST sequences. To provide comprehensive information for those putative TFs, we made extensive annotation at both family and gene levels. A brief introduction and key references were presented for each family. Functional domain information and cross-references to various well-known public databases were available for each identified TF. In addition, we predicted putative orthologs of those TFs among the 22 species. PlantTFDB has a simple interface to allow users to search the database by IDs or free texts, to make sequence similarity search against TFs of all or individual species, and to download TF sequences for local analysis. PMID:17933783

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.

Sequencing of cDNA Clones from the Genetic Map of Tomato (Lycopersicon esculentum)

PubMed Central

Ganal, Martin W.; Czihal, Rosemarie; Hannappel, Ulrich; Kloos, Dorothee-U.; Polley, Andreas; Ling, Hong-Qing

1998-01-01

The dense RFLP linkage map of tomato (Lycopersicon esculentum) contains >300 anonymous cDNA clones. Of those clones, 272 were partially or completely sequenced. The sequences were compared at the DNA and protein level to known genes in databases. For 57% of the clones, a significant match to previously described genes was found. The information will permit the conversion of those markers to STS markers and allow their use in PCR-based mapping experiments. Furthermore, it will facilitate the comparative mapping of genes across distantly related plant species by direct comparison of DNA sequences and map positions. [cDNA sequence data reported in this paper have been submitted to the EMBL database under accession nos. AA824695–AA825005 and the dbEST_Id database under accession nos. 1546519–1546862.] PMID:9724330

FOUNTAIN: A JAVA open-source package to assist large sequencing projects

PubMed Central

Buerstedde, Jean-Marie; Prill, Florian

2001-01-01

Background Better automation, lower cost per reaction and a heightened interest in comparative genomics has led to a dramatic increase in DNA sequencing activities. Although the large sequencing projects of specialized centers are supported by in-house bioinformatics groups, many smaller laboratories face difficulties managing the appropriate processing and storage of their sequencing output. The challenges include documentation of clones, templates and sequencing reactions, and the storage, annotation and analysis of the large number of generated sequences. Results We describe here a new program, named FOUNTAIN, for the management of large sequencing projects . FOUNTAIN uses the JAVA computer language and data storage in a relational database. Starting with a collection of sequencing objects (clones), the program generates and stores information related to the different stages of the sequencing project using a web browser interface for user input. The generated sequences are subsequently imported and annotated based on BLAST searches against the public databases. In addition, simple algorithms to cluster sequences and determine putative polymorphic positions are implemented. Conclusions A simple, but flexible and scalable software package is presented to facilitate data generation and storage for large sequencing projects. Open source and largely platform and database independent, we wish FOUNTAIN to be improved and extended in a community effort. PMID:11591214

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

Jackrel, Sara L.; Owens, Sarah M.; Gilbert, Jack A.

Plants in terrestrial and aquatic environments contain a diverse microbiome. Yet, the chloroplast and mitochondria organelles of the plant eukaryotic cell originate from free-living cyanobacteria and Rickettsiales. This represents a challenge for sequencing the plant microbiome with universal primers, as ~99% of 16S rRNA sequences may consist of chloroplast and mitochondrial sequences. Peptide nucleic acid clamps offer a potential solution by blocking amplification of host-associated sequences. We assessed the efficacy of chloroplast and mitochondria-blocking clamps against a range of microbial taxa from soil, freshwater and marine environments. While we found that the mitochondrial blocking clamps appear to be a robustmore » method for assessing animal-associated microbiota, Proteobacterial 16S rRNA binds to the chloroplast-blocking clamp, resulting in a strong sequencing bias against this group. We attribute this bias to a conserved 14-bp sequence in the Proteobacteria that matches the 17-bp chloroplast-blocking clamp sequence. By scanning the Greengenes database, we provide a reference list of nearly 1500 taxa that contain this 14-bp sequence, including 48 families such as the Rhodobacteraceae, Phyllobacteriaceae, Rhizobiaceae, Kiloniellaceae and Caulobacteraceae. To determine where these taxa are found in nature, we mapped this taxa reference list against the Earth Microbiome Project database. These taxa are abundant in a variety of environments, particularly aquatic and semiaquatic freshwater and marine habitats. To facilitate informed decisions on effective use of organelle-blocking clamps, we provide a searchable database of microbial taxa in the Greengenes and Silva databases matching various n-mer oligonucleotides of each PNA sequence.« less

Effect of the sequence data deluge on the performance of methods for detecting protein functional residues.

PubMed

Garrido-Martín, Diego; Pazos, Florencio

2018-02-27

The exponential accumulation of new sequences in public databases is expected to improve the performance of all the approaches for predicting protein structural and functional features. Nevertheless, this was never assessed or quantified for some widely used methodologies, such as those aimed at detecting functional sites and functional subfamilies in protein multiple sequence alignments. Using raw protein sequences as only input, these approaches can detect fully conserved positions, as well as those with a family-dependent conservation pattern. Both types of residues are routinely used as predictors of functional sites and, consequently, understanding how the sequence content of the databases affects them is relevant and timely. In this work we evaluate how the growth and change with time in the content of sequence databases affect five sequence-based approaches for detecting functional sites and subfamilies. We do that by recreating historical versions of the multiple sequence alignments that would have been obtained in the past based on the database contents at different time points, covering a period of 20 years. Applying the methods to these historical alignments allows quantifying the temporal variation in their performance. Our results show that the number of families to which these methods can be applied sharply increases with time, while their ability to detect potentially functional residues remains almost constant. These results are informative for the methods' developers and final users, and may have implications in the design of new sequencing initiatives.

Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor.

PubMed

Kohany, Oleksiy; Gentles, Andrew J; Hankus, Lukasz; Jurka, Jerzy

2006-10-25

Repbase is a reference database of eukaryotic repetitive DNA, which includes prototypic sequences of repeats and basic information described in annotations. Updating and maintenance of the database requires specialized tools, which we have created and made available for use with Repbase, and which may be useful as a template for other curated databases. We describe the software tools RepbaseSubmitter and Censor, which are designed to facilitate updating and screening the content of Repbase. RepbaseSubmitter is a java-based interface for formatting and annotating Repbase entries. It eliminates many common formatting errors, and automates actions such as calculation of sequence lengths and composition, thus facilitating curation of Repbase sequences. In addition, it has several features for predicting protein coding regions in sequences; searching and including Pubmed references in Repbase entries; and searching the NCBI taxonomy database for correct inclusion of species information and taxonomic position. Censor is a tool to rapidly identify repetitive elements by comparison to known repeats. It uses WU-BLAST for speed and sensitivity, and can conduct DNA-DNA, DNA-protein, or translated DNA-translated DNA searches of genomic sequence. Defragmented output includes a map of repeats present in the query sequence, with the options to report masked query sequence(s), repeat sequences found in the query, and alignments. Censor and RepbaseSubmitter are available as both web-based services and downloadable versions. They can be found at http://www.girinst.org/repbase/submission.html (RepbaseSubmitter) and http://www.girinst.org/censor/index.php (Censor).

The Génolevures database.

PubMed

Martin, Tiphaine; Sherman, David J; Durrens, Pascal

2011-01-01

The Génolevures online database (URL: http://www.genolevures.org) stores and provides the data and results obtained by the Génolevures Consortium through several campaigns of genome annotation of the yeasts in the Saccharomycotina subphylum (hemiascomycetes). This database is dedicated to large-scale comparison of these genomes, storing not only the different chromosomal elements detected in the sequences, but also the logical relations between them. The database is divided into a public part, accessible to anyone through Internet, and a private part where the Consortium members make genome annotations with our Magus annotation system; this system is used to annotate several related genomes in parallel. The public database is widely consulted and offers structured data, organized using a REST web site architecture that allows for automated requests. The implementation of the database, as well as its associated tools and methods, is evolving to cope with the influx of genome sequences produced by Next Generation Sequencing (NGS). Copyright © 2011 Académie des sciences. Published by Elsevier SAS. All rights reserved.

Indigenous species barcode database improves the identification of zooplankton

PubMed Central

Yang, Jianghua; Zhang, Wanwan; Sun, Jingying; Xie, Yuwei; Zhang, Yimin; Burton, G. Allen; Yu, Hongxia

2017-01-01

Incompleteness and inaccuracy of DNA barcode databases is considered an important hindrance to the use of metabarcoding in biodiversity analysis of zooplankton at the species-level. Species barcoding by Sanger sequencing is inefficient for organisms with small body sizes, such as zooplankton. Here mitochondrial cytochrome c oxidase I (COI) fragment barcodes from 910 freshwater zooplankton specimens (87 morphospecies) were recovered by a high-throughput sequencing platform, Ion Torrent PGM. Intraspecific divergence of most zooplanktons was < 5%, except Branchionus leydign (Rotifer, 14.3%), Trichocerca elongate (Rotifer, 11.5%), Lecane bulla (Rotifer, 15.9%), Synchaeta oblonga (Rotifer, 5.95%) and Schmackeria forbesi (Copepod, 6.5%). Metabarcoding data of 28 environmental samples from Lake Tai were annotated by both an indigenous database and NCBI Genbank database. The indigenous database improved the taxonomic assignment of metabarcoding of zooplankton. Most zooplankton (81%) with barcode sequences in the indigenous database were identified by metabarcoding monitoring. Furthermore, the frequency and distribution of zooplankton were also consistent between metabarcoding and morphology identification. Overall, the indigenous database improved the taxonomic assignment of zooplankton. PMID:28977035

HeLa Nucleic Acid Contamination in The Cancer Genome Atlas Leads to the Misidentification of Human Papillomavirus 18

PubMed Central

Cantalupo, Paul G.; Katz, Joshua P.

2015-01-01

ABSTRACT We searched The Cancer Genome Atlas (TCGA) database for viruses by comparing non-human reads present in transcriptome sequencing (RNA-Seq) and whole-exome sequencing (WXS) data to viral sequence databases. Human papillomavirus 18 (HPV18) is an etiologic agent of cervical cancer, and as expected, we found robust expression of HPV18 genes in cervical cancer samples. In agreement with previous studies, we also found HPV18 transcripts in non-cervical cancer samples, including those from the colon, rectum, and normal kidney. However, in each of these cases, HPV18 gene expression was low, and single-nucleotide variants and positions of genomic alignments matched the integrated portion of HPV18 present in HeLa cells. Chimeric reads that match a known virus-cell junction of HPV18 integrated in HeLa cells were also present in some samples. We hypothesize that HPV18 sequences in these non-cervical samples are due to nucleic acid contamination from HeLa cells. This finding highlights the problems that contamination presents in computational virus detection pipelines. IMPORTANCE Viruses associated with cancer can be detected by searching tumor sequence databases. Several studies involving searches of the TCGA database have reported the presence of HPV18, a known cause of cervical cancer, in a small number of additional cancers, including those of the rectum, kidney, and colon. We have determined that the sequences related to HPV18 in non-cervical samples are due to nucleic acid contamination from HeLa cells. To our knowledge, this is the first report of the misidentification of viruses in next-generation sequencing data of tumors due to contamination with a cancer cell line. These results raise awareness of the difficulty of accurately identifying viruses in human sequence databases. PMID:25631090

Using GenBank.

PubMed

Wheeler, David

2007-01-01

GenBank(R) is a comprehensive database of publicly available DNA sequences for more than 205,000 named organisms and for more than 60,000 within the embryophyta, obtained through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Daily data exchange with the European Molecular Biology Laboratory (EMBL) in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through the National Center for Biotechnology Information (NCBI) retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases with taxonomy, genome, mapping, protein structure, and domain information and the biomedical journal literature through PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available through FTP. GenBank usage scenarios ranging from local analyses of the data available through FTP to online analyses supported by the NCBI Web-based tools are discussed. To access GenBank and its related retrieval and analysis services, go to the NCBI Homepage at http://www.ncbi.nlm.nih.gov.

GenBank.

PubMed

Benson, Dennis A; Karsch-Mizrachi, Ilene; Lipman, David J; Ostell, James; Sayers, Eric W

2011-01-01

GenBank® is a comprehensive database that contains publicly available nucleotide sequences for more than 380,000 organisms named at the genus level or lower, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole genome shotgun (WGS) and environmental sampling 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 Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system that 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.

MPID-T2: a database for sequence-structure-function analyses of pMHC and TR/pMHC structures.

PubMed

Khan, Javed Mohammed; Cheruku, Harish Reddy; Tong, Joo Chuan; Ranganathan, Shoba

2011-04-15

Sequence-structure-function information is critical in understanding the mechanism of pMHC and TR/pMHC binding and recognition. A database for sequence-structure-function information on pMHC and TR/pMHC interactions, MHC-Peptide Interaction Database-TR version 2 (MPID-T2), is now available augmented with the latest PDB and IMGT/3Dstructure-DB data, advanced features and new parameters for the analysis of pMHC and TR/pMHC structures. http://biolinfo.org/mpid-t2. shoba.ranganathan@mq.edu.au Supplementary data are available at Bioinformatics online.

De novo assembly and characterization of the garlic (Allium sativum) bud transcriptome by Illumina sequencing.

PubMed

Sun, Xiudong; Zhou, Shumei; Meng, Fanlu; Liu, Shiqi

2012-10-01

Garlic is widely used as a spice throughout the world for the culinary value of its flavor and aroma, which are created by the chemical transformation of a series of organic sulfur compounds. To analyze the transcriptome of Allium sativum and discover the genes involved in sulfur metabolism, cDNAs derived from the total RNA of Allium sativum buds were analyzed by Illumina sequencing. Approximately 26.67 million 90 bp paired-end clean reads were achieved in two libraries. A total of 127,933 unigenes were generated by de novo assembly and were compared with the sequences in public databases. Of these, 45,286 unigenes had significant hits to the sequences in the Nr database, 29,514 showed significant similarity to known proteins in the Swiss-Prot database and, 20,706 and 21,952 unigenes had significant similarity to existing sequences in the KEGG and COG databases, respectively. Moreover, genes involved in organic sulfur biosynthesis were identified. These unigenes data will provide the foundation for research on gene expression, genomics and functional genomics in Allium sativum. Key message The obtained unigenes will provide the foundation for research on functional genomics in Allium sativum and its closely related species, and fill the gap of the existing plant EST database.

MetaMetaDB: a database and analytic system for investigating microbial habitability.

PubMed

Yang, Ching-chia; Iwasaki, Wataru

2014-01-01

MetaMetaDB (http://mmdb.aori.u-tokyo.ac.jp/) is a database and analytic system for investigating microbial habitability, i.e., how a prokaryotic group can inhabit different environments. The interaction between prokaryotes and the environment is a key issue in microbiology because distinct prokaryotic communities maintain distinct ecosystems. Because 16S ribosomal RNA (rRNA) sequences play pivotal roles in identifying prokaryotic species, a system that comprehensively links diverse environments to 16S rRNA sequences of the inhabitant prokaryotes is necessary for the systematic understanding of the microbial habitability. However, existing databases are biased to culturable prokaryotes and exhibit limitations in the comprehensiveness of the data because most prokaryotes are unculturable. Recently, metagenomic and 16S rRNA amplicon sequencing approaches have generated abundant 16S rRNA sequence data that encompass unculturable prokaryotes across diverse environments; however, these data are usually buried in large databases and are difficult to access. In this study, we developed MetaMetaDB (Meta-Metagenomic DataBase), which comprehensively and compactly covers 16S rRNA sequences retrieved from public datasets. Using MetaMetaDB, users can quickly generate hypotheses regarding the types of environments a prokaryotic group may be adapted to. We anticipate that MetaMetaDB will improve our understanding of the diversity and evolution of prokaryotes.

A Bioinformatics Workflow for Variant Peptide Detection in Shotgun Proteomics*

PubMed Central

Li, Jing; Su, Zengliu; Ma, Ze-Qiang; Slebos, Robbert J. C.; Halvey, Patrick; Tabb, David L.; Liebler, Daniel C.; Pao, William; Zhang, Bing

2011-01-01

Shotgun proteomics data analysis usually relies on database search. However, commonly used protein sequence databases do not contain information on protein variants and thus prevent variant peptides and proteins from been identified. Including known coding variations into protein sequence databases could help alleviate this problem. Based on our recently published human Cancer Proteome Variation Database, we have created a protein sequence database that comprehensively annotates thousands of cancer-related coding variants collected in the Cancer Proteome Variation Database as well as noncancer-specific ones from the Single Nucleotide Polymorphism Database (dbSNP). Using this database, we then developed a data analysis workflow for variant peptide identification in shotgun proteomics. The high risk of false positive variant identifications was addressed by a modified false discovery rate estimation method. Analysis of colorectal cancer cell lines SW480, RKO, and HCT-116 revealed a total of 81 peptides that contain either noncancer-specific or cancer-related variations. Twenty-three out of 26 variants randomly selected from the 81 were confirmed by genomic sequencing. We further applied the workflow on data sets from three individual colorectal tumor specimens. A total of 204 distinct variant peptides were detected, and five carried known cancer-related mutations. Each individual showed a specific pattern of cancer-related mutations, suggesting potential use of this type of information for personalized medicine. Compatibility of the workflow has been tested with four popular database search engines including Sequest, Mascot, X!Tandem, and MyriMatch. In summary, we have developed a workflow that effectively uses existing genomic data to enable variant peptide detection in proteomics. PMID:21389108

Tidying Up International Nucleotide Sequence Databases: Ecological, Geographical and Sequence Quality Annotation of ITS Sequences of Mycorrhizal Fungi

PubMed Central

Tedersoo, Leho; Abarenkov, Kessy; Nilsson, R. Henrik; Schüssler, Arthur; Grelet, Gwen-Aëlle; Kohout, Petr; Oja, Jane; Bonito, Gregory M.; Veldre, Vilmar; Jairus, Teele; Ryberg, Martin; Larsson, Karl-Henrik; Kõljalg, Urmas

2011-01-01

Sequence analysis of the ribosomal RNA operon, particularly the internal transcribed spacer (ITS) region, provides a powerful tool for identification of mycorrhizal fungi. The sequence data deposited in the International Nucleotide Sequence Databases (INSD) are, however, unfiltered for quality and are often poorly annotated with metadata. To detect chimeric and low-quality sequences and assign the ectomycorrhizal fungi to phylogenetic lineages, fungal ITS sequences were downloaded from INSD, aligned within family-level groups, and examined through phylogenetic analyses and BLAST searches. By combining the fungal sequence database UNITE and the annotation and search tool PlutoF, we also added metadata from the literature to these accessions. Altogether 35,632 sequences belonged to mycorrhizal fungi or originated from ericoid and orchid mycorrhizal roots. Of these sequences, 677 were considered chimeric and 2,174 of low read quality. Information detailing country of collection, geographical coordinates, interacting taxon and isolation source were supplemented to cover 78.0%, 33.0%, 41.7% and 96.4% of the sequences, respectively. These annotated sequences are publicly available via UNITE (http://unite.ut.ee/) for downstream biogeographic, ecological and taxonomic analyses. In European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena/), the annotated sequences have a special link-out to UNITE. We intend to expand the data annotation to additional genes and all taxonomic groups and functional guilds of fungi. PMID:21949797

An Ambystoma mexicanum EST sequencing project: analysis of 17,352 expressed sequence tags from embryonic and regenerating blastema cDNA libraries

PubMed Central

Habermann, Bianca; Bebin, Anne-Gaelle; Herklotz, Stephan; Volkmer, Michael; Eckelt, Kay; Pehlke, Kerstin; Epperlein, Hans Henning; Schackert, Hans Konrad; Wiebe, Glenis; Tanaka, Elly M

2004-01-01

Background The ambystomatid salamander, Ambystoma mexicanum (axolotl), is an important model organism in evolutionary and regeneration research but relatively little sequence information has so far been available. This is a major limitation for molecular studies on caudate development, regeneration and evolution. To address this lack of sequence information we have generated an expressed sequence tag (EST) database for A. mexicanum. Results Two cDNA libraries, one made from stage 18-22 embryos and the other from day-6 regenerating tail blastemas, generated 17,352 sequences. From the sequenced ESTs, 6,377 contigs were assembled that probably represent 25% of the expressed genes in this organism. Sequence comparison revealed significant homology to entries in the NCBI non-redundant database. Further examination of this gene set revealed the presence of genes involved in important cell and developmental processes, including cell proliferation, cell differentiation and cell-cell communication. On the basis of these data, we have performed phylogenetic analysis of key cell-cycle regulators. Interestingly, while cell-cycle proteins such as the cyclin B family display expected evolutionary relationships, the cyclin-dependent kinase inhibitor 1 gene family shows an unusual evolutionary behavior among the amphibians. Conclusions Our analysis reveals the importance of a comprehensive sequence set from a representative of the Caudata and illustrates that the EST sequence database is a rich source of molecular, developmental and regeneration studies. To aid in data mining, the ESTs have been organized into an easily searchable database that is freely available online. PMID:15345051

Plant Genome Resources at the National Center for Biotechnology Information

PubMed Central

Wheeler, David L.; Smith-White, Brian; Chetvernin, Vyacheslav; Resenchuk, Sergei; Dombrowski, Susan M.; Pechous, Steven W.; Tatusova, Tatiana; Ostell, James

2005-01-01

The National Center for Biotechnology Information (NCBI) integrates data from more than 20 biological databases through a flexible search and retrieval system called Entrez. A core Entrez database, Entrez Nucleotide, includes GenBank and is tightly linked to the NCBI Taxonomy database, the Entrez Protein database, and the scientific literature in PubMed. A suite of more specialized databases for genomes, genes, gene families, gene expression, gene variation, and protein domains dovetails with the core databases to make Entrez a powerful system for genomic research. Linked to the full range of Entrez databases is the NCBI Map Viewer, which displays aligned genetic, physical, and sequence maps for eukaryotic genomes including those of many plants. A specialized plant query page allow maps from all plant genomes covered by the Map Viewer to be searched in tandem to produce a display of aligned maps from several species. PlantBLAST searches against the sequences shown in the Map Viewer allow BLAST alignments to be viewed within a genomic context. In addition, precomputed sequence similarities, such as those for proteins offered by BLAST Link, enable fluid navigation from unannotated to annotated sequences, quickening the pace of discovery. NCBI Web pages for plants, such as Plant Genome Central, complete the system by providing centralized access to NCBI's genomic resources as well as links to organism-specific Web pages beyond NCBI. PMID:16010002

Job Aids: Descriptive Authoring Flowcharts for Phase II--DESIGN of the Instructional Systems Development Model.

ERIC Educational Resources Information Center

Schulz, Russel E.; Farrell, Jean R.

This resource guide for the use of job aids ("how-to-do-it" guidance) for activities identified in the second phase of the Instructional Systems Development Model (ISD) contains an introduction to the use of job aids, as well as descriptive authoring flowcharts for Blocks II.1 through II.4. The introduction includes definitions;…

Job Aids: Descriptive Authoring Flowcharts for Phase I--ANALYZE of the Instructional Systems Development Model.

ERIC Educational Resources Information Center

Schulz, Russel E.; Farrell, Jean R.

This resource guide for the use of job aids ("how-to-do-it" guidance) for activities identified in the first phase of the Instructional Systems Development Model (ISD) contains an introduction to the use of job aids, as well as descriptive authoring flowcharts for Blocks I.2 through I.5. The introduction includes definitions;…

Collaborative Efforts Result in a Successful Field Based Program for the Preparation of Secondary Teachers in Social Studies.

ERIC Educational Resources Information Center

Askins, Billy E.; Logan, Neal; Nelson, Jill

Collaborative efforts by Texas Tech University (TTU) and the Lubbock Independent School District (ISD) resulted in an innovative program to improve the preparation of secondary-level preservice teachers in social studies. The program is grounded in the realities of the social studies classroom. Students are organized by teaching field in a…

An Experienced Teacher's Model of Thinking and Teaching: An Ethnographic Study on Teacher Cognition.

ERIC Educational Resources Information Center

Moallem, Mahnaz

This study was designed to explore an expert teacher's model of thinking and teaching as it occurred within the social and cultural context of the classroom. The model was then compared with instructional systems design (ISD) to identify similarities and differences between them. To accomplish these goals, the study focused on the process and…

Development and Validation of a Web-Based Module to Teach Metacognitive Learning Strategies to Students in Higher Education

ERIC Educational Resources Information Center

Singh, Oma B.

2009-01-01

This study used a design based-research (DBR) methodology to examine how an Instructional Systematic Design (ISD) process such as ADDIE (Analysis, Design, Development, Implementation, Evaluation) can be employed to develop a web-based module to teach metacognitive learning strategies to students in higher education. The goal of the study was…

Training System Device Certification and Qualification Process

DTIC Science & Technology

2013-09-01

Engineering IPT Integrated Product Team ISD Instructional Systems Development ISEO In-Service Engineering Office KSAs Knowledge, Skills, and Attributes...Plan TES Tactical Engagement Simulation TPM Training Pipeline Managers T&R Training and Readiness TRR Test Readiness Review TS Training System...NAWCTSD) is the Navy’s source for a full range of innovative products and services that provide complete training solutions. This includes

Carl: A Case Study of a Gifted Student with Challenging Social Behaviors

ERIC Educational Resources Information Center

Zapotocky, Robin

2014-01-01

Robin Zapotocky is a first-year teacher in a fifth-grade classroom at Cannaday Elementary in Mesquite ISD, Mesquite TX. She graduated from Baylor University in the gifted and elementary dual certificate program, and first met Carl when she was student teaching in a gifted and talented pullout program for third- and fourth-grade gifted students.…

From Instructional Systems Design to Managing the Life Cycle of Knowledge in Organizations

ERIC Educational Resources Information Center

Salisbury, Mark

2008-01-01

This article describes a framework for managing the life cycle of knowledge in organizations. The framework emerges from years of work with the laboratories and facilities that are under the direction of the U.S. Department of Energy (DOE). The article begins by describing the instructional systems design (ISD) process and how it is used to…

Programming Design Guide for Computer Implementation of Job Aid for Selecting Instructional Setting. Final Report.

ERIC Educational Resources Information Center

Schulz, Russel E.; And Others

This Programming Design Guide (PDG) was developed to permit the offline Job Aid for Selecting Instructional Setting, which is one of 13 job aids presently available for use with the Instructional Systems Development (ISD) model, to be available in an inquiry-type, online version. It is intended to provide computer programmers with all of the…

The Effect of School Renaissance on TAAS Scores in the McKinney ISD

ERIC Educational Resources Information Center

Nunnery, John A.; Ross, Steven M.; Goldfeder, Elizabeth

2003-01-01

The present research is a third-party study of the effects of the School Renaissance (SR) comprehensive school reform (CSR) model on student achievement in 11 elementary and middle schools in Texas. The primary measures used in the study were the Texas Learning Index (TLI) reading and mathematics scores obtained through administration of the Texas…

Information Systems Development--ISD '94. Methods & Tools. Theory & Practice. Proceedings of the International Conference (4th, Bled, Slovenia, September 20-22, 1994).

ERIC Educational Resources Information Center

Zupancic, Joze, Ed.; Wrycza, Stanislaw, Ed.

These proceedings present 3 invited papers, 65 submitted papers, and 17 presentations on work in progress that were given at the Fourth International Conference on Information Systems Development. The three invited papers are: "Information Systems Planning in Small Business" (Georgios Doukidis, Panagiotis Lybereas, Robert D. Galliers);…

Job Aids: Descriptive Authoring Flowcharts for Phase III--DEVELOP of the Instructional Systems Development Model.

ERIC Educational Resources Information Center

Schulz, Russel E.; Farrell, Jean R.

This resource guide for the use of job aids ("how-to-do-it" guidance) for activities identified in the third phase of the Instructional Systems Development Model (ISD) contains an introduction to the use of job aids, as well as descriptive authoring flowcharts for Blocks III.1 through III.5. The introduction includes definitions;…

A Corporate Veto on Health Policy? Global Constitutionalism and Investor-State Dispute Settlement.

PubMed

Hawkins, Benjamin; Holden, Chris

2016-10-01

The importance of trade and investment agreements for health is now widely acknowledged in the literature, with much attention now focused on the impact of investor-state dispute settlement (ISDS) mechanisms. However, much of the analysis of such agreements in the health field remains largely descriptive. We theorize the implications of ISDS mechanisms for health policy by integrating the concept of global constitutionalism with veto point theory. It is argued that attempts to constitutionalize investment law, through a proliferation of International Investment Agreements (IIAs), has created a series of new veto points at which corporations may seek to block new policies aimed at protecting or enhancing public health. The multiplicity of new veto points in this global "spaghetti bowl" of IIAs creates opportunities for corporations to venue shop; that is, to exploit the agreements, and associated veto points, through which they are most likely to succeed in blocking or deterring new regulation. These concepts are illustrated with reference to two case studies of investor-state disputes involving a transnational tobacco company, but the implications of the analysis are of equal relevance for a range of other industries and health issues. Copyright © 2016 by Duke University Press.