Prevalence and Correlates of Suicidal Behavior Among New Soldiers in the U.S. Army: Results from the Army Study to Assess Risk and Resilience in Servicemembers (Army STARRS)

DTIC Science & Technology

2014-01-01

of Psy- chiatry, Uniformed Services University of the Health Sciences , Bethesda, Maryland 2Institute for Social Research, University of Michigan, Ann...Mental Health, Bethesda, Maryland 9Departments of Social and Behavioral Sciences , and Epidemi- ology, Harvard School of Public Health, Boston...Department of Psychiatry, Uniformed Services Uni- versity of the Health Sciences , 4301 Jones Bridge Road, Bethesda, MD 20814. E-mail: robert.ursano

Rotordynamic Instability Problems in High-Performance Turbomachinery. Proceedings of a Workshop (1st) Held at Texas A&M University, College Station, Texas, May 12-14, 1980.

DTIC Science & Technology

1980-08-01

Vibrations Stimulated by Lateral Forces in Sealing Gaps," In German, Institut ffir Thermische Str ~mungsmaschinen, Unwersitat Stuttgart. 26. Warner, R. E...investigations at the "Institut fOr Thermische Str ~mungsmaschinen at the Uni- versity of Stuttgart" are performed. This is done with the aim to point out the...Eigenschwingungen von Turbinenlaufern, angefacht durch die Spaltstr~ mung in Stopfbuchsen und Beschauflungen. Bull. de l’AIM 71 (1958) pp. 1039-1063 4

Models for Aircrew Safety Assessment: Uses, Limitations and Requirements (la Modelisation des conditions de securite des equipages: applications, limitations et cahiers des charges)

DTIC Science & Technology

1999-08-01

immediately, re- ducing venous return artifacts during the first beat of the simulation. tn+1 - W+ on c+ / \\ W_ on c_ t 1 Xi-l Xi+1 Figure 4...s) Figure 5: The effect of network complexity. The aortic pressure is shown in Figure 5 during the fifth beat for the networks with one and three...Mechanical Engineering Department, Uni- versity of Victoria. [19] Huyghe J.M., 1986, "Nonlinear Finite Element Models of The Beating Left

Boundary Layer Structure and Its Relation to Precipitation Over the St. Louis Area.

DTIC Science & Technology

1980-10-01

of METEORO LOGY SECTION 0i{1J ( 0I~) AT THE mp UNI VERSITY OV ILLINOIS0 SMISContract Report 241 T - BOUNDARY LAYER STRUCTURE AND ITS RELATION TO...PRECIPITATION OVER THE ST. LOUIS AREA Gary L. Achtemeier Meteorology Section Ill1inois State Water &uIvey, DTII CLeELEC T E C.> JAN 15 1981( Technical...in f r ’TNil PA&F rlhImm Does Rnteredl 𔄃. -. , .’.-..,. -.- -/" . ECumITYv CLASSFICATIOW Of TH t PAGE(Wfhn Date Entr,.e) 15529. 4-GS ?0. ABSTRACT

Benefit/Cost Analysis Between the Blue Cross and Blue Shield Federal Employee Health Insurance Program and the Military Health Services System Supplemental Champus Program

DTIC Science & Technology

1981-09-01

Rizzuto, my babysitter , whose long hours everyday allowed me to attend classes without worrying about my son, Andy; and my new bride, Roz, whose love...4 - , . ~ DTIO.,=I= EIECTE~l rl 1 FEB 1-7-1982 I III O UNITED STATES AIR FORCE AIR UNI VERSITY AIR FORCE INSTITUTE OF TECHNOLOGY ...WORK UNIT NUMBERS School of Systems and Logistics Air Force Institute of Technology , WPAFB OH II. CONTROLLING OFFICE NAME AND ADDRESS 12. REPORT DATE

A further look at the intergenerational transmission of violence: witnessing interparental violence in emerging adulthood.

PubMed

Black, David S; Sussman, Steve; Unger, Jennifer B

2010-06-01

The intergenerational transmission (IGT) of violence has been a main the oretical consideration to explain the link between interparental aggression in the family of origin and intimate partner violence (IPV) in subsequent intimate relationships. Studies have examined this theoretical link based on self reports of interparental violence witnessed during childhood and adolescence. However, no study has examined whether emerging adults who currently witness interparental violence are more likely to exhibit violence in their own intimate relationships. Data were analyzed from undergraduate students (N = 223) attending an ethnically diverse Southern California uni versity. Multivariate linear regression analyses were used to examine the impact of witnessing interparental violence on the physical and psycho logical IPV experienced in emerging adult relationships. The joint effects of witnessing both forms of interparental violence were also tested. Support for the intergenerational transmission of violence was identified for specific types of violence. Future directions of study and implications for prevention and treatment are offered.

Satellite Measurements Of OH Vibrational Populations

NASA Astrophysics Data System (ADS)

Martin-Torres, F. J.; Kaufmann, M.; Copeland, R. A.; López-Puertas, M.

Vibrationally excited OH molecules are generated in the atmosphere between 80 and 90 km by the reaction of hydrogen atoms with ozone and are important in the study of the Earth's mesospheric infrared emissions. Once produced, the OH either fluoresces or undergoes deactivation in collisions with the ambient species present at these alti- tudes. Over the past decade, significant progress has been made in measuring the vi- brational level dependence of the total removal rate constants for collisional processes in laboratory. Using these results we present an updated modelling of the vibrational populations of OH. The results of the model has been used to identify emission from the OH Meinel bands at 4.8mum in the measurements taken by the CRyogenic Infrared Spectrometer and Telescope (CRISTA). CRISTA was an infrared limb sounder designed by the Uni- versity of Wuppertal to measure infrared emissions of the Earth's atmosphere between 15-150 km that successfully completed two missions in 1994 and 1997. In addition, the results of the non-LTE modelling have been used to simulate the mea- surements that will be performed by the Michelson Interferometer for Passive At- mospheric Sounder (MIPAS)/ENVIromental SATellite (ENVISAT) instrument, to be launched the 1st March 2002.

Application of Box-Behnken Design and Response Surface Methodology for Surface Roughness Prediction Model of CP-Ti Powder Metallurgy Components Through WEDM

NASA Astrophysics Data System (ADS)

Das, Arunangsu; Sarkar, Susenjit; Karanjai, Malobika; Sutradhar, Goutam

2018-04-01

The present work was undertaken to investigate and characterize the machining parameters (such as surface roughness, etc.) of uni-axially pressed commercially pure titanium sintered powder metallurgy components. Powder was uni-axially pressed at designated pressure of 840 MPa to form cylindrical samples and the green compacts were sintered at 0.001 mbar for about 4 h with sintering temperature varying from 1350 to 1450 °C. The influence of the sintering temperature, pulse-on and pulse-off time at wire-EDM on the surface roughness of the preforms has been investigated thoroughly. Experiments were conducted under different machining parameters in a CNC operated wire-cut EDM. The surface roughness of the machined surface was measured and critically analysed. The optimum surface roughness was achieved under the conditions of 6 μs pulse-on time, 9 μs pulse-off time and at sintering temperature of 1450 °C.

UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein-DNA interactions.

PubMed

Hume, Maxwell A; Barrera, Luis A; Gisselbrecht, Stephen S; Bulyk, Martha L

2015-01-01

The Universal PBM Resource for Oligonucleotide Binding Evaluation (UniPROBE) serves as a convenient source of information on published data generated using universal protein-binding microarray (PBM) technology, which provides in vitro data about the relative DNA-binding preferences of transcription factors for all possible sequence variants of a length k ('k-mers'). The database displays important information about the proteins and displays their DNA-binding specificity data in terms of k-mers, position weight matrices and graphical sequence logos. This update to the database documents the growth of UniPROBE since the last update 4 years ago, and introduces a variety of new features and tools, including a new streamlined pipeline that facilitates data deposition by universal PBM data generators in the research community, a tool that generates putative nonbinding (i.e. negative control) DNA sequences for one or more proteins and novel motifs obtained by analyzing the PBM data using the BEEML-PBM algorithm for motif inference. The UniPROBE database is available at http://uniprobe.org. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Progress in Working Towards a More Sustainable Agri-Food Industry

EPA Science Inventory

The human health and environmental issues related to food, feed, and bio-based systems, range widely from greenhouse gas emissions and energy use to land use, water availability, soil quality, water quality and quantity, biodi-versity losses, and chemical exposure. Threats that s...

The new protein topology graph library web server.

PubMed

Schäfer, Tim; Scheck, Andreas; Bruneß, Daniel; May, Patrick; Koch, Ina

2016-02-01

We present a new, extended version of the Protein Topology Graph Library web server. The Protein Topology Graph Library describes the protein topology on the super-secondary structure level. It allows to compute and visualize protein ligand graphs and search for protein structural motifs. The new server features additional information on ligand binding to secondary structure elements, increased usability and an application programming interface (API) to retrieve data, allowing for an automated analysis of protein topology. The Protein Topology Graph Library server is freely available on the web at http://ptgl.uni-frankfurt.de. The website is implemented in PHP, JavaScript, PostgreSQL and Apache. It is supported by all major browsers. The VPLG software that was used to compute the protein ligand graphs and all other data in the database is available under the GNU public license 2.0 from http://vplg.sourceforge.net. tim.schaefer@bioinformatik.uni-frankfurt.de; ina.koch@bioinformatik.uni-frankfurt.de Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Unipept web services for metaproteomics analysis.

PubMed

Mesuere, Bart; Willems, Toon; Van der Jeugt, Felix; Devreese, Bart; Vandamme, Peter; Dawyndt, Peter

2016-06-01

Unipept is an open source web application that is designed for metaproteomics analysis with a focus on interactive datavisualization. It is underpinned by a fast index built from UniProtKB and the NCBI taxonomy that enables quick retrieval of all UniProt entries in which a given tryptic peptide occurs. Unipept version 2.4 introduced web services that provide programmatic access to the metaproteomics analysis features. This enables integration of Unipept functionality in custom applications and data processing pipelines. The web services are freely available at http://api.unipept.ugent.be and are open sourced under the MIT license. Unipept@ugent.be Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

The Pfam protein families database: towards a more sustainable future.

PubMed

Finn, Robert D; Coggill, Penelope; Eberhardt, Ruth Y; Eddy, Sean R; Mistry, Jaina; Mitchell, Alex L; Potter, Simon C; Punta, Marco; Qureshi, Matloob; Sangrador-Vegas, Amaia; Salazar, Gustavo A; Tate, John; Bateman, Alex

2016-01-04

In the last two years the Pfam database (http://pfam.xfam.org) has undergone a substantial reorganisation to reduce the effort involved in making a release, thereby permitting more frequent releases. Arguably the most significant of these changes is that Pfam is now primarily based on the UniProtKB reference proteomes, with the counts of matched sequences and species reported on the website restricted to this smaller set. Building families on reference proteomes sequences brings greater stability, which decreases the amount of manual curation required to maintain them. It also reduces the number of sequences displayed on the website, whilst still providing access to many important model organisms. Matches to the full UniProtKB database are, however, still available and Pfam annotations for individual UniProtKB sequences can still be retrieved. Some Pfam entries (1.6%) which have no matches to reference proteomes remain; we are working with UniProt to see if sequences from them can be incorporated into reference proteomes. Pfam-B, the automatically-generated supplement to Pfam, has been removed. The current release (Pfam 29.0) includes 16 295 entries and 559 clans. The facility to view the relationship between families within a clan has been improved by the introduction of a new tool. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

"Uni Has a Different Language?…?to the Real World": Demystifying Academic Culture and Discourse for Students from Low Socioeconomic Backgrounds

ERIC Educational Resources Information Center

McKay, Jade; Devlin, Marcia

2014-01-01

The Australian government has set ambitious targets for increased higher-education participation of people from low socioeconomic backgrounds. There is, thus, a pressing need to explore how best to empower these students with what they require to progress and succeed at university. The paper draws on a literature review and qualitative data from a…

antaRNA: ant colony-based RNA sequence design.

PubMed

Kleinkauf, Robert; Mann, Martin; Backofen, Rolf

2015-10-01

RNA sequence design is studied at least as long as the classical folding problem. Although for the latter the functional fold of an RNA molecule is to be found ,: inverse folding tries to identify RNA sequences that fold into a function-specific target structure. In combination with RNA-based biotechnology and synthetic biology ,: reliable RNA sequence design becomes a crucial step to generate novel biochemical components. In this article ,: the computational tool antaRNA is presented. It is capable of compiling RNA sequences for a given structure that comply in addition with an adjustable full range objective GC-content distribution ,: specific sequence constraints and additional fuzzy structure constraints. antaRNA applies ant colony optimization meta-heuristics and its superior performance is shown on a biological datasets. http://www.bioinf.uni-freiburg.de/Software/antaRNA CONTACT: backofen@informatik.uni-freiburg.de Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

The role of herbicides for enhancing productivity and conserving land for biodiversity in North America

Treesearch

Robert G. Wagner; Michael Newton; Elizabeth C. Cole; James H. Miller; Barry D. Shiver

2004-01-01

Herbicide technology has evolved with forest management in North America over the past 60 years and has become an integral part of modern forestry practice. Forest managers have prescribed herbicides to increase reforestation success and long-term timber yields. Wildlife managers and others interested in conserving biodi- versity, however, have often viewed herbicide...

The Proteins API: accessing key integrated protein and genome information.

PubMed

Nightingale, Andrew; Antunes, Ricardo; Alpi, Emanuele; Bursteinas, Borisas; Gonzales, Leonardo; Liu, Wudong; Luo, Jie; Qi, Guoying; Turner, Edd; Martin, Maria

2017-07-03

The Proteins API provides searching and programmatic access to protein and associated genomics data such as curated protein sequence positional annotations from UniProtKB, as well as mapped variation and proteomics data from large scale data sources (LSS). Using the coordinates service, researchers are able to retrieve the genomic sequence coordinates for proteins in UniProtKB. This, the LSS genomics and proteomics data for UniProt proteins is programmatically only available through this service. A Swagger UI has been implemented to provide documentation, an interface for users, with little or no programming experience, to 'talk' to the services to quickly and easily formulate queries with the services and obtain dynamically generated source code for popular programming languages, such as Java, Perl, Python and Ruby. Search results are returned as standard JSON, XML or GFF data objects. The Proteins API is a scalable, reliable, fast, easy to use RESTful services that provides a broad protein information resource for users to ask questions based upon their field of expertise and allowing them to gain an integrated overview of protein annotations available to aid their knowledge gain on proteins in biological processes. The Proteins API is available at (http://www.ebi.ac.uk/proteins/api/doc). © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Treatment of Hantavirus Pulmonary Syndrome

DTIC Science & Technology

2007-10-14

of Infectious Diseases, Ft. Detrick, MD, United States c Department of Internal Medicine, University of New Mexico , Albuquerque, NM, United States...Within ours the patient required mechanical ventilation and extracorporeal membrane xygenation (ECMO). Courtesy G. Mertz, University of New Mexico . hea...femoral artery and vein. The bed is versity of New Mexico . . Antiviral therapy Ribavirin was tested for efficacy in HFRS patients in China nd shown to

The Air Force and Diversity: The Awkward Embrace

DTIC Science & Technology

2014-06-01

Space Power Journal | 105 Streeter The Air Force and Diversity Feature eling an intelligence problem at the tactical level, through developing a...careers.2 Discordance exists between Air Force intentions vis-à-vis diversity and any effective programs and policies to retain and develop a di...though the service has initiated formal di- versity efforts, recommended policy and development programs may help develop and retain competent

Copper Soldiers: Forging New Roles for the Chilean Military

DTIC Science & Technology

2005-09-01

post of the Chief of Staff of the Armed Forces and Carabineros.” Finally, articles 95 and 96 created a National Security Council which included the...Nacional (RN) and the Unión Demócrata Independiente (UDI), felt an “independent security power”129 such as the military served as a check on the...Democracy: Latin America and the Caribbean in the Post -Cold War Era, ed. Jorge I. Domínguez (Pittsburgh: University of Pittsburgh Press, 1998), 131

MRUniNovo: an efficient tool for de novo peptide sequencing utilizing the hadoop distributed computing framework.

PubMed

Li, Chuang; Chen, Tao; He, Qiang; Zhu, Yunping; Li, Kenli

2017-03-15

Tandem mass spectrometry-based de novo peptide sequencing is a complex and time-consuming process. The current algorithms for de novo peptide sequencing cannot rapidly and thoroughly process large mass spectrometry datasets. In this paper, we propose MRUniNovo, a novel tool for parallel de novo peptide sequencing. MRUniNovo parallelizes UniNovo based on the Hadoop compute platform. Our experimental results demonstrate that MRUniNovo significantly reduces the computation time of de novo peptide sequencing without sacrificing the correctness and accuracy of the results, and thus can process very large datasets that UniNovo cannot. MRUniNovo is an open source software tool implemented in java. The source code and the parameter settings are available at http://bioinfo.hupo.org.cn/MRUniNovo/index.php. s131020002@hnu.edu.cn ; taochen1019@163.com. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Principles and Foundations for Fractionated Networked Cyber-Physical Systems

DTIC Science & Technology

2012-07-13

spectrum between autonomy to cooperation. Our distributed comput- ing model is based on distributed knowledge sharing, and makes very few assumptions but...over the computation without the need for explicit migration. Randomization techniques will make sure that enough di- versity is maintained to allow...small UAV testbed consisting of 10 inex- pensive quadcopters at SRI. Hard ware-wise, we added heat sinks to mitigate the impact of additional heat that

Thermodynamics and evolution.

PubMed

Demetrius, L

2000-09-07

The science of thermodynamics is concerned with understanding the properties of inanimate matter in so far as they are determined by changes in temperature. The Second Law asserts that in irreversible processes there is a uni-directional increase in thermodynamic entropy, a measure of the degree of uncertainty in the thermal energy state of a randomly chosen particle in the aggregate. The science of evolution is concerned with understanding the properties of populations of living matter in so far as they are regulated by changes in generation time. Directionality theory, a mathematical model of the evolutionary process, establishes that in populations subject to bounded growth constraints, there is a uni-directional increase in evolutionary entropy, a measure of the degree of uncertainty in the age of the immediate ancestor of a randomly chosen newborn. This article reviews the mathematical basis of directionality theory and analyses the relation between directionality theory and statistical thermodynamics. We exploit an analytic relation between temperature, and generation time, to show that the directionality principle for evolutionary entropy is a non-equilibrium extension of the principle of a uni-directional increase of thermodynamic entropy. The analytic relation between these directionality principles is consistent with the hypothesis of the equivalence of fundamental laws as one moves up the hierarchy, from a molecular ensemble where the thermodynamic laws apply, to a population of replicating entities (molecules, cells, higher organisms), where evolutionary principles prevail. Copyright 2000 Academic Press.

The Tracking of Referents in Discourse: Automated versus Attended Processes.

DTIC Science & Technology

1985-05-15

at :_uc. L -_.,ec tc seeaver and ,hearer in situ . e ,en t -te tank, ar the cashier c c r- ceck r,e. .--r c- tur . kr.ovedge or nrrr,at .e c . ts.." c...Participant coding ;n Y( agua . Unpubf ishe,1 doctora. 4 scertation, ’n~versity of Cal if, rn:a at Los Anneies. Fsner, M.I. & ran, O.S.M. <ds. .. Atter;tlon

Californium--palladium metal neutron source material

DOEpatents

Dahlen, B.L.; Mosly, W.C. Jr.; Smith, P.K.; Albenesius, E.L.

1974-01-22

Californium, as metal or oxide, is uniformly dispersed throughout a noble metal matrix, provided in compact, rod or wire form. A solution of californium values is added to palladium metal powder, dried, blended and pressed into a compact having a uni-form distribution of californium. The californium values are decomposed to californium oxide or metal by heating in an inert or reducing atmosphere. Sintering the compact to a high density closes the matrix around the dispersed californium. The sintered compact is then mechanically shaped into an elongated rod or wire form. (4 claims, no drawings) (Official Gazette)

VecScreen_plus_taxonomy: imposing a tax(onomy) increase on vector contamination screening.

PubMed

Schäffer, Alejandro A; Nawrocki, Eric P; Choi, Yoon; Kitts, Paul A; Karsch-Mizrachi, Ilene; McVeigh, Richard

2018-03-01

Nucleic acid sequences in public databases should not contain vector contamination, but many sequences in GenBank do (or did) contain vectors. The National Center for Biotechnology Information uses the program VecScreen to screen submitted sequences for contamination. Additional tools are needed to distinguish true-positive (contamination) from false-positive (not contamination) VecScreen matches. A principal reason for false-positive VecScreen matches is that the sequence and the matching vector subsequence originate from closely related or identical organisms (for example, both originate in Escherichia coli). We collected information on the taxonomy of sources of vector segments in the UniVec database used by VecScreen. We used that information in two overlapping software pipelines for retrospective analysis of contamination in GenBank and for prospective analysis of contamination in new sequence submissions. Using the retrospective pipeline, we identified and corrected over 8000 contaminated sequences in the nonredundant nucleotide database. The prospective analysis pipeline has been in production use since April 2017 to evaluate some new GenBank submissions. Data on the sources of UniVec entries were included in release 10.0 (ftp://ftp.ncbi.nih.gov/pub/UniVec/). The main software is freely available at https://github.com/aaschaffer/vecscreen_plus_taxonomy. aschaffe@helix.nih.gov. Supplementary data are available at Bioinformatics online. Published by Oxford University Press 2017. This work is written by US Government employees and are in the public domain in the US.

Moon-Mars Analogue Mission (EuroMoonMars 1 at the Mars Desert Research Station)

NASA Astrophysics Data System (ADS)

Lia Schlacht, Irene; Voute, Sara; Irwin, Stacy; Foing, Bernard H.; Stoker, Carol R.; Westenberg, Artemis

The Mars Desert Research Station (MDRS) is situated in an analogue habitat-based Martian environment, designed for missions to determine the knowledge and equipment necessary for successful future planetary exploration. For this purpose, a crew of six people worked and lived together in a closed-system environment. They performed habitability experiments within the dwelling and conducted Extra-Vehicular Activities (EVAs) for two weeks (20 Feb to 6 Mar 2010) and were guided externally by mission support, called "Earth" within the simulation. Crew 91, an international, mixed-gender, and multidisciplinary group, has completed several studies during the first mission of the EuroMoonMars campaign. The crew is composed of an Italian designer and human factors specialist, a Dutch geologist, an American physicist, and three French aerospace engineering students from Ecole de l'Air, all with ages between 21 and 31. Each crewmember worked on personal research and fulfilled a unique role within the group: commander, executive officer, engineer, health and safety officer, scientist, and journalist. The expedition focused on human factors, performance, communication, health and safety pro-tocols, and EVA procedures. The engineers' projects aimed to improve rover manoeuvrability, far-field communication, and data exchanges between the base and the rover or astronaut. The crew physicist evaluated dust control methods inside and outside the habitat. The geologist tested planetary geological sampling procedures. The crew designer investigated performance and overall habitability in the context of the Mars Habitability Experiment from the Extreme-Design group. During the mission the crew also participated in the Food Study and in the Ethospace study, managed by external groups. The poster will present crew dynamics, scientific results and daily schedule from a Human Factors perspective. Main co-sponsors and collaborators: ILEWG, ESA ESTEC, NASA Ames, Ecole de l'Air, SKOR, Extreme-Design, Universit` di Torino, MMS TU-Berlin, Space Florida, DAAD, Uni-a versity of Utrecht, The Mars Society.

Testing of the Prototype Mars Drill and Sample Acquisition System in the Mars Analog Site of the Antarctica's Dry Valleys

NASA Astrophysics Data System (ADS)

Zacny, K.; Paulsen, G.; McKay, C.; Glass, B. J.; Marinova, M.; Davila, A. F.; Pollard, W. H.; Jackson, A.

2011-12-01

We report on the testing of the one meter class prototype Mars drill and cuttings sampling system, called the IceBreaker in the Dry Valleys of Antarctica. The drill consists of a rotary-percussive drill head, a sampling auger with a bit at the end having an integrated temperature sensor, a Z-stage for advancing the auger into the ground, and a sampling station for moving the augered ice shavings or soil cuttings into a sample cup. In November/December of 2010, the IceBreaker drill was tested in the Uni-versity Valley (within the Beacon Valley region of the Antarctic Dry Valleys). University Valley is a good analog to the Northern Polar Regions of Mars because a layer of dry soil lies on top of either ice-cemeted ground or massive ice (depending on the location within the valley). That is exactly what the 2007 Phoenix mission discovered on Mars. The drill demonstrated drilling in ice-cemented ground and in massive ice at the 1-1-100-100 level; that is the drill reached 1 meter in 1 hour with 100 Watts of power and 100 Newton Weight on Bit. This corresponds to an average energy of 100 Whr. At the same time, the bit temperature measured by the bit thermocouple did not exceed more than 10 °C above the formation temperature. The temperature also never exceeded freezing, which minimizes chances of getting stuck and also of altering the materials that are being sampled and analyzed. The samples in the forms of cuttings were acquired every 10 cm intervals into sterile bags. These tests have shown that drilling on Mars, in ice cemented ground with limited power, energy and Weight on Bit, and collecting samples in discrete depth intervals is possible within the given mass, power, and energy levels of a Phoenix-size lander and within the duration of a Phoenix-like mission.

JPRS Report, China.

DTIC Science & Technology

1991-03-06

generation of leaders-to the trivial-the daily life, diet , be the "age of Chen Yun." Only when Chen Yun’s and health of some elderly people. One hidden...mouse and encumbered with the demands of JPRS-CAR-91-013 80 SOCIAL 6 March 1991 everyday living. His schoolmates say he is a vegetarian living expenses...shortchange them- versity C, there were 14 postdoctorates, some returned selves on diet basics. from abroad and some trained in China. Some did not stay at

The Bologna Annotation Resource (BAR 3.0): improving protein functional annotation.

PubMed

Profiti, Giuseppe; Martelli, Pier Luigi; Casadio, Rita

2017-07-03

BAR 3.0 updates our server BAR (Bologna Annotation Resource) for predicting protein structural and functional features from sequence. We increase data volume, query capabilities and information conveyed to the user. The core of BAR 3.0 is a graph-based clustering procedure of UniProtKB sequences, following strict pairwise similarity criteria (sequence identity ≥40% with alignment coverage ≥90%). Each cluster contains the available annotation downloaded from UniProtKB, GO, PFAM and PDB. After statistical validation, GO terms and PFAM domains are cluster-specific and annotate new sequences entering the cluster after satisfying similarity constraints. BAR 3.0 includes 28 869 663 sequences in 1 361 773 clusters, of which 22.2% (22 241 661 sequences) and 47.4% (24 555 055 sequences) have at least one validated GO term and one PFAM domain, respectively. 1.4% of the clusters (36% of all sequences) include PDB structures and the cluster is associated to a hidden Markov model that allows building template-target alignment suitable for structural modeling. Some other 3 399 026 sequences are singletons. BAR 3.0 offers an improved search interface, allowing queries by UniProtKB-accession, Fasta sequence, GO-term, PFAM-domain, organism, PDB and ligand/s. When evaluated on the CAFA2 targets, BAR 3.0 largely outperforms our previous version and scores among state-of-the-art methods. BAR 3.0 is publicly available and accessible at http://bar.biocomp.unibo.it/bar3. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

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/.

UniProtKB/Swiss-Prot, the Manually Annotated Section of the UniProt KnowledgeBase: How to Use the Entry View.

PubMed

Boutet, Emmanuel; Lieberherr, Damien; Tognolli, Michael; Schneider, Michel; Bansal, Parit; Bridge, Alan J; Poux, Sylvain; Bougueleret, Lydie; Xenarios, Ioannis

2016-01-01

The Universal Protein Resource (UniProt, http://www.uniprot.org ) consortium is an initiative of the SIB Swiss Institute of Bioinformatics (SIB), the European Bioinformatics Institute (EBI) and the Protein Information Resource (PIR) to provide the scientific community with a central resource for protein sequences and functional information. The UniProt consortium maintains the UniProt KnowledgeBase (UniProtKB), updated every 4 weeks, and several supplementary databases including the UniProt Reference Clusters (UniRef) and the UniProt Archive (UniParc).The Swiss-Prot section of the UniProt KnowledgeBase (UniProtKB/Swiss-Prot) contains publicly available expertly manually annotated protein sequences obtained from a broad spectrum of organisms. Plant protein entries are produced in the frame of the Plant Proteome Annotation Program (PPAP), with an emphasis on characterized proteins of Arabidopsis thaliana and Oryza sativa. High level annotations provided by UniProtKB/Swiss-Prot are widely used to predict annotation of newly available proteins through automatic pipelines.The purpose of this chapter is to present a guided tour of a UniProtKB/Swiss-Prot entry. We will also present some of the tools and databases that are linked to each entry.

An update on the Enzyme Portal: an integrative approach for exploring enzyme knowledge.

PubMed

Pundir, S; Onwubiko, J; Zaru, R; Rosanoff, S; Antunes, R; Bingley, M; Watkins, X; O'Donovan, C; Martin, M J

2017-03-01

Enzymes are a key part of life processes and are increasingly important for various areas of research such as medicine, biotechnology, bioprocessing and drug research. The goal of the Enzyme Portal is to provide an interface to all European Bioinformatics Institute (EMBL-EBI) data about enzymes (de Matos, P., et al. , (2013), BMC Bioinformatics , (1), 103). These data include enzyme function, sequence features and family classification, protein structure, reactions, pathways, small molecules, diseases and the associated literature. The sources of enzyme data are: the UniProt Knowledgebase (UniProtKB) (UniProt Consortium, 2015), the Protein Data Bank in Europe (PDBe), (Valenkar, S., et al ., Nucleic Acids Res. 2016; , D385-D395) Rhea-a database of enzyme-catalysed reactions (Morgat, A., et al .,  Nucleic Acids Res.  2015; , D459-D464), Reactome-a database of biochemical pathways (Fabregat, A., et al ., Nucleic Acids Res. 2016;  , D481-D487), IntEnz-a resource with enzyme nomenclature information (Fleischmann, A., et al ., Nucleic Acids Res.  2004 , D434-D437) and ChEBI (Hastings, J., et al .,  Nucleic Acids Res. 2013) and ChEMBL (Bento, A. P., et al ., Nucleic Acids Res.  2014 , 1083-1090)-resources which contain information about small-molecule chemistry and bioactivity. This article describes the redesign of Enzyme Portal and the increased functionality added to maximise integration and interpretation of these data. Use case examples of the Enzyme Portal and the versatile workflows its supports are illustrated. We welcome the suggestion of new resources for integration. © The Author 2017. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

UniGene Tabulator: a full parser for the UniGene format.

PubMed

Lenzi, Luca; Frabetti, Flavia; Facchin, Federica; Casadei, Raffaella; Vitale, Lorenza; Canaider, Silvia; Carinci, Paolo; Zannotti, Maria; Strippoli, Pierluigi

2006-10-15

UniGene Tabulator 1.0 provides a solution for full parsing of UniGene flat file format; it implements a structured graphical representation of each data field present in UniGene following import into a common database managing system usable in a personal computer. This database includes related tables for sequence, protein similarity, sequence-tagged site (STS) and transcript map interval (TXMAP) data, plus a summary table where each record represents a UniGene cluster. UniGene Tabulator enables full local management of UniGene data, allowing parsing, querying, indexing, retrieving, exporting and analysis of UniGene data in a relational database form, usable on Macintosh (OS X 10.3.9 or later) and Windows (2000, with service pack 4, XP, with service pack 2 or later) operating systems-based computers. The current release, including both the FileMaker runtime applications, is freely available at http://apollo11.isto.unibo.it/software/

Expanding the UniFrac Toolbox

PubMed Central

2016-01-01

The UniFrac distance metric is often used to separate groups in microbiome analysis, but requires a constant sequencing depth to work properly. Here we demonstrate that unweighted UniFrac is highly sensitive to rarefaction instance and to sequencing depth in uniform data sets with no clear structure or separation between groups. We show that this arises because of subcompositional effects. We introduce information UniFrac and ratio UniFrac, two new weightings that are not as sensitive to rarefaction and allow greater separation of outliers than classic unweighted and weighted UniFrac. With this expansion of the UniFrac toolbox, we hope to empower researchers to extract more varied information from their data. PMID:27632205

Magnetic properties of the UNiGe2 at low temperature

NASA Astrophysics Data System (ADS)

Ohashi, Kohei; Ohashi, Masashi; Sawabu, Masaki; Miyagawa, Masahiro; Maeta, Kae; Yamamura, Tomoo

2018-03-01

We report on the magnetic characterization of a novel ternary uranium intermetallic UNiGe2. When we assume that UNiGe2 has the orthorhombic structure of CeNiGe2-type which is same as that of UNiSi2, the lattice constants were obtained to be a = 3.97 Å, b = 16.48 Å, and c = 4.08 Å. The unit cell volume of UNiGe2 is larger than that of UNiSi2. It comes from the fact that the atomic radius of Ge is larger than that of Si. The temperature dependence of the magnetic susceptibility shows two peaks at T N=45 K and T N‧=65 K. Taking an account that UNi2Ge2 secondary phase exists in the compound, UNiGe2 is an antiferromagnet below T N while T N‧ may come from the antiferromagnetic order of UNi2Ge2. At 5 K, the slope of the magnetization curve increases as increasing the magnetic field up to 5 T, indicating the presence of a metamagnetic transition. The residual magnetization remains on the magnetization curve at 5 K, which may come from a week ferromagnetism of UNi2Ge2 at low temperature.

Medical Effects of Atomic Bombs. The Report of the Joint Commission for the Investigation of the Effects of the Atomic Bomb in Japan. Volume 3. Section 6. Hematology. Section 7. Studies on Bone Marrow Obtained by Biopsy

DTIC Science & Technology

1951-04-19

the general appearance of the atypical lymphocytes which a re seen i n infectious mononucleosis . plasm, some had abundbt, non-granular, palely...applied ape identical in appearance with the familiar "atypical. lymphocyte" of infectious mononucleosis , The di- versity of forms is even greater...1) Erythrocytes and Hemoglobin. w - I L The -effect of the radiation emitted by the atomic bomb on the erythro- m cytes is complicated by the

Boundary pressure of inter-connection of Fe-Ni-S melt in olivine based on in-situ X-ray tomography: Implication to core formation in asteroids

NASA Astrophysics Data System (ADS)

Terasaki, H.; Urakawa, S.; Uesugi, K.; Nakatsuka, A.; Funakoshi, K.; Ohtani, E.

2011-12-01

Interconnectivity of Fe-alloy melt in crystalline silicates is important property for the core formation mechanism in planetary interior. In previous studies, the interconnectivity of Fe-alloy melt has been studied based on textural observation of recovered samples from high pressure and temperature. However, there is no observation under high pressure and temperature. We have developed 80-ton uni-axial press for X-ray computed micro-tomography (X-CT) and performed X-CT measurement under high pressure (Urakawa et al. 2010). Here we report X-CT measurement of Fe-Ni-S melt in crystalline olivine and interconnectivity of the melt up to 3.5 GPa and 1273 K. X-CT measurements were carried out at BL20B2 beamline, SPring-8 synchrotron facility. The sample was powder mixture of Fe-Ni-S and olivine, which was enclosed in graphite capsule. Heating was performed using a cylindrical graphite furnace. Pressure was generated using opposed toroidal-shape WC anvil. The uni-axial press was set on the rotational stage and X-ray radiography image of the sample was collected using CCD camera from 0°to 180°with 0.3° step. 3-D image of the sample was obtained by reconstructing the 2-D radiography image. The 3-D CT image shows that the size of the Fe-Ni-S melt increased significantly compared to that before melting below 2.5 GPa, suggesting that the melt was interconnected in olivine crystals. On the other hand, 3-D texture of the sample at 3.5 GPa did not show difference from that before melting. Therefore, the boundary of inter-connection of Fe-Ni-S melt is likely to locate between 2.5 and 3.5 GPa. This result is important application for the core formation mechanism especially in small bodies, such as differentiated asteroids.

Mapping PDB chains to UniProtKB entries.

PubMed

Martin, Andrew C R

2005-12-01

UniProtKB/SwissProt is the main resource for detailed annotations of protein sequences. This database provides a jumping-off point to many other resources through the links it provides. Among others, these include other primary databases, secondary databases, the Gene Ontology and OMIM. While a large number of links are provided to Protein Data Bank (PDB) files, obtaining a regularly updated mapping between UniProtKB entries and PDB entries at the chain or residue level is not straightforward. In particular, there is no regularly updated resource which allows a UniProtKB/SwissProt entry to be identified for a given residue of a PDB file. We have created a completely automatically maintained database which maps PDB residues to residues in UniProtKB/SwissProt and UniProtKB/trEMBL entries. The protocol uses links from PDB to UniProtKB, from UniProtKB to PDB and a brute-force sequence scan to resolve PDB chains for which no annotated link is available. Finally the sequences from PDB and UniProtKB are aligned to obtain a residue-level mapping. The resource may be queried interactively or downloaded from http://www.bioinf.org.uk/pdbsws/.

Contact sponge water absorption test implemented for in situ measures

NASA Astrophysics Data System (ADS)

Gaggero, Laura; Scrivano, Simona

2016-04-01

The contact sponge method is a non-destructive in-situ methodology used to estimate a water uptake coefficient. The procedure, unlike other in-situ measurement was proven to be directly comparable to the water uptake laboratory measurements, and was registered as UNI 11432:2011. The UNI Normal procedure requires to use a sponge with known density, soaked in water, weighed, placed on the material for 1 minute (UNI 11432, 2011; Pardini & Tiano, 2004), then weighed again. Difficulties arise in operating on test samples or on materials with porosity varied for decay. While carrying on the test, fluctuations in the bearing of the environmental parameters were negligible, but not the pressure applied to the surface, that induced the release of different water amounts towards the material. For this reason we designed a metal piece of the same diameter of the plate carrying the sponge, to be screwed at the tip of a pocket penetrometer. With this instrument the sponge was kept in contact with the surface for 1 minute applying two different loads, at first pushed with 0.3 kg/cm2 in order to press the sponge, but not its holder, against the surface. Then, a load of 1.1 kg/ cm2 was applied, still avoiding deviating the load to the sponge holder. We applied both the current and our implemented method to determine the water absorption by contact sponge on 5 fresh rock types (4 limestones: Fine - and Coarse grained Pietra di Vicenza, Rosso Verona, Breccia Aurora, and the silicoclastic Macigno sandstone). The results show that 1) the current methodology imply manual skill and experience to produce a coherent set of data; the variable involved are in fact not only the imposed pressure but also the compression mechanics. 2) The control on the applied pressure allowed reproducible measurements. Moreover, 3) the use of a thicker sponge enabled to apply the method even on rougher surfaces, as the device holding the sponge is not in contact with the tested object. Finally, 4) the implemented measurements gave the possibility of a direct comparison with the capillary water absorption method. Pardini C. & Tiano P. 2004. Valutazione in situ dei trattamenti protettivi per il materiale lapideo, proposta di una nuova semplice metodologia. ARKOS, 5, 30-36. UNI 11432. 2011. Beni culturali Materiali lapidei naturali ed artificiali - Misura della capacita di assorbimento di acqua mediante spugna di contatto. P. 6.

ProtVista: visualization of protein sequence annotations.

PubMed

Watkins, Xavier; Garcia, Leyla J; Pundir, Sangya; Martin, Maria J

2017-07-01

ProtVista is a comprehensive visualization tool for the graphical representation of protein sequence features in the UniProt Knowledgebase, experimental proteomics and variation public datasets. The complexity and relationships in this wealth of data pose a challenge in interpretation. Integrative visualization approaches such as provided by ProtVista are thus essential for researchers to understand the data and, for instance, discover patterns affecting function and disease associations. ProtVista is a JavaScript component released as an open source project under the Apache 2 License. Documentation and source code are available at http://ebi-uniprot.github.io/ProtVista/ . martin@ebi.ac.uk. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

FRED 2: an immunoinformatics framework for Python.

PubMed

Schubert, Benjamin; Walzer, Mathias; Brachvogel, Hans-Philipp; Szolek, András; Mohr, Christopher; Kohlbacher, Oliver

2016-07-01

Immunoinformatics approaches are widely used in a variety of applications from basic immunological to applied biomedical research. Complex data integration is inevitable in immunological research and usually requires comprehensive pipelines including multiple tools and data sources. Non-standard input and output formats of immunoinformatics tools make the development of such applications difficult. Here we present FRED 2, an open-source immunoinformatics framework offering easy and unified access to methods for epitope prediction and other immunoinformatics applications. FRED 2 is implemented in Python and designed to be extendable and flexible to allow rapid prototyping of complex applications. FRED 2 is available at http://fred-2.github.io schubert@informatik.uni-tuebingen.de Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

ProbOnto: ontology and knowledge base of probability distributions.

PubMed

Swat, Maciej J; Grenon, Pierre; Wimalaratne, Sarala

2016-09-01

Probability distributions play a central role in mathematical and statistical modelling. The encoding, annotation and exchange of such models could be greatly simplified by a resource providing a common reference for the definition of probability distributions. Although some resources exist, no suitably detailed and complex ontology exists nor any database allowing programmatic access. ProbOnto, is an ontology-based knowledge base of probability distributions, featuring more than 80 uni- and multivariate distributions with their defining functions, characteristics, relationships and re-parameterization formulas. It can be used for model annotation and facilitates the encoding of distribution-based models, related functions and quantities. http://probonto.org mjswat@ebi.ac.uk Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

A Generalised Fault Protection Structure Proposed for Uni-grounded Low-Voltage AC Microgrids

NASA Astrophysics Data System (ADS)

Bui, Duong Minh; Chen, Shi-Lin; Lien, Keng-Yu; Jiang, Jheng-Lun

2016-04-01

This paper presents three main configurations of uni-grounded low-voltage AC microgrids. Transient situations of a uni-grounded low-voltage (LV) AC microgrid (MG) are simulated through various fault tests and operation transition tests between grid-connected and islanded modes. Based on transient simulation results, available fault protection methods are proposed for main and back-up protection of a uni-grounded AC microgrid. In addition, concept of a generalised fault protection structure of uni-grounded LVAC MGs is mentioned in the paper. As a result, main contributions of the paper are: (i) definition of different uni-grounded LVAC MG configurations; (ii) analysing transient responses of a uni-grounded LVAC microgrid through line-to-line faults, line-to-ground faults, three-phase faults and a microgrid operation transition test, (iii) proposing available fault protection methods for uni-grounded microgrids, such as: non-directional or directional overcurrent protection, under/over voltage protection, differential current protection, voltage-restrained overcurrent protection, and other fault protection principles not based on phase currents and voltages (e.g. total harmonic distortion detection of currents and voltages, using sequence components of current and voltage, 3I0 or 3V0 components), and (iv) developing a generalised fault protection structure with six individual protection zones to be suitable for different uni-grounded AC MG configurations.

Performance of a distributed superscalar storage server

NASA Technical Reports Server (NTRS)

Finestead, Arlan; Yeager, Nancy

1993-01-01

The RS/6000 performed well in our test environment. The potential exists for the RS/6000 to act as a departmental server for a small number of users, rather than as a high speed archival server. Multiple UniTree Disk Server's utilizing one UniTree Disk Server's utilizing one UniTree Name Server could be developed that would allow for a cost effective archival system. Our performance tests were clearly limited by the network bandwidth. The performance gathered by the LibUnix testing shows that UniTree is capable of exceeding ethernet speeds on an RS/6000 Model 550. The performance of FTP might be significantly faster if asked to perform across a higher bandwidth network. The UniTree Name Server also showed signs of being a potential bottleneck. UniTree sites that would require a high ratio of file creations and deletions to reads and writes would run into this bottleneck. It is possible to improve the UniTree Name Server performance by bypassing the UniTree LibUnix Library altogether and communicating directly with the UniTree Name Server and optimizing creations. Although testing was performed in a less than ideal environment, hopefully the performance statistics stated in this paper will give end-users a realistic idea as to what performance they can expect in this type of setup.

A novel nanobody-based target module for retargeting of T lymphocytes to EGFR-expressing cancer cells via the modular UniCAR platform

PubMed Central

Albert, Susann; Arndt, Claudia; Feldmann, Anja; Bachmann, Dominik; Koristka, Stefanie; Ludwig, Florian; Ziller-Walter, Pauline; Kegler, Alexandra; Gärtner, Sebastian; Schmitz, Marc; Ehninger, Armin; Cartellieri, Marc; Ehninger, Gerhard; Pietzsch, Hans-Jürgen; Steinbach, Jörg; Bachmann, Michael

2017-01-01

ABSTRACT Recent treatments of leukemias with chimeric antigen receptor (CAR) expressing T cells underline their impressive therapeutic potential. However, once adoptively transferred into patients, there is little scope left to shut them down after elimination of tumor cells or in case adverse side effects occur. This becomes of special relevance if they are directed against commonly expressed tumor associated antigens (TAAs) such as receptors of the ErbB family. To overcome this limitation, we recently established a modular CAR platform technology termed UniCAR. UniCARs are not directed against TAAs but instead against a unique peptide epitope on engineered recombinant targeting modules (TMs), which guide them to the target. In the absence of a TM UniCAR T cells are inactive. Thus an interruption of any UniCAR activity requires an elimination of unbound TM and the TM complexed with UniCAR T cells. Elimination of the latter one requires a disassembly of the UniCAR-TM complexes. Here, we describe a first nanobody (nb)-based TM directed against EGFR. The novel TM efficiently retargets UniCAR T cells to EGFR positive tumors and mediates highly efficient target-specific and target-dependent tumor cell lysis both in vitro and in vivo. After radiolabeling of the novel TM with 64Cu and 68Ga, we analyzed its biodistribution and clearance as well as the stability of the UniCAR-TM complexes. As expected unbound TM is rapidly eliminated while the elimination of the TM complexed with UniCAR T cells is delayed. Nonetheless, we show that UniCAR-TM complexes dissociate in vitro and in vivo in a concentration-dependent manner in line with the concept of a repeated stop and go retargeting of tumor cells via the UniCAR technology. PMID:28507794

78 FR 4467 - UniStar Nuclear Energy, Combined License Application for Calvert Cliffs Power Plant, Unit 3...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-22

... NUCLEAR REGULATORY COMMISSION [Docket No. 52-016; NRC-2008-0250] UniStar Nuclear Energy, Combined License Application for Calvert Cliffs Power Plant, Unit 3, Exemption 1.0 Background UniStar Nuclear Energy (UNE), on behalf of Calvert Cliffs Nuclear Project, LLC and UniStar Nuclear Operating Services...

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.

The UniProtKB guide to the human proteome

PubMed Central

Breuza, Lionel; Poux, Sylvain; Estreicher, Anne; Famiglietti, Maria Livia; Magrane, Michele; Tognolli, Michael; Bridge, Alan; Baratin, Delphine; Redaschi, Nicole

2016-01-01

Advances in high-throughput and advanced technologies allow researchers to routinely perform whole genome and proteome analysis. For this purpose, they need high-quality resources providing comprehensive gene and protein sets for their organisms of interest. Using the example of the human proteome, we will describe the content of a complete proteome in the UniProt Knowledgebase (UniProtKB). We will show how manual expert curation of UniProtKB/Swiss-Prot is complemented by expert-driven automatic annotation to build a comprehensive, high-quality and traceable resource. We will also illustrate how the complexity of the human proteome is captured and structured in UniProtKB. Database URL: www.uniprot.org PMID:26896845

SSMap: a new UniProt-PDB mapping resource for the curation of structural-related information in the UniProt/Swiss-Prot Knowledgebase.

PubMed

David, Fabrice P A; Yip, Yum L

2008-09-23

Sequences and structures provide valuable complementary information on protein features and functions. However, it is not always straightforward for users to gather information concurrently from the sequence and structure levels. The UniProt knowledgebase (UniProtKB) strives to help users on this undertaking by providing complete cross-references to Protein Data Bank (PDB) as well as coherent feature annotation using available structural information. In this study, SSMap - a new UniProt-PDB residue-residue level mapping - was generated. The primary objective of this mapping is not only to facilitate the two tasks mentioned above, but also to palliate a number of shortcomings of existent mappings. SSMap is the first isoform sequence-specific mapping resource and is up-to-date for UniProtKB annotation tasks. The method employed by SSMap differs from the other mapping resources in that it stresses on the correct reconstruction of the PDB sequence from structures, and on the correct attribution of a UniProtKB entry to each PDB chain by using a series of post-processing steps. SSMap was compared to other existing mapping resources in terms of the correctness of the attribution of PDB chains to UniProtKB entries, and of the quality of the pairwise alignments supporting the residue-residue mapping. It was found that SSMap shared about 80% of the mappings with other mapping sources. New and alternative mappings proposed by SSMap were mostly good as assessed by manual verification of data subsets. As for local pairwise alignments, it was shown that major discrepancies (both in terms of alignment lengths and boundaries), when present, were often due to differences in methodologies used for the mappings. SSMap provides an independent, good quality UniProt-PDB mapping. The systematic comparison conducted in this study allows the further identification of general problems in UniProt-PDB mappings so that both the coverage and the quality of the mappings can be systematically improved for the benefit of the scientific community. SSMap mapping is currently used to provide PDB cross-references in UniProtKB.

Impact of helicopter transport and hospital level on mortality of polytrauma patients.

PubMed

Biewener, Achim; Aschenbrenner, Ulf; Rammelt, Stefan; Grass, René; Zwipp, Hans

2004-01-01

Despite numerous studies analyzing this topic, specific advantages of helicopter transport of blunt polytrauma patients as compared with ground ambulances have not yet been identified unequivocally. Four possible pathways in 403 polytrauma patients (Injury Severity Score [ISS] > 16) who were in reach of the helicopter emergency medical service (HEMS) Dresden were analyzed as follows: HEMS-UNI group (n = 140), transfer by HEMS into a university hospital; AMB-REG group (n = 102), transfer by ground ambulance into a regional (Level II or III) hospital; AMB-UNI group (n = 70), transfer by ground ambulance into the university hospital; and INTER group (n = 91), transfer by ground ambulance into a regional hospital, followed by transfer to the university hospital. Scores used were the ISS and the TRISS. Tests used for statistical analysis included chi2 and Fisher's tests. Statistical significance was set at p > 0.05. Age, gender, and mean ISS (range, 33.3-35.6) revealed extensive homogeneity of the groups. Mortality of the AMB-REG group was almost doubled (41.2%) compared with HEMS-UNI (22.1%) patients (p = 0.002). The AMB-UNI group displayed the lowest mortality (15.7%, p = not significant). TRISS analysis (PRE-Chart) revealed identical outcome for AMB-UNI and HEMS-UNI patients. Rescue time averaged 90 +/- 29 minutes for HEMS-UNI patients, 68 +/- 25 minutes for AMB-UNI patients, and 69 +/- 26 minutes for the AMB-REG group. Primary transfer by HEMS into a Level I trauma center reduces mortality markedly. In principle, this benefit can be attributed to superior preclinical therapy, primary admission to a Level I trauma center, or both. However, the identical probability of survival of the AMB-UNI and HEMS-UNI groups in this and comparable studies does not confirm generally better survival rates on account of a more aggressive on-site approach.

75 FR 53292 - Combined Notice of Filings No. 1

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-31

...-000. Applicants: UniSource Energy Development Company. Description: UniSource Energy Development Company submits tariff filing per 35.12: Baseline Filing for UniSource Energy Development Company MBR... DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings No. 1 August...

UniNovo: a universal tool for de novo peptide sequencing.

PubMed

Jeong, Kyowon; Kim, Sangtae; Pevzner, Pavel A

2013-08-15

Mass spectrometry (MS) instruments and experimental protocols are rapidly advancing, but de novo peptide sequencing algorithms to analyze tandem mass (MS/MS) spectra are lagging behind. Although existing de novo sequencing tools perform well on certain types of spectra [e.g. Collision Induced Dissociation (CID) spectra of tryptic peptides], their performance often deteriorates on other types of spectra, such as Electron Transfer Dissociation (ETD), Higher-energy Collisional Dissociation (HCD) spectra or spectra of non-tryptic digests. Thus, rather than developing a new algorithm for each type of spectra, we develop a universal de novo sequencing algorithm called UniNovo that works well for all types of spectra or even for spectral pairs (e.g. CID/ETD spectral pairs). UniNovo uses an improved scoring function that captures the dependences between different ion types, where such dependencies are learned automatically using a modified offset frequency function. The performance of UniNovo is compared with PepNovo+, PEAKS and pNovo using various types of spectra. The results show that the performance of UniNovo is superior to other tools for ETD spectra and superior or comparable with others for CID and HCD spectra. UniNovo also estimates the probability that each reported reconstruction is correct, using simple statistics that are readily obtained from a small training dataset. We demonstrate that the estimation is accurate for all tested types of spectra (including CID, HCD, ETD, CID/ETD and HCD/ETD spectra of trypsin, LysC or AspN digested peptides). UniNovo is implemented in JAVA and tested on Windows, Ubuntu and OS X machines. UniNovo is available at http://proteomics.ucsd.edu/Software/UniNovo.html along with the manual.

On expert curation and scalability: UniProtKB/Swiss-Prot as a case study

PubMed Central

Arighi, Cecilia N; Magrane, Michele; Bateman, Alex; Wei, Chih-Hsuan; Lu, Zhiyong; Boutet, Emmanuel; Bye-A-Jee, Hema; Famiglietti, Maria Livia; Roechert, Bernd; UniProt Consortium, The

2017-01-01

Abstract Motivation Biological knowledgebases, such as UniProtKB/Swiss-Prot, constitute an essential component of daily scientific research by offering distilled, summarized and computable knowledge extracted from the literature by expert curators. While knowledgebases play an increasingly important role in the scientific community, their ability to keep up with the growth of biomedical literature is under scrutiny. Using UniProtKB/Swiss-Prot as a case study, we address this concern via multiple literature triage approaches. Results With the assistance of the PubTator text-mining tool, we tagged more than 10 000 articles to assess the ratio of papers relevant for curation. We first show that curators read and evaluate many more papers than they curate, and that measuring the number of curated publications is insufficient to provide a complete picture as demonstrated by the fact that 8000–10 000 papers are curated in UniProt each year while curators evaluate 50 000–70 000 papers per year. We show that 90% of the papers in PubMed are out of the scope of UniProt, that a maximum of 2–3% of the papers indexed in PubMed each year are relevant for UniProt curation, and that, despite appearances, expert curation in UniProt is scalable. Availability and implementation UniProt is freely available at http://www.uniprot.org/. Contact sylvain.poux@sib.swiss Supplementary information Supplementary data are available at Bioinformatics online. PMID:29036270

'Isotopo' a database application for facile analysis and management of mass isotopomer data.

PubMed

Ahmed, Zeeshan; Zeeshan, Saman; Huber, Claudia; Hensel, Michael; Schomburg, Dietmar; Münch, Richard; Eylert, Eva; Eisenreich, Wolfgang; Dandekar, Thomas

2014-01-01

The composition of stable-isotope labelled isotopologues/isotopomers in metabolic products can be measured by mass spectrometry and supports the analysis of pathways and fluxes. As a prerequisite, the original mass spectra have to be processed, managed and stored to rapidly calculate, analyse and compare isotopomer enrichments to study, for instance, bacterial metabolism in infection. For such applications, we provide here the database application 'Isotopo'. This software package includes (i) a database to store and process isotopomer data, (ii) a parser to upload and translate different data formats for such data and (iii) an improved application to process and convert signal intensities from mass spectra of (13)C-labelled metabolites such as tertbutyldimethylsilyl-derivatives of amino acids. Relative mass intensities and isotopomer distributions are calculated applying a partial least square method with iterative refinement for high precision data. The data output includes formats such as graphs for overall enrichments in amino acids. The package is user-friendly for easy and robust data management of multiple experiments. The 'Isotopo' software is available at the following web link (section Download): http://spp1316.uni-wuerzburg.de/bioinformatics/isotopo/. The package contains three additional files: software executable setup (installer), one data set file (discussed in this article) and one excel file (which can be used to convert data from excel to '.iso' format). The 'Isotopo' software is compatible only with the Microsoft Windows operating system. http://spp1316.uni-wuerzburg.de/bioinformatics/isotopo/. © The Author(s) 2014. Published by Oxford University Press.

An algorithm to detect and communicate the differences in computational models describing biological systems.

PubMed

Scharm, Martin; Wolkenhauer, Olaf; Waltemath, Dagmar

2016-02-15

Repositories support the reuse of models and ensure transparency about results in publications linked to those models. With thousands of models available in repositories, such as the BioModels database or the Physiome Model Repository, a framework to track the differences between models and their versions is essential to compare and combine models. Difference detection not only allows users to study the history of models but also helps in the detection of errors and inconsistencies. Existing repositories lack algorithms to track a model's development over time. Focusing on SBML and CellML, we present an algorithm to accurately detect and describe differences between coexisting versions of a model with respect to (i) the models' encoding, (ii) the structure of biological networks and (iii) mathematical expressions. This algorithm is implemented in a comprehensive and open source library called BiVeS. BiVeS helps to identify and characterize changes in computational models and thereby contributes to the documentation of a model's history. Our work facilitates the reuse and extension of existing models and supports collaborative modelling. Finally, it contributes to better reproducibility of modelling results and to the challenge of model provenance. The workflow described in this article is implemented in BiVeS. BiVeS is freely available as source code and binary from sems.uni-rostock.de. The web interface BudHat demonstrates the capabilities of BiVeS at budhat.sems.uni-rostock.de. © The Author 2015. Published by Oxford University Press.

A Dry Powder Process for Preparing Uni-Tape Prepreg from Polymer Powder Coated Filamentary Towpregs

NASA Technical Reports Server (NTRS)

Wilkinson, Steven P. (Inventor); Johnston, Norman J. (Inventor); Marchello, Joseph M. (Inventor)

1995-01-01

A process for preparing uni-tape prepreg from polymer powder coated filamentary towpregs is provided. A plurality of polymer powder coated filamentary towpregs are provided. The towpregs are collimated so that each towpreg is parallel. The sandwich is heated to a temperature wherein the polymer flows and intimately contacts the filaments and pressure is repeatedly applied perpendicularly to the sandwich with a longitudinal oscillating action wherein the filaments move apart and the polymer wets the filaments forming a uni-tape prepreg. The uni-tape prepreg is subsequently cooled.

Crew of Hubble Space Telescope servicing mission visits Europe

NASA Astrophysics Data System (ADS)

1994-01-01

The Hubble Space telescope servicing mission in December (STS-61) was a great success and the fully refurbished orbiting telescope produced absolutely remarkable first results just two weeks ago. The 7-member crew who carried out the mission will soon be in Europe to share their experience with the Press, ESA space specialists and the European space community. Public conferences will also be held in Switzerland, the home country of ESA astronaut Claude Nicollier. The visit of the STS-61 crew is scheduled as follows: Friday 11 February, 1994 - ESA Paris, France Presentation and Press Conference Location: ESA, 8/10 Rue Mario Nikis, 75015 Paris time: 16:00 hrs - 17:30 hrs contact: ESA, Public Relations Office Tel. (+33) 1 42 73 71 55 Fax. (+33) 1 42 73 76 90 Monday 14 February, 1994 - British Aerospace, Bristol, United Kingdom Presentation and Press Conference Location: British Aerospace, FPC 333, Filton, Bristol BS12 7QW time: 10:00 hrs - 12:00 hrs contact: BAe, Public Relations Tel. (+44) 272 36 33 69 Tel. (+44) 272 36 33 68 Tuesday 15 February, 1994 - ESA/ESTEC, Noordwijk, the Netherlands Presentation and Press Conference Location: Noordwijk Space Expo, Keplerlaan 3, 2201 AZ Noordwijk, the Netherlands time: 09:30 hrs - 12:00 hrs contact: ESTEC Public Relations Office Tel. (+31) 1719 8 3006 Fax. (+31) 1719 17 400 Wednesday 16 February, 1944 - ESO, Garching - Munich, Germany Presentation and Press Conference Location: European Southern Observatory, Karl- Schwarzschild-Str. 2, 85748 Garching -Munich, Germany time: to be decided contact: ESO Information Service Tel. (+49) 89 32 006 276 Fax. (+49) 89 320 23 62 Thursday 17 February, 1994 - Bern, Switzerland a. Presentation and Press Conference Location: Hotel Bern, Zeughausgasse 9, 3001 Bern, Switzerland time: 09:30 hrs contact: Press & Information Service of the Federal Dept. for Education & Sciences Tel. (+41) 31 322 80 34 Fax. (+41) 31 312 30 15 b. Public conference Location: University of Bern, Institute of Physics time: 18:00 hrs - 20:00 hrs Friday 18 February, 1994 - Geneva, Switzerland a. Presentation and Press Conference Location: Geneva Observatory, Chemin des Maillettes 51, 1290 Sauverny, Switzerland time: 10:00 hrs - 11:30 hrs contact: Press Service University of Geneva Tel. (+41) 22 705 77 17 Tel. (+41) 22 328 25 66 b. Public Conference Location: University of Geneva, Auditorium Piaget, Uni Dufour time: 18:00 hrs - 20:30 hrs For accreditation and further information on these events, please get in touch directly with the contact listed for each location.

TFmiR: a web server for constructing and analyzing disease-specific transcription factor and miRNA co-regulatory networks.

PubMed

Hamed, Mohamed; Spaniol, Christian; Nazarieh, Maryam; Helms, Volkhard

2015-07-01

TFmiR is a freely available web server for deep and integrative analysis of combinatorial regulatory interactions between transcription factors, microRNAs and target genes that are involved in disease pathogenesis. Since the inner workings of cells rely on the correct functioning of an enormously complex system of activating and repressing interactions that can be perturbed in many ways, TFmiR helps to better elucidate cellular mechanisms at the molecular level from a network perspective. The provided topological and functional analyses promote TFmiR as a reliable systems biology tool for researchers across the life science communities. TFmiR web server is accessible through the following URL: http://service.bioinformatik.uni-saarland.de/tfmir. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Multi-centre field evaluation of the performance of the Trinity Biotech Uni-Gold HIV 1/2 rapid test as a first-line screening assay for gay and bisexual men compared with 4th generation laboratory immunoassays.

PubMed

Keen, P; Conway, D P; Cunningham, P; McNulty, A; Couldwell, D L; Davies, S C; Smith, D E; Gray, J; Holt, M; O'Connor, C C; Read, P; Callander, D; Prestage, G; Guy, R

2017-01-01

The Trinity Biotech Uni-Gold HIV test (Uni-Gold) is often used as a supplementary rapid test in testing algorithms. To evaluate the operational performance of the Uni-Gold as a first-line screening test among gay and bisexual men (GBM) in a setting where 4th generation HIV laboratory assays are routinely used. We compared the performance of Uni-Gold with conventional HIV serology conducted in parallel among GBM attending 22 testing sites. Sensitivity was calculated separately for acute and established infection, defined using 4th generation screening Ag/Ab immunoassay (EIA) and Western blot results. Previous HIV testing history and results of supplementary 3rd generation HIV Ab EIA, and p24 antigen EIA were used to further characterise cases of acute infection. Of 10,793 specimens tested with Uni-Gold and conventional serology, 94 (0.90%, 95%CI:0.70-1.07) were confirmed as HIV-positive by conventional serology, and 37 (39.4%) were classified as acute infection. Uni-Gold sensitivity was 81.9% overall (77/94, 95%CI:72.6-89.1); 56.8% for acute infection (21/37, 95%CI:39.5-72.9) and 98.2% for established infection (56/57, 95%CI:90.6-100.0). Of 17 false non-reactive Uni-Gold results, 16 were acute infections, and of these seven were p24 antigen reactive but antibody negative. Uni-Gold specificity was 99.9% (10,692/10,699, 95%CI:99.9-100.0), PPV was 91.7% (95%CI:83.6-96.6) and NPV was 99.8% (95%CI:99.7-99.9), respectively. In this population, Uni-Gold had good specificity and sensitivity was high for established infections when compared to 4th generation laboratory assays, however sensitivity was lower in acute infections. Where rapid tests are used in populations with a high proportion of acute infections, additional testing strategies are needed to detect acute infections. Copyright © 2016 Elsevier B.V. All rights reserved.

Uninephrectomy in Rats on a Fixed Food Intake Potentiates Both Anorexia and Circulating Cytokine Subsets in Response to LPS.

PubMed

Arsenijevic, Denis; Montani, Jean-Pierre

2015-01-01

Recent human studies have suggested that mild reduction in kidney function can alter immune response and increase susceptibility to infection. The role of mild reduction in kidney function in altering susceptibility to bacterial lipopolysaccharide (LPS) responses was investigated in uninephrectomized rats compared to Sham-operated controls rats 4 weeks after surgery. Throughout the 4 weeks, all rats were maintained under mild food restriction at 90% of ad libitum intake to ensure the same caloric intake in both groups. In comparison to Sham, uninephrectomy (UniNX) potentiated LPS-induced anorexia by 2.1-fold. The circulating anorexigenic cytokines granulocyte-macrophage colony stimulating factor, interferon-γ, tumor necrosis factor-α, and complement-derived acylation-stimulating protein were elevated after LPS in UniNX animals compared to Sham animals. Interleukin(IL)1β and IL6 pro-inflammatory cytokines were transiently increased. Anti-inflammatory cytokines IL4 and IL10 did not differ or had a tendency to be lower in UniNX group compared to Sham animals. LPS-induced anorexia was associated with increased anorexigenic neuropeptides mRNA for pro-opiomelanocortin, corticotrophin-releasing factor, and cocaine-amphetamine-regulated transcript in the hypothalamus of both Sham and UniNX groups, but at higher levels in the UniNX group. Melanocortin-4-receptor mRNA was markedly increased in the UniNX group, which may have contributed to the enhanced anorexic response to LPS of the UniNX group. In summary, UniNX potentiates pro-inflammatory cytokine production, anorexia, and selected hypothalamic anorexigenic neuropeptides in response to LPS.

Pea Compound Leaf Architecture Is Regulated by Interactions among the Genes UNIFOLIATA, COCHLEATA, AFILA, and TENDRIL-LESS

PubMed Central

Gourlay, Campbell W.; Hofer, Julie M. I.; Ellis, T. H. Noel

2000-01-01

The compound leaf primordium of pea represents a marginal blastozone that initiates organ primordia, in an acropetal manner, from its growing distal region. The UNIFOLIATA (UNI) gene is important in marginal blastozone maintenance because loss or reduction of its function results in uni mutant leaves of reduced complexity. In this study, we show that UNI is expressed in the leaf blastozone over the period in which organ primordia are initiated and is downregulated at the time of leaf primordium determination. Prolonged UNI expression was associated with increased blastozone activity in the complex leaves of afila (af), cochleata (coch), and afila tendril-less (af tl) mutant plants. Our analysis suggests that UNI expression is negatively regulated by COCH in stipule primordia, by AF in proximal leaflet primordia, and by AF and TL in distal and terminal tendril primordia. We propose that the control of UNI expression by AF, TL, and COCH is important in the regulation of blastozone activity and pattern formation in the compound leaf primordium of the pea. PMID:10948249

UniPrime2: a web service providing easier Universal Primer design.

PubMed

Boutros, Robin; Stokes, Nicola; Bekaert, Michaël; Teeling, Emma C

2009-07-01

The UniPrime2 web server is a publicly available online resource which automatically designs large sets of universal primers when given a gene reference ID or Fasta sequence input by a user. UniPrime2 works by automatically retrieving and aligning homologous sequences from GenBank, identifying regions of conservation within the alignment, and generating suitable primers that can be used to amplify variable genomic regions. In essence, UniPrime2 is a suite of publicly available software packages (Blastn, T-Coffee, GramAlign, Primer3), which reduces the laborious process of primer design, by integrating these programs into a single software pipeline. Hence, UniPrime2 differs from previous primer design web services in that all steps are automated, linked, saved and phylogenetically delimited, only requiring a single user-defined gene reference ID or input sequence. We provide an overview of the web service and wet-laboratory validation of the primers generated. The system is freely accessible at: http://uniprime.batlab.eu. UniPrime2 is licenced under a Creative Commons Attribution Noncommercial-Share Alike 3.0 Licence.

The growth of the UniTree mass storage system at the NASA Center for Computational Sciences: Some lessons learned

NASA Technical Reports Server (NTRS)

Tarshish, Adina; Salmon, Ellen

1994-01-01

In October 1992, the NASA Center for Computational Sciences made its Convex-based UniTree system generally available to users. The ensuing months saw growth in every area. Within 26 months, data under UniTree control grew from nil to over 12 terabytes, nearly all of it stored on robotically mounted tape. HiPPI/UltraNet was added to enhance connectivity, and later HiPPI/TCP was added as well. Disks and robotic tape silos were added to those already under UniTree's control, and 18-track tapes were upgraded to 36-track. The primary data source for UniTree, the facility's Cray Y-MP/4-128, first doubled its processing power and then was replaced altogether by a C98/6-256 with nearly two-and-a-half times the Y-MP's combined peak gigaflops. The Convex/UniTree software was upgraded from version 1.5 to 1.7.5, and then to 1.7.6. Finally, the server itself, a Convex C3240, was upgraded to a C3830 with a second I/O bay, doubling the C3240's memory and capacity for I/O. This paper describes insights gained and reinforced with the burgeoning demands on the UniTree storage system and the significant increases in performance gained from the many upgrades.

76 FR 81994 - UniStar Nuclear Energy; Combined License Application for Calvert Cliffs Nuclear Power Plant, Unit...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-29

... NUCLEAR REGULATORY COMMISSION [Docket No. 52-016; NRC-2008-0250] UniStar Nuclear Energy; Combined License Application for Calvert Cliffs Nuclear Power Plant, Unit 3; Exemption 1.0 Background: UniStar Nuclear Energy (UNE) submitted to the U.S. Nuclear Regulatory Commission (NRC or the Commission ) a...

Larger low voltage zone in endocardial unipolar map compared with that in epicardial bipolar map indicates difficulty in eliminating ventricular tachycardia by catheter ablation.

PubMed

Miyamoto, Koji; Noda, Takashi; Satomi, Kazuhiro; Wada, Mitsuru; Nakajima, Ikutaro; Ishibashi, Kohei; Okamura, Hideo; Noguchi, Teruo; Anzai, Toshihisa; Yasuda, Satoshi; Ogawa, Hisao; Shimizu, Wataru; Aiba, Takeshi; Kamakura, Shiro; Kusano, Kengo

2016-08-01

Patients with ischemic and non-ischemic cardiomyopathy often have substrate for ventricular tachycardia (VT) in the endocardium (ENDO), epicardium (EPI), and/or intramural. Although it has been reported that the ENDO unipolar (UNI) voltage map is useful in detecting EPI substrate, its feasibility to detect intramural scarring and its usefulness in radiofrequency catheter ablation (RFCA) remain unclear. To assess the relationship between the left ventricle (LV) ENDO UNI voltage map and the LV EPI bipolar (BIP) voltage map, and to determine the usefulness of the ENDO UNI voltage map to guide RFCA for VT in patients with cardiomyopathy undergoing combined ENDO- and EPI RFCA. Eleven patients with VT undergoing detailed ENDO and EPI electroanatomical mapping of the LV were included (mean age 59 ± 11 years, 9 men). We assessed the value of the LV ENDO UNI voltage map in identifying EPI and/or intramural substrate in these 11 patients with non-ischemic or ischemic cardiomyopathy. The underlying heart disease was dilated cardiomyopathy in 4 patients, cardiac sarcoidosis in 3, hypertrophic cardiomyopathy in 2, and ischemic heart disease in 2 patients. The mean LV ejection fraction was 24 ± 7 %. The low voltage zone (LVZ) was defined as <1.5 mV for LV ENDO BIP electrograms (EGMs), <8.3 mV for LV ENDO UNI EGMs, and <1.0 mV for LV EPI BIP EGMs. The surface area of each LVZ was measured. We also measured the LVZ of the spatial overlap between ENDO UNI and EPI BIP voltage maps using the transparency mode on CARTO software. We performed RFCA at the ENDO and EPI based on activation and/or substrate maps, targeting the LVZ and/or abnormal EGMs. The LVZ was present in the LV ENDO BIP voltage map in 10 of 11 patients (42 ± 33 cm(2)), and in the LV ENDO UNI voltage map in 10 of 11 patients (72 ± 45 cm(2)). The LVZ was present in the EPI BIP voltage map in 9 of 11 patients (70 ± 61 cm(2)), and the LVZ in the ENDO UNI voltage map was also seen in all 9 patients. The location of the LVZ in the EPI BIP map matched that in 45 ± 28 % of ENDO UNI voltage maps. The LVZ in the ENDO UNI voltage map was larger than that in the EPI BIP voltage map in 6 of 11 patients, and RFCA failed in 5 of these 6 patients. In the remaining 5 patients with a smaller LVZ in the ENDO UNI voltage map compared with the EPI BIP voltage map or no LVZ both at ENDO UNI and EPI BIP voltage map, VT was successfully eliminated in 4 of 5 patients. The LV ENDO UNI voltage map is useful in detecting EPI substrate in patients with cardiomyopathy. A larger LVZ in the ENDO UNI voltage map compared to that in the EPI BIP voltage map may indicate the presence of intramural substrate, which leads to difficulty in eliminating VT, even with combined ENDO- and EPI RFCA.

Selective interference of grasp and space representations with number magnitude and serial order processing.

PubMed

van Dijck, Jean-Philippe; Fias, Wim; Andres, Michael

2015-10-01

It has been proposed that the metrics of space, time and other magnitudes relevant for action are coupled through a generalized magnitude system that also contribute to number representation. Several studies capitalized on stimulus-response compatibility effects to show that numbers map onto left-right representations and grasp representations as a function of their magnitude. However, the tasks typically used do not allow disentangling magnitude from serial order processing. Here, we devised a working memory (WM) task where participants had to remember random sequences of numbers and perform a precision/whole-hand grip (Experiment 1) or a uni-manual left/right button press (Experiment 2) in response to numbers presented during the retention interval. This task does allow differentiating the interference of number magnitude and serial order with each set of responses. Experiment 1 showed that precision grips were initiated faster than whole-hand grips in response to small numbers, irrespective of their serial position in WM. In contrast, Experiment 2 revealed an advantage of right over left button presses as serial position increased, without any influence of number magnitude. These findings demonstrate that grasping and left-right movements overlap with distinct dimensions of number processing. These findings are discussed in the light of different theories explaining the interactions between numbers, space and action.

Dry powder process for preparing uni-tape prepreg from polymer powder coated filamentary towpregs

NASA Technical Reports Server (NTRS)

Wilkinson, Steven P. (Inventor); Johnston, Norman J. (Inventor); Marchello, Joseph M. (Inventor)

1997-01-01

A process for preparing uni-tape prepreg from polymer powder coated filamentary towpregs is provided. A plurality of polymer powder coated filamentary towpregs are provided. The towpregs are collimated so that each towpreg is parallel. A material is applied to each side of the towpreg to form a sandwich. The sandwich is heated to a temperature wherein the polymer flows and intimately contacts the filaments and pressure is repeatedly applied perpendicularly to the sandwich with a longitudinal oscillating action wherein the filaments move apart and the polymer wets the filaments forming a uni-tape prepreg. The uni-tape prepreg is subsequently cooled.

The patient satisfaction questionnaire of EUprimecare project: measurement properties.

PubMed

Cimas, Marta; Ayala, Alba; García-Pérez, Sonia; Sarria-Santamera, Antonio; Forjaz, Maria João

2016-06-01

The measurement of patient satisfaction is considered an essential outcome indicator to evaluate health care quality. Patient satisfaction is considered a multi-dimensional construct, which would include a variety of domains. Although a large number of studies have proposed scales to measure patient satisfaction, there is a lack of psychometric information on them. This study aims to describe the psychometric properties of the Primary Care Satisfaction Scale (PCSS) of the EUprimecare project. A cross-sectional survey of patient satisfaction with primary care was carried out by telephone interview. Primary care services of Estonia, Finland, Germany, Hungary, Lithuania, Italy and Spain. A total of 3020 adult patients aged 18-65 years old attending primary care services. Classic psychometric properties were analysed and Rasch analysis was used to assess the following measurement properties: fit to the Rasch model; uni-dimensionality; reliability; differential item functioning (DIF) by gender, age, civil status, area of residency and country; local independency; adequacy of response scale; and scale targeting. To achieve good fit to the Rasch model, the original response scales of three items (1, 2 and 6) were rescored and Item 3 (waiting time in the room) was removed. The scale was uni-dimensional and Person Separation Index was 0.79, indicating a good reliability. All items were free from bias. PCSS linear measure displayed satisfactory convergent validity with overall satisfaction with primary care. PCSS, as a reliable and valid scale, could be used to measure patient satisfaction in primary care in Europe. © The Author 2016. Published by Oxford University Press in association with the International Society for Quality in Health Care; all rights reserved.

Understanding High Rate Behavior Through Low Rate Analog

DTIC Science & Technology

2014-04-28

uni- axial compression over all rates tested at 20 °C; (b) True yield stress as a function of strain rate...of temperature. (a) (b) Figure 11. Representative behaviour of PPVC-2. (a) True stress-true strain response in uni- axial compression over all...pages 33 of 78 (a) (b) Figure 15. Representative behaviour of PPVC-6. (a) True stress-true strain response in uni- axial compression

DiversePathsJ: diverse shortest paths for bioimage analysis.

PubMed

Uhlmann, Virginie; Haubold, Carsten; Hamprecht, Fred A; Unser, Michael

2018-02-01

We introduce a formulation for the general task of finding diverse shortest paths between two end-points. Our approach is not linked to a specific biological problem and can be applied to a large variety of images thanks to its generic implementation as a user-friendly ImageJ/Fiji plugin. It relies on the introduction of additional layers in a Viterbi path graph, which requires slight modifications to the standard Viterbi algorithm rules. This layered graph construction allows for the specification of various constraints imposing diversity between solutions. The software allows obtaining a collection of diverse shortest paths under some user-defined constraints through a convenient and user-friendly interface. It can be used alone or be integrated into larger image analysis pipelines. http://bigwww.epfl.ch/algorithms/diversepathsj. michael.unser@epfl.ch or fred.hamprecht@iwr.uni-heidelberg.de. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

GfaPy: a flexible and extensible software library for handling sequence graphs in Python.

PubMed

Gonnella, Giorgio; Kurtz, Stefan

2017-10-01

GFA 1 and GFA 2 are recently defined formats for representing sequence graphs, such as assembly, variation or splicing graphs. The formats are adopted by several software tools. Here, we present GfaPy, a software package for creating, parsing and editing GFA graphs using the programming language Python. GfaPy supports GFA 1 and GFA 2, using the same interface and allows for interconversion between both formats. The software package provides a simple interface for custom record types, which is an important new feature of GFA 2 (compared to GFA 1). This enables new applications of the format. GfaPy is available open source at https://github.com/ggonnella/gfapy and installable via pip. gonnella@zbh.uni-hamburg.de. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

UniPOPS: Unified data reduction suite

NASA Astrophysics Data System (ADS)

Maddalena, Ronald J.; Garwood, Robert W.; Salter, Christopher J.; Stobie, Elizabeth B.; Cram, Thomas R.; Morgan, Lorrie; Vance, Bob; Hudson, Jerome

2015-03-01

UniPOPS, a suite of programs and utilities developed at the National Radio Astronomy Observatory (NRAO), reduced data from the observatory's single-dish telescopes: the Tucson 12-m, the Green Bank 140-ft, and archived data from the Green Bank 300-ft. The primary reduction programs, 'line' (for spectral-line reduction) and 'condar' (for continuum reduction), used the People-Oriented Parsing Service (POPS) as the command line interpreter. UniPOPS unified previous analysis packages and provided new capabilities; development of UniPOPS continued within the NRAO until 2004 when the 12-m was turned over to the Arizona Radio Observatory (ARO). The submitted code is version 3.5 from 2004, the last supported by the NRAO.

Frequency Dependent Harmonic Powers in a Modified Uni-Traveling Carrier (MUTC) Photodetector

DTIC Science & Technology

2017-01-27

Naval Research Laboratory Washington, DC 20375-5320 NRL/MR/5651--17-9712 Frequency Dependent Harmonic Powers in a Modified Uni- Traveling Carrier...burden for this collection of information is estimated to average 1 hour per response, including the time for reviewing instructions, searching existing...Modified Uni- Traveling Carrier (MUTC) Photodetector Yue Hu,* Meredith N. Hutchinson, and Curtis R. Menyuk* Naval Research Laboratory 4555 Overlook

Investigating the mechanisms of glyphosate resistance in goosegrass (Eleusine indica (L.) Gaertn.) by RNA sequencing technology.

PubMed

Chen, Jingchao; Huang, Hongjuan; Wei, Shouhui; Huang, Zhaofeng; Wang, Xu; Zhang, Chaoxian

2017-01-01

Glyphosate is an important non-selective herbicide that is in common use worldwide. However, evolved glyphosate-resistant (GR) weeds significantly affect crop yields. Unfortunately, the mechanisms underlying resistance in GR weeds, such as goosegrass (Eleusine indica (L.) Gaertn.), an annual weed found worldwide, have not been fully elucidated. In this study, transcriptome analysis was conducted to further assess the potential mechanisms of glyphosate resistance in goosegrass. The RNA sequencing libraries generated 24 597 462 clean reads. De novo assembly analysis produced 48 852 UniGenes with an average length of 847 bp. All UniGenes were annotated using seven databases. Sixteen candidate differentially expressed genes selected by digital gene expression analysis were validated by quantitative real-time PCR (qRT-PCR). Among these UniGenes, the EPSPS and PFK genes were constitutively up-regulated in resistant (R) individuals and showed a higher copy number than that in susceptible (S) individuals. The expressions of four UniGenes relevant to photosynthesis were inhibited by glyphosate in S individuals, and this toxic response was confirmed by gas exchange analysis. Two UniGenes annotated as glutathione transferase (GST) were constitutively up-regulated in R individuals, and were induced by glyphosate both in R and S. In addition, the GST activities in R individuals were higher than in S. Our research confirmed that two UniGenes (PFK, EPSPS) were strongly associated with target resistance, and two GST-annotated UniGenes may play a role in metabolic glyphosate resistance in goosegrass. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

Baseline and Multimodal UAV GCS Interface Design

DTIC Science & Technology

2011-12-01

information queries). 2 Calhoun et al. (2004) Different musical chords and intervals. Priority level of a late-arriving UAV. 4 Graham and...tactors (the lower levels ones especially) would be on for much longer durations as the UAV’s attitude upset increases. 2.2.2.7.2 Uni- centred Circles...in uni- centred circles. Figure 2.12: Tactor formation for the uni- centred circles of tactors. In this type of display, the tactors which are

Congenital uni-leaflet mitral valve with severe stenosis: A case report with literature review.

PubMed

Zhang, Weixin; Wang, Yonghuai; Ma, Chunyan; Zhang, Zhiwei; Yang, Jun

2017-03-01

Numerical abnormalities of mitral leaflets is a special entity in congenital mitral malformations. Previously reported cases of uni-leaflet mitral valve were primarily related to absence or dysplasia of certain leaflets. We present a case here with mitral leaflets that were not divided into anterior and posterior as usual, but developed as an integral structure instead, which is different from previously documented cases of uni-leaflet mitral valves. Real time three-dimensional echocardiography (RT3DE) provides a visual presentation of the abnormal mitral structure which was confirmed by surgical operation. To the best of our knowledge, this unusual form of uni-leaflet mitral valve has not been reported yet. © 2017, Wiley Periodicals, Inc.

Finite element prediction on the chassis design of UniART4 racing car

NASA Astrophysics Data System (ADS)

Zaman, Z. I.; Basaruddin, K. S.; Basha, M. H.; Rahman, M. T. Abd; Daud, R.

2017-09-01

This paper presents the analysis and evaluation of the chassis design for University Automotive Racing Team No. 4 (UniART4) car based on finite element analysis. The existing UniART4 car chassis was measured and modelled geometrically using Solidwork before analysed in FEA software (ANSYS). Four types of static structural analysis were used to predict the chassis design capability under four different loading conditions; vertical bending, lateral bending, lateral torsion and horizontal lozenging. The results showed the chassis subjected to the highest stress and strain under horizontal lozenging, whereas the minimum stress and strain response was obtained under lateral bending. The present analysis result could provide valuable information in predicting the sustainability of the current UniART car chassis design.

NILES 94; International Conference Held in Cairo, Egypt on 26-30 March 1994

DTIC Science & Technology

1994-03-30

and the extreme against. Medicine, Cairo Uni., But the use of this modality in Anisometropia due to myopia Giza , Egypt. is an ideal indications...uncontrolled open angle Kaser EI-Aini School of glaucoma: IOP 26 mmHg or more despite maximal tolerated Medicine, Cairo Uni., Giza , medical therapy were treatd...of blood inhibited optical Medicine, Cairo Uni., Giza , breakdown and required a pasuse before completion Egypt. iridotomy, or other sitting is

MetaUniDec: High-Throughput Deconvolution of Native Mass Spectra

NASA Astrophysics Data System (ADS)

Reid, Deseree J.; Diesing, Jessica M.; Miller, Matthew A.; Perry, Scott M.; Wales, Jessica A.; Montfort, William R.; Marty, Michael T.

2018-04-01

The expansion of native mass spectrometry (MS) methods for both academic and industrial applications has created a substantial need for analysis of large native MS datasets. Existing software tools are poorly suited for high-throughput deconvolution of native electrospray mass spectra from intact proteins and protein complexes. The UniDec Bayesian deconvolution algorithm is uniquely well suited for high-throughput analysis due to its speed and robustness but was previously tailored towards individual spectra. Here, we optimized UniDec for deconvolution, analysis, and visualization of large data sets. This new module, MetaUniDec, centers around a hierarchical data format 5 (HDF5) format for storing datasets that significantly improves speed, portability, and file size. It also includes code optimizations to improve speed and a new graphical user interface for visualization, interaction, and analysis of data. To demonstrate the utility of MetaUniDec, we applied the software to analyze automated collision voltage ramps with a small bacterial heme protein and large lipoprotein nanodiscs. Upon increasing collisional activation, bacterial heme-nitric oxide/oxygen binding (H-NOX) protein shows a discrete loss of bound heme, and nanodiscs show a continuous loss of lipids and charge. By using MetaUniDec to track changes in peak area or mass as a function of collision voltage, we explore the energetic profile of collisional activation in an ultra-high mass range Orbitrap mass spectrometer. [Figure not available: see fulltext.

Open Online Courses in Public Health: experience from Peoples-uni.

PubMed

Heller, Richard F; Zurynski, Robert; Barrett, Alan; Oaiya, Omo; Madhok, Rajan

2017-01-01

Open Online Courses (OOCs) are offered by Peoples-uni at http://ooc.peoples-uni.org to complement the courses run on a separate site for academic credit at http://courses.peoples-uni.org. They provide a wide range of online learning resources beyond those usually found in credit bearing Public Health courses. They are self-paced, and students can enrol themselves at any time and utilise Open Educational Resources free of copyright restrictions.  In the two years that courses have been running, 1174 students from 100 countries have registered and among the 1597 enrolments in 14 courses, 15% gained a certificate of completion. Easily accessible and appealing to a wide geographical and professional audience, OOCs have the potential to play a part in establishing global Public Health capacity building programmes.

Open Online Courses in Public Health: experience from Peoples-uni

PubMed Central

Heller, Richard F.; Zurynski, Robert; Barrett, Alan; Oaiya, Omo; Madhok, Rajan

2017-01-01

Open Online Courses (OOCs) are offered by Peoples-uni at http://ooc.peoples-uni.org to complement the courses run on a separate site for academic credit at http://courses.peoples-uni.org. They provide a wide range of online learning resources beyond those usually found in credit bearing Public Health courses. They are self-paced, and students can enrol themselves at any time and utilise Open Educational Resources free of copyright restrictions.  In the two years that courses have been running, 1174 students from 100 countries have registered and among the 1597 enrolments in 14 courses, 15% gained a certificate of completion. Easily accessible and appealing to a wide geographical and professional audience, OOCs have the potential to play a part in establishing global Public Health capacity building programmes. PMID:28491283

Effect of Pd substitution for Ni on magnetism in UNiAl

NASA Astrophysics Data System (ADS)

Dremov, R. V.; Andreev, A. V.; Šebek, J.; Mushnikov, N. V.; Goto, T.; Havela, L.; Sechovský, V.; Shiokawa, Y.; Homma, Y.

1999-01-01

Itinerant 5f-electron antiferromagnet UNiAl ( TN=19.3 K) undergoes a metamagnetic transition in fields ( Bc≈11 T) applied along the c-axis of the hexagonal ZrNiAl-type structure. The same structure is preserved in the UNi 1- xPd xAl solid solutions x⩽0.4 characterized by isotropic lattice expansion with increasing x. The gradual increase of Bc and TN due to the Pd doping can be tentatively attributed to enhancement of antiferromagnetic exchange interactions.

Improvement in Renal Hemodynamics following Combined Angiotensin II Infusion and AT1R Blockade in Aged Female Sheep following Fetal Unilateral Nephrectomy

PubMed Central

Singh, Reetu R.; Lankadeva, Yugeesh R.

2013-01-01

Renin-angiotensin system (RAS) is a powerful modulator of renal hemodynamic and fluid homeostasis. Up-regulation in components of intra-renal RAS occurs with ageing. Recently we reported that 2 year old uninephrectomised (uni-x) female sheep have low renin hypertension and reduced renal function. By 5 years of age, these uni-x sheep had augmented decrease in renal blood flow (RBF) compared to sham. We hypothesised that this decrease in RBF in 5 year old uni-x sheep was due to an up-regulation in components of the intra-renal RAS. In this study, renal responses to angiotensin II (AngII) infusion and AngII type 1 receptor (AT1R) blockade were examined in the same 5 year old sheep. We also administered AngII in the presence of losartan to increase AngII bioavailability to the AT2R in order to understand AT2R contribution to renal function in this model. Uni-x animals had significantly lower renal cortical content of renin, AngII (∼40%) and Ang 1–7 (∼60%) and reduced cortical expression of AT1R gene than sham animals. In response to both AngII infusion and AT1R blockade via losartan, renal hemodynamic responses and tubular sodium excretion were significantly attenuated in uni-x animals compared to sham. However, AngII infusion in the presence of losartan caused ∼33% increase in RBF in uni-x sheep compared to ∼14% in sham (P<0.05). This was associated with a significant decrease in renal vascular resistance in the uni-x animals (22% vs 15%, P<0.05) without any changes in systemic blood pressure. The present study shows that majority of the intra-renal RAS components are suppressed in this model of low renin hypertension. However, increasing the availability of AngII to AT2R by AT1R blockade improved renal blood flow in uni-x sheep. This suggests that manipulation of the AT2R maybe a potential therapeutic target for treatment of renal dysfunction associated with a congenital nephron deficit. PMID:23840884

Infrastructure for the life sciences: design and implementation of the UniProt website.

PubMed

Jain, Eric; Bairoch, Amos; Duvaud, Severine; Phan, Isabelle; Redaschi, Nicole; Suzek, Baris E; Martin, Maria J; McGarvey, Peter; Gasteiger, Elisabeth

2009-05-08

The UniProt consortium was formed in 2002 by groups from the Swiss Institute of Bioinformatics (SIB), the European Bioinformatics Institute (EBI) and the Protein Information Resource (PIR) at Georgetown University, and soon afterwards the website http://www.uniprot.org was set up as a central entry point to UniProt resources. Requests to this address were redirected to one of the three organisations' websites. While these sites shared a set of static pages with general information about UniProt, their pages for searching and viewing data were different. To provide users with a consistent view and to cut the cost of maintaining three separate sites, the consortium decided to develop a common website for UniProt. Following several years of intense development and a year of public beta testing, the http://www.uniprot.org domain was switched to the newly developed site described in this paper in July 2008. The UniProt consortium is the main provider of protein sequence and annotation data for much of the life sciences community. The http://www.uniprot.org website is the primary access point to this data and to documentation and basic tools for the data. These tools include full text and field-based text search, similarity search, multiple sequence alignment, batch retrieval and database identifier mapping. This paper discusses the design and implementation of the new website, which was released in July 2008, and shows how it improves data access for users with different levels of experience, as well as to machines for programmatic access.http://www.uniprot.org/ is open for both academic and commercial use. The site was built with open source tools and libraries. Feedback is very welcome and should be sent to help@uniprot.org. The new UniProt website makes accessing and understanding UniProt easier than ever. The two main lessons learned are that getting the basics right for such a data provider website has huge benefits, but is not trivial and easy to underestimate, and that there is no substitute for using empirical data throughout the development process to decide on what is and what is not working for your users.

BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS.

PubMed

Hoff, Katharina J; Lange, Simone; Lomsadze, Alexandre; Borodovsky, Mark; Stanke, Mario

2016-03-01

Gene finding in eukaryotic genomes is notoriously difficult to automate. The task is to design a work flow with a minimal set of tools that would reach state-of-the-art performance across a wide range of species. GeneMark-ET is a gene prediction tool that incorporates RNA-Seq data into unsupervised training and subsequently generates ab initio gene predictions. AUGUSTUS is a gene finder that usually requires supervised training and uses information from RNA-Seq reads in the prediction step. Complementary strengths of GeneMark-ET and AUGUSTUS provided motivation for designing a new combined tool for automatic gene prediction. We present BRAKER1, a pipeline for unsupervised RNA-Seq-based genome annotation that combines the advantages of GeneMark-ET and AUGUSTUS. As input, BRAKER1 requires a genome assembly file and a file in bam-format with spliced alignments of RNA-Seq reads to the genome. First, GeneMark-ET performs iterative training and generates initial gene structures. Second, AUGUSTUS uses predicted genes for training and then integrates RNA-Seq read information into final gene predictions. In our experiments, we observed that BRAKER1 was more accurate than MAKER2 when it is using RNA-Seq as sole source for training and prediction. BRAKER1 does not require pre-trained parameters or a separate expert-prepared training step. BRAKER1 is available for download at http://bioinf.uni-greifswald.de/bioinf/braker/ and http://exon.gatech.edu/GeneMark/ katharina.hoff@uni-greifswald.de or borodovsky@gatech.edu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Simultaneous gene finding in multiple genomes.

PubMed

König, Stefanie; Romoth, Lars W; Gerischer, Lizzy; Stanke, Mario

2016-11-15

As the tree of life is populated with sequenced genomes ever more densely, the new challenge is the accurate and consistent annotation of entire clades of genomes. We address this problem with a new approach to comparative gene finding that takes a multiple genome alignment of closely related species and simultaneously predicts the location and structure of protein-coding genes in all input genomes, thereby exploiting negative selection and sequence conservation. The model prefers potential gene structures in the different genomes that are in agreement with each other, or-if not-where the exon gains and losses are plausible given the species tree. We formulate the multi-species gene finding problem as a binary labeling problem on a graph. The resulting optimization problem is NP hard, but can be efficiently approximated using a subgradient-based dual decomposition approach. The proposed method was tested on whole-genome alignments of 12 vertebrate and 12 Drosophila species. The accuracy was evaluated for human, mouse and Drosophila melanogaster and compared to competing methods. Results suggest that our method is well-suited for annotation of (a large number of) genomes of closely related species within a clade, in particular, when RNA-Seq data are available for many of the genomes. The transfer of existing annotations from one genome to another via the genome alignment is more accurate than previous approaches that are based on protein-spliced alignments, when the genomes are at close to medium distances. The method is implemented in C ++ as part of Augustus and available open source at http://bioinf.uni-greifswald.de/augustus/ CONTACT: stefaniekoenig@ymail.com or mario.stanke@uni-greifswald.deSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Predictors of persistent pain after total knee arthroplasty: a systematic review and meta-analysis.

PubMed

Lewis, G N; Rice, D A; McNair, P J; Kluger, M

2015-04-01

Several studies have identified clinical, psychosocial, patient characteristic, and perioperative variables that are associated with persistent postsurgical pain; however, the relative effect of these variables has yet to be quantified. The aim of the study was to provide a systematic review and meta-analysis of predictor variables associated with persistent pain after total knee arthroplasty (TKA). Included studies were required to measure predictor variables prior to or at the time of surgery, include a pain outcome measure at least 3 months post-TKA, and include a statistical analysis of the effect of the predictor variable(s) on the outcome measure. Counts were undertaken of the number of times each predictor was analysed and the number of times it was found to have a significant relationship with persistent pain. Separate meta-analyses were performed to determine the effect size of each predictor on persistent pain. Outcomes from studies implementing uni- and multivariable statistical models were analysed separately. Thirty-two studies involving almost 30 000 patients were included in the review. Preoperative pain was the predictor that most commonly demonstrated a significant relationship with persistent pain across uni- and multivariable analyses. In the meta-analyses of data from univariate models, the largest effect sizes were found for: other pain sites, catastrophizing, and depression. For data from multivariate models, significant effects were evident for: catastrophizing, preoperative pain, mental health, and comorbidities. Catastrophizing, mental health, preoperative knee pain, and pain at other sites are the strongest independent predictors of persistent pain after TKA. © The Author 2014. Published by Oxford University Press on behalf of the British Journal of Anaesthesia. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

PERMANOVA-S: association test for microbial community composition that accommodates confounders and multiple distances.

PubMed

Tang, Zheng-Zheng; Chen, Guanhua; Alekseyenko, Alexander V

2016-09-01

Recent advances in sequencing technology have made it possible to obtain high-throughput data on the composition of microbial communities and to study the effects of dysbiosis on the human host. Analysis of pairwise intersample distances quantifies the association between the microbiome diversity and covariates of interest (e.g. environmental factors, clinical outcomes, treatment groups). In the design of these analyses, multiple choices for distance metrics are available. Most distance-based methods, however, use a single distance and are underpowered if the distance is poorly chosen. In addition, distance-based tests cannot flexibly handle confounding variables, which can result in excessive false-positive findings. We derive presence-weighted UniFrac to complement the existing UniFrac distances for more powerful detection of the variation in species richness. We develop PERMANOVA-S, a new distance-based method that tests the association of microbiome composition with any covariates of interest. PERMANOVA-S improves the commonly-used Permutation Multivariate Analysis of Variance (PERMANOVA) test by allowing flexible confounder adjustments and ensembling multiple distances. We conducted extensive simulation studies to evaluate the performance of different distances under various patterns of association. Our simulation studies demonstrate that the power of the test relies on how well the selected distance captures the nature of the association. The PERMANOVA-S unified test combines multiple distances and achieves good power regardless of the patterns of the underlying association. We demonstrate the usefulness of our approach by reanalyzing several real microbiome datasets. miProfile software is freely available at https://medschool.vanderbilt.edu/tang-lab/software/miProfile z.tang@vanderbilt.edu or g.chen@vanderbilt.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

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

PubMed

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

2016-01-01

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

Linking metabolic network features to phenotypes using sparse group lasso.

PubMed

Samal, Satya Swarup; Radulescu, Ovidiu; Weber, Andreas; Fröhlich, Holger

2017-11-01

Integration of metabolic networks with '-omics' data has been a subject of recent research in order to better understand the behaviour of such networks with respect to differences between biological and clinical phenotypes. Under the conditions of steady state of the reaction network and the non-negativity of fluxes, metabolic networks can be algebraically decomposed into a set of sub-pathways often referred to as extreme currents (ECs). Our objective is to find the statistical association of such sub-pathways with given clinical outcomes, resulting in a particular instance of a self-contained gene set analysis method. In this direction, we propose a method based on sparse group lasso (SGL) to identify phenotype associated ECs based on gene expression data. SGL selects a sparse set of feature groups and also introduces sparsity within each group. Features in our model are clusters of ECs, and feature groups are defined based on correlations among these features. We apply our method to metabolic networks from KEGG database and study the association of network features to prostate cancer (where the outcome is tumor and normal, respectively) as well as glioblastoma multiforme (where the outcome is survival time). In addition, simulations show the superior performance of our method compared to global test, which is an existing self-contained gene set analysis method. R code (compatible with version 3.2.5) is available from http://www.abi.bit.uni-bonn.de/index.php?id=17. samal@combine.rwth-aachen.de or frohlich@bit.uni-bonn.de. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Role of Fetuin-A in Breast Tumor Cell Growth

DTIC Science & Technology

2009-03-01

UniRef100_Q0IIK2 289 390 1.4 Transferrin UniRef100_Q9GLY6 18 24 1.3 Inter- alpha -trypsin inhibitor heavy chain2 UniRef100_Q3SZ57 25 33 1.3 Alpha - fetoprotein ...the first time that cell attachment is mediated only by fetuin-A and not its major contaminant which is alpha -2-macroglobulin. We also show both...fetuin-A and alpha -2-macroglobulin can activate PI3 kinase/Akt. 15. SUBJECT TERMS Mammary tumors;fetuin-A;Polyoma middle T antigen; genotyping

Field comparison of OraQuick® ADVANCE Rapid HIV-1/2 antibody test and two blood-based rapid HIV antibody tests in Zambia

PubMed Central

2012-01-01

Background Zambia’s national HIV testing algorithm specifies use of two rapid blood based antibody assays, Determine®HIV-1/2 (Inverness Medical) and if positive then Uni-GoldTM Recombigen HIV-1/2 (Trinity Biotech). Little is known about the performance of oral fluid based HIV testing in Zambia. The aims of this study are two-fold: 1) to compare the diagnostic accuracy (sensitivity and specificity) under field conditions of the OraQuick® ADVANCE® Rapid HIV-1/2 (OraSure Technologies, Inc.) to two blood-based rapid antibody tests currently in use in the Zambia National Algorithm, and 2) to perform a cost analysis of large-scale field testing employing the OraQuick®. Methods This was a operational retrospective research of HIV testing and questionnaire data collected in 2010 as part of the ZAMSTAR (Zambia South Africa TB and AIDS reduction) study. Randomly sampled individuals in twelve communities were tested consecutively with OraQuick® test using oral fluid versus two blood-based rapid HIV tests, Determine® and Uni-GoldTM. A cost analysis of four algorithms from health systems perspective were performed: 1) Determine® and if positive, then Uni-GoldTM (Determine®/Uni-GoldTM); based on current algorithm, 2) Determine® and if positive, then OraQuick® (Determine®/OraQuick®), 3) OraQuick® and if positive, then Determine® (OraQuick®/Determine®), 4) OraQuick® and if positive, then Uni-GoldTM (OraQuick®/Uni-GoldTM). This information was then used to construct a model using a hypothetical population of 5,000 persons with varying prevalence of HIV infection from 1–30%. Results 4,458 participants received both a Determine® and OraQuick® test. The sensitivity and specificity of the OraQuick® test were 98.7 (95%CI, 97.5–99.4) and 99.8 (95%CI, 99.6–99.9), respectively when compared to HIV positive serostatus. The average unit costs per algorithm were US$3.76, US$4.03, US$7.35, and US$7.67 for Determine®/Uni-GoldTM, Determine®/OraQuick®, OraQuick®/Determine®, and OraQuick®/Uni-GoldTM, respectively, for an HIV prevalence of 15%. Conclusions An alternative HIV testing algorithm could include OraQuick® test which had a high sensitivity and specificity. The current Determine®/Uni-GoldTM testing algorithm is the least expensive when compared to Determine®/OraQuick®, OraQuick®/Determine®, and OraQuick®/Uni-GoldTM in the Zambian setting. From our field experience, oral fluid based testing offers many advantages over blood-based testing, especially with self testing on the horizon. PMID:22871032

Uni-directional optical pulses, temporal propagation, and spatial and temporal dispersion

NASA Astrophysics Data System (ADS)

Kinsler, P.

2018-02-01

I derive a temporally propagated uni-directional optical pulse equation valid in the few cycle limit. Temporal propagation is advantageous because it naturally preserves causality, unlike the competing spatially propagated models. The exact coupled bi-directional equations that this approach generates can be efficiently approximated down to a uni-directional form in cases where an optical pulse changes little over one optical cycle. They also permit a direct term-to-term comparison of the exact bi-directional theory with its corresponding approximate uni-directional theory. Notably, temporal propagation handles dispersion in a different way, and this difference serves to highlight existing approximations inherent in spatially propagated treatments of dispersion. Accordingly, I emphasise the need for future work in clarifying the limitations of the dispersion conversion required by these types of approaches; since the only alternative in the few cycle limit may be to resort to the much more computationally intensive full Maxwell equation solvers.

PWR steam generator chemical cleaning, Phase I. Final report

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

Rothstein, S.

1978-07-01

United Nuclear Industries (UNI) entered into a subcontract with Consolidated Edison Company of New York (Con Ed) on August 8, 1977, for the purpose of developing methods to chemically clean the secondary side tube to tube support crevices of the steam generators of Indian Point Nos. 1 and 2 PWR plants. This document represents the first reporting on activities performed for Phase I of this effort. Specifically, this report contains the results of a literature search performed by UNI for the purpose of determining state-of-the-art chemical solvents and methods for decontaminating nuclear reactor steam generators. The results of the searchmore » sought to accomplish two objectives: (1) identify solvents beyond those proposed at present by UNI and Con Ed for the test program, and (2) confirm the appropriateness of solvents and methods of decontamination currently in use by UNI.« less

Can Inferred Provenance and Its Visualisation Be Used to Detect Erroneous Annotation? A Case Study Using UniProtKB

PubMed Central

Bell, Michael J.; Collison, Matthew; Lord, Phillip

2013-01-01

A constant influx of new data poses a challenge in keeping the annotation in biological databases current. Most biological databases contain significant quantities of textual annotation, which often contains the richest source of knowledge. Many databases reuse existing knowledge; during the curation process annotations are often propagated between entries. However, this is often not made explicit. Therefore, it can be hard, potentially impossible, for a reader to identify where an annotation originated from. Within this work we attempt to identify annotation provenance and track its subsequent propagation. Specifically, we exploit annotation reuse within the UniProt Knowledgebase (UniProtKB), at the level of individual sentences. We describe a visualisation approach for the provenance and propagation of sentences in UniProtKB which enables a large-scale statistical analysis. Initially levels of sentence reuse within UniProtKB were analysed, showing that reuse is heavily prevalent, which enables the tracking of provenance and propagation. By analysing sentences throughout UniProtKB, a number of interesting propagation patterns were identified, covering over sentences. Over sentences remain in the database after they have been removed from the entries where they originally occurred. Analysing a subset of these sentences suggest that approximately are erroneous, whilst appear to be inconsistent. These results suggest that being able to visualise sentence propagation and provenance can aid in the determination of the accuracy and quality of textual annotation. Source code and supplementary data are available from the authors website at http://homepages.cs.ncl.ac.uk/m.j.bell1/sentence_analysis/. PMID:24143170

Out-of-autoclave manufacturing of a stiffened thermoplastic carbon fibre PEEK panel

NASA Astrophysics Data System (ADS)

Flanagan, M.; Goggins, J.; Doyle, A.; Weafer, B.; Ward, M.; Bizeul, M.; Canavan, R.; O'Bradaigh, C.; Doyle, K.; Harrison, N.

2017-10-01

Out-of-Autoclave manufacturing methods, specifically Automated Tape Placement (ATP) and induction welding, used in the fabrication of a stiffened thermoplastic demonstrator panel, are presented in this study. The demonstrator panel consists of two stiffeners induction welded to a flat skin, to form a typical load bearing aerospace sub-component. The skin of the panel is manufactured from uni-directional Carbon Fibre (CF) Polyetheretherkeytone (PEEK) using laser assisted Automated Tape Placement (ATP) and the stiffeners are press formed from woven CF-PEEK. The stiffeners are fusion bonded to the skin using a continuous induction welding process. A susceptor material is used at the interface to ensure the required heating is concentrated at the weldline. Microscopy was used to examine the manufactured coupons for defects. Destructive testing was carried out to evaluate the strength of the overall assembly. The work shows that assemblies manufactured using continuous induction welding and ATP are suitable for load bearing aerospace applications.

Kalium: a database of potassium channel toxins from scorpion venom.

PubMed

Kuzmenkov, Alexey I; Krylov, Nikolay A; Chugunov, Anton O; Grishin, Eugene V; Vassilevski, Alexander A

2016-01-01

Kalium (http://kaliumdb.org/) is a manually curated database that accumulates data on potassium channel toxins purified from scorpion venom (KTx). This database is an open-access resource, and provides easy access to pages of other databases of interest, such as UniProt, PDB, NCBI Taxonomy Browser, and PubMed. General achievements of Kalium are a strict and easy regulation of KTx classification based on the unified nomenclature supported by researchers in the field, removal of peptides with partial sequence and entries supported by transcriptomic information only, classification of β-family toxins, and addition of a novel λ-family. Molecules presented in the database can be processed by the Clustal Omega server using a one-click option. Molecular masses of mature peptides are calculated and available activity data are compiled for all KTx. We believe that Kalium is not only of high interest to professional toxinologists, but also of general utility to the scientific community.Database URL:http://kaliumdb.org/. © The Author(s) 2016. Published by Oxford University Press.

Sputnik: ad hoc distributed computation.

PubMed

Völkel, Gunnar; Lausser, Ludwig; Schmid, Florian; Kraus, Johann M; Kestler, Hans A

2015-04-15

In bioinformatic applications, computationally demanding algorithms are often parallelized to speed up computation. Nevertheless, setting up computational environments for distributed computation is often tedious. Aim of this project were the lightweight ad hoc set up and fault-tolerant computation requiring only a Java runtime, no administrator rights, while utilizing all CPU cores most effectively. The Sputnik framework provides ad hoc distributed computation on the Java Virtual Machine which uses all supplied CPU cores fully. It provides a graphical user interface for deployment setup and a web user interface displaying the current status of current computation jobs. Neither a permanent setup nor administrator privileges are required. We demonstrate the utility of our approach on feature selection of microarray data. The Sputnik framework is available on Github http://github.com/sysbio-bioinf/sputnik under the Eclipse Public License. hkestler@fli-leibniz.de or hans.kestler@uni-ulm.de Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

VisualCNA: a GUI for interactive constraint network analysis and protein engineering for improving thermostability.

PubMed

Rathi, Prakash Chandra; Mulnaes, Daniel; Gohlke, Holger

2015-07-15

Constraint network analysis (CNA) is a graph theory-based rigidity analysis approach for linking a biomolecule's structure, flexibility, (thermo)stability and function. Results from CNA are highly information-rich and require intuitive, synchronized and interactive visualization for a comprehensive analysis. We developed VisualCNA, an easy-to-use PyMOL plug-in that allows setup of CNA runs and analysis of CNA results linking plots with molecular graphics representations. From a practical viewpoint, the most striking feature of VisualCNA is that it facilitates interactive protein engineering aimed at improving thermostability. VisualCNA and its dependencies (CNA and FIRST software) are available free of charge under GPL and academic licenses, respectively. VisualCNA and CNA are available at http://cpclab.uni-duesseldorf.de/software; FIRST is available at http://flexweb.asu.edu. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

DOGMA: domain-based transcriptome and proteome quality assessment.

PubMed

Dohmen, Elias; Kremer, Lukas P M; Bornberg-Bauer, Erich; Kemena, Carsten

2016-09-01

Genome studies have become cheaper and easier than ever before, due to the decreased costs of high-throughput sequencing and the free availability of analysis software. However, the quality of genome or transcriptome assemblies can vary a lot. Therefore, quality assessment of assemblies and annotations are crucial aspects of genome analysis pipelines. We developed DOGMA, a program for fast and easy quality assessment of transcriptome and proteome data based on conserved protein domains. DOGMA measures the completeness of a given transcriptome or proteome and provides information about domain content for further analysis. DOGMA provides a very fast way to do quality assessment within seconds. DOGMA is implemented in Python and published under GNU GPL v.3 license. The source code is available on https://ebbgit.uni-muenster.de/domainWorld/DOGMA/ CONTACTS: e.dohmen@wwu.de or c.kemena@wwu.de Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Mapping proteins to disease terminologies: from UniProt to MeSH

PubMed Central

Mottaz, Anaïs; Yip, Yum L; Ruch, Patrick; Veuthey, Anne-Lise

2008-01-01

Background Although the UniProt KnowledgeBase is not a medical-oriented database, it contains information on more than 2,000 human proteins involved in pathologies. However, these annotations are not standardized, which impairs the interoperability between biological and clinical resources. In order to make these data easily accessible to clinical researchers, we have developed a procedure to link diseases described in the UniProtKB/Swiss-Prot entries to the MeSH disease terminology. Results We mapped disease names extracted either from the UniProtKB/Swiss-Prot entry comment lines or from the corresponding OMIM entry to the MeSH. Different methods were assessed on a benchmark set of 200 disease names manually mapped to MeSH terms. The performance of the retained procedure in term of precision and recall was 86% and 64% respectively. Using the same procedure, more than 3,000 disease names in Swiss-Prot were mapped to MeSH with comparable efficiency. Conclusions This study is a first attempt to link proteins in UniProtKB to the medical resources. The indexing we provided will help clinicians and researchers navigate from diseases to genes and from genes to diseases in an efficient way. The mapping is available at: . PMID:18460185

Switching CAR T cells on and off: a novel modular platform for retargeting of T cells to AML blasts

PubMed Central

Cartellieri, M; Feldmann, A; Koristka, S; Arndt, C; Loff, S; Ehninger, A; von Bonin, M; Bejestani, E P; Ehninger, G; Bachmann, M P

2016-01-01

The adoptive transfer of CD19-specific chimeric antigen receptor engineered T cells (CAR T cells) resulted in encouraging clinical trials in indolent B-cell malignancies. However, they also show the limitations of this fascinating technology: CAR T cells can lead to even life-threatening off-tumor, on-target side effects if CAR T cells crossreact with healthy tissues. Here, we describe a novel modular universal CAR platform technology termed UniCAR that reduces the risk of on-target side effects by a rapid and reversible control of CAR T-cell reactivity. The UniCAR system consists of two components: (1) a CAR for an inert manipulation of T cells and (2) specific targeting modules (TMs) for redirecting UniCAR T cells in an individualized time- and target-dependent manner. UniCAR T cells can be armed against different tumor targets simply by replacement of the respective TM for (1) targeting more than one antigen simultaneously or subsequently to enhance efficacy and (2) reducing the risk for development of antigen-loss tumor variants under treatment. Here we provide ‘proof of concept' for retargeting of UniCAR T cells to CD33- and/or CD123-positive acute myeloid leukemia blasts in vitro and in vivo. PMID:27518241

76 FR 21887 - Combined Notice of Filings #1

Federal Register 2010, 2011, 2012, 2013, 2014

2011-04-19

.... Applicants: UniSource Energy Development Company, UNS Electric, Inc. Description: Application pursuant to... re UniSource Energy Development Company et al. Filed Date: 04/07/2011. Accession Number: 20110411... DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings 1 Take notice...

76 FR 41785 - Combined Notice of Filings #1

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-15

.... Applicants: UniSource Energy Development Company. Description: Notification of Cancellation of Tolling Agreement of UniSource Energy Development. Filed Date: 07/01/2011. Accession Number: 20110701-5234. Comment... DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings 1 Take notice...

Enhanced Motor Imagery-Based BCI Performance via Tactile Stimulation on Unilateral Hand.

PubMed

Shu, Xiaokang; Yao, Lin; Sheng, Xinjun; Zhang, Dingguo; Zhu, Xiangyang

2017-01-01

Brain-computer interface (BCI) has attracted great interests for its effectiveness in assisting disabled people. However, due to the poor BCI performance, this technique is still far from daily-life applications. One of critical issues confronting BCI research is how to enhance BCI performance. This study aimed at improving the motor imagery (MI) based BCI accuracy by integrating MI tasks with unilateral tactile stimulation (Uni-TS). The effects were tested on both healthy subjects and stroke patients in a controlled study. Twenty-two healthy subjects and four stroke patients were recruited and randomly divided into a control-group and an enhanced-group. In the control-group, subjects performed two blocks of conventional MI tasks (left hand vs. right hand), with 80 trials in each block. In the enhanced-group, subjects also performed two blocks of MI tasks, but constant tactile stimulation was applied on the non-dominant/paretic hand during MI tasks in the second block. We found the Uni-TS significantly enhanced the contralateral cortical activations during MI of the stimulated hand, whereas it had no influence on activation patterns during MI of the non-stimulated hand. The two-class BCI decoding accuracy was significantly increased from 72.5% (MI without Uni-TS) to 84.7% (MI with Uni-TS) in the enhanced-group ( p < 0.001, paired t -test). Moreover, stroke patients in the enhanced-group achieved an accuracy >80% during MI with Uni-TS. This novel approach complements the conventional methods for BCI enhancement without increasing source information or complexity of signal processing. This enhancement via Uni-TS may facilitate clinical applications of MI-BCI.

A Multi-institutional Comparison of Adrenal Venous Sampling in Patients with Primary Aldosteronism: Caution Advised if Successful Bilateral Adrenal Vein Sampling is Not Achieved.

PubMed

Wang, Tracy S; Kline, Greg; Yen, Tina W; Yin, Ziyan; Liu, Ying; Rilling, William; So, Benny; Findling, James W; Evans, Douglas B; Pasieka, Janice L

2018-02-01

In patients with primary aldosteronism (PA), adrenal venous sampling (AVS) is recommended to differentiate between unilateral (UNI) or bilateral (BIL) adrenal disease. A recent study suggested that lateralization could be predicted, based on the ratio of aldosterone/cortisol levels (A/C) between the left adrenal vein (LAV) and inferior vena cava (IVC), with a 100% positive predictive value (PPV). This study aimed to validate those findings utilizing a larger, multi-institutional cohort. A retrospective review was performed of patients with PA who underwent AVS from 2 tertiary-care institutions. Laterality was predicted by an A/C ratio of >3:1 between the dominant and non-dominant adrenal. AVS results were compared to LAV/IVC ratios utilizing the published criteria (Lt ≥ 5.5; Rt ≤ 0.5). Of 222 patients, 124 (57%) had UNI and 98 (43%) had BIL disease based on AVS. AVS and LAV/IVC findings were concordant for laterality in 141 (64%) patients (69 UNI, 72 BIL). Using only the LAV/IVC ratio, 54 (24%) patients with UNI disease on AVS who underwent successful surgery would have been assumed to have BAH unless AVS was repeated, and 24 (11%) patients with BIL disease on AVS may have been incorrectly offered surgery (PPV 70%). Based on median LAV/IVC ratios (left 5.26; right 0.31; BIL 2.84), no LAV/IVC ratio accurately predicted laterality. This multi-institutional study of patients with both UNI and BIL PA failed to validate the previously reported PPV of LAV/IVC ratio for lateralization. Caution should be used in interpreting incomplete AVS data to differentiate between UNI versus BIL disease and strong consideration given to repeat AVS prior to adrenalectomy.

75 FR 20990 - Combined Notice of Filings # 1

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-22

...; ER98-1150-012. Applicants: Tucson Electric Power Company, UniSource Energy Development Company, UNS..., UNS Electric, Inc., UniSource Energy Development Company. Filed Date: 04/14/2010. Accession Number... DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings 1 April 15...

78 FR 6816 - Combined Notice of Filings #2

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-31

...: UniSource Energy Development Company. Description: UniSource Energy Development Company submits tariff... DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings 2 Take notice that the Commission received the following electric rate filings: Docket Numbers: ER10-2460-004; ER10...

Variable mode bi-directional and uni-directional computer communication system

DOEpatents

Cornett, Frank N.; Jenkins, Philip N.; Bowman, Terrance L.; Placek, Joseph M.; Thorson, Gregory M.

2004-12-14

A variable communication systems comprising a plurality of transceivers and a control circuit connected to the transceivers to configure the transceivers to operate in a bi-directional mode and a uni-directional mode at different times using different transfer methods to transfer data.

The ATLAS diboson resonance in non-supersymmetric SO(10)

DOE PAGES

Evans, Jason L.; Nagata, Natsumi; Olive, Keith A.; ...

2016-02-18

SO(10) grand uni cation accommodates intermediate gauge symmetries with which gauge coupling uni cation can be realized without supersymmetry. In this paper, we discuss the possibility that a new massive gauge boson associated with an intermediate gauge symmetry explains the excess observed in the diboson resonance search recently reported by the ATLAS experiment. The model we find has two intermediate symmetries, SU(4) C Ⓧ SU(2) L Ⓧ SU(2) R and SU(3) C Ⓧ SU(2) L Ⓧ SU(2)R Ⓧ U(1) B-L, where the latter gauge group is broken at the TeV scale. This model achieves gauge coupling uni cation with amore » uni cation scale su fficiently high to avoid proton decay. In addition, this model provides a good dark matter candidates, whose stability is guaranteed by a Z 2 symmetry present after the spontaneous breaking of the intermediate gauge symmetries. In addition, we discuss prospects for testing these models in the forthcoming LHC experiments and dark matter detection experiments.« less

Perceptions of students in different phases of medical education of the educational environment: Universiti Sultan Zainal Abidin

PubMed Central

Rahman, Nor Iza A; Aziz, Aniza Abd; Zulkifli, Zainal; Haj, Muhammad Arshad; Mohd Nasir, Farah Hanani Binti; Pergalathan, Sharvina; Hamidi, Muhammad Ismail; Ismail, Salwani; Simbak, Nordin Bin; Haque, Mainul

2015-01-01

Background The Dundee Ready Education Environment Measure (DREEM) was planned and designed to quantify the educational environment precisely for medical schools and health-related professional schools. DREEM is now considered a valid and reliable tool, which is globally accepted for measuring the medical educational environment. The educational environment encountered by students has an impact on satisfaction with the course of study, perceived sense of well-being, aspirations, and academic achievement. In addition to being measurable, the educational environment can also be changed, thus enhancing the quality of medical education and the environment, and the medical education process. The objective of this study was to assess the educational environment of the Universiti Sultan Zainal Abidin (UniSZA) undergraduate medical program from the students’ perspective. The study expected to explore UniSZA medical students’ overall perceptions, perceptions of learning, teachers, atmosphere, academic self-perception, and social self-perception using the DREEM questionnaire. Methods A cross-sectional survey was conducted to study the perceptions of the students toward the educational environment of UniSZA as a new medical school, using the DREEM questionnaire. All medical students of UniSZA from Years I–V enrolled in the Bachelor of Medicine and Bachelor of Surgery programs were the target population (n=270). Therefore, the universal sampling technique was used. The data were analyzed using the SPSS 20 software. This study obtained ethical clearance from the Faculty of Medicine and Health Sciences, UniSZA. Results A total of 195 out of 270 students responded. Respondents included 31% males and 69% females. The overall DREEM scores were significantly higher (P<0.001) for females than males. Conclusion The medical students at UniSZA showed a positive perception of their educational environment. The new medical faculty, established for only a few years, has achieved an above-average, conducive educational environment for students. Most of the students showed a positive perception for the entire five domains tested in the DREEM survey. Females were consistently satisfied with UniSZA’s educational environment, and self-perception was high, as compared to male undergraduates. PMID:25848333

Hierarchical Storage Management at the NASA Center for Computational Sciences: From UniTree to SAM-QFS

NASA Technical Reports Server (NTRS)

Salmon, Ellen; Tarshish, Adina; Palm, Nancy; Patel, Sanjay; Saletta, Marty; Vanderlan, Ed; Rouch, Mike; Burns, Lisa; Duffy, Daniel; Caine, Robert

2004-01-01

This paper presents the data management issues associated with a large center like the NCCS and how these issues are addressed. More specifically, the focus of this paper is on the recent transition from a legacy UniTree (Legato) system to a SAM-QFS (Sun) system. Therefore, this paper will describe the motivations, from both a hardware and software perspective, for migrating from one system to another. Coupled with the migration from UniTree into SAM-QFS, the complete mass storage environment was upgraded to provide high availability, redundancy, and enhanced performance. This paper will describe the resulting solution and lessons learned throughout the migration process.

The Urban Nutrition Initiative: Bringing Academically-Based Community Service to the University of Pennsylvania's Department of Anthropology

ERIC Educational Resources Information Center

Johnston, Francis E.; Harkavy, Ira; Barg, Frances; Gerber, Danny; Rulf, Jennifer

2004-01-01

The Urban Nutrition Initiative (UNI) is a University of Pennsylvania/West Philadelphia schools academically-based community service program that integrates academics, research, and service through service-learning and participatory action research. UNI is based academically within Penn's Department of Anthropology and administratively within the…

HAMAP in 2013, new developments in the protein family classification and annotation system

PubMed Central

Pedruzzi, Ivo; Rivoire, Catherine; Auchincloss, Andrea H.; Coudert, Elisabeth; Keller, Guillaume; de Castro, Edouard; Baratin, Delphine; Cuche, Béatrice A.; Bougueleret, Lydie; Poux, Sylvain; Redaschi, Nicole; Xenarios, Ioannis; Bridge, Alan

2013-01-01

HAMAP (High-quality Automated and Manual Annotation of Proteins—available at http://hamap.expasy.org/) is a system for the classification and annotation of protein sequences. It consists of a collection of manually curated family profiles for protein classification, and associated annotation rules that specify annotations that apply to family members. HAMAP was originally developed to support the manual curation of UniProtKB/Swiss-Prot records describing microbial proteins. Here we describe new developments in HAMAP, including the extension of HAMAP to eukaryotic proteins, the use of HAMAP in the automated annotation of UniProtKB/TrEMBL, providing high-quality annotation for millions of protein sequences, and the future integration of HAMAP into a unified system for UniProtKB annotation, UniRule. HAMAP is continuously updated by expert curators with new family profiles and annotation rules as new protein families are characterized. The collection of HAMAP family classification profiles and annotation rules can be browsed and viewed on the HAMAP website, which also provides an interface to scan user sequences against HAMAP profiles. PMID:23193261

Comparative study of flexural strength test methods on CAD/CAM Y-TZP dental ceramics

PubMed Central

Xu, Yongxiang; Han, Jianmin; Lin, Hong; An, Linan

2015-01-01

Clinically, fractures are the main cause of computer-aided design and computer-aided manufacturing (CAD/CAM) 3 mol%-yttria-stabilized tetragonal zirconia polycrystal (Y-TZP) all-ceramic dental restorations failure because of repetitive occlusal loading. The goal of this work is to study the effect of test methods and specimen’s size on the flexural strength of five ceramic products. Both bi-axial flexure test (BI) and uni-axial flexure tests (UNI), including three-point flexure test (3PF) and four-point flexure test (4PF), are used in this study. For all five products, the flexural strength is as follows: BI > 3PF > 4PF. Furthermore, specimens with smaller size (3PF-s) have higher values than the bigger ones (3PF). The difference between BI and UNI resulted from the edge flaws in ceramic specimens. The relationship between different UNI (including 3PF-s, 3PF and 4PF) can be explained according to Weibull statistical fracture theory. BI is recommended to evaluate the flexural strength of CAD/CAM Y-TZP dental ceramics. PMID:26816646

Comprehensive analysis of the N-glycan biosynthetic pathway using bioinformatics to generate UniCorn: A theoretical N-glycan structure database.

PubMed

Akune, Yukie; Lin, Chi-Hung; Abrahams, Jodie L; Zhang, Jingyu; Packer, Nicolle H; Aoki-Kinoshita, Kiyoko F; Campbell, Matthew P

2016-08-05

Glycan structures attached to proteins are comprised of diverse monosaccharide sequences and linkages that are produced from precursor nucleotide-sugars by a series of glycosyltransferases. Databases of these structures are an essential resource for the interpretation of analytical data and the development of bioinformatics tools. However, with no template to predict what structures are possible the human glycan structure databases are incomplete and rely heavily on the curation of published, experimentally determined, glycan structure data. In this work, a library of 45 human glycosyltransferases was used to generate a theoretical database of N-glycan structures comprised of 15 or less monosaccharide residues. Enzyme specificities were sourced from major online databases including Kyoto Encyclopedia of Genes and Genomes (KEGG) Glycan, Consortium for Functional Glycomics (CFG), Carbohydrate-Active enZymes (CAZy), GlycoGene DataBase (GGDB) and BRENDA. Based on the known activities, more than 1.1 million theoretical structures and 4.7 million synthetic reactions were generated and stored in our database called UniCorn. Furthermore, we analyzed the differences between the predicted glycan structures in UniCorn and those contained in UniCarbKB (www.unicarbkb.org), a database which stores experimentally described glycan structures reported in the literature, and demonstrate that UniCorn can be used to aid in the assignment of ambiguous structures whilst also serving as a discovery database. Copyright © 2016 Elsevier Ltd. All rights reserved.

Multisensory Integration Strategy for Modality-Specific Loss of Inhibition Control in Older Adults.

PubMed

Lee, Ahreum; Ryu, Hokyoung; Kim, Jae-Kwan; Jeong, Eunju

2018-04-11

Older adults are known to have lesser cognitive control capability and greater susceptibility to distraction than young adults. Previous studies have reported age-related problems in selective attention and inhibitory control, yielding mixed results depending on modality and context in which stimuli and tasks were presented. The purpose of the study was to empirically demonstrate a modality-specific loss of inhibitory control in processing audio-visual information with ageing. A group of 30 young adults (mean age = 25.23, Standar Desviation (SD) = 1.86) and 22 older adults (mean age = 55.91, SD = 4.92) performed the audio-visual contour identification task (AV-CIT). We compared performance of visual/auditory identification (Uni-V, Uni-A) with that of visual/auditory identification in the presence of distraction in counterpart modality (Multi-V, Multi-A). The findings showed a modality-specific effect on inhibitory control. Uni-V performance was significantly better than Multi-V, indicating that auditory distraction significantly hampered visual target identification. However, Multi-A performance was significantly enhanced compared to Uni-A, indicating that auditory target performance was significantly enhanced by visual distraction. Additional analysis showed an age-specific effect on enhancement between Uni-A and Multi-A depending on the level of visual inhibition. Together, our findings indicated that the loss of visual inhibitory control was beneficial for the auditory target identification presented in a multimodal context in older adults. A likely multisensory information processing strategy in the older adults was further discussed in relation to aged cognition.

UniBoard: generic hardware for radio astronomy signal processing

NASA Astrophysics Data System (ADS)

Hargreaves, J. E.

2012-09-01

UniBoard is a generic high-performance computing platform for radio astronomy, developed as a Joint Research Activity in the RadioNet FP7 Programme. The hardware comprises eight Altera Stratix IV Field Programmable Gate Arrays (FPGAs) interconnected by a high speed transceiver mesh. Each FPGA is connected to two DDR3 memory modules and three external 10Gbps ports. In addition, a total of 128 low voltage differential input lines permit connection to external ADC cards. The DSP capability of the board exceeds 644E9 complex multiply-accumulate operations per second. The first production run of eight boards was distributed to partners in The Netherlands, France, Italy, UK, China and Korea in May 2011, with a further production runs completed in December 2011 and early 2012. The function of the board is determined by the firmware loaded into its FPGAs. Current applications include beamformers, correlators, digital receivers, RFI mitigation for pulsar astronomy, and pulsar gating and search machines The new UniBoard based correlator for the European VLBI network (EVN) uses an FX architecture with half the resources of the board devoted to station based processing: delay and phase correction and channelization, and half to the correlation function. A single UniBoard can process a 64MHz band from 32 stations, 2 polarizations, sampled at 8 bit. Adding more UniBoards can expand the total bandwidth of the correlator. The design is able to process both prerecorded and real time (eVLBI) data.

Internet-Based Public Health E-Learning Student Perceptions: An Evaluation from the People's Open Access Education Initiative (Peoples-uni)

ERIC Educational Resources Information Center

Awofeso, Niyi; Philip, Keir; Heller, Richard F.

2012-01-01

Current public health training infrastructure and facilitators in most developing nations are insufficient relative to public health service delivery needs. We examined five areas of student perceptions of a web-based public health learning initiative, the Peoples-uni, which focused on: reasons for enrolling, learning expectations; technical…

Flight Performance of an Advanced Thermal Protection Material: Toughened Uni-Piece Fibrous Insulation

NASA Technical Reports Server (NTRS)

Leiser, Daniel B.; Gordon, Michael P.; Rasky, Daniel J. (Technical Monitor)

1995-01-01

The flight performance of a new class of low density, high temperature thermal protection materials (TPM) is described and compared to "standard" Space Shuttle TPM. This new functionally gradient material designated as Toughened Uni-Piece Fibrous Insulation (TUFI), was bonded on a removable panel attached to the base heat shield of Orbiter 105, Endeavour.

Flight Performance of an Advanced Thermal Protection Material: Toughened Uni-Piece Fibrous Insulation

NASA Technical Reports Server (NTRS)

Leiser, Daniel B.; Gordon, Michael P.; Rasky, Daniel J. (Technical Monitor)

1995-01-01

The flight performance of a new class of low density, high temperature, thermal protection materials (TPM), is described and compared to "standard" Space Shuttle TPM. This new functionally gradient material designated as Toughened Uni-Piece Fibrous Insulation (TUFI), was bonded on a removable panel attached to the base heatshield of Orbiter 105, Endeavor.

The growth of the UniTree mass storage system at the NASA Center for Computational Sciences

NASA Technical Reports Server (NTRS)

Tarshish, Adina; Salmon, Ellen

1993-01-01

In October 1992, the NASA Center for Computational Sciences made its Convex-based UniTree system generally available to users. The ensuing months saw the growth of near-online data from nil to nearly three terabytes, a doubling of the number of CPU's on the facility's Cray YMP (the primary data source for UniTree), and the necessity for an aggressive regimen for repacking sparse tapes and hierarchical 'vaulting' of old files to freestanding tape. Connectivity was enhanced as well with the addition of UltraNet HiPPI. This paper describes the increasing demands placed on the storage system's performance and throughput that resulted from the significant augmentation of compute-server processor power and network speed.

RepExplore: addressing technical replicate variance in proteomics and metabolomics data analysis.

PubMed

Glaab, Enrico; Schneider, Reinhard

2015-07-01

High-throughput omics datasets often contain technical replicates included to account for technical sources of noise in the measurement process. Although summarizing these replicate measurements by using robust averages may help to reduce the influence of noise on downstream data analysis, the information on the variance across the replicate measurements is lost in the averaging process and therefore typically disregarded in subsequent statistical analyses.We introduce RepExplore, a web-service dedicated to exploit the information captured in the technical replicate variance to provide more reliable and informative differential expression and abundance statistics for omics datasets. The software builds on previously published statistical methods, which have been applied successfully to biomedical omics data but are difficult to use without prior experience in programming or scripting. RepExplore facilitates the analysis by providing a fully automated data processing and interactive ranking tables, whisker plot, heat map and principal component analysis visualizations to interpret omics data and derived statistics. Freely available at http://www.repexplore.tk enrico.glaab@uni.lu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

FALCON: a toolbox for the fast contextualization of logical networks.

PubMed

De Landtsheer, Sébastien; Trairatphisan, Panuwat; Lucarelli, Philippe; Sauter, Thomas

2017-11-01

Mathematical modelling of regulatory networks allows for the discovery of knowledge at the system level. However, existing modelling tools are often computation-heavy and do not offer intuitive ways to explore the model, to test hypotheses or to interpret the results biologically. We have developed a computational approach to contextualize logical models of regulatory networks with biological measurements based on a probabilistic description of rule-based interactions between the different molecules. Here, we propose a Matlab toolbox, FALCON, to automatically and efficiently build and contextualize networks, which includes a pipeline for conducting parameter analysis, knockouts and easy and fast model investigation. The contextualized models could then provide qualitative and quantitative information about the network and suggest hypotheses about biological processes. FALCON is freely available for non-commercial users on GitHub under the GPLv3 licence. The toolbox, installation instructions, full documentation and test datasets are available at https://github.com/sysbiolux/FALCON. FALCON runs under Matlab (MathWorks) and requires the Optimization Toolbox. thomas.sauter@uni.lu. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Effects of small particle numbers on long-term behaviour in discrete biochemical systems.

PubMed

Kreyssig, Peter; Wozar, Christian; Peter, Stephan; Veloz, Tomás; Ibrahim, Bashar; Dittrich, Peter

2014-09-01

The functioning of many biological processes depends on the appearance of only a small number of a single molecular species. Additionally, the observation of molecular crowding leads to the insight that even a high number of copies of species do not guarantee their interaction. How single particles contribute to stabilizing biological systems is not well understood yet. Hence, we aim at determining the influence of single molecules on the long-term behaviour of biological systems, i.e. whether they can reach a steady state. We provide theoretical considerations and a tool to analyse Systems Biology Markup Language models for the possibility to stabilize because of the described effects. The theory is an extension of chemical organization theory, which we called discrete chemical organization theory. Furthermore we scanned the BioModels Database for the occurrence of discrete chemical organizations. To exemplify our method, we describe an application to the Template model of the mitotic spindle assembly checkpoint mechanism. http://www.biosys.uni-jena.de/Services.html. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

[Social and environmental vulnerability, flooding and repercussions on public health in underdeveloped regions: the case of the state of Alagoas, Brazil].

PubMed

Freire, Neison Cabral Ferreira; Bonfim, Cristine Vieira do; Natenzon, Claudia Eleonor

2014-09-01

The scope of this article is to analyze the social and environmental vulnerability of the population affected by disasters adopting the floods that occurred in the State of Alagoas in 2010 as a case study. For this, research was conducted in the Scielo and Medline databases as well as books, dissertations and theses. In addition, newspaper articles published in the local and national press about these floods were located and examined. A visit was made to some of the individuals who were affected by the flood and subsequently housed in the Santa Fé Prison Colony located in the municipality of União dos Palmares in the State of Alagoas. Among other aspects, the vulnerability is a consequence of the precarious living conditions of this population. However, even among the vulnerable there are some groups that are even more vulnerable without any possibility of changing a situation of chronic repetition of the disaster, perpetuating the vicious cycle of poverty and precarious living conditions.

Transcriptomic Analysis of Multipurpose Timber Yielding Tree Neolamarckia cadamba during Xylogenesis Using RNA-Seq.

PubMed

Ouyang, Kunxi; Li, Juncheng; Zhao, Xianhai; Que, Qingmin; Li, Pei; Huang, Hao; Deng, Xiaomei; Singh, Sunil Kumar; Wu, Ai-Min; Chen, Xiaoyang

2016-01-01

Neolamarckia cadamba is a fast-growing tropical hardwood tree that is used extensively for plywood and pulp production, light furniture fabrication, building materials, and as a raw material for the preparation of certain indigenous medicines. Lack of genomic resources hampers progress in the molecular breeding and genetic improvement of this multipurpose tree species. In this study, transcriptome profiling of differentiating stems was performed to understand N. cadamba xylogenesis. The N. cadamba transcriptome was sequenced using Illumina paired-end sequencing technology. This generated 42.49 G of raw data that was then de novo assembled into 55,432 UniGenes with a mean length of 803.2bp. Approximately 47.8% of the UniGenes (26,487) were annotated against publically available protein databases, among which 21,699 and 7,754 UniGenes were assigned to Gene Ontology categories (GO) and Clusters of Orthologous Groups (COG), respectively. 5,589 UniGenes could be mapped onto 116 pathways using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database. Among 6,202 UniGenes exhibiting differential expression during xylogenesis, 1,634 showed significantly higher levels of expression in the basal and middle stem segments compared to the apical stem segment. These genes included NAC and MYB transcription factors related to secondary cell wall biosynthesis, genes related to most metabolic steps of lignin biosynthesis, and CesA genes involved in cellulose biosynthesis. This study lays the foundation for further screening of key genes associated with xylogenesis in N. cadamba as well as enhancing our understanding of the mechanism of xylogenesis in fast-growing trees.

Multisensory Integration Strategy for Modality-Specific Loss of Inhibition Control in Older Adults

PubMed Central

Ryu, Hokyoung; Kim, Jae-Kwan; Jeong, Eunju

2018-01-01

Older adults are known to have lesser cognitive control capability and greater susceptibility to distraction than young adults. Previous studies have reported age-related problems in selective attention and inhibitory control, yielding mixed results depending on modality and context in which stimuli and tasks were presented. The purpose of the study was to empirically demonstrate a modality-specific loss of inhibitory control in processing audio-visual information with ageing. A group of 30 young adults (mean age = 25.23, Standard Deviation (SD) = 1.86) and 22 older adults (mean age = 55.91, SD = 4.92) performed the audio-visual contour identification task (AV-CIT). We compared performance of visual/auditory identification (Uni-V, Uni-A) with that of visual/auditory identification in the presence of distraction in counterpart modality (Multi-V, Multi-A). The findings showed a modality-specific effect on inhibitory control. Uni-V performance was significantly better than Multi-V, indicating that auditory distraction significantly hampered visual target identification. However, Multi-A performance was significantly enhanced compared to Uni-A, indicating that auditory target performance was significantly enhanced by visual distraction. Additional analysis showed an age-specific effect on enhancement between Uni-A and Multi-A depending on the level of visual inhibition. Together, our findings indicated that the loss of visual inhibitory control was beneficial for the auditory target identification presented in a multimodal context in older adults. A likely multisensory information processing strategy in the older adults was further discussed in relation to aged cognition. PMID:29641462

FcUni-RLuc: an engineered Renilla luciferase with Fc binding ability and light emission activity.

PubMed

Farzannia, A; Roghanian, R; Zarkesh-Esfahani, S H; Nazari, M; Emamzadeh, R

2015-03-07

A novel and advanced Fc-binding probe – FcUni-RLuc namely – has been produced and functionally assayed for labelling IgGs. The Fc antibody binding sequence – HWRGWV – was fused to Renilla luciferase, and the purified probe was employed for bioluminescence enzyme-linked immunoabsorbance assay of Her2 positive cells.

Comparative Growth Retarding Activity in Relation to Endogenous Tissue Concentration of Daminozide and a Pyrrolidino Analog (Uni-629) in Phaseolus vulgaris L. and Chrysanthemum morifolium Ramat

Treesearch

R.M. Sachs; J. DeBie; J.L. Michael; J.R. Frank; R.A. Creager

1975-01-01

N-pyrrolidino succinamic acid (Uni-F529) was considerably superior to succinic acid 2,2 dimethyl hydrazide (daiminozide. SADH) in inhihiting stem elongation in Phaseolus vulgaris L. `Black Valentine' and Chrysanthemum morifolium Ramat, `Bright Golden Anne'. This was true in winter or summer greenhouses. Under...

78 FR 4879 - Nine Mile Point 3 Nuclear Project, LLC and UniStar Nuclear Operating Services, LLC Combined...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-23

... Analysis Report (FSAR). On December 1, 2009, UniStar Nuclear Energy (UNE), acting on behalf of the COL... Exclusion From Environmental Review With respect to the exemption's impact on the quality of the human... relation to security issues. Therefore, the common defense and security is not impacted by this exemption...

Radio-frequency measurements of UNiX compounds (X=Al, Ga, Ge) in high magnetic fields

NASA Astrophysics Data System (ADS)

Alsmadi, A. M.; Alyones, S.; Mielke, C. H.; McDonald, R. D.; Zapf, V.; Altarawneh, M. M.; Lacerda, A.; Chang, S.; Adak, S.; Kothapalli, K.; Nakotte, H.

2009-11-01

We performed radio-frequency (RF) skin-depth measurements of antiferromagnetic UNiX compounds (X=Al, Ga, Ge) in magnetic fields up to 60 T and at temperatures between 1.4 to ~60 K. Magnetic fields are applied along different crystallographic directions and RF penetration-depth was measured using a tunnel-diode oscillator (TDO) circuit. The sample is coupled to the inductive element of a TDO resonant tank circuit, and the shift in the resonant frequency Δ f of the circuit is measured. The UNiX compounds exhibit field-induced magnetic transitions at low temperatures, and those transitions are accompanied by a drastic change in Δ f. The results of our skin-depth measurements were compared with previously published B- T phase diagrams for these three compounds.

75 FR 21373 - ULH Corp. (n/k/a UniHolding Corp.), Unapix Entertainment, Inc., Unicomp, Inc., and Unidyne Corp...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-23

... SECURITIES AND EXCHANGE COMMISSION [File No. 500-1] ULH Corp. (n/k/a UniHolding Corp.), Unapix Entertainment, Inc., Unicomp, Inc., and Unidyne Corp.; Order of Suspension of Trading April 21, 2010. It appears... Entertainment, Inc. because it has not filed any periodic reports since it filed a Form 10-Q for the period...

A glance at the history of uniportal video-assisted thoracic surgery.

PubMed

Mineo, Tommaso Claudio; Ambrogi, Vincenzo

2017-01-01

In the history of thoracic surgery, the advent of video-assisted thoracic surgery (VATS) had on effect equivalent to that provoked by a true revolution. VATS successfully allowed minor, major and complex procedures for various lung and mediastinal pathologies with small incision instead of the traditional accesses. These small incisions abolished ugly scars, generated less acute and chronic pain, reduced hospital stay and costs, allowed faster return to normal day life activities. Conventional VATS was initially performed through 3-4 ports and rapidly evolved to uniportal or single portal access [uniportal video-assisted thoracic surgery (uniVATS)]. First uniportal procedures were published in 2000. In 2010, uniportal technique for lobectomy was described. Focused experimental courses, live surgery events, the internet media favored the rapid diffusion of this technique over the world. Major and complex uniVATS lung resections involving segmentectomy, pneumonectomy, bronchoplasty and vascular reconstruction, redo VATS, en bloc chest wall resections have been accomplished with satisfactory outcomes. Interestingly, different uniportal approaches and techniques are emerging from a number of VATS centers particularly experienced in the mini-invasive thoracic surgery. As confidence grew, in 2014, the first uniVATS left upper lobectomy via the subxiphoid approach was reported. This novel technique is quite challenging but appropriate patient selection as well as availability of dedicated instruments allowed to perform procedures safely. The diffusion of uniVATS paralleled with the development of nonintubated awake anesthesia technique. In 2007 the first nonintubated lobectomy was described. In 2014 the first single port VATS lobectomy in a nonintubated patient with lung cancer of the right middle lobe was accomplished. The nonintubated uniVATS represents an intriguing technique, so that very experienced thoracoscopic surgeons may enroll to surgery elderly and high risk patients. Decreased postoperative pain and hospitalization, faster access to the radio-chemotherapy and diminished inflammatory response are important benefits of the modern approach to the thoracic pathologies. The history of uniVATS documented a constant and irresistible progress. This technique may further provide unthinkable surprises in next future.

Radio-frequency measurements of UNiX compounds (X= Al, Ga, Ge) in high magnetic fields

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

Mielke, Charles H; Mcdonald, David R; Zapf, Vivien

2009-01-01

We performed radio-frequency (RF) skin-depth measurements of antiferromagnetic UNiX compounds (X=Al, Ga, Ge) in magnetic fields up to 60 T and at temperatures between 1.4 to {approx}60 K. Magnetic fields are applied along different crystallographic directions and RF penetration-depth was measured using a tunnel-diode oscillator (TDO) circuit. The sample is coupled to the inductive element of a TDO resonant tank circuit, and the shift in the resonant frequency {Delta}f of the circuit is measured. The UNiX compounds exhibit field-induced magnetic transitions at low temperatures, and those transitions are accompanied by a drastic change in {Delta}f. The results of our skin-depthmore » measurements were compared with previously published B-T phase diagrams for these three compounds.« less

Analyzing the Web Services and UniFrame Paradigms

DTIC Science & Technology

2003-04-01

paradigm from a centralized one to a distributed one. Hence, the target environment is no more a centrally managed, but concerned with collaboration...lever (business logic level) and provide a new platform to build software for a distributed environment . UniFrame is a research project that aims to...EAI solutions provide tends to be complex and expensive, despite improving the overall communication. In addition, the EAI interfaces are not reusable

A Master Agreement between the State of Iowa Board of Regents and the Uni-United Faculty of University of Northern Iowa, July 1, 1987-June 30, 1989.

ERIC Educational Resources Information Center

Iowa State Board of Regents, Des Moines.

The collective bargaining agreement between the State of Iowa Board of Regents and the University of Northern Iowa Uni-United Faculty, an affiliate of the National Education Association, for the period July 1, 1987-June 30, 1989 is presented. Items covered in the agreement include: unit recognition; university facilities; faculty evaluation by…

Improvements in the Protein Identifier Cross-Reference service.

PubMed

Wein, Samuel P; Côté, Richard G; Dumousseau, Marine; Reisinger, Florian; Hermjakob, Henning; Vizcaíno, Juan A

2012-07-01

The Protein Identifier Cross-Reference (PICR) service is a tool that allows users to map protein identifiers, protein sequences and gene identifiers across over 100 different source databases. PICR takes input through an interactive website as well as Representational State Transfer (REST) and Simple Object Access Protocol (SOAP) services. It returns the results as HTML pages, XLS and CSV files. It has been in production since 2007 and has been recently enhanced to add new functionality and increase the number of databases it covers. Protein subsequences can be Basic Local Alignment Search Tool (BLAST) against the UniProt Knowledgebase (UniProtKB) to provide an entry point to the standard PICR mapping algorithm. In addition, gene identifiers from UniProtKB and Ensembl can now be submitted as input or mapped to as output from PICR. We have also implemented a 'best-guess' mapping algorithm for UniProt. In this article, we describe the usefulness of PICR, how these changes have been implemented, and the corresponding additions to the web services. Finally, we explain that the number of source databases covered by PICR has increased from the initial 73 to the current 102. New resources include several new species-specific Ensembl databases as well as the Ensembl Genome ones. PICR can be accessed at http://www.ebi.ac.uk/Tools/picr/.

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.

Treatment of sentence comprehension and production in aphasia: is there cross-modal generalisation?

PubMed

Adelt, Anne; Hanne, Sandra; Stadie, Nicole

2016-09-09

Exploring generalisation following treatment of language deficits in aphasia can provide insights into the functional relation of the cognitive processing systems involved. In the present study, we first review treatment outcomes of interventions targeting sentence processing deficits and, second report a treatment study examining the occurrence of practice effects and generalisation in sentence comprehension and production. In order to explore the potential linkage between processing systems involved in comprehending and producing sentences, we investigated whether improvements generalise within (i.e., uni-modal generalisation in comprehension or in production) and/or across modalities (i.e., cross-modal generalisation from comprehension to production or vice versa). Two individuals with aphasia displaying co-occurring deficits in sentence comprehension and production were trained on complex, non-canonical sentences in both modalities. Two evidence-based treatment protocols were applied in a crossover intervention study with sequence of treatment phases being randomly allocated. Both participants benefited significantly from treatment, leading to uni-modal generalisation in both comprehension and production. However, cross-modal generalisation did not occur. The magnitude of uni-modal generalisation in sentence production was related to participants' sentence comprehension performance prior to treatment. These findings support the assumption of modality-specific sub-systems for sentence comprehension and production, being linked uni-directionally from comprehension to production.

Magnetic properties and crystal structure of RENiA1 and UniA1 hydrides.

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

Bordallo, H. N.; Drulis, H.; Havela, L.

1999-08-11

RENiAl (RE = rare-earth metal) and UNiAl compounds crystallizing in the hexagonal ZrNiAl-type structure (space group P{bar 6}2m) can absorb up to 2 and 3 hydrogen (deuterium) atoms per formula unit, respectively. Hydrogenation leads to a notable lattice expansion and modification of magnetic properties. However, the impact of hydrogenation on magnetism is the opposite for 4f- and 5f-materials: TN(T{sub c})is lowered in the case of rare-earth hydrides, while for UNiAlH(D){sub x} it increases by an order of magnitude. Here we present results of magnetic and structure studies performed of these compounds, focusing on the correlation between magnetic and structural variationsmore » and discussing possible reasons of the striking difference in effect of hydrogenation on rare-earth and actinide intermetallics.« less

Influence of Shear Stiffness Degradation on Crack Paths in Uni-Directional Composite Laminates

NASA Technical Reports Server (NTRS)

Satyanarayana, Arunkumar; Bogert, Phil B.

2017-01-01

Influence of shear stiffness degradation in an element, due to damage, on crack paths in uni-directional laminates has been demonstrated. A new shear stiffness degradation approach to improve crack path prediction has been developed and implemented in an ABAQUS/Explicit frame work using VUMAT. Three progressive failure analysis models, built-in ABAQUS (TradeMark), original COmplete STress Reduction (COSTR) and the modified COSTR damage models have been utilized in this study to simulate crack paths in five unidirectional notched laminates, 15deg, 30deg, 45deg, 60deg and 75deg under uniaxial tension load. Results such as crack paths and load vs. edge displacement curves are documented in this report. Modified COSTR damage model shows better accuracy in predicting crack paths in all the uni-directional laminates compared to the ABAQUS (TradeMark) and the original COSTR damage models.

Reduction of hysteresis in solution-processed InGaZnO thin-film transistors through uni-directional pre-annealing

NASA Astrophysics Data System (ADS)

Kim, Young-Rae; Kwon, Jin-Hyuk; Vincent, Premkumar; Kim, Do-Kyung; Jeong, Hyeon-Seok; Hahn, Joonku; Bae, Jin-Hyuk; Park, Jaehoon

2018-01-01

The hysteresis of the solution-processed oxide thin-film transistors (TFTs) is fatal issue to interrupt stable operation. So, we came up with uni-directional pre-annealing to solve the problem. There are inevitable defects when solution-processed oxide TFTs are fabricated, due to the porosities by the solvent volatilization. Also oxygen vacancies needed for carrier generation in metal oxide semiconductor can be trap states inducing charge carrier trapping. Uni-directional pre-annealing improved the hysteresis, preventing randomly solvent evaporation and decreased the defects of the film. We can result in advanced stability of the solution-processed oxide TFTs, at the same time showing that the field effect mobility was enhanced from 3.35 cm2/Vs to 4.78 cm2/Vs simultaneously, and exhibiting better subthreshold swing from 0.89 V/dec to 0.23 V/dec.

A First Look at Surface Meteorology in the Arctic System Reanalysis

NASA Astrophysics Data System (ADS)

Slater, A. G.; Serreze, M. C.; Asr-Team, A.

2010-12-01

The Arctic System Reanalysis (ASR) is a joint venture between several universities (Ohio-State Uni., Uni. Colorado, Uni. Illinois UC, Uni. Alaska) and NCAR. It is a regional reanalysis that will span the period 2000-2010, possibly continuing into the future. Compared to current regional or global reanalyses it will have a spatial resolution twice that of prior efforts; a final product is expected to be an equal area projection of 15km grid boxes. The domain encompasses all the Arctic Ocean drainage areas. Several new reanalysis applications have been implemented, with some being Arctic specific - for example satellite derived sea ice age is translated into thickness and MODIS surface albedo is to be ingested. A preliminary ASR run has been performed for the period June 2007 - December 2008 at a reduced resolution of 30km. Here we make a comparison of all recent reanalysis products (NARR, MERRA, ERA-I, CFSRR) to both the ASR and observations at 350 surface stations in the Western Arctic; there is a major focus on Alaska. An intercomparison of surface variables (which are perhaps the most used reanalysis data) has been undertaken including temperature, humidity and solar radiation. Results indicate that the level of discrepancy between reanalysis data and observations is of similar magnitude as it is between all the reanalysis products; possibly suggesting that we have reached the limit of repersentativeness when comparing grid boxes to point measurements.

Tele-Manipulation with Two Asymmetric Slaves: Two Operators Perform Better Than One.

PubMed

van Oosterhout, Jeroen; Heemskerk, Cock J M; de Baar, Marco R; van der Helm, Frans C T; Abbink, David A

2018-01-01

Certain tele-manipulation tasks require manipulation by two asymmetric slaves, for example, a crane for hoisting and a dexterous robotic arm for fine manipulation. It is unclear how to best design human-in-the-loop control over two asymmetric slaves. The goal of this paper is to quantitatively compare the standard approach of two co-operating operators that each control a single subtask, to a single operator performing bi-manual control over the two subtasks, and a uni-manual control approach. In a human factors experiment, participants performed a heavy load maneuvering and mounting task using a vertical crane and a robotic arm. We hypothesize that bi-manual control yields worse task performance and control activity compared to co-operation, because of conflicting spatial and temporal constraints. Literature suggests that uni-manual operators should perform better than co-operation, as co-operators critically depend on each other's actions. However, other literature provides evidence that individual operators have limited capabilities in controlling asymmetric axes of two dynamic systems. The results show that the two co-operators perform the maneuvering and mounting task faster than either bi- or uni-manual operators. Compared to co-operators, uni-manual operators required more control activity for the vertical crane and less for the robotic arm. In conclusion, this study suggests that when controlling two asymmetric slaves, a co-operating pair of operators performs better than a single operator.

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

The Origin of Uni-axial Negative Thermal Expansion in a Layered Perovskite

NASA Astrophysics Data System (ADS)

Ablitt, Chris; Craddock, Sarah; Senn, Mark; Mostofi, Arash; Bristowe, Nicholas

Using first-principles calculations within the quasi-harmonic approximation (QHA), we explain the origin of experimentally observed uni-axial negative thermal expansion (NTE) in a layered perovskite: the Ruddlesden-Popper (RP) oxide Ca2MnO4, which has anti-ferromagnetic ordering at low temperatures and is closely related to Ca3Mn2O7, which exhibits hybrid improper ferroelectricity and uni-axial NTE in competing phases. Dynamic tilts of MnO6 octahedra, common in many complex oxides, drive the expansion of the a axis and contraction of the c axis of the tetragonal NTE phase. We find that ferroelastic RP phases with a frozen octahedral rotation are unusually compliant to particular combinations of strains along different axes. The atomic mechanism responsible is characteristic of the perovskite/rock-salt interfaces present in the RP structure. We show that the contribution from this anisotropic elasticity must be taken into account in order to accurately predict NTE over the temperature range observed in experiment. A similar compliance to cooperative strains is found in other systems with uni-axial NTE. The development of this mechanistic understanding of NTE in complex oxides may pave the way for designing tunable multifunctional materials. The authors would like to acknowledge support from the EPSRC and the Centre for Doctoral Training in Theory and Simulation of Materials.

Experimental Studies on Strength Behaviour of Notched Glass/Epoxy Laminated Composites under Uni-axial and Bi-axial Loading

NASA Astrophysics Data System (ADS)

Guptha, V. L. Jagannatha; Sharma, Ramesh S.

2017-11-01

The use of FRP composite materials in aerospace, aviation, marine, automotive and civil engineering industry has increased rapidly in recent years due to their high specific strength and stiffness properties. The structural members contrived from such composite materials are generally subjected to complex loading conditions and leads to multi-axial stress conditions at critical surface localities. Presence of notches, much required for joining process of composites, makes it further significant. The current practice of using uni-axial test data alone to validate proposed material models is inadequate leading to evaluation and consideration of bi-axial test data. In order to correlate the bi-axial strengths with the uni-axial strengths of GFRP composite laminates in the presence of a circular notch, bi-axial tests using four servo-hydraulic actuators with four load cells were carried out. To determine the in-plane strength parameters, bi-axial cruciform test specimen model was considered. Three different fibre orientations, namely, 0°, 45°, and 90° are considered with a central circular notch of 10 mm diameter in the present investigation. From the results obtained, it is observed that there is a reduction in strength of 5.36, 2.41 and 13.92% in 0°, 45°, and 90° fibre orientation, respectively, under bi-axial loading condition as compared to that of uni-axial loading in laminated composite.

TogoTable: cross-database annotation system using the Resource Description Framework (RDF) data model.

PubMed

Kawano, Shin; Watanabe, Tsutomu; Mizuguchi, Sohei; Araki, Norie; Katayama, Toshiaki; Yamaguchi, Atsuko

2014-07-01

TogoTable (http://togotable.dbcls.jp/) is a web tool that adds user-specified annotations to a table that a user uploads. Annotations are drawn from several biological databases that use the Resource Description Framework (RDF) data model. TogoTable uses database identifiers (IDs) in the table as a query key for searching. RDF data, which form a network called Linked Open Data (LOD), can be searched from SPARQL endpoints using a SPARQL query language. Because TogoTable uses RDF, it can integrate annotations from not only the reference database to which the IDs originally belong, but also externally linked databases via the LOD network. For example, annotations in the Protein Data Bank can be retrieved using GeneID through links provided by the UniProt RDF. Because RDF has been standardized by the World Wide Web Consortium, any database with annotations based on the RDF data model can be easily incorporated into this tool. We believe that TogoTable is a valuable Web tool, particularly for experimental biologists who need to process huge amounts of data such as high-throughput experimental output. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

WhopGenome: high-speed access to whole-genome variation and sequence data in R.

PubMed

Wittelsbürger, Ulrich; Pfeifer, Bastian; Lercher, Martin J

2015-02-01

The statistical programming language R has become a de facto standard for the analysis of many types of biological data, and is well suited for the rapid development of new algorithms. However, variant call data from population-scale resequencing projects are typically too large to be read and processed efficiently with R's built-in I/O capabilities. WhopGenome can efficiently read whole-genome variation data stored in the widely used variant call format (VCF) file format into several R data types. VCF files can be accessed either on local hard drives or on remote servers. WhopGenome can associate variants with annotations such as those available from the UCSC genome browser, and can accelerate the reading process by filtering loci according to user-defined criteria. WhopGenome can also read other Tabix-indexed files and create indices to allow fast selective access to FASTA-formatted sequence files. The WhopGenome R package is available on CRAN at http://cran.r-project.org/web/packages/WhopGenome/. A Bioconductor package has been submitted. lercher@cs.uni-duesseldorf.de. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Diagnostic accuracy of three monoclonal stool tests in a large series of untreated Helicobacter pylori infected patients.

PubMed

Lario, Sergio; Ramírez-Lázaro, María José; Montserrat, Antònia; Quílez, María Elisa; Junquera, Félix; Martínez-Bauer, Eva; Sanfeliu, Isabel; Brullet, Enric; Campo, Rafael; Segura, Ferran; Calvet, Xavier

2016-06-01

Immunochromatographic tests need to be improved in order to enhance their reliability. Recently, several new kits have appeared on the market. The objective was to evaluate the diagnostic accuracy of three monoclonal rapid stool tests - the new Uni-Gold™ H.pylori Antigen (Trinity Biotech, Ireland), the RAPID Hp StAR (Oxoid Ltd., UK) and the ImmunoCard STAT! HpSA (Meridian Diagnostics, USA) - for detecting H. pylori infection prior to eradication treatment. Diagnostic accuracy (sensitivity and specificity) and reliability (concordance between observers) were evaluated in 250 untreated consecutive dyspeptic patients. The gold standard for diagnosing H. pylori infection was defined as the concordance of two or more of rapid urease test (RUT), histopathology and urease breath test (UBT) or positive culture in isolation. Readings of immunochromatographic tests were performed by two different observers. Sensitivity, specificity, positive and negative predictive values and 95% confidence intervals were calculated. Sensitivity and specificity were compared using the McNemar test. The three tests showed a good correlation, with Kappa values>0.9. RAPID Hp StAR had a sensitivity of 91%-92% and a specificity ranging from 77% to 85%. Its sensitivity was higher than that of Uni-Gold™ H.pylori Antigen and ImmunoCard STAT! HpSA (p<0.01). Uni-Gold™ H.pylori Antigen kit showed a sensitivity of 83%, similar to ImmunoCard STAT! HpSA. Specificity of Uni-Gold™ H.pylori Antigen approached 90% (87-89%) and was superior to that of RAPID Hp StAR (p<0.01). Uni-Gold™ H.pylori Antigen and ImmunoCard STAT! HpSA present similar levels of diagnostic accuracy. RAPID Hp StAR was the most sensitive but less reliable of the three immunochromatographic stool tests. None are as accurate and reliable as UBT, RUT and histology. Copyright © 2016 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Integrating UniTree with the data migration API

NASA Technical Reports Server (NTRS)

Schrodel, David G.

1994-01-01

The Data Migration Application Programming Interface (DMAPI) has the potential to allow developers of open systems Hierarchical Storage Management (HSM) products to virtualize native file systems without the requirement to make changes to the underlying operating system. This paper describes advantages of virtualizing native file systems in hierarchical storage management systems, the DMAPI at a high level, what the goals are for the interface, and the integration of the Convex UniTree+HSM with DMAPI along with some of the benefits derived in the resulting product.

Microchemical and Structural Evidence for Space Weathering in Soils from Asteroid Itokawa

NASA Technical Reports Server (NTRS)

Thompson, M. S.; Christoffersen, R.; Zega, T. J.

2013-01-01

The chemistry, microstructure and optical properties of grains on the surfaces of airless bodies are continu-ously modified due to their interactions predominantly with solar energetic ions and micrometeorite impacts. Collectively known as space weathering, this phenomenon results in a discrepancy between remotely sensed spectra from asteroids and those ac-quired directly from meteorites. The return of pristine samples from the asteroid Itokawa provides insight into surface processes on airless bodies and will help in correlating remote sensing data with laboratory analysis of meteorites. Samples and Methods: We examined Itokawa samples RA-QD02-0042-01 and RA-QD-02-0042-02, ultramicrotomed sec-tions of a singular grain prepared by the Hayabusa sample cura-tion team. We analyzed these slices using a 200 keV JEOL 2010F transmission electron microscope (TEM) at Arizona State Uni-versity and a 200 keV JEOL 2500SE TEM at NASA JSC. Both field emission TEMs are equipped with energy-dispersive X-ray spectrometers (EDS) and scanning TEM (STEM) detectors. Results and Discussion: TEM observations reveal that the sectioned grain predominantly consists of a single crystal of low-Ca orthopyroxene, with subsidiary smaller regions of olivine, Fe-Ni sulfide, and Fe-Ni metal. EDS-spectrum imaging and high-resolution TEM (HRTEM) show local, nanocrystalline regions of the outermost 2 to 5 nm of the pyroxene are composed of an Fe-Mg-S-rich and Si- and O-depleted layer that is underlain by a 2- to 5-nm thick amorphous zone enriched in Si. These layers occur in multiple microtome slices and have uniform thicknesses. We also observe localized 'islands' of material on the surface of the pyroxene which HRTEM imaging indicates are amorphous and EDS measurements show are compositionally heterogeneous. A 10- to 60-nm thick partially amorphous zone occurs below the compositionally distinct rim. While this this zone is associated with the compositionally heterogeneous outer layer, it also occurs as a local stand-alone feature on the exterior rim of the grain. Ar-eas of the pyroxene grain rim also exhibit a vesicular texture. The TEM data indicate a complex history of space weather-ing for samples RA-QD02-0042-01 and -02. The outermost layer of nanocrystalline material with varied composition is consistent with previously suggested [3-4] chemical and structural pro-cessing by solar wind ions, with a possible additional role for im-pact vapor deposition [3-4]. The amorphous and compositionally distinct islands on the surface of this grain, similar to lunar glasses, suggest formation through vapor deposition via micrometeor-ite impact events. In comparison, the amorphization and vesicula-tion textures are likely a product of radiation damage from the solar wind. The depth and degree of amorphization, in conjunction with model calculations, will help provide an upper limit on exposure time for these particles.

Characterization of ichthyoplankton within the U.S. Geological Survey's Northeastern Gulf of Mexico study area - based on analysis of Southeast Area Monitoring and Assessment Program (SEAMAP) Sampling Surveys, 1982-1999. NEGOM ichthyoplankton synopsis final report

USGS Publications Warehouse

Lyczkowski-Shultz, Joanne; Hanisko, David S.; Sulak, Kenneth J.; Dennis, George D.

2004-01-01

This synthesis was undertaken to characterize the occurrence and abundance of fish eggs and larvae in the northeastern Gulf of Mexico (NEGOM) and to assess the region's relative importance in the early life history of fishes as compared to the entire U.S. Gulf of Mexico. Data for 66 selected taxa from 1,166 bongo and neuston net samples at 72 localities [comprising the UGSG NEGOM Ichthyoplankton Synopsis (UNIS) Study Area] were analyzed. These data were taken during annual Southeast Area Monitoring and Assessment Program (SEAMAP) gulfwide surveys from 1982-1999, and were summarized by the NMFS to accomplish this objective. Comparison of the UNIS Study Area with the overall SEAMAP survey area revealed that the larvae of 16 taxa occurred more frequently and were relatively more abundant in the UNIS Study Area than the entire SEAMAP survey area while for other taxa occurrence and relative abundance were comparable. These taxa represented fishes from mesopelagic, continental shelf, and reef assemblages reflecting the wide diversity of habitats available in the NEGOM and included the young of two important resource taxa, Rhomboplites aurorubens (vermilion snapper) and Seriola spp. (amberjacks). Distinct distribution patterns were observed among larvae in the UNIS Study Area that appear to be associated with the presence of the DeSoto Canyon. One notable pattern was the predominance of certain taxa to either the west or east of longitude 86.5-87.0o W. Larvae of several characteristic reef-fish families were most common to the east of this apparent zoogeographic faunal discontinuity. An alternative pattern was seen among taxa whose larvae occurred primarily at locations over depth contours outlining the canyon. Additionally, the UNIS Study Area contributed more fish eggs, total larvae, and zooplankton to survey totals than would be expected from the number of samples taken in the study area. This pattern was more evident during spring than fall surveys. It may relate to the close proximity of UNIS Study Area stations to the Mississippi River and the penetration of DeSoto Canyon, with its nutrient-rich deep slope water, into the inner shelf. The consistent presence of fish eggs throughout the NEGOM at mean abundances exceeding 100 eggs per 10 m? sea surface indicates that this region of the Gulf of Mexico is an important spawning area. The present synopsis has revealed that the NEGOM, as represented by the UNIS Study Area, should be considered an important, if not critical, habitat for the young stages of a diverse assemblage of fish taxa. The greatest biological deficiency in this synopsis is our current inability to identify the larvae of all species to a consistent taxonomic level.

Uni10: an open-source library for tensor network algorithms

NASA Astrophysics Data System (ADS)

Kao, Ying-Jer; Hsieh, Yun-Da; Chen, Pochung

2015-09-01

We present an object-oriented open-source library for developing tensor network algorithms written in C++ called Uni10. With Uni10, users can build a symmetric tensor from a collection of bonds, while the bonds are constructed from a list of quantum numbers associated with different quantum states. It is easy to label and permute the indices of the tensors and access a block associated with a particular quantum number. Furthermore a network class is used to describe arbitrary tensor network structure and to perform network contractions efficiently. We give an overview of the basic structure of the library and the hierarchy of the classes. We present examples of the construction of a spin-1 Heisenberg Hamiltonian and the implementation of the tensor renormalization group algorithm to illustrate the basic usage of the library. The library described here is particularly well suited to explore and fast prototype novel tensor network algorithms and to implement highly efficient codes for existing algorithms.

UniDA: Uniform Device Access Framework for Human Interaction Environments

PubMed Central

Varela, Gervasio; Paz-Lopez, Alejandro; Becerra, Jose Antonio; Vazquez-Rodriguez, Santiago; Duro, Richard José

2011-01-01

Human interaction environments (HIE) must be understood as any place where people carry out their daily life, including their work, family life, leisure and social life, interacting with technology to enhance or facilitate the experience. The integration of technology in these environments has been achieved in a disorderly and incompatible way, with devices operating in isolated islands with artificial edges delimited by the manufacturers. In this paper we are presenting the UniDA framework, an integral solution for the development of systems that require the integration and interoperation of devices and technologies in HIEs. It provides developers and installers with a uniform conceptual framework capable of modelling an HIE, together with a set of libraries, tools and devices to build distributed instrumentation networks with support for transparent integration of other technologies. A series of use case examples and a comparison to many of the existing technologies in the field has been included in order to show the benefits of using UniDA. PMID:22163700

UniDA: uniform device access framework for human interaction environments.

PubMed

Varela, Gervasio; Paz-Lopez, Alejandro; Becerra, Jose Antonio; Vazquez-Rodriguez, Santiago; Duro, Richard José

2011-01-01

Human interaction environments (HIE) must be understood as any place where people carry out their daily life, including their work, family life, leisure and social life, interacting with technology to enhance or facilitate the experience. The integration of technology in these environments has been achieved in a disorderly and incompatible way, with devices operating in isolated islands with artificial edges delimited by the manufacturers. In this paper we are presenting the UniDA framework, an integral solution for the development of systems that require the integration and interoperation of devices and technologies in HIEs. It provides developers and installers with a uniform conceptual framework capable of modelling an HIE, together with a set of libraries, tools and devices to build distributed instrumentation networks with support for transparent integration of other technologies. A series of use case examples and a comparison to many of the existing technologies in the field has been included in order to show the benefits of using UniDA.

Density and mixture fraction measurements in a GO2/GH2 uni-element rocket chamber

NASA Technical Reports Server (NTRS)

Moser, M. D.; Pal, S.; Santoro, R. J.

1994-01-01

In recent years, there has been a renewed interest in gas/gas injectors for rocket combustion. Specifically, the proposed new concept of full-flow oxygen rich preburner systems calls for the injection of both oxygen and hydrogen into the main chamber as gaseous propellants. The technology base for gas/gas injection must mature before actual booster class systems can be designed and fabricated. Since the data base for gas/gas injection is limited to studies focusing on the global parameters of small reaction engines, there is a critical need for experiment programs that emphasize studying the mixing and combustion characteristics of GO2 and GH2 propellants from a uni-element injector point of view. The experimental study of the combusting GO2/GH2 propellant combination in a uni-element rocket chamber also provides a simplified environment, in terms of both geometry and chemistry, that can be used to verify and validate computational fluid dynamic (CFD) models.

The use of the bi-factor model to test the uni-dimensionality of a battery of reasoning tests.

PubMed

Primi, Ricardo; Rocha da Silva, Marjorie Cristina; Rodrigues, Priscila; Muniz, Monalisa; Almeida, Leandro S

2013-02-01

The Battery of Reasoning Tests 5 (BPR-5) aims to assess the reasoning ability of individuals, using sub-tests with different formats and contents that require basic processes of inductive and deductive reasoning for their resolution. The BPR has three sequential forms: BPR-5i (for children from first to fifth grade), BPR-5 - Form A (for children from sixth to eighth grade) and BPR-5 - form B (for high school and undergraduate students). The present study analysed 412 questionnaires concerning BPR-5i, 603 questionnaires concerning BPR-5 - Form A and 1748 questionnaires concerning BPR-5 - Form B. The main goal was to test the uni-dimensionality of the battery and its tests in relation to items using the bi-factor model. Results suggest that the g factor loadings (extracted by the uni-dimensional model) do not change when the data is adjusted for a more flexible multi-factor model (bi-factor model). A general reasoning factor underlying different contents items is supported.

An approach to describing and analysing bulk biological annotation quality: a case study using UniProtKB.

PubMed

Bell, Michael J; Gillespie, Colin S; Swan, Daniel; Lord, Phillip

2012-09-15

Annotations are a key feature of many biological databases, used to convey our knowledge of a sequence to the reader. Ideally, annotations are curated manually, however manual curation is costly, time consuming and requires expert knowledge and training. Given these issues and the exponential increase of data, many databases implement automated annotation pipelines in an attempt to avoid un-annotated entries. Both manual and automated annotations vary in quality between databases and annotators, making assessment of annotation reliability problematic for users. The community lacks a generic measure for determining annotation quality and correctness, which we look at addressing within this article. Specifically we investigate word reuse within bulk textual annotations and relate this to Zipf's Principle of Least Effort. We use the UniProt Knowledgebase (UniProtKB) as a case study to demonstrate this approach since it allows us to compare annotation change, both over time and between automated and manually curated annotations. By applying power-law distributions to word reuse in annotation, we show clear trends in UniProtKB over time, which are consistent with existing studies of quality on free text English. Further, we show a clear distinction between manual and automated analysis and investigate cohorts of protein records as they mature. These results suggest that this approach holds distinct promise as a mechanism for judging annotation quality. Source code is available at the authors website: http://homepages.cs.ncl.ac.uk/m.j.bell1/annotation. phillip.lord@newcastle.ac.uk.

Utility of a thematic network in primary health care: a controlled interventional study in a rural area

PubMed Central

Coma del Corral, Maria Jesús; Abaigar Luquín, Pedro; Cordero Guevara, José; Olea Movilla, Angel; Torres Torres, Gerardo; Lozano Garcia, Javier

2005-01-01

Background UniNet is an Internet-based thematic network for a virtual community of users (VCU). It supports a virtual multidisciplinary community for physicians, focused on the improvement of clinical practice. This is a study of the effects of a thematic network such as UniNet on primary care medicine in a rural area, specifically as a platform of communication between specialists at the hospital and doctors in the rural area. Methods In order to study the effects of a thematic network such as UniNet on primary care medicine in a rural area, we designed an interventional study that included a control group. The measurements included the number of patient displacements due to disease, number of patient hospital stays and the number of prescriptions of drugs of low therapeutic utility and generic drug prescriptions by doctors. These data were analysed and compared with those of the control center. Results Our study showed positive changes in medical practice, reflected in the improvement of the evaluated parameters in the rural health area where the interventional study was carried out, compared with the control area. We discuss the strengths and weaknesses of UniNet as a potential medium to improve the quality of medical care in rural areas. Conclusion The rural doctors had an effective, useful, user-friendly and cheap source of medical information that may have contributed to the improvement observed in the medical quality indices. PMID:16042778

A Biomechanical Comparison of the Long Snap in Football Between High School and University Football Players.

PubMed

Chizewski, Michael G; Alexander, Marion J L

2015-08-01

Limited previous research was located that examined the technique of the long snap in football. The purpose of the study was to compare the joint movements, joint velocities, and body positions used to perform fast and accurate long snaps in high school (HS) and university (UNI) athletes. Ten HS and 10 UNI subjects were recruited for filming, each performing 10 snaps at a target with the fastest and most accurate trial being selected for subject analysis. Eighty-three variables were measured using Dartfish Team Pro 4.5.2 video analysis software, with statistical analysis performed using Microsoft Excel and SPSS 16.0. Several significant comparisons to long snapping technique between groups were noted during analysis; however, the body position and movement variables at release showed the greatest number of significant differences. The UNI athletes demonstrated significantly higher release velocity and left elbow extension velocity, with significantly lower release height and release angle than the HS group. Total snap time (release time + total flight time) was determined to have the strongest correlation to release velocity for the HS group (r = -0.915) and UNI group (r = -0.918). The study suggests HS long snappers may benefit from less elbow flexion and more knee flexion in the backswing (set position) to increase release velocity. University long snappers may benefit from increased left elbow extension range of motion during force production and decreased shoulder flexion at critical instant to increase long snap release velocity.

The arm posture in children with unilateral Cerebral Palsy is mainly related to antero-posterior gait instability.

PubMed

Meyns, Pieter; Duysens, Jacques; Desloovere, Kaat

2016-09-01

In this observational case-control study we aimed to determine whether altered arm postures in children with unilateral CP (uniCP) are related to gait instability in a specific direction. Antero-posterior and medio-lateral Foot Placement Estimator instability measures and arm posture measures (vertical and antero-posterior hand position, sagittal and frontal upper arm elevation angle) were determined in eleven uniCP (7 years-10 months) and twenty-four typically developing children (9 years-6 months) at two walking speeds. Spearman-rank correlation analyses were made to examine the relationship between antero-posterior and medio-lateral arm posture and gait instability. Arm posture in both planes was related to antero-posterior instability (e.g. sagittal and frontal upper arm elevation angle correlated moderately with antero-posterior instability; R=0.41, p<0.001, R=-0.47, p<0.001). In uniCP, increased antero-posterior instability was associated with a higher (R=-0.62, p=0.002) and more frontal position of the hemiplegic hand (R=-0.58, p=0.005), while the non-hemiplegic upper arm was rotated more backward (R=0.63, p=0.002) and both upper arms rotated more sideways (hemiplegic: R=-0.58, p=0.004; non-hemiplegic: R=-0.55, p=0.008). The altered non-hemiplegic (sagittal and frontal) arm posture in uniCP may be a compensation to reduce antero-posterior gait instability. Copyright © 2016 Elsevier B.V. All rights reserved.

Deep learning meets ontologies: experiments to anchor the cardiovascular disease ontology in the biomedical literature.

PubMed

Arguello Casteleiro, Mercedes; Demetriou, George; Read, Warren; Fernandez Prieto, Maria Jesus; Maroto, Nava; Maseda Fernandez, Diego; Nenadic, Goran; Klein, Julie; Keane, John; Stevens, Robert

2018-04-12

Automatic identification of term variants or acceptable alternative free-text terms for gene and protein names from the millions of biomedical publications is a challenging task. Ontologies, such as the Cardiovascular Disease Ontology (CVDO), capture domain knowledge in a computational form and can provide context for gene/protein names as written in the literature. This study investigates: 1) if word embeddings from Deep Learning algorithms can provide a list of term variants for a given gene/protein of interest; and 2) if biological knowledge from the CVDO can improve such a list without modifying the word embeddings created. We have manually annotated 105 gene/protein names from 25 PubMed titles/abstracts and mapped them to 79 unique UniProtKB entries corresponding to gene and protein classes from the CVDO. Using more than 14 M PubMed articles (titles and available abstracts), word embeddings were generated with CBOW and Skip-gram. We setup two experiments for a synonym detection task, each with four raters, and 3672 pairs of terms (target term and candidate term) from the word embeddings created. For Experiment I, the target terms for 64 UniProtKB entries were those that appear in the titles/abstracts; Experiment II involves 63 UniProtKB entries and the target terms are a combination of terms from PubMed titles/abstracts with terms (i.e. increased context) from the CVDO protein class expressions and labels. In Experiment I, Skip-gram finds term variants (full and/or partial) for 89% of the 64 UniProtKB entries, while CBOW finds term variants for 67%. In Experiment II (with the aid of the CVDO), Skip-gram finds term variants for 95% of the 63 UniProtKB entries, while CBOW finds term variants for 78%. Combining the results of both experiments, Skip-gram finds term variants for 97% of the 79 UniProtKB entries, while CBOW finds term variants for 81%. This study shows performance improvements for both CBOW and Skip-gram on a gene/protein synonym detection task by adding knowledge formalised in the CVDO and without modifying the word embeddings created. Hence, the CVDO supplies context that is effective in inducing term variability for both CBOW and Skip-gram while reducing ambiguity. Skip-gram outperforms CBOW and finds more pertinent term variants for gene/protein names annotated from the scientific literature.

Spectral statistics of the uni-modular ensemble

NASA Astrophysics Data System (ADS)

Joyner, Christopher H.; Smilansky, Uzy; Weidenmüller, Hans A.

2017-09-01

We investigate the spectral statistics of Hermitian matrices in which the elements are chosen uniformly from U(1) , called the uni-modular ensemble (UME), in the limit of large matrix size. Using three complimentary methods; a supersymmetric integration method, a combinatorial graph-theoretical analysis and a Brownian motion approach, we are able to derive expressions for 1 / N corrections to the mean spectral moments and also analyse the fluctuations about this mean. By addressing the same ensemble from three different point of view, we can critically compare their relative advantages and derive some new results.

170 GHz Uni-Traveling Carrier Photodiodes for InP-based photonic integrated circuits.

PubMed

Rouvalis, E; Chtioui, M; van Dijk, F; Lelarge, F; Fice, M J; Renaud, C C; Carpintero, G; Seeds, A J

2012-08-27

We demonstrate the capability of fabricating extremely high-bandwidth Uni-Traveling Carrier Photodiodes (UTC-PDs) using techniques that are suitable for active-passive monolithic integration with Multiple Quantum Well (MQW)-based photonic devices. The devices achieved a responsivity of 0.27 A/W, a 3-dB bandwidth of 170 GHz, and an output power of -9 dBm at 200 GHz. We anticipate that this work will deliver Photonic Integrated Circuits with extremely high bandwidth for optical communications and millimetre-wave applications.

UniDrug-target: a computational tool to identify unique drug targets in pathogenic bacteria.

PubMed

Chanumolu, Sree Krishna; Rout, Chittaranjan; Chauhan, Rajinder S

2012-01-01

Targeting conserved proteins of bacteria through antibacterial medications has resulted in both the development of resistant strains and changes to human health by destroying beneficial microbes which eventually become breeding grounds for the evolution of resistances. Despite the availability of more than 800 genomes sequences, 430 pathways, 4743 enzymes, 9257 metabolic reactions and protein (three-dimensional) 3D structures in bacteria, no pathogen-specific computational drug target identification tool has been developed. A web server, UniDrug-Target, which combines bacterial biological information and computational methods to stringently identify pathogen-specific proteins as drug targets, has been designed. Besides predicting pathogen-specific proteins essentiality, chokepoint property, etc., three new algorithms were developed and implemented by using protein sequences, domains, structures, and metabolic reactions for construction of partial metabolic networks (PMNs), determination of conservation in critical residues, and variation analysis of residues forming similar cavities in proteins sequences. First, PMNs are constructed to determine the extent of disturbances in metabolite production by targeting a protein as drug target. Conservation of pathogen-specific protein's critical residues involved in cavity formation and biological function determined at domain-level with low-matching sequences. Last, variation analysis of residues forming similar cavities in proteins sequences from pathogenic versus non-pathogenic bacteria and humans is performed. The server is capable of predicting drug targets for any sequenced pathogenic bacteria having fasta sequences and annotated information. The utility of UniDrug-Target server was demonstrated for Mycobacterium tuberculosis (H37Rv). The UniDrug-Target identified 265 mycobacteria pathogen-specific proteins, including 17 essential proteins which can be potential drug targets. UniDrug-Target is expected to accelerate pathogen-specific drug targets identification which will increase their success and durability as drugs developed against them have less chance to develop resistances and adverse impact on environment. The server is freely available at http://117.211.115.67/UDT/main.html. The standalone application (source codes) is available at http://www.bioinformatics.org/ftp/pub/bioinfojuit/UDT.rar.

Anti-Müllerian hormone (AMH) profiles as a novel biomarker to evaluate the existence of a functional cryptorchid testis in Japanese Black calves.

PubMed

Kitahara, Go; El-Sheikh Ali, Hossam; Sato, Tomohiro; Kobayashi, Ikuo; Hemmi, Koichiro; Shirao, Yuka; Kamimura, Shunichi

2012-01-01

Anti-Müllerian hormone (AMH) and testosterone (T) profiles in blood were investigated before and after an hCG stimulation test to assess their sensitivity and specificity for the existence of a functional cryptorchid testis in Japanese Black calves. The hCG (3,000 IU) was administered on Day 0, and peripheral blood was collected on Days 0 (just before hCG injection), 5 and 7 in intact male calves (Intact; n=19), bilateral castrated calves (Castrated; n=17), unilateral cryptorchid calves, which abdominal testis could been extracted (Uni-crypto; n=9). Castration of a descended testis was carried in the Castrated and Uni-Crypto groups on Day -14. The AMH detectability and the optimum cut-off point for T levels using the receiver operating characteristic curve were verified to characterize the cryptorchid testis. AMH values on Day 0 were 21.1 ± 5.1 and 29.0 ± 7.5 ng/ml in the Intact and Uni-crypto groups, respectively (Mean ± SEM). AMH levels were under the detection limit in the Castrated group (i.e., < 0.006 ng/ml). T showed its peak levels on Day 5 in the Intact group (26.8 ± 4.2 ng/ml), while it remained low in the Castrated group (< 0.9 ng/ml) and did not show a significant difference in the Uni-crypto group. The detectable levels for AMH was 0.006 ng/ml, and the optimum cut-off point for T was 0.9 ng/ml; the sensitivity and specificity for evaluation of testicular descent into the scrotum were 1.0 for both the AMH and T levels. The detection rates in the Uni-crypto group using them were 1.0 and 0.57 for AMH on Day 0 and T on Days 5 or 7, respectively. In conclusion, plasma AMH profiles could be used as a novel biomarker to evaluate the existence of a functional cryptorchid testis in Japanese Black calves.

Activations in gray and white matter are modulated by uni-manual responses during within and inter-hemispheric transfer: effects of response hand and right-handedness.

PubMed

Diwadkar, Vaibhav A; Bellani, Marcella; Chowdury, Asadur; Savazzi, Silvia; Perlini, Cinzia; Marinelli, Veronica; Zoccatelli, Giada; Alessandrini, Franco; Ciceri, Elisa; Rambaldelli, Gianluca; Ruggieri, Mirella; Carlo Altamura, A; Marzi, Carlo A; Brambilla, Paolo

2017-08-14

Because the visual cortices are contra-laterally organized, inter-hemispheric transfer tasks have been used to behaviorally probe how information briefly presented to one hemisphere of the visual cortex is integrated with responses resulting from the ipsi- or contra-lateral motor cortex. By forcing rapid information exchange across diverse regions, these tasks robustly activate not only gray matter regions, but also white matter tracts. It is likely that the response hand itself (dominant or non-dominant) modulates gray and white matter activations during within and inter-hemispheric transfer. Yet the role of uni-manual responses and/or right hand dominance in modulating brain activations during such basic tasks is unclear. Here we investigated how uni-manual responses with either hand modulated activations during a basic visuo-motor task (the established Poffenberger paradigm) alternating between inter- and within-hemispheric transfer conditions. In a large sample of strongly right-handed adults (n = 49), we used a factorial combination of transfer condition [Inter vs. Within] and response hand [Dominant(Right) vs. Non-Dominant (Left)] to discover fMRI-based activations in gray matter, and in narrowly defined white matter tracts. These tracts were identified using a priori probabilistic white matter atlases. Uni-manual responses with the right hand strongly modulated activations in gray matter, and notably in white matter. Furthermore, when responding with the left hand, activations during inter-hemispheric transfer were strongly predicted by the degree of right-hand dominance, with increased right-handedness predicting decreased fMRI activation. Finally, increasing age within the middle-aged sample was associated with a decrease in activations. These results provide novel evidence of complex relationships between uni-manual responses in right-handed subjects, and activations during within- and inter-hemispheric transfer suggest that the organization of the motor system exerts sophisticated functional effects. Moreover, our evidence of activation in white matter tracts is consistent with prior studies, confirming fMRI-detectable white matter activations which are systematically modulated by experimental condition.

EnzML: multi-label prediction of enzyme classes using InterPro signatures

PubMed Central

2012-01-01

Background Manual annotation of enzymatic functions cannot keep up with automatic genome sequencing. In this work we explore the capacity of InterPro sequence signatures to automatically predict enzymatic function. Results We present EnzML, a multi-label classification method that can efficiently account also for proteins with multiple enzymatic functions: 50,000 in UniProt. EnzML was evaluated using a standard set of 300,747 proteins for which the manually curated Swiss-Prot and KEGG databases have agreeing Enzyme Commission (EC) annotations. EnzML achieved more than 98% subset accuracy (exact match of all correct Enzyme Commission classes of a protein) for the entire dataset and between 87 and 97% subset accuracy in reannotating eight entire proteomes: human, mouse, rat, mouse-ear cress, fruit fly, the S. pombe yeast, the E. coli bacterium and the M. jannaschii archaebacterium. To understand the role played by the dataset size, we compared the cross-evaluation results of smaller datasets, either constructed at random or from specific taxonomic domains such as archaea, bacteria, fungi, invertebrates, plants and vertebrates. The results were confirmed even when the redundancy in the dataset was reduced using UniRef100, UniRef90 or UniRef50 clusters. Conclusions InterPro signatures are a compact and powerful attribute space for the prediction of enzymatic function. This representation makes multi-label machine learning feasible in reasonable time (30 minutes to train on 300,747 instances with 10,852 attributes and 2,201 class values) using the Mulan Binary Relevance Nearest Neighbours algorithm implementation (BR-kNN). PMID:22533924

Influence of ambient moisture on the compaction behavior of microcrystalline cellulose powder undergoing uni-axial compression and roller-compaction: a comparative study using near-infrared spectroscopy.

PubMed

Gupta, Abhay; Peck, Garnet E; Miller, Ronald W; Morris, Kenneth R

2005-10-01

This study evaluates the effect of variation in the ambient moisture on the compaction behavior of microcrystalline cellulose (MCC) powder. The study was conducted by comparing the physico-mechanical properties of, and the near infrared (NIR) spectra collected on, compacts prepared by roller compaction with those collected on simulated ribbons, that is, compacts prepared under uni-axial compression. Relative density, moisture content, tensile strength (TS), and Young modulus were used as key sample attributes for comparison. Samples prepared at constant roller compactor settings and feed mass showed constant density and a decrease in TS with increasing moisture content. Compacts prepared under uni-axial compression at constant pressure and compact mass showed the opposite effect, that is, density increased while TS remained almost constant with increasing moisture content. This suggests difference in the influence of moisture on the material under roller compaction, in which the roll gap (i.e., thickness and therefore density) remains almost constant, vs. under uni-axial compression, in which the thickness is free to change in response to the applied pressure. Key sample attributes were also related to the NIR spectra using multivariate data analysis by the partial least squares projection to latent structures (PLS). Good agreement was observed between the measured and the NIR-PLS predicted values for all key attributes for both, the roller compacted samples as well as the simulated ribbons. Copyright (c) 2005 Wiley-Liss, Inc. and the American Pharmacists Association

Performance evaluation of the automated nucleated red blood cell count of five commercial hematological analyzers.

PubMed

Da Rin, G; Vidali, M; Balboni, F; Benegiamo, A; Borin, M; Ciardelli, M L; Dima, F; Di Fabio, A; Fanelli, A; Fiorini, F; Francione, S; Germagnoli, L; Gioia, M; Lari, T; Lorubbio, M; Marini, A; Papa, A; Seghezzi, M; Solarino, L; Pipitone, S; Tilocca, E; Buoro, S

2017-12-01

Recent automated hematology analyzers (HAs) can identify and report nucleated red blood cells (NRBC) count as a separate population out of white blood cells (WBC). The aim of this study was to investigate the analytical performances of NRBC enumeration on five top of the range HAs. We evaluated the within-run and between-day precision, limit of blank (LoB), limit of detection (LoD), and limit of quantitation (LoQ) of XE-2100 and XN-module (Sysmex), ADVIA 2120i (Siemens), BC-6800 (Mindray), and UniCel DxH 800 (Beckman Coulter). Automated NRBC counts were also compared with optical microscopy (OM). The limits of detection for NRBC of the BC-6800, XN-module, XE-2100, UniCel DxH 800, and ADVIA 2120i are 0.035×10 9 /L, 0.019×10 9 /L, 0.067×10 9 /L, 0.038×10 9 /L, and 0.167×10 9 /L, respectively. Our data indicated excellent performance in terms of precision. The agreement with OM was excellent for BC-6800, XN-module, and XE-2100 (Bias 0.023, 0.019, and 0.033×10 9 /L, respectively). ADVIA 2120i displayed a significant constant error and UniCel DxH 800 both proportional and small constant error. Regards to NRBC counting, the performances shown by BC-6800, XN-module, and XE-2100 are excellent also a low count, ADVIA 2120i and UniCel DxH 800 need to be improved. © 2017 John Wiley & Sons Ltd.

High-responsivity vertical-illumination Si/Ge uni-traveling-carrier photodiodes based on silicon-on-insulator substrate.

PubMed

Li, Chong; Xue, ChunLai; Liu, Zhi; Cong, Hui; Cheng, Buwen; Hu, Zonghai; Guo, Xia; Liu, Wuming

2016-06-09

Si/Ge uni-traveling carrier photodiodes exhibit higher output current when space-charge effect is overcome and the thermal effects is suppressed. High current is beneficial for increasing the dynamic range of various microwave photonic systems and simplifying high-bit-rate digital receivers in many applications. From the point of view of packaging, detectors with vertical-illumination configuration can be easily handled by pick-and-place tools and are a popular choice for making photo-receiver modules. However, vertical-illumination Si/Ge uni-traveling carrier (UTC) devices suffer from inter-constraint between high speed and high responsivity. Here, we report a high responsivity vertical-illumination Si/Ge UTC photodiode based on a silicon-on-insulator substrate. When the transmission of the monolayer anti-reflection coating was maximum, the maximum absorption efficiency of the devices was 1.45 times greater than the silicon substrate owing to constructive interference. The Si/Ge UTC photodiode had a dominant responsivity at 1550 nm of 0.18 A/W, a 50% improvement even with a 25% thinner Ge absorption layer.

High-responsivity vertical-illumination Si/Ge uni-traveling-carrier photodiodes based on silicon-on-insulator substrate

PubMed Central

Li, Chong; Xue, ChunLai; Liu, Zhi; Cong, Hui; Cheng, Buwen; Hu, Zonghai; Guo, Xia; Liu, Wuming

2016-01-01

Si/Ge uni-traveling carrier photodiodes exhibit higher output current when space-charge effect is overcome and the thermal effects is suppressed. High current is beneficial for increasing the dynamic range of various microwave photonic systems and simplifying high-bit-rate digital receivers in many applications. From the point of view of packaging, detectors with vertical-illumination configuration can be easily handled by pick-and-place tools and are a popular choice for making photo-receiver modules. However, vertical-illumination Si/Ge uni-traveling carrier (UTC) devices suffer from inter-constraint between high speed and high responsivity. Here, we report a high responsivity vertical-illumination Si/Ge UTC photodiode based on a silicon-on-insulator substrate. When the transmission of the monolayer anti-reflection coating was maximum, the maximum absorption efficiency of the devices was 1.45 times greater than the silicon substrate owing to constructive interference. The Si/Ge UTC photodiode had a dominant responsivity at 1550 nm of 0.18 A/W, a 50% improvement even with a 25% thinner Ge absorption layer. PMID:27279426

29Si-NMR study of magnetic anisotropy and hyperfine interactions in the uranium-bsed ferromagnet UNiSi2

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

Sakai, Hironori; Baek, Seung H; Bauer, Eric D

2009-01-01

UNiSi{sub 2} orders ferromagnetically below T{sub Curie} = 95 K. This material crystallizes in the orthorhombic CeNiSi{sub 2}-type structure. The uranium atoms form double-layers, which are stacked along the crystallographic b axis (the longest axis). From magnetization measurement the easy (hard) magnetization axis is found to be the c axis (b axis). {sup 29}Si-NMR measurements have been performed in the paramagnetic state. In UNiSi{sub 2}, two crystallographic Si sites exist with orthorhombic local symmetry. The Knight shifts on each Si site have been estimated from the spectra of random and oriented powders. The transferred hyperfine couplings have been also derived.more » It is found that the transferred hyperfine coupling constants on each Si site are nearly isotropic, and that their Knight shift anisotropy comes from that of the bulk susceptibility. The nuclear-spin lattice relaxation rate 1/T{sub 1} shows temperature-independent behavior, which indicates the existence of localized 5f electron.« less

Coupled skinny baker's maps and the Kaplan-Yorke conjecture

NASA Astrophysics Data System (ADS)

Gröger, Maik; Hunt, Brian R.

2013-09-01

The Kaplan-Yorke conjecture states that for ‘typical’ dynamical systems with a physical measure, the information dimension and the Lyapunov dimension coincide. We explore this conjecture in a neighborhood of a system for which the two dimensions do not coincide because the system consists of two uncoupled subsystems. We are interested in whether coupling ‘typically’ restores the equality of the dimensions. The particular subsystems we consider are skinny baker's maps, and we consider uni-directional coupling. For coupling in one of the possible directions, we prove that the dimensions coincide for a prevalent set of coupling functions, but for coupling in the other direction we show that the dimensions remain unequal for all coupling functions. We conjecture that the dimensions prevalently coincide for bi-directional coupling. On the other hand, we conjecture that the phenomenon we observe for a particular class of systems with uni-directional coupling, where the information and Lyapunov dimensions differ robustly, occurs more generally for many classes of uni-directionally coupled systems (also called skew-product systems) in higher dimensions.

Linear Instability of a Uni-Directional Transversely Sheared Mean Flow

NASA Technical Reports Server (NTRS)

Wundrow, David W.

1996-01-01

The effect of spanwise-periodic mean-flow distortions (i.e. streamwise-vortex structures) on the evolution of small-amplitude, single-frequency instability waves in an otherwise two-dimensional shear flow is investigated. The streamwise-vortex structures are taken to be just weak enough so that the spatially growing instability waves behave (locally) like linear perturbations about a uni-directional transversely sheared mean flow. Numerical solutions are computed and discussed for both the mean flow and the instability waves. The influence of the streamwise-vortex wavelength on the properties of the most rapidly growing instability wave is also discussed.

A relationship between the effect of uni-univalent electrolytes on the structure of water and on its volatility

NASA Astrophysics Data System (ADS)

Marcus, Yizhak

2018-06-01

The effect of ions on the structure of water in dilute solutions, whether they are structure-makers or structure-breakers, is manifested also in the volatility of the water. For more than 40 uni-univalent electrolytes, there is a linearly increasing relationship between 2φ(m = 0.4) - φ(m = 0.2), where φ is the osmotic coefficient and m is the molality, and the difference between the viscosity B-coefficients of the cation and anion. Exceptions to this relationship are electrolytes with highly structure-making anions and with hydrophobic cations.

Moral and Ethical Decision Making

DTIC Science & Technology

2007-07-01

l’intermédiaire de divers navigateurs Web. L’échantillon se composait de 212 sujets, dont 121 femmes et 91 hommes , tous résidents des États-Unis. La...interrogés résidaient aux États-Unis. Parmi eux, il y avait 121 femmes et 91 hommes . La moyenne d’âge était de 47,89 ans et l’écart-type de 7,87. Le...participants de les remplir par l’intermédiaire de divers navigateurs Web. L’échantillon se composait de 212 sujets, dont 121 femmes et 91 hommes , tous

Constraint Preserving Schemes Using Potential-Based Fluxes. I. Multidimensional Transport Equations (PREPRINT)

DTIC Science & Technology

2010-01-01

i,j−∆t nEni ,j , u∗∗i,j =u ∗ i,j−∆t nEni ,j , un+1i,j = 1 2 (uni,j+u ∗∗ i,j ). (2.26) An alternative first-order accurate genuinely multi-dimensional...time stepping is the ex- tended Lax-Friedrichs type time stepping, un+1i,j = 1 8 (4uni,j+u n i+1,j+u n i,j+1+u n i−1,j+u n i,j−1)−∆t nEni ,j . (2.27) 13

PLAZA 3.0: an access point for plant comparative genomics.

PubMed

Proost, Sebastian; Van Bel, Michiel; Vaneechoutte, Dries; Van de Peer, Yves; Inzé, Dirk; Mueller-Roeber, Bernd; Vandepoele, Klaas

2015-01-01

Comparative sequence analysis has significantly altered our view on the complexity of genome organization and gene functions in different kingdoms. PLAZA 3.0 is designed to make comparative genomics data for plants available through a user-friendly web interface. Structural and functional annotation, gene families, protein domains, phylogenetic trees and detailed information about genome organization can easily be queried and visualized. Compared with the first version released in 2009, which featured nine organisms, the number of integrated genomes is more than four times higher, and now covers 37 plant species. The new species provide a wider phylogenetic range as well as a more in-depth sampling of specific clades, and genomes of additional crop species are present. The functional annotation has been expanded and now comprises data from Gene Ontology, MapMan, UniProtKB/Swiss-Prot, PlnTFDB and PlantTFDB. Furthermore, we improved the algorithms to transfer functional annotation from well-characterized plant genomes to other species. The additional data and new features make PLAZA 3.0 (http://bioinformatics.psb.ugent.be/plaza/) a versatile and comprehensible resource for users wanting to explore genome information to study different aspects of plant biology, both in model and non-model organisms. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

A comprehensive quality control workflow for paired tumor-normal NGS experiments.

PubMed

Schroeder, Christopher M; Hilke, Franz J; Löffler, Markus W; Bitzer, Michael; Lenz, Florian; Sturm, Marc

2017-06-01

Quality control (QC) is an important part of all NGS data analysis stages. Many available tools calculate QC metrics from different analysis steps of single sample experiments (raw reads, mapped reads and variant lists). Multi-sample experiments, as sequencing of tumor-normal pairs, require additional QC metrics to ensure validity of results. These multi-sample QC metrics still lack standardization. We therefore suggest a new workflow for QC of DNA sequencing of tumor-normal pairs. With this workflow well-known single-sample QC metrics and additional metrics specific for tumor-normal pairs can be calculated. The segmentation into different tools offers a high flexibility and allows reuse for other purposes. All tools produce qcML, a generic XML format for QC of -omics experiments. qcML uses quality metrics defined in an ontology, which was adapted for NGS. All QC tools are implemented in C ++ and run both under Linux and Windows. Plotting requires python 2.7 and matplotlib. The software is available under the 'GNU General Public License version 2' as part of the ngs-bits project: https://github.com/imgag/ngs-bits. christopher.schroeder@med.uni-tuebingen.de. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

SmartR: an open-source platform for interactive visual analytics for translational research data.

PubMed

Herzinger, Sascha; Gu, Wei; Satagopam, Venkata; Eifes, Serge; Rege, Kavita; Barbosa-Silva, Adriano; Schneider, Reinhard

2017-07-15

In translational research, efficient knowledge exchange between the different fields of expertise is crucial. An open platform that is capable of storing a multitude of data types such as clinical, pre-clinical or OMICS data combined with strong visual analytical capabilities will significantly accelerate the scientific progress by making data more accessible and hypothesis generation easier. The open data warehouse tranSMART is capable of storing a variety of data types and has a growing user community including both academic institutions and pharmaceutical companies. tranSMART, however, currently lacks interactive and dynamic visual analytics and does not permit any post-processing interaction or exploration. For this reason, we developed SmartR , a plugin for tranSMART, that equips the platform not only with several dynamic visual analytical workflows, but also provides its own framework for the addition of new custom workflows. Modern web technologies such as D3.js or AngularJS were used to build a set of standard visualizations that were heavily improved with dynamic elements. The source code is licensed under the Apache 2.0 License and is freely available on GitHub: https://github.com/transmart/SmartR . reinhard.schneider@uni.lu. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Alignment-Annotator web server: rendering and annotating sequence alignments.

PubMed

Gille, Christoph; Fähling, Michael; Weyand, Birgit; Wieland, Thomas; Gille, Andreas

2014-07-01

Alignment-Annotator is a novel web service designed to generate interactive views of annotated nucleotide and amino acid sequence alignments (i) de novo and (ii) embedded in other software. All computations are performed at server side. Interactivity is implemented in HTML5, a language native to web browsers. The alignment is initially displayed using default settings and can be modified with the graphical user interfaces. For example, individual sequences can be reordered or deleted using drag and drop, amino acid color code schemes can be applied and annotations can be added. Annotations can be made manually or imported (BioDAS servers, the UniProt, the Catalytic Site Atlas and the PDB). Some edits take immediate effect while others require server interaction and may take a few seconds to execute. The final alignment document can be downloaded as a zip-archive containing the HTML files. Because of the use of HTML the resulting interactive alignment can be viewed on any platform including Windows, Mac OS X, Linux, Android and iOS in any standard web browser. Importantly, no plugins nor Java are required and therefore Alignment-Anotator represents the first interactive browser-based alignment visualization. http://www.bioinformatics.org/strap/aa/ and http://strap.charite.de/aa/. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

LCR-eXXXplorer: a web platform to search, visualize and share data for low complexity regions in protein sequences.

PubMed

Kirmitzoglou, Ioannis; Promponas, Vasilis J

2015-07-01

Local compositionally biased and low complexity regions (LCRs) in amino acid sequences have initially attracted the interest of researchers due to their implication in generating artifacts in sequence database searches. There is accumulating evidence of the biological significance of LCRs both in physiological and in pathological situations. Nonetheless, LCR-related algorithms and tools have not gained wide appreciation across the research community, partly due to the fact that only a handful of user-friendly software is currently freely available. We developed LCR-eXXXplorer, an extensible online platform attempting to fill this gap. LCR-eXXXplorer offers tools for displaying LCRs from the UniProt/SwissProt knowledgebase, in combination with other relevant protein features, predicted or experimentally verified. Moreover, users may perform powerful queries against a custom designed sequence/LCR-centric database. We anticipate that LCR-eXXXplorer will be a useful starting point in research efforts for the elucidation of the structure, function and evolution of proteins with LCRs. LCR-eXXXplorer is freely available at the URL http://repeat.biol.ucy.ac.cy/lcr-exxxplorer. vprobon@ucy.ac.cy Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

The homogeneity effect on figure/ground perception in infancy.

PubMed

Takashima, Midori; Kanazawa, So; Yamaguchi, Masami K; Shiina, Ken

2014-02-01

We examined whether the homogeneity of the two profiles of Rubin's goblet affects figure/ground perception in infants. We modified the two profiles of Rubin's goblet in order to compare figure/ground perception under four test patterns: (1) two profiles painted with horizontal lines (horizontal-line condition), (2) two profiles painted middle gray (uni-color condition), (3) one profile painted light gray and the other dark gray (two-color condition), and (4) a goblet painted with concentric circles (concentric-circles condition). In the horizontal-line condition the homogeneity of the profile was strengthened, and in the two-color condition the homogeneity of the profile was weakened compared to the uni-color condition, which was an original Rubin's goblet. In the concentric-circles condition the homogeneity of the reversed areas of the horizontal-line were strengthened. After infants were familiarized with each Rubin's goblet, the infants were tested on their discrimination between the two profiles and the goblet in the post-familiarization test. In horizontal-line condition, uni-color condition and concentric-circles condition infants showed a novelty preference for the two profiles in the post-familiarization test. On the other hand, in the two-color condition no preference was observed in the post-familiarization test. This means that infants perceived the goblet as figure and the two profiles as ground in the horizontal-line condition, the uni-color condition and the concentric-circles condition. We found that infants could not perceive the goblet area as figure when the homogeneity of the two profiles was weakened. It can be said that figure/ground perception in infancy is not affected by strengthened homogeneity, but is affected by weakened homogeneity. Copyright © 2014 Elsevier Inc. All rights reserved.

Urinary nickel as bioindicator of workers' Ni exposure in a galvanizing plant in Brazil.

PubMed

Oliveira, J P; de Siqueira, M E; da Silva, C S

2000-01-01

We measured urinary nickel (U-Ni) in ten workers (97 samples) from a galvanizing plant that uses nickel sulfate, and in ten control subjects (55 samples) to examine the association between occupational exposure to airborne Ni and Ni absorption. Samples from the exposed group were taken before and after the work shift on 5 successive workdays. At the same time airborne Ni (A-Ni) was measured using personal samplers. Ni levels in biological material and in the airborne were determined by a graphite furnace atomic absorption spectrometry validated method. In the control group the urine samples were collected twice a day, in the before and after the work shift, on 3 successive days. Ni exposure low to moderate was detected in all the examined places in the plant, the airborne levels varying between 2.8 and 116.7 micrograms/m3 and the urine levels, from samples taken postshift, between 4.5 and 43.2 micrograms/g creatinine (mean 14.7 micrograms/g creatinine). Significant differences in U-Ni creatinine were seen between the exposed and control groups (Student's t test, P < or = 0.01). A significant correlation between U-Ni and A-Ni (r = 0.96; P < or = 0.001) was detected. No statistical difference was observed in U-Ni collected from exposed workers in the 5 successive days, but significant difference was observed between pre- and postshift samples. Urinary nickel may be used as a reliable internal dose bioindicator in biological monitoring of workers exposed to Ni sulfate in galvanizing plants regardless of the day of the workweek on which the samples are collected.

UniScan technology for innovative laboratory at a university for acquisition data from space in real-time

NASA Astrophysics Data System (ADS)

Gershenzon, V.; Gershenzon, O.; Sergeeva, M.; Ippolitov, V.; Targulyan, O.

2012-04-01

Keywords: Remote Sensing, UniScan ground station, Education, Monitoring. Remote Sensing Centers allowing real-time imagery acquisition from Earth observing satellites within the structure of Universities provides proper environment for innovative education. It delivers the efficient training for scientific and academic and teaching personnel, secure the role of the young professionals in science, education and hi-tech, and maintain the continuity of generations in science and education. Article is based on experience for creation such centers in more than 20 higher education institutions in Russia, Kazakhstan, and Spain on the base of UniScan ground station by R&D Center ScanEx. These stations serve as the basis for Earth monitoring from space providing the training and advanced training to produce the specialists having the state-of-the-art knowledge in Earth Remote Sensing and GIS, as well as the land-use monitoring and geo-data service for the economic operators in such diverse areas as the nature resource management, agriculture, land property management, disasters monitoring, etc. Currently our proposal of UniScan for universities all over the world allows to receive low resolution free of charge MODIS data from Terra and Aqua satellites, VIIRS from the NPP mission, and also high resolution optical images from EROS A and radar images from Radarsat-1 satellites, including the telemetry for the first year of operation, within the footprint of up to 2,500 kilometers in radius. Creation remote sensing centers at universities will lead to a new quality level for education and scientific studies and will enable to make education system in such innovation institutions open to modern research work and economy.

Formaldehyde methods comparison in the remote lower troposphere during the Mauna Loa Photochemistry Experiment 2

NASA Astrophysics Data System (ADS)

Heikes, B.; McCully, B.; Zhou, X.; Lee, Y.-N.; Mopper, K.; Chen, X.; Mackay, G.; Karecki, D.; Schiff, H.; Campos, T.; Atlas, E.

1996-06-01

Five methods for the measurement of CH2O vapor were compared under remote tropospheric conditions. The techniques included an aqueous-scrubber enzyme fluorescence method (URIcoil), TDLAS (UNI), 2,4-dinitrophenylhydrazine (DNPH) impregnated-cartridges (BNL/WSUcart), an aqueous-scrubber DNPH method (BNL/WSUcoil), and an unpublished aqueous-scrubber immobilized-enzyme fluorescence method (NCARbound). This was part of the Mauna Loa Observatory Photochemistry Experiment 2 (MLOPEX 2) which was performed in four ˜30-day intensives. In MLOPEX 2a (fall 1991), the URIcoil technique indicated higher concentrations relative to the BNL/WSUcoil which were higher than UNI. The limited number of NCARbound measurements for MLOPEX 2a were greater than the other measurements and least reliable. During MLOPEX 2b (winter 1992), URIcoil, UNI, BNL/WSUcoil, and NCAR-bound gave comparable measurements of CH2O with the latter again being consistently higher than the first three methods and its performance and reliability was improved over MLOPEX 2a. URIcoil and BNL/WSUcoil were comparable in MLOPEX 2c (spring 1992) and 2d (summer 1992), whereas BNL/WSUcart was consistently higher than both for these intensives. The major source of difference between techniques was ascribed to variations in the analytical-procedural field blanks. Calibration differences were the most likely cause of URIcoil being higher than BNL/WSUcoil and BNL/WSUcoil being higher than UNI during MLOPEX 2a. Lower free troposphere median concentrations were between 100 and 150 ppt for all seasons and without a seasonal trend. These values were a factor of 2 to 3 lower than model estimates for this study site and were in keeping with earlier work.

The effect of different posts on fracture strength of roots with vertical fracture and re-attached fragments.

PubMed

Ozcopur, B; Akman, S; Eskitascioglu, G; Belli, S

2010-08-01

The aim of this in vitro study was to test the effect of different post systems on fracture strength of roots with re-attached fragments. Root canals of eighty extracted single-rooted human teeth were instrumented (ProFile) and randomly divided into two groups. The roots in the first group were vertically cracked, and the fragments were re-attached using Super Bond C&B (Sun Medical, Tokya, Japan). The roots in the second group were kept sound. Obturation of the roots was performed with MetaSEAL (Sun Medical) and gutta-percha. Post spaces were prepared, and the roots were restored with one of the followings: UniCore (Ultradent), Everstick (Stick Tech), Ribbond (Ribbond), ParaPost (Coltene/Whaledent) (n = 10). Four mm high build-ups were created (Clearfil DC Bond Core; Kuraray, Tokyo, Japan). Compressive loading of the samples was performed after 24 h (1 mm min(-1)). Mean load necessary to fracture each sample was recorded (Newton) and statistically analysed (One-way anova, t-tests). ParaPost showed the highest fracture strength among the roots with re-attached fragments (P < 0.05). UniCore and ParaPost systems showed similar fracture strength in the sound roots (P > 0.05). Re-attached fragments significantly reduced the fracture strength of roots in UniCore group (P = 0.000). Ribbond post showed mostly repairable fractures. Metal post (ParaPost) showed the highest fracture strength in the roots with re-attached fragments; however, fracture pattern was 41% non-repairable. Re-attached fragments significantly reduced the fracture strength of the roots in UniCore group. Prefabricated posts showed similar fracture strength in the sound roots. Customized post systems EverStick and Ribbond showed mostly repairable failure after loading in sound roots or roots with re-attached fragments.

Associations between micronutrient intakes and gut microbiota in a group of adults with cystic fibrosis.

PubMed

Li, Li; Krause, Lutz; Somerset, Shawn

2017-08-01

Cystic fibrosis (CF) involves chronic inflammation and oxidative stress affecting mainly the respiratory and digestive systems. Survival rates for CF have improved with advances in treatment including nutritional interventions such as micronutrient supplementation. Diet can modulate gut microbiota in the general population with consequences on local and systemic immunity, and inflammation. The gut microbiota appears disrupted and may associate with pulmonary status in CF. This study investigated associations between micronutrient intakes and gut microbiota variations in a group of adults with CF. Faecal microbiota of sixteen free-living adults with CF was profiled by 16ss rDNA sequencing on the GS-FLX platform. Associations were tested between UniFrac distances of faecal microbiota and time-corresponding micronutrient intakes. Associations between relative abundances of bacterial taxa and micronutrient intakes (those showing significant associations with UniFrac distances) were examined by Spearman correlation. Unweighted UniFrac distances were associated with intakes of potassium and antioxidant vitamins C, E and beta-carotene equivalents, whereas weighted UniFrac distances were associated with antioxidant vitamins riboflavin, niacin equivalents, beta-carotene equivalents and vitamin A equivalents. Intakes of beta-carotene equivalents, vitamin C, vitamin E, niacin equivalents and riboflavin correlated negatively with Bacteroides and/or its corresponding higher level taxa. Intakes of beta-carotene equivalents and vitamin E also positively correlated with Firmicutes and specific taxa belonging to Firmicutes. Some micronutrients, particularly antioxidant vitamins, correlated with gut microbiota variations in the studied cohort. Further research is required to clarify whether antioxidant vitamin intakes can influence CF gut microbiota and potential clinical/therapeutic implications in CF. Copyright © 2016 Elsevier Ltd and European Society for Clinical Nutrition and Metabolism. All rights reserved.

Characterization of the thermal conductivity for Advanced Toughened Uni-piece Fibrous Insulations

NASA Technical Reports Server (NTRS)

Stewart, David A.; Leiser, Daniel B.

1993-01-01

Advanced Toughened Uni-piece Fibrous Insulations (TUFI) is discussed in terms of their thermal response to an arc-jet air stream. A modification of the existing Ames thermal conductivity program to predict the thermal response of these functionally gradient materials is described in the paper. The modified program was used to evaluate the effect of density, surface porosity, and density gradient through the TUFI materials on the thermal response of these insulations. Predictions using a finite-difference code and calculated thermal conductivity values from the modified program were compared with in-depth temperature measurements taken from TUFI insulations during short exposures to arc-jet hypersonic air streams.

Study on Energy Absorption Capacity of Steel-Polyester Hybrid Fiber Reinforced Concrete Under Uni-axial Compression

NASA Astrophysics Data System (ADS)

Chella Gifta, C.; Prabavathy, S.

2018-05-01

This work presents the energy absorption capacity of hybrid fiber reinforced concrete made with hooked end steel fibers (0.5 and 0.75%) and straight polyester fibers (0.5, 0.8, 1.0 and 2.0%). Compressive toughness (energy absorption capacity) under uni-axial compression was evaluated on 100 × 200 mm size cylindrical specimens with varying steel and polyester fiber content. Efficiency of the hybrid fiber reinforcement is studied with respect to fiber type, size and volume fractions in this investigation. The vertical displacement under uni-axial compression was measured under the applied loads and the load-deformation curves were plotted. From these curves the toughness values were calculated and the results were compared with steel and polyester as individual fibers. The hybridization of 0.5% steel + 0.5% polyester performed well in post peak region due to the addition of polyester fibers with steel fibers and the energy absorption value was 23% greater than 0.5% steel FRC. Peak stress values were also higher in hybrid series than single fiber and based on the results it is concluded that hybrid fiber reinforcement improves the toughness characteristics of concrete without affecting workability.

Effects of small particle numbers on long-term behaviour in discrete biochemical systems

PubMed Central

Ibrahim, Bashar; Dittrich, Peter

2014-01-01

Motivation: The functioning of many biological processes depends on the appearance of only a small number of a single molecular species. Additionally, the observation of molecular crowding leads to the insight that even a high number of copies of species do not guarantee their interaction. How single particles contribute to stabilizing biological systems is not well understood yet. Hence, we aim at determining the influence of single molecules on the long-term behaviour of biological systems, i.e. whether they can reach a steady state. Results: We provide theoretical considerations and a tool to analyse Systems Biology Markup Language models for the possibility to stabilize because of the described effects. The theory is an extension of chemical organization theory, which we called discrete chemical organization theory. Furthermore we scanned the BioModels Database for the occurrence of discrete chemical organizations. To exemplify our method, we describe an application to the Template model of the mitotic spindle assembly checkpoint mechanism. Availability and implementation: http://www.biosys.uni-jena.de/Services.html. Contact: bashar.ibrahim@uni-jena.de or dittrich@minet.uni-jena.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25161236

Home delivery of heat-stable vaccines in Indonesia: outreach immunization with a prefilled, single-use injection device.

PubMed Central

Sutanto, A.; Suarnawa, I. M.; Nelson, C. M.; Stewart, T.; Soewarso, T. I.

1999-01-01

Extending immunization coverage to underserved populations will require innovative immunization strategies. This study evaluated one such strategy: the use of a prefilled, single-use injection device for outreach immunization by village midwives. The device, UniJect, is designed to prevent refilling or reuse. Stored at ambient temperatures for up to 1 month in midwives' homes, vaccine-filled UniJect devices were immediately available for outreach. Between July 1995 and April 1996, 110 midwives on the Indonesia islands of Lombok and Bali visited the homes of newborn infants to deliver hepatitis B vaccine to the infants and tetanus toxoid to their mothers. Observations and interviews showed that the midwives used the device properly and safely to administer approximately 10,000 sterile injections in home settings. There were no problems with excessive heat exposure during the storage or delivery of vaccine. Injection recipients and midwives expressed a strong preference for the UniJect device over a standard syringe. Use of the prefilled device outside the cold chain simplified the logistics and facilitated the speed and efficiency of home visits, while the single-dose format minimized vaccine wastage. PMID:10083709

BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins.

PubMed

van Heel, Auke J; de Jong, Anne; Song, Chunxu; Viel, Jakob H; Kok, Jan; Kuipers, Oscar P

2018-05-21

Interest in secondary metabolites such as RiPPs (ribosomally synthesized and posttranslationally modified peptides) is increasing worldwide. To facilitate the research in this field we have updated our mining web server. BAGEL4 is faster than its predecessor and is now fully independent from ORF-calling. Gene clusters of interest are discovered using the core-peptide database and/or through HMM motifs that are present in associated context genes. The databases used for mining have been updated and extended with literature references and links to UniProt and NCBI. Additionally, we have included automated promoter and terminator prediction and the option to upload RNA expression data, which can be displayed along with the identified clusters. Further improvements include the annotation of the context genes, which is now based on a fast blast against the prokaryote part of the UniRef90 database, and the improved web-BLAST feature that dynamically loads structural data such as internal cross-linking from UniProt. Overall BAGEL4 provides the user with more information through a user-friendly web-interface which simplifies data evaluation. BAGEL4 is freely accessible at http://bagel4.molgenrug.nl.

METSP: a maximum-entropy classifier based text mining tool for transporter-substrate identification with semistructured text.

PubMed

Zhao, Min; Chen, Yanming; Qu, Dacheng; Qu, Hong

2015-01-01

The substrates of a transporter are not only useful for inferring function of the transporter, but also important to discover compound-compound interaction and to reconstruct metabolic pathway. Though plenty of data has been accumulated with the developing of new technologies such as in vitro transporter assays, the search for substrates of transporters is far from complete. In this article, we introduce METSP, a maximum-entropy classifier devoted to retrieve transporter-substrate pairs (TSPs) from semistructured text. Based on the high quality annotation from UniProt, METSP achieves high precision and recall in cross-validation experiments. When METSP is applied to 182,829 human transporter annotation sentences in UniProt, it identifies 3942 sentences with transporter and compound information. Finally, 1547 confidential human TSPs are identified for further manual curation, among which 58.37% pairs with novel substrates not annotated in public transporter databases. METSP is the first efficient tool to extract TSPs from semistructured annotation text in UniProt. This tool can help to determine the precise substrates and drugs of transporters, thus facilitating drug-target prediction, metabolic network reconstruction, and literature classification.

Malaysian Twin Registry.

PubMed

Jahanfar, Shayesteh; Jaffar, Sharifah Halimah

2013-02-01

The National Malaysian Twin Registry was established in Royal College of Medicine, Perak, University Kuala Lumpur (UniKL) in June 2008 through a grant provided by UniKL. The general objective is to facilitate scientific research involving participation of twins and their family members in order to answer questions of health and wellbeing relevant to Malaysians. Recruitment is done via mass media, poster, and pamphlets. We now have 266 adult and 204 children twins registered. Several research projects including reproductive health study of twins and the role of co-bedding on growth and development of children are carried out. Registry holds annual activities for twins and seeks to provide health-related information for twins. We seek international collaboration.

Magnetic anisotropy on the single crystal UNi4B probed by 11B NMR

NASA Astrophysics Data System (ADS)

Kishimoto, Yasuki; Matsuno, Haruki; Kotegawa, Hisashi; Tou, Hideki; Saito, Hiraku; Amitsuka, Hiroshi; Homma, Yoshiya; Nakamura, Ai; Li, Dexin; Honda, Fuminori; Aoki, Dai

2018-05-01

We have performed a susceptibility M / H and 11B NMR measurements to investigate the static magnetic anisotropy of a single crystal UNi4B. The Knight shift 11K and the hyperfine coupling constant Ahf evaluated by 11K- M / H plot show anisotropic behavior between H ∥ [ 11 2 bar 0 ] and H ∥ [ 0001 ] , reflecting the bulk susceptibility. The evaluated transferred term Atr of Ahf for H ∥ [ 11 2 bar 0 ] is much larger than the one for H ∥ [ 0001 ] . The strong hybridization in the [0001]-plane due to a itinerant 5f-electron is strongly associated with the unique magnetic structure in this compound.

Modeling and simulation of queuing system for customer service improvement: A case study

NASA Astrophysics Data System (ADS)

Xian, Tan Chai; Hong, Chai Weng; Hawari, Nurul Nazihah

2016-10-01

This study aims to develop a queuing model at UniMall by using discrete event simulation approach in analyzing the service performance that affects customer satisfaction. The performance measures that considered in this model are such as the average time in system, the total number of student served, the number of student in waiting queue, the waiting time in queue as well as the maximum length of buffer. ARENA simulation software is used to develop a simulation model and the output is analyzed. Based on the analysis of output, it is recommended that management of UniMall consider introducing shifts and adding another payment counter in the morning.

[Validation of plasma creatinine measurement on UniCel DxC 600 according to LAB GTA 04 recommendation].

PubMed

Chianea, Denis; Renard, Christophe; Garcia, Carine; Mbongo, Elvire; Monpeurt, Corine; Vest, Philippe

2010-01-01

The accreditation process, according to NF EN ISO 15189, implies a prior evaluation of the new reagent on-site for the implementation of each new assay technique. Thus, our new standardized method for determination of creatinine (non compensated method) in plasma or serum on UniCel DxC 600 (Beckman Coulter) has been tested according to LAB GTA 04 protocol. The reagent meets the quality criteria recommended by Valtec protocol, except fidelity with the low concentration standard (50 micromol/L). Besides there is no problem of results transferability with the two other techniques used in the laboratory (Jaffe compensated and enzymatic methods performed on Cobas Integra 800).

PDBe: Protein Data Bank in Europe

PubMed Central

Velankar, S.; Alhroub, Y.; Best, C.; Caboche, S.; Conroy, M. J.; Dana, J. M.; Fernandez Montecelo, M. A.; van Ginkel, G.; Golovin, A.; Gore, S. P.; Gutmanas, A.; Haslam, P.; Hendrickx, P. M. S.; Heuson, E.; Hirshberg, M.; John, M.; Lagerstedt, I.; Mir, S.; Newman, L. E.; Oldfield, T. J.; Patwardhan, A.; Rinaldi, L.; Sahni, G.; Sanz-García, E.; Sen, S.; Slowley, R.; Suarez-Uruena, A.; Swaminathan, G. J.; Symmons, M. F.; Vranken, W. F.; Wainwright, M.; Kleywegt, G. J.

2012-01-01

The Protein Data Bank in Europe (PDBe; pdbe.org) is a partner in the Worldwide PDB organization (wwPDB; wwpdb.org) and as such actively involved in managing the single global archive of biomacromolecular structure data, the PDB. In addition, PDBe develops tools, services and resources to make structure-related data more accessible to the biomedical community. Here we describe recently developed, extended or improved services, including an animated structure-presentation widget (PDBportfolio), a widget to graphically display the coverage of any UniProt sequence in the PDB (UniPDB), chemistry- and taxonomy-based PDB-archive browsers (PDBeXplore), and a tool for interactive visualization of NMR structures, corresponding experimental data as well as validation and analysis results (Vivaldi). PMID:22110033

The Proteins API: accessing key integrated protein and genome information

PubMed Central

Antunes, Ricardo; Alpi, Emanuele; Gonzales, Leonardo; Liu, Wudong; Luo, Jie; Qi, Guoying; Turner, Edd

2017-01-01

Abstract The Proteins API provides searching and programmatic access to protein and associated genomics data such as curated protein sequence positional annotations from UniProtKB, as well as mapped variation and proteomics data from large scale data sources (LSS). Using the coordinates service, researchers are able to retrieve the genomic sequence coordinates for proteins in UniProtKB. This, the LSS genomics and proteomics data for UniProt proteins is programmatically only available through this service. A Swagger UI has been implemented to provide documentation, an interface for users, with little or no programming experience, to ‘talk’ to the services to quickly and easily formulate queries with the services and obtain dynamically generated source code for popular programming languages, such as Java, Perl, Python and Ruby. Search results are returned as standard JSON, XML or GFF data objects. The Proteins API is a scalable, reliable, fast, easy to use RESTful services that provides a broad protein information resource for users to ask questions based upon their field of expertise and allowing them to gain an integrated overview of protein annotations available to aid their knowledge gain on proteins in biological processes. The Proteins API is available at (http://www.ebi.ac.uk/proteins/api/doc). PMID:28383659

Deep learning for tumor classification in imaging mass spectrometry.

PubMed

Behrmann, Jens; Etmann, Christian; Boskamp, Tobias; Casadonte, Rita; Kriegsmann, Jörg; Maaß, Peter

2018-04-01

Tumor classification using imaging mass spectrometry (IMS) data has a high potential for future applications in pathology. Due to the complexity and size of the data, automated feature extraction and classification steps are required to fully process the data. Since mass spectra exhibit certain structural similarities to image data, deep learning may offer a promising strategy for classification of IMS data as it has been successfully applied to image classification. Methodologically, we propose an adapted architecture based on deep convolutional networks to handle the characteristics of mass spectrometry data, as well as a strategy to interpret the learned model in the spectral domain based on a sensitivity analysis. The proposed methods are evaluated on two algorithmically challenging tumor classification tasks and compared to a baseline approach. Competitiveness of the proposed methods is shown on both tasks by studying the performance via cross-validation. Moreover, the learned models are analyzed by the proposed sensitivity analysis revealing biologically plausible effects as well as confounding factors of the considered tasks. Thus, this study may serve as a starting point for further development of deep learning approaches in IMS classification tasks. https://gitlab.informatik.uni-bremen.de/digipath/Deep_Learning_for_Tumor_Classification_in_IMS. jbehrmann@uni-bremen.de or christianetmann@uni-bremen.de. Supplementary data are available at Bioinformatics online.

Potential for false positive HIV test results with the serial rapid HIV testing algorithm.

PubMed

Baveewo, Steven; Kamya, Moses R; Mayanja-Kizza, Harriet; Fatch, Robin; Bangsberg, David R; Coates, Thomas; Hahn, Judith A; Wanyenze, Rhoda K

2012-03-19

Rapid HIV tests provide same-day results and are widely used in HIV testing programs in areas with limited personnel and laboratory infrastructure. The Uganda Ministry of Health currently recommends the serial rapid testing algorithm with Determine, STAT-PAK, and Uni-Gold for diagnosis of HIV infection. Using this algorithm, individuals who test positive on Determine, negative to STAT-PAK and positive to Uni-Gold are reported as HIV positive. We conducted further testing on this subgroup of samples using qualitative DNA PCR to assess the potential for false positive tests in this situation. Of the 3388 individuals who were tested, 984 were HIV positive on two consecutive tests, and 29 were considered positive by a tiebreaker (positive on Determine, negative on STAT-PAK, and positive on Uni-Gold). However, when the 29 samples were further tested using qualitative DNA PCR, 14 (48.2%) were HIV negative. Although this study was not primarily designed to assess the validity of rapid HIV tests and thus only a subset of the samples were retested, the findings show a potential for false positive HIV results in the subset of individuals who test positive when a tiebreaker test is used in serial testing. These findings highlight a need for confirmatory testing for this category of individuals.

Potential for false positive HIV test results with the serial rapid HIV testing algorithm

PubMed Central

2012-01-01

Background Rapid HIV tests provide same-day results and are widely used in HIV testing programs in areas with limited personnel and laboratory infrastructure. The Uganda Ministry of Health currently recommends the serial rapid testing algorithm with Determine, STAT-PAK, and Uni-Gold for diagnosis of HIV infection. Using this algorithm, individuals who test positive on Determine, negative to STAT-PAK and positive to Uni-Gold are reported as HIV positive. We conducted further testing on this subgroup of samples using qualitative DNA PCR to assess the potential for false positive tests in this situation. Results Of the 3388 individuals who were tested, 984 were HIV positive on two consecutive tests, and 29 were considered positive by a tiebreaker (positive on Determine, negative on STAT-PAK, and positive on Uni-Gold). However, when the 29 samples were further tested using qualitative DNA PCR, 14 (48.2%) were HIV negative. Conclusion Although this study was not primarily designed to assess the validity of rapid HIV tests and thus only a subset of the samples were retested, the findings show a potential for false positive HIV results in the subset of individuals who test positive when a tiebreaker test is used in serial testing. These findings highlight a need for confirmatory testing for this category of individuals. PMID:22429706

Examination of a Thermally Viable Structure for an Unconventional Uni-Leg Mg2Si Thermoelectric Power Generator

NASA Astrophysics Data System (ADS)

Sakamoto, Tatsuya; Iida, Tsutomu; Taguchi, Yutaka; Kurosaki, Shota; Hayatsu, Yusuke; Nishio, Keishi; Kogo, Yasuo; Takanashi, Yoshifumi

2012-06-01

We have fabricated an unconventional uni-leg structure thermoelectric generator (TEG) element using quad thermoelectric (TE) chips of Sb-doped n-Mg2Si, which were prepared by a plasma-activated sintering process. The power curve characteristics, the effect of aging up to 500 h, and the thermal gradients at several points on the module were investigated. The observed maximum output power with the heat source at 975 K and the heat sink at 345 K was 341 mW, from which the Δ T for the TE chip was calculated to be about 333 K. In aging testing in air ambient, a remarkable feature of the results was that there was no notable change from the initial resistance of the TEG module for as long as 500 h. The thermal distribution for the fabricated uni-leg TEG element was analyzed by finite-element modeling using ANSYS software. To tune the calculation parameters of ANSYS, such as the thermal conductance properties of the corresponding coupled materials in the module, precise measurements of the temperature at various probe points on the module were made. Then, meticulous verification between the measured temperature values and the results calculated by ANSYS was carried out to optimize the parameters.

Usefulness of an Internet-based thematic learning network: comparison of effectiveness with traditional teaching.

PubMed

Coma Del Corral, María Jesús; Guevara, José Cordero; Luquin, Pedro Abáigar; Peña, Horacio J; Mateos Otero, Juan José

2006-03-01

UniNet is an Internet-based thematic network for a virtual community of users (VCU). It supports one multidisciplinary community of doctoral students, who receive most of the courses on the network. The evident advantages of distance learning by Internet, in terms of costs, comfort, etc., require a previous evaluation of the system, focusing on the learning outcomes of the student. The aim was to evaluate the real learning of the students of doctorate courses, by comparing the effectiveness of distance learning in UniNet with traditional classroom-based teaching. Five doctorate courses were taught simultaneously to two independent groups of students in two ways: one, through the UniNet Network, and the other in a traditional classroom. The academic knowledge of students was evaluated at the beginning and end of each course. The difference in score was considered as a knowledge increase. The comparison was made using Student's t-test for independent groups. There were no significant statistical differences in the outcomes of the two groups of students. This suggests that both teaching systems were equivalent in increasing the knowledge of the students. Both educational methods, the traditional system and the online system in a thematic network, are effective and similar for increasing knowledge.

Towards Spectral Library-free MALDI-TOF MS Bacterial Identification.

PubMed

Cheng, Ding; Qiao, Liang; Horvatovich, Péter

2018-05-11

Bacterial identification is of great importance in clinical diagnosis, environmental monitoring and food safety control. Among various strategies, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has drawn significant interests, and has been clinically used. Nevertheless, current bioinformatics solutions use spectral libraries for the identification of bacterial strains. Spectral library generation requires acquisition of MALDI-TOF spectra from monoculture bacterial colonies, which is time-consuming and not possible for many species and strains. We propose a strategy for bacterial typing by MALDI-TOF using protein sequences from public database, i.e. UniProt. Ten genes were identified to encode proteins most often observed by MALD-TOF from bacteria through 500 times repeated a 10-fold double cross-validation procedure, using 403 MALDI-TOF spectra corresponding to 14 genera, 81 species and 403 strains, and the protein sequences of 1276 species in UniProt. The 10 genes were then used to annotate peaks on MALDI-TOF spectra of bacteria for bacterial identification. With the approach, bacteria can be identified at the genus level by searching against a database containing the protein sequences of 42 genera of bacteria from UniProt. Our approach identified 84.1% of the 403 spectra correctly at the genus level. Source code of the algorithm is available at https://github.com/dipcarbon/BacteriaMSLF.

An emerging cyberinfrastructure for biodefense pathogen and pathogen-host data.

PubMed

Zhang, C; Crasta, O; Cammer, S; Will, R; Kenyon, R; Sullivan, D; Yu, Q; Sun, W; Jha, R; Liu, D; Xue, T; Zhang, Y; Moore, M; McGarvey, P; Huang, H; Chen, Y; Zhang, J; Mazumder, R; Wu, C; Sobral, B

2008-01-01

The NIAID-funded Biodefense Proteomics Resource Center (RC) provides storage, dissemination, visualization and analysis capabilities for the experimental data deposited by seven Proteomics Research Centers (PRCs). The data and its publication is to support researchers working to discover candidates for the next generation of vaccines, therapeutics and diagnostics against NIAID's Category A, B and C priority pathogens. The data includes transcriptional profiles, protein profiles, protein structural data and host-pathogen protein interactions, in the context of the pathogen life cycle in vivo and in vitro. The database has stored and supported host or pathogen data derived from Bacillus, Brucella, Cryptosporidium, Salmonella, SARS, Toxoplasma, Vibrio and Yersinia, human tissue libraries, and mouse macrophages. These publicly available data cover diverse data types such as mass spectrometry, yeast two-hybrid (Y2H), gene expression profiles, X-ray and NMR determined protein structures and protein expression clones. The growing database covers over 23 000 unique genes/proteins from different experiments and organisms. All of the genes/proteins are annotated and integrated across experiments using UniProt Knowledgebase (UniProtKB) accession numbers. The web-interface for the database enables searching, querying and downloading at the level of experiment, group and individual gene(s)/protein(s) via UniProtKB accession numbers or protein function keywords. The system is accessible at http://www.proteomicsresource.org/.

Fungal genome resources at NCBI.

PubMed

Robbertse, B; Tatusova, T

2011-09-01

The National Center for Biotechnology Information (NCBI) is well known for the nucleotide sequence archive, GenBank and sequence analysis tool BLAST. However, NCBI integrates many types of biomolecular data from variety of sources and makes it available to the scientific community as interactive web resources as well as organized releases of bulk data. These tools are available to explore and compare fungal genomes. Searching all databases with Fungi [organism] at http://www.ncbi.nlm.nih.gov/ is the quickest way to find resources of interest with fungal entries. Some tools though are resources specific and can be indirectly accessed from a particular database in the Entrez system. These include graphical viewers and comparative analysis tools such as TaxPlot, TaxMap and UniGene DDD (found via UniGene Homepage). Gene and BioProject pages also serve as portals to external data such as community annotation websites, BioGrid and UniProt. There are many different ways of accessing genomic data at NCBI. Depending on the focus and goal of research projects or the level of interest, a user would select a particular route for accessing genomic databases and resources. This review article describes methods of accessing fungal genome data and provides examples that illustrate the use of analysis tools.

Using distant supervised learning to identify protein subcellular localizations from full-text scientific articles.

PubMed

Zheng, Wu; Blake, Catherine

2015-10-01

Databases of curated biomedical knowledge, such as the protein-locations reflected in the UniProtKB database, provide an accurate and useful resource to researchers and decision makers. Our goal is to augment the manual efforts currently used to curate knowledge bases with automated approaches that leverage the increased availability of full-text scientific articles. This paper describes experiments that use distant supervised learning to identify protein subcellular localizations, which are important to understand protein function and to identify candidate drug targets. Experiments consider Swiss-Prot, the manually annotated subset of the UniProtKB protein knowledge base, and 43,000 full-text articles from the Journal of Biological Chemistry that contain just under 11.5 million sentences. The system achieves 0.81 precision and 0.49 recall at sentence level and an accuracy of 57% on held-out instances in a test set. Moreover, the approach identifies 8210 instances that are not in the UniProtKB knowledge base. Manual inspection of the 50 most likely relations showed that 41 (82%) were valid. These results have immediate benefit to researchers interested in protein function, and suggest that distant supervision should be explored to complement other manual data curation efforts. Copyright © 2015 Elsevier Inc. All rights reserved.

Study of the Forced Response of a Clamped Circular Plate Coupled to a Uni-Dimensional Acoustic Cavity

NASA Astrophysics Data System (ADS)

Curà, F.; Curti, G.; Mantovani, M.

1996-03-01

The subject of this paper is an experimental and analytical study of a structural-acoustical coupling problem. To simplify the issue, the analytical model considered here consists of a uni-dimensional acoustic cavity coupled to a one-degree-of-freedom system (mass, spring and damper). An harmonic excitation force is applied to the mass of the oscillator. In the theoretical analysis, the uni-dimensional cavity is subjected, in correspondence of its end sections, to boundary conditions, which are either the usual ones (closed or open ended) or those deriving from the coupling with the oscillator. This simple model proved to be very useful to investigate the influence of the variation of both the geometrical parameters (i.e., the length of the cavity) and the physical parameters (i.e., mass, damping coefficient and stiffness of the oscillator). The analytical results are compared to those obtained experimentally on a real coupled system, consisting of a cavity enclosed by an acoustically rigid steel cylinder, closed at one end by a movable, acoustically rigid piston and at the other end by a flexible plate, clamped around its edge by the cylinder. Thus the length of the cavity can be varied by simply moving the rigid piston.

The BioExtract Server: a web-based bioinformatic workflow platform

PubMed Central

Lushbough, Carol M.; Jennewein, Douglas M.; Brendel, Volker P.

2011-01-01

The BioExtract Server (bioextract.org) is an open, web-based system designed to aid researchers in the analysis of genomic data by providing a platform for the creation of bioinformatic workflows. Scientific workflows are created within the system by recording tasks performed by the user. These tasks may include querying multiple, distributed data sources, saving query results as searchable data extracts, and executing local and web-accessible analytic tools. The series of recorded tasks can then be saved as a reproducible, sharable workflow available for subsequent execution with the original or modified inputs and parameter settings. Integrated data resources include interfaces to the National Center for Biotechnology Information (NCBI) nucleotide and protein databases, the European Molecular Biology Laboratory (EMBL-Bank) non-redundant nucleotide database, the Universal Protein Resource (UniProt), and the UniProt Reference Clusters (UniRef) database. The system offers access to numerous preinstalled, curated analytic tools and also provides researchers with the option of selecting computational tools from a large list of web services including the European Molecular Biology Open Software Suite (EMBOSS), BioMoby, and the Kyoto Encyclopedia of Genes and Genomes (KEGG). The system further allows users to integrate local command line tools residing on their own computers through a client-side Java applet. PMID:21546552

DESM: portal for microbial knowledge exploration systems.

PubMed

Salhi, Adil; Essack, Magbubah; Radovanovic, Aleksandar; Marchand, Benoit; Bougouffa, Salim; Antunes, Andre; Simoes, Marta Filipa; Lafi, Feras F; Motwalli, Olaa A; Bokhari, Ameerah; Malas, Tariq; Amoudi, Soha Al; Othum, Ghofran; Allam, Intikhab; Mineta, Katsuhiko; Gao, Xin; Hoehndorf, Robert; C Archer, John A; Gojobori, Takashi; Bajic, Vladimir B

2016-01-04

Microorganisms produce an enormous variety of chemical compounds. It is of general interest for microbiology and biotechnology researchers to have means to explore information about molecular and genetic basis of functioning of different microorganisms and their ability for bioproduction. To enable such exploration, we compiled 45 topic-specific knowledgebases (KBs) accessible through DESM portal (www.cbrc.kaust.edu.sa/desm). The KBs contain information derived through text-mining of PubMed information and complemented by information data-mined from various other resources (e.g. ChEBI, Entrez Gene, GO, KOBAS, KEGG, UniPathways, BioGrid). All PubMed records were indexed using 4,538,278 concepts from 29 dictionaries, with 1 638 986 records utilized in KBs. Concepts used are normalized whenever possible. Most of the KBs focus on a particular type of microbial activity, such as production of biocatalysts or nutraceuticals. Others are focused on specific categories of microorganisms, e.g. streptomyces or cyanobacteria. KBs are all structured in a uniform manner and have a standardized user interface. Information exploration is enabled through various searches. Users can explore statistically most significant concepts or pairs of concepts, generate hypotheses, create interactive networks of associated concepts and export results. We believe DESM will be a useful complement to the existing resources to benefit microbiology and biotechnology research. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

The EMBL-EBI bioinformatics web and programmatic tools framework.

PubMed

Li, Weizhong; Cowley, Andrew; Uludag, Mahmut; Gur, Tamer; McWilliam, Hamish; Squizzato, Silvano; Park, Young Mi; Buso, Nicola; Lopez, Rodrigo

2015-07-01

Since 2009 the EMBL-EBI Job Dispatcher framework has provided free access to a range of mainstream sequence analysis applications. These include sequence similarity search services (https://www.ebi.ac.uk/Tools/sss/) such as BLAST, FASTA and PSI-Search, multiple sequence alignment tools (https://www.ebi.ac.uk/Tools/msa/) such as Clustal Omega, MAFFT and T-Coffee, and other sequence analysis tools (https://www.ebi.ac.uk/Tools/pfa/) such as InterProScan. Through these services users can search mainstream sequence databases such as ENA, UniProt and Ensembl Genomes, utilising a uniform web interface or systematically through Web Services interfaces (https://www.ebi.ac.uk/Tools/webservices/) using common programming languages, and obtain enriched results with novel visualisations. Integration with EBI Search (https://www.ebi.ac.uk/ebisearch/) and the dbfetch retrieval service (https://www.ebi.ac.uk/Tools/dbfetch/) further expands the usefulness of the framework. New tools and updates such as NCBI BLAST+, InterProScan 5 and PfamScan, new categories such as RNA analysis tools (https://www.ebi.ac.uk/Tools/rna/), new databases such as ENA non-coding, WormBase ParaSite, Pfam and Rfam, and new workflow methods, together with the retirement of depreciated services, ensure that the framework remains relevant to today's biological community. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software.

PubMed

Kriventseva, Evgenia V; Tegenfeldt, Fredrik; Petty, Tom J; Waterhouse, Robert M; Simão, Felipe A; Pozdnyakov, Igor A; Ioannidis, Panagiotis; Zdobnov, Evgeny M

2015-01-01

Orthology, refining the concept of homology, is the cornerstone of evolutionary comparative studies. With the ever-increasing availability of genomic data, inference of orthology has become instrumental for generating hypotheses about gene functions crucial to many studies. This update of the OrthoDB hierarchical catalog of orthologs (http://www.orthodb.org) covers 3027 complete genomes, including the most comprehensive set of 87 arthropods, 61 vertebrates, 227 fungi and 2627 bacteria (sampling the most complete and representative genomes from over 11,000 available). In addition to the most extensive integration of functional annotations from UniProt, InterPro, GO, OMIM, model organism phenotypes and COG functional categories, OrthoDB uniquely provides evolutionary annotations including rates of ortholog sequence divergence, copy-number profiles, sibling groups and gene architectures. We re-designed the entirety of the OrthoDB website from the underlying technology to the user interface, enabling the user to specify species of interest and to select the relevant orthology level by the NCBI taxonomy. The text searches allow use of complex logic with various identifiers of genes, proteins, domains, ontologies or annotation keywords and phrases. Gene copy-number profiles can also be queried. This release comes with the freely available underlying ortholog clustering pipeline (http://www.orthodb.org/software). © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites.

PubMed

Ribeiro, António J M; Holliday, Gemma L; Furnham, Nicholas; Tyzack, Jonathan D; Ferris, Katherine; Thornton, Janet M

2018-01-04

M-CSA (Mechanism and Catalytic Site Atlas) is a database of enzyme active sites and reaction mechanisms that can be accessed at www.ebi.ac.uk/thornton-srv/m-csa. Our objectives with M-CSA are to provide an open data resource for the community to browse known enzyme reaction mechanisms and catalytic sites, and to use the dataset to understand enzyme function and evolution. M-CSA results from the merging of two existing databases, MACiE (Mechanism, Annotation and Classification in Enzymes), a database of enzyme mechanisms, and CSA (Catalytic Site Atlas), a database of catalytic sites of enzymes. We are releasing M-CSA as a new website and underlying database architecture. At the moment, M-CSA contains 961 entries, 423 of these with detailed mechanism information, and 538 with information on the catalytic site residues only. In total, these cover 81% (195/241) of third level EC numbers with a PDB structure, and 30% (840/2793) of fourth level EC numbers with a PDB structure, out of 6028 in total. By searching for close homologues, we are able to extend M-CSA coverage of PDB and UniProtKB to 51 993 structures and to over five million sequences, respectively, of which about 40% and 30% have a conserved active site. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

PolySearch2: a significantly improved text-mining system for discovering associations between human diseases, genes, drugs, metabolites, toxins and more.

PubMed

Liu, Yifeng; Liang, Yongjie; Wishart, David

2015-07-01

PolySearch2 (http://polysearch.ca) is an online text-mining system for identifying relationships between biomedical entities such as human diseases, genes, SNPs, proteins, drugs, metabolites, toxins, metabolic pathways, organs, tissues, subcellular organelles, positive health effects, negative health effects, drug actions, Gene Ontology terms, MeSH terms, ICD-10 medical codes, biological taxonomies and chemical taxonomies. PolySearch2 supports a generalized 'Given X, find all associated Ys' query, where X and Y can be selected from the aforementioned biomedical entities. An example query might be: 'Find all diseases associated with Bisphenol A'. To find its answers, PolySearch2 searches for associations against comprehensive collections of free-text collections, including local versions of MEDLINE abstracts, PubMed Central full-text articles, Wikipedia full-text articles and US Patent application abstracts. PolySearch2 also searches 14 widely used, text-rich biological databases such as UniProt, DrugBank and Human Metabolome Database to improve its accuracy and coverage. PolySearch2 maintains an extensive thesaurus of biological terms and exploits the latest search engine technology to rapidly retrieve relevant articles and databases records. PolySearch2 also generates, ranks and annotates associative candidates and present results with relevancy statistics and highlighted key sentences to facilitate user interpretation. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

SANSparallel: interactive homology search against Uniprot.

PubMed

Somervuo, Panu; Holm, Liisa

2015-07-01

Proteins evolve by mutations and natural selection. The network of sequence similarities is a rich source for mining homologous relationships that inform on protein structure and function. There are many servers available to browse the network of homology relationships but one has to wait up to a minute for results. The SANSparallel webserver provides protein sequence database searches with immediate response and professional alignment visualization by third-party software. The output is a list, pairwise alignment or stacked alignment of sequence-similar proteins from Uniprot, UniRef90/50, Swissprot or Protein Data Bank. The stacked alignments are viewed in Jalview or as sequence logos. The database search uses the suffix array neighborhood search (SANS) method, which has been re-implemented as a client-server, improved and parallelized. The method is extremely fast and as sensitive as BLAST above 50% sequence identity. Benchmarks show that the method is highly competitive compared to previously published fast database search programs: UBLAST, DIAMOND, LAST, LAMBDA, RAPSEARCH2 and BLAT. The web server can be accessed interactively or programmatically at http://ekhidna2.biocenter.helsinki.fi/cgi-bin/sans/sans.cgi. It can be used to make protein functional annotation pipelines more efficient, and it is useful in interactive exploration of the detailed evidence supporting the annotation of particular proteins of interest. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Effects of forming temperature and sintering rate to the final properties of FeCuAl powder compacts formed through uniaxial die compaction process

NASA Astrophysics Data System (ADS)

Rahman, M. M.; Ismail, M. A.; Sopyan, I.; Rahman, H. Y.

2018-01-01

This paper presents the outcomes of an experimental investigation on the effects of forming temperature and sintering schedule to the final characteristics of FeCuAl powder mass formed at different temperature and sintered at different schedule. A lab-scale uni-axial die compaction rig was designed and fabricated which enabled the compaction of powder mass at room temperature as well as elevated temperature. Iron (Fe) powder ASC 100.29 was mechanically mixed with other elemental powders, namely copper (Cu), and aluminum (Al) for 60 minutes and compacted at three different temperature, i.e., 30°C, 150°C, and 200°C by applying 425 MPa of simultaneous downward and upward axial loading to generate green compacts. The as-pressed samples were inspected visually and the defect-free green compacts were subsequently sintered in an argon gas fired furnace at 800°C for 60 min at three different heating/cooling rates, i.e., 5, 10, and 15°C/min, respectively. The sintered samples were then characterised for their physical, electrical, and mechanical properties. The microstructures of the sintered samples were also analysed. The results revealed that a forming temperature of 150°C and a sintering rate of 10°C/min could produce a product with better characteristics.

Database resources of the National Center for Biotechnology Information.

PubMed

2016-01-04

The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank(®) nucleic acid sequence database and the PubMed database of citations and abstracts for published life science journals. Additional NCBI resources focus on literature (PubMed Central (PMC), Bookshelf and PubReader), health (ClinVar, dbGaP, dbMHC, the Genetic Testing Registry, HIV-1/Human Protein Interaction Database and MedGen), genomes (BioProject, Assembly, Genome, BioSample, dbSNP, dbVar, Epigenomics, the Map Viewer, Nucleotide, Probe, RefSeq, Sequence Read Archive, the Taxonomy Browser and the Trace Archive), genes (Gene, Gene Expression Omnibus (GEO), HomoloGene, PopSet and UniGene), proteins (Protein, the Conserved Domain Database (CDD), COBALT, Conserved Domain Architecture Retrieval Tool (CDART), the Molecular Modeling Database (MMDB) and Protein Clusters) and chemicals (Biosystems and the PubChem suite of small molecule databases). The Entrez system provides search and retrieval operations for most of these databases. Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized datasets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov. Published by Oxford University Press on behalf of Nucleic Acids Research 2015. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Database resources of the National Center for Biotechnology Information.

PubMed

2015-01-01

The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank(®) nucleic acid sequence database and the PubMed database of citations and abstracts for published life science journals. Additional NCBI resources focus on literature (Bookshelf, PubMed Central (PMC) and PubReader); medical genetics (ClinVar, dbMHC, the Genetic Testing Registry, HIV-1/Human Protein Interaction Database and MedGen); genes and genomics (BioProject, BioSample, dbSNP, dbVar, Epigenomics, Gene, Gene Expression Omnibus (GEO), Genome, HomoloGene, the Map Viewer, Nucleotide, PopSet, Probe, RefSeq, Sequence Read Archive, the Taxonomy Browser, Trace Archive and UniGene); and proteins and chemicals (Biosystems, COBALT, the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), the Molecular Modeling Database (MMDB), Protein Clusters, Protein and the PubChem suite of small molecule databases). The Entrez system provides search and retrieval operations for many of these databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at http://www.ncbi.nlm.nih.gov. Published by Oxford University Press on behalf of Nucleic Acids Research 2014. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Effects of La2O3 content and particle size on the long-term stability and thermal cycling property of La2O3-dispersed SUS430 alloys for SOFC interconnect materials

NASA Astrophysics Data System (ADS)

Lee, Jung-Won; Mehran, Muhammad Taqi; Song, Rak-Hyun; Lee, Seung-Bok; Lee, Jong-Won; Lim, Tak-Hyoung; Park, Seok-Joo; Hong, Jong-Eun; Shim, Joon-Hyung

2017-11-01

We developed oxide-dispersed alloys as interconnect materials for a solid oxide fuel cell by adding La2O3 to SUS430 ferritic steels. For this purpose, we prepared two types of La2O3 with different particle sizes and added different amounts of La2O3 to SUS430 powder. Then, we mixed the powders using a high energy ball mill, so that nano-sized as well as micro-sized oxide particles were able to mix uniformly with the SUS430 powders. After preparing hexahedral green samples using uni-axial and cold isostatic presses, we were finally able to obtain oxide-dispersed alloys having high relative densities after firing at 1,400 °C under hydrogen atmosphere. The nano-sized La2O3 dispersed alloys showed properties superior to those of micro-sized dispersed alloys in terms of long-term stability and thermal cycling. Moreover, we determined the optimum amounts of added La2O3. Finally we were able to develop a new oxide-dispersed alloy showing excellent properties of low area specific resistance (16.23 mΩ cm2) after 1000 h at 800 °C, and no degradation after 10 iterations of thermal cycling under oxidizing atmosphere.

Brain Events Underlying Episodic Memory Changes in Aging: A Longitudinal Investigation of Structural and Functional Connectivity.

PubMed

Fjell, Anders M; Sneve, Markus H; Storsve, Andreas B; Grydeland, Håkon; Yendiki, Anastasia; Walhovd, Kristine B

2016-03-01

Episodic memories are established and maintained by close interplay between hippocampus and other cortical regions, but degradation of a fronto-striatal network has been suggested to be a driving force of memory decline in aging. We wanted to directly address how changes in hippocampal-cortical versus striatal-cortical networks over time impact episodic memory with age. We followed 119 healthy participants (20-83 years) for 3.5 years with repeated tests of episodic verbal memory and magnetic resonance imaging for quantification of functional and structural connectivity and regional brain atrophy. While hippocampal-cortical functional connectivity predicted memory change in young, changes in cortico-striatal functional connectivity were related to change in recall in older adults. Within each age group, effects of functional and structural connectivity were anatomically closely aligned. Interestingly, the relationship between functional connectivity and memory was strongest in the age ranges where the rate of reduction of the relevant brain structure was lowest, implying selective impacts of the different brain events on memory. Together, these findings suggest a partly sequential and partly simultaneous model of brain events underlying cognitive changes in aging, where different functional and structural events are more or less important in various time windows, dismissing a simple uni-factorial view on neurocognitive aging. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Unrealistic phylogenetic trees may improve phylogenetic footprinting.

PubMed

Nettling, Martin; Treutler, Hendrik; Cerquides, Jesus; Grosse, Ivo

2017-06-01

The computational investigation of DNA binding motifs from binding sites is one of the classic tasks in bioinformatics and a prerequisite for understanding gene regulation as a whole. Due to the development of sequencing technologies and the increasing number of available genomes, approaches based on phylogenetic footprinting become increasingly attractive. Phylogenetic footprinting requires phylogenetic trees with attached substitution probabilities for quantifying the evolution of binding sites, but these trees and substitution probabilities are typically not known and cannot be estimated easily. Here, we investigate the influence of phylogenetic trees with different substitution probabilities on the classification performance of phylogenetic footprinting using synthetic and real data. For synthetic data we find that the classification performance is highest when the substitution probability used for phylogenetic footprinting is similar to that used for data generation. For real data, however, we typically find that the classification performance of phylogenetic footprinting surprisingly increases with increasing substitution probabilities and is often highest for unrealistically high substitution probabilities close to one. This finding suggests that choosing realistic model assumptions might not always yield optimal predictions in general and that choosing unrealistically high substitution probabilities close to one might actually improve the classification performance of phylogenetic footprinting. The proposed PF is implemented in JAVA and can be downloaded from https://github.com/mgledi/PhyFoo. : martin.nettling@informatik.uni-halle.de. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation.

PubMed

Ruffier, Magali; Kähäri, Andreas; Komorowska, Monika; Keenan, Stephen; Laird, Matthew; Longden, Ian; Proctor, Glenn; Searle, Steve; Staines, Daniel; Taylor, Kieron; Vullo, Alessandro; Yates, Andrew; Zerbino, Daniel; Flicek, Paul

2017-01-01

The Ensembl software resources are a stable infrastructure to store, access and manipulate genome assemblies and their functional annotations. The Ensembl 'Core' database and Application Programming Interface (API) was our first major piece of software infrastructure and remains at the centre of all of our genome resources. Since its initial design more than fifteen years ago, the number of publicly available genomic, transcriptomic and proteomic datasets has grown enormously, accelerated by continuous advances in DNA-sequencing technology. Initially intended to provide annotation for the reference human genome, we have extended our framework to support the genomes of all species as well as richer assembly models. Cross-referenced links to other informatics resources facilitate searching our database with a variety of popular identifiers such as UniProt and RefSeq. Our comprehensive and robust framework storing a large diversity of genome annotations in one location serves as a platform for other groups to generate and maintain their own tailored annotation. We welcome reuse and contributions: our databases and APIs are publicly available, all of our source code is released with a permissive Apache v2.0 licence at http://github.com/Ensembl and we have an active developer mailing list ( http://www.ensembl.org/info/about/contact/index.html ). http://www.ensembl.org. © The Author(s) 2017. Published by Oxford University Press.

RNAcentral: A vision for an international database of RNA sequences

PubMed Central

Bateman, Alex; Agrawal, Shipra; Birney, Ewan; Bruford, Elspeth A.; Bujnicki, Janusz M.; Cochrane, Guy; Cole, James R.; Dinger, Marcel E.; Enright, Anton J.; Gardner, Paul P.; Gautheret, Daniel; Griffiths-Jones, Sam; Harrow, Jen; Herrero, Javier; Holmes, Ian H.; Huang, Hsien-Da; Kelly, Krystyna A.; Kersey, Paul; Kozomara, Ana; Lowe, Todd M.; Marz, Manja; Moxon, Simon; Pruitt, Kim D.; Samuelsson, Tore; Stadler, Peter F.; Vilella, Albert J.; Vogel, Jan-Hinnerk; Williams, Kelly P.; Wright, Mathew W.; Zwieb, Christian

2011-01-01

During the last decade there has been a great increase in the number of noncoding RNA genes identified, including new classes such as microRNAs and piRNAs. There is also a large growth in the amount of experimental characterization of these RNA components. Despite this growth in information, it is still difficult for researchers to access RNA data, because key data resources for noncoding RNAs have not yet been created. The most pressing omission is the lack of a comprehensive RNA sequence database, much like UniProt, which provides a comprehensive set of protein knowledge. In this article we propose the creation of a new open public resource that we term RNAcentral, which will contain a comprehensive collection of RNA sequences and fill an important gap in the provision of biomedical databases. We envision RNA researchers from all over the world joining a federated RNAcentral network, contributing specialized knowledge and databases. RNAcentral would centralize key data that are currently held across a variety of databases, allowing researchers instant access to a single, unified resource. This resource would facilitate the next generation of RNA research and help drive further discoveries, including those that improve food production and human and animal health. We encourage additional RNA database resources and research groups to join this effort. We aim to obtain international network funding to further this endeavor. PMID:21940779

Experiences From NASA/Langley's DMSS Project

NASA Technical Reports Server (NTRS)

1996-01-01

There is a trend in institutions with high performance computing and data management requirements to explore mass storage systems with peripherals directly attached to a high speed network. The Distributed Mass Storage System (DMSS) Project at the NASA Langley Research Center (LaRC) has placed such a system into production use. This paper will present the experiences, both good and bad, we have had with this system since putting it into production usage. The system is comprised of: 1) National Storage Laboratory (NSL)/UniTree 2.1, 2) IBM 9570 HIPPI attached disk arrays (both RAID 3 and RAID 5), 3) IBM RS6000 server, 4) HIPPI/IPI3 third party transfers between the disk array systems and the supercomputer clients, a CRAY Y-MP and a CRAY 2, 5) a "warm spare" file server, 6) transition software to convert from CRAY's Data Migration Facility (DMF) based system to DMSS, 7) an NSC PS32 HIPPI switch, and 8) a STK 4490 robotic library accessed from the IBM RS6000 block mux interface. This paper will cover: the performance of the DMSS in the following areas: file transfer rates, migration and recall, and file manipulation (listing, deleting, etc.); the appropriateness of a workstation class of file server for NSL/UniTree with LaRC's present storage requirements in mind the role of the third party transfers between the supercomputers and the DMSS disk array systems in DMSS; a detailed comparison (both in performance and functionality) between the DMF and DMSS systems LaRC's enhancements to the NSL/UniTree system administration environment the mechanism for DMSS to provide file server redundancy the statistics on the availability of DMSS the design and experiences with the locally developed transparent transition software which allowed us to make over 1.5 million DMF files available to NSL/UniTree with minimal system outage

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

Cloning and expression of vgb gene in Bacillus cereus, improve phenol and p-nitrophenol biodegradation

NASA Astrophysics Data System (ADS)

Vélez-Lee, Angel Eduardo; Cordova-Lozano, Felipe; Bandala, Erick R.; Sanchez-Salas, Jose Luis

2016-02-01

In this work, the vgb gene from Vitrocilla stercoraria was used to genetically modify a Bacillus cereus strain isolated from pulp and paper wastewater effluent. The gene was cloned in a multicopy plasmid (pUB110) or uni-copy gene using a chromosome integrative vector (pTrpBG1). B. cereus and its recombinant strains were used for phenol and p-nitrophenol biodegradation using aerobic or micro-aerobic conditions and two different temperatures (i.e. 37 and 25 °C). Complete (100%) phenol degradation was obtained for the strain where the multicopy of vgb gene was present, 98% for the strain where uni-copy gene was present and 45% for wild type strain for the same experimental conditions (i.e. 37 °C and aerobic condition). For p-nitrophenol degradation at the same conditions, the strain with the multi-copy vgb gene was capable to achieve 50% of biodegradation, ˜100% biodegradation was obtained using the uni-copy strain and ˜24% for wild type strain. When the micro-aerobic condition was tested, the biodegradation yield showed a significant decreased. The biodegradation trend observed for aerobic was similar for micro-aerobic assessments: the modified strains showed higher degradation rates when compared with wild type strain. For all experimental conditions, the highest p-nitrophenol degradation was observed using the strain with uni-copy of vgb gene. Besides the increase of biodegradative capability of the strain, insertion of the vgb gene was observed able to modify other morphological characteristics such as avoiding the typical flake formation in the B. cereus culture. In both cases, the modification seems to be related with the enhancement of oxygen supply to the cells generated by the vgb gene insertion. The application of the genetically modified microorganism (GMM) to the biodegradation of pollutants in contaminated water possesses high potential as an environmentally friendly technology to facing this emergent problem.

Evaluation of simple rapid HIV assays and development of national rapid HIV test algorithms in Dar es Salaam, Tanzania

PubMed Central

2009-01-01

Background Suitable algorithms based on a combination of two or more simple rapid HIV assays have been shown to have a diagnostic accuracy comparable to double enzyme-linked immunosorbent assay (ELISA) or double ELISA with Western Blot strategies. The aims of this study were to evaluate the performance of five simple rapid HIV assays using whole blood samples from HIV-infected patients, pregnant women, voluntary counseling and testing attendees and blood donors, and to formulate an alternative confirmatory strategy based on rapid HIV testing algorithms suitable for use in Tanzania. Methods Five rapid HIV assays: Determine™ HIV-1/2 (Inverness Medical), SD Bioline HIV 1/2 3.0 (Standard Diagnostics Inc.), First Response HIV Card 1–2.0 (PMC Medical India Pvt Ltd), HIV1/2 Stat-Pak Dipstick (Chembio Diagnostic System, Inc) and Uni-Gold™ HIV-1/2 (Trinity Biotech) were evaluated between June and September 2006 using 1433 whole blood samples from hospital patients, pregnant women, voluntary counseling and testing attendees and blood donors. All samples that were reactive on all or any of the five rapid assays and 10% of non-reactive samples were tested on a confirmatory Inno-Lia HIV I/II immunoblot assay (Immunogenetics). Results Three hundred and ninety samples were confirmed HIV-1 antibody positive, while 1043 were HIV negative. The sensitivity at initial testing of Determine, SD Bioline and Uni-Gold™ was 100% (95% CI; 99.1–100) while First Response and Stat-Pak had sensitivity of 99.5% (95% CI; 98.2–99.9) and 97.7% (95% CI; 95.7–98.9), respectively, which increased to 100% (95% CI; 99.1–100) on repeat testing. The initial specificity of the Uni-Gold™ assay was 100% (95% CI; 99.6–100) while specificities were 99.6% (95% CI; 99–99.9), 99.4% (95% CI; 98.8–99.7), 99.6% (95% CI; 99–99.9) and 99.8% (95% CI; 99.3–99.9) for Determine, SD Bioline, First Response and Stat-Pak assays, respectively. There was no any sample which was concordantly false positive in Uni-Gold™, Determine and SD Bioline assays. Conclusion An alternative confirmatory HIV testing strategy based on initial testing on either SD Bioline or Determine assays followed by testing of reactive samples on the Determine or SD Bioline gave 100% sensitivity (95% CI; 99.1–100) and 100% specificity (95% CI; 96–99.1) with Uni-Gold™ as tiebreaker for discordant results. PMID:19226452

Rapid Immuno-Chromatographic Assay for the Detection of Antibodies to HIV Compare with Elisa among Voluntary and Replacement Blood Donor of Mymensingh Medical College Hospital.

PubMed

Chakrabarty, P; Rudra, S; Hossain, M A; Begum, S A; Mirza, T T; Rudra, M

2015-04-01

Suitable algorithms based on a combination of two or more simple rapid HIV assays have been shown to have a diagnostic accuracy comparable to double enzyme-linked immunosorbent assay (ELISA) or double ELISA with Western Blot strategies. The aims of this study were to evaluate the performance of five simple rapid HIV assays using whole blood samples from voluntary and replacement blood donors & HIV-infected patients (positive samples from BSMMU, Dhaka). Five rapid HIV assays: Determine™ HIV-1/2 (Inverness Medical), SD Bioline HIV 1/2 3.0 (Standard Diagnostics Inc.), First Response HIV Card 1-2.0 (PMC Medical India Pvt Ltd.), HIV1/2 Stat-Pak Dipstick (Chembio Diagnostic System, Inc) and Uni-Gold™ HIV-1/2 (Biotech) were evaluated between 1st February to 30th June, 2013 using 400 whole blood samples from voluntary and replacement blood donors. All samples that were reactive on all or any of the five rapid assays and 10% of non-reactive samples were tested on a confirmatory Inno-Lia HIV I/II immunoblot assay (Immunogenetics). Only 01 sample including ten positive samples from BSMMU were confirmed HIV-1 antibody positive, while 399 were HIV negative. The sensitivity at initial testing of Determine, SD Bioline and Uni-Gold™ was 100% (95% CI; 99.1-100) while First Response and Stat-Pak had sensitivity of 99.5% (95% CI; 98.2-99.9) and 97.7% (95% CI; 95.7-98.9) respectively, which increased to 100% (95% CI; 99.1-100) on repeat testing. The initial specificity of the Uni-Gold™ assay was 100% (95% CI; 99.6-100) while specificities were 99.6% (95% CI; 99-99.9), 99.4% (95% CI; 98.8-99.7), 99.6% (95% CI; 99-99.9) and 99.8% (95% CI; 99.3-99.9) for Determine, SD Bioline, First Response and Stat-Pak assays, respectively. There was no any sample which was concordantly false positive in Uni-Gold™, Determine and SD Bioline assays. An alternative confirmatory HIV testing strategy based on initial testing on either SD Bioline or Determine assays followed by testing of reactive samples on the Determine or SD Bioline gave 100% sensitivity (95% CI; 99.1-100) and 100% specificity (95% CI; 96-99.1) with Uni-Gold™ as tiebreaker for discordant results.

Evaluation of simple rapid HIV assays and development of national rapid HIV test algorithms in Dar es Salaam, Tanzania.

PubMed

Lyamuya, Eligius F; Aboud, Said; Urassa, Willy K; Sufi, Jaffer; Mbwana, Judica; Ndugulile, Faustin; Massambu, Charles

2009-02-18

Suitable algorithms based on a combination of two or more simple rapid HIV assays have been shown to have a diagnostic accuracy comparable to double enzyme-linked immunosorbent assay (ELISA) or double ELISA with Western Blot strategies. The aims of this study were to evaluate the performance of five simple rapid HIV assays using whole blood samples from HIV-infected patients, pregnant women, voluntary counseling and testing attendees and blood donors, and to formulate an alternative confirmatory strategy based on rapid HIV testing algorithms suitable for use in Tanzania. Five rapid HIV assays: Determine HIV-1/2 (Inverness Medical), SD Bioline HIV 1/2 3.0 (Standard Diagnostics Inc.), First Response HIV Card 1-2.0 (PMC Medical India Pvt Ltd), HIV1/2 Stat-Pak Dipstick (Chembio Diagnostic System, Inc) and Uni-Gold HIV-1/2 (Trinity Biotech) were evaluated between June and September 2006 using 1433 whole blood samples from hospital patients, pregnant women, voluntary counseling and testing attendees and blood donors. All samples that were reactive on all or any of the five rapid assays and 10% of non-reactive samples were tested on a confirmatory Inno-Lia HIV I/II immunoblot assay (Immunogenetics). Three hundred and ninety samples were confirmed HIV-1 antibody positive, while 1043 were HIV negative. The sensitivity at initial testing of Determine, SD Bioline and Uni-Gold was 100% (95% CI; 99.1-100) while First Response and Stat-Pak had sensitivity of 99.5% (95% CI; 98.2-99.9) and 97.7% (95% CI; 95.7-98.9), respectively, which increased to 100% (95% CI; 99.1-100) on repeat testing. The initial specificity of the Uni-Gold assay was 100% (95% CI; 99.6-100) while specificities were 99.6% (95% CI; 99-99.9), 99.4% (95% CI; 98.8-99.7), 99.6% (95% CI; 99-99.9) and 99.8% (95% CI; 99.3-99.9) for Determine, SD Bioline, First Response and Stat-Pak assays, respectively. There was no any sample which was concordantly false positive in Uni-Gold, Determine and SD Bioline assays. An alternative confirmatory HIV testing strategy based on initial testing on either SD Bioline or Determine assays followed by testing of reactive samples on the Determine or SD Bioline gave 100% sensitivity (95% CI; 99.1-100) and 100% specificity (95% CI; 96-99.1) with Uni-Gold as tiebreaker for discordant results.

Two interactive Bioinformatics courses at the Bielefeld University Bioinformatics Server.

PubMed

Sczyrba, Alexander; Konermann, Susanne; Giegerich, Robert

2008-05-01

Conferences in computational biology continue to provide tutorials on classical and new methods in the field. This can be taken as an indicator that education is still a bottleneck in our field's process of becoming an established scientific discipline. Bielefeld University has been one of the early providers of bioinformatics education, both locally and via the internet. The Bielefeld Bioinformatics Server (BiBiServ) offers a variety of older and new materials. Here, we report on two online courses made available recently, one introductory and one on the advanced level: (i) SADR: Sequence Analysis with Distributed Resources (http://bibiserv.techfak.uni-bielefeld.de/sadr/) and (ii) ADP: Algebraic Dynamic Programming in Bioinformatics (http://bibiserv.techfak.uni-bielefeld.de/dpcourse/).

Brain network dysfunction in youth with obsessive-compulsive disorder induced by simple uni-manual behavior: The role of the dorsal anterior cingulate cortex

PubMed Central

Friedman, Amy L.; Burgess, Ashley; Ramaseshan, Karthik; Easter, Phil; Khatib, Dalal; Chowdury, Asadur; Arnold, Paul D.; Hanna, Gregory L.; Rosenberg, David R.; Diwadkar, Vaibhav A.

2017-01-01

In an effort to elucidate differences in functioning brain networks between youth with obsessive-compulsive disorder and controls, we used fMRI signals to analyze brain network interactions of the dorsal anterior cingulate cortex (dACC) during visually coordinated motor responses. Subjects made a uni-manual response to briefly presented probes, at periodic (allowing participants to maintain a “motor set”) or random intervals (demanding reactive responses). Network interactions were assessed using psycho-physiological interaction (PPI), a basic model of functional connectivity evaluating modulatory effects of the dACC in the context of each task condition. Across conditions, OCD were characterized by hyper-modulation by the dACC, with loci alternatively observed as both condition-general and condition-specific. Thus, dynamically driven task demands during simple uni-manual motor control induce compensatory network interactions in cortical-thalamic regions in OCD. These findings support previous research in OCD showing compensatory network interactions during complex memory tasks, but establish that these network effects are observed during basic sensorimotor processing. Thus, these patterns of network dysfunction may in fact be independent of the complexity of tasks used to induce brain network activity. Hypothesis-driven approaches coupled with sophisticated network analyses are a highly valuable approach in using fMRI to uncover mechanisms in disorders like OCD. PMID:27992792

UniEuk: Time to Speak a Common Language in Protistology!

PubMed

Berney, Cédric; Ciuprina, Andreea; Bender, Sara; Brodie, Juliet; Edgcomb, Virginia; Kim, Eunsoo; Rajan, Jeena; Parfrey, Laura Wegener; Adl, Sina; Audic, Stéphane; Bass, David; Caron, David A; Cochrane, Guy; Czech, Lucas; Dunthorn, Micah; Geisen, Stefan; Glöckner, Frank Oliver; Mahé, Frédéric; Quast, Christian; Kaye, Jonathan Z; Simpson, Alastair G B; Stamatakis, Alexandros; Del Campo, Javier; Yilmaz, Pelin; de Vargas, Colomban

2017-05-01

Universal taxonomic frameworks have been critical tools to structure the fields of botany, zoology, mycology, and bacteriology as well as their large research communities. Animals, plants, and fungi have relatively solid, stable morpho-taxonomies built over the last three centuries, while bacteria have been classified for the last three decades under a coherent molecular taxonomic framework. By contrast, no such common language exists for microbial eukaryotes, even though environmental '-omics' surveys suggest that protists make up most of the organismal and genetic complexity of our planet's ecosystems! With the current deluge of eukaryotic meta-omics data, we urgently need to build up a universal eukaryotic taxonomy bridging the protist -omics age to the fragile, centuries-old body of classical knowledge that has effectively linked protist taxa to morphological, physiological, and ecological information. UniEuk is an open, inclusive, community-based and expert-driven international initiative to build a flexible, adaptive universal taxonomic framework for eukaryotes. It unites three complementary modules, EukRef, EukBank, and EukMap, which use phylogenetic markers, environmental metabarcoding surveys, and expert knowledge to inform the taxonomic framework. The UniEuk taxonomy is directly implemented in the European Nucleotide Archive at EMBL-EBI, ensuring its broad use and long-term preservation as a reference taxonomy for eukaryotes. © 2017 The Author(s) Journal of Eukaryotic Microbiology published by Wiley Periodicals, Inc. on behalf of International Society of Protistologists.

An emerging cyberinfrastructure for biodefense pathogen and pathogen–host data

PubMed Central

Zhang, C.; Crasta, O.; Cammer, S.; Will, R.; Kenyon, R.; Sullivan, D.; Yu, Q.; Sun, W.; Jha, R.; Liu, D.; Xue, T.; Zhang, Y.; Moore, M.; McGarvey, P.; Huang, H.; Chen, Y.; Zhang, J.; Mazumder, R.; Wu, C.; Sobral, B.

2008-01-01

The NIAID-funded Biodefense Proteomics Resource Center (RC) provides storage, dissemination, visualization and analysis capabilities for the experimental data deposited by seven Proteomics Research Centers (PRCs). The data and its publication is to support researchers working to discover candidates for the next generation of vaccines, therapeutics and diagnostics against NIAID's Category A, B and C priority pathogens. The data includes transcriptional profiles, protein profiles, protein structural data and host–pathogen protein interactions, in the context of the pathogen life cycle in vivo and in vitro. The database has stored and supported host or pathogen data derived from Bacillus, Brucella, Cryptosporidium, Salmonella, SARS, Toxoplasma, Vibrio and Yersinia, human tissue libraries, and mouse macrophages. These publicly available data cover diverse data types such as mass spectrometry, yeast two-hybrid (Y2H), gene expression profiles, X-ray and NMR determined protein structures and protein expression clones. The growing database covers over 23 000 unique genes/proteins from different experiments and organisms. All of the genes/proteins are annotated and integrated across experiments using UniProt Knowledgebase (UniProtKB) accession numbers. The web-interface for the database enables searching, querying and downloading at the level of experiment, group and individual gene(s)/protein(s) via UniProtKB accession numbers or protein function keywords. The system is accessible at http://www.proteomicsresource.org/. PMID:17984082

Physically-Based Reduced Order Modelling of a Uni-Axial Polysilicon MEMS Accelerometer

PubMed Central

Ghisi, Aldo; Mariani, Stefano; Corigliano, Alberto; Zerbini, Sarah

2012-01-01

In this paper, the mechanical response of a commercial off-the-shelf, uni-axial polysilicon MEMS accelerometer subject to drops is numerically investigated. To speed up the calculations, a simplified physically-based (beams and plate), two degrees of freedom model of the movable parts of the sensor is adopted. The capability and the accuracy of the model are assessed against three-dimensional finite element simulations, and against outcomes of experiments on instrumented samples. It is shown that the reduced order model provides accurate outcomes as for the system dynamics. To also get rather accurate results in terms of stress fields within regions that are prone to fail upon high-g shocks, a correction factor is proposed by accounting for the local stress amplification induced by re-entrant corners. PMID:23202031

Databases and Associated Tools for Glycomics and Glycoproteomics.

PubMed

Lisacek, Frederique; Mariethoz, Julien; Alocci, Davide; Rudd, Pauline M; Abrahams, Jodie L; Campbell, Matthew P; Packer, Nicolle H; Ståhle, Jonas; Widmalm, Göran; Mullen, Elaine; Adamczyk, Barbara; Rojas-Macias, Miguel A; Jin, Chunsheng; Karlsson, Niclas G

2017-01-01

The access to biodatabases for glycomics and glycoproteomics has proven to be essential for current glycobiological research. This chapter presents available databases that are devoted to different aspects of glycobioinformatics. This includes oligosaccharide sequence databases, experimental databases, 3D structure databases (of both glycans and glycorelated proteins) and association of glycans with tissue, disease, and proteins. Specific search protocols are also provided using tools associated with experimental databases for converting primary glycoanalytical data to glycan structural information. In particular, researchers using glycoanalysis methods by U/HPLC (GlycoBase), MS (GlycoWorkbench, UniCarb-DB, GlycoDigest), and NMR (CASPER) will benefit from this chapter. In addition we also include information on how to utilize glycan structural information to query databases that associate glycans with proteins (UniCarbKB) and with interactions with pathogens (SugarBind).

Conference B.Bettelheim

ScienceCinema

None

2017-12-09

Le Dr.Bruno Bettelheim, psychologue américain, d'origine viennoise, a passé son doctorat en psychologie à l'université de Vienne. Il émigra aux Etats-Unis et enseigna la psychologie au Rockford College en Illinois et la psychologie de l'éducation à L'université de Chicago, où il dirigea également l'institut orthogénique Sonia-Shankman pour le traitement des enfants psychotiques. Cet homme a bouleversé la compréhension des relations parents et enfants en y introduisant la psychanalyse. Basé sur ses expériences aux Etats-Unis,il nous parle des changements dans la structure de la famille et ses conséquences pour la relation entre enfants et parents.

Design optimization of rear uprights for UniMAP Automotive Racing Team Formula SAE racing car

NASA Astrophysics Data System (ADS)

Azmeer, M.; Basha, M. H.; Hamid, M. F.; Rahman, M. T. A.; Hashim, M. S. M.

2017-10-01

In an automobile, the rear upright are used to provide a physical mounting and links the suspension arms to the hub and wheel assembly. In this work, static structural and shape optimization analysis for rear upright for UniMAP’s Formula SAE racing car had been done using ANSYS software with the objective to reduce weight while maintaining the structural strength of the vehicle upright. During the shape optimization process, the component undergoes 25%, 50% and 75 % weight reduction in order to find the best optimal shape of the upright. The final design of the upright is developed considering the weight reduction, structural integrity and the manufacturability. The final design achieved 21 % weight reduction and is able to withstand several loads.

The La Unión Au ± Cu prospect, Camagüey District, Cuba: fluid inclusion and stable isotope evidence for ore-forming processes

NASA Astrophysics Data System (ADS)

Santana, Miriela María Ulloa; Moura, Márcia Abrahão; Olivo, Gema R.; Botelho, Nilson Francisquini; Kyser, T. Kurtis; Bühn, Bernhard

2011-01-01

The Camagüey district, Cuba, is known for its epithermal precious metal deposits in a Cretaceous volcanic arc setting. Recently, the La Unión prospect was discovered in the southern part of the district, containing gold and minor copper mineralization interpreted as porphyry type. Mineralization is hosted in a 73.0 ± 1.5 Ma calc-alkaline I-type oxidized porphyry quartz diorite intrusive within volcanic and volcaniclastic rocks of the early Cretaceous Guáimaro Formation. The porphyry is affected by propylitic alteration and crosscut by a network of quartz and carbonate veinlets and veins. Chlorite, epidote, sericite, quartz, and pyrite are the main minerals in the early veins which are cut by late carbonate and zeolite veins. Late barite pseudomorphously replaces pyrite. Gold is associated with pyrite as disseminations in the altered quartz diorite and in the veins, occurring as inclusions or filling fractures in pyrite with 4 g/t Au in bulk samples, and up to 900 ppm Au in in pyrite. Fluid inclusion and oxygen isotope data are consistent with a H2O-NaCl-(KCl) mineralizing fluid, derived from the quartz diorite magma, and trapped at least at 425°C and 1.2 kbar. This primary fluid unmixed into two fluid phases, a hypersaline aqueous fluid and a low-salinity vapor-rich fluid. Boiling during cooling may have played an important role in metal precipitation. Pyrite δ34S values for the La Unión prospect range between 0.71‰ and 1.31‰, consistent with a homogeneous magmatic sulfur source. The fluids in equilibrium with the mineralized rocks have estimated δ18O values from 8‰ to 11.8‰, calculated for a temperature range of 480-505°C. The tectonic environment of the La Unión prospect, its high gold and low copper contents, the physical-chemical characteristics of the mineralizing fluids and the isotopic signature of the alteration minerals and fluids indicate that the La Unión gold mineralization is similar to the porphyry gold type, even though the ore-related epidote-chlorite alteration can be classified as propylitic and not the classic potassic and/or phyllic alteration. The low copper contents in the prospect could be due to a mineralizing fluid previously saturated in copper, which is indicated by trapped chalcopyrite crystals in high-temperature fluid inclusions. The low-temperature paragenesis, represented by carbonate, zeolite and barite, indicates epithermal overprint. The study shows the potential for other gold porphyry-type deposits in the Cretaceous volcanoplutonic arc of Cuba.

Bacillus anthracis o-succinylbenzoyl-CoA synthetase: reaction kinetics and a novel inhibitor mimicking its reaction intermediate †

PubMed Central

Tian, Yang; Suk, Dae-Hwan; Cai, Feng; Crich, David; Mesecar, Andrew D.

2009-01-01

O-succinylbenzoyl-CoA (OSB-CoA) synthetase (EC 6.2.1.26) catalyzes the ATP-dependent condensation of o-succinylbenzoate (OSB) and CoA to form OSB-CoA, the fourth step of the menaquinone biosynthetic pathway in Bacillus anthracis. Gene knockout studies have highlighted this enzyme as a potential target for the discovery of new antibiotics. Here we report the first studies on the kinetic mechanism of B. anthracis OSB-CoA synthetase, classifying it as an ordered Bi Uni Uni Bi ping-pong mechanism. Through a series of pre-steady-state and steady-state kinetic studies in conjunction with direct-binding studies, it is demonstrated that CoA, the last substrate to bind, strongly activates the first half-reaction after the first round of turnover. The activation of the first-half reaction is most likely achieved by CoA stabilizing conformations of the enzyme in the ‘F’ form, which slowly isomerize back to the E form. Thus, the kinetic mechanism of OSB-CoA synthetase may be more accurately described as an ordered Bi Uni Uni Bi Iso ping-pong mechanism. The substrate specificity of OSB-CoA synthetase was probed using a series of OSB analogs with alterations in the carboxylate groups. OSB-CoA shows a strong preference for OSB over all of the analogs tested as none were active except 4-(2-trifluoromethylphenyl)-4-oxobutyric acid which exhibited a 100-fold decrease in kcat/Km. Based on an understanding of OSB-CoA synthetase’s kinetic mechanism and substrate specificity, a reaction intermediate analog of OSB-AMP, 5’-O-(N-(2-trifluoromethylphenyl)-4-oxobutyl) adenosine sulfonamide (TFMP-butyl-AMS), was designed and synthesized. This inhibitor was found to be an uncompetitive inhibitor to CoA and a mixed-type inhibitor to ATP and OSB with low micromolar inhibition constants. Collectively, these results should serve as an important forerunner to more detailed and extensive inhibitor design studies aimed at developing lead compounds against the OSB-CoA synthetase class of enzymes. PMID:18973344

Bacillus anthracis o-succinylbenzoyl-CoA synthetase: reaction kinetics and a novel inhibitor mimicking its reaction intermediate.

PubMed

Tian, Yang; Suk, Dae-Hwan; Cai, Feng; Crich, David; Mesecar, Andrew D

2008-11-25

o-Succinylbenzoyl-CoA (OSB-CoA) synthetase (EC 6.2.1.26) catalyzes the ATP-dependent condensation of o-succinylbenzoate (OSB) and CoA to form OSB-CoA, the fourth step of the menaquinone biosynthetic pathway in Bacillus anthracis. Gene knockout studies have highlighted this enzyme as a potential target for the discovery of new antibiotics. Here we report the first studies on the kinetic mechanism of B. anthracis OSB-CoA synthetase, classifying it as an ordered bi uni uni bi ping-pong mechanism. Through a series of pre-steady-state and steady-state kinetic studies in conjunction with direct binding studies, it is demonstrated that CoA, the last substrate to bind, strongly activates the first half-reaction after the first round of turnover. The activation of the first half-reaction is most likely achieved by CoA stabilizing conformations of the enzyme in the "F" form, which slowly isomerize back to the E form. Thus, the kinetic mechanism of OSB-CoA synthetase may be more accurately described as an ordered bi uni uni bi iso ping-pong mechanism. The substrate specificity of OSB-CoA synthetase was probed using a series of OSB analogues with alterations in the carboxylate groups. OSB-CoA shows a strong preference for OSB over all of the analogues tested as none were active except 4-[2-(trifluoromethyl)phenyl]-4-oxobutyric acid which exhibited a 100-fold decrease in k(cat)/K(m). On the basis of an understanding of OSB-CoA synthetase's kinetic mechanism and substrate specificity, a reaction intermediate analogue of OSB-AMP, 5'-O-{N-[2-(trifluoromethyl)phenyl]-4-oxobutyl}adenosine sulfonamide (TFMP-butyl-AMS), was designed and synthesized. This inhibitor was found to be an uncompetitive inhibitor to CoA and a mixed-type inhibitor to ATP and OSB with low micromolar inhibition constants. Collectively, these results should serve as an important forerunner to more detailed and extensive inhibitor design studies aimed at developing lead compounds against the OSB-CoA synthetase class of enzymes.

Uni-directional consumer-resource theory characterizing transitions of interaction outcomes

USGS Publications Warehouse

Wang, Y.; DeAngelis, D.L.; Holland, J.N.

2011-01-01

A resource is considered here to be a biotic population that helps to maintain the population growth of its consumers, whereas a consumer utilizes a resource and in turn decreases its growth rate. Bi-directional consumer-resource (C-R) interactions have been the object of recent theory. In these interactions, each species acts, in some respects, as both a consumer and a resource of the other, which is the basis of many mutualisms. In uni-directional C-R interactions between two species, one acts as a consumer and the other as a material and/or energy resource, while neither acts as both. The relationship between insect pollinator/seed parasites and the host plant is an example of the latter interaction type of C-R, as the insect provides no material resource to the plant (though it provides a pollination service). In this paper we consider a different variation of the uni-directional C-R interaction, in which the resource species has both positive and negative effects on the consumer species, while the consumer has only a negative effect on the resource. A predator-prey system in which the prey is able to kill or consume predator eggs or larvae is an example. Our aim is to demonstrate mechanisms by which interaction outcomes of this system vary with different conditions, and thus to extend the uni-directional C-R theory established by Holland and DeAngelis (2009). By the analysis of a specific two-species system, it is shown that there is no periodic solution of the system, and the parameter (factor) space can be divided into six regions, which correspond to predation/parasitism, amensalism, and competition. The interaction outcomes of the system transition smoothly when the parameters are changed continuously in the six regions and/or initial densities of the species vary in a smooth fashion. Varying a pair of parameters can also result in the transitions. The analysis leads to both conditions under which the species approach their maximal densities, and explanations for phenomena in experiments by Urabe and Sterner (1996). ?? 2011 .

Evaluation and Optimization of a Supercritical Carbon Dioxide Power Conversion Cycle for Nuclear Applications

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

Edwin A. Harvego; Michael G. McKellar

2011-05-01

There have been a number of studies involving the use of gases operating in the supercritical mode for power production and process heat applications. Supercritical carbon dioxide (CO2) is particularly attractive because it is capable of achieving relatively high power conversion cycle efficiencies in the temperature range between 550°C and 750°C. Therefore, it has the potential for use with any type of high-temperature nuclear reactor concept, assuming reactor core outlet temperatures of at least 550°C. The particular power cycle investigated in this paper is a supercritical CO2 Recompression Brayton Cycle. The CO2 Recompression Brayton Cycle can be used as eithermore » a direct or indirect power conversion cycle, depending on the reactor type and reactor outlet temperature. The advantage of this cycle when compared to the helium Brayton Cycle is the lower required operating temperature; 550°C versus 850°C. However, the supercritical CO2 Recompression Brayton Cycle requires an operating pressure in the range of 20 MPa, which is considerably higher than the required helium Brayton cycle operating pressure of 8 MPa. This paper presents results of analyses performed using the UniSim process analyses software to evaluate the performance of the supercritical CO2 Brayton Recompression Cycle for different reactor outlet temperatures. The UniSim model assumed a 600 MWt reactor power source, which provides heat to the power cycle at a maximum temperature of between 550°C and 750°C. The UniSim model used realistic component parameters and operating conditions to model the complete power conversion system. CO2 properties were evaluated, and the operating range for the cycle was adjusted to take advantage of the rapidly changing conditions near the critical point. The UniSim model was then optimized to maximize the power cycle thermal efficiency at the different maximum power cycle operating temperatures. The results of the analyses showed that power cycle thermal efficiencies in the range of 40 to 50% can be achieved.« less

Professionalism perspectives among medical students of a novel medical graduate school in Malaysia.

PubMed

Haque, Mainul; Zulkifli, Zainal; Haque, Seraj Zohurul; Kamal, Zubair M; Salam, Abdus; Bhagat, Vidya; Alattraqchi, Ahmed Ghazi; Rahman, Nor Iza A

2016-01-01

Defining professionalism in this constantly evolving world is not easy. How do you measure degrees of benevolence and compassion? If it is so obvious to our profession, what professionalism is, then why is it so difficult to teach it to medical students and residents? Today's definition of medical professionalism is evolving - from autonomy to accountability, from expert opinion to evidence-based medicine, and from self-interest to teamwork and shared responsibility. However, medical professionalism is defined as the basis for the trust in the patient-physician relationship, caring and compassion, insight, openness, respect for patient dignity, confidentiality, autonomy, presence, altruism, and those qualities that lead to trust-competence, integrity, honesty, morality, and ethical conduct. The purpose of this study is to explore professionalism in terms of its fundamental elements among medical students of Universiti Sultan Zainal Abidin (UniSZA). This was a cross-sectional study carried out on medical students of UniSZA. The study population included preclinical and clinical medical students of UniSZA from Year I to Year V of academic session 2014/2015. The simple random sampling technique was used to select the sample. Data were collected using a validated instrument. The data were then compiled and analyzed using SPSS Version 21. Out of 165 questionnaires distributed randomly among Year I to Year V medical students of UniSZA, 144 returned, giving a response rate of 87%. Among the study participants, 38% (54) and 62% (90) were males and females, respectively. The grand total score was 170.92±19.08. A total of 166.98±20.15 and 173.49±18.09 were the total professionalism score of male and female study participants, respectively, with no statistically significant (P=0.61) differences. This study found almost similar levels of familiarity with all fundamental issues of professionalism with no statistically (P>0.05) significant differences. Medical faculty members should give more effort for the professional development of medical doctor. Henceforth, researchers believe and expect that the country will produce more rational and holistic medical doctors.

Professionalism perspectives among medical students of a novel medical graduate school in Malaysia

PubMed Central

Haque, Mainul; Zulkifli, Zainal; Haque, Seraj Zohurul; Kamal, Zubair M; Salam, Abdus; Bhagat, Vidya; Alattraqchi, Ahmed Ghazi; Rahman, Nor Iza A

2016-01-01

Defining professionalism in this constantly evolving world is not easy. How do you measure degrees of benevolence and compassion? If it is so obvious to our profession, what professionalism is, then why is it so difficult to teach it to medical students and residents? Today’s definition of medical professionalism is evolving – from autonomy to accountability, from expert opinion to evidence-based medicine, and from self-interest to teamwork and shared responsibility. However, medical professionalism is defined as the basis for the trust in the patient–physician relationship, caring and compassion, insight, openness, respect for patient dignity, confidentiality, autonomy, presence, altruism, and those qualities that lead to trust-competence, integrity, honesty, morality, and ethical conduct. The purpose of this study is to explore professionalism in terms of its fundamental elements among medical students of Universiti Sultan Zainal Abidin (UniSZA). This was a cross-sectional study carried out on medical students of UniSZA. The study population included preclinical and clinical medical students of UniSZA from Year I to Year V of academic session 2014/2015. The simple random sampling technique was used to select the sample. Data were collected using a validated instrument. The data were then compiled and analyzed using SPSS Version 21. Out of 165 questionnaires distributed randomly among Year I to Year V medical students of UniSZA, 144 returned, giving a response rate of 87%. Among the study participants, 38% (54) and 62% (90) were males and females, respectively. The grand total score was 170.92±19.08. A total of 166.98±20.15 and 173.49±18.09 were the total professionalism score of male and female study participants, respectively, with no statistically significant (P=0.61) differences. This study found almost similar levels of familiarity with all fundamental issues of professionalism with no statistically (P>0.05) significant differences. Medical faculty members should give more effort for the professional development of medical doctor. Henceforth, researchers believe and expect that the country will produce more rational and holistic medical doctors. PMID:27524927

miRPathDB: a new dictionary on microRNAs and target pathways.

PubMed

Backes, Christina; Kehl, Tim; Stöckel, Daniel; Fehlmann, Tobias; Schneider, Lara; Meese, Eckart; Lenhof, Hans-Peter; Keller, Andreas

2017-01-04

In the last decade, miRNAs and their regulatory mechanisms have been intensively studied and many tools for the analysis of miRNAs and their targets have been developed. We previously presented a dictionary on single miRNAs and their putative target pathways. Since then, the number of miRNAs has tripled and the knowledge on miRNAs and targets has grown substantially. This, along with changes in pathway resources such as KEGG, leads to an improved understanding of miRNAs, their target genes and related pathways. Here, we introduce the miRNA Pathway Dictionary Database (miRPathDB), freely accessible at https://mpd.bioinf.uni-sb.de/ With the database we aim to complement available target pathway web-servers by providing researchers easy access to the information which pathways are regulated by a miRNA, which miRNAs target a pathway and how specific these regulations are. The database contains a large number of miRNAs (2595 human miRNAs), different miRNA target sets (14 773 experimentally validated target genes as well as 19 281 predicted targets genes) and a broad selection of functional biochemical categories (KEGG-, WikiPathways-, BioCarta-, SMPDB-, PID-, Reactome pathways, functional categories from gene ontology (GO), protein families from Pfam and chromosomal locations totaling 12 875 categories). In addition to Homo sapiens, also Mus musculus data are stored and can be compared to human target pathways. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

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

Bae, Euiyoung; Bingman, Craig A.; Aceti, David J.

LOC79017 (MW 21.0 kDa, residues 1-188) was annotated as a hypothetical protein encoded by Homo sapiens chromosome 7 open reading frame 24. It was selected as a target by the Center for Eukaryotic Structural Genomics (CESG) because it did not share more than 30% sequence identity with any protein for which the three-dimensional structure is known. The biological function of the protein has not been established yet. Parts of LOC79017 were identified as members of uncharacterized Pfam families (residues 1-95 as PB006073 and residues 104-180 as PB031696). BLAST searches revealed homologues of LOC79017 in many eukaryotes, but none of themmore » have been functionally characterized. Here, we report the crystal structure of H. sapiens protein LOC79017 (UniGene code Hs.530024, UniProt code O75223, CESG target number go.35223).« less

Improvements to quality of needle coke by controlled carbonized conditions

NASA Astrophysics Data System (ADS)

Liu, Dong; Lou, Bin; Yu, Ran; Chen, Qingtai; Li, Zhiheng; Zhang, Yadong

2018-06-01

In this study, the selected aromatic-rich fraction derived from hydrocracking tail oil was carbonized and further improvement in the quality of resultant coke was achieved by promoting temperature at the solidification stage. In comparison with conventional process carried out isothermally and isobarically, the coupling analysis between formation and subsequent uni-axial orientation of mesophase textures during the controlled process was systematically discussed on the basis of the mutual relevance among mesophase texture evolution, gas evolution rate and solidification rate of intermediates. The results show that on the premise that formation of bulk mesophase, appropriate rate of gas evolution at a right time of solidification contributes to fine produces fine fibrous mesophase aligned uni-axially and less pores. Moreover, the intermediates with solidification index of 2˜6 are suitable for deformation induced by gas evolution.

Performance and Stability Characteristics of a Uni-Element Swirl Injector for Oxygen-Rich Stage Combustion Cycles

NASA Technical Reports Server (NTRS)

Pal, S.; Kalitan, D.; Woodward, R. D.; Santoro, R. J.

2004-01-01

A uni-element liquid propellant combustion performance and instability study for liquid RP-1 and hot oxygen-rich pre-burner products was conducted, at a chamber pressure of about 1000 psi. using flush and recessed swirl injectors. High-frequency pressure transducer measurements were analyzed to yield the characteristic frequencies which were compared to expected frequencies of the chamber. Modes, which were discovered to be present within the main chamber included, the first longitudinal, detected at approximately 1950 Hz, and the second longitudinal mode at approximately 3800 Hz. An additional first longitudinal quarter wave mode was measured at a frequency of approximately 23000 Hz for the recessed swirl injector configuration. The characteristic instabilities resulting from these experiments were relatively weak averaging 0.2% to 0.3% of the chamber pressure.

The Bologna Annotation Resource (BAR 3.0): improving protein functional annotation

PubMed Central

Casadio, Rita

2017-01-01

Abstract BAR 3.0 updates our server BAR (Bologna Annotation Resource) for predicting protein structural and functional features from sequence. We increase data volume, query capabilities and information conveyed to the user. The core of BAR 3.0 is a graph-based clustering procedure of UniProtKB sequences, following strict pairwise similarity criteria (sequence identity ≥40% with alignment coverage ≥90%). Each cluster contains the available annotation downloaded from UniProtKB, GO, PFAM and PDB. After statistical validation, GO terms and PFAM domains are cluster-specific and annotate new sequences entering the cluster after satisfying similarity constraints. BAR 3.0 includes 28 869 663 sequences in 1 361 773 clusters, of which 22.2% (22 241 661 sequences) and 47.4% (24 555 055 sequences) have at least one validated GO term and one PFAM domain, respectively. 1.4% of the clusters (36% of all sequences) include PDB structures and the cluster is associated to a hidden Markov model that allows building template-target alignment suitable for structural modeling. Some other 3 399 026 sequences are singletons. BAR 3.0 offers an improved search interface, allowing queries by UniProtKB-accession, Fasta sequence, GO-term, PFAM-domain, organism, PDB and ligand/s. When evaluated on the CAFA2 targets, BAR 3.0 largely outperforms our previous version and scores among state-of-the-art methods. BAR 3.0 is publicly available and accessible at http://bar.biocomp.unibo.it/bar3. PMID:28453653

LipidHome: a database of theoretical lipids optimized for high throughput mass spectrometry lipidomics.

PubMed

Foster, Joseph M; Moreno, Pablo; Fabregat, Antonio; Hermjakob, Henning; Steinbeck, Christoph; Apweiler, Rolf; Wakelam, Michael J O; Vizcaíno, Juan Antonio

2013-01-01

Protein sequence databases are the pillar upon which modern proteomics is supported, representing a stable reference space of predicted and validated proteins. One example of such resources is UniProt, enriched with both expertly curated and automatic annotations. Taken largely for granted, similar mature resources such as UniProt are not available yet in some other "omics" fields, lipidomics being one of them. While having a seasoned community of wet lab scientists, lipidomics lies significantly behind proteomics in the adoption of data standards and other core bioinformatics concepts. This work aims to reduce the gap by developing an equivalent resource to UniProt called 'LipidHome', providing theoretically generated lipid molecules and useful metadata. Using the 'FASTLipid' Java library, a database was populated with theoretical lipids, generated from a set of community agreed upon chemical bounds. In parallel, a web application was developed to present the information and provide computational access via a web service. Designed specifically to accommodate high throughput mass spectrometry based approaches, lipids are organised into a hierarchy that reflects the variety in the structural resolution of lipid identifications. Additionally, cross-references to other lipid related resources and papers that cite specific lipids were used to annotate lipid records. The web application encompasses a browser for viewing lipid records and a 'tools' section where an MS1 search engine is currently implemented. LipidHome can be accessed at http://www.ebi.ac.uk/apweiler-srv/lipidhome.

Comparative study of unilateral versus bilateral inferior oblique recession/anteriorization in unilateral inferior oblique overaction.

PubMed

Mostafa, Attiat M; Kassem, Rehab R

2018-05-01

To compare the effect of, and the rate of subsequent development of iatrogenic antielevation syndrome after, unilateral versus bilateral inferior oblique graded recession-anteriorization to treat unilateral inferior oblique overaction. Thirty-four patients with unilateral inferior oblique overaction were included in a randomized prospective study. Patients were equally divided into 2 groups. Group UNI underwent unilateral, group BI bilateral, inferior oblique graded recession-anteriorization. A successful outcome was defined as orthotropia, or within 2 ∆ of a residual hypertropia, in the absence of signs of antielevation syndrome, residual inferior oblique overaction, V-pattern, dissociated vertical deviation, or ocular torticollis. A successful outcome was achieved in 11 (64.7%) and 13 (76.5%) patients in groups UNI and BI, respectively (p = 0.452). Antielevation syndrome was diagnosed as the cause of surgical failure in 6 (35.3%) and 2 (11.8%) patients, in groups UNI and BI, respectively (p = 0.106). The cause of surgical failure in the other 2 patients in group BI was due to persistence of ocular torticollis and hypertropia in a patient with superior oblique palsy and a residual V-pattern and hypertropia in the other patient. The differences between unilateral and bilateral inferior oblique graded recession-anteriorization are insignificant. Unilateral surgery has a higher tendency for the subsequent development of antielevation syndrome. Bilateral surgery may still become complicated by antielevation syndrome, although at a lower rate. In addition, bilateral surgery had a higher rate of undercorrection. Further studies on a larger sample are encouraged.

ManUniCast: A Community Weather and Air-Quality Forecasting Teaching Portal

NASA Astrophysics Data System (ADS)

Schultz, David M.; Anderson, Stuart; Fairman, Jonathan G.; Lowe, Douglas; McFiggans, Gordon; Lee, Elsa; Seo-Zindy, Ryo

2014-05-01

Manunicast was borne out of the needs of our teaching program: students were entering a world where environmental prediction via numerical model was an essential skill, but were not exposed to the production or output of such models. Our site is an educational testbed to explain to students and the public how weather, air-quality, and air-chemistry forecasts are made using real-time predictions as examples. As far as we know, this site provides the first freely available real-time predictions for the UK. We perform two simulations a day over three domains using the most popular, freely available, community atmospheric mesoscale and chemistry models WRF-ARW and WRF-Chem: 1. a WRF-ARW domain over the North Atlantic and western Europe (20-km horizontal grid spacing) 2. a WRF-ARW domain over the UK and Ireland (4-km grid spacing, nested within the 20-km domain) 3. a WRF-Chem domain over the UK and Ireland (12-km grid spacing) Called ManUniCast (Manchester University Forecast), we offer a suite of products from horizontal maps, time series at stations (meteograms), skew-T-logp charts, and cross sections to help students better visualize the weather and the relationships between the various fields more effectively, specifically through the ability to overlay and fade between different plotted products. This presentation discusses how we funded and built ManUniCast, the struggles we faced, and its use in our classes.

Functional recovery differences after stroke rehabilitation in patients with uni- or bilateral hemiparesis

PubMed Central

Bindawas, Saad M.; Mawajdeh, Hussam M.; Vennu, Vishal S.; Alhaidary, Hisham M.

2017-01-01

Objective: To examine the functional recovery differences after stroke rehabilitation in patients with uni- or bilateral hemiparesis. Methods: In this retrospective study, we included data from the medical record of all 383 patients with uni- or bilateral hemiparesis after stroke who were admitted to King Fahad Medical City-Rehabilitation Hospital between 2008 and 2014 in Riyadh, Kingdom of Saudi Arabia. According to the site of hemiparesis, we classified patients into 3 groups: right hemiparesis (n=208), left hemiparesis (n=157), and bilateral hemipareses (n=18). The patients (n=49) who did not have either site of hemiparesis were excluded. The Functional Independence Measures (FIM) instrument was used to assess the score at admission and discharge. A post hoc test was conducted to examine the functional recovery differences between groups. Multiple regression analyses were used to confirm the findings. Results: Amongst the three groups, there were significant (p<0.05) differences in the total-FIM score as well as motor- and cognitive-FIM sub-scores between admission and discharge of stroke rehabilitation. The differences were significantly greater in the bilateral hemipareses group than in either unilateral hemiparesis group. Multiple regression analyses also confirmed that the site of hemiparesis significantly (p<0.05) differs in the total-FIM score as well as motor-FIM and cognitive-FIM sub-scores. Conclusion: Our results demonstrate that differences in functional recovery after stroke rehabilitation may be influenced by the site of hemiparesis after stroke. PMID:28678212

Green Chemistry Challenge: 2017 Small Business Award

EPA Pesticide Factsheets

Green Chemistry Challenge 2017 award winner, UniEnergy,improved a vanadium redox flow battery to double the energy density, have a broader operating temperature range, a smaller footprint, reduced chemical usage, and very little capacity degradation.

Accident/incident bulletin : calendar year 1994

DOT National Transportation Integrated Search

1995-08-01

The FRA Guide for Preparing Accident/Incident Reports was reprinted in 1993. It : incorporates many suggestions received from representatives of various segments of the : railroad safety community. The primary goal of this revision was to improve uni...

Enhanced performance for the analysis of prostaglandins and thromboxanes by liquid chromatography-tandem mass spectrometry using a new atmospheric pressure ionization source.

PubMed

Lubin, Arnaud; Geerinckx, Suzy; Bajic, Steve; Cabooter, Deirdre; Augustijns, Patrick; Cuyckens, Filip; Vreeken, Rob J

2016-04-01

Eicosanoids, including prostaglandins and thromboxanes are lipid mediators synthetized from polyunsaturated fatty acids. They play an important role in cell signaling and are often reported as inflammatory markers. LC-MS/MS is the technique of choice for the analysis of these compounds, often in combination with advanced sample preparation techniques. Here we report a head to head comparison between an electrospray ionization source (ESI) and a new atmospheric pressure ionization source (UniSpray). The performance of both interfaces was evaluated in various matrices such as human plasma, pig colon and mouse colon. The UniSpray source shows an increase in method sensitivity up to a factor 5. Equivalent to better linearity and repeatability on various matrices as well as an increase in signal intensity were observed in comparison to ESI. Copyright © 2016 Elsevier B.V. All rights reserved.

Analysis of a front suspension system for UniART FSAE car using FEA

NASA Astrophysics Data System (ADS)

Zaidie, M. N. A.; Hashim, M. S. M.; Tasyrif, M.; Basha, M. H.; Ibrahim, I.; Kamaruddin, N. S.; Shahriman, A. B.

2017-10-01

In recent years, many research works from institutions that participated in Formula SAE had highlighted on suspension systems. The aim is to improve the system in term of performance and robustness. However, every suspension system for a racing car is tailored to the car itself. Thus, this paper proposes a new design for front suspension system for UniART FSAE car. The new design was than being compared to the previous suspension system for enhancement. The analysis covered in this paper based on several conditions such as braking, cornering and bumping condition and was carried out using finite element analysis. Each main component for the suspension system such as lower arm, upper arm and knuckle has been analysed in term of strength and performance. From the results, the proposed new design of the suspension system has improved in term of strength and performance compared to the previous suspension system.

Unification and new particles at the LHC

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

Arkani-Hamed, Nima; D’Agnolo, Raffaele Tito; Low, Matthew

Precision gauge coupling uni cation is one of the primary quantitative successes of low energy or split supersymmetry. Preserving this success puts severe restrictions on possible matter and gauge sectors that might appear at collider-accessible energies. In this study we enumerate new gauge sectors which are compatible with uni cation, consisting of horizontal gauge groups acting on vector-like matter charged under the Standard Model. Interestingly, almost all of these theories are in the supersymmetric conformal window at high energies and con ne quickly after the superpartners are decoupled. For a range of scalar masses compatible with both moderately tuned andmore » minimally split supersymmetry, the con ning dynamics happen at the multi-TeV scale, leading to a spectrum of multiple spin-0 and spin-1 resonances accessible to the LHC, with unusual quantum numbers and striking decay patterns.« less

InGaAsP-based uni-travelling carrier photodiode structure grown by solid source molecular beam epitaxy.

PubMed

Natrella, Michele; Rouvalis, Efthymios; Liu, Chin-Pang; Liu, Huiyun; Renaud, Cyril C; Seeds, Alwyn J

2012-08-13

We report the first InGaAsP-based uni-travelling carrier photodiode structure grown by Solid Source Molecular Beam Epitaxy; the material contains layers of InGaAsP as thick as 300 nm and a 120 nm thick InGaAs absorber. Large area vertically illuminated test devices have been fabricated and characterised; the devices exhibited 0.1 A/W responsivity at 1550 nm, 12.5 GHz -3 dB bandwidth and -5.8 dBm output power at 10 GHz for a photocurrent of 4.8 mA. The use of Solid Source Molecular Beam Epitaxy enables the major issue associated with the unintentional diffusion of zinc in Metal Organic Vapour Phase Epitaxy to be overcome and gives the benefit of the superior control provided by MBE growth techniques without the costs and the risks of handling toxic gases of Gas Source Molecular Beam Epitaxy.

Application of information technology to the National Launch System

NASA Technical Reports Server (NTRS)

Mauldin, W. T.; Smith, Carolyn L.; Monk, Jan C.; Davis, Steve; Smith, Marty E.

1992-01-01

The approach to the development of the Unified Information System (UNIS) to provide in a timely manner all the information required to manage, design, manufacture, integrate, test, launch, operate, and support the Advanced Launch System (NLS), as well as the current and planned capabilities are described. STESYM, the Space Transportation Main Engine (STME) development program, is comprised of a collection of data models which can be grouped into two primary models: the Engine Infrastructure Model (ENGIM) and the Engine Integrated Cast Model (ENGICOM). ENGIM is an end-to-end model of the infrastructure needed to perform the fabrication, assembly, and testing of the STEM program and its components. Together, UNIS and STESYM are to provide NLS managers and engineers with the ability to access various types and files of data quickly and use that data to assess the capabilities of the STEM program.

A case study: semantic integration of gene-disease associations for type 2 diabetes mellitus from literature and biomedical data resources.

PubMed

Rebholz-Schuhmann, Dietrich; Grabmüller, Christoph; Kavaliauskas, Silvestras; Croset, Samuel; Woollard, Peter; Backofen, Rolf; Filsell, Wendy; Clark, Dominic

2014-07-01

In the Semantic Enrichment of the Scientific Literature (SESL) project, researchers from academia and from life science and publishing companies collaborated in a pre-competitive way to integrate and share information for type 2 diabetes mellitus (T2DM) in adults. This case study exposes benefits from semantic interoperability after integrating the scientific literature with biomedical data resources, such as UniProt Knowledgebase (UniProtKB) and the Gene Expression Atlas (GXA). We annotated scientific documents in a standardized way, by applying public terminological resources for diseases and proteins, and other text-mining approaches. Eventually, we compared the genetic causes of T2DM across the data resources to demonstrate the benefits from the SESL triple store. Our solution enables publishers to distribute their content with little overhead into remote data infrastructures, such as into any Virtual Knowledge Broker. Copyright © 2013. Published by Elsevier Ltd.

Twinning European and South Asian river basins to enhance capacity and implement adaptive integrated water resources management approaches - results from the EC-project BRAHMATWINN

NASA Astrophysics Data System (ADS)

Flügel, W.-A.

2011-04-01

The EC-project BRAHMATWINN was carrying out a harmonised integrated water resources management (IWRM) approach as addressed by the European Water Initiative (EWI) in headwater river systems of alpine mountain massifs of the twinning Upper Danube River Basin (UDRB) and the Upper Brahmaputra River Basins (UBRB) in Europe and Southeast Asia respectively. Social and natural scientists in cooperation with water law experts and local stakeholders produced the project outcomes presented in Chapter 2 till Chapter 10 of this publication. BRAHMATWINN applied a holistic approach towards IWRM comprising climate modelling, socio-economic and governance analysis and concepts together with methods and integrated tools of applied Geoinformatics. A detailed description of the deliverables produced by the BRAHMATWINN project is published on the project homepage http://www.brahmatwinn.uni-jena.de.

DIEGO: detection of differential alternative splicing using Aitchison's geometry.

PubMed

Doose, Gero; Bernhart, Stephan H; Wagener, Rabea; Hoffmann, Steve

2018-03-15

Alternative splicing is a biological process of fundamental importance in most eukaryotes. It plays a pivotal role in cell differentiation and gene regulation and has been associated with a number of different diseases. The widespread availability of RNA-Sequencing capacities allows an ever closer investigation of differentially expressed isoforms. However, most tools for differential alternative splicing (DAS) analysis do not take split reads, i.e. the most direct evidence for a splice event, into account. Here, we present DIEGO, a compositional data analysis method able to detect DAS between two sets of RNA-Seq samples based on split reads. The python tool DIEGO works without isoform annotations and is fast enough to analyze large experiments while being robust and accurate. We provide python and perl parsers for common formats. The software is available at: www.bioinf.uni-leipzig.de/Software/DIEGO. steve@bioinf.uni-leipzig.de. Supplementary data are available at Bioinformatics online.

Unification and new particles at the LHC

DOE PAGES

Arkani-Hamed, Nima; D’Agnolo, Raffaele Tito; Low, Matthew; ...

2016-11-14

Precision gauge coupling uni cation is one of the primary quantitative successes of low energy or split supersymmetry. Preserving this success puts severe restrictions on possible matter and gauge sectors that might appear at collider-accessible energies. In this study we enumerate new gauge sectors which are compatible with uni cation, consisting of horizontal gauge groups acting on vector-like matter charged under the Standard Model. Interestingly, almost all of these theories are in the supersymmetric conformal window at high energies and con ne quickly after the superpartners are decoupled. For a range of scalar masses compatible with both moderately tuned andmore » minimally split supersymmetry, the con ning dynamics happen at the multi-TeV scale, leading to a spectrum of multiple spin-0 and spin-1 resonances accessible to the LHC, with unusual quantum numbers and striking decay patterns.« less

Test and Analyses of a Composite Multi-Bay Fuselage Panel Under Uni-Axial Compression

NASA Technical Reports Server (NTRS)

Li, Jian; Baker, Donald J.

2004-01-01

A composite panel containing three stringers and two frames cut from a vacuum-assisted resin transfer molded (VaRTM) stitched fuselage article was tested under uni-axial compression loading. The stringers and frames divided the panel into six bays with two columns of three bays each along the compressive loading direction. The two frames were supported at the ends with pins to restrict the out-of-plane translation. The free edges of the panel were constrained by knife-edges. The panel was modeled with shell finite elements and analyzed with ABAQUS nonlinear solver. The nonlinear predictions were compared with the test results in out-of-plane displacements, back-to-back surface strains on stringer flanges and back-to-back surface strains at the centers of the skin-bays. The analysis predictions were in good agreement with the test data up to post-buckling.

Abscinazole-F1, a conformationally restricted analogue of the plant growth retardant uniconazole and an inhibitor of ABA 8'-hydroxylase CYP707A with no growth-retardant effect.

PubMed

Todoroki, Yasushi; Kobayashi, Kyotaro; Shirakura, Minaho; Aoyama, Hikaru; Takatori, Kokichi; Nimitkeatkai, Hataitip; Jin, Mei-Hong; Hiramatsu, Saori; Ueno, Kotomi; Kondo, Satoru; Mizutani, Masaharu; Hirai, Nobuhiro

2009-09-15

To develop a specific inhibitor of abscisic acid (ABA) 8'-hydroxylase, a key enzyme in the catabolism of ABA, a plant hormone involved in stress tolerance, seed dormancy, and other various physiological events, we designed and synthesized conformationally restricted analogues of uniconazole (UNI), a well-known plant growth retardant, which inhibits a biosynthetic enzyme (ent-kaurene oxidase) of gibberellin as well as ABA 8'-hydroxylase. Although most of these analogues were less effective than UNI in inhibition of ABA 8'-hydroxylase and rice seedling growth, we found that a lactol-bridged analogue with an imidazole is a potent inhibitor of ABA 8'-hydroxylase but not of plant growth. This compound, abscinazole-F1, induced drought tolerance in apple seedlings upon spray treatment with a 10 microM solution.

Modelling Growth and Form of the Scleractinian Coral Pocillopora verrucosa and the Influence of Hydrodynamics

PubMed Central

Chindapol, Nol; Kaandorp, Jaap A.; Cronemberger, Carolina; Mass, Tali; Genin, Amatzia

2013-01-01

The growth of scleractinian corals is strongly influenced by the effect of water motion. Corals are known to have a high level of phenotypic variation and exhibit a diverse range of growth forms, which often contain a high level of geometric complexity. Due to their complex shape, simulation models represent an important option to complement experimental studies of growth and flow. In this work, we analyzed the impact of flow on coral's morphology by an accretive growth model coupled with advection-diffusion equations. We performed simulations under no-flow and uni-directional flow setup with the Reynolds number constant. The relevant importance of diffusion to advection was investigated by varying the diffusion coefficient, rather than the flow speed in Péclet number. The flow and transport equations were coupled and solved using COMSOL Multiphysics. We then compared the simulated morphologies with a series of Computed Tomography (CT) scans of scleractinian corals Pocillopora verrucosa exposed to various flow conditions in the in situ controlled flume setup. As a result, we found a similar trend associated with the increasing Péclet for both simulated forms and in situ corals; that is uni-directional current tends to facilitate asymmetrical growth response resulting in colonies with branches predominantly developed in the upstream direction. A closer look at the morphological traits yielded an interesting property about colony symmetry and plasticity induced by uni-directional flow. Both simulated and in situ corals exhibit a tendency where the degree of symmetry decreases and compactification increases in conjunction with the augmented Péclet thus indicates the significant importance of hydrodynamics. PMID:23326222

Cross-modal perceptual load: the impact of modality and individual differences.

PubMed

Sandhu, Rajwant; Dyson, Benjamin James

2016-05-01

Visual distractor processing tends to be more pronounced when the perceptual load (PL) of a task is low compared to when it is high [perpetual load theory (PLT); Lavie in J Exp Psychol Hum Percept Perform 21(3):451-468, 1995]. While PLT is well established in the visual domain, application to cross-modal processing has produced mixed results, and the current study was designed in an attempt to improve previous methodologies. First, we assessed PLT using response competition, a typical metric from the uni-modal domain. Second, we looked at the impact of auditory load on visual distractors, and of visual load on auditory distractors, within the same individual. Third, we compared individual uni- and cross-modal selective attention abilities, by correlating performance with the visual Attentional Network Test (ANT). Fourth, we obtained a measure of the relative processing efficiency between vision and audition, to investigate whether processing ease influences the extent of distractor processing. Although distractor processing was evident during both attend auditory and attend visual conditions, we found that PL did not modulate processing of either visual or auditory distractors. We also found support for a correlation between the uni-modal (visual) ANT and our cross-modal task but only when the distractors were visual. Finally, although auditory processing was more impacted by visual distractors, our measure of processing efficiency only accounted for this asymmetry in the auditory high-load condition. The results are discussed with respect to the continued debate regarding the shared or separate nature of processing resources across modalities.

Towards the Interoperability of Web, Database, and Mass Storage Technologies for Petabyte Archives

NASA Technical Reports Server (NTRS)

Moore, Reagan; Marciano, Richard; Wan, Michael; Sherwin, Tom; Frost, Richard

1996-01-01

At the San Diego Supercomputer Center, a massive data analysis system (MDAS) is being developed to support data-intensive applications that manipulate terabyte sized data sets. The objective is to support scientific application access to data whether it is located at a Web site, stored as an object in a database, and/or storage in an archival storage system. We are developing a suite of demonstration programs which illustrate how Web, database (DBMS), and archival storage (mass storage) technologies can be integrated. An application presentation interface is being designed that integrates data access to all of these sources. We have developed a data movement interface between the Illustra object-relational database and the NSL UniTree archival storage system running in a production mode at the San Diego Supercomputer Center. With this interface, an Illustra client can transparently access data on UniTree under the control of the Illustr DBMS server. The current implementation is based on the creation of a new DBMS storage manager class, and a set of library functions that allow the manipulation and migration of data stored as Illustra 'large objects'. We have extended this interface to allow a Web client application to control data movement between its local disk, the Web server, the DBMS Illustra server, and the UniTree mass storage environment. This paper describes some of the current approaches successfully integrating these technologies. This framework is measured against a representative sample of environmental data extracted from the San Diego Ba Environmental Data Repository. Practical lessons are drawn and critical research areas are highlighted.

A Low-cost Beam Profiler Based On Cerium-doped Silica Fibers

NASA Astrophysics Data System (ADS)

Potkins, David Edward; Braccini, Saverio; Nesteruk, Konrad Pawel; Carzaniga, Tommaso Stefano; Vedda, Anna; Chiodini, Norberto; Timmermans, Jacob; Melanson, Stephane; Dehnel, Morgan Patrick

A beam profiler called the Universal Beam Monitor (UniBEaM) has been developed by D-Pace Inc. (Canada) and the Albert Einstein Center for Fundamental Physics, Laboratory for High Energy Physics, University of Bern (Switzerland). The device is based on passing 100 to 600 micron cerium-doped optical fibers through a particle beam. Visible scintillation light from the sensor fibers is transmitted over distances of tens of meters to the light sensors with minimal signal loss and no susceptibility to electromagnetic fields. The probe has an insertion length of only 70 mm. The software plots the beam intensity distribution in the horizontal and vertical planes, and calculates the beam location and integrated profile area, which correlates well with total beam current. UniBEaM has a large dynamic range, operating with beam currents of ∼pA to mA, and a large range of particle kinetic energies of ∼keV to GeV, depending on the absorbed power density. Test data are presented for H- beams at 25keV for 500 μA, and H+ beams at 18MeV for 50pA to 10 μA. Maximum absorbed power density of the optical fiber before thermal damage is discussed in relation to dE/dx energy deposition as a function of particle type and kinetic energy. UniBEaM is well suited for a wide variety of beamlines including discovery science applications, radio-pharmaceutical production, hadron therapy, industrial ion beam applications including ion implantation, industrial electron beams, and ion source testing.

Push-out bond strengths of fiber-reinforced composite posts with various resin cements according to the root level

PubMed Central

Chang, Hoon-Sang; Noh, Young-Sin; Lee, Yoon; Min, Kyung-San

2013-01-01

PURPOSE The aim of this study was to determine whether the push-out bond strengths between the radicular dentin and fiber reinforced-composite (FRC) posts with various resin cements decreased or not, according to the coronal, middle or apical level of the root. MATERIALS AND METHODS FRC posts were cemented with one of five resin cement groups (RelyX Unicem: Uni, Contax with activator & LuxaCore-Dual: LuA, Contax & LuxaCore-Dual: Lu, Panavia F 2.0: PA, Super-Bond C&B: SB) into extracted human mandibular premolars. The roots were sliced into discs at the coronal, middle and apical levels. Push-out bond strength tests were performed with a universal testing machine at a crosshead speed of 0.5 mm/min, and the failure aspect was analyzed. RESULTS There were no significant differences (P>.05) in the bond strengths of the different resin cements at the coronal level, but there were significant differences in the bond strengths at the middle and apical levels (P<.05). Only the Uni and LuA cements did not show any significant decrease in their bond strengths at all the root levels (P>.05); all other groups had a significant decrease in bond strength at the middle or apical level (P<.05). The failure aspect was dominantly cohesive at the coronal level of all resin cements (P<.05), whereas it was dominantly adhesive at the apical level. CONCLUSION All resin cement groups showed decreases in bond strengths at the middle or apical level except LuA and Uni. PMID:24049569

Linking microarray reporters with protein functions.

PubMed

Gaj, Stan; van Erk, Arie; van Haaften, Rachel I M; Evelo, Chris T A

2007-09-26

The analysis of microarray experiments requires accurate and up-to-date functional annotation of the microarray reporters to optimize the interpretation of the biological processes involved. Pathway visualization tools are used to connect gene expression data with existing biological pathways by using specific database identifiers that link reporters with elements in the pathways. This paper proposes a novel method that aims to improve microarray reporter annotation by BLASTing the original reporter sequences against a species-specific EMBL subset, that was derived from and crosslinked back to the highly curated UniProt database. The resulting alignments were filtered using high quality alignment criteria and further compared with the outcome of a more traditional approach, where reporter sequences were BLASTed against EnsEMBL followed by locating the corresponding protein (UniProt) entry for the high quality hits. Combining the results of both methods resulted in successful annotation of > 58% of all reporter sequences with UniProt IDs on two commercial array platforms, increasing the amount of Incyte reporters that could be coupled to Gene Ontology terms from 32.7% to 58.3% and to a local GenMAPP pathway from 9.6% to 16.7%. For Agilent, 35.3% of the total reporters are now linked towards GO nodes and 7.1% on local pathways. Our methods increased the annotation quality of microarray reporter sequences and allowed us to visualize more reporters using pathway visualization tools. Even in cases where the original reporter annotation showed the correct description the new identifiers often allowed improved pathway and Gene Ontology linking. These methods are freely available at http://www.bigcat.unimaas.nl/public/publications/Gaj_Annotation/.

21 CFR 888.3535 - Knee joint femorotibial (uni-compartmental) metal/polymer porous-coated uncemented prosthesis.

Code of Federal Regulations, 2014 CFR

2014-04-01

... across-the-joint. This generic type of device is designed to achieve biological fixation to bone without the use of bone cement. This identification includes fixed-bearing knee prostheses where the ultra...

21 CFR 888.3535 - Knee joint femorotibial (uni-compartmental) metal/polymer porous-coated uncemented prosthesis.

Code of Federal Regulations, 2013 CFR

2013-04-01

... across-the-joint. This generic type of device is designed to achieve biological fixation to bone without the use of bone cement. This identification includes fixed-bearing knee prostheses where the ultra...

21 CFR 888.3535 - Knee joint femorotibial (uni-compartmental) metal/polymer porous-coated uncemented prosthesis.

Code of Federal Regulations, 2012 CFR

2012-04-01

... across-the-joint. This generic type of device is designed to achieve biological fixation to bone without the use of bone cement. This identification includes fixed-bearing knee prostheses where the ultra...

21 CFR 888.3535 - Knee joint femorotibial (uni-compartmental) metal/polymer porous-coated uncemented prosthesis.

Code of Federal Regulations, 2011 CFR

2011-04-01

... across-the-joint. This generic type of device is designed to achieve biological fixation to bone without the use of bone cement. This identification includes fixed-bearing knee prostheses where the ultra...

21 CFR 888.3535 - Knee joint femorotibial (uni-compartmental) metal/polymer porous-coated uncemented prosthesis.

Code of Federal Regulations, 2010 CFR

2010-04-01

... across-the-joint. This generic type of device is designed to achieve biological fixation to bone without the use of bone cement. This identification includes fixed-bearing knee prostheses where the ultra...

Materials Data on U(Ni2P)2 (SG:136) by Materials Project

DOE Data Explorer

Kristin Persson

2015-02-09

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Developing Real-Time Emissions Estimates for Enhanced Air Quality Forecasting

EPA Science Inventory

Exploring the relationship between ambient temperature, energy demand, and electric generating unit point source emissions and potential techniques for incorporating real-time information on the modulating effects of these variables using the Mid-Atlantic/Northeast Visibility Uni...

Maize databases

USDA-ARS?s Scientific Manuscript database

This chapter is a succinct overview of maize data held in the species-specific database MaizeGDB (the Maize Genomics and Genetics Database), and selected multi-species data repositories, such as Gramene/Ensembl Plants, Phytozome, UniProt and the National Center for Biotechnology Information (NCBI), ...

Text Mining Genotype-Phenotype Relationships from Biomedical Literature for Database Curation and Precision Medicine.

PubMed

Singhal, Ayush; Simmons, Michael; Lu, Zhiyong

2016-11-01

The practice of precision medicine will ultimately require databases of genes and mutations for healthcare providers to reference in order to understand the clinical implications of each patient's genetic makeup. Although the highest quality databases require manual curation, text mining tools can facilitate the curation process, increasing accuracy, coverage, and productivity. However, to date there are no available text mining tools that offer high-accuracy performance for extracting such triplets from biomedical literature. In this paper we propose a high-performance machine learning approach to automate the extraction of disease-gene-variant triplets from biomedical literature. Our approach is unique because we identify the genes and protein products associated with each mutation from not just the local text content, but from a global context as well (from the Internet and from all literature in PubMed). Our approach also incorporates protein sequence validation and disease association using a novel text-mining-based machine learning approach. We extract disease-gene-variant triplets from all abstracts in PubMed related to a set of ten important diseases (breast cancer, prostate cancer, pancreatic cancer, lung cancer, acute myeloid leukemia, Alzheimer's disease, hemochromatosis, age-related macular degeneration (AMD), diabetes mellitus, and cystic fibrosis). We then evaluate our approach in two ways: (1) a direct comparison with the state of the art using benchmark datasets; (2) a validation study comparing the results of our approach with entries in a popular human-curated database (UniProt) for each of the previously mentioned diseases. In the benchmark comparison, our full approach achieves a 28% improvement in F1-measure (from 0.62 to 0.79) over the state-of-the-art results. For the validation study with UniProt Knowledgebase (KB), we present a thorough analysis of the results and errors. Across all diseases, our approach returned 272 triplets (disease-gene-variant) that overlapped with entries in UniProt and 5,384 triplets without overlap in UniProt. Analysis of the overlapping triplets and of a stratified sample of the non-overlapping triplets revealed accuracies of 93% and 80% for the respective categories (cumulative accuracy, 77%). We conclude that our process represents an important and broadly applicable improvement to the state of the art for curation of disease-gene-variant relationships.

UNITEC SENS-IT

EPA Science Inventory

The UniTec Sens-It is a small gas-sensing device that can measure volatile organic compounds (VOCs). This sensor is used to measure VOCs in applications such as urban air quality, roadside pollution, and (solid waste) landfill monitoring. This operating procedure explains what yo...

USDOT Tier 1 University Transportation Center Program progress performance report #5.

DOT National Transportation Integrated Search

2016-04-29

MarTREC is a USDOT Tier 1 University Transportation Center funded in September 30, 2013 : under MAP-21. Our consortium consists of the University of Arkansas (UARK), Fayetteville, AR; : Jackson State University (JSU), Jackson, MS; Louisiana State Uni...

DeepLoc: prediction of protein subcellular localization using deep learning.

PubMed

Almagro Armenteros, José Juan; Sønderby, Casper Kaae; Sønderby, Søren Kaae; Nielsen, Henrik; Winther, Ole

2017-11-01

The prediction of eukaryotic protein subcellular localization is a well-studied topic in bioinformatics due to its relevance in proteomics research. Many machine learning methods have been successfully applied in this task, but in most of them, predictions rely on annotation of homologues from knowledge databases. For novel proteins where no annotated homologues exist, and for predicting the effects of sequence variants, it is desirable to have methods for predicting protein properties from sequence information only. Here, we present a prediction algorithm using deep neural networks to predict protein subcellular localization relying only on sequence information. At its core, the prediction model uses a recurrent neural network that processes the entire protein sequence and an attention mechanism identifying protein regions important for the subcellular localization. The model was trained and tested on a protein dataset extracted from one of the latest UniProt releases, in which experimentally annotated proteins follow more stringent criteria than previously. We demonstrate that our model achieves a good accuracy (78% for 10 categories; 92% for membrane-bound or soluble), outperforming current state-of-the-art algorithms, including those relying on homology information. The method is available as a web server at http://www.cbs.dtu.dk/services/DeepLoc. Example code is available at https://github.com/JJAlmagro/subcellular_localization. The dataset is available at http://www.cbs.dtu.dk/services/DeepLoc/data.php. jjalma@dtu.dk. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Resolving the problem of multiple accessions of the same transcript deposited across various public databases.

PubMed

Weirick, Tyler; John, David; Uchida, Shizuka

2017-03-01

Maintaining the consistency of genomic annotations is an increasingly complex task because of the iterative and dynamic nature of assembly and annotation, growing numbers of biological databases and insufficient integration of annotations across databases. As information exchange among databases is poor, a 'novel' sequence from one reference annotation could be annotated in another. Furthermore, relationships to nearby or overlapping annotated transcripts are even more complicated when using different genome assemblies. To better understand these problems, we surveyed current and previous versions of genomic assemblies and annotations across a number of public databases containing long noncoding RNA. We identified numerous discrepancies of transcripts regarding their genomic locations, transcript lengths and identifiers. Further investigation showed that the positional differences between reference annotations of essentially the same transcript could lead to differences in its measured expression at the RNA level. To aid in resolving these problems, we present the algorithm 'Universal Genomic Accession Hash (UGAHash)' and created an open source web tool to encourage the usage of the UGAHash algorithm. The UGAHash web tool (http://ugahash.uni-frankfurt.de) can be accessed freely without registration. The web tool allows researchers to generate Universal Genomic Accessions for genomic features or to explore annotations deposited in the public databases of the past and present versions. We anticipate that the UGAHash web tool will be a valuable tool to check for the existence of transcripts before judging the newly discovered transcripts as novel. © The Author 2016. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

SIBIS: a Bayesian model for inconsistent protein sequence estimation.

PubMed

Khenoussi, Walyd; Vanhoutrève, Renaud; Poch, Olivier; Thompson, Julie D

2014-09-01

The prediction of protein coding genes is a major challenge that depends on the quality of genome sequencing, the accuracy of the model used to elucidate the exonic structure of the genes and the complexity of the gene splicing process leading to different protein variants. As a consequence, today's protein databases contain a huge amount of inconsistency, due to both natural variants and sequence prediction errors. We have developed a new method, called SIBIS, to detect such inconsistencies based on the evolutionary information in multiple sequence alignments. A Bayesian framework, combined with Dirichlet mixture models, is used to estimate the probability of observing specific amino acids and to detect inconsistent or erroneous sequence segments. We evaluated the performance of SIBIS on a reference set of protein sequences with experimentally validated errors and showed that the sensitivity is significantly higher than previous methods, with only a small loss of specificity. We also assessed a large set of human sequences from the UniProt database and found evidence of inconsistency in 48% of the previously uncharacterized sequences. We conclude that the integration of quality control methods like SIBIS in automatic analysis pipelines will be critical for the robust inference of structural, functional and phylogenetic information from these sequences. Source code, implemented in C on a linux system, and the datasets of protein sequences are freely available for download at http://www.lbgi.fr/∼julie/SIBIS. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

77 FR 31608 - Combined Notice of Filings #1

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-29

..., Inc., UniSource Energy Development Company. Description: Change in Status Filing Tucson Electric Power... DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings 1 Take notice that the Commission received the following electric rate filings: Docket Numbers: ER10-1556-005...

77 FR 76023 - Combined Notice of Filings #1

Federal Register 2010, 2011, 2012, 2013, 2014

2012-12-26

..., UNS Electric, Inc., UniSource Energy Development Company. Description: Triennial Market Power Update... DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings 1 Take notice... County Wind Energy, LLC. Description: Gray County Wind and Ensign Wind Shared Facilities Agreement to be...

Complex Event Extraction using DRUM

DTIC Science & Technology

2015-10-01

towards tackling these challenges . Figure 9. Evaluation results for eleven teams. The diamond ◆ represents the results of our system. The two topmost...Proceedings of the Joint SIGDAT Conference on Empirical Methods in Natural Language Processing and Very Large Corpora (EMNLP/ VLC -2000). The UniProt

Registration of 'Thunder CL' Wheat

USDA-ARS?s Scientific Manuscript database

'Thunder CL' (Reg. No. CV- , PI XXXXXX) hard white winter wheat (Triticum aestivum L.) was developed by the Colorado Agricultural Experiment Station and released in August 2008 through a marketing agreement with the Colorado Wheat Research Foundation. In addition to researchers at Colorado State Uni...

An update on the Enzyme Portal: an integrative approach for exploring enzyme knowledge

PubMed Central

Onwubiko, J.; Zaru, R.; Rosanoff, S.; Antunes, R.; Bingley, M.; Watkins, X.; O'Donovan, C.; Martin, M. J.

2017-01-01

Abstract Enzymes are a key part of life processes and are increasingly important for various areas of research such as medicine, biotechnology, bioprocessing and drug research. The goal of the Enzyme Portal is to provide an interface to all European Bioinformatics Institute (EMBL-EBI) data about enzymes (de Matos, P., et al., (2013), BMC Bioinformatics, 14 (1), 103). These data include enzyme function, sequence features and family classification, protein structure, reactions, pathways, small molecules, diseases and the associated literature. The sources of enzyme data are: the UniProt Knowledgebase (UniProtKB) (UniProt Consortium, 2015), the Protein Data Bank in Europe (PDBe), (Valenkar, S., et al., Nucleic Acids Res.2016; 44, D385–D395) Rhea—a database of enzyme-catalysed reactions (Morgat, A., et al., Nucleic Acids Res. 2015; 43, D459-D464), Reactome—a database of biochemical pathways (Fabregat, A., et al., Nucleic Acids Res. 2016; 44, D481–D487), IntEnz—a resource with enzyme nomenclature information (Fleischmann, A., et al., Nucleic Acids Res. 2004 32, D434–D437) and ChEBI (Hastings, J., et al., Nucleic Acids Res. 2013) and ChEMBL (Bento, A. P., et al., Nucleic Acids Res. 201442, 1083–1090)—resources which contain information about small-molecule chemistry and bioactivity. This article describes the redesign of Enzyme Portal and the increased functionality added to maximise integration and interpretation of these data. Use case examples of the Enzyme Portal and the versatile workflows its supports are illustrated. We welcome the suggestion of new resources for integration. PMID:28158609

Investigation of Voronoi diagram based direction choices using uni- and bi-directional trajectory data

NASA Astrophysics Data System (ADS)

Xiao, Yao; Chraibi, Mohcine; Qu, Yunchao; Tordeux, Antoine; Gao, Ziyou

2018-05-01

In a crowd, individuals make different motion choices such as "moving to destination," "following another pedestrian," and "making a detour." For the sake of convenience, the three direction choices are respectively called destination direction, following direction, and detour direction in this paper. Here, it is found that the featured direction choices could be inspired by the shape characteristics of the Voronoi diagram. To be specific, in the Voronoi cell of a pedestrian, the direction to a Voronoi node is regarded as a potential "detour" direction and the direction perpendicular to a Voronoi link is regarded as a potential "following" direction. A pedestrian generally owns several alternative Voronoi nodes and Voronoi links in a Voronoi cell, and the optimal detour and following direction are determined by considering related factors such as deviation. Plus the destination direction which is directly pointing to the destination, the three basic direction choices are defined in a Voronoi cell. In order to evaluate the Voronoi diagram based basic directions, the empirical trajectory data in both uni- and bi-directional flow experiments are extracted. A time series method considering the step frequency is used to reduce the original trajectories' swaying phenomena which might disturb the recognition of actual forward direction. The deviations between the empirical velocity direction and the basic directions are investigated, and each velocity direction is classified into a basic direction or regarded as an inexplicable direction according to the deviations. The analysis results show that each basic direction could be a potential direction choice for a pedestrian. The combination of the three basic directions could cover most empirical velocity direction choices in both uni- and bi-directional flow experiments.

The mitochondrial DNA history of a former native American village in northern Uruguay.

PubMed

Sans, Mónica; Mones, Pablo; Figueiro, Gonzalo; Barreto, Isabel; Motti, Josefina M B; Coble, Michael D; Bravi, Claudio M; Hidalgo, Pedro C

2015-01-01

In 1828, between 8,000 and 15,000 Indians from the Jesuit Missions were brought to Uruguay. There, they were settled in a village, presently named Bella Unión, in the northwest corner of the country. According to historic sources, the Indians abandoned the settlement shortly thereafter, with the village subsequently repopulated by "criollos" and immigrants from abroad. As a first approach to reconstruct the genetic history of the population, data about the living population genetic structure will be used. Based on the analysis of the maternal lineages of the inhabitants of Bella Unión, and of those from two nearby villages, we expect to partially answer what happened with the first and subsequent inhabitants. We analyzed the maternal lineages of the present inhabitants of Bella Unión and neighboring localities through the sequencing of the mitochondrial DNA control region. A total of 64.3%, 5.7%, and 30% of the mtDNAs were of Native, African, and West Eurasian origin, respectively. These figures are quite similar to that of the population of Tacuarembó, which is located in northeastern Uruguay. The four main Native American founding haplogroups were detected, with B2 being the most frequent, while some rare subhaplogroups (B2h, C1b2, D1f1) were also found. When compared with other Native American sequences, near- matches most consistently pointed to an Amazonian Indian origin which, when considered with historical evidence, suggested a probable Guaraní-Missionary-related origin. The data support the existence of a relationship between the historic and present inhabitants of the extreme northwest Uruguay, with a strong contribution of Native Americans to the mitochondrial DNA diversity observed there. © 2014 Wiley Periodicals, Inc.

Neural Activity Patterns in the Human Brain Reflect Tactile Stickiness Perception.

PubMed

Kim, Junsuk; Yeon, Jiwon; Ryu, Jaekyun; Park, Jang-Yeon; Chung, Soon-Cheol; Kim, Sung-Phil

2017-01-01

Our previous human fMRI study found brain activations correlated with tactile stickiness perception using the uni-variate general linear model (GLM) (Yeon et al., 2017). Here, we conducted an in-depth investigation on neural correlates of sticky sensations by employing a multivoxel pattern analysis (MVPA) on the same dataset. In particular, we statistically compared multi-variate neural activities in response to the three groups of sticky stimuli: A supra-threshold group including a set of sticky stimuli that evoked vivid sticky perception; an infra-threshold group including another set of sticky stimuli that barely evoked sticky perception; and a sham group including acrylic stimuli with no physically sticky property. Searchlight MVPAs were performed to search for local activity patterns carrying neural information of stickiness perception. Similar to the uni-variate GLM results, significant multi-variate neural activity patterns were identified in postcentral gyrus, subcortical (basal ganglia and thalamus), and insula areas (insula and adjacent areas). Moreover, MVPAs revealed that activity patterns in posterior parietal cortex discriminated the perceptual intensities of stickiness, which was not present in the uni-variate analysis. Next, we applied a principal component analysis (PCA) to the voxel response patterns within identified clusters so as to find low-dimensional neural representations of stickiness intensities. Follow-up clustering analyses clearly showed separate neural grouping configurations between the Supra- and Infra-threshold groups. Interestingly, this neural categorization was in line with the perceptual grouping pattern obtained from the psychophysical data. Our findings thus suggest that different stickiness intensities would elicit distinct neural activity patterns in the human brain and may provide a neural basis for the perception and categorization of tactile stickiness.

Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data.

PubMed

Chung, Dongjun; Kuan, Pei Fen; Li, Bo; Sanalkumar, Rajendran; Liang, Kun; Bresnick, Emery H; Dewey, Colin; Keleş, Sündüz

2011-07-01

Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is rapidly replacing chromatin immunoprecipitation combined with genome-wide tiling array analysis (ChIP-chip) as the preferred approach for mapping transcription-factor binding sites and chromatin modifications. The state of the art for analyzing ChIP-seq data relies on using only reads that map uniquely to a relevant reference genome (uni-reads). This can lead to the omission of up to 30% of alignable reads. We describe a general approach for utilizing reads that map to multiple locations on the reference genome (multi-reads). Our approach is based on allocating multi-reads as fractional counts using a weighted alignment scheme. Using human STAT1 and mouse GATA1 ChIP-seq datasets, we illustrate that incorporation of multi-reads significantly increases sequencing depths, leads to detection of novel peaks that are not otherwise identifiable with uni-reads, and improves detection of peaks in mappable regions. We investigate various genome-wide characteristics of peaks detected only by utilization of multi-reads via computational experiments. Overall, peaks from multi-read analysis have similar characteristics to peaks that are identified by uni-reads except that the majority of them reside in segmental duplications. We further validate a number of GATA1 multi-read only peaks by independent quantitative real-time ChIP analysis and identify novel target genes of GATA1. These computational and experimental results establish that multi-reads can be of critical importance for studying transcription factor binding in highly repetitive regions of genomes with ChIP-seq experiments.

Functional Conservation of PISTILLATA Activity in a Pea Homolog Lacking the PI Motif1

PubMed Central

Berbel, Ana; Navarro, Cristina; Ferrándiz, Cristina; Cañas, Luis Antonio; Beltrán, José-Pío; Madueño, Francisco

2005-01-01

Current understanding of floral development is mainly based on what we know from Arabidopsis (Arabidopsis thaliana) and Antirrhinum majus. However, we can learn more by comparing developmental mechanisms that may explain morphological differences between species. A good example comes from the analysis of genes controlling flower development in pea (Pisum sativum), a plant with more complex leaves and inflorescences than Arabidopsis and Antirrhinum, and a different floral ontogeny. The analysis of UNIFOLIATA (UNI) and STAMINA PISTILLOIDA (STP), the pea orthologs of LEAFY and UNUSUAL FLORAL ORGANS, has revealed a common link in the regulation of flower and leaf development not apparent in Arabidopsis. While the Arabidopsis genes mainly behave as key regulators of flower development, where they control the expression of B-function genes, UNI and STP also contribute to the development of the pea compound leaf. Here, we describe the characterization of P. sativum PISTILLATA (PsPI), a pea MADS-box gene homologous to B-function genes like PI and GLOBOSA (GLO), from Arabidopsis and Antirrhinum, respectively. PsPI encodes for an atypical PI-type polypeptide that lacks the highly conserved C-terminal PI motif. Nevertheless, constitutive expression of PsPI in tobacco (Nicotiana tabacum) and Arabidopsis shows that it can specifically replace the function of PI, being able to complement the strong pi-1 mutant. Accordingly, PsPI expression in pea flowers, which is dependent on STP, is identical to PI and GLO. Interestingly, PsPI is also transiently expressed in young leaves, suggesting a role of PsPI in pea leaf development, a possibility that fits with the established role of UNI and STP in the control of this process. PMID:16113230

dbWFA: a web-based database for functional annotation of Triticum aestivum transcripts

PubMed Central

Vincent, Jonathan; Dai, Zhanwu; Ravel, Catherine; Choulet, Frédéric; Mouzeyar, Said; Bouzidi, M. Fouad; Agier, Marie; Martre, Pierre

2013-01-01

The functional annotation of genes based on sequence homology with genes from model species genomes is time-consuming because it is necessary to mine several unrelated databases. The aim of the present work was to develop a functional annotation database for common wheat Triticum aestivum (L.). The database, named dbWFA, is based on the reference NCBI UniGene set, an expressed gene catalogue built by expressed sequence tag clustering, and on full-length coding sequences retrieved from the TriFLDB database. Information from good-quality heterogeneous sources, including annotations for model plant species Arabidopsis thaliana (L.) Heynh. and Oryza sativa L., was gathered and linked to T. aestivum sequences through BLAST-based homology searches. Even though the complexity of the transcriptome cannot yet be fully appreciated, we developed a tool to easily and promptly obtain information from multiple functional annotation systems (Gene Ontology, MapMan bin codes, MIPS Functional Categories, PlantCyc pathway reactions and TAIR gene families). The use of dbWFA is illustrated here with several query examples. We were able to assign a putative function to 45% of the UniGenes and 81% of the full-length coding sequences from TriFLDB. Moreover, comparison of the annotation of the whole T. aestivum UniGene set along with curated annotations of the two model species assessed the accuracy of the annotation provided by dbWFA. To further illustrate the use of dbWFA, genes specifically expressed during the early cell division or late storage polymer accumulation phases of T. aestivum grain development were identified using a clustering analysis and then annotated using dbWFA. The annotation of these two sets of genes was consistent with previous analyses of T. aestivum grain transcriptomes and proteomes. Database URL: urgi.versailles.inra.fr/dbWFA/ PMID:23660284

The Psychometric Properties of the Generalized Anxiety Disorder-7 scale in Hispanic Americans with English or Spanish Language Preference

PubMed Central

Mills, Sarah D.; Fox, Rina S.; Malcarne, Vanessa L.; Roesch, Scott C.; Champagne, Brian R.; Sadler, Georgia Robins

2014-01-01

The Generalized Anxiety Disorder-7 scale (GAD-7) is a self-report questionnaire that is widely used to screen for anxiety. The GAD-7 has been translated into numerous languages, including Spanish. Previous studies evaluating the structural validity of the English and Spanish versions indicate a uni-dimensional factor structure in both languages. However, the psychometric properties of the Spanish language version have yet to be evaluated in samples outside of Spain, and the measure has not been tested for use among Hispanic Americans. This study evaluated the reliability, structural validity, and convergent validity of the English and Spanish language versions of the GAD-7 for Hispanic Americans in the United States. A community sample of 436 Hispanic Americans with an English (n = 210) or Spanish (n = 226) language preference completed the GAD-7. Multiple-group confirmatory factor analysis (CFA) was used to examine the goodness of fit of the uni-dimensional factor structure of the GAD-7 across language-preference groups. Results from the multiple-group CFA indicated a similar unidimensional factor structure with equivalent response patterns and item intercepts, but different variances, across language-preference groups. Internal consistency was good for both English and Spanish language-preference groups. The GAD-7 also evidenced good convergent validity as demonstrated by significant correlations in expected directions with the Perceived Stress Scale, the Patient Health Questionnaire-9, and the Physical health domain of the World Health Organization Quality of Life-BREF assessment. The uni-dimensional GAD-7 is suitable for use among Hispanic Americans with an English or Spanish language preference. PMID:25045957

Neural Activity Patterns in the Human Brain Reflect Tactile Stickiness Perception

PubMed Central

Kim, Junsuk; Yeon, Jiwon; Ryu, Jaekyun; Park, Jang-Yeon; Chung, Soon-Cheol; Kim, Sung-Phil

2017-01-01

Our previous human fMRI study found brain activations correlated with tactile stickiness perception using the uni-variate general linear model (GLM) (Yeon et al., 2017). Here, we conducted an in-depth investigation on neural correlates of sticky sensations by employing a multivoxel pattern analysis (MVPA) on the same dataset. In particular, we statistically compared multi-variate neural activities in response to the three groups of sticky stimuli: A supra-threshold group including a set of sticky stimuli that evoked vivid sticky perception; an infra-threshold group including another set of sticky stimuli that barely evoked sticky perception; and a sham group including acrylic stimuli with no physically sticky property. Searchlight MVPAs were performed to search for local activity patterns carrying neural information of stickiness perception. Similar to the uni-variate GLM results, significant multi-variate neural activity patterns were identified in postcentral gyrus, subcortical (basal ganglia and thalamus), and insula areas (insula and adjacent areas). Moreover, MVPAs revealed that activity patterns in posterior parietal cortex discriminated the perceptual intensities of stickiness, which was not present in the uni-variate analysis. Next, we applied a principal component analysis (PCA) to the voxel response patterns within identified clusters so as to find low-dimensional neural representations of stickiness intensities. Follow-up clustering analyses clearly showed separate neural grouping configurations between the Supra- and Infra-threshold groups. Interestingly, this neural categorization was in line with the perceptual grouping pattern obtained from the psychophysical data. Our findings thus suggest that different stickiness intensities would elicit distinct neural activity patterns in the human brain and may provide a neural basis for the perception and categorization of tactile stickiness. PMID:28936171

Near- and far-field infrasound monitoring in the Mediterranean area

NASA Astrophysics Data System (ADS)

Campus, Paola; Marchetti, Emanuele; Le Pichon, Alexis; Wallenstein, Nicolau; Ripepe, Maurizio; Kallel, Mohamed; Mialle, Pierrick

2013-04-01

The Mediterranean area is characterized by a number of very interesting sources of infrasound signals and offers a promising playground for the development of a deeper understanding of such sources and of the associated propagation models. The progress in the construction and certification of infrasound arrays belonging to the International Monitoring System (IMS) of the Comprehensive Nuclear-Test-Ban Treaty (CTBT) in the vicinity of this area has been complemented, in the last decade, by the construction of infrasound arrays established by several European research groups. The University of Florence (UniFi) plays a crucial role for the detection of infrasound signals in the Mediterranean area, having deployed since several years two infrasound arrays on Stromboli and Etna volcanoes, and, more recently, three infrasound arrays in the Alpine area of NW Italy and one infrasound array on the Apennines (Mount Amiata), designed and established in the framework of the ARISE Project. The IMS infrasound arrays IS42 (Graciosa, Azores, Portugal) and IS48 (Kesra, Tunisia) recorded, since the time of their certification, a number of far-field events which can be correlated with some near-field records of the infrasound arrays belonging to UniFi. An analysis of the results and potentialities of infrasound source's detections in near and far-field realized by IS42, IS48 and UniFi arrays in the Mediterranean area, with special focus on volcanic events is presented. The combined results deriving from the analysis of data recorded by the Unifi arrays and by the IS42 and IS48 arrays, in collaboration with the Department of Analyse et Surveillance (CEA/DASE), will generate a synergy which will certainly contribute to the progress of the ARISE Project.

[Accidents among postmen using motorbikes for mail deliveries in Tuscany in the period 2007-2009].

PubMed

Chellini, Elisabetta; Cortini, Barbara; Mameli, Marina; Abbarchi, M; Dei, Simona; Rossi, Oriana; Zallocco, A

2014-01-01

Health risks for postmen using motorbikes for mail delivery may be influenced by stability, weight and ease of handling of the vehicle, traffic and slippery or irregular road surface. To describe accidents that occurred among postmen in Tuscany and evaluate how many of these would have been prevented using the UNI EN 13595/2004 safety jacket. Record linkage of data obtained from the employer--the main mail delivery company in Italy--and from the Italian Workers Compensation Authority on accidents that occurred in postmen in Tuscany who used motorbikes for deliveries during the period 2007-2009. Accident rates (with CI 95%) by age, sex, year and province were calculated; the differences were evaluated using chi2 test. 1,342 accidents requiring at least 3 days' sick absence were recorded in postmen in Tuscany in the period 2007-2009, with an increasing trend in young men. The average accident rate was 17.6 per 100 workers, with 42,419 sick absence days. The female rate was higher compared to men (19.4%, CI 95% 18.03-20.79 in women vs 15.5%, CI 95%: 14.15-16.89 in men). 68% of accidents occurred driving a motorbike. The index of severity was 6.79, which was higher than that calculated by INAIL for the whole Tuscan transport and communication work sector (5.31). 309 accidents (11,021 sick absence days) could have been mitigated or avoided using UNI EN 13595/2004 safety jackets (47% spinal, 30% shoulder, 23% elbow, arm and forearm). The frequency of accidents in postmen using motorbikes is extremely high. Several serious accidents could have been prevented using the UNI EN 13595/2004 safety jackets, suggesting the need to make their use obligatory by these workers.

Linking microarray reporters with protein functions

PubMed Central

Gaj, Stan; van Erk, Arie; van Haaften, Rachel IM; Evelo, Chris TA

2007-01-01

Background The analysis of microarray experiments requires accurate and up-to-date functional annotation of the microarray reporters to optimize the interpretation of the biological processes involved. Pathway visualization tools are used to connect gene expression data with existing biological pathways by using specific database identifiers that link reporters with elements in the pathways. Results This paper proposes a novel method that aims to improve microarray reporter annotation by BLASTing the original reporter sequences against a species-specific EMBL subset, that was derived from and crosslinked back to the highly curated UniProt database. The resulting alignments were filtered using high quality alignment criteria and further compared with the outcome of a more traditional approach, where reporter sequences were BLASTed against EnsEMBL followed by locating the corresponding protein (UniProt) entry for the high quality hits. Combining the results of both methods resulted in successful annotation of > 58% of all reporter sequences with UniProt IDs on two commercial array platforms, increasing the amount of Incyte reporters that could be coupled to Gene Ontology terms from 32.7% to 58.3% and to a local GenMAPP pathway from 9.6% to 16.7%. For Agilent, 35.3% of the total reporters are now linked towards GO nodes and 7.1% on local pathways. Conclusion Our methods increased the annotation quality of microarray reporter sequences and allowed us to visualize more reporters using pathway visualization tools. Even in cases where the original reporter annotation showed the correct description the new identifiers often allowed improved pathway and Gene Ontology linking. These methods are freely available at http://www.bigcat.unimaas.nl/public/publications/Gaj_Annotation/. PMID:17897448

Extraction and Production of Omega-3 from UniMAP Puyu (Jade Perch) and Mackarel

NASA Astrophysics Data System (ADS)

Nur Izzati, I.; Zainab, H.; Nornadhiratulhusna, M.; Chee Hann, Y.; Khairunissa Syairah, A. S.; Amira Farzana, S.

2018-03-01

Extraction techniques to extract fish oil from various types of fish are numerous but not widely accepted because of the use of chemicals that may be harmful to health. In this study, fish oil is extracted using a technique of Microwave-Assisted Extraction, which uses only water. The optimum conditions required for the production of fish oil for extraction is carried out by examining three parameters such as microwave power (300-700W), extraction time (10-30 min) and amount of water used (70-190ml). Optimum conditions were determined after using design of experiments (DOE). The optimum condition obtained was 300 W for microwave power, 10 minutes extraction time and 190 milliliter amounts of water used. Fourier transform infrared spectroscopy (FTIR) was used to analyze the functional groups of fish oil. Two types of fish such as Jade Perch or UniMAP Puyu and Indian Mackerel were used. A standard omega-3 oil sample (Blackmores) purchased from pharmacy was also determined to confirm the presence of omega-3 oil in these fishes. Similar compounds were present in Jade Perch and Indian Mackerel as compared to the standard. Therefore, there were presence of omega-3 fish oil in the two types of fish. From this study, omega-3 in UniMAP Puyu fish was higher compared to Indian Mackerel fish. However, based on the FTIR analysis, besides the presence of omega-3, the two fishes also contain other functional groups such as alkanes, alkenes, aldehyde, ketones and many others. The yield of fish oil for the Jade Perch was low compared to Indian Mackerel which was 9% while Indian Mackerel was 10 %.

75 FR 13757 - Combined Notice of Filings #1

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-23

..., Inc.; UniSource Energy Development Company. Description: Tucson Electric Power Co. submits a... DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings 1 March 16....P. Morgan Ventures Energy Corporation, BE Allegheny LLC, BE CA LLC, BE Ironwood LLC,BE KJ LLC, BE...

ETV Program Report: Coatings for Wastewater Collection Systems - Epoxy Tec International, Inc., CPP RC3

EPA Science Inventory

The Epoxytec, Inc. CPP™ epoxy coating used for wastewater collection system rehabilitation was evaluated by EPA’s Environmental Technology Verification Program under laboratory conditions at the Center for Innovative Grouting Material and Technology (CIGMAT) Laboratory at the Uni...

INTEGRATION OF HEAT PUMPS IN PERVAPORATION SYSTEMS FOR IMPROVED ENERGY EFFICIENCY

EPA Science Inventory

The removal of organic compounds from water by pervaporation is highly energy efficient when the separation factor offered by the pervaporation process is high. In cases where the separation factor is relatively small, consequential amounts of water permeate the membrane per uni...

VizieR Online Data Catalog: Sub-millimeter spectra of 2-hydroxyacetonitrile (Margules+, 2017)

NASA Astrophysics Data System (ADS)

Margules, L.; McGuire, B. A.; Senent, M. L.; Motiyenko, R. A.; Remijan, A.; Guillemin, J. C.

2017-02-01

Measured frequencies and residuals from the global fit of the submillimeter-wave data for 2-hydroxyacetonitrile and files used for SPFIT. Detailled explanations on SPFIT could be found at https://www.astro.uni-koeln.de/cdms/pickett (4 data files).

When a hit sounds like a kiss: An electrophysiological exploration of semantic processing in visual narrative.

PubMed

Manfredi, Mirella; Cohn, Neil; Kutas, Marta

2017-06-01

Researchers have long questioned whether information presented through different sensory modalities involves distinct or shared semantic systems. We investigated uni-sensory cross-modal processing by recording event-related brain potentials to words replacing the climactic event in a visual narrative sequence (comics). We compared Onomatopoeic words, which phonetically imitate action sounds (Pow!), with Descriptive words, which describe an action (Punch!), that were (in)congruent within their sequence contexts. Across two experiments, larger N400s appeared to Anomalous Onomatopoeic or Descriptive critical panels than to their congruent counterparts, reflecting a difficulty in semantic access/retrieval. Also, Descriptive words evinced a greater late frontal positivity compared to Onomatopoetic words, suggesting that, though plausible, they may be less predictable/expected in visual narratives. Our results indicate that uni-sensory cross-model integration of word/letter-symbol strings within visual narratives elicit ERP patterns typically observed for written sentence processing, thereby suggesting the engagement of similar domain-independent integration/interpretation mechanisms. Copyright © 2017 Elsevier Inc. All rights reserved.

In-vivo x-ray micro-imaging and micro-CT with the Medipix2 semiconductor detector at UniAndes

NASA Astrophysics Data System (ADS)

Caicedo, I.; Avila, C.; Gomez, B.; Bula, C.; Roa, C.; Sanabria, J.

2012-02-01

This poster contains the procedure to obtain micro-CTs and to image moving samples using the Medipix2 detector, with its corresponding results. The high granularity of the detector makes it suitable for micro-CT. We used commercial software (Octopus) to do the 3D reconstruction of the samples in the first place, and we worked on modifying free reconstruction software afterwards. Medipix has a very fast response ( ~ hundreds of nanoseconds) and high sensibility. These features allow obtaining nearly in-vivo high resolution (55m * 55m) images. We used an exposure time of 0.1 s for each frame, and the resulting images were animated. The High Energy Physics Group at UniAndes is a member of the Medipix3 collaboration. Its research activities are focused on developing set-ups for biomedical applications and particle tracking using the Medipix2 and Timepix detectors, and assessing the feasibility of the Medipix3 detector for future applications.

A six-month prospective evaluation of personality traits, psychiatric symptoms and quality of life in ayahuasca-naïve subjects.

PubMed

Barbosa, Paulo Cesar Ribeiro; Cazorla, Irene Maurício; Giglio, Joel Sales; Strassman, Rick

2009-09-01

The authors assessed 23 subjects immediately before and six months (27.5 weeks) after their first ayahuasca experience in an urban Brazilian religious setting, either Santo Daime (N = 15) or União do Vegetal (N = 8). Measures included scores on instruments assessing psychiatric symptoms, personality variables and quality of life. Independent variables were the frequency of ayahuasca use throughout the period and the length of ayahuasca wash-out after six months. Santo Daime subjects had a significant reduction of minor psychiatric symptoms, improvement of mental health, and a change in attitude towards more confidence and optimism. The União do Vegetal group had a significant decrease in physical pain, and attitude change towards more independence. Independence was positively correlated with the frequency of ayahuasca use and negatively correlated with the wash-out period. We discuss possible mechanisms by which these changes may occur and suggest areas for future research.

Unmarked: An R package for fitting hierarchical models of wildlife occurrence and abundance

USGS Publications Warehouse

Fiske, I.J.; Chandler, R.B.

2011-01-01

Ecological research uses data collection techniques that are prone to substantial and unique types of measurement error to address scientic questions about species abundance and distribution. These data collection schemes include a number of survey methods in which unmarked individuals are counted, or determined to be present, at spatially- referenced sites. Examples include site occupancy sampling, repeated counts, distance sampling, removal sampling, and double observer sampling. To appropriately analyze these data, hierarchical models have been developed to separately model explanatory variables of both a latent abundance or occurrence process and a conditional detection process. Because these models have a straightforward interpretation paralleling mecha- nisms under which the data arose, they have recently gained immense popularity. The common hierarchical structure of these models is well-suited for a unied modeling in- terface. The R package unmarked provides such a unied modeling framework, including tools for data exploration, model tting, model criticism, post-hoc analysis, and model comparison.

Publisher Correction: A Co3O4-CDots-C3N4 three component electrocatalyst design concept for efficient and tunable CO2 reduction to syngas.

PubMed

Guo, Sijie; Zhao, Siqi; Wu, Xiuqin; Li, Hao; Zhou, Yunjie; Zhu, Cheng; Yang, Nianjun; Jiang, Xin; Gao, Jin; Bai, Liang; Liu, Yang; Lifshitz, Yeshayahu; Lee, Shuit-Tong; Kang, Zhenhui

2018-02-08

The original HTML version of this Article omitted to list Yeshayahu Lifshitz as a corresponding author and incorrectly listed Shuit-Tong Lee as a corresponding author.Correspondingly, the original PDF version of this Article incorrectly stated that "Correspondence and requests for materials should be addressed to X.J. (email: xin.jiang@uni-siegen.de), or to Y.L. (email: yangl@suda.edu.cn), or to S.-T.L. (email: shayli@technion.ac.il), or to Z.K. (email: zhkang@suda.edu.cn)", instead of the correct "Correspondence and requests for materials should be addressed to X.J. (email: xin.jiang@uni-siegen.de), or to Y. Liu (email: yangl@suda.edu.cn), or to Y. Lifshitz (email: shayli@technion.ac.il), or to Z.K. (email: zhkang@suda.edu.cn)".This has now been corrected in the PDF and HTML versions of the Article.

Spring-back of Thick Uni-Directional Carbon Fibre Reinforced Composite Laminate for Aircraft Structure Application

NASA Astrophysics Data System (ADS)

Zakaria, M.; Aminanda, Y.; Rashidi, S. A.; Mat Sah, M. A.

2018-04-01

The springback phenomena of CFRP after curing process through autoclave manufacturing method results on the out of tolerance for its utilisation in aerospace industry. This paper relates to the measurements of springback for Uni-directional flat laminate as a first steps to the springback study for the real aircraft composite laminate structures. A flat laminate with dimension of 300 mm x 300 mm, 400 mm x 400 mm and 500mm x 500 mm with different number of ply; 20, 24 and 28 are manufactured. The choice of dimension and number of lay-up corresponds to the dimension and lay-up of rib structure. After process, the springbacks are measured using 3D scanner (optical-based three-dimensional) with an accuracy of 42 micrometers to obtain an accurate measurement. The analysis of the effect of dimension and number of ply to the magnitude of springback are presented within the range of specimen studied in this work.

When a hit sounds like a kiss: an electrophysiological exploration of semantic processing in visual narrative

PubMed Central

Manfredi, Mirella; Cohn, Neil; Kutas, Marta

2017-01-01

Researchers have long questioned whether information presented through different sensory modalities involves distinct or shared semantic systems. We investigated uni-sensory cross-modal processing by recording event-related brain potentials to words replacing the climactic event in a visual narrative sequence (comics). We compared Onomatopoeic words, which phonetically imitate action sounds (Pow!), with Descriptive words, which describe an action (Punch!), that were (in)congruent within their sequence contexts. Across two experiments, larger N400s appeared to Anomalous Onomatopoeic or Descriptive critical panels than to their congruent counterparts, reflecting a difficulty in semantic access/retrieval. Also, Descriptive words evinced a greater late frontal positivity compared to Onomatopoetic words, suggesting that, though plausible, they may be less predictable/expected in visual narratives. Our results indicate that uni-sensory cross-model integration of word/letter-symbol strings within visual narratives elicit ERP patterns typically observed for written sentence processing, thereby suggesting the engagement of similar domain-independent integration/interpretation mechanisms. PMID:28242517

A2TiF 5· nH 2O ( A=K, Rb, or Cs; n=0 or 1): Synthesis, structure, characterization, and calculations of three new uni-dimensional titanium fluorides

NASA Astrophysics Data System (ADS)

Jo, Vinna; Woo Lee, Dong; Koo, Hyun-Joo; Ok, Kang Min

2011-04-01

Three new uni-dimensional alkali metal titanium fluoride materials, A2TiF 5· nH 2O ( A=K, Rb, or Cs; n=0 or 1) have been synthesized by hydrothermal reactions. The structures of A2TiF 5· nH 2O have been determined by single-crystal X-ray diffraction. The Ti 4+ cations have been reduced to Ti 3+ during the synthesis reactions. All three A2TiF 5· nH 2O materials contain novel 1-D chain structures that are composed of the slightly distorted Ti 3+F 6 corner-sharing octahedra attributable to the Jahn-Teller distortion. The coordination environment of the alkali metal cations plays an important role to determine the degree of turning in the chain structures. Complete structural analyses, Infrared and UV-vis diffuse reflectance spectra, and thermal analyses are presented, as are electronic structure calculations.

ChromA: signal-based retention time alignment for chromatography–mass spectrometry data

PubMed Central

Hoffmann, Nils; Stoye, Jens

2009-01-01

Summary: We describe ChromA, a web-based alignment tool for chromatography–mass spectrometry data from the metabolomics and proteomics domains. Users can supply their data in open and standardized file formats for retention time alignment using dynamic time warping with different configurable local distance and similarity functions. Additionally, user-defined anchors can be used to constrain and speedup the alignment. A neighborhood around each anchor can be added to increase the flexibility of the constrained alignment. ChromA offers different visualizations of the alignment for easier qualitative interpretation and comparison of the data. For the multiple alignment of more than two data files, the center-star approximation is applied to select a reference among input files to align to. Availability: ChromA is available at http://bibiserv.techfak.uni-bielefeld.de/chroma. Executables and source code under the L-GPL v3 license are provided for download at the same location. Contact: stoye@techfak.uni-bielefeld.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:19505941

KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats.

PubMed

Wrzodek, Clemens; Dräger, Andreas; Zell, Andreas

2011-08-15

The KEGG PATHWAY database provides a widely used service for metabolic and nonmetabolic pathways. It contains manually drawn pathway maps with information about the genes, reactions and relations contained therein. To store these pathways, KEGG uses KGML, a proprietary XML-format. Parsers and translators are needed to process the pathway maps for usage in other applications and algorithms. We have developed KEGGtranslator, an easy-to-use stand-alone application that can visualize and convert KGML formatted XML-files into multiple output formats. Unlike other translators, KEGGtranslator supports a plethora of output formats, is able to augment the information in translated documents (e.g. MIRIAM annotations) beyond the scope of the KGML document, and amends missing components to fragmentary reactions within the pathway to allow simulations on those. KEGGtranslator is freely available as a Java(™) Web Start application and for download at http://www.cogsys.cs.uni-tuebingen.de/software/KEGGtranslator/. KGML files can be downloaded from within the application. clemens.wrzodek@uni-tuebingen.de Supplementary data are available at Bioinformatics online.

A Unified Equation of State on a Microscopic Basis : Implications for Neutron Stars Structure and Cooling

NASA Astrophysics Data System (ADS)

Burgio, G. F.

2018-03-01

We discuss the structure of Neutron Stars by modelling the homogeneous nuclear matter of the core by a suitable microscopic Equation of State, based on the Brueckner-Hartree-Fock many-body theory, and the crust, including the pasta phase, by the BCPM energy density functional which is based on the same Equation of State. This allows for a uni ed description of the Neutron Star matter over a wide density range. A comparison with other uni ed approaches is discussed. With the same Equation of State, which features strong direct Urca processes and using consistent nuclear pairing gaps as well as effective masses, we model neutron star cooling, in particular the current rapid cooldown of the neutron star Cas A. We nd that several scenarios are possible to explain the features of Cas A, but only large and extended proton 1 S 0 gaps and small neutron 3 PF 2 gaps can accommodate also the major part of the complete current cooling data.

Memory-efficient RNA energy landscape exploration

PubMed Central

Mann, Martin; Kucharík, Marcel; Flamm, Christoph; Wolfinger, Michael T.

2014-01-01

Motivation: Energy landscapes provide a valuable means for studying the folding dynamics of short RNA molecules in detail by modeling all possible structures and their transitions. Higher abstraction levels based on a macro-state decomposition of the landscape enable the study of larger systems; however, they are still restricted by huge memory requirements of exact approaches. Results: We present a highly parallelizable local enumeration scheme that enables the computation of exact macro-state transition models with highly reduced memory requirements. The approach is evaluated on RNA secondary structure landscapes using a gradient basin definition for macro-states. Furthermore, we demonstrate the need for exact transition models by comparing two barrier-based approaches, and perform a detailed investigation of gradient basins in RNA energy landscapes. Availability and implementation: Source code is part of the C++ Energy Landscape Library available at http://www.bioinf.uni-freiburg.de/Software/. Contact: mmann@informatik.uni-freiburg.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24833804

Transitions of interaction outcomes in a uni-directional consumer-resource system

USGS Publications Warehouse

Wang, Y.; DeAngelis, D.L.

2011-01-01

A uni-directional consumer-resource system of two species is analyzed. Our aim is to understand the mechanisms that determine how the interaction outcomes depend on the context of the interaction; that is, on the model parameters. The dynamic behavior of the model is described and, in particular, it is demonstrated that no periodic orbits exist. Then the parameter (factor) space is shown to be divided into four regions, which correspond to the four forms of interaction outcomes; i.e. mutualism, commensalism, parasitism and amensalism. It is shown that the interaction outcomes of the system transition smoothly among these four forms when the parameters of the system are varied continuously. Varying each parameter individually or varying pairs of parameters can also lead to smooth transitions between the interaction outcomes. The analysis leads to both conditions for which each species achieves its maximal density, and situations in which periodic oscillations of the interaction outcomes emerge. ?? 2011 Elsevier Ltd.

Topology optimized design of functionally graded piezoelectric ultrasonic transducers

NASA Astrophysics Data System (ADS)

Rubio, Wilfredo Montealegre; Buiochi, Flávio; Adamowski, Julio Cezar; Silva, Emílio C. N.

2010-01-01

This work presents a new approach to systematically design piezoelectric ultrasonic transducers based on Topology Optimization Method (TOM) and Functionally Graded Material (FGM) concepts. The main goal is to find the optimal material distribution of Functionally Graded Piezoelectric Ultrasonic Transducers, to achieve the following requirements: (i) the transducer must be designed to have a multi-modal or uni-modal frequency response, which defines the kind of generated acoustic wave, either short pulse or continuous wave, respectively; (ii) the transducer is required to oscillate in a thickness extensional mode or piston-like mode, aiming at acoustic wave generation applications. Two kinds of piezoelectric materials are mixed for producing the FGM transducer. Material type 1 represents a PZT-5A piezoelectric ceramic and material type 2 represents a PZT-5H piezoelectric ceramic. To illustrate the proposed method, two Functionally Graded Piezoelectric Ultrasonic Transducers are designed. The TOM has shown to be a useful tool for designing Functionally Graded Piezoelectric Ultrasonic Transducers with uni-modal or multi-modal dynamic behavior.

Computational clustering for viral reference proteomes

PubMed Central

Chen, Chuming; Huang, Hongzhan; Mazumder, Raja; Natale, Darren A.; McGarvey, Peter B.; Zhang, Jian; Polson, Shawn W.; Wang, Yuqi; Wu, Cathy H.

2016-01-01

Motivation: The enormous number of redundant sequenced genomes has hindered efforts to analyze and functionally annotate proteins. As the taxonomy of viruses is not uniformly defined, viral proteomes pose special challenges in this regard. Grouping viruses based on the similarity of their proteins at proteome scale can normalize against potential taxonomic nomenclature anomalies. Results: We present Viral Reference Proteomes (Viral RPs), which are computed from complete virus proteomes within UniProtKB. Viral RPs based on 95, 75, 55, 35 and 15% co-membership in proteome similarity based clusters are provided. Comparison of our computational Viral RPs with UniProt’s curator-selected Reference Proteomes indicates that the two sets are consistent and complementary. Furthermore, each Viral RP represents a cluster of virus proteomes that was consistent with virus or host taxonomy. We provide BLASTP search and FTP download of Viral RP protein sequences, and a browser to facilitate the visualization of Viral RPs. Availability and implementation: http://proteininformationresource.org/rps/viruses/ Contact: chenc@udel.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27153712

Mass-transfer limitations for immobilized enzyme-catalyzed kinetic resolution of racemate in a fixed-bed reactor.

PubMed

Xiu, G H; Jiang, L; Li, P

2001-07-05

A mathematical model has been developed for immobilized enzyme-catalyzed kinetic resolution of racemate in a fixed-bed reactor in which the enzyme-catalyzed reaction (the irreversible uni-uni competitive Michaelis-Menten kinetics is chosen as an example) was coupled with intraparticle diffusion, external mass transfer, and axial dispersion. The effects of mass-transfer limitations, competitive inhibition of substrates, deactivation on the enzyme effective enantioselectivity, and the optical purity and yield of the desired product are examined quantitatively over a wide range of parameters using the orthogonal collocation method. For a first-order reaction, an analytical solution is derived from the mathematical model for slab-, cylindrical-, and spherical-enzyme supports. Based on the analytical solution for the steady-state resolution process, a new concise formulation is presented to predict quantitatively the mass-transfer limitations on enzyme effective enantioselectivity and optical purity and yield of the desired product for a continuous steady-state kinetic resolution process in a fixed-bed reactor. Copyright 2001 John Wiley & Sons, Inc.

Utility of light scatter in the morphological analysis of sperm

EPA Science Inventory

We were able to differentiate the morphologically diverse sperm nuclei of four animal species by using an Ortho flow cytometer to detect the forward light scatter from a red (helium-neon) laser. Cytograms depicting the axial light loss and forward red scatter signals revealed uni...

Maximizing industry benefit through cooperation between federal, state and private-sector floricultural research efforts

USDA-ARS?s Scientific Manuscript database

he USDA-ARS Greenhouse Production Research Group was established to provide a federally funded research emphasis on greenhouse crop production. It has focused on broad production issues (nutrition, water management, and energy conservation) by coordinating research between in-house researchers, Uni...

Measurement: The Boon and Bane of Investigating Religion.

ERIC Educational Resources Information Center

Gorsuch, Richard L.

1984-01-01

A major problem of research into religion is whether religion is uni- or multi-dimensional; a model maintaining the advantages of both approaches is suggested with general religiousness as a broad construct (higher order factor) that is subdivided into a set of more specific factors. (CMG)

Modelling Drug Administration Regimes for Asthma: A Romanian Experience

ERIC Educational Resources Information Center

Andras, Szilard; Szilagyi, Judit

2010-01-01

In this article, we present a modelling activity, which was a part of the project DQME II (Developing Quality in Mathematics Education, for more details see http://www.dqime.uni-dortmund.de) and some general observations regarding the maladjustments and rational errors arising in such type of activities.

Body Size Changes of Royal Australian Air Force Aircrew: 1971 - 2005

DTIC Science & Technology

2009-08-01

International Airport (2004). Adam completed his Physiotherapy Degree in 2008 at the University of South Australia. Adam currently works as a physiotherapist...Australia (UniSA) School of Health Sciences student pool and personal contacts (e.g. friends, family and work colleagues). All subjects were fully informed

Channels: Runtime System Infrastructure for Security-typed Languages

DTIC Science & Technology

2008-10-01

Milan , Italy, September 2005. Springer-Verlag. [2] D. E. Bell and L. J. LaPadula. Secure computer system: Uni- fied exposition and Multics...Proceedings of the USENIX Annual Technical Conference, Santa Clara, CA, USA, June 2007. To appear. [9] S. Kamara, S. Fahmy, E. Schultz , F. Kerschbaum, and

Ischemia-induced endothelial cell swelling and mitochondrial dysfunction are attenuated by dietary polyphenols in vitro

USDA-ARS?s Scientific Manuscript database

Polyphenols possess anti-oxidant and anti-inflammatory properties. Oxidative stress (OS) and inflammation have been implicated in the pathogenesis of cytotoxic brain edema in cerebral ischemia. In addition, OS and pro-inflammatory cytokines also damage the endothelial cells and the neurovascular uni...

ENVIRONMENTAL RESEARCH IN RESPONSE TO 9/11 AND HOMELAND SECURITY

EPA Science Inventory

The terrorist attacks on September 11, 2001 resulted in a disaster unlike any other on U.S. soil. The collapse of the World Trade Center (WTC) towers and the underground fires that burned for months required the efforts of numerous Federal, State and local agencies as well as uni...

USE OF WILDLIFE MORTALITY DATA TO QUALIFY RISKS TO POPULATIONS ACROSS SPACE AND TIME

EPA Science Inventory

Common loon (Gavia immer) populations have declined from historic levels in New England and despite recent range-wide increases; mortality has increased in some areas. To identify and quantify the causes of disease and death in New England loons, the Wildlife Clinic at Tufts Uni...

A Study of the High Strain-Rate Behaviour of GRP Composites

DTIC Science & Technology

1998-01-01

rate. In contrast, results reported by Armenakas and Sciammarella [9] and Daniel and Liber [24] on uni-directional (UD) glass/epoxy material showed...pp. 85-98. [9] A.E. Armenakas and C.A. Sciammarella , ’Response of glass-fibre-reinforced epoxy specimens to high rates of tensile loading

VizieR Online Data Catalog: 15NH2 amidogen radical rotational spectrum (M

NASA Astrophysics Data System (ADS)

Margules, L.; Martin-Drumel, M. A.; Pirali, O.; Bailleux, S.; Wlodarczak, G.; Roy, P.; Roueff, E.; Gerin, M.

2016-04-01

Measured frequencies and residuals from the global fit of the Infrared, and submillimeter-wave data for 15NH2 and files used for SPFIT. Detailled explanations on SPFIT could be found at https://www.astro.uni-koeln.de/cdms/pickett (4 data files).

Climate change : observations on the potential role of carbon offsets in climate change legislation

DOT National Transportation Integrated Search

2009-03-05

Currently, carbon offsets are generated, bought, and sold in two types of markets. In markets such as the United States, which does not have binding limits on emissions, the market is referred to as a voluntary market. Conversely, in the European Uni...

RADON REMOVAL USING POINT-OF-ENTRY WATER TREATMENT TECHNIQUES

EPA Science Inventory

The purpose of the EPA Cooperative Agreement was to evaluate the performance of POE granular activated carbon (GAC), and diffused bubble and bubble place aeration systems treating a ground water supply containing radon (35,620 ±6,717 pCi/L). The pattern of loading to the uni...

A Methodology for Evaluating Advanced Operator Workstation Accommodation

DTIC Science & Technology

2006-11-01

the actual area of right and left hands used in uni-manual tasks was not symmetrical around the body median ( Gabbard and Rabb, 2000; Stins, 11...Applied Physiology, 90, 480-488. Gabbard , C. & Rabb, C. (2000). What determines choice of limb for unimanual reaching movements? The journal of General

Moving Hands, Moving Entities

ERIC Educational Resources Information Center

Setti, Annalisa; Borghi, Anna M.; Tessari, Alessia

2009-01-01

In this study we investigated with a priming paradigm whether uni and bimanual actions presented as primes differently affected language processing. Animals' (self-moving entities) and plants' (not self-moving entities) names were used as targets. As prime we used grasping hands, presented both as static images and videos. The results showed an…

Is NAA reduction in normal contralateral cerebral tissue in stroke patients dependent on underlying risk factors?

PubMed

Walker, P M; Ben Salem, D; Giroud, M; Brunotte, F

2006-05-01

This retrospective study investigated the dependence of N-acetyl aspartate (NAA) ratios on risk factors for cerebral vasculopathy such as sex, age, hypertension, diabetes mellitus, carotid stenosis, and dyslipidaemia, which may have affected brain vessels and induced metabolic brain abnormalities prior to stroke. We hypothesise that in stroke patients metabolic alterations in the apparently normal contralateral brain are dependent on the presence or not of such risk factors. Fifty nine patients (31 male, 28 female: 58.8+/-16.1 years old) with cortical middle cerebral artery (MCA) territory infarction were included. Long echo time chemical shift imaging spectroscopy was carried out on a Siemens 1.5 T Magnetom Vision scanner using a multi-voxel PRESS technique. Metabolite ratios (NAA/choline, NAA/creatine, lactate/choline, etc) were studied using uni- and multivariate analyses with respect to common risk factors. The influence of age, stroke lesion size, and time since stroke was studied using a linear regression approach. Age, sex, and hypertension all appeared to individually influence metabolite ratios, although only hypertension was significant after multivariate analysis. In both basal ganglia and periventricular white matter regions in apparently normal contralateral brain, the NAA/choline ratio was significantly lower in hypertensive (1.37+/-0.16 and 1.50+/-0.19, respectively) than in normotensive patients (1.72+/-0.19 and 1.85+/-0.15, respectively). Regarding MCA infarction, contralateral tissue remote from the lesion behaves abnormally in the presence of hypertension, the NAA ratios in hypertensive patients being significantly lower. These data suggest that hypertension may compromise the use of contralateral tissue data as a reference for comparison with ischaemic tissue.

Fast integration-based prediction bands for ordinary differential equation models.

PubMed

Hass, Helge; Kreutz, Clemens; Timmer, Jens; Kaschek, Daniel

2016-04-15

To gain a deeper understanding of biological processes and their relevance in disease, mathematical models are built upon experimental data. Uncertainty in the data leads to uncertainties of the model's parameters and in turn to uncertainties of predictions. Mechanistic dynamic models of biochemical networks are frequently based on nonlinear differential equation systems and feature a large number of parameters, sparse observations of the model components and lack of information in the available data. Due to the curse of dimensionality, classical and sampling approaches propagating parameter uncertainties to predictions are hardly feasible and insufficient. However, for experimental design and to discriminate between competing models, prediction and confidence bands are essential. To circumvent the hurdles of the former methods, an approach to calculate a profile likelihood on arbitrary observations for a specific time point has been introduced, which provides accurate confidence and prediction intervals for nonlinear models and is computationally feasible for high-dimensional models. In this article, reliable and smooth point-wise prediction and confidence bands to assess the model's uncertainty on the whole time-course are achieved via explicit integration with elaborate correction mechanisms. The corresponding system of ordinary differential equations is derived and tested on three established models for cellular signalling. An efficiency analysis is performed to illustrate the computational benefit compared with repeated profile likelihood calculations at multiple time points. The integration framework and the examples used in this article are provided with the software package Data2Dynamics, which is based on MATLAB and freely available at http://www.data2dynamics.org helge.hass@fdm.uni-freiburg.de Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Wikidata as a semantic framework for the Gene Wiki initiative.

PubMed

Burgstaller-Muehlbacher, Sebastian; Waagmeester, Andra; Mitraka, Elvira; Turner, Julia; Putman, Tim; Leong, Justin; Naik, Chinmay; Pavlidis, Paul; Schriml, Lynn; Good, Benjamin M; Su, Andrew I

2016-01-01

Open biological data are distributed over many resources making them challenging to integrate, to update and to disseminate quickly. Wikidata is a growing, open community database which can serve this purpose and also provides tight integration with Wikipedia. In order to improve the state of biological data, facilitate data management and dissemination, we imported all human and mouse genes, and all human and mouse proteins into Wikidata. In total, 59,721 human genes and 73,355 mouse genes have been imported from NCBI and 27,306 human proteins and 16,728 mouse proteins have been imported from the Swissprot subset of UniProt. As Wikidata is open and can be edited by anybody, our corpus of imported data serves as the starting point for integration of further data by scientists, the Wikidata community and citizen scientists alike. The first use case for these data is to populate Wikipedia Gene Wiki infoboxes directly from Wikidata with the data integrated above. This enables immediate updates of the Gene Wiki infoboxes as soon as the data in Wikidata are modified. Although Gene Wiki pages are currently only on the English language version of Wikipedia, the multilingual nature of Wikidata allows for usage of the data we imported in all 280 different language Wikipedias. Apart from the Gene Wiki infobox use case, a SPARQL endpoint and exporting functionality to several standard formats (e.g. JSON, XML) enable use of the data by scientists. In summary, we created a fully open and extensible data resource for human and mouse molecular biology and biochemistry data. This resource enriches all the Wikipedias with structured information and serves as a new linking hub for the biological semantic web. Database URL: https://www.wikidata.org/. © The Author(s) 2016. Published by Oxford University Press.

Fast and accurate phylogeny reconstruction using filtered spaced-word matches.

PubMed

Leimeister, Chris-André; Sohrabi-Jahromi, Salma; Morgenstern, Burkhard

2017-04-01

Word-based or 'alignment-free' algorithms are increasingly used for phylogeny reconstruction and genome comparison, since they are much faster than traditional approaches that are based on full sequence alignments. Existing alignment-free programs, however, are less accurate than alignment-based methods. We propose Filtered Spaced Word Matches (FSWM) , a fast alignment-free approach to estimate phylogenetic distances between large genomic sequences. For a pre-defined binary pattern of match and don't-care positions, FSWM rapidly identifies spaced word-matches between input sequences, i.e. gap-free local alignments with matching nucleotides at the match positions and with mismatches allowed at the don't-care positions. We then estimate the number of nucleotide substitutions per site by considering the nucleotides aligned at the don't-care positions of the identified spaced-word matches. To reduce the noise from spurious random matches, we use a filtering procedure where we discard all spaced-word matches for which the overall similarity between the aligned segments is below a threshold. We show that our approach can accurately estimate substitution frequencies even for distantly related sequences that cannot be analyzed with existing alignment-free methods; phylogenetic trees constructed with FSWM distances are of high quality. A program run on a pair of eukaryotic genomes of a few hundred Mb each takes a few minutes. The program source code for FSWM including a documentation, as well as the software that we used to generate artificial genome sequences are freely available at http://fswm.gobics.de/. chris.leimeister@stud.uni-goettingen.de. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

Partitioned learning of deep Boltzmann machines for SNP data.

PubMed

Hess, Moritz; Lenz, Stefan; Blätte, Tamara J; Bullinger, Lars; Binder, Harald

2017-10-15

Learning the joint distributions of measurements, and in particular identification of an appropriate low-dimensional manifold, has been found to be a powerful ingredient of deep leaning approaches. Yet, such approaches have hardly been applied to single nucleotide polymorphism (SNP) data, probably due to the high number of features typically exceeding the number of studied individuals. After a brief overview of how deep Boltzmann machines (DBMs), a deep learning approach, can be adapted to SNP data in principle, we specifically present a way to alleviate the dimensionality problem by partitioned learning. We propose a sparse regression approach to coarsely screen the joint distribution of SNPs, followed by training several DBMs on SNP partitions that were identified by the screening. Aggregate features representing SNP patterns and the corresponding SNPs are extracted from the DBMs by a combination of statistical tests and sparse regression. In simulated case-control data, we show how this can uncover complex SNP patterns and augment results from univariate approaches, while maintaining type 1 error control. Time-to-event endpoints are considered in an application with acute myeloid leukemia patients, where SNP patterns are modeled after a pre-screening based on gene expression data. The proposed approach identified three SNPs that seem to jointly influence survival in a validation dataset. This indicates the added value of jointly investigating SNPs compared to standard univariate analyses and makes partitioned learning of DBMs an interesting complementary approach when analyzing SNP data. A Julia package is provided at 'http://github.com/binderh/BoltzmannMachines.jl'. binderh@imbi.uni-freiburg.de. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

dbPTM 2016: 10-year anniversary of a resource for post-translational modification of proteins.

PubMed

Huang, Kai-Yao; Su, Min-Gang; Kao, Hui-Ju; Hsieh, Yun-Chung; Jhong, Jhih-Hua; Cheng, Kuang-Hao; Huang, Hsien-Da; Lee, Tzong-Yi

2016-01-04

Owing to the importance of the post-translational modifications (PTMs) of proteins in regulating biological processes, the dbPTM (http://dbPTM.mbc.nctu.edu.tw/) was developed as a comprehensive database of experimentally verified PTMs from several databases with annotations of potential PTMs for all UniProtKB protein entries. For this 10th anniversary of dbPTM, the updated resource provides not only a comprehensive dataset of experimentally verified PTMs, supported by the literature, but also an integrative interface for accessing all available databases and tools that are associated with PTM analysis. As well as collecting experimental PTM data from 14 public databases, this update manually curates over 12 000 modified peptides, including the emerging S-nitrosylation, S-glutathionylation and succinylation, from approximately 500 research articles, which were retrieved by text mining. As the number of available PTM prediction methods increases, this work compiles a non-homologous benchmark dataset to evaluate the predictive power of online PTM prediction tools. An increasing interest in the structural investigation of PTM substrate sites motivated the mapping of all experimental PTM peptides to protein entries of Protein Data Bank (PDB) based on database identifier and sequence identity, which enables users to examine spatially neighboring amino acids, solvent-accessible surface area and side-chain orientations for PTM substrate sites on tertiary structures. Since drug binding in PDB is annotated, this update identified over 1100 PTM sites that are associated with drug binding. The update also integrates metabolic pathways and protein-protein interactions to support the PTM network analysis for a group of proteins. Finally, the web interface is redesigned and enhanced to facilitate access to this resource. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Gender and Migration Background in Intergenerational Educational Mobility

ERIC Educational Resources Information Center

Schneebaum, Alyssa; Rumplmaier, Bernhard; Altzinger, Wilfried

2016-01-01

We employ 2011 European Union Statistics on Income and Living Conditions survey data for Austria to perform uni- and multivariate econometric analyses to study the role of gender and migration background (MB) in intergenerational educational mobility. We find that there is more persistence in the educational attainment of girls relative to their…

75 FR 51992 - Combined Notice of Filings #1

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-24

...: ER98-1150-011; ER07-1232-003; ER07-964-002. Applicants: Tucson Electric Company; UniSource Energy... DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings 1 August 16... Ventures Energy Corporation, BE Allegheny LLC, BE CA LLC, BE Ironwood LLC, BE KJ LLC, BE Alabama LLC, BE...

West Europe Report, Science & Technology, No. 151

DTIC Science & Technology

1983-08-02

francs) Valeur ( 7 ) cumulee (en millions de francs) Effectifs construisant les robots Japon ( 9 ) 11 000 43 000 4 750 70 000 780 2 600 3...application robot r1 (16) (assemblage) autres applications (17) (18U , , n L-ÜJ Japon (191)^3 Etats-Unis )E23 Allemagne federäle Autres MM

ASBESTOS-INDUCED ACTIVATION OF SIGNALING PATHWAYS IN HUMAN BRONCHIAL EPITHELIAL CELLS

EPA Science Inventory

Title: Asbestos-Induced Activation of Signaling Pathways in Human
Bronchial Epithelial Cells

X. Wang, MD 1, J. M. Samet, PhD 2 and A. J. Ghio, MD 2. 1 Center for
Environmental Medicine, Asthma and Lung Biology, University of North
Carolina, Chapel Hill, NC, Uni...

Use of carbon fiber reinforced polymer (CFRP) with CFRP anchors for shear-strengthening and design recommendations/quality control procedures for CFRP anchors.

DOT National Transportation Integrated Search

2017-03-01

The objective of the study was to demonstrate the feasibility of using bi-directional layouts of CFRP for shear : strengthening of bridge girders. In a previous project (0-6306), it was demonstrated that uni-directional CFRP : strips and CFRP anchors...

78 FR 76607 - Combined Notice of Filings #2

Federal Register 2010, 2011, 2012, 2013, 2014

2013-12-18

... DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings 2 Take notice that the Commission received the following electric rate filings: Docket Numbers: ER10-2564-002; ER10-2600-002; ER10-2289-002. Applicants: Tucson Electric Power Company, UNS Electric, Inc., UniSource Energy Development Company. Description: Second...

Teaching in Hanoi

ERIC Educational Resources Information Center

Larsen, Sarah

2006-01-01

The author of this article shares her teaching experience in the United Nations International School (UNIS) of Hanoi, a prestigious school offering an International Baccalaureate program from Kindergarten to Grade 12. It is one of only two UN schools in the world, the other being in New York City. On the first day of school, her 18 students filed…

Leading Change: Applying Change Management Approaches to Engage Students in Blended Learning

ERIC Educational Resources Information Center

Quinn, Diana; Amer, Yousef; Lonie, Anne; Blackmore, Kim; Thompson, Lauren; Pettigrove, Malcolm

2012-01-01

The Australian National University (ANU) and the University of South Australia (UniSA) have embarked on Federally-funded project to collaborate in the design, development and delivery of a range of undergraduate and postgraduate courses in engineering. The collaboration investigates new ways to bring together the strengths and discipline expertise…

Misc Tandem Pix

Science.gov Websites

looking east.jpg 183 KB UNIS Ion Source 111 KB MP-7 Low Energy.jpg 138 KB MP-7 Object West.jpg 117 KB MP-7 Object Middle.jpg 120 KB MP-7 Object East.jpg 142 KB MP-7 Image.jpg 151 KB SEU area in TR-4 looking

DesUni: University Entrepreneurship Education through Design Thinking

ERIC Educational Resources Information Center

Nielsen, Suna Løwe; Stovang, Pia

2015-01-01

Purpose: In recent years there has been growing focus on the innovative and profit generating value of design thinking in a businesses. This attention is also reflected in business education. The basic thesis is that design thinking is particular relevant to entrepreneurship education. The purpose of this paper is to propose a teaching model,…

Blended Teaching and Learning in the School of Science and Technology of UniSIM

ERIC Educational Resources Information Center

Toon, Andrew John; Samir, Attallah; Kheng, Jennifer Huang Mui; Chew, Lim Kin; Vythilingam, Moorthy; Kiat, Stephen Low Wee

2009-01-01

Purpose: The purpose of this paper is to investigate the blended learning preferences under which adult students study mathematics, electronics and industry certificate examinations like project management and e-SAP (systems, applications and products). Design/methodology/approach: The study is based on four case studies in mathematics,…

Field Responsive, Center Specific: A Model for Collaborative Partnerships.

ERIC Educational Resources Information Center

Hawkes, Richard R.; Stahlhut, Richard G.

A description is given of the Regional Partnership Program, a field-responsive, center-specific model established at the University of Northern Iowa (UNI) designed to oversee clinical field experiences for student teachers. This cooperative partnership calls for a resident tenure track professor to be placed in a geographic area away from the main…

Champion or Chump: Using a Book-Length Case Study to Evaluate a Mythical Principal

ERIC Educational Resources Information Center

Pace, Nicholas J.; Gilson, Timothy W.

2013-01-01

This study examined how 130 participants enrolled in the University of Northern Iowa (UNI) principalship program completed a standards-based evaluation after reading a book-length case study of a mythical principal. Application of the Iowa Standards for School Leaders (ISSL), which mirror the Interstate School Leadership Licensure Consortium…

Global gene expression in channel catfish after vaccination with an attenuated Edwardsiella ictaluri

USDA-ARS?s Scientific Manuscript database

To understand the global gene expression in channel catfish after immersion vaccination with an attenuated Edwardsiella ictaluri (AquaVac ESCTM), microarray analysis of 65,182 UniGene transcripts were performed. With a filter of false-discovery rate less than 0.05 and fold change greater than 2, a t...

76 FR 80972 - Biweekly Notice; Applications and Amendments to Facility Operating Licenses Involving No...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-27

...), a subsidiary of UniStar Nuclear Energy, LLC. Basis for proposed no significant hazards consideration... Frequency Control Program in accordance with guidance in Nuclear Energy Institute (NEI) 04-10, ``Risk... with 10 CFR 51.22. Therefore, pursuant to 10 CFR 51.22(b), no environmental impact statement or...

Perceptual Salience and Children's Multidimensional Problem Solving

ERIC Educational Resources Information Center

Odom, Richard D.; Corbin, David W.

1973-01-01

Uni- and multidimensional processing of 6- to 9-year olds was studied using recall tasks in which an array of stimuli was reconstructed to match a model array. Results indicated that both age groups were able to solve multidimensional problems, but that solution rate was retarded by the unidimensional processing of highly salient dimensions.…

ARSENIC REMOVAL FROM DRINKING WATER BY ADSORPTIVE MEDIA, USEPA DEMONSTRATION PROJECT AT RIMROCK, AZ, SIX-MONTH EVALUATION REPORT

EPA Science Inventory

This report documents the activities performed during and the results obtained from the first six months of the arsenic removal treatment technology demonstration project at Rimrock, AZ. The objectives of the project are to evaluate the effectiveness of AdEdge Arsenic Package Uni...

The Spectrum of School--University Partnerships: A Typology of Organizational Learning Systems

ERIC Educational Resources Information Center

Callahan, Jamie L.; Martin, Dorian

2007-01-01

School-university partnerships are not uni-dimensional projects. Success in these partnerships can be found in loosely-coupled systems such as client-server partnerships and in more tightly-coupled systems such as collaborative development centers. Using a comparative case study approach, we explore two school-university partnership case studies…

Spatial Analysis of Market Economy Innovations in the Former Soviet Union: The Case of Commodity Exchanges

DTIC Science & Technology

1992-10-06

current cooperative movement in the former Soviet Uni’n can be traced to a law adopted in November, 1986 which permitted family members residing...the labor joined the cooperative movement in 1988. Uzbekistan, the largest of the Central Asian republics, claims only one exchange in Tashkent

East Europe Report, Economic and Industrial Affairs.

DTIC Science & Technology

1984-05-10

Women’s wear, girls ’ wear, men’s wear, uni- forms /continued on following page/ 21 Combine Established Employees VEB’s in the Combined...and handles for purses and luggage Stockings,socks, panty - hose, women’s and children’s slips Belt bands,conveyer belts,textile filters of manmade

Affective Learning in Higher Education: A Regional Perspective

ERIC Educational Resources Information Center

Evans, Nina; Ziaian, Tahereh; Sawyer, Janet; Gillham, David

2013-01-01

A pilot study was conducted in a regional university setting to promote awareness of the value of affective teaching and learning amongst staff and students. Academic staff and students from diverse disciplines at University of South Australia's (UniSA) Centre for Regional Engagement (CRE) were recruited to the study. The research investigated…

Knowledge Contribution in Virtual Communities: Accounting for Multiple Dimensions of Social Presence through Social Identity

ERIC Educational Resources Information Center

Shen, Kathy Ning; Yu, Angela Yan; Khalifa, Mohamed

2010-01-01

Integrating social presence theory and social identity theory, this study brings system design and social influence aspects together to explain their joint effects on knowledge contribution in virtual communities (VCs). Different from most prior information systems (IS) research that adopts a uni-dimensional approach and restricts social presence…

Bending patterns of chlamydomonas flagella: III. A radial spoke head deficient mutant and a central pair deficient mutant.

PubMed

Brokaw, C J; Luck, D J

1985-01-01

Flash photomicrography at frequencies up to 300 Hz and computer-assisted image analysis have been used to obtain parameters describing the flagellar bending patterns of mutants of Chlamydomonas reinhardtii. All strains contained the uni1 mutation, to facilitate photography. The radial spoke head deficient mutant pf17, and the central pair deficient mutant, pf15, in combination with suppressor mutations that restore motility without restoring the ultrastructural or biochemical deficiencies, both generate forward mode bending patterns with increased shear amplitude and decreased asymmetry relative to the "wild-type" uni1 flagella described previously. In the reverse beating mode, the suppressed pf17 mutants generate reverse bending patterns with large shear amplitudes. Reverse beating of the suppressed pf15 mutants is rare. There is a reciprocal relationship between increased shear amplitude and decreased beat frequency, so that the velocity of sliding between flagellar microtubules is not increased by an increase in shear amplitude. The suppressor mutations alone cause decreased frequency and sliding velocity in both forward and reverse mode beating, with little change in shear amplitude or symmetry.

Uni-Morbid and Co-Occurring Marijuana and Tobacco Use: Examination of Concurrent Associations with Negative Mood States

PubMed Central

Bonn-Miller, Marcel O.; Zvolensky, Michael J.; Johnson, Kirsten A.

2010-01-01

The aim of the current investigation was to examine uni-morbid and co-occurring tobacco and marijuana use in relation to the negative emotional symptoms of anxiety and depression. Participants were 250 adult individuals (132 female; mage = 22.43, SD = 9.00), falling into one of four non-overlapping substance use categories: tobacco use only (n = 39), marijuana use only (n = 62), co-occurring tobacco and marijuana use (n = 82), and neither tobacco nor marijuana use (n = 67). Results revealed three key findings. First, tobacco-only using individuals reported significantly greater negative affectivity than any of the other groups. Second, tobacco-only users reported greater anxious arousal symptoms than either the marijuana or non-substance-using groups, but not the combined group. Third, tobacco-only users reported greater levels of depressive symptoms than either marijuana users or non-substance-users. These findings provide novel information about tobacco and marijuana use, and how these variables relate to the experience of general and specific types of negative emotional symptoms. PMID:20390700

UniEnt: uniform entropy model for the dynamics of a neuronal population

NASA Astrophysics Data System (ADS)

Hernandez Lahme, Damian; Nemenman, Ilya

Sensory information and motor responses are encoded in the brain in a collective spiking activity of a large number of neurons. Understanding the neural code requires inferring statistical properties of such collective dynamics from multicellular neurophysiological recordings. Questions of whether synchronous activity or silence of multiple neurons carries information about the stimuli or the motor responses are especially interesting. Unfortunately, detection of such high order statistical interactions from data is especially challenging due to the exponentially large dimensionality of the state space of neural collectives. Here we present UniEnt, a method for the inference of strengths of multivariate neural interaction patterns. The method is based on the Bayesian prior that makes no assumptions (uniform a priori expectations) about the value of the entropy of the observed multivariate neural activity, in contrast to popular approaches that maximize this entropy. We then study previously published multi-electrode recordings data from salamander retina, exposing the relevance of higher order neural interaction patterns for information encoding in this system. This work was supported in part by Grants JSMF/220020321 and NSF/IOS/1208126.

[The pharmaceutical industry in the industrial chemical group: the National Union of Chemical-Pharmaceutical Laboratories (1919-1936)].

PubMed

Nozal, Raúl Rodríquez

2011-01-01

The pharmaceutical industry associations, as it happened with other businesses, had a significant rise during the dictatorship of Primo de Rivera and II Republic. The 'Cámara Nacional de Industrias Químicas', in Barcelona, represented the national chemical industry to its ultimate assimilation by the 'Organización Sindical' in 1939. In this association, matters relating to pharmaceutical products -- which we will especially deal with in this work -- were managed by the 'Unión Nacional de Laboratorios Químico-Farmacéuticos', which defended the interests of pharmaceutical companies in the presence of government authorities, using the resources and mechanisms also managed by business pressure groups. The inclusion of industrial pharmacy in the Chemical lobby separated the pharmaceutical industry from traditional exercise and its corporate environment. this created ups and downs, conflicts of interests and finally, love and hate relationships with their colleagues of the pharmacy work placement and, of course, with the association that represented them: the 'Unión Farmacéutica Nacional'.

SNPdbe: constructing an nsSNP functional impacts database.

PubMed

Schaefer, Christian; Meier, Alice; Rost, Burkhard; Bromberg, Yana

2012-02-15

Many existing databases annotate experimentally characterized single nucleotide polymorphisms (SNPs). Each non-synonymous SNP (nsSNP) changes one amino acid in the gene product (single amino acid substitution;SAAS). This change can either affect protein function or be neutral in that respect. Most polymorphisms lack experimental annotation of their functional impact. Here, we introduce SNPdbe-SNP database of effects, with predictions of computationally annotated functional impacts of SNPs. Database entries represent nsSNPs in dbSNP and 1000 Genomes collection, as well as variants from UniProt and PMD. SAASs come from >2600 organisms; 'human' being the most prevalent. The impact of each SAAS on protein function is predicted using the SNAP and SIFT algorithms and augmented with experimentally derived function/structure information and disease associations from PMD, OMIM and UniProt. SNPdbe is consistently updated and easily augmented with new sources of information. The database is available as an MySQL dump and via a web front end that allows searches with any combination of organism names, sequences and mutation IDs. http://www.rostlab.org/services/snpdbe.

Surrogate Based Uni/Multi-Objective Optimization and Distribution Estimation Methods

NASA Astrophysics Data System (ADS)

Gong, W.; Duan, Q.; Huo, X.

2017-12-01

Parameter calibration has been demonstrated as an effective way to improve the performance of dynamic models, such as hydrological models, land surface models, weather and climate models etc. Traditional optimization algorithms usually cost a huge number of model evaluations, making dynamic model calibration very difficult, or even computationally prohibitive. With the help of a serious of recently developed adaptive surrogate-modelling based optimization methods: uni-objective optimization method ASMO, multi-objective optimization method MO-ASMO, and probability distribution estimation method ASMO-PODE, the number of model evaluations can be significantly reduced to several hundreds, making it possible to calibrate very expensive dynamic models, such as regional high resolution land surface models, weather forecast models such as WRF, and intermediate complexity earth system models such as LOVECLIM. This presentation provides a brief introduction to the common framework of adaptive surrogate-based optimization algorithms of ASMO, MO-ASMO and ASMO-PODE, a case study of Common Land Model (CoLM) calibration in Heihe river basin in Northwest China, and an outlook of the potential applications of the surrogate-based optimization methods.

Processing and Testing of Thermoplastic Composite Cylindrical Shells Fabricated by Automated Fiber Placement

NASA Technical Reports Server (NTRS)

Hulcher, Anthony Bruce; McGowan, David M.; Grimsley, Brian W.; Johnston, Norman J.; Gordon, Gail H. (Technical Monitor)

2001-01-01

Two 61-cm-diameter eight-ply quasi-isotropic IM7/PEEK cylindrical shells were fabricated by automated fiber placement the NASA Langley Research Center using only infrared radiant heat to preheat the substrate and incoming composite uni-tape. The shells were characterized by ultrasonic c-scans for overall consolidation quality, and by optical microscopy and acid digestion for void content. Compression tests were also performed. Although the material used in the study was of generally poor quality due to numerous splits and dry fiber regions, the process was able to achieve a net reduction in void content in the as-placed component. Microscopy of the composite shells revealed well-consolidated, void-free interfaces. The two cylinders were then tested in uni-axial compression in a 1334 kN-capacity hydraulic test machine until buckling occurred. A geometrically nonlinear finite element analysis was conducted, and the differences between the predicted and measured values were 18.0 and 25.8%, respectively. Inclusion of measured imperfections of the cylinder into the analysis is expected to reduce these differences.

Lyophilized sustained release mucoadhesive chitosan sponges for buccal buspirone hydrochloride delivery: formulation and in vitro evaluation.

PubMed

Kassem, Mohamed A A; ElMeshad, Aliaa N; Fares, Ahmed R

2015-06-01

This work aims to prepare sustained release buccal mucoadhesive lyophilized chitosan sponges of buspirone hydrochloride (BH) to improve its systemic bioavailability. Chitosan sponges were prepared using simple casting/freeze-drying technique according to 3(2) factorial design where chitosan grade was set at three levels (low, medium, and high molecular weight), and concentration of chitosan solution at three levels (0.5, 1, and 2%). Mucoadhesion force, ex vivo mucoadhesion time, percent BH released after 8 h (Q8h), and time for release of 50% BH (T50%) were chosen as dependent variables. Additional BH cup and core buccal chitosan sponge were prepared to achieve uni-directional BH release toward the buccal mucosa. Sponges were evaluated in terms of drug content, surface pH, scanning electron microscopy, swelling index, mucoadhesion strength, ex vivo mucoadhesion time, and in vitro drug release. Cup and core sponge (HCH 0.5E) were able to adhere to the buccal mucosa for 8 h. It showed Q8h of 68.89% and exhibited a uni-directional drug release profile following Higuchi diffusion model.

A Theoretical Model for Estimation of Yield Strength of Fiber Metal Laminate

NASA Astrophysics Data System (ADS)

Bhat, Sunil; Nagesh, Suresh; Umesh, C. K.; Narayanan, S.

2017-08-01

The paper presents a theoretical model for estimation of yield strength of fiber metal laminate. Principles of elasticity and formulation of residual stress are employed to determine the stress state in metal layer of the laminate that is found to be higher than the stress applied over the laminate resulting in reduced yield strength of the laminate in comparison with that of the metal layer. The model is tested over 4A-3/2 Glare laminate comprising three thin aerospace 2014-T6 aluminum alloy layers alternately bonded adhesively with two prepregs, each prepreg built up of three uni-directional glass fiber layers laid in longitudinal and transverse directions. Laminates with prepregs of E-Glass and S-Glass fibers are investigated separately under uni-axial tension. Yield strengths of both the Glare variants are found to be less than that of aluminum alloy with use of S-Glass fiber resulting in higher laminate yield strength than with the use of E-Glass fiber. Results from finite element analysis and tensile tests conducted over the laminates substantiate the theoretical model.

BoolNet--an R package for generation, reconstruction and analysis of Boolean networks.

PubMed

Müssel, Christoph; Hopfensitz, Martin; Kestler, Hans A

2010-05-15

As the study of information processing in living cells moves from individual pathways to complex regulatory networks, mathematical models and simulation become indispensable tools for analyzing the complex behavior of such networks and can provide deep insights into the functioning of cells. The dynamics of gene expression, for example, can be modeled with Boolean networks (BNs). These are mathematical models of low complexity, but have the advantage of being able to capture essential properties of gene-regulatory networks. However, current implementations of BNs only focus on different sub-aspects of this model and do not allow for a seamless integration into existing preprocessing pipelines. BoolNet efficiently integrates methods for synchronous, asynchronous and probabilistic BNs. This includes reconstructing networks from time series, generating random networks, robustness analysis via perturbation, Markov chain simulations, and identification and visualization of attractors. The package BoolNet is freely available from the R project at http://cran.r-project.org/ or http://www.informatik.uni-ulm.de/ni/mitarbeiter/HKestler/boolnet/ under Artistic License 2.0. hans.kestler@uni-ulm.de Supplementary data are available at Bioinformatics online.

APPRIS 2017: principal isoforms for multiple gene sets

PubMed Central

Rodriguez-Rivas, Juan; Di Domenico, Tomás; Vázquez, Jesús; Valencia, Alfonso

2018-01-01

Abstract The APPRIS database (http://appris-tools.org) uses protein structural and functional features and information from cross-species conservation to annotate splice isoforms in protein-coding genes. APPRIS selects a single protein isoform, the ‘principal’ isoform, as the reference for each gene based on these annotations. A single main splice isoform reflects the biological reality for most protein coding genes and APPRIS principal isoforms are the best predictors of these main proteins isoforms. Here, we present the updates to the database, new developments that include the addition of three new species (chimpanzee, Drosophila melangaster and Caenorhabditis elegans), the expansion of APPRIS to cover the RefSeq gene set and the UniProtKB proteome for six species and refinements in the core methods that make up the annotation pipeline. In addition APPRIS now provides a measure of reliability for individual principal isoforms and updates with each release of the GENCODE/Ensembl and RefSeq reference sets. The individual GENCODE/Ensembl, RefSeq and UniProtKB reference gene sets for six organisms have been merged to produce common sets of splice variants. PMID:29069475

5 Gbps wireless transmission link with an optically pumped uni-traveling carrier photodiode mixer at the receiver.

PubMed

Mohammad, Ahmad W; Shams, Haymen; Balakier, Katarzyna; Graham, Chris; Natrella, Michele; Seeds, Alwyn J; Renaud, Cyril C

2018-02-05

We report the first demonstration of a uni-traveling carrier photodiode (UTC-PD) used as a 5 Gbps wireless receiver. In this experiment, a 35.1 GHz carrier was electrically modulated with 5 Gbps non-return with zero on-off keying (NRZ-OOK) data and transmitted wirelessly over a distance of 1.3 m. At the receiver, a UTC-PD was used as an optically pumped mixer (OPM) to down-convert the received radio frequency (RF) signal to an intermediate frequency (IF) of 11.7 GHz, before it was down-converted to the baseband using an electronic mixer. The recovered data show a clear eye diagram, and a bit error rate (BER) of less than 10 -8 was measured. The conversion loss of the UTC-PD optoelectronic mixer has been measured at 22 dB. The frequency of the local oscillator (LO) used for the UTC-PD is defined by the frequency spacing between the two optical tones, which can be broadly tuneable offering the frequency agility of this photodiode-based receiver.

Experimental Results From Stitched Composite Multi-Bay Fuselage Panels Tested Under Uni-Axial Compression

NASA Technical Reports Server (NTRS)

Baker, Donald J.

2004-01-01

The experimental results from two stitched VARTM composite panels tested under uni-axial compression loading are presented. The curved panels are divided by frames and stringers into five or six bays with a column of three bays along the compressive loading direction. The frames are supported at the ends to resist out-of-plane translation. Back-to-back strain gages are used to record the strain and displacement transducers were used to record the out-of-plane displacements. In addition a full-field measurement technique that utilizes a camera-based-stero-vision system was used to record displacements. The panels were loaded in increments to determine the first bay to buckle. Loading was discontinued at limit load and the panels were removed from the test machine for impact testing. After impacting at 20 ft-lbs to 25 ft-lbs of energy with a spherical indenter, the panels were loaded in compression until failure. Impact testing reduced the axial stiffness 4 percent and less than 1 percent. Postbuckled axial panel stiffness was 52 percent and 70 percent of the pre-buckled stiffness.

A Comparison of Secondary Chemistry Courses and Chemistry Teacher Preparation Programs in Iowa and Saint Petersburg, Russia

NASA Astrophysics Data System (ADS)

Sanger, Michael J.; Brincks, Erik L.; Phelps, Amy J.; Pak, Maria S.; Lyovkin, Antony N.

2001-09-01

This paper, which is a result of the collaboration between the University of Northern Iowa (UNI) in Cedar Falls, Iowa, and Herzen State Pedagogical University of Russia in Saint Petersburg, compares the 7-12 chemistry courses in Iowa and Saint Petersburg and the chemistry teacher preparation programs at UNI and Herzen. Differences in the 7-12 chemistry courses include curriculum design (spiral versus layer cake), students' extracurricular activities, and access to technology in the classroom. Differences in the chemistry teacher preparation programs include the number of methods and chemistry content courses required, the number of chemistry teaching majors, the proportion of teaching majors enrolled in the different natural science programs, and the typical minors and endorsements received by these majors. Although we noted many differences in chemistry instruction between Iowa and Saint Petersburg, the secondary and college instructors still face many similar issues, which include overcoming student chemophobia, improving students' algorithmic and problem-solving skills, improving students' conceptual understanding at the particulate level, and dealing with shortages in qualified secondary science teachers.

Development of a Mechatronic Syringe Pump to Control Fluid Flow in a Microfluidic Device Based on Polyimide Film

NASA Astrophysics Data System (ADS)

Sek Tee, Kian; Sharil Saripan, Muhammad; Yap, Hiung Yin; Fhong Soon, Chin

2017-08-01

With the advancement in microfluidic technology, fluid flow control for syringe pump is always essential. In this paper, a mechatronic syringe pump will be developed and customized to control the fluid flow in a poly-dimethylsiloxane (PDMS) microfluidic device based on a polyimide laminating film. The syringe pump is designed to drive fluid with flow rates of 100 and 1000 μl/min which intended to drive continuous fluid in a polyimide based microfluidic device. The electronic system consists of an Arduino microcontroller board and a uni-polar stepper motor. In the system, the uni-polar stepper motor was coupled to a linear slider attached to the plunger of a syringe pump. As the motor rotates, the plunger pumps the liquid out of the syringe. The accuracy of the fluid flow rate was determined by adjusting the number of micro-step/revolution to drive the stepper motor to infuse fluid into the microfluidic device. With the precise control of the electronic system, the syringe pump could accurately inject fluid volume at 100 and 1000 μl/min into a microfluidic device.

Performance of different theories for the angular distribution of bremsstrahlung produced by keV electrons incident upon a target

NASA Astrophysics Data System (ADS)

Omar, Artur; Andreo, Pedro; Poludniowski, Gavin

2018-07-01

Different theories of the intrinsic bremsstrahlung angular distribution (i.e., the shape function) have been evaluated using Monte Carlo calculations for various target materials and incident electron energies between 20 keV and 300 keV. The shape functions considered were the plane-wave first Born approximation cross sections (i) 2BS [high-energy result, screened nucleus], (ii) 2BN [general result, bare nucleus], (iii) KM [2BS modified to emulate 2BN], and (iv) SIM [leading term of 2BN]; (v) expression based on partial-waves expansion, KQP; and (vi) a uniform spherical distribution, UNI [a common approximation in certain analytical models]. The shape function was found to have an important impact on the bremsstrahlung emerging from thin foil targets in which the incident electrons undergo few elastic scatterings before exiting the target material. For thick transmission and reflection targets the type of shape function had less importance, as the intrinsic bremsstrahlung angular distribution was masked by the diffuse directional distribution of multiple scattered electrons. Predictions made using the 2BN and KQP theories were generally in good agreement, suggesting that the effect of screening and the constraints of the Born approximation on the intrinsic angular distribution may be acceptable. The KM and SIM shape functions deviated notably from KQP for low electron energies (< 50 keV), while 2BS and UNI performed poorly over most of the energy range considered; the 2BS shape function was found to be too forward-focused in emission, while UNI was not forward-focused enough. The results obtained emphasize the importance of the intrinsic bremsstrahlung angular distribution for theoretical predictions of x-ray emission, which is relevant in various applied disciplines, including x-ray crystallography, electron-probe microanalysis, security and industrial inspection, medical imaging, as well as low- and medium (orthovoltage) energy radiotherapy.

Effects of framework design and layering material on fracture strength of implant-supported zirconia-based molar crowns.

PubMed

Kamio, Shingo; Komine, Futoshi; Taguchi, Kohei; Iwasaki, Taro; Blatz, Markus B; Matsumura, Hideo

2015-12-01

To evaluate the effects of framework design and layering material on the fracture strength of implant-supported zirconia-based molar crowns. Sixty-six titanium abutments (GingiHue Post) were tightened onto dental implants (Implant Lab Analog). These abutment-implant complexes were randomly divided into three groups (n = 22) according to the design of the zirconia framework (Katana), namely, uniform-thickness (UNI), anatomic (ANA), and supported anatomic (SUP) designs. The specimens in each design group were further divided into two subgroups (n = 11): zirconia-based all-ceramic restorations (ZAC group) and zirconia-based restorations with an indirect composite material (Estenia C&B) layered onto the zirconia framework (ZIC group). All crowns were cemented on implant abutments, after which the specimens were tested for fracture resistance. The data were analyzed with the Kruskal-Wallis test and the Mann-Whitney U-test with the Bonferroni correction (α = 0.05). The following mean fracture strength values (kN) were obtained in UNI design, ANA design, and SUP design, respectively: Group ZAC, 3.78, 6.01, 6.50 and Group ZIC, 3.15, 5.65, 5.83. In both the ZAC and ZIC groups, fracture strength was significantly lower for the UNI design than the other two framework designs (P = 0.001). Fracture strength did not significantly differ (P > 0.420) between identical framework designs in the ZAC and ZIC groups. A framework design with standardized layer thickness and adequate support of veneer by zirconia frameworks, as in the ANA and SUP designs, increases fracture resistance in implant-supported zirconia-based restorations under conditions of chewing attrition. Indirect composite material and porcelain perform similarly as layering materials on zirconia frameworks. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Opportunities of probabilistic flood loss models

NASA Astrophysics Data System (ADS)

Schröter, Kai; Kreibich, Heidi; Lüdtke, Stefan; Vogel, Kristin; Merz, Bruno

2016-04-01

Oftentimes, traditional uni-variate damage models as for instance depth-damage curves fail to reproduce the variability of observed flood damage. However, reliable flood damage models are a prerequisite for the practical usefulness of the model results. Innovative multi-variate probabilistic modelling approaches are promising to capture and quantify the uncertainty involved and thus to improve the basis for decision making. In this study we compare the predictive capability of two probabilistic modelling approaches, namely Bagging Decision Trees and Bayesian Networks and traditional stage damage functions. For model evaluation we use empirical damage data which are available from computer aided telephone interviews that were respectively compiled after the floods in 2002, 2005, 2006 and 2013 in the Elbe and Danube catchments in Germany. We carry out a split sample test by sub-setting the damage records. One sub-set is used to derive the models and the remaining records are used to evaluate the predictive performance of the model. Further we stratify the sample according to catchments which allows studying model performance in a spatial transfer context. Flood damage estimation is carried out on the scale of the individual buildings in terms of relative damage. The predictive performance of the models is assessed in terms of systematic deviations (mean bias), precision (mean absolute error) as well as in terms of sharpness of the predictions the reliability which is represented by the proportion of the number of observations that fall within the 95-quantile and 5-quantile predictive interval. The comparison of the uni-variable Stage damage function and the multivariable model approach emphasises the importance to quantify predictive uncertainty. With each explanatory variable, the multi-variable model reveals an additional source of uncertainty. However, the predictive performance in terms of precision (mbe), accuracy (mae) and reliability (HR) is clearly improved in comparison to uni-variable Stage damage function. Overall, Probabilistic models provide quantitative information about prediction uncertainty which is crucial to assess the reliability of model predictions and improves the usefulness of model results.

FastRNABindR: Fast and Accurate Prediction of Protein-RNA Interface Residues.

PubMed

El-Manzalawy, Yasser; Abbas, Mostafa; Malluhi, Qutaibah; Honavar, Vasant

2016-01-01

A wide range of biological processes, including regulation of gene expression, protein synthesis, and replication and assembly of many viruses are mediated by RNA-protein interactions. However, experimental determination of the structures of protein-RNA complexes is expensive and technically challenging. Hence, a number of computational tools have been developed for predicting protein-RNA interfaces. Some of the state-of-the-art protein-RNA interface predictors rely on position-specific scoring matrix (PSSM)-based encoding of the protein sequences. The computational efforts needed for generating PSSMs severely limits the practical utility of protein-RNA interface prediction servers. In this work, we experiment with two approaches, random sampling and sequence similarity reduction, for extracting a representative reference database of protein sequences from more than 50 million protein sequences in UniRef100. Our results suggest that random sampled databases produce better PSSM profiles (in terms of the number of hits used to generate the profile and the distance of the generated profile to the corresponding profile generated using the entire UniRef100 data as well as the accuracy of the machine learning classifier trained using these profiles). Based on our results, we developed FastRNABindR, an improved version of RNABindR for predicting protein-RNA interface residues using PSSM profiles generated using 1% of the UniRef100 sequences sampled uniformly at random. To the best of our knowledge, FastRNABindR is the only protein-RNA interface residue prediction online server that requires generation of PSSM profiles for query sequences and accepts hundreds of protein sequences per submission. Our approach for determining the optimal BLAST database for a protein-RNA interface residue classification task has the potential of substantially speeding up, and hence increasing the practical utility of, other amino acid sequence based predictors of protein-protein and protein-DNA interfaces.

The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases.

PubMed

Côté, Richard G; Jones, Philip; Martens, Lennart; Kerrien, Samuel; Reisinger, Florian; Lin, Quan; Leinonen, Rasko; Apweiler, Rolf; Hermjakob, Henning

2007-10-18

Each major protein database uses its own conventions when assigning protein identifiers. Resolving the various, potentially unstable, identifiers that refer to identical proteins is a major challenge. This is a common problem when attempting to unify datasets that have been annotated with proteins from multiple data sources or querying data providers with one flavour of protein identifiers when the source database uses another. Partial solutions for protein identifier mapping exist but they are limited to specific species or techniques and to a very small number of databases. As a result, we have not found a solution that is generic enough and broad enough in mapping scope to suit our needs. We have created the Protein Identifier Cross-Reference (PICR) service, a web application that provides interactive and programmatic (SOAP and REST) access to a mapping algorithm that uses the UniProt Archive (UniParc) as a data warehouse to offer protein cross-references based on 100% sequence identity to proteins from over 70 distinct source databases loaded into UniParc. Mappings can be limited by source database, taxonomic ID and activity status in the source database. Users can copy/paste or upload files containing protein identifiers or sequences in FASTA format to obtain mappings using the interactive interface. Search results can be viewed in simple or detailed HTML tables or downloaded as comma-separated values (CSV) or Microsoft Excel (XLS) files suitable for use in a local database or a spreadsheet. Alternatively, a SOAP interface is available to integrate PICR functionality in other applications, as is a lightweight REST interface. We offer a publicly available service that can interactively map protein identifiers and protein sequences to the majority of commonly used protein databases. Programmatic access is available through a standards-compliant SOAP interface or a lightweight REST interface. The PICR interface, documentation and code examples are available at http://www.ebi.ac.uk/Tools/picr.

Effects of Heavy-Resistance Strength and Balance Training on Unilateral and Bilateral Leg Strength Performance in Old Adults

PubMed Central

Beurskens, Rainer; Gollhofer, Albert; Muehlbauer, Thomas; Cardinale, Marco; Granacher, Urs

2015-01-01

The term “bilateral deficit” (BLD) has been used to describe a reduction in performance during bilateral contractions when compared to the sum of identical unilateral contractions. In old age, maximal isometric force production (MIF) decreases and BLD increases indicating the need for training interventions to mitigate this impact in seniors. In a cross-sectional approach, we examined age-related differences in MIF and BLD in young (age: 20–30 years) and old adults (age: >65 years). In addition, a randomized-controlled trial was conducted to investigate training-specific effects of resistance vs. balance training on MIF and BLD of the leg extensors in old adults. Subjects were randomly assigned to resistance training (n = 19), balance training (n = 14), or a control group (n = 20). Bilateral heavy-resistance training for the lower extremities was performed for 13 weeks (3 × / week) at 80% of the one repetition maximum. Balance training was conducted using predominately unilateral exercises on wobble boards, soft mats, and uneven surfaces for the same duration. Pre- and post-tests included uni- and bilateral measurements of maximal isometric leg extension force. At baseline, young subjects outperformed older adults in uni- and bilateral MIF (all p < .001; d = 2.61–3.37) and in measures of BLD (p < .001; d = 2.04). We also found significant increases in uni- and bilateral MIF after resistance training (all p < .001, d = 1.8-5.7) and balance training (all p < .05, d = 1.3-3.2). In addition, BLD decreased following resistance (p < .001, d = 3.4) and balance training (p < .001, d = 2.6). It can be concluded that both training regimens resulted in increased MIF and decreased BLD of the leg extensors (HRT-group more than BAL-group), almost reaching the levels of young adults. PMID:25695770

PICKLE 2.0: A human protein-protein interaction meta-database employing data integration via genetic information ontology

PubMed Central

Gioutlakis, Aris; Klapa, Maria I.

2017-01-01

It has been acknowledged that source databases recording experimentally supported human protein-protein interactions (PPIs) exhibit limited overlap. Thus, the reconstruction of a comprehensive PPI network requires appropriate integration of multiple heterogeneous primary datasets, presenting the PPIs at various genetic reference levels. Existing PPI meta-databases perform integration via normalization; namely, PPIs are merged after converted to a certain target level. Hence, the node set of the integrated network depends each time on the number and type of the combined datasets. Moreover, the irreversible a priori normalization process hinders the identification of normalization artifacts in the integrated network, which originate from the nonlinearity characterizing the genetic information flow. PICKLE (Protein InteraCtion KnowLedgebasE) 2.0 implements a new architecture for this recently introduced human PPI meta-database. Its main novel feature over the existing meta-databases is its approach to primary PPI dataset integration via genetic information ontology. Building upon the PICKLE principles of using the reviewed human complete proteome (RHCP) of UniProtKB/Swiss-Prot as the reference protein interactor set, and filtering out protein interactions with low probability of being direct based on the available evidence, PICKLE 2.0 first assembles the RHCP genetic information ontology network by connecting the corresponding genes, nucleotide sequences (mRNAs) and proteins (UniProt entries) and then integrates PPI datasets by superimposing them on the ontology network without any a priori transformations. Importantly, this process allows the resulting heterogeneous integrated network to be reversibly normalized to any level of genetic reference without loss of the original information, the latter being used for identification of normalization biases, and enables the appraisal of potential false positive interactions through PPI source database cross-checking. The PICKLE web-based interface (www.pickle.gr) allows for the simultaneous query of multiple entities and provides integrated human PPI networks at either the protein (UniProt) or the gene level, at three PPI filtering modes. PMID:29023571

Mutants Resistant to anti-Microtubule Herbicides Map to a Locus on the Uni Linkage Group in Chlamydomonas Reinhardtii

PubMed Central

James, S. W.; Ranum, LPW.; Silflow, C. D.; Lefebvre, P. A.

1988-01-01

We have used genetic analysis to study the mode of action of two anti-microtubule herbicides, amiprophos-methyl (APM) and oryzalin (ORY). Over 200 resistant mutants were selected by growth on APM- or ORY-containing plates. The 21 independently isolated mutants examined in this study are 3- to 8-fold resistant to APM and are strongly cross-resistant to ORY and butamiphos, a close analog of APM. Two Mendelian genes, apm1 and apm2, are defined by linkage and complementation analysis. There are 20 alleles of apm1 and one temperature-sensitive lethal (33°) allele of apm2. Mapping by two-factor crosses places apm1 6.5 cM centromere proximal to uni1 and within 4 cM of pf7 on the uni linkage group, a genetically circular linkage group comprising genes which affect flagellar assembly or function; apm2 maps near the centromere of linkage group VIII. Allele-specific synthetic lethality is observed in crosses between apm2 and alleles of apm1. Also, self crosses of apm2 are zygotic lethal, whereas crosses of nine apm1 alleles inter se result in normal germination and tetrad viability. The mutants are recessive to their wild-type alleles but doubly heterozygous diploids (apm1 +/+ apm2) made with apm2 and any of 15 apm1 alleles display partial intergenic noncomplementation, expressed as intermediate resistance. Diploids homozygous for mutant alleles of apm1 are 4-6-fold resistant to APM and ORY; diploids homozygous for apm2 are ts(-) and 2-fold resistant to the herbicides. Doubly heterozygous diploids complement the ts(-) phenotype of apm2, but they are typically 1.5-2-fold resistant to APM and ORY. From the results described we suggest that the gene products of apm1 and apm2 may interact directly or function in the same structure or process. PMID:8608924

SuperSAGE analysis of the Nicotiana attenuata transcriptome after fatty acid-amino acid elicitation (FAC): identification of early mediators of insect responses

PubMed Central

2010-01-01

Background Plants trigger and tailor defense responses after perception of the oral secretions (OS) of attacking specialist lepidopteran larvae. Fatty acid-amino acid conjugates (FACs) in the OS of the Manduca sexta larvae are necessary and sufficient to elicit the herbivory-specific responses in Nicotiana attenuata, an annual wild tobacco species. How FACs are perceived and activate signal transduction mechanisms is unknown. Results We used SuperSAGE combined with 454 sequencing to quantify the early transcriptional changes elicited by the FAC N-linolenoyl-glutamic acid (18:3-Glu) and virus induced gene silencing (VIGS) to examine the function of candidate genes in the M. sexta-N. attenuata interaction. The analysis targeted mRNAs encoding regulatory components: rare transcripts with very rapid FAC-elicited kinetics (increases within 60 and declines within 120 min). From 12,744 unique Tag sequences identified (UniTags), 430 and 117 were significantly up- and down-regulated ≥ 2.5-fold, respectively, after 18:3-Glu elicitation compared to wounding. Based on gene ontology classification, more than 25% of the annotated UniTags corresponded to putative regulatory components, including 30 transcriptional regulators and 22 protein kinases. Quantitative PCR analysis was used to analyze the FAC-dependent regulation of a subset of 27 of these UniTags and for most of them a rapid and transient induction was confirmed. Six FAC-regulated genes were functionally characterized by VIGS and two, a putative lipid phosphate phosphatase (LPP) and a protein of unknown function, were identified as important mediators of the M. sexta-N. attenuata interaction. Conclusions The analysis of the early changes in the transcriptome of N. attenuata after FAC elicitation using SuperSAGE/454 has identified regulatory genes involved in insect-specific mediated responses in plants. Moreover, it has provided a foundation for the identification of additional novel regulators associated with this process. PMID:20398280

[In Process Citation].

PubMed

Guzmán-Mercado, Elizabeth; Vásquez-Garibay, Edgar M; Troyo-Sanroman, Rogelio; Romero-Velarde, Enrique

2016-03-25

Objetivo: identificar los hábitos alimentarios de adolescentes embarazadas en cuatro estados civiles diferentes: casada, cohabita con una pareja, soltera sin pareja y soltera con una pareja. Métodos: en estudio transversal, se incluyeron 321 adolescentes embarazadas de 13-19 años que acudieron al Hospital Civil de Guadalajara Dr. Juan I Menchaca, Guadalajara (Jalisco, México). Se encontraban sanas, en cualquier trimestre del embarazo y pertenecían a un nivel socioe-conómico bajo o medio-bajo. El estado civil se estratificó en: casadas; en unión libre; soltera con una pareja y soltera sin pareja. Se incluyeron datos socio-demográficos, económicos y de hábitos de alimentación. Se utilizaron pruebas de ANOVA, pruebas post-hoc para Chi 2 , razón de momios y modelos de regresión logística. Resultados: la frecuencia de las adolescentes casadas fue de 9,3%, 59,8% en unión libre, 15,3% eran solteras sin pareja y 15,6% solteras con pareja. La baja escolaridad (RM 2,6 [1,5-4,4]) y la ocupación en el hogar (RM 4,47 [1,99-10,0]) predominaron entre las adolescentes en unión libre; la ocupación en el hogar (RM 0,28 [0,127-0,61]) y cenar sin compañía (RM 4,12 [1,62-10,8]) fueron significativamente más frecuentes en adolescentes sin pareja. El consumo de verduras fue menor en las adolescentes casadas y en quienes cohabitaban con pareja; el consumo de frijoles y pan dulce fue menor en adolescentes embarazadas casadas. Conclusión: debido a que ciertas variables y hábitos de alimentación mostraron diferencias entre los grupos es pertinente analizar las adolescentes embarazadas de acuerdo a su estado civil.

Integrated Analysis and Visualization of Group Differences in Structural and Functional Brain Connectivity: Applications in Typical Ageing and Schizophrenia.

PubMed

Langen, Carolyn D; White, Tonya; Ikram, M Arfan; Vernooij, Meike W; Niessen, Wiro J

2015-01-01

Structural and functional brain connectivity are increasingly used to identify and analyze group differences in studies of brain disease. This study presents methods to analyze uni- and bi-modal brain connectivity and evaluate their ability to identify differences. Novel visualizations of significantly different connections comparing multiple metrics are presented. On the global level, "bi-modal comparison plots" show the distribution of uni- and bi-modal group differences and the relationship between structure and function. Differences between brain lobes are visualized using "worm plots". Group differences in connections are examined with an existing visualization, the "connectogram". These visualizations were evaluated in two proof-of-concept studies: (1) middle-aged versus elderly subjects; and (2) patients with schizophrenia versus controls. Each included two measures derived from diffusion weighted images and two from functional magnetic resonance images. The structural measures were minimum cost path between two anatomical regions according to the "Statistical Analysis of Minimum cost path based Structural Connectivity" method and the average fractional anisotropy along the fiber. The functional measures were Pearson's correlation and partial correlation of mean regional time series. The relationship between structure and function was similar in both studies. Uni-modal group differences varied greatly between connectivity types. Group differences were identified in both studies globally, within brain lobes and between regions. In the aging study, minimum cost path was highly effective in identifying group differences on all levels; fractional anisotropy and mean correlation showed smaller differences on the brain lobe and regional levels. In the schizophrenia study, minimum cost path and fractional anisotropy showed differences on the global level and within brain lobes; mean correlation showed small differences on the lobe level. Only fractional anisotropy and mean correlation showed regional differences. The presented visualizations were helpful in comparing and evaluating connectivity measures on multiple levels in both studies.

The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases

PubMed Central

Côté, Richard G; Jones, Philip; Martens, Lennart; Kerrien, Samuel; Reisinger, Florian; Lin, Quan; Leinonen, Rasko; Apweiler, Rolf; Hermjakob, Henning

2007-01-01

Background Each major protein database uses its own conventions when assigning protein identifiers. Resolving the various, potentially unstable, identifiers that refer to identical proteins is a major challenge. This is a common problem when attempting to unify datasets that have been annotated with proteins from multiple data sources or querying data providers with one flavour of protein identifiers when the source database uses another. Partial solutions for protein identifier mapping exist but they are limited to specific species or techniques and to a very small number of databases. As a result, we have not found a solution that is generic enough and broad enough in mapping scope to suit our needs. Results We have created the Protein Identifier Cross-Reference (PICR) service, a web application that provides interactive and programmatic (SOAP and REST) access to a mapping algorithm that uses the UniProt Archive (UniParc) as a data warehouse to offer protein cross-references based on 100% sequence identity to proteins from over 70 distinct source databases loaded into UniParc. Mappings can be limited by source database, taxonomic ID and activity status in the source database. Users can copy/paste or upload files containing protein identifiers or sequences in FASTA format to obtain mappings using the interactive interface. Search results can be viewed in simple or detailed HTML tables or downloaded as comma-separated values (CSV) or Microsoft Excel (XLS) files suitable for use in a local database or a spreadsheet. Alternatively, a SOAP interface is available to integrate PICR functionality in other applications, as is a lightweight REST interface. Conclusion We offer a publicly available service that can interactively map protein identifiers and protein sequences to the majority of commonly used protein databases. Programmatic access is available through a standards-compliant SOAP interface or a lightweight REST interface. The PICR interface, documentation and code examples are available at . PMID:17945017

SuperSAGE analysis of the Nicotiana attenuata transcriptome after fatty acid-amino acid elicitation (FAC): identification of early mediators of insect responses.

PubMed

Gilardoni, Paola A; Schuck, Stefan; Jüngling, Ruth; Rotter, Björn; Baldwin, Ian T; Bonaventure, Gustavo

2010-04-14

Plants trigger and tailor defense responses after perception of the oral secretions (OS) of attacking specialist lepidopteran larvae. Fatty acid-amino acid conjugates (FACs) in the OS of the Manduca sexta larvae are necessary and sufficient to elicit the herbivory-specific responses in Nicotiana attenuata, an annual wild tobacco species. How FACs are perceived and activate signal transduction mechanisms is unknown. We used SuperSAGE combined with 454 sequencing to quantify the early transcriptional changes elicited by the FAC N-linolenoyl-glutamic acid (18:3-Glu) and virus induced gene silencing (VIGS) to examine the function of candidate genes in the M. sexta-N. attenuata interaction. The analysis targeted mRNAs encoding regulatory components: rare transcripts with very rapid FAC-elicited kinetics (increases within 60 and declines within 120 min). From 12,744 unique Tag sequences identified (UniTags), 430 and 117 were significantly up- and down-regulated >or= 2.5-fold, respectively, after 18:3-Glu elicitation compared to wounding. Based on gene ontology classification, more than 25% of the annotated UniTags corresponded to putative regulatory components, including 30 transcriptional regulators and 22 protein kinases. Quantitative PCR analysis was used to analyze the FAC-dependent regulation of a subset of 27 of these UniTags and for most of them a rapid and transient induction was confirmed. Six FAC-regulated genes were functionally characterized by VIGS and two, a putative lipid phosphate phosphatase (LPP) and a protein of unknown function, were identified as important mediators of the M. sexta-N. attenuata interaction. The analysis of the early changes in the transcriptome of N. attenuata after FAC elicitation using SuperSAGE/454 has identified regulatory genes involved in insect-specific mediated responses in plants. Moreover, it has provided a foundation for the identification of additional novel regulators associated with this process.

EuroPineDB: a high-coverage web database for maritime pine transcriptome

PubMed Central

2011-01-01

Background Pinus pinaster is an economically and ecologically important species that is becoming a woody gymnosperm model. Its enormous genome size makes whole-genome sequencing approaches are hard to apply. Therefore, the expressed portion of the genome has to be characterised and the results and annotations have to be stored in dedicated databases. Description EuroPineDB is the largest sequence collection available for a single pine species, Pinus pinaster (maritime pine), since it comprises 951 641 raw sequence reads obtained from non-normalised cDNA libraries and high-throughput sequencing from adult (xylem, phloem, roots, stem, needles, cones, strobili) and embryonic (germinated embryos, buds, callus) maritime pine tissues. Using open-source tools, sequences were optimally pre-processed, assembled, and extensively annotated (GO, EC and KEGG terms, descriptions, SNPs, SSRs, ORFs and InterPro codes). As a result, a 10.5× P. pinaster genome was covered and assembled in 55 322 UniGenes. A total of 32 919 (59.5%) of P. pinaster UniGenes were annotated with at least one description, revealing at least 18 466 different genes. The complete database, which is designed to be scalable, maintainable, and expandable, is freely available at: http://www.scbi.uma.es/pindb/. It can be retrieved by gene libraries, pine species, annotations, UniGenes and microarrays (i.e., the sequences are distributed in two-colour microarrays; this is the only conifer database that provides this information) and will be periodically updated. Small assemblies can be viewed using a dedicated visualisation tool that connects them with SNPs. Any sequence or annotation set shown on-screen can be downloaded. Retrieval mechanisms for sequences and gene annotations are provided. Conclusions The EuroPineDB with its integrated information can be used to reveal new knowledge, offers an easy-to-use collection of information to directly support experimental work (including microarray hybridisation), and provides deeper knowledge on the maritime pine transcriptome. PMID:21762488

UniSat-5: a space-based optical system for space debris monitoring

NASA Astrophysics Data System (ADS)

Di Roberto, Riccardo; Cappelletti, Chantal

2012-07-01

Micro-satellite missions, thanks to the miniaturization process of electronic components, now have a broader range of applications. Gauss Group at School of Aerospace Engineering has been a pioneer in educational micro-satellites, namely with UNISAT and EDUSAT missions. Moreover it has been long involved in space debris related studies, such as optical observations as well as mitigation. A new project is under development for a compact digital imaging system. The purpose will be in situ observation of space debris on board Unisat-5 micro-satellite. One of the key elements of observing on orbit is that many atmospheric phenomena would be avoided, such as diffraction and EM absorption. Hence images would gain more contrast and solar spectral irradiance would be higher for the whole visible spectrum Earlier limitations of power and instrument size prevented the inclusion of these payloads in educational satellite missions. The system is composed of an optical tube, a camera, C band and S band transceivers and two antennas. The system is independent from the rest of the spacecraft. The optical tube is a Schmidt-Cassegrain reflector, and the magnitude limit is 13. The camera is equipped with a panchromatic 5Mpix sensor, capable of direct video streaming, as well as local storage of recorded images. The transceivers operate on ISM 2.4GHz and 5 GHz Wi-Fi bands, and they provide stand-alone communication capabilities to the payload, and Unisat-5 OBDH can switch between the two. Both transceivers are connected to their respective custom-designed patch antenna. The ground segment is constituted of a high gain antenna dish, which will use the same transceiver on board the spacecraft as the feed, in order to establish a TCP/IP wireless link. Every component of this system is a consumer grade product. Therefore price reduction of cutting edge imaging technology now allows the use of professional instruments, that combined with the new wireless technology developed for commercially available RF equipment, allows for an affordable, stand-alone system for digital imaging in space. The space debris observation will work in pair with the attitude determination system, as well as the orbit determination system. UniSat-5 micro-satellite will be launched during Q4 2012 by a Kosmotras DNEPR LV, and it will be injected in a Sun Synchronous Orbit. UniSat-5 will be a the first university satellite for space debris monitoring, and it will test the technology for the future design of a formation flight for on orbit optical debris detection. This paper deals with the space debris observation system boarded on UniSat-5 and the observation strategies adopted considering the mission proposed.

Inventory of Military Real Property

DTIC Science & Technology

1966-12-21

priate manner. The covers used for binding will be of a stiff hard - back material of sufficient strength to permit stowing on edge within file cabinets...SYRMBH0L S FO OM UNI TS O F MEV.A SOUBA 5241/01. UINT SF MEASSURE SYMBOL SlTJ OF IERS//IS AC acresl .. O A. aaiyKilonolt-saperrn, rapacity (KVA) B/D

An Interdisciplinary Evaluation of Transactive Memory in Distributed Cyber Teams

ERIC Educational Resources Information Center

Mancuso, Vincent Francis

2012-01-01

In the modern workplace, collaboration is no longer only a face-to-face process. When working together, it is common for teams to rely on technology and operate across geographic, temporal and cultural boundaries. Most research, when looking at distributed teams, takes a uni-disciplinary perspective and fails to address the entire problem space.…

Microsatellite DNA in genomic survey sequences and UniGenes of loblolly pine

Treesearch

Craig S Echt; Surya Saha; Dennis L Deemer; C Dana Nelson

2011-01-01

Genomic DNA sequence databases are a potential and growing resource for simple sequence repeat (SSR) marker development in loblolly pine (Pinus taeda L.). Loblolly pine also has many expressed sequence tags (ESTs) available for microsatellite (SSR) marker development. We compared loblolly pine SSR densities in genome survey sequences (GSSs) to those in non-redundant...

Center for Regenerative Biology and Medicine at Mount Desert Island Biological Laboratory

DTIC Science & Technology

2012-06-01

Code Axolotl microRNAs Zebrafish Polypterus 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF...controlled in both Polypterus and axolotl samples. These comparisons revealed a total of 2779 shared genes that are significantly upregulated during...UPREGULATED DOWNREGULATED Figure 1: Venn diagram of UniProt protein sequence IDs among Axolotl and Polypterus contigs that were up-regulated

Predicting the flexure response of wood-plastic composites from uni-axial and shear data using a finite-element model

Treesearch

Scott E. Hamel; John C. Hermanson; Steven M. Cramer

2014-01-01

Wood-plastic composites (WPCs), commonly used in residential decks and railings, exhibit mechanical behavior that is bimodal, anisotropic, and nonlinear viscoelastic. They exhibit different stress-strain responses to tension and compression, both of which are nonlinear. Their mechanical properties vary with respect to extrusion direction, their deformation under...

Modality and Task Switching Interactions using Bi-Modal and Bivalent Stimuli

ERIC Educational Resources Information Center

Sandhu, Rajwant; Dyson, Benjamin J.

2013-01-01

Investigations of concurrent task and modality switching effects have to date been studied under conditions of uni-modal stimulus presentation. As such, it is difficult to directly compare resultant task and modality switching effects, as the stimuli afford both tasks on each trial, but only one modality. The current study investigated task and…

Thermal conductivity of some common forest fuels

Treesearch

G.M. Byram; W.L. Fons

1952-01-01

This study was designed to obtain thermal conductivity of som common forest fuels which hitherto had defied such efforts because of their shape, size, or structure. Dry leaves and decayed. wood (punk) were modified so that conductivity measurements could be made by a thin plate uni-directional heat flow calibration stand, Resultss of these measurements are compatible...

DETERMINATION OF URINARY TRIVALENT ARSENICALS (MMASIII AND DMASIII) IN INDIVIDUALS CHRONICALLY EXPOSED TO ARSENIC

EPA Science Inventory

DETERMINATION OF URINARY TRIVALENT ARSENICALS (MMAsIII and DMAsIII) IN INDIVIDUALS CHRONICALLY EXPOSED TO ARSENIC.
L. M. Del Razo1, M. Styblo2, W. R. Cullen3, and D.J. Thomas4.
1Toxicology Section, Cinvestav-IPN, Mexico, D.F., 2Univ. North Carolina, Chapel Hill, NC; 3Uni...

An Observational Approach to Testing Bi-Directional Parent-Child Interactions as Influential to Child Eating and Weight

ERIC Educational Resources Information Center

Demir, Defne; Skouteris, Helen; Dell'Aquila, Daniela; Aksan, Nazan; McCabe, Marita P.; Ricciardelli, Lina A.; Milgrom, Jeannette; Baur, Louise A.

2012-01-01

Obesity among children has been on the rise globally for the past few decades. Previous research has centred mainly on self/parent-reported measures examining only uni-directional parental feeding styles and practices. Recent discussions in the literature have raised the importance of bi-directional parent-child interactions in influencing…

76 FR 81992 - PPL Bell Bend, LLC; Combined License Application for Bell Bend Nuclear Power Plant; Exemption

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-29

... License Application for Bell Bend Nuclear Power Plant; Exemption 1.0 Background PPL Bell Bend, LLC... for Nuclear Power Plants.'' This reactor is to be identified as Bell Bend Nuclear Power Plant (BBNPP... based upon the U.S. EPR reference COL (RCOL) application for UniStar's Calvert Cliffs Nuclear Power...

Assessment of the effects of horizontal grid resolution on long-term air quality trends using coupled WRF-CMAQ simulations

EPA Science Inventory

The objective of this study is to determine the adequacy of using a relatively coarse horizontal resolution (i.e. 36 km) to simulate long-term trends of pollutant concentrations and radiation variables with the coupled WRF-CMAQ model. WRF-CMAQ simulations over the continental Uni...

Democratic Nation Building in the Arc of Crisis: The Case of the Presidential Election in Afghanistan

DTIC Science & Technology

2006-01-01

astrologer waiting for loaves of bread at a bakery in Qalat, know that the new Afghan Constitution allows them full personal rights. But he still says he must...of nearly all development indices, has no extended tradition of uni- versal franchise , and has experienced almost a quarter century of continual

Let's Start in Our Own Backyard: Children's Engagement with Science through the Natural Environment

ERIC Educational Resources Information Center

Alexander, Athalie; Russo, Sharon

2010-01-01

Capitalising on areas in which teachers feel most comfortable, the teaching of Biology, environmental education or nature to young children can be an alternative way of introducing and understanding Science. A "Citizen Science" program currently being run by the University of South Australia (UniSA) may be an appropriate starting point.…

Arthropod fauna of the United Arab Emirates: Order Hymenoptera, family Figitidae

USDA-ARS?s Scientific Manuscript database

No thorough documentation of the figitid fauna has ever been undertaken for the whole of the Arabian Peninsula. To this end, presented here is a list of species documented from the fieldwork of Antonius van Harten and colleagues, as well as a key and diagnoses for all genera of Figitidae in the Uni...

Smoking Cessation: Uni-Modal and Multi-Modal Hypnotic and Non-Hypnotic Approaches.

ERIC Educational Resources Information Center

Habicht, Manuela H.

A survey of Queensland's population in 1993 determined that 24% of the adults were smokers. National data compiled in 1992 indicated that 72% of the drug-related deaths were related to tobacco use. In light of the need for effective smoking cessation approaches, a literature review was undertaken to determine the efficacy of hypnotic and…

Hierarchical storage management system evaluation

NASA Technical Reports Server (NTRS)

Woodrow, Thomas S.

1993-01-01

The Numerical Aerodynamic Simulation (NAS) Program at NASA Ames Research Center has been developing a hierarchical storage management system, NAStore, for some 6 years. This evaluation compares functionality, performance, reliability, and other factors of NAStore and three commercial alternatives. FileServ is found to be slightly better overall than NAStore and DMF. UniTree is found to be severely lacking in comparison.

Lateralized Implicit Sequence Learning in Uni- and Bi-Manual Conditions

ERIC Educational Resources Information Center

Schmitz, Remy; Pasquali, Antoine; Cleeremans, Axel; Peigneux, Philippe

2013-01-01

It has been proposed that the right hemisphere (RH) is better suited to acquire novel material whereas the left hemisphere (LH) is more able to process well-routinized information. Here, we ask whether this potential dissociation also manifests itself in an implicit learning task. Using a lateralized version of the serial reaction time task (SRT),…

Atorvastatin decreases menaquinone-4 formation in C57Bl6 male mice

USDA-ARS?s Scientific Manuscript database

Vitamin K is a fat-soluble vitamin found in two forms, phylloquinone (PK) and menaquinones. The two forms differ in saturation and length of their side chain. Menaquinone-4 (MK4) is a unique menaquinone because it is: (1) formed from dietary PK by means of tissue-specific conversion; and (2) has uni...

The Mediating Effects of Parenting Behaviors on Maternal Affect and Reports of Children's Behavior

ERIC Educational Resources Information Center

Karazsia, Bryan T.; Wildman, Beth G.

2009-01-01

Parenting behaviors have received ample support as a mediator of the relationship between maternal affect and child behavior problems. The majority of these research efforts were based on a uni-dimensional conceptualization of maternal mood, even though decades of theory and research suggest that mood is multidimensional. We examined the mediating…

Writing and Reading Multiplicity in the Uni-Verse: Engagements with Mathematics through Poetry

ERIC Educational Resources Information Center

Radakovic, Nenad; Jagger, Susan; Jao, Limin

2018-01-01

In this article, we explore the reading and writing of mathematical poetry from our experiences as mathematics teacher educators. First, we outline how our own engagement with mathematical poetry encouraged us to incorporate it into our teaching of pre-service teachers. We describe how our initial disappointment with the mathematical content of…

"La unión hace la fuerza": Community Organizing in Adult Education for Immigrants

ERIC Educational Resources Information Center

Carlock, Russell H., Jr.

2016-01-01

Adult English as a second language (ESL) educators have struggled to move beyond skills-based instruction to implement more student-centered, contextualized pedagogy that prepares students to become active citizens and to solve real-world problems, even as the growing number of immigrants make adult education increasingly important for determining…

Educational Expenditure in France, Japan and the United Kingdom. Les Depenses d'enseignement en France, au Japon et au Royaume-Uni.

ERIC Educational Resources Information Center

Levy-Garboua, Louis; And Others

This study is intended to improve analyses of the cost of education at both the national level and in international comparisons. Hitherto, international comparisons of educational costs have been hindered by the fact that governmental education budgets often include many noninstructional costs while excluding adult education costs and private…

Recasting Postcolonial Citizenship through Civic Education: Critical Perspectives on Zambia

ERIC Educational Resources Information Center

Abdi, Ali A.; Shizha, Edward; Bwalya, Ignatio

2006-01-01

Since the early 1990s and, perhaps, as one effect of the emergence of the uni-polar world, there have been a lot of "democratizing" activities in the Sub-Saharan context, with Zambia, a central African country of about 10 million, at the forefront of these processes. While democracy, in one form or another, has come to Zambia,…

China: A Country Study.

DTIC Science & Technology

1980-09-01

China. Washington: National Science Foundation, 1961. _ ’ Resarch and Development in Communist China: Mood, Management , and Measurement." Pages 549-78...publications manager , who gave this book thoughtful attention through a series of production stages. Grateful acknowledgment is given to Marty Ittner, who... Strategy , and Tactics-Organization and Equip- ment-Reeruitment and Conditions of Servioe-Uni- forms and Insignia of Rank-Training-THE PLACE OF THE MILITARY

High Cycle Fatigue (HCF) Science and Technology Program 2000 Annual Report

DTIC Science & Technology

2000-01-01

in an area of deep compressive stress. • Results of industry and government testing have indicated the ability to stop crack initiation and...fatigue crack nucleation process with the cyclic deformation behavior of the alloy for different microstructures and crystallographic texture ... texture combinations investigated, bimodal fine uni-rolled and lamellar cross-rolled displayed superior fatigue properties to the remaining four

77 FR 1748 - Atomic Safety and Licensing Board; Calvert Cliffs 3 Nuclear Project, LLC, and UniStar Nuclear...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-01-11

... observe this evidentiary hearing. However, all signs, banners, posters, demonstrations, and displays are... required by NRC policy, signs, banners, posters, and displays not larger than 18 x 18 will be permitted at..., banner, poster or display affixed to a stick, or similar device, will not be permitted at the oral...

Inflammatory Markers and Breast Cancer Risk

DTIC Science & Technology

2011-07-01

breast cancer [26, 27] or cytologic atypia [28], while another observed elevated IL-6 levels among breast cancer cases with insulin resistance [29...Relation between insulin resistance and serum concentrations of IL-6 and TNF- alpha in overweight or obese women with early stage breast cancer...without oophorectomy, hysterectomy with uni- or bilateral oophorectomy), prior breast biopsy (no, yes), ever been pregnant (no, yes), and

Parent weight change predicts child weight change in family-based weight control program for pre-school children (Buffalo healthy tots)

USDA-ARS?s Scientific Manuscript database

Title: PARENT WEIGHT CHANGE PREDICTS CHILD WEIGHT CHANGE IN FAMILY-BASED WEIGHT CONTROL PROGRAM FOR PRE-SCHOOL CHILDREN (BUFFALO HEALTHY TOTS), Teresa Quattrin, MOl, James N Roemmich, PhDI, Rocco Paluch, MAl, Jihnhee Yu, PhD2, Leonard H Epstein, PhDI and Michelle A Ecker, RD, CDEI . lpediatrics, Uni...

An Investigation into Why Students from Regional South Australia Choose to Study Business Programs in the Capital City

ERIC Educational Resources Information Center

Sawyer, Janet; Ellis, Bronwyn

2011-01-01

Although Business undergraduate studies are available at the University of South Australia's (UniSA) Centre for Regional Engagement (CRE), both at the Whyalla Campus and the Mount Gambier Regional Centre (MGRC), many students from regional South Australia choose to undertake Business degrees in Adelaide, the state capital, rather than locally.…

An Analysis of the Effects of Instructional Methods Upon Selected Outcomes of Instruction in an Interdisciplinary Science Unit.

ERIC Educational Resources Information Center

Thomas, Barbara Schalk

Studied was the effect of instructional method on educational outcomes in an interdisciplinary science uni t taught to 143 eighth grade students of earth science. Compared were the didactic and guided discovery methods of teaching. Also analyzed were the interactions of methods with student characteristics including sex, intelligence, creativity,…

Guidelines for Developing and Inserting Material Properties into the Code 65 Composite Material Database

DTIC Science & Technology

2011-12-01

kind of base fiber used Fab-ric uni, stitched, weave, woven roving, textile form, tape, prepreg Laminate Schedu le [0]10 [0]14 [0]36 Manufacturing...roving, textile form, tape, prepreg Laminate Schedule [0]10 [0]14 [0]36 Manufacturing Date 2006 Test Facility/Date 2007 Program of Record AHM&ST...9 Laminate Schedule .......................................................................................................10 Cure

Target Presentation Methodology for Tactical Field Evaluations

DTIC Science & Technology

1976-10-01

to making their observations. Finally, Sternberp and Banks J (during an investigation of search effectiveness with passive night vision...factors are likely to be more important in the acquisition process. ^J. Stemberg and J. Banks . Search Fffcstivcncss viih hwoive Nipht Vision...differently-colored low-contrast uni- forms (green field uniform and black pajama -type uniform) in a Jungle environment. They found that the

A Qualitative Study of the Lived Experiences of Disabled Post-Transition Students in Higher Education Institutions in Northern Ireland

ERIC Educational Resources Information Center

Redpath, Jennifer; Kearney, Patricia; Nicholl, Peter; Mulvenna, Maurice; Wallace, Jonathan; Martin, Suzanne

2013-01-01

This article provides a systematic analysis of 13 in-depth interviews of disabled students from universities in Northern Ireland. Undertaken as part of the Uni4U initiative, the findings presented describe barriers experienced by students with disabilities to participation in higher education. The students provided comments concerning their…

University for All Programs (ProUni): Engagement, Satisfaction, and Employability

ERIC Educational Resources Information Center

Felicetti, Vera Lucia

2017-01-01

A training at Higher Education level needs, in addition to improve the skills specific in the area chosen, to develop a set of skills and/or personal attributes that make him or her more likely to succeed in the profession. In this context, this paper was developed and has the objective to identify the relationships between engagement,…

76 FR 32994 - Nine Mile Point 3 Nuclear Project, LLC and Unistar Nuclear Operating Services, LLC; Combined...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-07

... December 1, 2009, UniStar Nuclear Energy (UNE), which is acting on behalf of the COL applicants Nine Mile... impacted by this exemption. Special Circumstances Special circumstances, in accordance with 10 CFR 50.12(a... exemption from 10 CFR 50.71(e)(3)(iii) exist. Eligibility for Categorical Exclusion From Environmental...

Getting Alice through the door: social science research and natural resource management

Treesearch

Alan W. Ewert

1995-01-01

A number of trends are altering the role of science in natural resource management. These trends include the growing political power of science, the recognition that most natural resource problems are extremely complex and not prone to uni-dimensional solutions, and the increasing need to integrate an understanding of the human component into the planning and decision-...

Going on to Uni? Access and Participation in University for Students from Backgrounds of Disadvantage

ERIC Educational Resources Information Center

Wilks, Judith; Wilson, Katie

2012-01-01

This article reports on a research project that investigated the aspirations of primary and secondary school students about access to, and participation in higher education. The research was undertaken at schools in low socio-economic status regional and rural areas of north-eastern New South Wales. The paper discusses the background to the…

The art of space-time

NASA Astrophysics Data System (ADS)

Cartlidge, Edwin

2018-01-01

The Museo Na­zionale delle Arti del XXI Secolo (MAXXI; National Museum of 21st Century Arts) in Rome has chosen Einstein as the figurehead of its latest exhibition, enti­tled Gravity. Imaging the Uni­verse After Einstein. Running until 29 April 2018, the exhibition explores "the meeting point of the current understanding of the cos­mos and contemporary art and thinking."

The Pfam protein families database.

PubMed

Punta, Marco; Coggill, Penny C; Eberhardt, Ruth Y; Mistry, Jaina; Tate, John; Boursnell, Chris; Pang, Ningze; Forslund, Kristoffer; Ceric, Goran; Clements, Jody; Heger, Andreas; Holm, Liisa; Sonnhammer, Erik L L; Eddy, Sean R; Bateman, Alex; Finn, Robert D

2012-01-01

Pfam is a widely used database of protein families, currently containing more than 13,000 manually curated protein families as of release 26.0. Pfam is available via servers in the UK (http://pfam.sanger.ac.uk/), the USA (http://pfam.janelia.org/) and Sweden (http://pfam.sbc.su.se/). Here, we report on changes that have occurred since our 2010 NAR paper (release 24.0). Over the last 2 years, we have generated 1840 new families and increased coverage of the UniProt Knowledgebase (UniProtKB) to nearly 80%. Notably, we have taken the step of opening up the annotation of our families to the Wikipedia community, by linking Pfam families to relevant Wikipedia pages and encouraging the Pfam and Wikipedia communities to improve and expand those pages. We continue to improve the Pfam website and add new visualizations, such as the 'sunburst' representation of taxonomic distribution of families. In this work we additionally address two topics that will be of particular interest to the Pfam community. First, we explain the definition and use of family-specific, manually curated gathering thresholds. Second, we discuss some of the features of domains of unknown function (also known as DUFs), which constitute a rapidly growing class of families within Pfam.

ddPCRclust - An R package and Shiny app for automated analysis of multiplexed ddPCR data.

PubMed

Brink, Benedikt G; Meskas, Justin; Brinkman, Ryan R

2018-03-09

Droplet digital PCR (ddPCR) is an emerging technology for quantifying DNA. By partitioning the target DNA into ∼20000 droplets, each serving as its own PCR reaction compartment, a very high sensitivity of DNA quantification can be achieved. However, manual analysis of the data is time consuming and algorithms for automated analysis of non-orthogonal, multiplexed ddPCR data are unavailable, presenting a major bottleneck for the advancement of ddPCR transitioning from low-throughput to high- throughput. ddPCRclust is an R package for automated analysis of data from Bio-Rad's droplet digital PCR systems (QX100 and QX200). It can automatically analyse and visualise multiplexed ddPCR experiments with up to four targets per reaction. Results are on par with manual analysis, but only take minutes to compute instead of hours. The accompanying Shiny app ddPCRvis provides easy access to the functionalities of ddPCRclust through a web-browser based GUI. R package: https://github.com/bgbrink/ddPCRclust; Interface: https://github.com/bgbrink/ddPCRvis/; Web: https://bibiserv.cebitec.uni-bielefeld.de/ddPCRvis/. bbrink@cebitec.uni-bielefeld.de.

Tanglegrams for rooted phylogenetic trees and networks

PubMed Central

Scornavacca, Celine; Zickmann, Franziska; Huson, Daniel H.

2011-01-01

Motivation: In systematic biology, one is often faced with the task of comparing different phylogenetic trees, in particular in multi-gene analysis or cospeciation studies. One approach is to use a tanglegram in which two rooted phylogenetic trees are drawn opposite each other, using auxiliary lines to connect matching taxa. There is an increasing interest in using rooted phylogenetic networks to represent evolutionary history, so as to explicitly represent reticulate events, such as horizontal gene transfer, hybridization or reassortment. Thus, the question arises how to define and compute a tanglegram for such networks. Results: In this article, we present the first formal definition of a tanglegram for rooted phylogenetic networks and present a heuristic approach for computing one, called the NN-tanglegram method. We compare the performance of our method with existing tree tanglegram algorithms and also show a typical application to real biological datasets. For maximum usability, the algorithm does not require that the trees or networks are bifurcating or bicombining, or that they are on identical taxon sets. Availability: The algorithm is implemented in our program Dendroscope 3, which is freely available from www.dendroscope.org. Contact: scornava@informatik.uni-tuebingen.de; huson@informatik.uni-tuebingen.de PMID:21685078

[A particular anthropometric method for the study of accessibility of a workstation].

PubMed

Molinaro, V; Del Ferraro, S

2008-01-01

One of the main factors which can involve musculo-skeletal disorders is the assumption of awkward postures. These lasts can be caused, in some cases, by a no-suitable collocation of some devices which are indispensable for the work. It is possible to evaluate if the chosen collocation is adequate or not by studying the accessibility of the workstation with a special regard for the accessibility of the devices placed inside the workstation. EN ISO 14738:2002 is a specific standard which has been adopted in Italy as UNI EN ISO 14738:2004. This standard gives some useful requirements, in terms of accessibility, to design a workstation at no-mobile machinery. In this study, the authors have analyzed a check out workstation by following the requirements described in UNI EN ISO 14738:2004. Critical aspects, related to the organization both of the work activities either of the workstation, have been highlighted taking into account standard criteria. Finally the authors make a new design of the check out workstation trying to optimize device collocation in order to reduce awkward postures. The new configuration has been investigated by applying the criteria mentioned in the standard.

The unique peptidome: Taxon-specific tryptic peptides as biomarkers for targeted metaproteomics.

PubMed

Mesuere, Bart; Van der Jeugt, Felix; Devreese, Bart; Vandamme, Peter; Dawyndt, Peter

2016-09-01

The Unique Peptide Finder (http://unipept.ugent.be/peptidefinder) is an interactive web application to quickly hunt for tryptic peptides that are unique to a particular species, genus, or any other taxon. Biodiversity within the target taxon is represented by a set of proteomes selected from a monthly updated list of complete and nonredundant UniProt proteomes, supplemented with proprietary proteomes loaded into persistent local browser storage. The software computes and visualizes pan and core peptidomes as unions and intersections of tryptic peptides occurring in the selected proteomes. In addition, it also computes and displays unique peptidomes as the set of all tryptic peptides that occur in all selected proteomes but not in any UniProt record not assigned to the target taxon. As a result, the unique peptides can serve as robust biomarkers for the target taxon, for example, in targeted metaproteomics studies. Computations are extremely fast since they are underpinned by the Unipept database, the lowest common ancestor algorithm implemented in Unipept and modern web technologies that facilitate in-browser data storage and parallel processing. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Comparison of methods for calculating conditional expectations of sufficient statistics for continuous time Markov chains.

PubMed

Tataru, Paula; Hobolth, Asger

2011-12-05

Continuous time Markov chains (CTMCs) is a widely used model for describing the evolution of DNA sequences on the nucleotide, amino acid or codon level. The sufficient statistics for CTMCs are the time spent in a state and the number of changes between any two states. In applications past evolutionary events (exact times and types of changes) are unaccessible and the past must be inferred from DNA sequence data observed in the present. We describe and implement three algorithms for computing linear combinations of expected values of the sufficient statistics, conditioned on the end-points of the chain, and compare their performance with respect to accuracy and running time. The first algorithm is based on an eigenvalue decomposition of the rate matrix (EVD), the second on uniformization (UNI), and the third on integrals of matrix exponentials (EXPM). The implementation in R of the algorithms is available at http://www.birc.au.dk/~paula/. We use two different models to analyze the accuracy and eight experiments to investigate the speed of the three algorithms. We find that they have similar accuracy and that EXPM is the slowest method. Furthermore we find that UNI is usually faster than EVD.

The Edinburgh Postnatal Depression Scale: Screening Tool for Postpartum Anxiety as Well? Findings from a Confirmatory Factor Analysis of the Hebrew Version.

PubMed

Bina, Rena; Harrington, Donna

2016-04-01

The Edinburgh Postnatal Depression Scale (EPDS) was originally created as a uni-dimensional scale to screen for postpartum depression (PPD); however, evidence from various studies suggests that it is a multi-dimensional scale measuring mainly anxiety in addition to depression. The factor structure of the EPDS seems to differ across various language translations, raising questions regarding its stability. This study examined the factor structure of the Hebrew version of the EPDS to assess whether it is uni- or multi-dimensional. Seven hundred and fifteen (n = 715) women were screened at 6 weeks postpartum using the Hebrew version of the EPDS. Confirmatory factor analysis (CFA) was used to test four models derived from the literature. Of the four CFA models tested, a 9-item two factor model fit the data best, with one factor representing an underlying depression construct and the other representing an underlying anxiety construct. for Practice The Hebrew version of the EPDS appears to consist of depression and anxiety sub-scales. Given the widespread PPD screening initiatives, anxiety symptoms should be addressed in addition to depressive symptoms, and a short scale, such as the EPDS, assessing both may be efficient.

Fast Detection of Copper Content in Rice by Laser-Induced Breakdown Spectroscopy with Uni- and Multivariate Analysis.

PubMed

Liu, Fei; Ye, Lanhan; Peng, Jiyu; Song, Kunlin; Shen, Tingting; Zhang, Chu; He, Yong

2018-02-27

Fast detection of heavy metals is very important for ensuring the quality and safety of crops. Laser-induced breakdown spectroscopy (LIBS), coupled with uni- and multivariate analysis, was applied for quantitative analysis of copper in three kinds of rice (Jiangsu rice, regular rice, and Simiao rice). For univariate analysis, three pre-processing methods were applied to reduce fluctuations, including background normalization, the internal standard method, and the standard normal variate (SNV). Linear regression models showed a strong correlation between spectral intensity and Cu content, with an R 2 more than 0.97. The limit of detection (LOD) was around 5 ppm, lower than the tolerance limit of copper in foods. For multivariate analysis, partial least squares regression (PLSR) showed its advantage in extracting effective information for prediction, and its sensitivity reached 1.95 ppm, while support vector machine regression (SVMR) performed better in both calibration and prediction sets, where R c 2 and R p 2 reached 0.9979 and 0.9879, respectively. This study showed that LIBS could be considered as a constructive tool for the quantification of copper contamination in rice.

Fast Detection of Copper Content in Rice by Laser-Induced Breakdown Spectroscopy with Uni- and Multivariate Analysis

PubMed Central

Ye, Lanhan; Song, Kunlin; Shen, Tingting

2018-01-01

Fast detection of heavy metals is very important for ensuring the quality and safety of crops. Laser-induced breakdown spectroscopy (LIBS), coupled with uni- and multivariate analysis, was applied for quantitative analysis of copper in three kinds of rice (Jiangsu rice, regular rice, and Simiao rice). For univariate analysis, three pre-processing methods were applied to reduce fluctuations, including background normalization, the internal standard method, and the standard normal variate (SNV). Linear regression models showed a strong correlation between spectral intensity and Cu content, with an R2 more than 0.97. The limit of detection (LOD) was around 5 ppm, lower than the tolerance limit of copper in foods. For multivariate analysis, partial least squares regression (PLSR) showed its advantage in extracting effective information for prediction, and its sensitivity reached 1.95 ppm, while support vector machine regression (SVMR) performed better in both calibration and prediction sets, where Rc2 and Rp2 reached 0.9979 and 0.9879, respectively. This study showed that LIBS could be considered as a constructive tool for the quantification of copper contamination in rice. PMID:29495445

The thyrotropin receptor mutation database: update 2003.

PubMed

Führer, Dagmar; Lachmund, Peter; Nebel, Istvan-Tibor; Paschke, Ralf

2003-12-01

In 1999 we have created a TSHR mutation database compiling TSHR mutations with their basic characteristics and associated clinical conditions (www.uni-leipzig.de/innere/tshr). Since then, more than 2887 users from 36 countries have logged into the TSHR mutation database and have contributed several valuable suggestions for further improvement of the database. We now present an updated and extended version of the TSHR database to which several novel features have been introduced: 1. detailed functional characteristics on all 65 mutations (43 activating and 22 inactivating mutations) reported to date, 2. 40 pedigrees with detailed information on molecular aspects, clinical courses and treatment options in patients with gain-of-function and loss-of-function germline TSHR mutations, 3. a first compilation of site-directed mutagenesis studies, 4. references with Medline links, 5. a user friendly search tool for specific database searches, user-specific database output and 6. an administrator tool for the submission of novel TSHR mutations. The TSHR mutation database is installed as one of the locus specific HUGO mutation databases. It is listed under index TSHR 603372 (http://ariel.ucs.unimelb.edu.au/~cotton/glsdbq.htm) and can be accessed via www.uni-leipzig.de/innere/tshr.

UniVIO: A Multiple Omics Database with Hormonome and Transcriptome Data from Rice

PubMed Central

Sakurai, Tetsuya; Sakakibara, Hitoshi

2013-01-01

Plant hormones play important roles as signaling molecules in the regulation of growth and development by controlling the expression of downstream genes. Since the hormone signaling system represents a complex network involving functional cross-talk through the mutual regulation of signaling and metabolism, a comprehensive and integrative analysis of plant hormone concentrations and gene expression is important for a deeper understanding of hormone actions. We have developed a database named Uniformed Viewer for Integrated Omics (UniVIO: http://univio.psc.riken.jp/), which displays hormone-metabolome (hormonome) and transcriptome data in a single formatted (uniformed) heat map. At the present time, hormonome and transcriptome data obtained from 14 organ parts of rice plants at the reproductive stage and seedling shoots of three gibberellin signaling mutants are included in the database. The hormone concentration and gene expression data can be searched by substance name, probe ID, gene locus ID or gene description. A correlation search function has been implemented to enable users to obtain information of correlated substance accumulation and gene expression. In the correlation search, calculation method, range of correlation coefficient and plant samples can be selected freely. PMID:23314752

Reuse of steel slag in bituminous paving mixtures.

PubMed

Sorlini, Sabrina; Sanzeni, Alex; Rondi, Luca

2012-03-30

This paper presents a comprehensive study to evaluate the mechanical properties and environmental suitability of electric arc furnace (EAF) steel slag in bituminous paving mixtures. A variety of tests were executed on samples of EAF slag to characterize the physical, geometrical, mechanical and chemical properties as required by UNI EN specifications, focusing additionally on the volumetric expansion associated with hydration of free CaO and MgO. Five bituminous mixtures of aggregates for flexible road pavement were designed containing up to 40% of EAF slag and were tested to determine Marshall stability and indirect tensile strength. The leaching behaviour of slag samples and bituminous mixtures was evaluated according to the UNI EN leaching test. The tested slag showed satisfactory physical and mechanical properties and a release of pollutants generally below the limits set by the Italian code. Tests on volume stability of fresh materials confirmed that a period of 2-3 months is necessary to reduce effects of oxides hydration. The results of tests performed on bituminous mixtures with EAF slag were comparable with the performance of mixtures containing natural aggregates and the leaching tests provided satisfactory results. Copyright © 2012 Elsevier B.V. All rights reserved.

The salt-responsive transcriptome of chickpea roots and nodules via deepSuperSAGE

PubMed Central

2011-01-01

Background The combination of high-throughput transcript profiling and next-generation sequencing technologies is a prerequisite for genome-wide comprehensive transcriptome analysis. Our recent innovation of deepSuperSAGE is based on an advanced SuperSAGE protocol and its combination with massively parallel pyrosequencing on Roche's 454 sequencing platform. As a demonstration of the power of this combination, we have chosen the salt stress transcriptomes of roots and nodules of the third most important legume crop chickpea (Cicer arietinum L.). While our report is more technology-oriented, it nevertheless addresses a major world-wide problem for crops generally: high salinity. Together with low temperatures and water stress, high salinity is responsible for crop losses of millions of tons of various legume (and other) crops. Continuously deteriorating environmental conditions will combine with salinity stress to further compromise crop yields. As a good example for such stress-exposed crop plants, we started to characterize salt stress responses of chickpeas on the transcriptome level. Results We used deepSuperSAGE to detect early global transcriptome changes in salt-stressed chickpea. The salt stress responses of 86,919 transcripts representing 17,918 unique 26 bp deepSuperSAGE tags (UniTags) from roots of the salt-tolerant variety INRAT-93 two hours after treatment with 25 mM NaCl were characterized. Additionally, the expression of 57,281 transcripts representing 13,115 UniTags was monitored in nodules of the same plants. From a total of 144,200 analyzed 26 bp tags in roots and nodules together, 21,401 unique transcripts were identified. Of these, only 363 and 106 specific transcripts, respectively, were commonly up- or down-regulated (>3.0-fold) under salt stress in both organs, witnessing a differential organ-specific response to stress. Profiting from recent pioneer works on massive cDNA sequencing in chickpea, more than 9,400 UniTags were able to be linked to UniProt entries. Additionally, gene ontology (GO) categories over-representation analysis enabled to filter out enriched biological processes among the differentially expressed UniTags. Subsequently, the gathered information was further cross-checked with stress-related pathways. From several filtered pathways, here we focus exemplarily on transcripts associated with the generation and scavenging of reactive oxygen species (ROS), as well as on transcripts involved in Na+ homeostasis. Although both processes are already very well characterized in other plants, the information generated in the present work is of high value. Information on expression profiles and sequence similarity for several hundreds of transcripts of potential interest is now available. Conclusions This report demonstrates, that the combination of the high-throughput transcriptome profiling technology SuperSAGE with one of the next-generation sequencing platforms allows deep insights into the first molecular reactions of a plant exposed to salinity. Cross validation with recent reports enriched the information about the salt stress dynamics of more than 9,000 chickpea ESTs, and enlarged their pool of alternative transcripts isoforms. As an example for the high resolution of the employed technology that we coin deepSuperSAGE, we demonstrate that ROS-scavenging and -generating pathways undergo strong global transcriptome changes in chickpea roots and nodules already 2 hours after onset of moderate salt stress (25 mM NaCl). Additionally, a set of more than 15 candidate transcripts are proposed to be potential components of the salt overly sensitive (SOS) pathway in chickpea. Newly identified transcript isoforms are potential targets for breeding novel cultivars with high salinity tolerance. We demonstrate that these targets can be integrated into breeding schemes by micro-arrays and RT-PCR assays downstream of the generation of 26 bp tags by SuperSAGE. PMID:21320317

The salt-responsive transcriptome of chickpea roots and nodules via deepSuperSAGE.

PubMed

Molina, Carlos; Zaman-Allah, Mainassara; Khan, Faheema; Fatnassi, Nadia; Horres, Ralf; Rotter, Björn; Steinhauer, Diana; Amenc, Laurie; Drevon, Jean-Jacques; Winter, Peter; Kahl, Günter

2011-02-14

The combination of high-throughput transcript profiling and next-generation sequencing technologies is a prerequisite for genome-wide comprehensive transcriptome analysis. Our recent innovation of deepSuperSAGE is based on an advanced SuperSAGE protocol and its combination with massively parallel pyrosequencing on Roche's 454 sequencing platform. As a demonstration of the power of this combination, we have chosen the salt stress transcriptomes of roots and nodules of the third most important legume crop chickpea (Cicer arietinum L.). While our report is more technology-oriented, it nevertheless addresses a major world-wide problem for crops generally: high salinity. Together with low temperatures and water stress, high salinity is responsible for crop losses of millions of tons of various legume (and other) crops. Continuously deteriorating environmental conditions will combine with salinity stress to further compromise crop yields. As a good example for such stress-exposed crop plants, we started to characterize salt stress responses of chickpeas on the transcriptome level. We used deepSuperSAGE to detect early global transcriptome changes in salt-stressed chickpea. The salt stress responses of 86,919 transcripts representing 17,918 unique 26 bp deepSuperSAGE tags (UniTags) from roots of the salt-tolerant variety INRAT-93 two hours after treatment with 25 mM NaCl were characterized. Additionally, the expression of 57,281 transcripts representing 13,115 UniTags was monitored in nodules of the same plants. From a total of 144,200 analyzed 26 bp tags in roots and nodules together, 21,401 unique transcripts were identified. Of these, only 363 and 106 specific transcripts, respectively, were commonly up- or down-regulated (>3.0-fold) under salt stress in both organs, witnessing a differential organ-specific response to stress.Profiting from recent pioneer works on massive cDNA sequencing in chickpea, more than 9,400 UniTags were able to be linked to UniProt entries. Additionally, gene ontology (GO) categories over-representation analysis enabled to filter out enriched biological processes among the differentially expressed UniTags. Subsequently, the gathered information was further cross-checked with stress-related pathways. From several filtered pathways, here we focus exemplarily on transcripts associated with the generation and scavenging of reactive oxygen species (ROS), as well as on transcripts involved in Na+ homeostasis. Although both processes are already very well characterized in other plants, the information generated in the present work is of high value. Information on expression profiles and sequence similarity for several hundreds of transcripts of potential interest is now available. This report demonstrates, that the combination of the high-throughput transcriptome profiling technology SuperSAGE with one of the next-generation sequencing platforms allows deep insights into the first molecular reactions of a plant exposed to salinity. Cross validation with recent reports enriched the information about the salt stress dynamics of more than 9,000 chickpea ESTs, and enlarged their pool of alternative transcripts isoforms. As an example for the high resolution of the employed technology that we coin deepSuperSAGE, we demonstrate that ROS-scavenging and -generating pathways undergo strong global transcriptome changes in chickpea roots and nodules already 2 hours after onset of moderate salt stress (25 mM NaCl). Additionally, a set of more than 15 candidate transcripts are proposed to be potential components of the salt overly sensitive (SOS) pathway in chickpea. Newly identified transcript isoforms are potential targets for breeding novel cultivars with high salinity tolerance. We demonstrate that these targets can be integrated into breeding schemes by micro-arrays and RT-PCR assays downstream of the generation of 26 bp tags by SuperSAGE.

Glutamate quantification by PRESS or MEGA-PRESS: Validation, repeatability, and concordance.

PubMed

van Veenendaal, Tamar M; Backes, Walter H; van Bussel, Frank C G; Edden, Richard A E; Puts, Nicolaas A J; Aldenkamp, Albert P; Jansen, Jacobus F A

2018-05-01

While PRESS is often employed to measure glutamate concentrations, MEGA-PRESS enables simultaneous Glx (glutamate and glutamine) and GABA measurements. This study aimed to compare validation, repeatability, and concordance of different approaches for glutamate quantification at 3T to aid future studies in their selection of the appropriate sequence and quantification method. Nine phantoms with different glutamate and glutamine concentrations and five healthy participants were scanned twice to assess respectively the validation and repeatability of measurements with PRESS and MEGA-PRESS. To assess concordance between the different methods, results from 95 human participants were compared. PRESS, MEGA-PRESS (i.e. difference), and the MEGA-PRESS OFF spectra were analyzed with both LCModel and Gannet. In vitro, excellent agreement was shown between actual and measured glutamate concentrations for all measurements (r>0.98). In vivo CVs were better for PRESS (2.9%) than MEGA-PRESS (4.9%) and MEGA-PRESS OFF (4.2%). However, the concordance between the sequences was low (PRESS and MEGA-PRESS OFF, r=0.3) to modest (MEGA-PRESS versus MEGA-PRESS OFF, r=0.8). Both PRESS and MEGA-PRESS can be employed to measure in vivo glutamate concentrations, although PRESS shows a better repeatability. Comparisons between in vivo glutamate measures of different sequences however need to be interpreted cautiously. Copyright © 2018 Elsevier Inc. All rights reserved.

University Presses: Problems and Prospects.

ERIC Educational Resources Information Center

Meeker, Robert B.

Historical information on university presses and their problems are considered. University presses in the United States have their roots in 15th century England when the Oxford University Press was established in 1478. The first U.S. press to use the term "university press" was Cornell University; the press operated from 1869 until it…

The Center for Regenerative Biology and Medicine at Mount Desert Island Biological Laboratory

DTIC Science & Technology

2015-08-01

TERMS limb regeneration Positional Memory Code Axolotl microRNAs Zebrafish Polypterus 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT 18...injury induced regeneration of limbs/appendage tissues in Ambystoma ( axolotl ) and Polypterus animals. The defining feature of limb/appendage...downregulated in UPREGULATED DOWNREGULATED Figure 1: Venn diagram of UniProt protein sequence IDs among Axolotl and Polypterus contigs that

76 FR 3927 - Ameren Missouri; Combined License Application for Callaway Plant Unit 2; Exemption

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-21

... for a single unit of AREVA NP's U.S. EPR in accordance with the requirements of Title 10 of the Code... application is based upon and linked to the U.S. EPR reference COL (RCOL) application for UniStar's Calvert... U.S. EPR. 2.0 Request/Action The regulations specified in 10 CFR 50.71(e)(3)(iii) require that an...

Preliminary Evaluation of Methods for Classifying Forest Site Productivity Based on Species Composition in Western North Carolina

Treesearch

W. Henry McNab; F. Thomas Lloyd; David L. Loftis

2002-01-01

The species indicator approach to forest site classification was evaluated for 210 relatively undisturbed plots established by the USDA Forest Service Forest Inventory and Analysis uni (FIA) in western North Carolina. Plots were classified by low, medium, and high levels of productivity based on 10-year individual tree basal area increment data standardized for initial...

On the Law of Inertia. Translation of: Ueber das Beharrungsgesetz

NASA Astrophysics Data System (ADS)

Lange, Ludwig

2014-04-01

This article is a translation of Ludwig Lange: "Ueber das Beharrungsgesetz" in: Berichte ueber Verhandlungen der Koenigl. Saechsischen Gesellschaft der Wissenschaften, math.-physik. Klasse (Leipzig, 1885), SS. 333-351. Translated by Herbert Pfister, Institut für Theoretische Physik, Universität Tübingen, Auf der Morgenstelle 14, 72076 Tübingen, Germany; herbert.pfister@uni-tuebingen.de. Kind assistance by Julian Barbour is acknowledged.

"Because Uni Is Totally Different than What You Do at TAFE": Protective Strategies and Provisions for Diploma Students Traversing Their First Professional Experience Placement at University

ERIC Educational Resources Information Center

Hadley, Fay; Andrews, Rebecca

2015-01-01

Students who enrol in a Bachelor of Education (Early Childhood Education) at the Institute of Early Childhood, Macquarie University, with a Diploma in Children's Services attained from a Technical and Further Education (TAFE) institution or a Registered Training Organisation (RTO) often experience challenges in their first professional experience…

STS (Space Transportation System) Task Simulator.

DTIC Science & Technology

1985-08-15

3 Clohessy - Wiltshire Coordinate System • • -1 1- .M 1°... "p ’. -. .’- 0 . _ -~:Q ~. ... . .o. ., 1. INTRODUCTION The Space Transportation System...motion is obtained by applying the Clohessy - Wiltshire equations for terminal rendezvous/docking with the earth modeled as a uni- form sphere...rotational accelerations to the present quaternions. The Clohessy - Wiltshire equations for terminal rendezvous/dockinq are used to model orbital drift

Endocannabinoids as a Target for the Treatment of Traumatic Brain Injury

DTIC Science & Technology

2016-01-01

an RNeasy Plus Uni- versal Mini Kit (Qiagen, Valencia, CA), according to the manu- facturer’s instructions. Total RNA was reverse transcribed using...one-way ANOVA. 18 Figure 10. Mini excitatory post-synaptic currents (mEPSCs) recorded from rat cortex (site...stress sensitivity, anhedonia, impulse control deficits, sleep disturbances, and pain sensitivity.6–10 The initial mechanical insult induces increased

Dual and self-curing potential of self-adhesive resin cements as thin films.

PubMed

Moraes, R R; Boscato, N; Jardim, P S; Schneider, L F J

2011-01-01

In this study, the dual- and self-curing potential of self-adhesive resin cements (SARCs) as thin, clinically-relevant cement films was investigated. The SARCs tested were: BisCem (BSC; Bisco), Maxcem Elite (MXE; Kerr), RelyX Unicem clicker (UNI; 3M ESPE), seT capsule (SET; SDI), and SmartCem 2 (SC2; Dentsply Caulk). The conventional cement RelyX ARC (3M ESPE) was tested as a reference. The degree of conversion (DC) as a function of time was evaluated by real-time Fourier transform infrared spectroscopy with an attenuated total reflectance (ATR) device. The cements were either photoactivated for 40 seconds (dual-cure mode) or not photoactivated (self-cure mode). The cement film thickness was 50 ± 10 μm. The DC (%) was evaluated 1, 5, 10, 15, 20, 25, and 30 minutes after placing the cement on the ATR cell. Data for DC as a function of time were analyzed by two-way repeated measures analysis of variance (ANOVA). DC values at 30 minutes for the self- and dual-cure modes were submitted to one-way ANOVA. Post hoc comparisons were performed using the Student-Newman-Keuls test (p<0.05). The rate and the extent of conversion were lower for the SARCs compared with the conventional cement. Means ± standard deviations (SD) for the dual-cure mode at 30 minutes were: 75 ± 5 (ARC)a, 73 ± 8 (SET)a, 61 ± 4 (MXE)b, 51 ± 9 (BSC)c, 51 ± 4 (UNI)c, and 48 ± 3 (SC2)c, while in the self-cure mode means and SD were 62 ± 6 (ARC)a, 54 ± 3 (MXE)b, 40 ± 6 (SC2)c, 35 ± 2 (UNI)c, 35 ± 3 (SET)c, and 11 ± 3 (BSC)d. The DC for the dual-cure mode was generally higher than the self-cure, irrespective of the time. Discrepancies in DC between the dual- and self-cure modes from 11% to 79% were observed. In conclusion, SARCs may present slower rate of polymerization and lower final DC than conventional resin cements, in either the dual- or self-cure mode.

Intercomparison of OMI NO2 and HCHO air mass factor calculations: recommendations and best practices for retrievals

NASA Astrophysics Data System (ADS)

Lorente Delgado, Alba; Klaas Boersma, Folkert; Hilboll, Andreas; Richter, Andreas; Yu, Huan; van Roozendael, Michel; Dörner, Steffen; Wagner, Thomas; Barkley, Michael; Lamsal, Lok; Lin, Jintai; Liu, Mengyao

2016-04-01

We present a detailed comparison of the air mass factor (AMF) calculation process used by various research groups for OMI satellite retrievals of NO2 and HCHO. Although satellite retrievals have strongly improved over the last decades, there is still a need to better understand and reduce the uncertainties associated with every retrieval step of satellite data products, such as the AMF calculation. Here we compare and evaluate the different approaches used to calculate AMFs by several scientific groups (KNMI (WUR), IASB-BIRA, IUP-UNI. BREMEN, MPI-C, NASA GSFC, LEICESTER UNI. and PEKING UNI.). Each group calculated altitude dependent (box-) AMFs and clear sky and total tropospheric AMFs for several OMI orbits. First, European groups computed AMFs for one OMI orbit using common settings for the choice of surface albedo data, terrain height, cloud treatment and a priori vertical profile. Second, every group computed AMFs for two complete days in different seasons using preferred settings for the ancillary data and cloud treatment as a part of a Round Robin exercise. Box-AMFs comparison showed good consistency and underlined the importance of a correct treatment of the physical processes affecting the effective light path and the vertical discretization of the atmosphere. Using common settings, tropospheric NO2 AMFs in polluted pixels on average agreed within 4.7% whereas in remote pixels agreed within 3.5%. Using preferred settings relative differences between AMFs increase up to 15-30%. This increase is traced back to the different choices and assumptions made throughout the AMF calculation, which affect the final AMF values and thus the uncertainty in the AMF calculation. Differences between state of the art cloud treatment approaches highlight the importance of an accurate cloud correction: total and clear sky AMFs in polluted conditions differ by up to 40% depending on the retrieval scenario. Based on the comparison results, specific recommendations on best practices are given and they will be used in QA4ECV community effort retrieval algorithm to be applied in past and future UV/Vis instrumentation for generating quality assured multi decadal NO2 and HCHO records.

The CE3R Network: current status and future perspectives

NASA Astrophysics Data System (ADS)

Lenhardt, Wolfgang; Pesaresi, Damiano; Živčić, Mladen; Costa, Giovanni; Kuk, Kresimir; Bondár, István; Duni, Llambro; Spacek, Petr

2016-04-01

In order to improve the monitoring of seismic activities in the border regions and to enhance the collaboration between countries and seismological institutions in Central Europe, the Environment Agency of the Slovenian Republic (ARSO), the Italian National Institute for Oceanography and Experimental Geophysics (OGS), the University of Trieste (UniTS) and the Austrian Central Institute for Meteorology and Geodynamics (ZAMG) established in 2001 the "South Eastern Alps Transfrontier Seismological Network". In May 2014 ARSO, OGS, UniTS and ZAMG agreed to formalize the transfrontier network, to name it "Central and East European Earthquake Research Network", (CE3RN or CE3R Network) in order to locate it geographically since cross-border networks can be established in other areas of the world and to expand their cooperation, including institutions in other countries. The University of Zagreb (UniZG) joined CE3RN in October 2014. The Kövesligethy Radó Seismological Observatory (KRSZO) of the Hungarian Academy of Sciences joined CE3RN in October 2015. The Institute of Geosciences, Energy, Water and Environment (IGEWE) of the Polytechnic University of Tirana joined CE3RN in November 2015. The Institute of Physics of the Earth (IPE) of the Masaryk University in Brno joined CE3RN in November 2015. CE3RN Parties intend to formalize and possibly extend their ongoing cooperation in the field of seismological data acquisition, exchange and use for seismological and earthquake engineering and civil protection purposes. The purpose of this cooperation is to retain and expand the existing cross-border network, specify the rules of conduct in the network management, improvements, extensions and enlargements, enhance seismological research in the region, and support civil protection activities. Since the formal establishment of CE3RN, several common projects have been completed, like the SeismoSAT project for the seismic data center connection over satellite funded by the Interreg IV-A Italy-Austria program, and the Earthquake Early Warning System (EEWS) PRESTo@CE3RN. We will here briefly introduce original and new CE3RN Parties, with a synthesis of the common results achieved so far and an indication of possible future developments.

A graph kernel approach for alignment-free domain–peptide interaction prediction with an application to human SH3 domains

PubMed Central

Kundu, Kousik; Costa, Fabrizio; Backofen, Rolf

2013-01-01

Motivation: State-of-the-art experimental data for determining binding specificities of peptide recognition modules (PRMs) is obtained by high-throughput approaches like peptide arrays. Most prediction tools applicable to this kind of data are based on an initial multiple alignment of the peptide ligands. Building an initial alignment can be error-prone, especially in the case of the proline-rich peptides bound by the SH3 domains. Results: Here, we present a machine-learning approach based on an efficient graph-kernel technique to predict the specificity of a large set of 70 human SH3 domains, which are an important class of PRMs. The graph-kernel strategy allows us to (i) integrate several types of physico-chemical information for each amino acid, (ii) consider high-order correlations between these features and (iii) eliminate the need for an initial peptide alignment. We build specialized models for each human SH3 domain and achieve competitive predictive performance of 0.73 area under precision-recall curve, compared with 0.27 area under precision-recall curve for state-of-the-art methods based on position weight matrices. We show that better models can be obtained when we use information on the noninteracting peptides (negative examples), which is currently not used by the state-of-the art approaches based on position weight matrices. To this end, we analyze two strategies to identify subsets of high confidence negative data. The techniques introduced here are more general and hence can also be used for any other protein domains, which interact with short peptides (i.e. other PRMs). Availability: The program with the predictive models can be found at http://www.bioinf.uni-freiburg.de/Software/SH3PepInt/SH3PepInt.tar.gz. We also provide a genome-wide prediction for all 70 human SH3 domains, which can be found under http://www.bioinf.uni-freiburg.de/Software/SH3PepInt/Genome-Wide-Predictions.tar.gz. Contact: backofen@informatik.uni-freiburg.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23813002

New Design Concept for an Excavator Arms by Using Composite Material

NASA Astrophysics Data System (ADS)

Solazzi, L.; Assi, A.; Ceresoli, F.

2018-06-01

The purpose of the present paper is to lightweight design an excavator arms, by using a different materials and in particular composite material. Specifically, the research is based on the study of a commercial excavator, by determining its geometry and analyzing the load conditions to which it is exposed. These are determined in relation to either the load diagram of the machine or the possible utilities of the excavator, such as the rotation of the machine. The materials used and implemented in the different analytical and numerical elaborations are classic construction steel S 355 (UNI EN 10025-3), high-resistance steel S 890 (UNI EN 10025-6), aluminum Al 6063 T6 (UNI EN 573-3) and the composite material made by carbon fiber and epoxy resin. The adopted constraints for the design of new arms with different materials, non-conventional for these applications, are numerous. The new solutions must present a safety factor either with respect to the yield tensile strength or to the critical load of buckling greater than or equal to the one determined for the excavator in its original geometrical conformation. Another criterion, which has heavily conditioned the geometry of the arms, was given by the fact that the developed solutions must present a very similar value of the maximum displacement in the different load conditions analyzed. A new geometry for arms made by composite material was developed. It was an elliptical conic section, instead of the classic rectangular section, in order to use the filament winding technological process. As for the adoption of the composite material, we focused on the study and the design of this material as long as the interaction with the extremities (made of aluminum) which are interfaced either with the link between the arms or with the elements of the hydraulic plant which serves for the arms movement. From the results developed, it emerges that the solution developed by adopting composite materials is the one that permits the maximum weight reduction for all arms, about 68.1%, which can be seen as an increment of the maximum mass transportable about 45.5% i.e. passing from 5000 kg to 7277 kg.

The 2016 NIST Speaker Recognition Evaluation

DTIC Science & Technology

2017-08-20

The 2016 NIST Speaker Recognition Evaluation Seyed Omid Sadjadi1,∗, Timothée Kheyrkhah1,†, Audrey Tong1, Craig Greenberg1, Douglas Reynolds2, Elliot...recent in an ongoing series of speaker recognition evaluations (SRE) to foster research in ro- bust text-independent speaker recognition, as well as...online evaluation platform, a fixed training data condition, more variability in test segment duration (uni- formly distributed between 10s and 60s

Low-Level Outflow Potential of Non-Tornadic Thunderstorms Inferred from Single-Doppler Radar

DTIC Science & Technology

1988-01-01

10) MNGATE(3) , MIGATE (3) ,NFLD,ELCNT, * + BD.ANGE .ERANGE COMMON/PARMS/IVOL,KVOL,SN ,FN COMMON/WNITS! ITJNT, JUN17 ,KUN DIMENSION R01(3) ,DRI(3) ,MPG(3... MIGATE (ILOOP) NO (IOOP) - NXIATE (ILOOP) -MNGITE(ILOOP) +1I!8 FCAGNTINUE E RED(UNI ) AZ 1),NIT DO 1 ILOP-1,NLD DONUNT 58 LOP1,N(IOOP)N K~~~EI UNIT) BICNT

Properties of Urea-Doped Ice in the CRREL Test Basin,

DTIC Science & Technology

1983-03-01

thickness versus initial ice thickness at start of warm-up ................ 7 9. Thin sections of urea-doped ice...following section ) on the mechanical properties of the tank, essential for achieving an ice sheet of uni- the model ice was investigated. In particular...Figure 1. elastic foundation: Measurements ~i 7 A 1 f 2 Temperature As mentioned in the preceding section , water and temperature was measured with a 1/50

Precision Airdrop (Largage de precision)

DTIC Science & Technology

2005-12-01

NAVIGATION TO A PRECISION AIRDROP OVERVIEW RTO-AG-300-V24 2 - 9 the point from various compass headings. As the tests are conducted, the resultant...rate. This approach avoids including a magnetic compass for the heading reference, which has difficulties due to local changes in the magnetic field...Scientifica della Difesa ROYAUME-UNI Via XX Settembre 123 Dstl Knowledge Services ESPAGNE 00187 Roma Information Centre, Building 247 SDG TECEN / DGAM

Daring to Care: The Role of Culturally Relevant Care in Mentoring Black and Latino Male High School Students

ERIC Educational Resources Information Center

Watson, Wanda; Sealey-Ruiz, Yolanda; Jackson, Iesha

2016-01-01

This study seeks to challenge the uni-dimensional way care in school is written about by highlighting an often overlooked aspect of care--the kind that students do for each other. Data is drawn from focus groups conducted with the youth participants and founder of Umoja Network for Young Men (UMOJA), an all-male, school-based mentoring program for…

Environmental and Cultural Impact. Proposed Tennessee Colony Reservoir, Trinity River, Texas. Volume I. Summary Report.

DTIC Science & Technology

1972-01-01

high populations of phytoplankton and periphyton , indi- cate excessive eutrophic conditions. Rates of primary production are comparatively high. The...species of algae in the phytoplankton and periphyton are those .commonly associated with organic pollution, and the high numbers for total coliform...uni- quely important geological areas within or adjacent to the proposed project area. Other geologically related pheno- 4 I mena and of potential

DeepText2GO: Improving large-scale protein function prediction with deep semantic text representation.

PubMed

You, Ronghui; Huang, Xiaodi; Zhu, Shanfeng

2018-06-06

As of April 2018, UniProtKB has collected more than 115 million protein sequences. Less than 0.15% of these proteins, however, have been associated with experimental GO annotations. As such, the use of automatic protein function prediction (AFP) to reduce this huge gap becomes increasingly important. The previous studies conclude that sequence homology based methods are highly effective in AFP. In addition, mining motif, domain, and functional information from protein sequences has been found very helpful for AFP. Other than sequences, alternative information sources such as text, however, may be useful for AFP as well. Instead of using BOW (bag of words) representation in traditional text-based AFP, we propose a new method called DeepText2GO that relies on deep semantic text representation, together with different kinds of available protein information such as sequence homology, families, domains, and motifs, to improve large-scale AFP. Furthermore, DeepText2GO integrates text-based methods with sequence-based ones by means of a consensus approach. Extensive experiments on the benchmark dataset extracted from UniProt/SwissProt have demonstrated that DeepText2GO significantly outperformed both text-based and sequence-based methods, validating its superiority. Copyright © 2018 Elsevier Inc. All rights reserved.

Modular rate laws for enzymatic reactions: thermodynamics, elasticities and implementation.

PubMed

Liebermeister, Wolfram; Uhlendorf, Jannis; Klipp, Edda

2010-06-15

Standard rate laws are a key requisite for systematically turning metabolic networks into kinetic models. They should provide simple, general and biochemically plausible formulae for reaction velocities and reaction elasticities. At the same time, they need to respect thermodynamic relations between the kinetic constants and the metabolic fluxes and concentrations. We present a family of reversible rate laws for reactions with arbitrary stoichiometries and various types of regulation, including mass-action, Michaelis-Menten and uni-uni reversible Hill kinetics as special cases. With a thermodynamically safe parameterization of these rate laws, parameter sets obtained by model fitting, sampling or optimization are guaranteed to lead to consistent chemical equilibrium states. A reformulation using saturation values yields simple formulae for rates and elasticities, which can be easily adjusted to the given stationary flux distributions. Furthermore, this formulation highlights the role of chemical potential differences as thermodynamic driving forces. We compare the modular rate laws to the thermodynamic-kinetic modelling formalism and discuss a simplified rate law in which the reaction rate directly depends on the reaction affinity. For automatic handling of modular rate laws, we propose a standard syntax and semantic annotations for the Systems Biology Markup Language. An online tool for inserting the rate laws into SBML models is freely available at www.semanticsbml.org. Supplementary data are available at Bioinformatics online.

Lifespan development of the bilateral deficit in a simple reaction time task.

PubMed

Vieluf, Solveig; Aschersleben, Gisa; Panzer, Stefan

2017-04-01

Performing an action at a maximum speed or with a maximum strength simultaneously with two limbs leads to a lower performance than the sum of unimanual performances. This phenomenon is known as bilateral deficit. There is some evidence that the bilateral deficit changes over the lifespan, in a way that children and older adults show lower deficits than young adults. Inverse developmental changes of childrens' and older adults' brain structures connecting both hemispheres, i.e., the corpus callosum, might importantly contribute to this phenomenon. The seemingly similar developments have been observed with different experimental protocols in the different age groups, respectively. To test for similarities and differences in changes of the bilateral deficit at critical periods of the lifespan development of bimanual actions, children, young adults, and older adults performed a simple reaction time task uni- and bimanually. Reaction times and the resulting bilateral deficit, as well as reaction time variability were analyzed. As expected, reaction times were different for the young adults between the uni- and the bimanual task. Children and older adults performed both conditions with similar reaction times. However, a difference in the direction of the %bilateral deficit occurred between the two age groups. The findings demonstrated an absence of the bilateral deficit for children, but not for younger and older adults.

Multi-phasic bi-directional chemotactic responses of the growth cone

PubMed Central

Naoki, Honda; Nishiyama, Makoto; Togashi, Kazunobu; Igarashi, Yasunobu; Hong, Kyonsoo; Ishii, Shin

2016-01-01

The nerve growth cone is bi-directionally attracted and repelled by the same cue molecules depending on the situations, while other non-neural chemotactic cells usually show uni-directional attraction or repulsion toward their specific cue molecules. However, how the growth cone differs from other non-neural cells remains unclear. Toward this question, we developed a theory for describing chemotactic response based on a mathematical model of intracellular signaling of activator and inhibitor. Our theory was first able to clarify the conditions of attraction and repulsion, which are determined by balance between activator and inhibitor, and the conditions of uni- and bi-directional responses, which are determined by dose-response profiles of activator and inhibitor to the guidance cue. With biologically realistic sigmoidal dose-responses, our model predicted tri-phasic turning response depending on intracellular Ca2+ level, which was then experimentally confirmed by growth cone turning assays and Ca2+ imaging. Furthermore, we took a reverse-engineering analysis to identify balanced regulation between CaMKII (activator) and PP1 (inhibitor) and then the model performance was validated by reproducing turning assays with inhibitions of CaMKII and PP1. Thus, our study implies that the balance between activator and inhibitor underlies the multi-phasic bi-directional turning response of the growth cone. PMID:27808115

Dental plaque development on a hydroxyapatite disk in young adults observed by using a barcoded pyrosequencing approach

PubMed Central

Takeshita, Toru; Yasui, Masaki; Shibata, Yukie; Furuta, Michiko; Saeki, Yoji; Eshima, Nobuoki; Yamashita, Yoshihisa

2015-01-01

Dental plaque is a dynamic microbial biofilm ecosystem that comprises hundreds of species including difficult-to-cultivate bacteria. We observed the assembly of a plaque bacterial community through 16S rRNA gene analysis. Plaque samples that accumulated on a hydroxyapatite disk for 1, 2, 3, 4, 5, and 7 days with saliva on day 0 were collected from 19 young adults using a removable resin splint. Quantitative PCR analysis showed that the total bacterial amount gradually increased and reached a plateau on day 4. Barcoded pyrosequencing analysis revealed that the microbial richness and diversity particularly increased between days 5 and 7. A principal coordinate analysis plot based on unweighted UniFrac showed the community assembly in a time-related manner, which became increasingly similar to the salivary microbiota. Facultative anaerobic bacteria such as Streptococcus, Neisseria, Abiotrophia, Gemella, and Rothia were predominant in the plaque bacterial community in the earlier days, whereas obligate anaerobes, such as Porphyromonas, Fusobacterium, Prevotella, and Capnocytophaga showed increased dominance on later days. UniFrac analysis also demonstrated that dental caries experience had a significant effect on the assembly process. Our results reveal the development pattern of the plaque bacterial community as well as the inter-individual differences associated with dental caries experience. PMID:25633431

Elastic coupling of limb joints enables faster bipedal walking

PubMed Central

Dean, J.C.; Kuo, A.D.

2008-01-01

The passive dynamics of bipedal limbs alone are sufficient to produce a walking motion, without need for control. Humans augment these dynamics with muscles, actively coordinated to produce stable and economical walking. Present robots using passive dynamics walk much slower, perhaps because they lack elastic muscles that couple the joints. Elastic properties are well known to enhance running gaits, but their effect on walking has yet to be explored. Here we use a computational model of dynamic walking to show that elastic joint coupling can help to coordinate faster walking. In walking powered by trailing leg push-off, the model's speed is normally limited by a swing leg that moves too slowly to avoid stumbling. A uni-articular spring about the knee allows faster but uneconomical walking. A combination of uni-articular hip and knee springs can speed the legs for improved speed and economy, but not without the swing foot scuffing the ground. Bi-articular springs coupling the hips and knees can yield high economy and good ground clearance similar to humans. An important parameter is the knee-to-hip moment arm that greatly affects the existence and stability of gaits, and when selected appropriately can allow for a wide range of speeds. Elastic joint coupling may contribute to the economy and stability of human gait. PMID:18957360