WorldWideScience

Sample records for connecting sequence information

  1. Spreading Sequence System for Full Connectivity Relay Network

    Science.gov (United States)

    Kwon, Hyuck M. (Inventor); Yang, Jie (Inventor); Pham, Khanh D. (Inventor)

    2018-01-01

    Fully connected uplink and downlink fully connected relay network systems using pseudo-noise spreading and despreading sequences subjected to maximizing the signal-to-interference-plus-noise ratio. The relay network systems comprise one or more transmitting units, relays, and receiving units connected via a communication network. The transmitting units, relays, and receiving units each may include a computer for performing the methods and steps described herein and transceivers for transmitting and/or receiving signals. The computer encodes and/or decodes communication signals via optimum adaptive PN sequences found by employing Cholesky decompositions and singular value decompositions (SVD). The PN sequences employ channel state information (CSI) to more effectively and more securely computing the optimal sequences.

  2. MedlinePlus Connect: Technical Information

    Science.gov (United States)

    ... MedlinePlus Connect → Technical Information URL of this page: https://medlineplus.gov/connect/technical.html MedlinePlus Connect: Technical ... will change.) Old URLs New URLs Web Application https://apps.nlm.nih.gov/medlineplus/services/mpconnect.cfm? ...

  3. Information decomposition method to analyze symbolical sequences

    International Nuclear Information System (INIS)

    Korotkov, E.V.; Korotkova, M.A.; Kudryashov, N.A.

    2003-01-01

    The information decomposition (ID) method to analyze symbolical sequences is presented. This method allows us to reveal a latent periodicity of any symbolical sequence. The ID method is shown to have advantages in comparison with application of the Fourier transformation, the wavelet transform and the dynamic programming method to look for latent periodicity. Examples of the latent periods for poetic texts, DNA sequences and amino acids are presented. Possible origin of a latent periodicity for different symbolical sequences is discussed

  4. Sequencing Information Management System (SIMS). Final report

    Energy Technology Data Exchange (ETDEWEB)

    Fields, C.

    1996-02-15

    A feasibility study to develop a requirements analysis and functional specification for a data management system for large-scale DNA sequencing laboratories resulted in a functional specification for a Sequencing Information Management System (SIMS). This document reports the results of this feasibility study, and includes a functional specification for a SIMS relational schema. The SIMS is an integrated information management system that supports data acquisition, management, analysis, and distribution for DNA sequencing laboratories. The SIMS provides ad hoc query access to information on the sequencing process and its results, and partially automates the transfer of data between laboratory instruments, analysis programs, technical personnel, and managers. The SIMS user interfaces are designed for use by laboratory technicians, laboratory managers, and scientists. The SIMS is designed to run in a heterogeneous, multiplatform environment in a client/server mode. The SIMS communicates with external computational and data resources via the internet.

  5. Autonomous informational stability in connective tissues.

    Science.gov (United States)

    Brand, R A

    1992-02-01

    No coherent theories currently explain connective tissue stability (i.e. 'memory') as well as spatial and temporal adaptability in the face of continual flux of its constituents. Furthermore, explanations of stability based exclusively upon DNA raise certain inherent problems, particularly with the spatial concordance of somatic tissues. As an alternative explanation, it is hypothesized that while connective tissue cells produce extracellular protein precursors through DNA-dependent processes, the assembly, location, orientation and configuration of the extracellular macromolecules as well as their degree of cell attachment depend primarily upon local micro-environmental conditions and/or self-organization rather than strictly cellular processes. The resulting extracellular matrix (ECM) serves as a time- and spatially-variable filter about each cell to afford a relatively consistent micro-environment for all similar cells, regardless of the more variable macro-environment. By insuring a consistent set of signals to the cell, the filter provides a non-genetic memory complementary to genetic memory. The half-lives of constituent molecules define the duration of the filter, allowing the filter to adapt to new environmental demands, yet to maintain a consistent milieu for the cell. The cell/matrix construct permits local, self-optimizing, non-deterministic tissue autonomy obviating the need to postulate certain intricate mechanisms coordinating spatial morphology and temporal behavior.

  6. Connecting Formal and Informal Learning Experiences

    Science.gov (United States)

    O'Mahony, Timothy Kieran

    The learning study reports on part of a larger project being lead by the author. In this dissertation I explore one goal of this project---to understand effects on student learning outcomes as a function of using different methods for connecting out-of-school experiential learning with formal school-based instruction. There is a long history of assuming that "experience is the best teacher"(e.g. Aristotle, 360 BC; Dewey, 1934; Kolb, 1997; Pliny, AD 77). As a practical geographer I endorsed that assumption throughout my teaching career, paying attention to local topography, physical features, and natural resources in the geographic hinterland. I was particularly interested in understanding the impact of the physical landscape on humankind, and reciprocally, noting humankind's widespread impressions on the natural world. Until I began this research project, I assumed that everyone else paid a similar attention to immediate surroundings. The work that I describe in this dissertation emerges out of a conviction that there are many degrees of truth to the idea that experience is a great teacher. Its effectiveness seems to depend on how one's "experience" is mediated, and how "learning from it" is defined. This motivated me to think about design principles for linking people's experiences to learning. I began to explore, experimentally, how I might enhance people's abilities to notice, represent, and discuss their experiences in order to better learn from them. This study investigated how different ways of connecting outdoor learning experiences to formal schooling impacts students' performance. I studied high-school students in outdoor settings as they engaged in evocative issues of learning pertaining to consequential everyday life encounters. Different kinds of "expert mediation" were introduced and tested as the students engaged in investigative activities around the science of dam removal and habitat restoration. I measured outcomes with the aid of pre- and

  7. Connections, Information and Reality: Thinking about the internet of things

    Directory of Open Access Journals (Sweden)

    Ben Van Lier

    2011-10-01

    Full Text Available The number of connections between people, organizations and technology is proliferating rapidly, and the amount of information they produce, exchange and share is increasing accordingly. These connections and the information they produce are defining and shaping our daily life and work and our perception of reality. Computers in all forms are becoming smaller and less visible, but they are omnipresent. This development of information technology ‘everyware’, as Greenfield calls it, is also referred to as ubiquitous computing. With the development of ubiquitous computing, computers not only disappear from our perception, but also from our experience. When these new and almost invisible technological devices are tied together, for instance in the Internet of Things, the information resulting from that connection will be more than the sum of its parts. The Internet is the place where subjects are connected and where they exchange and share information. With the development of the ‘Internet of things’, the Internet will also connect objects and enable them to exchange and share information. In this Internet of the future, subjects and objects are more and more connected in random coalitions and networks on the basis of information. These new connections and their seamless exchanging and sharing of information will challenge traditional organizational structures. The information produced in networks will be used for changes to our existing reality and will help create a new reality. Will this development of subjects and objects connected in networks raise new questions and challenges for science and for the development of knowledge within a changing reality?

  8. Management Information, Decision Sciences, and Financial Economics : a connection

    NARCIS (Netherlands)

    C-L. Chang (Chia-Lin); M.J. McAleer (Michael); W.-K. Wong (Wing-Keung)

    2018-01-01

    markdownabstractThe paper provides a brief review of the connecting literature in management information, decision sciences, and financial economics, and discusses some research that is related to the three cognate disciplines. Academics could develop theoretical models and subsequent

  9. An information theory framework for dynamic functional domain connectivity.

    Science.gov (United States)

    Vergara, Victor M; Miller, Robyn; Calhoun, Vince

    2017-06-01

    Dynamic functional network connectivity (dFNC) analyzes time evolution of coherent activity in the brain. In this technique dynamic changes are considered for the whole brain. This paper proposes an information theory framework to measure information flowing among subsets of functional networks call functional domains. Our method aims at estimating bits of information contained and shared among domains. The succession of dynamic functional states is estimated at the domain level. Information quantity is based on the probabilities of observing each dynamic state. Mutual information measurement is then obtained from probabilities across domains. Thus, we named this value the cross domain mutual information (CDMI). Strong CDMIs were observed in relation to the subcortical domain. Domains related to sensorial input, motor control and cerebellum form another CDMI cluster. Information flow among other domains was seldom found. Other methods of dynamic connectivity focus on whole brain dFNC matrices. In the current framework, information theory is applied to states estimated from pairs of multi-network functional domains. In this context, we apply information theory to measure information flow across functional domains. Identified CDMI clusters point to known information pathways in the basal ganglia and also among areas of sensorial input, patterns found in static functional connectivity. In contrast, CDMI across brain areas of higher level cognitive processing follow a different pattern that indicates scarce information sharing. These findings show that employing information theory to formally measured information flow through brain domains reveals additional features of functional connectivity. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. Motor sequence learning-induced neural efficiency in functional brain connectivity.

    Science.gov (United States)

    Karim, Helmet T; Huppert, Theodore J; Erickson, Kirk I; Wollam, Mariegold E; Sparto, Patrick J; Sejdić, Ervin; VanSwearingen, Jessie M

    2017-02-15

    Previous studies have shown the functional neural circuitry differences before and after an explicitly learned motor sequence task, but have not assessed these changes during the process of motor skill learning. Functional magnetic resonance imaging activity was measured while participants (n=13) were asked to tap their fingers to visually presented sequences in blocks that were either the same sequence repeated (learning block) or random sequences (control block). Motor learning was associated with a decrease in brain activity during learning compared to control. Lower brain activation was noted in the posterior parietal association area and bilateral thalamus during the later periods of learning (not during the control). Compared to the control condition, we found the task-related motor learning was associated with decreased connectivity between the putamen and left inferior frontal gyrus and left middle cingulate brain regions. Motor learning was associated with changes in network activity, spatial extent, and connectivity. Copyright © 2016 Elsevier B.V. All rights reserved.

  11. High value of ecological information for river connectivity restoration

    Science.gov (United States)

    Sethi, Suresh; O'Hanley, Jesse R.; Gerken, Jonathon; Ashline, Joshua; Bradley, Catherine

    2017-01-01

    ContextEfficient restoration of longitudinal river connectivity relies on barrier mitigation prioritization tools that incorporate stream network spatial structure to maximize ecological benefits given limited resources. Typically, ecological benefits of barrier mitigation are measured using proxies such as the amount of accessible riverine habitat.ObjectivesWe developed an optimization approach for barrier mitigation planning which directly incorporates the ecology of managed taxa, and applied it to an urbanizing salmon-bearing watershed in Alaska.MethodsA novel river connectivity metric that exploits information on the distribution and movement of managed taxon was embedded into a barrier prioritization framework to identify optimal mitigation actions given limited restoration budgets. The value of ecological information on managed taxa was estimated by comparing costs to achieve restoration targets across alternative barrier prioritization approaches.ResultsBarrier mitigation solutions informed by life history information outperformed those using only river connectivity proxies, demonstrating high value of ecological information for watershed restoration. In our study area, information on salmon ecology was typically valued at 0.8–1.2 M USD in costs savings to achieve a given benefit level relative to solutions derived only from stream network information, equating to 16–28% of the restoration budget.ConclusionsInvesting in ecological studies may achieve win–win outcomes of improved understanding of aquatic ecology and greater watershed restoration efficiency.

  12. Image encryption using random sequence generated from generalized information domain

    International Nuclear Information System (INIS)

    Zhang Xia-Yan; Wu Jie-Hua; Zhang Guo-Ji; Li Xuan; Ren Ya-Zhou

    2016-01-01

    A novel image encryption method based on the random sequence generated from the generalized information domain and permutation–diffusion architecture is proposed. The random sequence is generated by reconstruction from the generalized information file and discrete trajectory extraction from the data stream. The trajectory address sequence is used to generate a P-box to shuffle the plain image while random sequences are treated as keystreams. A new factor called drift factor is employed to accelerate and enhance the performance of the random sequence generator. An initial value is introduced to make the encryption method an approximately one-time pad. Experimental results show that the random sequences pass the NIST statistical test with a high ratio and extensive analysis demonstrates that the new encryption scheme has superior security. (paper)

  13. The"minimum information about an environmental sequence" (MIENS) specification

    Energy Technology Data Exchange (ETDEWEB)

    Yilmaz, P.; Kottmann, R.; Field, D.; Knight, R.; Cole, J.R.; Amaral-Zettler, L.; Gilbert, J.A.; Karsch-Mizrachi, I.; Johnston, A.; Cochrane, G.; Vaughan, R.; Hunter, C.; Park, J.; Morrison, N.; Rocca-Serra, P.; Sterk, P.; Arumugam, M.; Baumgartner, L.; Birren, B.W.; Blaser, M.J.; Bonazzi, V.; Bork, P.; Buttigieg, P. L.; Chain, P.; Costello, E.K.; Huot-Creasy, H.; Dawyndt, P.; DeSantis, T.; Fierer, N.; Fuhrman, J.; Gallery, R.E.; Gibbs, R.A.; Giglio, M.G.; Gil, I. San; Gonzalez, A.; Gordon, J.I.; Guralnick, R.; Hankeln, W.; Highlander, S.; Hugenholtz, P.; Jansson, J.; Kennedy, J.; Knights, D.; Koren, O.; Kuczynski, J.; Kyrpides, N.; Larsen, R.; Lauber, C.L.; Legg, T.; Ley, R.E.; Lozupone, C.A.; Ludwig, W.; Lyons, D.; Maguire, E.; Methe, B.A.; Meyer, F.; Nakieny, S.; Nelson, K.E.; Nemergut, D.; Neufeld, J.D.; Pace, N.R.; Palanisamy, G.; Peplies, J.; Peterson, J.; Petrosino, J.; Proctor, L.; Raes, J.; Ratnasingham, S.; Ravel, J.; Relman, D.A.; Assunta-Sansone, S.; Schriml, L.; Sodergren, E.; Spor, A.; Stombaugh, J.; Tiedje, J.M.; Ward, D.V.; Weinstock, G.M.; Wendel, D.; White, O.; Wikle, A.; Wortman, J.R.; Glockner, F.O.; Bushman, F.D.; Charlson, E.; Gevers, D.; Kelley, S.T.; Neubold, L.K.; Oliver, A.E.; Pruesse, E.; Quast, C.; Schloss, P.D.; Sinha, R.; Whitely, A.

    2010-10-15

    We present the Genomic Standards Consortium's (GSC) 'Minimum Information about an ENvironmental Sequence' (MIENS) standard for describing marker genes. Adoption of MIENS will enhance our ability to analyze natural genetic diversity across the Tree of Life as it is currently being documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere.

  14. 78 FR 34175 - Proposed Information Collection (Request for Employment Information in Connection With Claim for...

    Science.gov (United States)

    2013-06-06

    ... techniques or the use of other forms of information technology. Title: Request for Employment Information in... (Request for Employment Information in Connection With Claim for Disability Benefits) Activity: Comment...: Extension of a currently approved collection. Abstract: VA Form 21-4192 is used to request employment...

  15. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

    DEFF Research Database (Denmark)

    Yilmaz, Pelin; Kottmann, Renzo; Field, Dawn

    2011-01-01

    Here we present a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences--the minimum information about a marker gene sequence (MIMARKS). We also introduce a system for describing the environment from which a biological sample originates. The 'environment...

  16. PIMS sequencing extension: a laboratory information management system for DNA sequencing facilities

    Directory of Open Access Journals (Sweden)

    Baldwin Stephen A

    2011-03-01

    Full Text Available Abstract Background Facilities that provide a service for DNA sequencing typically support large numbers of users and experiment types. The cost of services is often reduced by the use of liquid handling robots but the efficiency of such facilities is hampered because the software for such robots does not usually integrate well with the systems that run the sequencing machines. Accordingly, there is a need for software systems capable of integrating different robotic systems and managing sample information for DNA sequencing services. In this paper, we describe an extension to the Protein Information Management System (PIMS that is designed for DNA sequencing facilities. The new version of PIMS has a user-friendly web interface and integrates all aspects of the sequencing process, including sample submission, handling and tracking, together with capture and management of the data. Results The PIMS sequencing extension has been in production since July 2009 at the University of Leeds DNA Sequencing Facility. It has completely replaced manual data handling and simplified the tasks of data management and user communication. Samples from 45 groups have been processed with an average throughput of 10000 samples per month. The current version of the PIMS sequencing extension works with Applied Biosystems 3130XL 96-well plate sequencer and MWG 4204 or Aviso Theonyx liquid handling robots, but is readily adaptable for use with other combinations of robots. Conclusions PIMS has been extended to provide a user-friendly and integrated data management solution for DNA sequencing facilities that is accessed through a normal web browser and allows simultaneous access by multiple users as well as facility managers. The system integrates sequencing and liquid handling robots, manages the data flow, and provides remote access to the sequencing results. The software is freely available, for academic users, from http://www.pims-lims.org/.

  17. PIMS sequencing extension: a laboratory information management system for DNA sequencing facilities.

    Science.gov (United States)

    Troshin, Peter V; Postis, Vincent Lg; Ashworth, Denise; Baldwin, Stephen A; McPherson, Michael J; Barton, Geoffrey J

    2011-03-07

    Facilities that provide a service for DNA sequencing typically support large numbers of users and experiment types. The cost of services is often reduced by the use of liquid handling robots but the efficiency of such facilities is hampered because the software for such robots does not usually integrate well with the systems that run the sequencing machines. Accordingly, there is a need for software systems capable of integrating different robotic systems and managing sample information for DNA sequencing services. In this paper, we describe an extension to the Protein Information Management System (PIMS) that is designed for DNA sequencing facilities. The new version of PIMS has a user-friendly web interface and integrates all aspects of the sequencing process, including sample submission, handling and tracking, together with capture and management of the data. The PIMS sequencing extension has been in production since July 2009 at the University of Leeds DNA Sequencing Facility. It has completely replaced manual data handling and simplified the tasks of data management and user communication. Samples from 45 groups have been processed with an average throughput of 10000 samples per month. The current version of the PIMS sequencing extension works with Applied Biosystems 3130XL 96-well plate sequencer and MWG 4204 or Aviso Theonyx liquid handling robots, but is readily adaptable for use with other combinations of robots. PIMS has been extended to provide a user-friendly and integrated data management solution for DNA sequencing facilities that is accessed through a normal web browser and allows simultaneous access by multiple users as well as facility managers. The system integrates sequencing and liquid handling robots, manages the data flow, and provides remote access to the sequencing results. The software is freely available, for academic users, from http://www.pims-lims.org/.

  18. Critical connections: personal learning environments and information literacy

    Directory of Open Access Journals (Sweden)

    Alison Hicks

    2015-01-01

    Full Text Available Personal learning environments (PLEs and critical information literacies (CILs are two concepts that have been presented as responses to the challenges of the rich and complex information landscape. While both approaches support learners’ critical engagement with new information environments, each was developed within a different field. This paper connects and contrasts PLEs and CILs in order to explore the design of pedagogical responses to the information environment. Through a careful examination of PLE and CIL literature, the paper demonstrates that information literacy education intersects with the concepts and goals of PLEs. As such, the authors suggest that PLE scholarship informed by CIL scholarship, and vice versa, will yield a deeper understanding of modern learning contexts as well as a more holistic and responsive learner framework. The example of the research assignment will be used to demonstrate the viability of this approach. With these propositions, the authors invite educators, librarians and information technologists to engage in a dialogue about these concepts and the potential for pedagogical change.

  19. Negative sequence current control in wind power plants with VSC-HVDC connection

    DEFF Research Database (Denmark)

    Chaudhary, Sanjay; Teodorescu, Remus; Rodriguez, Pedro

    2012-01-01

    Large offshore wind power plants may have multi-MW wind turbine generators (WTG) equipped with full-scale converters (FSC) and voltage source converter (VSC) based high voltaage direct-current (HVDC) transmission for grid connection. The power electronic converters in theWTG-FSC and the VSC......-HVDC allow fast current control in the offshore grid. This paper presents a method of controlling the negative sequence current injection into the offshore grid from the VSC-HVDC as well as WTG-FSCs. This would minimize the power oscillations and hence reduce the dc voltage overshoots in the VSC-HVDC system...... as well as in the WTG-FSCs; especially when the offshore grid is unbalanced due to asymmetric faults. The formulation for negative sequence current injection is mathematically derived and then implemented in electromagnetic transients (EMT) simulation model. The simulated results show that the negative...

  20. Human genome and genetic sequencing research and informed consent

    International Nuclear Information System (INIS)

    Iwakawa, Mayumi

    2003-01-01

    On March 29, 2001, the Ethical Guidelines for Human Genome and Genetic Sequencing Research were established. They have intended to serve as ethical guidelines for all human genome and genetic sequencing research practice, for the purpose of upholding respect for human dignity and rights and enforcing use of proper methods in the pursuit of human genome and genetic sequencing research, with the understanding and cooperation of the public. The RadGenomics Project has prepared a research protocol and informed consent document that follow these ethical guidelines. We have endeavored to protect the privacy of individual information, and have established a procedure for examination of research practices by an ethics committee. Here we report our procedure in order to offer this concept to the patients. (authors)

  1. MACSIMS : multiple alignment of complete sequences information management system

    Directory of Open Access Journals (Sweden)

    Plewniak Frédéric

    2006-06-01

    Full Text Available Abstract Background In the post-genomic era, systems-level studies are being performed that seek to explain complex biological systems by integrating diverse resources from fields such as genomics, proteomics or transcriptomics. New information management systems are now needed for the collection, validation and analysis of the vast amount of heterogeneous data available. Multiple alignments of complete sequences provide an ideal environment for the integration of this information in the context of the protein family. Results MACSIMS is a multiple alignment-based information management program that combines the advantages of both knowledge-based and ab initio sequence analysis methods. Structural and functional information is retrieved automatically from the public databases. In the multiple alignment, homologous regions are identified and the retrieved data is evaluated and propagated from known to unknown sequences with these reliable regions. In a large-scale evaluation, the specificity of the propagated sequence features is estimated to be >99%, i.e. very few false positive predictions are made. MACSIMS is then used to characterise mutations in a test set of 100 proteins that are known to be involved in human genetic diseases. The number of sequence features associated with these proteins was increased by 60%, compared to the features available in the public databases. An XML format output file allows automatic parsing of the MACSIM results, while a graphical display using the JalView program allows manual analysis. Conclusion MACSIMS is a new information management system that incorporates detailed analyses of protein families at the structural, functional and evolutionary levels. MACSIMS thus provides a unique environment that facilitates knowledge extraction and the presentation of the most pertinent information to the biologist. A web server and the source code are available at http://bips.u-strasbg.fr/MACSIMS/.

  2. Representation of protein-sequence information by amino acid subalphabets

    DEFF Research Database (Denmark)

    Andersen, C.A.F.; Brunak, Søren

    2004-01-01

    -sequence information, using machine learning strategies, where the primary goal is the discovery of novel powerful representations for use in AI techniques. In the case of proteins and the 20 different amino acids they typically contain, it is also a secondary goal to discover how the current selection of amino acids...

  3. Biocompatibility Evaluation of EndoSequence Root Repair Paste in the Connective Tissue of Rats.

    Science.gov (United States)

    Taha, Nessrin A; Safadi, Rima A; Alwedaie, Manal S

    2016-10-01

    The aim of this study was to evaluate the subcutaneous connective tissue response to EndoSequence root repair paste (Brasseler, Savannah, GA) compared with mineral trioxide aggregate (MTA). Thirty-six Wistar rats each received 3 sterile tubes, containing 1 of the tested materials and control. The animals were killed 1, 3 and 6 weeks after implantation. The specimens were evaluated histologically for type of inflammation, intensity and extent of inflammatory cells, foreign body reaction, fibrous capsule thickness, perivascular fragments, calcific deposits and vascular congestion. EndoSequence provoked severe inflammation after 1 week, which was significantly different from MTA and control (P ˂ .05), with fragmented particles and foreign body reaction. MTA showed tissue-tolerance features almost comparable to control. EndoSequence was significantly more irritating than MTA and control at 1 and 3 weeks in terms of severity and extent of inflammation. After 6 weeks it displayed more biocompatible characteristics. Copyright © 2016 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

  4. Applications of statistical physics and information theory to the analysis of DNA sequences

    Science.gov (United States)

    Grosse, Ivo

    2000-10-01

    DNA carries the genetic information of most living organisms, and the of genome projects is to uncover that genetic information. One basic task in the analysis of DNA sequences is the recognition of protein coding genes. Powerful computer programs for gene recognition have been developed, but most of them are based on statistical patterns that vary from species to species. In this thesis I address the question if there exist universal statistical patterns that are different in coding and noncoding DNA of all living species, regardless of their phylogenetic origin. In search for such species-independent patterns I study the mutual information function of genomic DNA sequences, and find that it shows persistent period-three oscillations. To understand the biological origin of the observed period-three oscillations, I compare the mutual information function of genomic DNA sequences to the mutual information function of stochastic model sequences. I find that the pseudo-exon model is able to reproduce the mutual information function of genomic DNA sequences. Moreover, I find that a generalization of the pseudo-exon model can connect the existence and the functional form of long-range correlations to the presence and the length distributions of coding and noncoding regions. Based on these theoretical studies I am able to find an information-theoretical quantity, the average mutual information (AMI), whose probability distributions are significantly different in coding and noncoding DNA, while they are almost identical in all studied species. These findings show that there exist universal statistical patterns that are different in coding and noncoding DNA of all studied species, and they suggest that the AMI may be used to identify genes in different living species, irrespective of their taxonomic origin.

  5. Protein Function Prediction Based on Sequence and Structure Information

    KAUST Repository

    Smaili, Fatima Z.

    2016-05-25

    The number of available protein sequences in public databases is increasing exponentially. However, a significant fraction of these sequences lack functional annotation which is essential to our understanding of how biological systems and processes operate. In this master thesis project, we worked on inferring protein functions based on the primary protein sequence. In the approach we follow, 3D models are first constructed using I-TASSER. Functions are then deduced by structurally matching these predicted models, using global and local similarities, through three independent enzyme commission (EC) and gene ontology (GO) function libraries. The method was tested on 250 “hard” proteins, which lack homologous templates in both structure and function libraries. The results show that this method outperforms the conventional prediction methods based on sequence similarity or threading. Additionally, our method could be improved even further by incorporating protein-protein interaction information. Overall, the method we use provides an efficient approach for automated functional annotation of non-homologous proteins, starting from their sequence.

  6. Immunization Information System and Informatics to Promote Immunizations: Perspective From Minnesota Immunization Information Connection.

    Science.gov (United States)

    Muscoplat, Miriam Halstead; Rajamani, Sripriya

    2017-01-01

    The vision for management of immunization information is availability of real-time consolidated data and services for all ages, to clinical, public health, and other stakeholders. This is being executed through Immunization Information Systems (IISs), which are population-based and confidential computerized systems present in most US states and territories. Immunization Information Systems offer many functionalities, such as immunization assessment reports, client follow-up, reminder/recall feature, vaccine management tools, state-supplied vaccine ordering, comprehensive immunization history, clinical decision support/vaccine forecasting and recommendations, data processing, and data exchange. This perspective article will present various informatics tools in an IIS, in the context of the Minnesota Immunization Information Connection.

  7. LTD windows of the STDP learning rule and synaptic connections having a large transmission delay enable robust sequence learning amid background noise.

    Science.gov (United States)

    Hayashi, Hatsuo; Igarashi, Jun

    2009-06-01

    Spike-timing-dependent synaptic plasticity (STDP) is a simple and effective learning rule for sequence learning. However, synapses being subject to STDP rules are readily influenced in noisy circumstances because synaptic conductances are modified by pre- and postsynaptic spikes elicited within a few tens of milliseconds, regardless of whether those spikes convey information or not. Noisy firing existing everywhere in the brain may induce irrelevant enhancement of synaptic connections through STDP rules and would result in uncertain memory encoding and obscure memory patterns. We will here show that the LTD windows of the STDP rules enable robust sequence learning amid background noise in cooperation with a large signal transmission delay between neurons and a theta rhythm, using a network model of the entorhinal cortex layer II with entorhinal-hippocampal loop connections. The important element of the present model for robust sequence learning amid background noise is the symmetric STDP rule having LTD windows on both sides of the LTP window, in addition to the loop connections having a large signal transmission delay and the theta rhythm pacing activities of stellate cells. Above all, the LTD window in the range of positive spike-timing is important to prevent influences of noise with the progress of sequence learning.

  8. Always look on both sides: phylogenetic information conveyed by simple sequence repeat allele sequences.

    Directory of Open Access Journals (Sweden)

    Stéphanie Barthe

    Full Text Available Simple sequence repeat (SSR markers are widely used tools for inferences about genetic diversity, phylogeography and spatial genetic structure. Their applications assume that variation among alleles is essentially caused by an expansion or contraction of the number of repeats and that, accessorily, mutations in the target sequences follow the stepwise mutation model (SMM. Generally speaking, PCR amplicon sizes are used as direct indicators of the number of SSR repeats composing an allele with the data analysis either ignoring the extent of allele size differences or assuming that there is a direct correlation between differences in amplicon size and evolutionary distance. However, without precisely knowing the kind and distribution of polymorphism within an allele (SSR and the associated flanking region (FR sequences, it is hard to say what kind of evolutionary message is conveyed by such a synthetic descriptor of polymorphism as DNA amplicon size. In this study, we sequenced several SSR alleles in multiple populations of three divergent tree genera and disentangled the types of polymorphisms contained in each portion of the DNA amplicon containing an SSR. The patterns of diversity provided by amplicon size variation, SSR variation itself, insertions/deletions (indels, and single nucleotide polymorphisms (SNPs observed in the FRs were compared. Amplicon size variation largely reflected SSR repeat number. The amount of variation was as large in FRs as in the SSR itself. The former contributed significantly to the phylogenetic information and sometimes was the main source of differentiation among individuals and populations contained by FR and SSR regions of SSR markers. The presence of mutations occurring at different rates within a marker's sequence offers the opportunity to analyse evolutionary events occurring on various timescales, but at the same time calls for caution in the interpretation of SSR marker data when the distribution of within

  9. CISAPS: Complex Informational Spectrum for the Analysis of Protein Sequences

    Directory of Open Access Journals (Sweden)

    Charalambos Chrysostomou

    2015-01-01

    Full Text Available Complex informational spectrum analysis for protein sequences (CISAPS and its web-based server are developed and presented. As recent studies show, only the use of the absolute spectrum in the analysis of protein sequences using the informational spectrum analysis is proven to be insufficient. Therefore, CISAPS is developed to consider and provide results in three forms including absolute, real, and imaginary spectrum. Biologically related features to the analysis of influenza A subtypes as presented as a case study in this study can also appear individually either in the real or imaginary spectrum. As the results presented, protein classes can present similarities or differences according to the features extracted from CISAPS web server. These associations are probable to be related with the protein feature that the specific amino acid index represents. In addition, various technical issues such as zero-padding and windowing that may affect the analysis are also addressed. CISAPS uses an expanded list of 611 unique amino acid indices where each one represents a different property to perform the analysis. This web-based server enables researchers with little knowledge of signal processing methods to apply and include complex informational spectrum analysis to their work.

  10. Risk-Informed Selection of Steel Connections for Seismic Zones

    Directory of Open Access Journals (Sweden)

    De León-Escobedo D.

    2011-04-01

    Full Text Available The findings about the fragile behavior of steel welded connections after the Northridge 1994 earthquake, specially for frames designed to withstand lateral force, has brought an amount of new attention to the design and safety issues of the welded connections for structures located on seismic zones. In México, practitioners and designers are wondering about the seismic effectiveness of the several kinds of connections as used in steel structures. A decision must be made to balance the safety required with the costs incurred after exceeding the serviceability limit state. Structural reliability techniques provide the proper framework to include the inherent uncertainties into the design process. Registered motions after the 1985 Mexico City earthquake are properly scaled according to the seismic hazard curve for soft soil in Mexico City. Earthquake occurrence is modeled as a Poisson process and the expected life-cycle cost is taken as the decision criteria. Parametric analyses allow the identification of dominant variables and ranges where one option is more recommendable than the other one. The proposed formulation may support designers and builders for the decision making process about the selection of the convenient connection type for the seismic zones with soft soil in Mexico City.

  11. The minimum information about a genome sequence (MIGS) specification

    Science.gov (United States)

    Field, Dawn; Garrity, George; Gray, Tanya; Morrison, Norman; Selengut, Jeremy; Sterk, Peter; Tatusova, Tatiana; Thomson, Nicholas; Allen, Michael J; Angiuoli, Samuel V; Ashburner, Michael; Axelrod, Nelson; Baldauf, Sandra; Ballard, Stuart; Boore, Jeffrey; Cochrane, Guy; Cole, James; Dawyndt, Peter; De Vos, Paul; dePamphilis, Claude; Edwards, Robert; Faruque, Nadeem; Feldman, Robert; Gilbert, Jack; Gilna, Paul; Glöckner, Frank Oliver; Goldstein, Philip; Guralnick, Robert; Haft, Dan; Hancock, David; Hermjakob, Henning; Hertz-Fowler, Christiane; Hugenholtz, Phil; Joint, Ian; Kagan, Leonid; Kane, Matthew; Kennedy, Jessie; Kowalchuk, George; Kottmann, Renzo; Kolker, Eugene; Kravitz, Saul; Kyrpides, Nikos; Leebens-Mack, Jim; Lewis, Suzanna E; Li, Kelvin; Lister, Allyson L; Lord, Phillip; Maltsev, Natalia; Markowitz, Victor; Martiny, Jennifer; Methe, Barbara; Mizrachi, Ilene; Moxon, Richard; Nelson, Karen; Parkhill, Julian; Proctor, Lita; White, Owen; Sansone, Susanna-Assunta; Spiers, Andrew; Stevens, Robert; Swift, Paul; Taylor, Chris; Tateno, Yoshio; Tett, Adrian; Turner, Sarah; Ussery, David; Vaughan, Bob; Ward, Naomi; Whetzel, Trish; Gil, Ingio San; Wilson, Gareth; Wipat, Anil

    2008-01-01

    With the quantity of genomic data increasing at an exponential rate, it is imperative that these data be captured electronically, in a standard format. Standardization activities must proceed within the auspices of open-access and international working bodies. To tackle the issues surrounding the development of better descriptions of genomic investigations, we have formed the Genomic Standards Consortium (GSC). Here, we introduce the minimum information about a genome sequence (MIGS) specification with the intent of promoting participation in its development and discussing the resources that will be required to develop improved mechanisms of metadata capture and exchange. As part of its wider goals, the GSC also supports improving the ‘transparency’ of the information contained in existing genomic databases. PMID:18464787

  12. The minimum information about a genome sequence (MIGS) specification

    DEFF Research Database (Denmark)

    Field, D; Garrity, G; Gray, T

    2008-01-01

    With the quantity of genomic data increasing at an exponential rate, it is imperative that these data be captured electronically, in a standard format. Standardization activities must proceed within the auspices of open-access and international working bodies. To tackle the issues surrounding the...... that will be required to develop improved mechanisms of metadata capture and exchange. As part of its wider goals, the GSC also supports improving the 'transparency' of the information contained in existing genomic databases....... the development of better descriptions of genomic investigations, we have formed the Genomic Standards Consortium (GSC). Here, we introduce the minimum information about a genome sequence (MIGS) specification with the intent of promoting participation in its development and discussing the resources...

  13. Information-Theoretical Analysis of EEG Microstate Sequences in Python

    Directory of Open Access Journals (Sweden)

    Frederic von Wegner

    2018-06-01

    Full Text Available We present an open-source Python package to compute information-theoretical quantities for electroencephalographic data. Electroencephalography (EEG measures the electrical potential generated by the cerebral cortex and the set of spatial patterns projected by the brain's electrical potential on the scalp surface can be clustered into a set of representative maps called EEG microstates. Microstate time series are obtained by competitively fitting the microstate maps back into the EEG data set, i.e., by substituting the EEG data at a given time with the label of the microstate that has the highest similarity with the actual EEG topography. As microstate sequences consist of non-metric random variables, e.g., the letters A–D, we recently introduced information-theoretical measures to quantify these time series. In wakeful resting state EEG recordings, we found new characteristics of microstate sequences such as periodicities related to EEG frequency bands. The algorithms used are here provided as an open-source package and their use is explained in a tutorial style. The package is self-contained and the programming style is procedural, focusing on code intelligibility and easy portability. Using a sample EEG file, we demonstrate how to perform EEG microstate segmentation using the modified K-means approach, and how to compute and visualize the recently introduced information-theoretical tests and quantities. The time-lagged mutual information function is derived as a discrete symbolic alternative to the autocorrelation function for metric time series and confidence intervals are computed from Markov chain surrogate data. The software package provides an open-source extension to the existing implementations of the microstate transform and is specifically designed to analyze resting state EEG recordings.

  14. Exploiting sequence and stability information for directing nanobody stability engineering.

    Science.gov (United States)

    Kunz, Patrick; Flock, Tilman; Soler, Nicolas; Zaiss, Moritz; Vincke, Cécile; Sterckx, Yann; Kastelic, Damjana; Muyldermans, Serge; Hoheisel, Jörg D

    2017-09-01

    Variable domains of camelid heavy-chain antibodies, commonly named nanobodies, have high biotechnological potential. In view of their broad range of applications in research, diagnostics and therapy, engineering their stability is of particular interest. One important aspect is the improvement of thermostability, because it can have immediate effects on conformational stability, protease resistance and aggregation propensity of the protein. We analyzed the sequences and thermostabilities of 78 purified nanobody binders. From this data, potentially stabilizing amino acid variations were identified and studied experimentally. Some mutations improved the stability of nanobodies by up to 6.1°C, with an average of 2.3°C across eight modified nanobodies. The stabilizing mechanism involves an improvement of both conformational stability and aggregation behavior, explaining the variable degree of stabilization in individual molecules. In some instances, variations predicted to be stabilizing actually led to thermal destabilization of the proteins. The reasons for this contradiction between prediction and experiment were investigated. The results reveal a mutational strategy to improve the biophysical behavior of nanobody binders and indicate a species-specificity of nanobody architecture. This study illustrates the potential and limitations of engineering nanobody thermostability by merging sequence information with stability data, an aspect that is becoming increasingly important with the recent development of high-throughput biophysical methods. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  15. Comprehensive Information Retrieval and Model Input Sequence (CIRMIS)

    International Nuclear Information System (INIS)

    Friedrichs, D.R.

    1977-04-01

    The Comprehensive Information Retrieval and Model Input Sequence (CIRMIS) was developed to provide the research scientist with man--machine interactive capabilities in a real-time environment, and thereby produce results more quickly and efficiently. The CIRMIS system was originally developed to increase data storage and retrieval capabilities and ground-water model control for the Hanford site. The overall configuration, however, can be used in other areas. The CIRMIS system provides the user with three major functions: retrieval of well-based data, special application for manipulating surface data or background maps, and the manipulation and control of ground-water models. These programs comprise only a portion of the entire CIRMIS system. A complete description of the CIRMIS system is given in this report. 25 figures, 7 tables

  16. An Analysis of Delay-based and Integrator-based Sequence Detectors for Grid-Connected Converters

    DEFF Research Database (Denmark)

    Khazraj, Hesam; Silva, Filipe Miguel Faria da; Bak, Claus Leth

    2017-01-01

    -signal cancellation operators are the main members of the delay-based sequence detectors. The aim of this paper is to provide a theoretical and experimental comparative study between integrator and delay based sequence detectors. The theoretical analysis is conducted based on the small-signal modelling......Detecting and separating positive and negative sequence components of the grid voltage or current is of vital importance in the control of grid-connected power converters, HVDC systems, etc. To this end, several techniques have been proposed in recent years. These techniques can be broadly...... classified into two main classes: The integrator-based techniques and Delay-based techniques. The complex-coefficient filter-based technique, dual second-order generalized integrator-based method, multiple reference frame approach are the main members of the integrator-based sequence detector and the delay...

  17. Connected or informed?: Local Twitter networking in a London neighbourhood

    Directory of Open Access Journals (Sweden)

    John Bingham-Hall

    2015-08-01

    Full Text Available This paper asks whether geographically localised, or ‘hyperlocal’, uses of Twitter succeed in creating peer-to-peer neighbourhood networks or simply act as broadcast media at a reduced scale. Literature drawn from the smart cities discourse and from a UK research project into hyperlocal media, respectively, take on these two opposing interpretations. Evidence gathered in the case study presented here is consistent with the latter, and on this basis we criticise the notion that hyperlocal social media can be seen as a community in itself. We demonstrate this by creating a network map of Twitter followers of a popular hyperlocal blog in Brockley, southeast London. We describe various attributes of this network including its average degree and clustering coefficient to suggest that a small and highly connected cluster of visible local entities such as businesses form a clique at the centre of this network, with individual residents following these but not one another. We then plot the locations of these entities and demonstrate that sub-communities in the network are formed due to close geographical proximity between smaller sets of businesses. These observations are illustrated with qualitative evidence from interviews with users who suggest instead that rather than being connected to one another they benefit from what has been described as ‘neighbourhood storytelling’. Despite the limitations of working with Twitter data, we propose that this multi-modal approach offers a valuable way to investigate the experience of using social media as a communication tool in urban neighbourhoods.

  18. Connecting Hazard Analysts and Risk Managers to Sensor Information.

    Science.gov (United States)

    Le Cozannet, Gonéri; Hosford, Steven; Douglas, John; Serrano, Jean-Jacques; Coraboeuf, Damien; Comte, Jérémie

    2008-06-11

    Hazard analysts and risk managers of natural perils, such as earthquakes, landslides and floods, need to access information from sensor networks surveying their regions of interest. However, currently information about these networks is difficult to obtain and is available in varying formats, thereby restricting accesses and consequently possibly leading to decision-making based on limited information. As a response to this issue, state-of-the-art interoperable catalogues are being currently developed within the framework of the Group on Earth Observations (GEO) workplan. This article provides an overview of the prototype catalogue that was developed to improve access to information about the sensor networks surveying geological hazards (geohazards), such as earthquakes, landslides and volcanoes.

  19. Brain activity and cognition: a connection from thermodynamics and information theory.

    Science.gov (United States)

    Collell, Guillem; Fauquet, Jordi

    2015-01-01

    The connection between brain and mind is an important scientific and philosophical question that we are still far from completely understanding. A crucial point to our work is noticing that thermodynamics provides a convenient framework to model brain activity, whereas cognition can be modeled in information-theoretical terms. In fact, several models have been proposed so far from both approaches. A second critical remark is the existence of deep theoretical connections between thermodynamics and information theory. In fact, some well-known authors claim that the laws of thermodynamics are nothing but principles in information theory. Unlike in physics or chemistry, a formalization of the relationship between information and energy is currently lacking in neuroscience. In this paper we propose a framework to connect physical brain and cognitive models by means of the theoretical connections between information theory and thermodynamics. Ultimately, this article aims at providing further insight on the formal relationship between cognition and neural activity.

  20. Brain activity and cognition: a connection from thermodynamics and information theory

    Science.gov (United States)

    Collell, Guillem; Fauquet, Jordi

    2015-01-01

    The connection between brain and mind is an important scientific and philosophical question that we are still far from completely understanding. A crucial point to our work is noticing that thermodynamics provides a convenient framework to model brain activity, whereas cognition can be modeled in information-theoretical terms. In fact, several models have been proposed so far from both approaches. A second critical remark is the existence of deep theoretical connections between thermodynamics and information theory. In fact, some well-known authors claim that the laws of thermodynamics are nothing but principles in information theory. Unlike in physics or chemistry, a formalization of the relationship between information and energy is currently lacking in neuroscience. In this paper we propose a framework to connect physical brain and cognitive models by means of the theoretical connections between information theory and thermodynamics. Ultimately, this article aims at providing further insight on the formal relationship between cognition and neural activity. PMID:26136709

  1. Global Information Justice: Rights, Responsibilities, and Caring Connections.

    Science.gov (United States)

    Smith, Martha

    2001-01-01

    Explains the concept of global information justice and describes it as an ethical ideal, as an organizing principle for a model for analysis, and as a direction for policy making. Discusses the use of new technologies; access to technology; ownership; privacy; security; community; and the Universal Declaration of Human Rights. (Author/LRW)

  2. Connecting Information Literacy and Social Justice: Why and How

    Science.gov (United States)

    Saunders, Laura

    2017-01-01

    Libraries have a long, though not uncomplicated, history with social justice and social advocacy. The new ACRL "Framework for Information Literacy," which is more conceptual and flexible than the original Standards, offers an opportunity for librarians to approach teaching and learning from a social justice perspective. Indeed, the…

  3. A Poster Assignment Connects Information Literacy and Writing Skills

    Science.gov (United States)

    Waters, Natalie

    2015-01-01

    This paper describes the implementation of a poster assignment in a writing and information literacy course required for undergraduate Life Sciences and Environmental Biology majors with the Faculty of Agricultural and Environmental Sciences at McGill University. The assignment was introduced in response to weaknesses identified through course…

  4. Always Connected at Work? : The Role of Information Novelty and Individual Needs

    NARCIS (Netherlands)

    De Jonge, Kiki M.M.; Rietzschel, Eric F.; Van Yperen, Nico W.

    2015-01-01

    Purpose: As a result of new ICT developments, many workers are almost constantly connected to job-relevant information and co-workers, regardless of when or where they are working. Depending on workers’ psychological needs, constantly being connected may be perceived as favorable (e.g., when it

  5. Context-Aware Writing Support for SNS: Connecting Formal and Informal Learning

    Science.gov (United States)

    Waragai, Ikumi; Kurabayashi, Shuichi; Ohta, Tatsuya; Raindl, Marco; Kiyoki, Yasushi; Tokuda, Hideyuki

    2014-01-01

    This paper presents another stage in a series of research efforts by the authors to develop an experience-connected mobile language learning environment, bridging formal and informal learning. Building on a study in which the authors tried to connect classroom learning (of German in Japan) with learners' real life experiences abroad by having…

  6. Distress vocalization sequences broadcasted by bats carry redundant information.

    Science.gov (United States)

    Hechavarría, Julio C; Beetz, M Jerome; Macias, Silvio; Kössl, Manfred

    2016-07-01

    Distress vocalizations (also known as alarm or screams) are an important component of the vocal repertoire of a number of animal species, including bats, humans, monkeys and birds, among others. Although the behavioral relevance of distress vocalizations is undeniable, at present, little is known about the rules that govern vocalization production when in alarmful situations. In this article, we show that when distressed, bats of the species Carollia perspicillata produce repetitive vocalization sequences in which consecutive syllables are likely to be similar to one another regarding their physical attributes. The uttered distress syllables are broadband (12-73 kHz) with most of their energy focussing at 23 kHz. Distress syllables are short (~4 ms), their average sound pressure level is close to 70 dB SPL, and they are produced at high repetition rates (every 14 ms). We discuss that, because of their physical attributes, bat distress vocalizations could serve a dual purpose: (1) advertising threatful situations to conspecifics, and (2) informing the threatener that the bats are ready to defend themselves. We also discuss possible advantages of advertising danger/discomfort using repetitive utterances, a calling strategy that appears to be ubiquitous across the animal kingdom.

  7. Mitochondrial DNA sequencing of cat hair: an informative forensic tool.

    Science.gov (United States)

    Tarditi, Christy R; Grahn, Robert A; Evans, Jeffrey J; Kurushima, Jennifer D; Lyons, Leslie A

    2011-01-01

    Approximately 81.7 million cats are in 37.5 million U.S. households. Shed fur can be criminal evidence because of transfer to victims, suspects, and/or their belongings. To improve cat hairs as forensic evidence, the mtDNA control region from single hairs, with and without root tags, was sequenced. A dataset of a 402-bp control region segment from 174 random-bred cats representing four U.S. geographic areas was generated to determine the informativeness of the mtDNA region. Thirty-two mtDNA mitotypes were observed ranging in frequencies from 0.6-27%. Four common types occurred in all populations. Low heteroplasmy, 1.7%, was determined. Unique mitotypes were found in 18 individuals, 10.3% of the population studied. The calculated discrimination power implied that 8.3 of 10 randomly selected individuals can be excluded by this region. The genetic characteristics of the region and the generated dataset support the use of this cat mtDNA region in forensic applications. 2010 American Academy of Forensic Sciences. Published 2010. This article is a U.S. Government work and is in the public domain in the U.S.A.

  8. News from the Library: Stay connected and informed, try Mendeley!

    CERN Multimedia

    CERN Library

    2012-01-01

    Mendeley is a free bibliographic reference manager and academic social network. This online platform enables researchers to discover scientific publications and to collaborate with others online.   Mendeley helps you to organize the papers you read, share them with colleagues, and create bibliographies and reference lists. These papers can be accessed anywhere and on any electronic device. Mendeley currently has over 1.7 million active users in the world. It contains, therefore, a large crowd-sourced information library, with over 242 million documents. Recently, the software has opened up new pathways for collaboration and interaction between individual students and researchers and their institutions' libraries. The fee-based institutional edition of Mendeley not only allows access to the Library's online resources, but also facilitates communication and collaboration within your group on the platform. The CERN Library has now opened a free trial to the Me...

  9. Exploring the connections between green economy and informal economy in South Africa

    Directory of Open Access Journals (Sweden)

    Suzanne Smit

    2015-11-01

    Full Text Available The notion of an inclusive green economy in the context of sustainable development and poverty eradication requires an approach that engages with the informal economy. However, the informal economy is generally ignored or undervalued in discussions on the green economy. This paper set out to bolster this argument by identifying the ways in which the green economy and the informal economy may be connected by establishing the extent to which policies and plans relating to green economy connect with the informal economy, and recognising several informal green activities. The barriers and opportunities for connecting the two spheres were also explored as well as possible ways in which such activities may be supported at different levels of organisation. In the case of South Africa, many informal green activities that contribute to sustainable livelihoods are recognised. However, issues pertaining to procedure, process and participation hinder the transition to a truly inclusive green economy.

  10. Hellmann–Feynman connection for the relative Fisher information

    Energy Technology Data Exchange (ETDEWEB)

    Venkatesan, R.C., E-mail: ravi@systemsresearchcorp.com [Systems Research Corporation, Aundh, Pune 411007 (India); Plastino, A., E-mail: plastino@fisica.unlp.edu.ar [IFLP, National University La Plata & National Research (CONICET) C. C., 727 1900, La Plata (Argentina)

    2015-08-15

    The (i) reciprocity relations for the relative Fisher information (RFI, hereafter) and (ii) a generalized RFI–Euler theorem are self-consistently derived from the Hellmann–Feynman theorem. These new reciprocity relations generalize the RFI–Euler theorem and constitute the basis for building up a mathematical Legendre transform structure (LTS, hereafter), akin to that of thermodynamics, that underlies the RFI scenario. This demonstrates the possibility of translating the entire mathematical structure of thermodynamics into a RFI-based theoretical framework. Virial theorems play a prominent role in this endeavor, as a Schrödinger-like equation can be associated to the RFI. Lagrange multipliers are determined invoking the RFI–LTS link and the quantum mechanical virial theorem. An appropriate ansatz allows for the inference of probability density functions (pdf’s, hereafter) and energy-eigenvalues of the above mentioned Schrödinger-like equation. The energy-eigenvalues obtained here via inference are benchmarked against established theoretical and numerical results. A principled theoretical basis to reconstruct the RFI-framework from the FIM framework is established. Numerical examples for exemplary cases are provided. - Highlights: • Legendre transform structure for the RFI is obtained with the Hellmann–Feynman theorem. • Inference of the energy-eigenvalues of the SWE-like equation for the RFI is accomplished. • Basis for reconstruction of the RFI framework from the FIM-case is established. • Substantial qualitative and quantitative distinctions with prior studies are discussed.

  11. Protein Function Prediction Based on Sequence and Structure Information

    KAUST Repository

    Smaili, Fatima Z.

    2016-01-01

    operate. In this master thesis project, we worked on inferring protein functions based on the primary protein sequence. In the approach we follow, 3D models are first constructed using I-TASSER. Functions are then deduced by structurally matching

  12. Event Sequence Analysis of the Air Intelligence Agency Information Operations Center Flight Operations

    National Research Council Canada - National Science Library

    Larsen, Glen

    1998-01-01

    This report applies Event Sequence Analysis, methodology adapted from aircraft mishap investigation, to an investigation of the performance of the Air Intelligence Agency's Information Operations Center (IOC...

  13. Functional region prediction with a set of appropriate homologous sequences-an index for sequence selection by integrating structure and sequence information with spatial statistics

    Science.gov (United States)

    2012-01-01

    Background The detection of conserved residue clusters on a protein structure is one of the effective strategies for the prediction of functional protein regions. Various methods, such as Evolutionary Trace, have been developed based on this strategy. In such approaches, the conserved residues are identified through comparisons of homologous amino acid sequences. Therefore, the selection of homologous sequences is a critical step. It is empirically known that a certain degree of sequence divergence in the set of homologous sequences is required for the identification of conserved residues. However, the development of a method to select homologous sequences appropriate for the identification of conserved residues has not been sufficiently addressed. An objective and general method to select appropriate homologous sequences is desired for the efficient prediction of functional regions. Results We have developed a novel index to select the sequences appropriate for the identification of conserved residues, and implemented the index within our method to predict the functional regions of a protein. The implementation of the index improved the performance of the functional region prediction. The index represents the degree of conserved residue clustering on the tertiary structure of the protein. For this purpose, the structure and sequence information were integrated within the index by the application of spatial statistics. Spatial statistics is a field of statistics in which not only the attributes but also the geometrical coordinates of the data are considered simultaneously. Higher degrees of clustering generate larger index scores. We adopted the set of homologous sequences with the highest index score, under the assumption that the best prediction accuracy is obtained when the degree of clustering is the maximum. The set of sequences selected by the index led to higher functional region prediction performance than the sets of sequences selected by other sequence

  14. Cognitive Connected Vehicle Information System Design Requirement for Safety: Role of Bayesian Artificial Intelligence

    Directory of Open Access Journals (Sweden)

    Ata Khan

    2013-04-01

    Full Text Available Intelligent transportation systems (ITS are gaining acceptance around the world and the connected vehicle component of ITS is recognized as a high priority research and development area in many technologically advanced countries. Connected vehicles are expected to have the capability of safe, efficient and eco-driving operations whether these are under human control or in the adaptive machine control mode of operations. The race is on to design the capability to operate in connected traffic environment. The operational requirements can be met with cognitive vehicle design features made possible by advances in artificial intelligence-supported methodology, improved understanding of human factors, and advances in communication technology. This paper describes cognitive features and their information system requirements. The architecture of an information system is presented that supports the features of the cognitive connected vehicle. For better focus, information processing capabilities are specified and the role of Bayesian artificial intelligence is defined for data fusion. Example applications illustrate the role of information systems in integrating intelligent technology, Bayesian artificial intelligence, and abstracted human factors. Concluding remarks highlight the role of the information system and Bayesian artificial intelligence in the design of a new generation of cognitive connected vehicle.

  15. Highly accurate fluorogenic DNA sequencing with information theory-based error correction.

    Science.gov (United States)

    Chen, Zitian; Zhou, Wenxiong; Qiao, Shuo; Kang, Li; Duan, Haifeng; Xie, X Sunney; Huang, Yanyi

    2017-12-01

    Eliminating errors in next-generation DNA sequencing has proved challenging. Here we present error-correction code (ECC) sequencing, a method to greatly improve sequencing accuracy by combining fluorogenic sequencing-by-synthesis (SBS) with an information theory-based error-correction algorithm. ECC embeds redundancy in sequencing reads by creating three orthogonal degenerate sequences, generated by alternate dual-base reactions. This is similar to encoding and decoding strategies that have proved effective in detecting and correcting errors in information communication and storage. We show that, when combined with a fluorogenic SBS chemistry with raw accuracy of 98.1%, ECC sequencing provides single-end, error-free sequences up to 200 bp. ECC approaches should enable accurate identification of extremely rare genomic variations in various applications in biology and medicine.

  16. A Novel Computational Method for Detecting DNA Methylation Sites with DNA Sequence Information and Physicochemical Properties.

    Science.gov (United States)

    Pan, Gaofeng; Jiang, Limin; Tang, Jijun; Guo, Fei

    2018-02-08

    DNA methylation is an important biochemical process, and it has a close connection with many types of cancer. Research about DNA methylation can help us to understand the regulation mechanism and epigenetic reprogramming. Therefore, it becomes very important to recognize the methylation sites in the DNA sequence. In the past several decades, many computational methods-especially machine learning methods-have been developed since the high-throughout sequencing technology became widely used in research and industry. In order to accurately identify whether or not a nucleotide residue is methylated under the specific DNA sequence context, we propose a novel method that overcomes the shortcomings of previous methods for predicting methylation sites. We use k -gram, multivariate mutual information, discrete wavelet transform, and pseudo amino acid composition to extract features, and train a sparse Bayesian learning model to do DNA methylation prediction. Five criteria-area under the receiver operating characteristic curve (AUC), Matthew's correlation coefficient (MCC), accuracy (ACC), sensitivity (SN), and specificity-are used to evaluate the prediction results of our method. On the benchmark dataset, we could reach 0.8632 on AUC, 0.8017 on ACC, 0.5558 on MCC, and 0.7268 on SN. Additionally, the best results on two scBS-seq profiled mouse embryonic stem cells datasets were 0.8896 and 0.9511 by AUC, respectively. When compared with other outstanding methods, our method surpassed them on the accuracy of prediction. The improvement of AUC by our method compared to other methods was at least 0.0399 . For the convenience of other researchers, our code has been uploaded to a file hosting service, and can be downloaded from: https://figshare.com/s/0697b692d802861282d3.

  17. A Novel Computational Method for Detecting DNA Methylation Sites with DNA Sequence Information and Physicochemical Properties

    Directory of Open Access Journals (Sweden)

    Gaofeng Pan

    2018-02-01

    Full Text Available DNA methylation is an important biochemical process, and it has a close connection with many types of cancer. Research about DNA methylation can help us to understand the regulation mechanism and epigenetic reprogramming. Therefore, it becomes very important to recognize the methylation sites in the DNA sequence. In the past several decades, many computational methods—especially machine learning methods—have been developed since the high-throughout sequencing technology became widely used in research and industry. In order to accurately identify whether or not a nucleotide residue is methylated under the specific DNA sequence context, we propose a novel method that overcomes the shortcomings of previous methods for predicting methylation sites. We use k-gram, multivariate mutual information, discrete wavelet transform, and pseudo amino acid composition to extract features, and train a sparse Bayesian learning model to do DNA methylation prediction. Five criteria—area under the receiver operating characteristic curve (AUC, Matthew’s correlation coefficient (MCC, accuracy (ACC, sensitivity (SN, and specificity—are used to evaluate the prediction results of our method. On the benchmark dataset, we could reach 0.8632 on AUC, 0.8017 on ACC, 0.5558 on MCC, and 0.7268 on SN. Additionally, the best results on two scBS-seq profiled mouse embryonic stem cells datasets were 0.8896 and 0.9511 by AUC, respectively. When compared with other outstanding methods, our method surpassed them on the accuracy of prediction. The improvement of AUC by our method compared to other methods was at least 0.0399 . For the convenience of other researchers, our code has been uploaded to a file hosting service, and can be downloaded from: https://figshare.com/s/0697b692d802861282d3.

  18. Effects of informed consent for individual genome sequencing on relevant knowledge.

    Science.gov (United States)

    Kaphingst, K A; Facio, F M; Cheng, M-R; Brooks, S; Eidem, H; Linn, A; Biesecker, B B; Biesecker, L G

    2012-11-01

    Increasing availability of individual genomic information suggests that patients will need knowledge about genome sequencing to make informed decisions, but prior research is limited. In this study, we examined genome sequencing knowledge before and after informed consent among 311 participants enrolled in the ClinSeq™ sequencing study. An exploratory factor analysis of knowledge items yielded two factors (sequencing limitations knowledge; sequencing benefits knowledge). In multivariable analysis, high pre-consent sequencing limitations knowledge scores were significantly related to education [odds ratio (OR): 8.7, 95% confidence interval (CI): 2.45-31.10 for post-graduate education, and OR: 3.9; 95% CI: 1.05, 14.61 for college degree compared with less than college degree] and race/ethnicity (OR: 2.4, 95% CI: 1.09, 5.38 for non-Hispanic Whites compared with other racial/ethnic groups). Mean values increased significantly between pre- and post-consent for the sequencing limitations knowledge subscale (6.9-7.7, p benefits knowledge subscale (7.0-7.5, p < 0.0001); increase in knowledge did not differ by sociodemographic characteristics. This study highlights gaps in genome sequencing knowledge and underscores the need to target educational efforts toward participants with less education or from minority racial/ethnic groups. The informed consent process improved genome sequencing knowledge. Future studies could examine how genome sequencing knowledge influences informed decision making. © 2012 John Wiley & Sons A/S.

  19. Equivalence between the Arquès-Walsh sequence formula and the number of connected Feynman diagrams for every perturbation order in the fermionic many-body problem

    Science.gov (United States)

    Castro, E.

    2018-02-01

    From the perturbative expansion of the exact Green function, an exact counting formula is derived to determine the number of different types of connected Feynman diagrams. This formula coincides with the Arquès-Walsh sequence formula in the rooted map theory, supporting the topological connection between Feynman diagrams and rooted maps. A classificatory summing-terms approach is used, in connection to discrete mathematical theory.

  20. Personal Web home pages of adolescents with cancer: self-presentation, information dissemination, and interpersonal connection.

    Science.gov (United States)

    Suzuki, Lalita K; Beale, Ivan L

    2006-01-01

    The content of personal Web home pages created by adolescents with cancer is a new source of information about this population of potential benefit to oncology nurses and psychologists. Individual Internet elements found on 21 home pages created by youths with cancer (14-22 years old) were rated for cancer-related self-presentation, information dissemination, and interpersonal connection. Examples of adolescents' online narratives were also recorded. Adolescents with cancer used various Internet elements on their home pages for cancer-related self-presentation (eg, welcome messages, essays, personal history and diary pages, news articles, and poetry), information dissemination (e.g., through personal interest pages, multimedia presentations, lists, charts, and hyperlinks), and interpersonal connection (eg, guestbook entries). Results suggest that various elements found on personal home pages are being used by a limited number of young patients with cancer for self-expression, information access, and contact with peers.

  1. Elman RNN based classification of proteins sequences on account of their mutual information.

    Science.gov (United States)

    Mishra, Pooja; Nath Pandey, Paras

    2012-10-21

    In the present work we have employed the method of estimating residue correlation within the protein sequences, by using the mutual information (MI) of adjacent residues, based on structural and solvent accessibility properties of amino acids. The long range correlation between nonadjacent residues is improved by constructing a mutual information vector (MIV) for a single protein sequence, like this each protein sequence is associated with its corresponding MIVs. These MIVs are given to Elman RNN to obtain the classification of protein sequences. The modeling power of MIV was shown to be significantly better, giving a new approach towards alignment free classification of protein sequences. We also conclude that sequence structural and solvent accessible property based MIVs are better predictor. Copyright © 2012 Elsevier Ltd. All rights reserved.

  2. Human α2-HS-glycoprotein: the A and B chains with a connecting sequence are encoded by a single mRNA transcript

    International Nuclear Information System (INIS)

    Lee, C.C.; Bowman, B.H.; Yang, F.

    1987-01-01

    The α 2 -HS-glycoprotein (AHSG) is a plasma protein reported to play roles in bone mineralization and in the immune response. It is composed of two subunits, the A and B chains. Recombinant plasmids containing human cDNA AHSG have been isolated by screening an adult human liver library with a mixed oligonucleotide probe. The cDNA clones containing AHSG inserts span approximately 1.5 kilobase pairs and include the entire AHSG coding sequence, demonstrating that the A and B chains are encoded by a single mRNA transcript. The cDNA sequence predicts an 18-amino-acid signal peptide, followed by the A-chain sequence of AHSG. A heretofore unseen connecting sequence of 40 amino acids was deduced between the A- and B-chain sequences. The connecting sequence demonstrates the unique amino acid doublets and collagen triplets found in the A and B chains; it is not homologous with other reported amino acid sequences. The connecting sequence may be cleaved in a posttranslational step by limited proteolysis before mature AHSG is released into the circulation or may vary in its presence because of alternative processing. The AHSG cDNA was utilized for mapping the AHSG gene to the 3q21→qter region of human chromosome 3. The availability of the AHSG cDNA clone will facilitate the analysis of its genetic control and gene expression during development and bone formation

  3. Identifying Statistical Dependence in Genomic Sequences via Mutual Information Estimates

    Directory of Open Access Journals (Sweden)

    Wojciech Szpankowski

    2007-12-01

    Full Text Available Questions of understanding and quantifying the representation and amount of information in organisms have become a central part of biological research, as they potentially hold the key to fundamental advances. In this paper, we demonstrate the use of information-theoretic tools for the task of identifying segments of biomolecules (DNA or RNA that are statistically correlated. We develop a precise and reliable methodology, based on the notion of mutual information, for finding and extracting statistical as well as structural dependencies. A simple threshold function is defined, and its use in quantifying the level of significance of dependencies between biological segments is explored. These tools are used in two specific applications. First, they are used for the identification of correlations between different parts of the maize zmSRp32 gene. There, we find significant dependencies between the 5′ untranslated region in zmSRp32 and its alternatively spliced exons. This observation may indicate the presence of as-yet unknown alternative splicing mechanisms or structural scaffolds. Second, using data from the FBI's combined DNA index system (CODIS, we demonstrate that our approach is particularly well suited for the problem of discovering short tandem repeats—an application of importance in genetic profiling.

  4. IMITATING MODEL OF ASSIMILATION AND FORGETTING OF THE LOGICALLY CONNECTED INFORMATION

    Directory of Open Access Journals (Sweden)

    Robert Valerievich Mayer

    2017-09-01

    Full Text Available The educational material we present as a set of a number of information blocks consisting of learning material elements (LMEs; therefore its assimilation and forgetting occurs differently, than in the Ebbinghaus’s experiments. The purpose of the article is constructing of a computer model of assimilation and forgetting of the logically connected information allowing: 1 to prove the fast rise of understanding while training; 2 to receive the forgetting curve for the comprehended information. The modeling methods help to receive the graphs of the knowledge level dependence on time. It is shown, that the processes of assimilation and forgetting occurs according to the logistic law.

  5. Connecting Inspiration with Information: Studio Art Students and Information Literacy Instruction

    Directory of Open Access Journals (Sweden)

    Katie Greer

    2015-06-01

    Full Text Available This article discusses the partnership between the library and the studio art faculty at [Institution name], that led to the integration of information literacy instruction into the studio art curriculum. The author outlines the importance of information literacy to artistic practice and student success, and discusses the program of instruction and learning outcomes. Early assessment of student needs and the program’s effectiveness, using both citation analysis and anecdotal feedback, reveals that the program has contributed to the maturation of student research and inquiry skills, and positively affected the relationship between the department and the library, and provides preliminary conclusions about undergraduate studio art information behaviors. An ongoing further program of study to more fully describe the information needs of undergraduate studio art students is also outlined.

  6. DeepProbe: Information Directed Sequence Understanding and Chatbot Design via Recurrent Neural Networks

    OpenAIRE

    Yin, Zi; Chang, Keng-hao; Zhang, Ruofei

    2017-01-01

    Information extraction and user intention identification are central topics in modern query understanding and recommendation systems. In this paper, we propose DeepProbe, a generic information-directed interaction framework which is built around an attention-based sequence to sequence (seq2seq) recurrent neural network. DeepProbe can rephrase, evaluate, and even actively ask questions, leveraging the generative ability and likelihood estimation made possible by seq2seq models. DeepProbe makes...

  7. Corporate Social Responsibility in the Dynamic Information Age of Inter-Systems Connectivity

    OpenAIRE

    Arvind Ashta

    2009-01-01

    The Information Age, with its new technologies, is accompanied by an accelerating shift in work relations, of which this article focuses on connectivity, interdependence and dynamism. Along with this change in relations, new ethical cultures and responsibilities are evolving at different levels: individual, corporate, governmental, NGO, and global. This article zooms in on theoretical developments related to Corporate Social Responsibility to see how they have evolved to adapt to the new mode...

  8. Subfamily logos: visualization of sequence deviations at alignment positions with high information content

    Directory of Open Access Journals (Sweden)

    Beitz Eric

    2006-06-01

    Full Text Available Abstract Background Recognition of relevant sequence deviations can be valuable for elucidating functional differences between protein subfamilies. Interesting residues at highly conserved positions can then be mutated and experimentally analyzed. However, identification of such sites is tedious because automated approaches are scarce. Results Subfamily logos visualize subfamily-specific sequence deviations. The display is similar to classical sequence logos but extends into the negative range. Positive, upright characters correspond to residues which are characteristic for the subfamily, negative, upside-down characters to residues typical for the remaining sequences. The symbol height is adjusted to the information content of the alignment position. Residues which are conserved throughout do not appear. Conclusion Subfamily logos provide an intuitive display of relevant sequence deviations. The method has proven to be valid using a set of 135 aligned aquaporin sequences in which established subfamily-specific positions were readily identified by the algorithm.

  9. Functional connectivity and information flow of the respiratory neural network in chronic obstructive pulmonary disease.

    Science.gov (United States)

    Yu, Lianchun; De Mazancourt, Marine; Hess, Agathe; Ashadi, Fakhrul R; Klein, Isabelle; Mal, Hervé; Courbage, Maurice; Mangin, Laurence

    2016-08-01

    Breathing involves a complex interplay between the brainstem automatic network and cortical voluntary command. How these brain regions communicate at rest or during inspiratory loading is unknown. This issue is crucial for several reasons: (i) increased respiratory loading is a major feature of several respiratory diseases, (ii) failure of the voluntary motor and cortical sensory processing drives is among the mechanisms that precede acute respiratory failure, (iii) several cerebral structures involved in responding to inspiratory loading participate in the perception of dyspnea, a distressing symptom in many disease. We studied functional connectivity and Granger causality of the respiratory network in controls and patients with chronic obstructive pulmonary disease (COPD), at rest and during inspiratory loading. Compared with those of controls, the motor cortex area of patients exhibited decreased connectivity with their contralateral counterparts and no connectivity with the brainstem. In the patients, the information flow was reversed at rest with the source of the network shifted from the medulla towards the motor cortex. During inspiratory loading, the system was overwhelmed and the motor cortex became the sink of the network. This major finding may help to understand why some patients with COPD are prone to acute respiratory failure. Network connectivity and causality were related to lung function and illness severity. We validated our connectivity and causality results with a mathematical model of neural network. Our findings suggest a new therapeutic strategy involving the modulation of brain activity to increase motor cortex functional connectivity and improve respiratory muscles performance in patients. Hum Brain Mapp 37:2736-2754, 2016. © 2016 The Authors Human Brain Mapping Published by Wiley Periodicals, Inc. © 2016 The Authors Human Brain Mapping Published by Wiley Periodicals, Inc.

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

    Science.gov (United States)

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

    1997-01-01

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

  11. A method for partitioning the information contained in a protein sequence between its structure and function.

    Science.gov (United States)

    Possenti, Andrea; Vendruscolo, Michele; Camilloni, Carlo; Tiana, Guido

    2018-05-23

    Proteins employ the information stored in the genetic code and translated into their sequences to carry out well-defined functions in the cellular environment. The possibility to encode for such functions is controlled by the balance between the amount of information supplied by the sequence and that left after that the protein has folded into its structure. We study the amount of information necessary to specify the protein structure, providing an estimate that keeps into account the thermodynamic properties of protein folding. We thus show that the information remaining in the protein sequence after encoding for its structure (the 'information gap') is very close to what needed to encode for its function and interactions. Then, by predicting the information gap directly from the protein sequence, we show that it may be possible to use these insights from information theory to discriminate between ordered and disordered proteins, to identify unknown functions, and to optimize artificially-designed protein sequences. This article is protected by copyright. All rights reserved. © 2018 Wiley Periodicals, Inc.

  12. MEG connectivity analysis in patients with Alzheimer's disease using cross mutual information and spectral coherence.

    Science.gov (United States)

    Alonso, Joan Francesc; Poza, Jesús; Mañanas, Miguel Angel; Romero, Sergio; Fernández, Alberto; Hornero, Roberto

    2011-01-01

    Alzheimer's disease (AD) is an irreversible brain disorder which represents the most common form of dementia in western countries. An early and accurate diagnosis of AD would enable to develop new strategies for managing the disease; however, nowadays there is no single test that can accurately predict the development of AD. In this sense, only a few studies have focused on the magnetoencephalographic (MEG) AD connectivity patterns. This study compares brain connectivity in terms of linear and nonlinear couplings by means of spectral coherence and cross mutual information function (CMIF), respectively. The variables defined from these functions provide statistically significant differences (p CMIF. The results suggest that AD is characterized by both decreases and increases of functional couplings in different frequency bands as well as by an increase in regularity, that is, more evident statistical deterministic relationships in AD patients' MEG connectivity. The significant differences obtained indicate that AD could disturb brain interactions causing abnormal brain connectivity and operation. Furthermore, the combination of coherence and CMIF features to perform a diagnostic test based on logistic regression improved the tests based on individual variables for its robustness.

  13. Magnetic resonance for T-staging of nasopharyngeal carcinoma. The most informative pair of sequences

    International Nuclear Information System (INIS)

    Lau, Kam Y.; Kan, Wai K.; Sze, Wai M.

    2004-01-01

    The objective of this study was to evaluate the most informative pair of sequences in magnetic resonance (MR) for T-staging of nasopharyngeal carcinoma (NPC). The MR images of 134 patients with newly diagnosed NRC, from 1996 to 2002, were retrospectively reviewed. All the patients were scanned using 1.5 Tesla MR systems. The images of the nasopharynx were reviewed by two qualified radiologists to determine the positive findings and the T-stage by Union Internationale Contre le Cancer (UICC) (6th edition) System, using each sequence separately. The T-stage derived from a single MR sequence was then compared with the T-stage based on the five selected sequences to assess the number and percentage of patients who were being understaged. Therefore, the overall percentage accuracy of each single sequence could be determined. A pair of sequences providing information to achieve almost 100% diagnostic accuracy was then derived. The overall percentage accuracy of five individual sequences of the nasopharynx is as follows: contrast-enhanced (CE) fat suppression (FS) axial T1 (94.8%), CE FS coronal T1 (88.1%), FS axial T2 (85.8%), non-contrast enhanced (NE) axial T1 (78.4%) and NE coronal T1 (77.6%). CE FS axial T1 has the best accuracy. All the structures that are missed in CE FS axial T1 which lead to apparent understaging, are appreciated in NE axial T1-weighted images. Individual sequences supplement each other in the NPC staging. CE FS axial T1 is the most informative individual sequence. Combination of CE FS axial T1 and NE axial T1 of the nasopharynx provides sufficient information to achieve almost 100% diagnostic accuracy in T-staging; therefore, both should be included in the MR-staging protocol. (author)

  14. Brain connectivity during encoding and retrieval of spatial information: individual differences in navigation skills.

    Science.gov (United States)

    Sharma, Greeshma; Gramann, Klaus; Chandra, Sushil; Singh, Vijander; Mittal, Alok Prakash

    2017-09-01

    Emerging evidence suggests that the variations in the ability to navigate through any real or virtual environment are accompanied by distinct underlying cortical activations in multiple regions of the brain. These activations may appear due to the use of different frame of reference (FOR) for representing an environment. The present study investigated the brain dynamics in the good and bad navigators using Graph Theoretical analysis applied to low-density electroencephalography (EEG) data. Individual navigation skills were rated according to the performance in a virtual reality (VR)-based navigation task and the effect of navigator's proclivity towards a particular FOR on the navigation performance was explored. Participants were introduced to a novel virtual environment that they learned from a first-person or an aerial perspective and were subsequently assessed on the basis of efficiency with which they learnt and recalled. The graph theoretical parameters, path length (PL), global efficiency (GE), and clustering coefficient (CC) were computed for the functional connectivity network in the theta and alpha frequency bands. During acquisition of the spatial information, good navigators were distinguished by a lower degree of dispersion in the functional connectivity compared to the bad navigators. Within the groups of good and bad navigators, better performers were characterised by the formation of multiple hubs at various sites and the percentage of connectivity or small world index. The proclivity towards a specific FOR during exploration of a new environment was not found to have any bearing on the spatial learning. These findings may have wider implications for how the functional connectivity in the good and bad navigators differs during spatial information acquisition and retrieval in the domains of rescue operations and defence systems.

  15. Multivariate information-theoretic measures reveal directed information structure and task relevant changes in fMRI connectivity.

    Science.gov (United States)

    Lizier, Joseph T; Heinzle, Jakob; Horstmann, Annette; Haynes, John-Dylan; Prokopenko, Mikhail

    2011-02-01

    The human brain undertakes highly sophisticated information processing facilitated by the interaction between its sub-regions. We present a novel method for interregional connectivity analysis, using multivariate extensions to the mutual information and transfer entropy. The method allows us to identify the underlying directed information structure between brain regions, and how that structure changes according to behavioral conditions. This method is distinguished in using asymmetric, multivariate, information-theoretical analysis, which captures not only directional and non-linear relationships, but also collective interactions. Importantly, the method is able to estimate multivariate information measures with only relatively little data. We demonstrate the method to analyze functional magnetic resonance imaging time series to establish the directed information structure between brain regions involved in a visuo-motor tracking task. Importantly, this results in a tiered structure, with known movement planning regions driving visual and motor control regions. Also, we examine the changes in this structure as the difficulty of the tracking task is increased. We find that task difficulty modulates the coupling strength between regions of a cortical network involved in movement planning and between motor cortex and the cerebellum which is involved in the fine-tuning of motor control. It is likely these methods will find utility in identifying interregional structure (and experimentally induced changes in this structure) in other cognitive tasks and data modalities.

  16. Background information to the installers guide for small scale mains connected PV

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2002-07-01

    This report contains background information used by BRE, EA Technology, Halcrows and Sundog when compiling guidance for the UK's New and Renewable Energy Programme on the installation of small-scale photovoltaics (PV) in buildings. The report considers: relevant standards; general safety issues; fire and safety issues, including the fire resistance of PV modules; PV module ratings such as maximum voltage and maximum current; DC cabling; the DC disconnect; the DC junction box; fault analysis; general and AC side earthing; DC earthing; lightning and surge suppression; inverters; AC modules; AC systems; getting connection; mounting options; and installation issues.

  17. Prediction of glutathionylation sites in proteins using minimal sequence information and their experimental validation.

    Science.gov (United States)

    Pal, Debojyoti; Sharma, Deepak; Kumar, Mukesh; Sandur, Santosh K

    2016-09-01

    S-glutathionylation of proteins plays an important role in various biological processes and is known to be protective modification during oxidative stress. Since, experimental detection of S-glutathionylation is labor intensive and time consuming, bioinformatics based approach is a viable alternative. Available methods require relatively longer sequence information, which may prevent prediction if sequence information is incomplete. Here, we present a model to predict glutathionylation sites from pentapeptide sequences. It is based upon differential association of amino acids with glutathionylated and non-glutathionylated cysteines from a database of experimentally verified sequences. This data was used to calculate position dependent F-scores, which measure how a particular amino acid at a particular position may affect the likelihood of glutathionylation event. Glutathionylation-score (G-score), indicating propensity of a sequence to undergo glutathionylation, was calculated using position-dependent F-scores for each amino-acid. Cut-off values were used for prediction. Our model returned an accuracy of 58% with Matthew's correlation-coefficient (MCC) value of 0.165. On an independent dataset, our model outperformed the currently available model, in spite of needing much less sequence information. Pentapeptide motifs having high abundance among glutathionylated proteins were identified. A list of potential glutathionylation hotspot sequences were obtained by assigning G-scores and subsequent Protein-BLAST analysis revealed a total of 254 putative glutathionable proteins, a number of which were already known to be glutathionylated. Our model predicted glutathionylation sites in 93.93% of experimentally verified glutathionylated proteins. Outcome of this study may assist in discovering novel glutathionylation sites and finding candidate proteins for glutathionylation.

  18. Alpha-gamma phase amplitude coupling subserves information transfer during perceptual sequence learning.

    Science.gov (United States)

    Tzvi, Elinor; Bauhaus, Leon J; Kessler, Till U; Liebrand, Matthias; Wöstmann, Malte; Krämer, Ulrike M

    2018-03-01

    Cross-frequency coupling is suggested to serve transfer of information between wide-spread neuronal assemblies and has been shown to underlie many cognitive functions including learning and memory. In previous work, we found that alpha (8-13 Hz) - gamma (30-48 Hz) phase amplitude coupling (αγPAC) is decreased during sequence learning in bilateral frontal cortex and right parietal cortex. We interpreted this to reflect decreased demands for visuo-motor mapping once the sequence has been encoded. In the present study, we put this hypothesis to the test by adding a "simple" condition to the standard serial reaction time task (SRTT) with minimal needs for visuo-motor mapping. The standard SRTT in our paradigm entailed a perceptual sequence allowing for implicit learning of a sequence of colors with randomly assigned motor responses. Sequence learning in this case was thus not associated with reduced demands for visuo-motor mapping. Analysis of oscillatory power revealed a learning-related alpha decrease pointing to a stronger recruitment of occipito-parietal areas when encoding the perceptual sequence. Replicating our previous findings but in contrast to our hypothesis, αγPAC was decreased in sequence compared to random trials over right frontal and parietal cortex. It also tended to be smaller compared to trials requiring a simple motor sequence. We additionally analyzed αγPAC in resting-state data of a separate cohort. PAC in electrodes over right parietal cortex was significantly stronger compared to sequence trials and tended to be higher compared to simple and random trials of the SRTT data. We suggest that αγPAC in right parietal cortex reflects a "default-mode" brain state, which gets perturbed to allow for encoding of visual regularities into memory. Copyright © 2018 Elsevier Inc. All rights reserved.

  19. MIToS.jl: mutual information tools for protein sequence analysis in the Julia language

    DEFF Research Database (Denmark)

    Zea, Diego J.; Anfossi, Diego; Nielsen, Morten

    2017-01-01

    Motivation: MIToS is an environment for mutual information analysis and a framework for protein multiple sequence alignments (MSAs) and protein structures (PDB) management in Julia language. It integrates sequence and structural information through SIFTS, making Pfam MSAs analysis straightforward....... MIToS streamlines the implementation of any measure calculated from residue contingency tables and its optimization and testing in terms of protein contact prediction. As an example, we implemented and tested a BLOSUM62-based pseudo-count strategy in mutual information analysis. Availability...... and Implementation: The software is totally implemented in Julia and supported for Linux, OS X and Windows. It’s freely available on GitHub under MIT license: http://mitos.leloir.org.ar. Contacts:diegozea@gmail.com or cmb@leloir.org.ar Supplementary information: Supplementary data are available at Bioinformatics...

  20. Sequencing Genetics Information: Integrating Data into Information Literacy for Undergraduate Biology Students

    Science.gov (United States)

    MacMillan, Don

    2010-01-01

    This case study describes an information literacy lab for an undergraduate biology course that leads students through a range of resources to discover aspects of genetic information. The lab provides over 560 students per semester with the opportunity for hands-on exploration of resources in steps that simulate the pathways of higher-level…

  1. A Teaching-Learning Sequence of Colour Informed by History and Philosophy of Science

    Science.gov (United States)

    Maurício, Paulo; Valente, Bianor; Chagas, Isabel

    2017-01-01

    In this work, we present a teaching-learning sequence on colour intended to a pre-service elementary teacher programme informed by History and Philosophy of Science. Working in a socio-constructivist framework, we made an excursion on the history of colour. Our excursion through history of colour, as well as the reported misconception on colour…

  2. Information-Theoretic Properties of Auditory Sequences Dynamically Influence Expectation and Memory.

    Science.gov (United States)

    Agres, Kat; Abdallah, Samer; Pearce, Marcus

    2018-01-01

    A basic function of cognition is to detect regularities in sensory input to facilitate the prediction and recognition of future events. It has been proposed that these implicit expectations arise from an internal predictive coding model, based on knowledge acquired through processes such as statistical learning, but it is unclear how different types of statistical information affect listeners' memory for auditory stimuli. We used a combination of behavioral and computational methods to investigate memory for non-linguistic auditory sequences. Participants repeatedly heard tone sequences varying systematically in their information-theoretic properties. Expectedness ratings of tones were collected during three listening sessions, and a recognition memory test was given after each session. Information-theoretic measures of sequential predictability significantly influenced listeners' expectedness ratings, and variations in these properties had a significant impact on memory performance. Predictable sequences yielded increasingly better memory performance with increasing exposure. Computational simulations using a probabilistic model of auditory expectation suggest that listeners dynamically formed a new, and increasingly accurate, implicit cognitive model of the information-theoretic structure of the sequences throughout the experimental session. Copyright © 2017 Cognitive Science Society, Inc.

  3. MendeLIMS: a web-based laboratory information management system for clinical genome sequencing.

    Science.gov (United States)

    Grimes, Susan M; Ji, Hanlee P

    2014-08-27

    Large clinical genomics studies using next generation DNA sequencing require the ability to select and track samples from a large population of patients through many experimental steps. With the number of clinical genome sequencing studies increasing, it is critical to maintain adequate laboratory information management systems to manage the thousands of patient samples that are subject to this type of genetic analysis. To meet the needs of clinical population studies using genome sequencing, we developed a web-based laboratory information management system (LIMS) with a flexible configuration that is adaptable to continuously evolving experimental protocols of next generation DNA sequencing technologies. Our system is referred to as MendeLIMS, is easily implemented with open source tools and is also highly configurable and extensible. MendeLIMS has been invaluable in the management of our clinical genome sequencing studies. We maintain a publicly available demonstration version of the application for evaluation purposes at http://mendelims.stanford.edu. MendeLIMS is programmed in Ruby on Rails (RoR) and accesses data stored in SQL-compliant relational databases. Software is freely available for non-commercial use at http://dna-discovery.stanford.edu/software/mendelims/.

  4. Improving probe set selection for microbial community analysis by leveraging taxonomic information of training sequences

    Directory of Open Access Journals (Sweden)

    Jiang Tao

    2011-10-01

    Full Text Available Abstract Background Population levels of microbial phylotypes can be examined using a hybridization-based method that utilizes a small set of computationally-designed DNA probes targeted to a gene common to all. Our previous algorithm attempts to select a set of probes such that each training sequence manifests a unique theoretical hybridization pattern (a binary fingerprint to a probe set. It does so without taking into account similarity between training gene sequences or their putative taxonomic classifications, however. We present an improved algorithm for probe set selection that utilizes the available taxonomic information of training gene sequences and attempts to choose probes such that the resultant binary fingerprints cluster into real taxonomic groups. Results Gene sequences manifesting identical fingerprints with probes chosen by the new algorithm are more likely to be from the same taxonomic group than probes chosen by the previous algorithm. In cases where they are from different taxonomic groups, underlying DNA sequences of identical fingerprints are more similar to each other in probe sets made with the new versus the previous algorithm. Complete removal of large taxonomic groups from training data does not greatly decrease the ability of probe sets to distinguish those groups. Conclusions Probe sets made from the new algorithm create fingerprints that more reliably cluster into biologically meaningful groups. The method can readily distinguish microbial phylotypes that were excluded from the training sequences, suggesting novel microbes can also be detected.

  5. Improving probe set selection for microbial community analysis by leveraging taxonomic information of training sequences.

    Science.gov (United States)

    Ruegger, Paul M; Della Vedova, Gianluca; Jiang, Tao; Borneman, James

    2011-10-10

    Population levels of microbial phylotypes can be examined using a hybridization-based method that utilizes a small set of computationally-designed DNA probes targeted to a gene common to all. Our previous algorithm attempts to select a set of probes such that each training sequence manifests a unique theoretical hybridization pattern (a binary fingerprint) to a probe set. It does so without taking into account similarity between training gene sequences or their putative taxonomic classifications, however. We present an improved algorithm for probe set selection that utilizes the available taxonomic information of training gene sequences and attempts to choose probes such that the resultant binary fingerprints cluster into real taxonomic groups. Gene sequences manifesting identical fingerprints with probes chosen by the new algorithm are more likely to be from the same taxonomic group than probes chosen by the previous algorithm. In cases where they are from different taxonomic groups, underlying DNA sequences of identical fingerprints are more similar to each other in probe sets made with the new versus the previous algorithm. Complete removal of large taxonomic groups from training data does not greatly decrease the ability of probe sets to distinguish those groups. Probe sets made from the new algorithm create fingerprints that more reliably cluster into biologically meaningful groups. The method can readily distinguish microbial phylotypes that were excluded from the training sequences, suggesting novel microbes can also be detected.

  6. Information performances and illative sequences: Sequential organization of explanations of chemical phase equilibrium

    Science.gov (United States)

    Brown, Nathaniel James Swanton

    While there is consensus that conceptual change is surprisingly difficult, many competing theories of conceptual change co-exist in the literature. This dissertation argues that this discord is partly the result of an inadequate account of the unwritten rules of human social interaction that underlie the field's preferred methodology---semi-structured interviewing. To better understand the contributions of interaction during explanations, I analyze eight undergraduate general chemistry students as they attempt to explain to various people, for various reasons, why phenomena involving chemical phase equilibrium occur. Using the methods of interaction analysis, I characterize the unwritten, but systematic, rules that these participants follow as they explain. The result is a description of the contributions of interaction to explaining. Each step in each explanation is a jointly performed expression of a subject-predicate relation, an interactive accomplishment I call an information performance (in-form, for short). Unlike clauses, in-forms need not have a coherent grammatical structure. Unlike speaker turns, in-forms have the clear function of expressing information. Unlike both clauses and speaker turns, in-forms are a co-construction, jointly performed by both the primary speaker and the other interlocutor. The other interlocutor strongly affects the form and content of each explanation by giving or withholding feedback at the end of each in-form, moments I call feedback-relevant places. While in-forms are the bricks out of which the explanation is constructed, they are secured by a series of inferential links I call an illative sequence. Illative sequences are forward-searching, starting with a remembered fact or observation and following a chain of inferences in the hope it leads to the target phenomenon. The participants treat an explanation as a success if the illative sequence generates an in-form that describes the phenomenon. If the illative sequence does

  7. Modeling habitat connectivity to inform reintroductions: a case study with the Chiricahua Leopard Frog

    Science.gov (United States)

    Jarchow, Christopher J.; Hossack, Blake R.; Sigafus, Brent H.; Schwalbe, Cecil R.; Muths, Erin L.

    2016-01-01

    Managing species with intensive tools such as reintroduction may focus on single sites or entire landscapes. For vagile species, long-term persistence will require colonization and establishment in neighboring habitats. Therefore, both suitable colonization sites and suitable dispersal corridors between sites are required. Assessment of landscapes for both requirements can contribute to ranking and selection of reintroduction areas, thereby improving management success. Following eradication of invasive American Bullfrogs (Lithobates catesbeianus) from most of Buenos Aires National Wildlife Refuge (BANWR; Arizona, United States), larval Chiricahua Leopard Frogs (Lithobates chiricahuensis) from a private pond were reintroduced into three stock ponds. Populations became established at all three reintroduction sites followed by colonization of neighboring ponds in subsequent years. Our aim was to better understand colonization patterns by the federally threatened L. chiricahuensis which could help inform other reintroduction efforts. We assessed the influence of four landscape features on colonization. Using surveys from 2007 and information about the landscape, we developed a habitat connectivity model, based on electrical circuit theory, that identified potential dispersal corridors after explicitly accounting for imperfect detection of frogs. Landscape features provided little insight into why some sites were colonized and others were not, results that are likely because of the uniformity of the BANWR landscape. While corridor modeling may be effective in more-complex landscapes, our results suggest focusing on local habitat will be more useful at BANWR. We also illustrate that existing data, even when limited in spatial or temporal resolution, can provide information useful in formulating management actions.

  8. Multi-scale coding of genomic information: From DNA sequence to genome structure and function

    International Nuclear Information System (INIS)

    Arneodo, Alain; Vaillant, Cedric; Audit, Benjamin; Argoul, Francoise; D'Aubenton-Carafa, Yves; Thermes, Claude

    2011-01-01

    Understanding how chromatin is spatially and dynamically organized in the nucleus of eukaryotic cells and how this affects genome functions is one of the main challenges of cell biology. Since the different orders of packaging in the hierarchical organization of DNA condition the accessibility of DNA sequence elements to trans-acting factors that control the transcription and replication processes, there is actually a wealth of structural and dynamical information to learn in the primary DNA sequence. In this review, we show that when using concepts, methodologies, numerical and experimental techniques coming from statistical mechanics and nonlinear physics combined with wavelet-based multi-scale signal processing, we are able to decipher the multi-scale sequence encoding of chromatin condensation-decondensation mechanisms that play a fundamental role in regulating many molecular processes involved in nuclear functions.

  9. MedlinePlus Connect: Linking Patient Portals and Electronic Health Records to Health Information

    Science.gov (United States)

    ... Here: Home → MedlinePlus Connect URL of this page: https://medlineplus.gov/connect/overview.html MedlinePlus Connect Linking ... will change.) Old URLs New URLs Web Application https://apps.nlm.nih.gov/medlineplus/services/mpconnect.cfm? ...

  10. 76 FR 2755 - Proposed Information Collection (Statement in Support of Claim for Service Connection for Post...

    Science.gov (United States)

    2011-01-14

    ... (Statement in Support of Claim for Service Connection for Post-Traumatic Stress Disorder (PTSD) and Statement in Support of Claim for Service Connection for Post-Traumatic Stress Disorder (PTSD) Secondary to... to substantiate claims for service connection post-traumatic stress disorder (PTSD). DATES: Written...

  11. Refined repetitive sequence searches utilizing a fast hash function and cross species information retrievals

    Directory of Open Access Journals (Sweden)

    Reneker Jeff

    2005-05-01

    Full Text Available Abstract Background Searching for small tandem/disperse repetitive DNA sequences streamlines many biomedical research processes. For instance, whole genomic array analysis in yeast has revealed 22 PHO-regulated genes. The promoter regions of all but one of them contain at least one of the two core Pho4p binding sites, CACGTG and CACGTT. In humans, microsatellites play a role in a number of rare neurodegenerative diseases such as spinocerebellar ataxia type 1 (SCA1. SCA1 is a hereditary neurodegenerative disease caused by an expanded CAG repeat in the coding sequence of the gene. In bacterial pathogens, microsatellites are proposed to regulate expression of some virulence factors. For example, bacteria commonly generate intra-strain diversity through phase variation which is strongly associated with virulence determinants. A recent analysis of the complete sequences of the Helicobacter pylori strains 26695 and J99 has identified 46 putative phase-variable genes among the two genomes through their association with homopolymeric tracts and dinucleotide repeats. Life scientists are increasingly interested in studying the function of small sequences of DNA. However, current search algorithms often generate thousands of matches – most of which are irrelevant to the researcher. Results We present our hash function as well as our search algorithm to locate small sequences of DNA within multiple genomes. Our system applies information retrieval algorithms to discover knowledge of cross-species conservation of repeat sequences. We discuss our incorporation of the Gene Ontology (GO database into these algorithms. We conduct an exhaustive time analysis of our system for various repetitive sequence lengths. For instance, a search for eight bases of sequence within 3.224 GBases on 49 different chromosomes takes 1.147 seconds on average. To illustrate the relevance of the search results, we conduct a search with and without added annotation terms for the

  12. Phylum-Level Conservation of Regulatory Information in Nematodes despite Extensive Non-coding Sequence Divergence

    Science.gov (United States)

    Gordon, Kacy L.; Arthur, Robert K.; Ruvinsky, Ilya

    2015-01-01

    Gene regulatory information guides development and shapes the course of evolution. To test conservation of gene regulation within the phylum Nematoda, we compared the functions of putative cis-regulatory sequences of four sets of orthologs (unc-47, unc-25, mec-3 and elt-2) from distantly-related nematode species. These species, Caenorhabditis elegans, its congeneric C. briggsae, and three parasitic species Meloidogyne hapla, Brugia malayi, and Trichinella spiralis, represent four of the five major clades in the phylum Nematoda. Despite the great phylogenetic distances sampled and the extensive sequence divergence of nematode genomes, all but one of the regulatory elements we tested are able to drive at least a subset of the expected gene expression patterns. We show that functionally conserved cis-regulatory elements have no more extended sequence similarity to their C. elegans orthologs than would be expected by chance, but they do harbor motifs that are important for proper expression of the C. elegans genes. These motifs are too short to be distinguished from the background level of sequence similarity, and while identical in sequence they are not conserved in orientation or position. Functional tests reveal that some of these motifs contribute to proper expression. Our results suggest that conserved regulatory circuitry can persist despite considerable turnover within cis elements. PMID:26020930

  13. Phylum-Level Conservation of Regulatory Information in Nematodes despite Extensive Non-coding Sequence Divergence.

    Directory of Open Access Journals (Sweden)

    Kacy L Gordon

    2015-05-01

    Full Text Available Gene regulatory information guides development and shapes the course of evolution. To test conservation of gene regulation within the phylum Nematoda, we compared the functions of putative cis-regulatory sequences of four sets of orthologs (unc-47, unc-25, mec-3 and elt-2 from distantly-related nematode species. These species, Caenorhabditis elegans, its congeneric C. briggsae, and three parasitic species Meloidogyne hapla, Brugia malayi, and Trichinella spiralis, represent four of the five major clades in the phylum Nematoda. Despite the great phylogenetic distances sampled and the extensive sequence divergence of nematode genomes, all but one of the regulatory elements we tested are able to drive at least a subset of the expected gene expression patterns. We show that functionally conserved cis-regulatory elements have no more extended sequence similarity to their C. elegans orthologs than would be expected by chance, but they do harbor motifs that are important for proper expression of the C. elegans genes. These motifs are too short to be distinguished from the background level of sequence similarity, and while identical in sequence they are not conserved in orientation or position. Functional tests reveal that some of these motifs contribute to proper expression. Our results suggest that conserved regulatory circuitry can persist despite considerable turnover within cis elements.

  14. [Study on quality evaluation of sequence and SSR information in transcriptome of Astragalus membranacus].

    Science.gov (United States)

    Chang, Yue; Yang, Song; Liu, Zhen-Peng; Ren, Wei-Chao; Liu, Jie; Ma, Wei

    2016-04-01

    In this study, 454/Roche GS FLX sequencing technology was used to obtain the data of the Astragalus membranaceus. Four hundred and fifty-four Sequencing System Software was applied to carry out the transcription of the group from scratch. Using MISA tools, 9 893 unigenes were selected for the sequence of the genome of A. membranaceus, and the information of SSR locus was analyzed. According to the result, the average length of reads was 413 bp, about 86% of the reads was involved in the splicing, the length of the N50 was 1 205 bp, the number of unigenes was measured by the whole transcript. 1 729 SSR loci in the A. membranaceus transcriptome were searched, the occurrence frequency of SSR was 9.24%, the frequency of SSR in the whole transcriptome was 13.42%, the average length of SSR was 7.97 kb. One hundred and twenty-seven kinds of core repeat sequences were found, the dominant type was TG/AC type of dinucleotide, it appeared to account for 4.25% of the total SSR locus. The results of the sequence of the transcription of the A. membranaceus transcriptome revealed the overall expression, and a large number of unigenessequence was obtained, and the SSR locus in the genome of the A. membranaceus is high, and the type is diverse, and the polymorphism of the gene is high. Copyright© by the Chinese Pharmaceutical Association.

  15. Towards rationally redesigning bacterial signaling systems using information encoded in abundant sequence data

    Science.gov (United States)

    Cheng, Ryan; Morcos, Faruck; Levine, Herbert; Onuchic, Jose

    2014-03-01

    An important challenge in biology is to distinguish the subset of residues that allow bacterial two-component signaling (TCS) proteins to preferentially interact with their correct TCS partner such that they can bind and transfer signal. Detailed knowledge of this information would allow one to search sequence-space for mutations that can systematically tune the signal transmission between TCS partners as well as re-encode a TCS protein to preferentially transfer signals to a non-partner. Motivated by the notion that this detailed information is found in sequence data, we explore the mutual sequence co-evolution between signaling partners to infer how mutations can positively or negatively alter their interaction. Using Direct Coupling Analysis (DCA) for determining evolutionarily conserved interprotein interactions, we apply a DCA-based metric to quantify mutational changes in the interaction between TCS proteins and demonstrate that it accurately correlates with experimental mutagenesis studies probing the mutational change in the in vitro phosphotransfer. Our methodology serves as a potential framework for the rational design of TCS systems as well as a framework for the system-level study of protein-protein interactions in sequence-rich systems. This research has been supported by the NSF INSPIRE award MCB-1241332 and by the CTBP sponsored by the NSF (Grant PHY-1308264).

  16. Sequence exploration reveals information bias among molecular markers used in phylogenetic reconstruction for Colletotrichum species.

    Science.gov (United States)

    Rampersad, Sephra N; Hosein, Fazeeda N; Carrington, Christine Vf

    2014-01-01

    The Colletotrichum gloeosporioides species complex is among the most destructive fungal plant pathogens in the world, however, identification of isolates of quarantine importance to the intra-specific level is confounded by a number of factors that affect phylogenetic reconstruction. Information bias and quality parameters were investigated to determine whether nucleotide sequence alignments and phylogenetic trees accurately reflect the genetic diversity and phylogenetic relatedness of individuals. Sequence exploration of GAPDH, ACT, TUB2 and ITS markers indicated that the query sequences had different patterns of nucleotide substitution but were without evidence of base substitution saturation. Regions of high entropy were much more dispersed in the ACT and GAPDH marker alignments than for the ITS and TUB2 markers. A discernible bimodal gap in the genetic distance frequency histograms was produced for the ACT and GAPDH markers which indicated successful separation of intra- and inter-specific sequences in the data set. Overall, analyses indicated clear differences in the ability of these markers to phylogenetically separate individuals to the intra-specific level which coincided with information bias.

  17. Connecting Informal and Formal Learning Experiences in the Age of Participatory Media: Commentary on Bull et al. (2008)

    Science.gov (United States)

    Greenhow, Christine

    2008-01-01

    The recent editorial in this journal by Bull et al. ("Connecting Informal and Formal Learning Experiences in the Age of Participatory Media" Vol 8, Iss 2) discussed the challenges of bridging formal learning practices and informal learning opportunities within the context of today's Web-enhanced world. In this commentary, Christine…

  18. Application of the accident management information needs methodology to a severe accident sequence

    International Nuclear Information System (INIS)

    Ward, L.W.; Hanson, D.J.; Nelson, W.R.; Solberg, D.E.

    1989-01-01

    The U.S. Nuclear Regulatory Commission (NRC) is conducting an Accident Management Research Program that emphasizes the application of severe accident research results to enhance the capability of plant operating personnel to effectively manage severe accidents. A methodology to identify and assess the information needs of the operating staff of a nuclear power plant during a severe accident has been developed as part of the research program designed to resolve this issue. The methodology identifies the information needs of the plant personnel during a wide range of accident conditions, the existing plant measurements capable of supplying these information needs and what, if any minor additions to instrument and display systems would enhance the capability to manage accidents, known limitations on the capability of these measurements to function properly under the conditions that will be present during a wide range of severe accidents, and areas in which the information systems could mislead plant personnel. This paper presents an application of this methodology to a severe accident sequence to demonstrate its use in identifying the information which is available for management of the event. The methodology has been applied to a severe accident sequence in a Pressurized Water Reactor with a large dry containment. An examination of the capability of the existing measurements was then performed to determine whether the information needs can be supplied

  19. Impact of connected vehicle guidance information on network-wide average travel time

    Directory of Open Access Journals (Sweden)

    Jiangfeng Wang

    2016-12-01

    Full Text Available With the emergence of connected vehicle technologies, the potential positive impact of connected vehicle guidance on mobility has become a research hotspot by data exchange among vehicles, infrastructure, and mobile devices. This study is focused on micro-modeling and quantitatively evaluating the impact of connected vehicle guidance on network-wide travel time by introducing various affecting factors. To evaluate the benefits of connected vehicle guidance, a simulation architecture based on one engine is proposed representing the connected vehicle–enabled virtual world, and connected vehicle route guidance scenario is established through the development of communication agent and intelligent transportation systems agents using connected vehicle application programming interface considering the communication properties, such as path loss and transmission power. The impact of connected vehicle guidance on network-wide travel time is analyzed by comparing with non-connected vehicle guidance in response to different market penetration rate, following rate, and congestion level. The simulation results explore that average network-wide travel time in connected vehicle guidance shows a significant reduction versus that in non–connected vehicle guidance. Average network-wide travel time in connected vehicle guidance have an increase of 42.23% comparing to that in non-connected vehicle guidance, and average travel time variability (represented by the coefficient of variance increases as the travel time increases. Other vital findings include that higher penetration rate and following rate generate bigger savings of average network-wide travel time. The savings of average network-wide travel time increase from 17% to 38% according to different congestion levels, and savings of average travel time in more serious congestion have a more obvious improvement for the same penetration rate or following rate.

  20. Clinical decision support for whole genome sequence information leveraging a service-oriented architecture: a prototype.

    Science.gov (United States)

    Welch, Brandon M; Rodriguez-Loya, Salvador; Eilbeck, Karen; Kawamoto, Kensaku

    2014-01-01

    Whole genome sequence (WGS) information could soon be routinely available to clinicians to support the personalized care of their patients. At such time, clinical decision support (CDS) integrated into the clinical workflow will likely be necessary to support genome-guided clinical care. Nevertheless, developing CDS capabilities for WGS information presents many unique challenges that need to be overcome for such approaches to be effective. In this manuscript, we describe the development of a prototype CDS system that is capable of providing genome-guided CDS at the point of care and within the clinical workflow. To demonstrate the functionality of this prototype, we implemented a clinical scenario of a hypothetical patient at high risk for Lynch Syndrome based on his genomic information. We demonstrate that this system can effectively use service-oriented architecture principles and standards-based components to deliver point of care CDS for WGS information in real-time.

  1. Cognitive Connected Vehicle Information System Design Requirement for Safety: Role of Bayesian Artificial Intelligence

    OpenAIRE

    Ata Khan

    2013-01-01

    Intelligent transportation systems (ITS) are gaining acceptance around the world and the connected vehicle component of ITS is recognized as a high priority research and development area in many technologically advanced countries. Connected vehicles are expected to have the capability of safe, efficient and eco-driving operations whether these are under human control or in the adaptive machine control mode of operations. The race is on to design the capability to operate in connected traffic ...

  2. On the Concept of Cis-regulatory Information: From Sequence Motifs to Logic Functions

    Science.gov (United States)

    Tarpine, Ryan; Istrail, Sorin

    The regulatory genome is about the “system level organization of the core genomic regulatory apparatus, and how this is the locus of causality underlying the twin phenomena of animal development and animal evolution” (E.H. Davidson. The Regulatory Genome: Gene Regulatory Networks in Development and Evolution, Academic Press, 2006). Information processing in the regulatory genome is done through regulatory states, defined as sets of transcription factors (sequence-specific DNA binding proteins which determine gene expression) that are expressed and active at the same time. The core information processing machinery consists of modular DNA sequence elements, called cis-modules, that interact with transcription factors. The cis-modules “read” the information contained in the regulatory state of the cell through transcription factor binding, “process” it, and directly or indirectly communicate with the basal transcription apparatus to determine gene expression. This endowment of each gene with the information-receiving capacity through their cis-regulatory modules is essential for the response to every possible regulatory state to which it might be exposed during all phases of the life cycle and in all cell types. We present here a set of challenges addressed by our CYRENE research project aimed at studying the cis-regulatory code of the regulatory genome. The CYRENE Project is devoted to (1) the construction of a database, the cis-Lexicon, containing comprehensive information across species about experimentally validated cis-regulatory modules; and (2) the software development of a next-generation genome browser, the cis-Browser, specialized for the regulatory genome. The presentation is anchored on three main computational challenges: the Gene Naming Problem, the Consensus Sequence Bottleneck Problem, and the Logic Function Inference Problem.

  3. Moving target detection based on temporal-spatial information fusion for infrared image sequences

    Science.gov (United States)

    Toing, Wu-qin; Xiong, Jin-yu; Zeng, An-jun; Wu, Xiao-ping; Xu, Hao-peng

    2009-07-01

    Moving target detection and localization is one of the most fundamental tasks in visual surveillance. In this paper, through analyzing the advantages and disadvantages of the traditional approaches about moving target detection, a novel approach based on temporal-spatial information fusion is proposed for moving target detection. The proposed method combines the spatial feature in single frame and the temporal properties within multiple frames of an image sequence of moving target. First, the method uses the spatial image segmentation for target separation from background and uses the local temporal variance for extracting targets and wiping off the trail artifact. Second, the logical "and" operator is used to fuse the temporal and spatial information. In the end, to the fusion image sequence, the morphological filtering and blob analysis are used to acquire exact moving target. The algorithm not only requires minimal computation and memory but also quickly adapts to the change of background and environment. Comparing with other methods, such as the KDE, the Mixture of K Gaussians, etc., the simulation results show the proposed method has better validity and higher adaptive for moving target detection, especially in infrared image sequences with complex illumination change, noise change, and so on.

  4. Balancing Health Information Exchange and Privacy Governance from a Patient-Centred Connected Health and Telehealth Perspective.

    Science.gov (United States)

    Kuziemsky, Craig E; Gogia, Shashi B; Househ, Mowafa; Petersen, Carolyn; Basu, Arindam

    2018-04-22

    Connected healthcare is an essential part of patient-centred care delivery. Technology such as telehealth is a critical part of connected healthcare. However, exchanging health information brings the risk of privacy issues. To better manage privacy risks we first need to understand the different patterns of patient-centred care in order to tailor solutions to address privacy risks.  Drawing upon published literature, we develop a business model to enable patient-centred care via telehealth. The model identifies three patient-centred connected health patterns. We then use the patterns to analyse potential privacy risks and possible solutions from different types of telehealth delivery.  Connected healthcare raises the risk of unwarranted access to health data and related invasion of privacy. However, the risk and extent of privacy issues differ according to the pattern of patient-centred care delivery and the type of particular challenge as they enable the highest degree of connectivity and thus the greatest potential for privacy breaches.  Privacy issues are a major concern in telehealth systems and patients, providers, and administrators need to be aware of these privacy issues and have guidance on how to manage them. This paper integrates patient-centred connected health care, telehealth, and privacy risks to provide an understanding of how risks vary across different patterns of patient-centred connected health and different types of telehealth delivery. Georg Thieme Verlag KG Stuttgart.

  5. 76 FR 16039 - Agency Information Collection (Statement in Support of Claim for Service Connection for PTSD...

    Science.gov (United States)

    2011-03-22

    ... (Statement in Support of Claim for Service Connection for PTSD) Under OMB Review AGENCY: Veterans Benefits...: Titles: a. Statement in Support of Claim for Service Connection for Post- Traumatic Stress Disorder (PTSD... Disorder (PTSD) Secondary to Personal Assault, VA Form 21-0781a. OMB Control Number: 2900-0659. Type of...

  6. How could disclosing incidental information from whole-genome sequencing affect patient behavior?

    Science.gov (United States)

    Christensen, Kurt D; Green, Robert C

    2013-06-01

    In this article, we argue that disclosure of incidental findings from whole-genome sequencing has the potential to motivate individuals to change health behaviors through psychological mechanisms that differ from typical risk assessment interventions. Their ability to do so, however, is likely to be highly contingent upon the nature of the incidental findings and how they are disclosed, the context of the disclosure and the characteristics of the patient. Moreover, clinicians need to be aware that behavioral responses may occur in unanticipated ways. This article argues for commentators and policy makers to take a cautious but optimistic perspective while empirical evidence is collected through ongoing research involving whole-genome sequencing and the disclosure of incidental information.

  7. Informing conservation management about structural versus functional connectivity: a case-study of Cross River gorillas.

    Science.gov (United States)

    Imong, Inaoyom; Robbins, Martha M; Mundry, Roger; Bergl, Richard; Kühl, Hjalmar S

    2014-10-01

    Connectivity among subpopulations is vital for the persistence of small and fragmented populations. For management interventions to be effective conservation planners have to make the critical distinction between structural connectivity (based on landscape structure) and functional connectivity (which considers both landscape structure and organism-specific behavioral attributes) which can differ considerably within a given context. We assessed spatial and temporal changes in structural and functional connectivity of the Cross River gorilla Gorilla gorilla diehli (CRG) population in a 12,000 km(2) landscape in the Nigeria-Cameroon border region over a 23-year period, comparing two periods: 1987-2000 and 2000-2010. Despite substantial forest connections between occupied areas, genetic evidence shows that only limited dispersal occurs among CRG subpopulations. We used remotely sensed land-cover data and simulated human pressure (using a spatially explicit agent-based model) to assess human impact on connectivity of the CRG population. We calculated cost-weighted distances between areas occupied by gorillas as measures of connectivity (structural based on land-cover only, functional based on both land-cover and simulated human pressure). Whereas structural connectivity decreased by 5% over the 23-year period, functional connectivity decreased by 11%, with both decreasing more during the latter compared to the earlier period. Our results highlight the increasing threat of isolation of CRG subpopulations due to human disturbance, and provide insight into how increasing human influence may lead to functional isolation of wildlife populations despite habitat continuity, a pressing and common issue in tropical Africa often not accounted for when deciding management interventions. In addition to quantifying threats to connectivity, our study provides crucial evidence for management authorities to identify actions that are more likely to be effective for conservation of

  8. A Proposed Clinical Decision Support Architecture Capable of Supporting Whole Genome Sequence Information

    Directory of Open Access Journals (Sweden)

    Brandon M. Welch

    2014-04-01

    Full Text Available Whole genome sequence (WGS information may soon be widely available to help clinicians personalize the care and treatment of patients. However, considerable barriers exist, which may hinder the effective utilization of WGS information in a routine clinical care setting. Clinical decision support (CDS offers a potential solution to overcome such barriers and to facilitate the effective use of WGS information in the clinic. However, genomic information is complex and will require significant considerations when developing CDS capabilities. As such, this manuscript lays out a conceptual framework for a CDS architecture designed to deliver WGS-guided CDS within the clinical workflow. To handle the complexity and breadth of WGS information, the proposed CDS framework leverages service-oriented capabilities and orchestrates the interaction of several independently-managed components. These independently-managed components include the genome variant knowledge base, the genome database, the CDS knowledge base, a CDS controller and the electronic health record (EHR. A key design feature is that genome data can be stored separately from the EHR. This paper describes in detail: (1 each component of the architecture; (2 the interaction of the components; and (3 how the architecture attempts to overcome the challenges associated with WGS information. We believe that service-oriented CDS capabilities will be essential to using WGS information for personalized medicine.

  9. A proposed clinical decision support architecture capable of supporting whole genome sequence information.

    Science.gov (United States)

    Welch, Brandon M; Loya, Salvador Rodriguez; Eilbeck, Karen; Kawamoto, Kensaku

    2014-04-04

    Whole genome sequence (WGS) information may soon be widely available to help clinicians personalize the care and treatment of patients. However, considerable barriers exist, which may hinder the effective utilization of WGS information in a routine clinical care setting. Clinical decision support (CDS) offers a potential solution to overcome such barriers and to facilitate the effective use of WGS information in the clinic. However, genomic information is complex and will require significant considerations when developing CDS capabilities. As such, this manuscript lays out a conceptual framework for a CDS architecture designed to deliver WGS-guided CDS within the clinical workflow. To handle the complexity and breadth of WGS information, the proposed CDS framework leverages service-oriented capabilities and orchestrates the interaction of several independently-managed components. These independently-managed components include the genome variant knowledge base, the genome database, the CDS knowledge base, a CDS controller and the electronic health record (EHR). A key design feature is that genome data can be stored separately from the EHR. This paper describes in detail: (1) each component of the architecture; (2) the interaction of the components; and (3) how the architecture attempts to overcome the challenges associated with WGS information. We believe that service-oriented CDS capabilities will be essential to using WGS information for personalized medicine.

  10. 26 CFR 301.6103(n)-2T - Disclosure of return information in connection with written contracts among the IRS...

    Science.gov (United States)

    2010-04-01

    ... (temporary). 301.6103(n)-2T Section 301.6103(n)-2T Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF... Returns Returns and Records § 301.6103(n)-2T Disclosure of return information in connection with written...) General rule. (1) Pursuant to the provisions of sections 6103(n) and 7623 of the Internal Revenue Code and...

  11. Reduction of Interhemispheric Functional Connectivity in Sensorimotor and Visual Information Processing Pathways in Schizophrenia

    Directory of Open Access Journals (Sweden)

    Xu Lang

    2016-01-01

    Conclusions: Interhemispheric functional connectivity in the sensorimotor and visual processing pathways was reduced in patients with schizophrenia, but this reduction was unrelated to the disease state; thus, this reduction may serve as a trait marker of schizophrenia.

  12. Population Connectivity Measures of Fishery-Targeted Coral Reef Species to Inform Marine Reserve Network Design in Fiji.

    Science.gov (United States)

    Eastwood, Erin K; López, Elora H; Drew, Joshua A

    2016-01-25

    Coral reef fish serve as food sources to coastal communities worldwide, yet are vulnerable to mounting anthropogenic pressures like overfishing and climate change. Marine reserve networks have become important tools for mitigating these pressures, and one of the most critical factors in determining their spatial design is the degree of connectivity among different populations of species prioritized for protection. To help inform the spatial design of an expanded reserve network in Fiji, we used rapidly evolving mitochondrial genes to investigate connectivity patterns of three coral reef species targeted by fisheries in Fiji: Epinephelus merra (Serranidae), Halichoeres trimaculatus (Labridae), and Holothuria atra (Holothuriidae). The two fish species, E. merra and Ha. trimaculatus, exhibited low genetic structuring and high amounts of gene flow, whereas the sea cucumber Ho. atra displayed high genetic partitioning and predominantly westward gene flow. The idiosyncratic patterns observed among these species indicate that patterns of connectivity in Fiji are likely determined by a combination of oceanographic and ecological characteristics. Our data indicate that in the cases of species with high connectivity, other factors such as representation or political availability may dictate where reserves are placed. In low connectivity species, ensuring upstream and downstream connections is critical.

  13. Accessible surface area of proteins from purely sequence information and the importance of global features

    Science.gov (United States)

    Faraggi, Eshel; Zhou, Yaoqi; Kloczkowski, Andrzej

    2014-03-01

    We present a new approach for predicting the accessible surface area of proteins. The novelty of this approach lies in not using residue mutation profiles generated by multiple sequence alignments as descriptive inputs. Rather, sequential window information and the global monomer and dimer compositions of the chain are used. We find that much of the lost accuracy due to the elimination of evolutionary information is recouped by the use of global features. Furthermore, this new predictor produces similar results for proteins with or without sequence homologs deposited in the Protein Data Bank, and hence shows generalizability. Finally, these predictions are obtained in a small fraction (1/1000) of the time required to run mutation profile based prediction. All these factors indicate the possible usability of this work in de-novo protein structure prediction and in de-novo protein design using iterative searches. Funded in part by the financial support of the National Institutes of Health through Grants R01GM072014 and R01GM073095, and the National Science Foundation through Grant NSF MCB 1071785.

  14. Designing for scale: optimising the health information system architecture for mobile maternal health messaging in South Africa (MomConnect).

    Science.gov (United States)

    Seebregts, Christopher; Dane, Pierre; Parsons, Annie Neo; Fogwill, Thomas; Rogers, Debbie; Bekker, Marcha; Shaw, Vincent; Barron, Peter

    2018-01-01

    MomConnect is a national initiative coordinated by the South African National Department of Health that sends text-based mobile phone messages free of charge to pregnant women who voluntarily register at any public healthcare facility in South Africa. We describe the system design and architecture of the MomConnect technical platform, planned as a nationally scalable and extensible initiative. It uses a health information exchange that can connect any standards-compliant electronic front-end application to any standards-compliant electronic back-end database. The implementation of the MomConnect technical platform, in turn, is a national reference application for electronic interoperability in line with the South African National Health Normative Standards Framework. The use of open content and messaging standards enables the architecture to include any application adhering to the selected standards. Its national implementation at scale demonstrates both the use of this technology and a key objective of global health information systems, which is to achieve implementation scale. The system's limited clinical information, initially, allowed the architecture to focus on the base standards and profiles for interoperability in a resource-constrained environment with limited connectivity and infrastructural capacity. Maintenance of the system requires mobilisation of national resources. Future work aims to use the standard interfaces to include data from additional applications as well as to extend and interface the framework with other public health information systems in South Africa. The development of this platform has also shown the benefits of interoperability at both an organisational and technical level in South Africa.

  15. Spectral Sequences of Type Ia Supernovae. I. Connecting Normal and Subluminous SNe Ia and the Presence of Unburned Carbon

    Energy Technology Data Exchange (ETDEWEB)

    Heringer, E.; Kerkwijk, M. H. van [Department of Astronomy and Astrophysics, University of Toronto, 50 Saint George Street, Toronto, ON M5S 3H4 (Canada); Sim, S. A. [Astrophysics Research Centre, School of Mathematics and Physics, Queens University Belfast, Belfast BT7 1NN (United Kingdom); Kerzendorf, W. E. [European Southern Observatory (ESO), Karl-Schwarzschild-Straße 2, D-85748 Garching (Germany)

    2017-09-01

    Type Ia supernovae (SNe Ia) are generally agreed to arise from thermonuclear explosions of carbon–oxygen white dwarfs. The actual path to explosion, however, remains elusive, with numerous plausible parent systems and explosion mechanisms suggested. Observationally, SNe Ia have multiple subclasses, distinguished by their light curves and spectra. This raises the question of whether these indicate that multiple mechanisms occur in nature or that explosions have a large but continuous range of physical properties. We revisit the idea that normal and 91bg-like SNe can be understood as part of a spectral sequence in which changes in temperature dominate. Specifically, we find that a single ejecta structure is sufficient to provide reasonable fits of both the normal SN Ia SN 2011fe and the 91bg-like SN 2005bl, provided that the luminosity and thus temperature of the ejecta are adjusted appropriately. This suggests that the outer layers of the ejecta are similar, thus providing some support for a common explosion mechanism. Our spectral sequence also helps to shed light on the conditions under which carbon can be detected in premaximum SN Ia spectra—we find that emission from iron can “fill in” the carbon trough in cool SNe Ia. This may indicate that the outer layers of the ejecta of events in which carbon is detected are relatively metal-poor compared to events in which carbon is not detected.

  16. Importance of Viral Sequence Length and Number of Variable and Informative Sites in Analysis of HIV Clustering.

    Science.gov (United States)

    Novitsky, Vlad; Moyo, Sikhulile; Lei, Quanhong; DeGruttola, Victor; Essex, M

    2015-05-01

    To improve the methodology of HIV cluster analysis, we addressed how analysis of HIV clustering is associated with parameters that can affect the outcome of viral clustering. The extent of HIV clustering and tree certainty was compared between 401 HIV-1C near full-length genome sequences and subgenomic regions retrieved from the LANL HIV Database. Sliding window analysis was based on 99 windows of 1,000 bp and 45 windows of 2,000 bp. Potential associations between the extent of HIV clustering and sequence length and the number of variable and informative sites were evaluated. The near full-length genome HIV sequences showed the highest extent of HIV clustering and the highest tree certainty. At the bootstrap threshold of 0.80 in maximum likelihood (ML) analysis, 58.9% of near full-length HIV-1C sequences but only 15.5% of partial pol sequences (ViroSeq) were found in clusters. Among HIV-1 structural genes, pol showed the highest extent of clustering (38.9% at a bootstrap threshold of 0.80), although it was significantly lower than in the near full-length genome sequences. The extent of HIV clustering was significantly higher for sliding windows of 2,000 bp than 1,000 bp. We found a strong association between the sequence length and proportion of HIV sequences in clusters, and a moderate association between the number of variable and informative sites and the proportion of HIV sequences in clusters. In HIV cluster analysis, the extent of detectable HIV clustering is directly associated with the length of viral sequences used, as well as the number of variable and informative sites. Near full-length genome sequences could provide the most informative HIV cluster analysis. Selected subgenomic regions with a high extent of HIV clustering and high tree certainty could also be considered as a second choice.

  17. A Scaffold Analysis Tool Using Mate-Pair Information in Genome Sequencing

    Directory of Open Access Journals (Sweden)

    Pan-Gyu Kim

    2008-01-01

    Full Text Available We have developed a Windows-based program, ConPath, as a scaffold analyzer. ConPath constructs scaffolds by ordering and orienting separate sequence contigs by exploiting the mate-pair information between contig-pairs. Our algorithm builds directed graphs from link information and traverses them to find the longest acyclic graphs. Using end read pairs of fixed-sized mate-pair libraries, ConPath determines relative orientations of all contigs, estimates the gap size of each adjacent contig pair, and reports wrong assembly information by validating orientations and gap sizes. We have utilized ConPath in more than 10 microbial genome projects, including Mannheimia succiniciproducens and Vibro vulnificus, where we verified contig assembly and identified several erroneous contigs using the four types of error defined in ConPath. Also, ConPath supports some convenient features and viewers that permit investigation of each contig in detail; these include contig viewer, scaffold viewer, edge information list, mate-pair list, and the printing of complex scaffold structures.

  18. Diluted connectivity in pattern association networks facilitates the recall of information from the hippocampus to the neocortex.

    Science.gov (United States)

    Rolls, Edmund T

    2015-01-01

    The recall of information stored in the hippocampus involves a series of corticocortical backprojections via the entorhinal cortex, parahippocampal gyrus, and one or more neocortical stages. Each stage is considered to be a pattern association network, with the retrieval cue at each stage the firing of neurons in the previous stage. The leading factor that determines the capacity of this multistage pattern association backprojection pathway is the number of connections onto any one neuron, which provides a quantitative basis for why there are as many backprojections between adjacent stages in the hierarchy as forward projections. The issue arises of why this multistage backprojection system uses diluted connectivity. One reason is that a multistage backprojection system with expansion of neuron numbers at each stage enables the hippocampus to address during recall the very large numbers of neocortical neurons, which would otherwise require hippocampal neurons to make very large numbers of synapses if they were directly onto neocortical neurons. The second reason is that as shown here, diluted connectivity in the backprojection pathways reduces the probability of more than one connection onto a receiving neuron in the backprojecting pathways, which otherwise reduces the capacity of the system, that is the number of memories that can be recalled from the hippocampus to the neocortex. For similar reasons, diluted connectivity is advantageous in pattern association networks in other brain systems such as the orbitofrontal cortex and amygdala; for related reasons, in autoassociation networks in, for example, the hippocampal CA3 and the neocortex; and for the different reason that diluted connectivity facilitates the operation of competitive networks in forward-connected cortical systems. © 2015 Elsevier B.V. All rights reserved.

  19. Informational and linguistic analysis of large genomic sequence collections via efficient Hadoop cluster algorithms.

    Science.gov (United States)

    Ferraro Petrillo, Umberto; Roscigno, Gianluca; Cattaneo, Giuseppe; Giancarlo, Raffaele

    2018-06-01

    Information theoretic and compositional/linguistic analysis of genomes have a central role in bioinformatics, even more so since the associated methodologies are becoming very valuable also for epigenomic and meta-genomic studies. The kernel of those methods is based on the collection of k-mer statistics, i.e. how many times each k-mer in {A,C,G,T}k occurs in a DNA sequence. Although this problem is computationally very simple and efficiently solvable on a conventional computer, the sheer amount of data available now in applications demands to resort to parallel and distributed computing. Indeed, those type of algorithms have been developed to collect k-mer statistics in the realm of genome assembly. However, they are so specialized to this domain that they do not extend easily to the computation of informational and linguistic indices, concurrently on sets of genomes. Following the well-established approach in many disciplines, and with a growing success also in bioinformatics, to resort to MapReduce and Hadoop to deal with 'Big Data' problems, we present KCH, the first set of MapReduce algorithms able to perform concurrently informational and linguistic analysis of large collections of genomic sequences on a Hadoop cluster. The benchmarking of KCH that we provide indicates that it is quite effective and versatile. It is also competitive with respect to the parallel and distributed algorithms highly specialized to k-mer statistics collection for genome assembly problems. In conclusion, KCH is a much needed addition to the growing number of algorithms and tools that use MapReduce for bioinformatics core applications. The software, including instructions for running it over Amazon AWS, as well as the datasets are available at http://www.di-srv.unisa.it/KCH. umberto.ferraro@uniroma1.it. Supplementary data are available at Bioinformatics online.

  20. Globalization: Ecological consequences of global-scale connectivity in people, resources and information

    Science.gov (United States)

    Globalization is a phenomenon affecting all facets of the Earth System. Within the context of ecological systems, it is becoming increasingly apparent that global connectivity among terrestrial systems, the atmosphere, and oceans is driving many ecological dynamics at finer scales and pushing thresh...

  1. Location of core diagnostic information across various sequences in brain MRI and implications for efficiency of MRI scanner utilization.

    Science.gov (United States)

    Sharma, Aseem; Chatterjee, Arindam; Goyal, Manu; Parsons, Matthew S; Bartel, Seth

    2015-04-01

    Targeting redundancy within MRI can improve its cost-effective utilization. We sought to quantify potential redundancy in our brain MRI protocols. In this retrospective review, we aggregated 207 consecutive adults who underwent brain MRI and reviewed their medical records to document clinical indication, core diagnostic information provided by MRI, and its clinical impact. Contributory imaging abnormalities constituted positive core diagnostic information whereas absence of imaging abnormalities constituted negative core diagnostic information. The senior author selected core sequences deemed sufficient for extraction of core diagnostic information. For validating core sequences selection, four readers assessed the relative ease of extracting core diagnostic information from the core sequences. Potential redundancy was calculated by comparing the average number of core sequences to the average number of sequences obtained. Scanning had been performed using 9.4±2.8 sequences over 37.3±12.3 minutes. Core diagnostic information was deemed extractable from 2.1±1.1 core sequences, with an assumed scanning time of 8.6±4.8 minutes, reflecting a potential redundancy of 74.5%±19.1%. Potential redundancy was least in scans obtained for treatment planning (14.9%±25.7%) and highest in scans obtained for follow-up of benign diseases (81.4%±12.6%). In 97.4% of cases, all four readers considered core diagnostic information to be either easily extractable from core sequences or the ease to be equivalent to that from the entire study. With only one MRI lacking clinical impact (0.48%), overutilization did not seem to contribute to potential redundancy. High potential redundancy that can be targeted for more efficient scanner utilization exists in brain MRI protocols.

  2. The role of INGVterremoti blog in information management during the earthquake sequence in central Italy

    Directory of Open Access Journals (Sweden)

    Maurizio Pignone

    2017-01-01

    Full Text Available In this paper, we describe the role the INGVterremoti blog in information management during the first part of the earthquake sequence in central Italy (August 24 to September 30. In the last four years, we have been working on the INGVterremoti blog in order to provide quick updates on the ongoing seismic activity in Italy and in-depth scientific information. These include articles on specific historical earthquakes, seismic hazard, geological interpretations, source models from different type of data, effects at the surface, and so on. We have delivered information in quasi-real-time also about all the recent magnitude M≥4.0 earthquakes in Italy, the strongest events in the Mediterranean and in the world. During the 2016 central Italy, the INGVterremoti blog has continuously released information about seismic sequences with three types of posts: i updates on the ongoing seismic activity; ii reports on the activities carried out by the INGV teams in the field and any other working groups; iii in-depth scientific articles describing some specific analysis and results. All the blog posts have been shared automatically and in real time on the other social media of the INGVterremoti platform, also to counter the bad information and to fight rumors. These include Facebook, Twitter and INGVterremoti App on IOS and Android. As well, both the main INGV home page (http://www.ingv.it and the INGV earthquake portal (http://terremoti.ingv.it have published the contents of the blog on dedicated pages that were fed automatically. The work done day by day on the INGVterremoti blog has been coordinated with the INGV Press Office that has written several press releases based on the contents of the blog. Since August 24, 53 articles were published on the blog they have had more than 1.9 million views and 1 million visitors. The peak in the number of views, which was more than 800,000 in a single day, was registered on August 24, 2016, following the M 6

  3. LigandRFs: random forest ensemble to identify ligand-binding residues from sequence information alone

    KAUST Repository

    Chen, Peng

    2014-12-03

    Background Protein-ligand binding is important for some proteins to perform their functions. Protein-ligand binding sites are the residues of proteins that physically bind to ligands. Despite of the recent advances in computational prediction for protein-ligand binding sites, the state-of-the-art methods search for similar, known structures of the query and predict the binding sites based on the solved structures. However, such structural information is not commonly available. Results In this paper, we propose a sequence-based approach to identify protein-ligand binding residues. We propose a combination technique to reduce the effects of different sliding residue windows in the process of encoding input feature vectors. Moreover, due to the highly imbalanced samples between the ligand-binding sites and non ligand-binding sites, we construct several balanced data sets, for each of which a random forest (RF)-based classifier is trained. The ensemble of these RF classifiers forms a sequence-based protein-ligand binding site predictor. Conclusions Experimental results on CASP9 and CASP8 data sets demonstrate that our method compares favorably with the state-of-the-art protein-ligand binding site prediction methods.

  4. Position-specific prediction of methylation sites from sequence conservation based on information theory.

    Science.gov (United States)

    Shi, Yinan; Guo, Yanzhi; Hu, Yayun; Li, Menglong

    2015-07-23

    Protein methylation plays vital roles in many biological processes and has been implicated in various human diseases. To fully understand the mechanisms underlying methylation for use in drug design and work in methylation-related diseases, an initial but crucial step is to identify methylation sites. The use of high-throughput bioinformatics methods has become imperative to predict methylation sites. In this study, we developed a novel method that is based only on sequence conservation to predict protein methylation sites. Conservation difference profiles between methylated and non-methylated peptides were constructed by the information entropy (IE) in a wider neighbor interval around the methylation sites that fully incorporated all of the environmental information. Then, the distinctive neighbor residues were identified by the importance scores of information gain (IG). The most representative model was constructed by support vector machine (SVM) for Arginine and Lysine methylation, respectively. This model yielded a promising result on both the benchmark dataset and independent test set. The model was used to screen the entire human proteome, and many unknown substrates were identified. These results indicate that our method can serve as a useful supplement to elucidate the mechanism of protein methylation and facilitate hypothesis-driven experimental design and validation.

  5. Prediction of membrane transport proteins and their substrate specificities using primary sequence information.

    Directory of Open Access Journals (Sweden)

    Nitish K Mishra

    Full Text Available Membrane transport proteins (transporters move hydrophilic substrates across hydrophobic membranes and play vital roles in most cellular functions. Transporters represent a diverse group of proteins that differ in topology, energy coupling mechanism, and substrate specificity as well as sequence similarity. Among the functional annotations of transporters, information about their transporting substrates is especially important. The experimental identification and characterization of transporters is currently costly and time-consuming. The development of robust bioinformatics-based methods for the prediction of membrane transport proteins and their substrate specificities is therefore an important and urgent task.Support vector machine (SVM-based computational models, which comprehensively utilize integrative protein sequence features such as amino acid composition, dipeptide composition, physico-chemical composition, biochemical composition, and position-specific scoring matrices (PSSM, were developed to predict the substrate specificity of seven transporter classes: amino acid, anion, cation, electron, protein/mRNA, sugar, and other transporters. An additional model to differentiate transporters from non-transporters was also developed. Among the developed models, the biochemical composition and PSSM hybrid model outperformed other models and achieved an overall average prediction accuracy of 76.69% with a Mathews correlation coefficient (MCC of 0.49 and a receiver operating characteristic area under the curve (AUC of 0.833 on our main dataset. This model also achieved an overall average prediction accuracy of 78.88% and MCC of 0.41 on an independent dataset.Our analyses suggest that evolutionary information (i.e., the PSSM and the AAIndex are key features for the substrate specificity prediction of transport proteins. In comparison, similarity-based methods such as BLAST, PSI-BLAST, and hidden Markov models do not provide accurate predictions

  6. Pornographic information of Internet views detection method based on the connected areas

    Science.gov (United States)

    Wang, Huibai; Fan, Ajie

    2017-01-01

    Nowadays online porn video broadcasting and downloading is very popular. In view of the widespread phenomenon of Internet pornography, this paper proposed a new method of pornographic video detection based on connected areas. Firstly, decode the video into a serious of static images and detect skin color on the extracted key frames. If the area of skin color reaches a certain threshold, use the AdaBoost algorithm to detect the human face. Judge the connectivity of the human face and the large area of skin color to determine whether detect the sensitive area finally. The experimental results show that the method can effectively remove the non-pornographic videos contain human who wear less. This method can improve the efficiency and reduce the workload of detection.

  7. Neural activity, neural connectivity, and the processing of emotionally valenced information in older adults: links with life satisfaction.

    Science.gov (United States)

    Waldinger, Robert J; Kensinger, Elizabeth A; Schulz, Marc S

    2011-09-01

    This study examines whether differences in late-life well-being are linked to how older adults encode emotionally valenced information. Using fMRI with 39 older adults varying in life satisfaction, we examined how viewing positive and negative images would affect activation and connectivity of an emotion-processing network. Participants engaged most regions within this network more robustly for positive than for negative images, but within the PFC this effect was moderated by life satisfaction, with individuals higher in satisfaction showing lower levels of activity during the processing of positive images. Participants high in satisfaction showed stronger correlations among network regions-particularly between the amygdala and other emotion processing regions-when viewing positive, as compared with negative, images. Participants low in satisfaction showed no valence effect. Findings suggest that late-life satisfaction is linked with how emotion-processing regions are engaged and connected during processing of valenced information. This first demonstration of a link between neural recruitment and late-life well-being suggests that differences in neural network activation and connectivity may account for the preferential encoding of positive information seen in some older adults.

  8. Using Edge Voxel Information to Improve Motion Regression for rs-fMRI Connectivity Studies.

    Science.gov (United States)

    Patriat, Rémi; Molloy, Erin K; Birn, Rasmus M

    2015-11-01

    Recent fMRI studies have outlined the critical impact of in-scanner head motion, particularly on estimates of functional connectivity. Common strategies to reduce the influence of motion include realignment as well as the inclusion of nuisance regressors, such as the 6 realignment parameters, their first derivatives, time-shifted versions of the realignment parameters, and the squared parameters. However, these regressors have limited success at noise reduction. We hypothesized that using nuisance regressors consisting of the principal components (PCs) of edge voxel time series would be better able to capture slice-specific and nonlinear signal changes, thus explaining more variance, improving data quality (i.e., lower DVARS and temporal SNR), and reducing the effect of motion on default-mode network connectivity. Functional MRI data from 22 healthy adult subjects were preprocessed using typical motion regression approaches as well as nuisance regression derived from edge voxel time courses. Results were evaluated in the presence and absence of both global signal regression and motion censoring. Nuisance regressors derived from signal intensity time courses at the edge of the brain significantly improved motion correction compared to using only the realignment parameters and their derivatives. Of the models tested, only the edge voxel regression models were able to eliminate significant differences in default-mode network connectivity between high- and low-motion subjects regardless of the use of global signal regression or censoring.

  9. Connecting people and information: how an African special library is building bridges

    CSIR Research Space (South Africa)

    Halland, Y

    2009-04-30

    Full Text Available : How an African Special Library is Building Bridges Yvonne Halland, BA Library Science Strategic Information Resources Coordinator CSIR Information Services Pretoria, South Africa Member, Science & Technology Division Noxolo Mniki... delivery, information literacy training and knowledge management. Although the CSIR library was at one time regarded as the top science & technology library in the country, the upward spiralling costs of information resources over the last twenty...

  10. Correction of projective distortion in long-image-sequence mosaics without prior information

    Science.gov (United States)

    Yang, Chenhui; Mao, Hongwei; Abousleman, Glen; Si, Jennie

    2010-04-01

    Image mosaicking is the process of piecing together multiple video frames or still images from a moving camera to form a wide-area or panoramic view of the scene being imaged. Mosaics have widespread applications in many areas such as security surveillance, remote sensing, geographical exploration, agricultural field surveillance, virtual reality, digital video, and medical image analysis, among others. When mosaicking a large number of still images or video frames, the quality of the resulting mosaic is compromised by projective distortion. That is, during the mosaicking process, the image frames that are transformed and pasted to the mosaic become significantly scaled down and appear out of proportion with respect to the mosaic. As more frames continue to be transformed, important target information in the frames can be lost since the transformed frames become too small, which eventually leads to the inability to continue further. Some projective distortion correction techniques make use of prior information such as GPS information embedded within the image, or camera internal and external parameters. Alternatively, this paper proposes a new algorithm to reduce the projective distortion without using any prior information whatsoever. Based on the analysis of the projective distortion, we approximate the projective matrix that describes the transformation between image frames using an affine model. Using singular value decomposition, we can deduce the affine model scaling factor that is usually very close to 1. By resetting the image scale of the affine model to 1, the transformed image size remains unchanged. Even though the proposed correction introduces some error in the image matching, this error is typically acceptable and more importantly, the final mosaic preserves the original image size after transformation. We demonstrate the effectiveness of this new correction algorithm on two real-world unmanned air vehicle (UAV) sequences. The proposed method is

  11. Through Increasing "Information Literacy" Capital and Habitus (Agency): The Complementary Impact on Composition Skills When Appropriately Sequenced

    Science.gov (United States)

    Karas, Timothy

    2017-01-01

    Through a case study approach of a cohort of community college students at a single community college, the impact on success rates in composition courses was analyzed based on the sequence of completing an information literacy course. Two student cohorts were sampled based on completing an information literacy course prior to, or concurrently with…

  12. Information about radiation dose and risks in connection with radiological examinations: what patients would like to know

    International Nuclear Information System (INIS)

    Ukkola, Leila; Oikarinen, Heljae; Haapea, Marianne; Tervonen, Osmo; Henner, Anja; Honkanen, Hilkka

    2016-01-01

    To find out patients' wishes for the content and sources of the information concerning radiological procedures. A questionnaire providing quantitative and qualitative data was prepared. It comprised general information, dose and risks of radiation, and source of information. Two tables demonstrating different options to indicate the dose or risks were also provided. Patients could give one or many votes. Altogether, 147 patients (18-85 years) were interviewed after different radiological examinations using these devices. 95 % (139/147) of the patients wished for dose and risk information. Symbols (78/182 votes) and verbal scale (56/182) were preferred to reveal the dose, while verbal (83/164) and numerical scale (55/164) on the risk of fatal cancer were preferred to indicate the risks. Wishes concerning the course, options and purpose of the examination were also expressed. Prescriber (3.9 on a scale 1-5), information letter (3.8) and radiographer (3.3) were the preferred sources. Patients aged 66-85 years were reluctant to choose electronic channels. Apart from general information, patients wish for dose and risk information in connection with radiological examinations. The majority preferred symbols to indicate dose and verbal scales to indicate risks, and the preferred source of information was the prescriber or information letter. (orig.)

  13. HR Connect

    Data.gov (United States)

    US Agency for International Development — HR Connect is the USAID HR personnel system which allows HR professionals to process HR actions related to employee's personal and position information. This system...

  14. Classification of early-stage non-small cell lung cancer by weighing gene expression profiles with connectivity information.

    Science.gov (United States)

    Zhang, Ao; Tian, Suyan

    2018-05-01

    Pathway-based feature selection algorithms, which utilize biological information contained in pathways to guide which features/genes should be selected, have evolved quickly and become widespread in the field of bioinformatics. Based on how the pathway information is incorporated, we classify pathway-based feature selection algorithms into three major categories-penalty, stepwise forward, and weighting. Compared to the first two categories, the weighting methods have been underutilized even though they are usually the simplest ones. In this article, we constructed three different genes' connectivity information-based weights for each gene and then conducted feature selection upon the resulting weighted gene expression profiles. Using both simulations and a real-world application, we have demonstrated that when the data-driven connectivity information constructed from the data of specific disease under study is considered, the resulting weighted gene expression profiles slightly outperform the original expression profiles. In summary, a big challenge faced by the weighting method is how to estimate pathway knowledge-based weights more accurately and precisely. Only until the issue is conquered successfully will wide utilization of the weighting methods be impossible. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. An integrated native mass spectrometry and top-down proteomics method that connects sequence to structure and function of macromolecular complexes

    Science.gov (United States)

    Li, Huilin; Nguyen, Hong Hanh; Ogorzalek Loo, Rachel R.; Campuzano, Iain D. G.; Loo, Joseph A.

    2018-02-01

    Mass spectrometry (MS) has become a crucial technique for the analysis of protein complexes. Native MS has traditionally examined protein subunit arrangements, while proteomics MS has focused on sequence identification. These two techniques are usually performed separately without taking advantage of the synergies between them. Here we describe the development of an integrated native MS and top-down proteomics method using Fourier-transform ion cyclotron resonance (FTICR) to analyse macromolecular protein complexes in a single experiment. We address previous concerns of employing FTICR MS to measure large macromolecular complexes by demonstrating the detection of complexes up to 1.8 MDa, and we demonstrate the efficacy of this technique for direct acquirement of sequence to higher-order structural information with several large complexes. We then summarize the unique functionalities of different activation/dissociation techniques. The platform expands the ability of MS to integrate proteomics and structural biology to provide insights into protein structure, function and regulation.

  16. Practical Problems in Connection with the Planning and Introduction of Information Systems. Technical Report.

    Science.gov (United States)

    Klose, Traugott

    Major reforms brought about in July 1969 at the Free University of Berlin in its organization, planning, and decision making are reviewed. Specific problems are addressed, such as plans for introducing an information system on technical data and space use, plans for an information system on personnel employed by the university, and plans for an…

  17. From Collections to Connections: Building a Revised Platform for Library and Information Science

    Science.gov (United States)

    Audunson, Ragnar; Aabo, Svanhild

    2013-01-01

    Introduction: The paper discusses the often-repeated assertion that digitization makes libraries and librarians redundant by giving everyone access to the information they need without having to rely upon librarians as information middlemen. Method: Relevant articles both from research literature and from discussions in the public sphere…

  18. Information and communication technology: connecting the public and first responders during disasters.

    Science.gov (United States)

    Buzzelli, Michelle M; Morgan, Paula; Muschek, Alexander G; Macgregor-Skinner, Gavin

    2014-01-01

    Lack of success in disaster recovery occurs for many reasons, with one predominant catalyst for catastrophic failure being flawed and inefficient communication systems. Increased occurrences of devastating environmental hazards and human-caused disasters will continue to promulgate throughout the United States and around the globe as a result of the continuous intensive urbanization forcing human population into more concentrated and interconnected societies. With the rapid evolutions in technology and the advent of Information and communication technology (ICT) interfaces such as Facebook, Twitter, Flickr, Myspace, and Smartphone technology, communication is no longer a unidirectional source of information traveling from the newsroom to the public. In the event of a disaster, time critical information can be exchanged to and from any person or organization simultaneously with the capability to receive feedback. A literature review of current information regarding the use of ICT as information infrastructures in disaster management during human-caused and natural disasters will be conducted. This article asserts that the integrated use of ICTs as multidirectional information sharing tools throughout the disaster cycle will increase a community's resiliency and supplement the capabilities of first responders and emergency management officials by providing real-time updates and information needed to assist and recover from a disaster.

  19. Analysis on the urban street network of Korea: Connections between topology and meta-information

    Science.gov (United States)

    Lee, Byoung-Hwa; Jung, Woo-Sung

    2018-05-01

    Cities consist of infrastructure that enables transportation, which can be considered as topology in abstract terms. Once cities are physically organized in terms of infrastructure, people interact with each other to form the values, which can be regarded as the meta-information of the cities. The topology and meta-information coevolve together as the cities are developed. In this study, we investigate the relationship between the topology and meta-information for a street network, which has aspects of both a complex network and planar graph. The degree of organization of a street structure determines the efficiency and productivity of the city in that they act as blood vessels to transport people, goods, and information. We analyze the topological aspect of a street network using centralities including the betweenness, closeness, straightness, and information. We classify the cities into several groups that share common meta-information based on the centrality, indicating that the topological factor of the street structure is closely related to meta-information through coevolution. We also obtain the coevolution in the planned cities using the regularity. Another footprint is the relation between the street segment length and the population, which shows the sublinear scaling.

  20. RStrucFam: a web server to associate structure and cognate RNA for RNA-binding proteins from sequence information.

    Science.gov (United States)

    Ghosh, Pritha; Mathew, Oommen K; Sowdhamini, Ramanathan

    2016-10-07

    RNA-binding proteins (RBPs) interact with their cognate RNA(s) to form large biomolecular assemblies. They are versatile in their functionality and are involved in a myriad of processes inside the cell. RBPs with similar structural features and common biological functions are grouped together into families and superfamilies. It will be useful to obtain an early understanding and association of RNA-binding property of sequences of gene products. Here, we report a web server, RStrucFam, to predict the structure, type of cognate RNA(s) and function(s) of proteins, where possible, from mere sequence information. The web server employs Hidden Markov Model scan (hmmscan) to enable association to a back-end database of structural and sequence families. The database (HMMRBP) comprises of 437 HMMs of RBP families of known structure that have been generated using structure-based sequence alignments and 746 sequence-centric RBP family HMMs. The input protein sequence is associated with structural or sequence domain families, if structure or sequence signatures exist. In case of association of the protein with a family of known structures, output features like, multiple structure-based sequence alignment (MSSA) of the query with all others members of that family is provided. Further, cognate RNA partner(s) for that protein, Gene Ontology (GO) annotations, if any and a homology model of the protein can be obtained. The users can also browse through the database for details pertaining to each family, protein or RNA and their related information based on keyword search or RNA motif search. RStrucFam is a web server that exploits structurally conserved features of RBPs, derived from known family members and imprinted in mathematical profiles, to predict putative RBPs from sequence information. Proteins that fail to associate with such structure-centric families are further queried against the sequence-centric RBP family HMMs in the HMMRBP database. Further, all other essential

  1. Forced phase-locked states and information retrieval in a two-layer network of oscillatory neurons with directional connectivity

    International Nuclear Information System (INIS)

    Kazantsev, Victor; Pimashkin, Alexey

    2007-01-01

    We propose two-layer architecture of associative memory oscillatory network with directional interlayer connectivity. The network is capable to store information in the form of phase-locked (in-phase and antiphase) oscillatory patterns. The first (input) layer takes an input pattern to be recognized and their units are unidirectionally connected with all units of the second (control) layer. The connection strengths are weighted using the Hebbian rule. The output (retrieved) patterns appear as forced-phase locked states of the control layer. The conditions are found and analytically expressed for pattern retrieval in response on incoming stimulus. It is shown that the system is capable to recover patterns with a certain level of distortions or noises in their profiles. The architecture is implemented with the Kuramoto phase model and using synaptically coupled neural oscillators with spikes. It is found that the spiking model is capable to retrieve patterns using the spiking phase that translates memorized patterns into the spiking phase shifts at different time scales

  2. Functional connectivity measures after psilocybin inform a novel hypothesis of early psychosis.

    Science.gov (United States)

    Carhart-Harris, Robin L; Leech, Robert; Erritzoe, David; Williams, Tim M; Stone, James M; Evans, John; Sharp, David J; Feilding, Amanda; Wise, Richard G; Nutt, David J

    2013-11-01

    Psilocybin is a classic psychedelic and a candidate drug model of psychosis. This study measured the effects of psilocybin on resting-state network and thalamocortical functional connectivity (FC) using functional magnetic resonance imaging (fMRI). Fifteen healthy volunteers received intravenous infusions of psilocybin and placebo in 2 task-free resting-state scans. Primary analyses focused on changes in FC between the default-mode- (DMN) and task-positive network (TPN). Spontaneous activity in the DMN is orthogonal to spontaneous activity in the TPN, and it is well known that these networks support very different functions (ie, the DMN supports introspection, whereas the TPN supports externally focused attention). Here, independent components and seed-based FC analyses revealed increased DMN-TPN FC and so decreased DMN-TPN orthogonality after psilocybin. Increased DMN-TPN FC has been found in psychosis and meditatory states, which share some phenomenological similarities with the psychedelic state. Increased DMN-TPN FC has also been observed in sedation, as has decreased thalamocortical FC, but here we found preserved thalamocortical FC after psilocybin. Thus, we propose that thalamocortical FC may be related to arousal, whereas DMN-TPN FC is related to the separateness of internally and externally focused states. We suggest that this orthogonality is compromised in early psychosis, explaining similarities between its phenomenology and that of the psychedelic state and supporting the utility of psilocybin as a model of early psychosis.

  3. Plastid, nuclear and reverse transcriptase sequences in the mitochondrial genome of Oenothera: is genetic information transferred between organelles via RNA?

    Science.gov (United States)

    Schuster, W; Brennicke, A

    1987-01-01

    We describe an open reading frame (ORF) with high homology to reverse transcriptase in the mitochondrial genome of Oenothera. This ORF displays all the characteristics of an active plant mitochondrial gene with a possible ribosome binding site and 39% T in the third codon position. It is located between a sequence fragment from the plastid genome and one of nuclear origin downstream from the gene encoding subunit 5 of the NADH dehydrogenase. The nuclear derived sequence consists of 528 nucleotides from the small ribosomal RNA and contains an expansion segment unique to nuclear rRNAs. The plastid sequence contains part of the ribosomal protein S4 and the complete tRNA(Ser). The observation that only transcribed sequences have been found i more than one subcellular compartment in higher plants suggests that interorganellar transfer of genetic information may occur via RNA and subsequent local reverse transcription and genomic integration. PMID:14650433

  4. Shape theory. Functional connections of information, energy, and temperature in phasics and physiology; Gestalttheorie. Funktionelle Zusammenhaenge von Information, Energie und Temperatur in Physik und Physiologie

    Energy Technology Data Exchange (ETDEWEB)

    Wengel, Claus

    2012-11-01

    Starting from the phenomenon of the information input and the information output system in the central nervous system, which was conceived in physiology, as well as from the phenomenon of the disturbance oc consciousness, which was in neuropsychiatry psychopathometrically and by this quantitatively determinable, the author was occupied by the general question: How systems can be described, which possess and exchange temperature, energy, and information? A connection of thermodynamics and information theory was found and presented in this work. It came to the redefinition of several quantities, which can be applied both in mathematical physics and in mathematical physiology. First the negentropy was defined in fact as first partial derivation of the total information on the absolute temperature. Further definitions follow: That of the shape (measured in bit.J/K), that of the action (measured in bit.J), as well that of the structure (measured in bit.J/K{sup 2}). Functional connections of information, energy, and temperature as well as of further quantities became recognizable and were written. Mathematical physics were thereby enriched, also by conservation laws. But also mathematical physiology was extended. Here diseases like the inflammatory diseases catatonia, epilepsy, tumor, vegetative dystonies, anorexy, dementia, as well as the phenomenon vitality and the phenomenon sleeping were comprehended by formulas. As consequences resulted proposals resulted for the prophylaxis and for the therapy and for the design of a live-preserving and live-elongating way of life. These proposals are in the sections, which treat the diseases, detailedly listed and derived. Furthermore a first law of psychodynamics was formulated - in analogy to the first law of thermodynamics.

  5. Semantics for interoperability of distributed data and models: Foundations for better-connected information

    NARCIS (Netherlands)

    Villa, Ferdinando; Balbi, Stefano; Athanasiadis, I.N.; Caracciolo, Caterina

    2017-01-01

    Correct and reliable linkage of independently produced information is a requirement to enable sophisticated applications and processing workflows. These can ultimately help address the challenges posed by complex systems (such as socio-ecological systems), whose many components can only be described

  6. Information and Communication Technology in Education: Getting Chinese Connected for Learning

    Science.gov (United States)

    Li, Xiaobin

    2013-01-01

    This article provides an overview of the current development of information and communication technology (ICT) utilized in Chinese education. Specifically, the article describes and discusses the impact contemporary ICT has on Chinese elementary and secondary education, as well as the existing challenges in ICT application. The article also…

  7. Connecting the Dots: Enduring Challenges in the Nation’s Information Sharing Environment

    Science.gov (United States)

    2010-05-12

    communities of interest. Finally, the drawing’s canvas overlays the multiple layers of government at play, from foreign partners, federal, state, local...e.g., a cell phone or portable electronic device tied to an individual) and digit referring to biometric information (e.g., one’s fingerprints , or

  8. Think Warm Thoughts: Plan Ahead for Summertime Information Literacy Programs! The College Connection

    Science.gov (United States)

    Kasowitz-Scheer, Abby

    2009-01-01

    It's winter! While it is frosty outside, one can at least think warm thoughts by starting now to plan ahead for summer information literacy programs. This article is designed to provide some ideas for planning next summer's reading, sleuthing, and research programs. It features a variety of programs organized by academic librarians this past…

  9. Schemata as Scaffolding for the Representation of Information in Connected Discourse

    Science.gov (United States)

    Anderson, Richard C.; And Others

    1978-01-01

    As predicted, foods from categories typical of most people's restaurant schemata (conceptual framework) were better recalled by undergraduates who read a restaurant narrative, than those reading about supermarkets, a less structured schemata. Findings confirm Ausubel's notion that information which fits slots in a conceptual framework is more…

  10. Not All Order Memory Is Equal: Test Demands Reveal Dissociations in Memory for Sequence Information

    Science.gov (United States)

    Jonker, Tanya R.; MacLeod, Colin M.

    2017-01-01

    Remembering the order of a sequence of events is a fundamental feature of episodic memory. Indeed, a number of formal models represent temporal context as part of the memory system, and memory for order has been researched extensively. Yet, the nature of the code(s) underlying sequence memory is still relatively unknown. Across 4 experiments that…

  11. Situation models and memory: the effects of temporal and causal information on recall sequence.

    Science.gov (United States)

    Brownstein, Aaron L; Read, Stephen J

    2007-10-01

    Participants watched an episode of the television show Cheers on video and then reported free recall. Recall sequence followed the sequence of events in the story; if one concept was observed immediately after another, it was recalled immediately after it. We also made a causal network of the show's story and found that recall sequence followed causal links; effects were recalled immediately after their causes. Recall sequence was more likely to follow causal links than temporal sequence, and most likely to follow causal links that were temporally sequential. Results were similar at 10-minute and 1-week delayed recall. This is the most direct and detailed evidence reported on sequential effects in recall. The causal network also predicted probability of recall; concepts with more links and concepts on the main causal chain were most likely to be recalled. This extends the causal network model to more complex materials than previous research.

  12. School Health Connection Goes Electronic: Developing a Health Information Management System for New Orleans' School-Based Health Centers. Program Results Report

    Science.gov (United States)

    Rastorfer, Darl

    2011-01-01

    From February 2008 through April 2011, School Health Connection, a program of the Louisiana Public Health Institute, developed an electronic health information management system for newly established school-based health centers in Greater New Orleans. School Health Connection was established as part of a broader effort to restore community health…

  13. Assessing hydraulic connections across a complex sequence of volcanic rocks - Analysis of U-20 WW multiple-well aquifer test, Pahute Mesa, Nevada National Security Site, Nevada

    Science.gov (United States)

    Garcia, C. Amanda; Fenelon, Joseph M.; Halford, Keith J.; Reiner, Steven R.; Laczniak, Randell J.

    2011-01-01

    Groundwater beneath Pahute Mesa flows through a complexly layered sequence of volcanic rock aquifers and confining units that have been faulted into distinct structural blocks. Hydraulic property estimates of rocks and structures in this flow system are necessary to assess radionuclide migration near underground nuclear testing areas. The U.S. Geological Survey (USGS) used a 12 month (October 1, 2008— October 1, 2009) intermittent pumping schedule of well U-20 WW and continuously monitored water levels in observation wells ER-20-6 #3, UE-20bh 1, and U-20bg as a multi-well aquifer test to evaluate hydraulic connections across structural blocks, bulk hydraulic properties of volcanic rocks, and the hydraulic significance of a major fault. Measured water levels were approximated using synthetic water levels generated from an analytical model. Synthetic water levels are a summation of environmental water-level fluctuations and a Theis (1935) transform of the pumping signal from flow rate to water-level change. Drawdown was estimated by summing residual differences between measured and synthetic water levels and the Theis-transformed pumping signal from April to September 2009. Drawdown estimates were used in a three‑dimensional numerical model to estimate hydraulic properties of distinct aquifers, confining units, and a major fault.

  14. So you want to share your science…. Connecting to the world of informal science learning.

    Science.gov (United States)

    Alpert, Carol Lynn

    2018-04-25

    Scientists can reap personal rewards through collaborations with science and natural history museums, zoos, botanical gardens, aquaria, parks, and nature preserves, and, while doing so, help to advance science literacy and broaden participation in the natural sciences. Beyond volunteer opportunities, which allow scientists to contribute their knowledge and passion within the context of existing programs and activities, there are also opportunities for scientists to bring their knowledge and resources to the design and implementation of new learning experiences for visitors to these informal science learning organizations (ISLOs). Well-designed education outreach plans that leverage the expertise and broad audiences of ISLOs can also enhance the prospects of research grant proposals made to agencies such as National Science Foundation, which encourage researchers to pay careful attention to the broader impacts of their research as well as its intellectual merit. Few scientists, however, have had the opportunity to become familiar with the pedagogy and design of informal or 'free-choice' science learning, and fewer still know how to go about the process of collaborating with ISLO's in developing and implementing effective programs, exhibits, and other learning experiences. This article, written by an experienced science museum professional, provides guidance for individual scientists and research groups interested in pursuing effective education outreach collaborations with science museums and other ISLOs. When prospective partners begin discussions early in the proposal development process, they increase the likelihood of successful outcomes in funding, implementation, and impact. A strategic planning worksheet is provided, along with a carefully-selected set of further resources to guide the design and planning of informal science learning experiences.

  15. Information Theory - The Bridge Connecting Bounded Rational Game Theory and Statistical Physics

    Science.gov (United States)

    Wolpert, David H.

    2005-01-01

    A long-running difficulty with conventional game theory has been how to modify it to accommodate the bounded rationality of all red-world players. A recurring issue in statistical physics is how best to approximate joint probability distributions with decoupled (and therefore far more tractable) distributions. This paper shows that the same information theoretic mathematical structure, known as Product Distribution (PD) theory, addresses both issues. In this, PD theory not only provides a principle formulation of bounded rationality and a set of new types of mean field theory in statistical physics; it also shows that those topics are fundamentally one and the same.

  16. TRX-LOGOS - a graphical tool to demonstrate DNA information content dependent upon backbone dynamics in addition to base sequence.

    Science.gov (United States)

    Fortin, Connor H; Schulze, Katharina V; Babbitt, Gregory A

    2015-01-01

    It is now widely-accepted that DNA sequences defining DNA-protein interactions functionally depend upon local biophysical features of DNA backbone that are important in defining sites of binding interaction in the genome (e.g. DNA shape, charge and intrinsic dynamics). However, these physical features of DNA polymer are not directly apparent when analyzing and viewing Shannon information content calculated at single nucleobases in a traditional sequence logo plot. Thus, sequence logos plots are severely limited in that they convey no explicit information regarding the structural dynamics of DNA backbone, a feature often critical to binding specificity. We present TRX-LOGOS, an R software package and Perl wrapper code that interfaces the JASPAR database for computational regulatory genomics. TRX-LOGOS extends the traditional sequence logo plot to include Shannon information content calculated with regard to the dinucleotide-based BI-BII conformation shifts in phosphate linkages on the DNA backbone, thereby adding a visual measure of intrinsic DNA flexibility that can be critical for many DNA-protein interactions. TRX-LOGOS is available as an R graphics module offered at both SourceForge and as a download supplement at this journal. To demonstrate the general utility of TRX logo plots, we first calculated the information content for 416 Saccharomyces cerevisiae transcription factor binding sites functionally confirmed in the Yeastract database and matched to previously published yeast genomic alignments. We discovered that flanking regions contain significantly elevated information content at phosphate linkages than can be observed at nucleobases. We also examined broader transcription factor classifications defined by the JASPAR database, and discovered that many general signatures of transcription factor binding are locally more information rich at the level of DNA backbone dynamics than nucleobase sequence. We used TRX-logos in combination with MEGA 6.0 software

  17. High-density rhesus macaque oligonucleotide microarray design using early-stage rhesus genome sequence information and human genome annotations

    Directory of Open Access Journals (Sweden)

    Magness Charles L

    2007-01-01

    Full Text Available Abstract Background Until recently, few genomic reagents specific for non-human primate research have been available. To address this need, we have constructed a macaque-specific high-density oligonucleotide microarray by using highly fragmented low-pass sequence contigs from the rhesus genome project together with the detailed sequence and exon structure of the human genome. Using this method, we designed oligonucleotide probes to over 17,000 distinct rhesus/human gene orthologs and increased by four-fold the number of available genes relative to our first-generation expressed sequence tag (EST-derived array. Results We constructed a database containing 248,000 exon sequences from 23,000 human RefSeq genes and compared each human exon with its best matching sequence in the January 2005 version of the rhesus genome project list of 486,000 DNA contigs. Best matching rhesus exon sequences for each of the 23,000 human genes were then concatenated in the proper order and orientation to produce a rhesus "virtual transcriptome." Microarray probes were designed, one per gene, to the region closest to the 3' untranslated region (UTR of each rhesus virtual transcript. Each probe was compared to a composite rhesus/human transcript database to test for cross-hybridization potential yielding a final probe set representing 18,296 rhesus/human gene orthologs, including transcript variants, and over 17,000 distinct genes. We hybridized mRNA from rhesus brain and spleen to both the EST- and genome-derived microarrays. Besides four-fold greater gene coverage, the genome-derived array also showed greater mean signal intensities for genes present on both arrays. Genome-derived probes showed 99.4% identity when compared to 4,767 rhesus GenBank sequence tag site (STS sequences indicating that early stage low-pass versions of complex genomes are of sufficient quality to yield valuable functional genomic information when combined with finished genome information from

  18. Sequence- vs. chip-assisted genomic selection: accurate biological information is advised.

    Science.gov (United States)

    Pérez-Enciso, Miguel; Rincón, Juan C; Legarra, Andrés

    2015-05-09

    The development of next-generation sequencing technologies (NGS) has made the use of whole-genome sequence data for routine genetic evaluations possible, which has triggered a considerable interest in animal and plant breeding fields. Here, we investigated whether complete or partial sequence data can improve upon existing SNP (single nucleotide polymorphism) array-based selection strategies by simulation using a mixed coalescence - gene-dropping approach. We simulated 20 or 100 causal mutations (quantitative trait nucleotides, QTN) within 65 predefined 'gene' regions, each 10 kb long, within a genome composed of ten 3-Mb chromosomes. We compared prediction accuracy by cross-validation using a medium-density chip (7.5 k SNPs), a high-density (HD, 17 k) and sequence data (335 k). Genetic evaluation was based on a GBLUP method. The simulations showed: (1) a law of diminishing returns with increasing number of SNPs; (2) a modest effect of SNP ascertainment bias in arrays; (3) a small advantage of using whole-genome sequence data vs. HD arrays i.e. ~4%; (4) a minor effect of NGS errors except when imputation error rates are high (≥20%); and (5) if QTN were known, prediction accuracy approached 1. Since this is obviously unrealistic, we explored milder assumptions. We showed that, if all SNPs within causal genes were included in the prediction model, accuracy could also dramatically increase by ~40%. However, this criterion was highly sensitive to either misspecification (including wrong genes) or to the use of an incomplete gene list; in these cases, accuracy fell rapidly towards that reached when all SNPs from sequence data were blindly included in the model. Our study shows that, unless an accurate prior estimate on the functionality of SNPs can be included in the predictor, there is a law of diminishing returns with increasing SNP density. As a result, use of whole-genome sequence data may not result in a highly increased selection response over high

  19. Importance of the temporal structure of movement sequences on the ability of monkeys to use serial order information.

    Science.gov (United States)

    Deffains, Marc; Legallet, Eric; Apicella, Paul

    2011-10-01

    also used in the repeated sequence. This performance advantage was most prominently detectable when temporal prediction of forthcoming target stimuli was optimized. Taken together, the present findings demonstrate that the monkey's capacity to make use of serial order information to speed task performance was dependent on the temporal structure of the motor sequence.

  20. A Technical Evaluation of Wireless Connectivity from Patient Monitors to an Anesthesia Information Management System During Intensive Care Unit Surgery.

    Science.gov (United States)

    Simpao, Allan F; Galvez, Jorge A; England, W Randall; Wartman, Elicia C; Scott, James H; Hamid, Michael M; Rehman, Mohamed A; Epstein, Richard H

    2016-02-01

    Surgical procedures performed at the bedside in the neonatal intensive care unit (NICU) at The Children's Hospital of Philadelphia were documented using paper anesthesia records in contrast to the operating rooms, where an anesthesia information management system (AIMS) was used for all cases. This was largely because of logistical problems related to connecting cables between the bedside monitors and our portable AIMS workstations. We implemented an AIMS for documentation in the NICU using wireless adapters to transmit data from bedside monitoring equipment to a portable AIMS workstation. Testing of the wireless AIMS during simulation in the presence of an electrosurgical generator showed no evidence of interference with data transmission. Thirty NICU surgical procedures were documented via the wireless AIMS. Two wireless cases exhibited brief periods of data loss; one case had an extended data gap because of adapter power failure. In comparison, in a control group of 30 surgical cases in which wired connections were used, there were no data gaps. The wireless AIMS provided a simple, unobtrusive, portable alternative to paper records for documenting anesthesia records during NICU bedside procedures.

  1. Connecting Knowledge, Belief, Values and Action: Informing Climate Literacy by Using Autobiographies to Articulate Environmental Worldviews

    Science.gov (United States)

    Owens, M. A.

    2011-12-01

    human beings above nature. The creation stories of Genesis have been used both implicitly and explicitly to justify domination and exploitation of the earth and its resources. Autobiographies may be used as a reflective pedagogical tool to help students to identify various components of their respective environmental worldviews that may influence their overall environmental and climate literacy. Narrative responses to guiding questions prompt students to reflect on beliefs, trust, and values. This research will inform the development of culturally relevant and scientifically sound approaches to climate change education.

  2. Symmetries of a generic utricular projection: neural connectivity and the distribution of utricular information.

    Science.gov (United States)

    Chartrand, Thomas; McCollum, Gin; Hanes, Douglas A; Boyle, Richard D

    2016-02-01

    Sensory contribution to perception and action depends on both sensory receptors and the organization of pathways (or projections) reaching the central nervous system. Unlike the semicircular canals that are divided into three discrete sensitivity directions, the utricle has a relatively complicated anatomical structure, including sensitivity directions over essentially 360° of a curved, two-dimensional disk. The utricle is not flat, and we do not assume it to be. Directional sensitivity of individual utricular afferents decreases in a cosine-like fashion from peak excitation for movement in one direction to a null or near null response for a movement in an orthogonal direction. Directional sensitivity varies slowly between neighboring cells except within the striolar region that separates the medial from the lateral zone, where the directional selectivity abruptly reverses along the reversal line. Utricular primary afferent pathways reach the vestibular nuclei and cerebellum and, in many cases, converge on target cells with semicircular canal primary afferents and afference from other sources. Mathematically, some canal pathways are known to be characterized by symmetry groups related to physical space. These groups structure rotational information and movement. They divide the target neural center into distinct populations according to the innervation patterns they receive. Like canal pathways, utricular pathways combine symmetries from the utricle with those from target neural centers. This study presents a generic set of transformations drawn from the known structure of the utricle and therefore likely to be found in utricular pathways, but not exhaustive of utricular pathway symmetries. This generic set of transformations forms a 32-element group that is a semi-direct product of two simple abelian groups. Subgroups of the group include order-four elements corresponding to discrete rotations. Evaluation of subgroups allows us to functionally identify the

  3. An HMM posterior decoder for sequence feature prediction that includes homology information

    DEFF Research Database (Denmark)

    Käll, Lukas; Krogh, Anders Stærmose; Sonnhammer, Erik L. L.

    2005-01-01

    Motivation: When predicting sequence features like transmembrane topology, signal peptides, coil-coil structures, protein secondary structure or genes, extra support can be gained from homologs. Results: We present here a general hidden Markov model (HMM) decoding algorithm that combines probabil......Motivation: When predicting sequence features like transmembrane topology, signal peptides, coil-coil structures, protein secondary structure or genes, extra support can be gained from homologs. Results: We present here a general hidden Markov model (HMM) decoding algorithm that combines......://phobius.cgb.ki.se/poly.html . An implementation of the algorithm is available on request from the authors....

  4. Toward allotetraploid cotton genome assembly: integration of a high-density molecular genetic linkage map with DNA sequence information

    Science.gov (United States)

    2012-01-01

    Background Cotton is the world’s most important natural textile fiber and a significant oilseed crop. Decoding cotton genomes will provide the ultimate reference and resource for research and utilization of the species. Integration of high-density genetic maps with genomic sequence information will largely accelerate the process of whole-genome assembly in cotton. Results In this paper, we update a high-density interspecific genetic linkage map of allotetraploid cultivated cotton. An additional 1,167 marker loci have been added to our previously published map of 2,247 loci. Three new marker types, InDel (insertion-deletion) and SNP (single nucleotide polymorphism) developed from gene information, and REMAP (retrotransposon-microsatellite amplified polymorphism), were used to increase map density. The updated map consists of 3,414 loci in 26 linkage groups covering 3,667.62 cM with an average inter-locus distance of 1.08 cM. Furthermore, genome-wide sequence analysis was finished using 3,324 informative sequence-based markers and publicly-available Gossypium DNA sequence information. A total of 413,113 EST and 195 BAC sequences were physically anchored and clustered by 3,324 sequence-based markers. Of these, 14,243 ESTs and 188 BACs from different species of Gossypium were clustered and specifically anchored to the high-density genetic map. A total of 2,748 candidate unigenes from 2,111 ESTs clusters and 63 BACs were mined for functional annotation and classification. The 337 ESTs/genes related to fiber quality traits were integrated with 132 previously reported cotton fiber quality quantitative trait loci, which demonstrated the important roles in fiber quality of these genes. Higher-level sequence conservation between different cotton species and between the A- and D-subgenomes in tetraploid cotton was found, indicating a common evolutionary origin for orthologous and paralogous loci in Gossypium. Conclusion This study will serve as a valuable genomic resource

  5. Connected Traveler

    Energy Technology Data Exchange (ETDEWEB)

    2016-06-01

    The Connected Traveler framework seeks to boost the energy efficiency of personal travel and the overall transportation system by maximizing the accuracy of predicted traveler behavior in response to real-time feedback and incentives. It is anticipated that this approach will establish a feedback loop that 'learns' traveler preferences and customizes incentives to meet or exceed energy efficiency targets by empowering individual travelers with information needed to make energy-efficient choices and reducing the complexity required to validate transportation system energy savings. This handout provides an overview of NREL's Connected Traveler project, including graphics, milestones, and contact information.

  6. HemeBIND: a novel method for heme binding residue prediction by combining structural and sequence information

    Directory of Open Access Journals (Sweden)

    Hu Jianjun

    2011-05-01

    Full Text Available Abstract Background Accurate prediction of binding residues involved in the interactions between proteins and small ligands is one of the major challenges in structural bioinformatics. Heme is an essential and commonly used ligand that plays critical roles in electron transfer, catalysis, signal transduction and gene expression. Although much effort has been devoted to the development of various generic algorithms for ligand binding site prediction over the last decade, no algorithm has been specifically designed to complement experimental techniques for identification of heme binding residues. Consequently, an urgent need is to develop a computational method for recognizing these important residues. Results Here we introduced an efficient algorithm HemeBIND for predicting heme binding residues by integrating structural and sequence information. We systematically investigated the characteristics of binding interfaces based on a non-redundant dataset of heme-protein complexes. It was found that several sequence and structural attributes such as evolutionary conservation, solvent accessibility, depth and protrusion clearly illustrate the differences between heme binding and non-binding residues. These features can then be separately used or combined to build the structure-based classifiers using support vector machine (SVM. The results showed that the information contained in these features is largely complementary and their combination achieved the best performance. To further improve the performance, an attempt has been made to develop a post-processing procedure to reduce the number of false positives. In addition, we built a sequence-based classifier based on SVM and sequence profile as an alternative when only sequence information can be used. Finally, we employed a voting method to combine the outputs of structure-based and sequence-based classifiers, which demonstrated remarkably better performance than the individual classifier alone

  7. Automatic Time Sequence Alignment in Contrast Enhanced MRI by Maximization of Mutual Information

    National Research Council Canada - National Science Library

    Positano, Vicenzo

    2001-01-01

    The use of contrast medium allows joining the high-resolution anatomical information provided by standard magnetic resonance with functional information obtained by means of the diffusion of contrast...

  8. Timing and sequencing of events marking the transition to adulthood in two informal settlements in Nairobi, Kenya.

    Science.gov (United States)

    Beguy, Donatien; Kabiru, Caroline W; Zulu, Eliya M; Ezeh, Alex C

    2011-06-01

    Young people living in poor urban informal settlements face unique challenges as they transition to adulthood. This exploratory paper uses retrospective information from the baseline survey of a 3-year prospective study to examine the timing and sequencing of four key markers (first sex, marriage, birth, and independent housing) of the transition to adulthood among 3,944 adolescents in two informal settlements in Nairobi city, Kenya. Event history analysis techniques are employed to examine the timing of the events. Results indicate that there is no significant gender difference with regard to first sexual debut among adolescents. For many boys and girls, the first sexual experience occurs outside of marriage or other union. For males, the sequencing of entry begins with entry into first sex, followed by independent housing. Conversely, for females, the sequencing begins with first sex and then parenthood. Apart from sexual debut, the patterns of entry into union and parenthood do not differ much from what was observed for Nairobi as a whole. The space constraints that typify the two slums may have influenced the pattern of leaving home observed. We discuss these and other findings in light of their implications for young people's health and well-being in resource-poor settings in urban areas.

  9. Ion torrent personal genome machine sequencing for genomic typing of Neisseria meningitidis for rapid determination of multiple layers of typing information.

    Science.gov (United States)

    Vogel, Ulrich; Szczepanowski, Rafael; Claus, Heike; Jünemann, Sebastian; Prior, Karola; Harmsen, Dag

    2012-06-01

    Neisseria meningitidis causes invasive meningococcal disease in infants, toddlers, and adolescents worldwide. DNA sequence-based typing, including multilocus sequence typing, analysis of genetic determinants of antibiotic resistance, and sequence typing of vaccine antigens, has become the standard for molecular epidemiology of the organism. However, PCR of multiple targets and consecutive Sanger sequencing provide logistic constraints to reference laboratories. Taking advantage of the recent development of benchtop next-generation sequencers (NGSs) and of BIGSdb, a database accommodating and analyzing genome sequence data, we therefore explored the feasibility and accuracy of Ion Torrent Personal Genome Machine (PGM) sequencing for genomic typing of meningococci. Three strains from a previous meningococcus serogroup B community outbreak were selected to compare conventional typing results with data generated by semiconductor chip-based sequencing. In addition, sequencing of the meningococcal type strain MC58 provided information about the general performance of the technology. The PGM technology generated sequence information for all target genes addressed. The results were 100% concordant with conventional typing results, with no further editing being necessary. In addition, the amount of typing information, i.e., nucleotides and target genes analyzed, could be substantially increased by the combined use of genome sequencing and BIGSdb compared to conventional methods. In the near future, affordable and fast benchtop NGS machines like the PGM might enable reference laboratories to switch to genomic typing on a routine basis. This will reduce workloads and rapidly provide information for laboratory surveillance, outbreak investigation, assessment of vaccine preventability, and antibiotic resistance gene monitoring.

  10. An Observational Study of Children's Involvement in Informed Consent for Exome Sequencing Research.

    Science.gov (United States)

    Miller, Victoria A; Werner-Lin, Allison; Walser, Sarah A; Biswas, Sawona; Bernhardt, Barbara A

    2017-02-01

    The goal of this study was to examine children's involvement in consent sessions for exome sequencing research and associations of involvement with provider and parent communication. Participants included 44 children (8-17 years) from five cohorts who were offered participation in an exome sequencing study. The consent sessions were audiotaped, transcribed, and coded. Providers attempted to facilitate the child's involvement in the majority (73%) of sessions, and most (75%) children also verbally participated. Provider facilitation was strongly associated with likelihood of child participation. These findings underscore that strategies such as asking for children's opinions and soliciting their questions show respect for children and may increase the likelihood that they are engaged and involved in decisions about research participation.

  11. Combining information from linkage and association mapping for next-generation sequencing longitudinal family data.

    Science.gov (United States)

    Balliu, Brunilda; Uh, Hae-Won; Tsonaka, Roula; Boehringer, Stefan; Helmer, Quinta; Houwing-Duistermaat, Jeanine J

    2014-01-01

    In this analysis, we investigate the contributions that linkage-based methods, such as identical-by-descent mapping, can make to association mapping to identify rare variants in next-generation sequencing data. First, we identify regions in which cases share more segments identical-by-descent around a putative causal variant than do controls. Second, we use a two-stage mixed-effect model approach to summarize the single-nucleotide polymorphism data within each region and include them as covariates in the model for the phenotype. We assess the impact of linkage disequilibrium in determining identical-by-descent states between individuals by using markers with and without linkage disequilibrium for the first part and the impact of imputation in testing for association by using imputed genome-wide association studies or raw sequence markers for the second part. We apply the method to next-generation sequencing longitudinal family data from Genetic Association Workshop 18 and identify a significant region at chromosome 3: 40249244-41025167 (p-value = 2.3 × 10(-3)).

  12. Schizophrenia alters intra-network functional connectivity in the caudate for detecting speech under informational speech masking conditions.

    Science.gov (United States)

    Zheng, Yingjun; Wu, Chao; Li, Juanhua; Li, Ruikeng; Peng, Hongjun; She, Shenglin; Ning, Yuping; Li, Liang

    2018-04-04

    Speech recognition under noisy "cocktail-party" environments involves multiple perceptual/cognitive processes, including target detection, selective attention, irrelevant signal inhibition, sensory/working memory, and speech production. Compared to health listeners, people with schizophrenia are more vulnerable to masking stimuli and perform worse in speech recognition under speech-on-speech masking conditions. Although the schizophrenia-related speech-recognition impairment under "cocktail-party" conditions is associated with deficits of various perceptual/cognitive processes, it is crucial to know whether the brain substrates critically underlying speech detection against informational speech masking are impaired in people with schizophrenia. Using functional magnetic resonance imaging (fMRI), this study investigated differences between people with schizophrenia (n = 19, mean age = 33 ± 10 years) and their matched healthy controls (n = 15, mean age = 30 ± 9 years) in intra-network functional connectivity (FC) specifically associated with target-speech detection under speech-on-speech-masking conditions. The target-speech detection performance under the speech-on-speech-masking condition in participants with schizophrenia was significantly worse than that in matched healthy participants (healthy controls). Moreover, in healthy controls, but not participants with schizophrenia, the strength of intra-network FC within the bilateral caudate was positively correlated with the speech-detection performance under the speech-masking conditions. Compared to controls, patients showed altered spatial activity pattern and decreased intra-network FC in the caudate. In people with schizophrenia, the declined speech-detection performance under speech-on-speech masking conditions is associated with reduced intra-caudate functional connectivity, which normally contributes to detecting target speech against speech masking via its functions of suppressing masking-speech signals.

  13. Application of the accident management information needs methodology to a severe accident sequence

    International Nuclear Information System (INIS)

    Ward, L.W.; Hanson, D.J.; Nelson, W.R.; Solberg, D.E.

    1989-01-01

    The U.S. Nuclear Regulatory Commission is conducting an accident management research program that emphasizes the use of severe accident research to enhance the ability of plant operating personnel to effectively manage severe accidents. Hence, it is necessary to ensure that the plant instrumentation and information systems adequately provide this information to the operating staff during accident conditions. A methodology to identify and assess the information needs of the operating staff of a nuclear power plant during a severe accident has been developed. The methodology identifies (a) the information needs of the plant personnel during a wide range of accident conditions, (b) the existing plant measurements capable of supplying these information needs and minor additions to instrument and display systems that would enhance management capabilities, (c) measurement capabilities and limitations during severe accident conditions, and (d) areas in which the information systems could mislead plant personnel

  14. Application of the accident management information needs methodology to a severe accident sequence

    Energy Technology Data Exchange (ETDEWEB)

    Ward, L.W.; Hanson, D.J.; Nelson, W.R. (Idaho National Engineering Laboratory, Idaho Falls (USA)); Solberg, D.E. (Nuclear Regulatory Commission, Washington, DC (USA))

    1989-11-01

    The U.S. Nuclear Regulatory Commission is conducting an accident management research program that emphasizes the use of severe accident research to enhance the ability of plant operating personnel to effectively manage severe accidents. Hence, it is necessary to ensure that the plant instrumentation and information systems adequately provide this information to the operating staff during accident conditions. A methodology to identify and assess the information needs of the operating staff of a nuclear power plant during a severe accident has been developed. The methodology identifies (a) the information needs of the plant personnel during a wide range of accident conditions, (b) the existing plant measurements capable of supplying these information needs and minor additions to instrument and display systems that would enhance management capabilities, (c) measurement capabilities and limitations during severe accident conditions, and (d) areas in which the information systems could mislead plant personnel.

  15. Simplifying complex sequence information: a PCP-consensus protein binds antibodies against all four Dengue serotypes.

    Science.gov (United States)

    Bowen, David M; Lewis, Jessica A; Lu, Wenzhe; Schein, Catherine H

    2012-09-14

    Designing proteins that reflect the natural variability of a pathogen is essential for developing novel vaccines and drugs. Flaviviruses, including Dengue (DENV) and West Nile (WNV), evolve rapidly and can "escape" neutralizing monoclonal antibodies by mutation. Designing antigens that represent many distinct strains is important for DENV, where infection with a strain from one of the four serotypes may lead to severe hemorrhagic disease on subsequent infection with a strain from another serotype. Here, a DENV physicochemical property (PCP)-consensus sequence was derived from 671 unique sequences from the Flavitrack database. PCP-consensus proteins for domain 3 of the envelope protein (EdomIII) were expressed from synthetic genes in Escherichia coli. The ability of the purified consensus proteins to bind polyclonal antibodies generated in response to infection with strains from each of the four DENV serotypes was determined. The initial consensus protein bound antibodies from DENV-1-3 in ELISA and Western blot assays. This sequence was altered in 3 steps to incorporate regions of maximum variability, identified as significant changes in the PCPs, characteristic of DENV-4 strains. The final protein was recognized by antibodies against all four serotypes. Two amino acids essential for efficient binding to all DENV antibodies are part of a discontinuous epitope previously defined for a neutralizing monoclonal antibody. The PCP-consensus method can significantly reduce the number of experiments required to define a multivalent antigen, which is particularly important when dealing with pathogens that must be tested at higher biosafety levels. Copyright © 2012 Elsevier Ltd. All rights reserved.

  16. A Proteomic Workflow Using High-Throughput De Novo Sequencing Towards Complementation of Genome Information for Improved Comparative Crop Science.

    Science.gov (United States)

    Turetschek, Reinhard; Lyon, David; Desalegn, Getinet; Kaul, Hans-Peter; Wienkoop, Stefanie

    2016-01-01

    The proteomic study of non-model organisms, such as many crop plants, is challenging due to the lack of comprehensive genome information. Changing environmental conditions require the study and selection of adapted cultivars. Mutations, inherent to cultivars, hamper protein identification and thus considerably complicate the qualitative and quantitative comparison in large-scale systems biology approaches. With this workflow, cultivar-specific mutations are detected from high-throughput comparative MS analyses, by extracting sequence polymorphisms with de novo sequencing. Stringent criteria are suggested to filter for confidential mutations. Subsequently, these polymorphisms complement the initially used database, which is ready to use with any preferred database search algorithm. In our example, we thereby identified 26 specific mutations in two cultivars of Pisum sativum and achieved an increased number (17 %) of peptide spectrum matches.

  17. Controlling the structure of sequence-defined poly(phosphodiester)s for optimal MS/MS reading of digital information.

    Science.gov (United States)

    Amalian, J-A; Al Ouahabi, A; Cavallo, G; König, N F; Poyer, S; Lutz, J-F; Charles, L

    2017-11-01

    Digital polymers are monodisperse chains with a controlled sequence of co-monomers, defined as letters of an alphabet, and are used to store information at the molecular level. Reading such messages is hence a sequencing task that can be efficiently achieved by tandem mass spectrometry. To improve their readability, structure of sequence-controlled synthetic polymers can be optimized, based on considerations regarding their fragmentation behavior. This strategy is described here for poly(phosphodiester)s, which were synthesized as monodisperse chains with more than 100 units but exhibited extremely complex dissociation spectra. In these polymers, two repeating units that differ by a simple H/CH 3 variation were defined as the 0 and 1 bit of the ASCII code and spaced by a phosphate moiety. They were readily ionized in negative ion mode electrospray but dissociated via cleavage at all phosphate bonds upon collisional activation. Although allowing a complete sequence coverage of digital poly(phosphodiester)s, this fragmentation behavior was not efficient for macromolecules with more than 50 co-monomers, and data interpretation was very tedious. The structure of these polymers was then modified by introducing alkoxyamine linkages at appropriate location throughout the chain. A first design consisted of placing these low dissociation energy bonds between each monomeric bit: while cleavage of this sole bond greatly simplified MS/MS spectra, efficient sequencing was limited to chains with up to about 50 units. In contrast, introduction of alkoxyamine bonds between each byte (i.e. a set of eight co-monomers) was a more successful strategy. Long messages (so far, up to 8 bytes) could be read in MS 3 experiments, where single-byte containing fragments released during the first activation stage were further dissociated for sequencing. The whole sequence of such byte-truncated poly(phosphodiester)s could be easily re-constructed based on a mass tagging system which permits

  18. Geographic information systems supporting the solution of emergencies and their connection to self-actuated notification systems

    Science.gov (United States)

    Reil, Adam; Bureš, Luděk; Roub, Radek; Hejduk, Tomáš; Novák, Pavel

    2015-04-01

    area of Lety on the Berounka River. Two sets of certified maps were created: (1) The map of endangered properties 1 - grid of depths, and (2) The map of endangered properties 2 - grid of flow rates. The maps were created from the discharge of 500 m3/s to 1460 m3/s at intervals of 60 m3/s. Two additional discharge values were 1500 m3/s and a calibration discharge of 990 m3/s. In total, thirty-eight maps were created the foundation of which was an orthophotograph map where endangered properties were plotted together with inundation areas. The next step will now be a specific proposal for data store version. The data store will be placed on the web interface where scenarios will be possible to display according to the selected discharge. At the same time, information will be available about the current discharge in the given watercourse. The web interface will be publicly accessible and will be connected to IRS. This study was supported from the Project VG20132015127 as a part of the Security Research conducted by the Ministry of the Interior of the Czech Republic. Keywords: IRS, MIKE 21C, flood

  19. Implications of Informal Education Experiences for Mathematics Teachers' Ability to Make Connections beyond Formal Classroom

    Science.gov (United States)

    Popovic, Gorjana; Lederman, Judith S.

    2015-01-01

    The Common Core Standard for Mathematical Practice 4: Model with Mathematics specifies that mathematically proficient students are able to make connections between school mathematics and its applications to solving real-world problems. Hence, mathematics teachers are expected to incorporate connections between mathematical concepts they teach and…

  20. Magnifying visual target information and the role of eye movements in motor sequence learning.

    Science.gov (United States)

    Massing, Matthias; Blandin, Yannick; Panzer, Stefan

    2016-01-01

    An experiment investigated the influence of eye movements on learning a simple motor sequence task when the visual display was magnified. The task was to reproduce a 1300 ms spatial-temporal pattern of elbow flexions and extensions. The spatial-temporal pattern was displayed in front of the participants. Participants were randomly assigned to four groups differing on eye movements (free to use their eyes/instructed to fixate) and the visual display (small/magnified). All participants had to perform a pre-test, an acquisition phase, a delayed retention test, and a transfer test. The results indicated that participants in each practice condition increased their performance during acquisition. The participants who were permitted to use their eyes in the magnified visual display outperformed those who were instructed to fixate on the magnified visual display. When a small visual display was used, the instruction to fixate induced no performance decrements compared to participants who were permitted to use their eyes during acquisition. The findings demonstrated that a spatial-temporal pattern can be learned without eye movements, but being permitting to use eye movements facilitates the response production when the visual angle is increased. Copyright © 2015 Elsevier B.V. All rights reserved.

  1. The Coding of Biological Information: From Nucleotide Sequence to Protein Recognition

    Science.gov (United States)

    Štambuk, Nikola

    The paper reviews the classic results of Swanson, Dayhoff, Grantham, Blalock and Root-Bernstein, which link genetic code nucleotide patterns to the protein structure, evolution and molecular recognition. Symbolic representation of the binary addresses defining particular nucleotide and amino acid properties is discussed, with consideration of: structure and metric of the code, direct correspondence between amino acid and nucleotide information, and molecular recognition of the interacting protein motifs coded by the complementary DNA and RNA strands.

  2. Integrating genomic information with protein sequence and 3D atomic level structure at the RCSB protein data bank.

    Science.gov (United States)

    Prlic, Andreas; Kalro, Tara; Bhattacharya, Roshni; Christie, Cole; Burley, Stephen K; Rose, Peter W

    2016-12-15

    The Protein Data Bank (PDB) now contains more than 120,000 three-dimensional (3D) structures of biological macromolecules. To allow an interpretation of how PDB data relates to other publicly available annotations, we developed a novel data integration platform that maps 3D structural information across various datasets. This integration bridges from the human genome across protein sequence to 3D structure space. We developed novel software solutions for data management and visualization, while incorporating new libraries for web-based visualization using SVG graphics. The new views are available from http://www.rcsb.org and software is available from https://github.com/rcsb/. andreas.prlic@rcsb.orgSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

  3. The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences

    Science.gov (United States)

    Portales-Casamar, Elodie; Arenillas, David; Lim, Jonathan; Swanson, Magdalena I.; Jiang, Steven; McCallum, Anthony; Kirov, Stefan; Wasserman, Wyeth W.

    2009-01-01

    The PAZAR database unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. The flexible PAZAR schema permits the representation of diverse information derived from experiments ranging from biochemical protein–DNA binding to cellular reporter gene assays. Data collections can be made available to the public, or restricted to specific system users. The data ‘boutiques’ within the shopping-mall-inspired system facilitate the analysis of genomics data and the creation of predictive models of gene regulation. Since its initial release, PAZAR has grown in terms of data, features and through the addition of an associated package of software tools called the ORCA toolkit (ORCAtk). ORCAtk allows users to rapidly develop analyses based on the information stored in the PAZAR system. PAZAR is available at http://www.pazar.info. ORCAtk can be accessed through convenient buttons located in the PAZAR pages or via our website at http://www.cisreg.ca/ORCAtk. PMID:18971253

  4. Acceptability of, and Information Needs Regarding, Next-Generation Sequencing in People Tested for Hereditary Cancer: A Qualitative Study.

    Science.gov (United States)

    Meiser, Bettina; Storey, Ben; Quinn, Veronica; Rahman, Belinda; Andrews, Lesley

    2016-04-01

    Next generation sequencing (NGS) for patients at risk of hereditary cancer syndromes can also identify non-cancer related mutations, as well as variants of unknown significance. This study aimed to determine what benefits and shortcomings patients perceive in relation to NGS, as well as their interest and information preferences in regards to such testing. Eligible patients had previously received inconclusive results from clinical mutation testing for cancer susceptibility. Semi-structured telephone interviews were subjected to qualitative analysis guided by the approach developed by Miles and Huberman. The majority of the 19 participants reported they would be interested in panel/genomic testing. Advantages identified included that it would enable better preparation and allow implementation of individualized preventative strategies, with few disadvantages mentioned. Almost all participants said they would want all results, not just those related to their previous diagnosis. Participants felt that a face-to-face discussion supplemented by an information booklet would be the best way to convey information and achieve informed consent. All participants wanted their information stored and reviewed in accordance with new developments. Although the findings indicate strong interest among these individuals, it seems that the consent process, and the interpretation and communication of results will be areas that will require revision to meet the needs of patients.

  5. Massively parallel sequencing of 165 ancestry informative SNPs in two Chinese Tibetan-Burmese minority ethnicities.

    Science.gov (United States)

    Wang, Zheng; He, Guanglin; Luo, Tao; Zhao, Xueying; Liu, Jing; Wang, Mengge; Zhou, Di; Chen, Xu; Li, Chengtao; Hou, Yiping

    2018-05-01

    The Tibeto-Burman language, one subfamily of the Sino-Tibetan languages, is spoken by over 60 million people all over East Asia. Yet the ethnic origin and genetic architecture of Tibeto-Burman speaking populations remain largely unexplored. In the present study, 169 Chinese individuals from Tibeto-Burman speaking populations (two ethnic groups: Tibetan and Yi) in four different geographic regions in western China were analyzed using the Precision ID Ancestry Panel (165 AISNPs) and the Ion PGM System. The performance and corresponding forensic statistical parameters of this AISNPs panel were investigated. Comprehensive population genetic comparisons (143 populations based on Kidd' SNPs, 92 populations on the basis of Seldin' SNPs and 31 populations based on the Precision ID Ancestry Panel) and ancestry inference were further performed. Sequencing performance demonstrated that the Precision ID Ancestry Panel is effective and robust. Forensic characteristics suggested that this panel not only can be used for ancestry estimation of Tibeto-Burman populations but also for individual identification. Tibetan and Yi shared a common genetic ancestry origin but experienced the complex history of gene flow, local adaptation, and isolation, and constructed the specific genetic landscape of human genetic diversity of Highlander and Lowlander populations. Tibetan-Burman populations and other East Asian populations showed sufficient genetic difference and could be distinguished into three distinct groups. Furthermore, analysis of population structure revealed that significant genetic difference was existed inter-continent populations and strong genetic affinity was observed within-continent populations. Additional population-specific AISNPs and a relatively more comprehensive database with sufficient reference population data remain necessary to get better-scale resolution within a geographically proximate populations in East Asia. Copyright © 2018 Elsevier B.V. All rights

  6. Perceived connections between information and communication technology use and mental symptoms among young adults - a qualitative study.

    Science.gov (United States)

    Thomée, Sara; Dellve, Lotta; Härenstam, Annika; Hagberg, Mats

    2010-02-12

    Prospective associations have been found between high use of information and communication technology (ICT) and reported mental symptoms among young adult university students, but the causal mechanisms are unclear. Our aim was to explore possible explanations for associations between high ICT use and symptoms of depression, sleep disorders, and stress among young adults in order to propose a model of possible pathways to mental health effects that can be tested epidemiologically. We conducted a qualitative interview study with 16 women and 16 men (21-28 years), recruited from a cohort of university students on the basis of reporting high computer (n = 28) or mobile phone (n = 20) use at baseline and reporting mental symptoms at the one-year follow-up. Semi-structured interviews were performed, with open-ended questions about possible connections between the use of computers and mobile phones, and stress, depression, and sleep disturbances. The interview data were analyzed with qualitative content analysis and summarized in a model. Central factors appearing to explain high quantitative ICT use were personal dependency, and demands for achievement and availability originating from the domains of work, study, social life, and individual aspirations. Consequences included mental overload, neglect of other activities and personal needs, time pressure, role conflicts, guilt feelings, social isolation, physical symptoms, worry about electromagnetic radiation, and economic problems. Qualitative aspects (destructive communication and information) were also reported, with consequences including vulnerability, misunderstandings, altered values, and feelings of inadequacy. User problems were a source of frustration. Altered ICT use as an effect of mental symptoms was reported, as well as possible positive effects of ICT on mental health. The concepts and ideas of the young adults with high ICT use and mental symptoms generated a model of possible paths for associations

  7. Perceived connections between information and communication technology use and mental symptoms among young adults - a qualitative study

    Directory of Open Access Journals (Sweden)

    Hagberg Mats

    2010-02-01

    Full Text Available Abstract Background Prospective associations have been found between high use of information and communication technology (ICT and reported mental symptoms among young adult university students, but the causal mechanisms are unclear. Our aim was to explore possible explanations for associations between high ICT use and symptoms of depression, sleep disorders, and stress among young adults in order to propose a model of possible pathways to mental health effects that can be tested epidemiologically. Methods We conducted a qualitative interview study with 16 women and 16 men (21-28 years, recruited from a cohort of university students on the basis of reporting high computer (n = 28 or mobile phone (n = 20 use at baseline and reporting mental symptoms at the one-year follow-up. Semi-structured interviews were performed, with open-ended questions about possible connections between the use of computers and mobile phones, and stress, depression, and sleep disturbances. The interview data were analyzed with qualitative content analysis and summarized in a model. Results Central factors appearing to explain high quantitative ICT use were personal dependency, and demands for achievement and availability originating from the domains of work, study, social life, and individual aspirations. Consequences included mental overload, neglect of other activities and personal needs, time pressure, role conflicts, guilt feelings, social isolation, physical symptoms, worry about electromagnetic radiation, and economic problems. Qualitative aspects (destructive communication and information were also reported, with consequences including vulnerability, misunderstandings, altered values, and feelings of inadequacy. User problems were a source of frustration. Altered ICT use as an effect of mental symptoms was reported, as well as possible positive effects of ICT on mental health. Conclusions The concepts and ideas of the young adults with high ICT use and mental

  8. An information-theoretic approach to the modeling and analysis of whole-genome bisulfite sequencing data.

    Science.gov (United States)

    Jenkinson, Garrett; Abante, Jordi; Feinberg, Andrew P; Goutsias, John

    2018-03-07

    DNA methylation is a stable form of epigenetic memory used by cells to control gene expression. Whole genome bisulfite sequencing (WGBS) has emerged as a gold-standard experimental technique for studying DNA methylation by producing high resolution genome-wide methylation profiles. Statistical modeling and analysis is employed to computationally extract and quantify information from these profiles in an effort to identify regions of the genome that demonstrate crucial or aberrant epigenetic behavior. However, the performance of most currently available methods for methylation analysis is hampered by their inability to directly account for statistical dependencies between neighboring methylation sites, thus ignoring significant information available in WGBS reads. We present a powerful information-theoretic approach for genome-wide modeling and analysis of WGBS data based on the 1D Ising model of statistical physics. This approach takes into account correlations in methylation by utilizing a joint probability model that encapsulates all information available in WGBS methylation reads and produces accurate results even when applied on single WGBS samples with low coverage. Using the Shannon entropy, our approach provides a rigorous quantification of methylation stochasticity in individual WGBS samples genome-wide. Furthermore, it utilizes the Jensen-Shannon distance to evaluate differences in methylation distributions between a test and a reference sample. Differential performance assessment using simulated and real human lung normal/cancer data demonstrate a clear superiority of our approach over DSS, a recently proposed method for WGBS data analysis. Critically, these results demonstrate that marginal methods become statistically invalid when correlations are present in the data. This contribution demonstrates clear benefits and the necessity of modeling joint probability distributions of methylation using the 1D Ising model of statistical physics and of

  9. Intelligent Access to Sequence and Structure Databases (IASSD) - an interface for accessing information from major web databases.

    Science.gov (United States)

    Ganguli, Sayak; Gupta, Manoj Kumar; Basu, Protip; Banik, Rahul; Singh, Pankaj Kumar; Vishal, Vineet; Bera, Abhisek Ranjan; Chakraborty, Hirak Jyoti; Das, Sasti Gopal

    2014-01-01

    With the advent of age of big data and advances in high throughput technology accessing data has become one of the most important step in the entire knowledge discovery process. Most users are not able to decipher the query result that is obtained when non specific keywords or a combination of keywords are used. Intelligent access to sequence and structure databases (IASSD) is a desktop application for windows operating system. It is written in Java and utilizes the web service description language (wsdl) files and Jar files of E-utilities of various databases such as National Centre for Biotechnology Information (NCBI) and Protein Data Bank (PDB). Apart from that IASSD allows the user to view protein structure using a JMOL application which supports conditional editing. The Jar file is freely available through e-mail from the corresponding author.

  10. Designing for scale: optimising the health information system architecture for mobile maternal health messaging in South Africa (MomConnect)

    CSIR Research Space (South Africa)

    Seebregts, C

    2018-04-01

    Full Text Available MomConnect is a national initiative coordinated by the South African National Department of Health that sends text-based mobile phone messages free of charge to pregnant women who voluntarily register at any public healthcare facility in South...

  11. PINGU: PredIction of eNzyme catalytic residues usinG seqUence information.

    Directory of Open Access Journals (Sweden)

    Priyadarshini P Pai

    Full Text Available Identification of catalytic residues can help unveil interesting attributes of enzyme function for various therapeutic and industrial applications. Based on their biochemical roles, the number of catalytic residues and sequence lengths of enzymes vary. This article describes a prediction approach (PINGU for such a scenario. It uses models trained using physicochemical properties and evolutionary information of 650 non-redundant enzymes (2136 catalytic residues in a support vector machines architecture. Independent testing on 200 non-redundant enzymes (683 catalytic residues in predefined prediction settings, i.e., with non-catalytic per catalytic residue ranging from 1 to 30, suggested that the prediction approach was highly sensitive and specific, i.e., 80% or above, over the incremental challenges. To learn more about the discriminatory power of PINGU in real scenarios, where the prediction challenge is variable and susceptible to high false positives, the best model from independent testing was used on 60 diverse enzymes. Results suggested that PINGU was able to identify most catalytic residues and non-catalytic residues properly with 80% or above accuracy, sensitivity and specificity. The effect of false positives on precision was addressed in this study by application of predicted ligand-binding residue information as a post-processing filter. An overall improvement of 20% in F-measure and 0.138 in Correlation Coefficient with 16% enhanced precision could be achieved. On account of its encouraging performance, PINGU is hoped to have eventual applications in boosting enzyme engineering and novel drug discovery.

  12. Informed consent for exome sequencing research in families with genetic disease: the emerging issue of incidental findings.

    Science.gov (United States)

    Bergner, Amanda L; Bollinger, Juli; Raraigh, Karen S; Tichnell, Crystal; Murray, Brittney; Blout, Carrie Lynn; Telegrafi, Aida Bytyci; James, Cynthia A

    2014-11-01

    Genomic sequencing technology is increasingly used in genetic research. Studies of informed consent for exome and genome sequencing (ES/GS) research have largely involved hypothetical scenarios or healthy individuals enrolling in population-based studies. Studies have yet to explore the consent experiences of adults with inherited disease. We conducted a qualitative interview study of 15 adults recently enrolled in a large-scale ES/GS study (11 affected adults, four parents of affected children). Our study had two goals: (1) to explore three theoretical barriers to consent for ES/GS research (interpretive/technical complexity, possibility of incidental findings, and risks of loss of privacy); and (2) to explore how interviewees experienced the consent process. Interviewees could articulate study goals and processes, describe incidental findings, discuss risks of privacy loss, and reflect on their consent experience. Few expected the study would identify the genetic cause of their condition. All elected to receive incidental findings. Interviewees acknowledged paying little attention to potential implications of incidental findings in light of more pressing goals of supporting research regarding their own medical conditions. Interviewees suggested that experience living with a genetic condition prepared them to adjust to incidental findings. Interviewees also expressed little concern about loss of confidentiality of study data. Some experienced the consent process as very long. None desired reconsent prior to return of study results. Families with inherited disease likely would benefit from a consent process in which study risks and benefits were discussed in the context of prior experiences with genetic research and genetic disease. © 2014 Wiley Periodicals, Inc.

  13. A tale of two anomalies: Depletion, dispersion, and the connection between the stellar lithium spread and inflated radii on the pre-main sequence

    Energy Technology Data Exchange (ETDEWEB)

    Somers, Garrett; Pinsonneault, Marc H., E-mail: somers@astronomy.ohio-state.edu, E-mail: pinsono@astronomy.ohio-state.edu [Department of Astronomy, The Ohio State University, 140 West 18th Avenue, Columbus, OH 43201 (United States)

    2014-07-20

    We investigate lithium depletion in standard stellar models (SSMs) and main sequence (MS) open clusters, and explore the origin of the Li dispersion in young, cool stars of equal mass, age, and composition. We first demonstrate that SSMs accurately predict the Li abundances of solar analogs at the zero-age main sequence (ZAMS) within theoretical uncertainties. We then measure the rate of MS Li depletion by removing the [Fe/H]-dependent ZAMS Li pattern from three well-studied clusters, and comparing the detrended data. MS depletion is found to be mass-dependent, in the sense of more depletion at low mass. A dispersion in Li abundance at fixed T{sub eff} is nearly universal, and sets in by ∼200 Myr. We discuss mass and age dispersion trends, and the pattern is mixed. We argue that metallicity impacts the ZAMS Li pattern, in agreement with theoretical expectations but contrary to the findings of some previous studies, and suggest Li as a test of cluster metallicity. Finally, we argue that a radius dispersion in stars of fixed mass and age, during the epoch of pre-MS Li destruction, is responsible for the spread in Li abundances and the correlation between rotation and Li in young cool stars, most well known in the Pleiades. We calculate stellar models, inflated to match observed radius anomalies in magnetically active systems, and the resulting range of Li abundances reproduces the observed patterns of young clusters. We discuss ramifications for pre-MS evolutionary tracks and age measurements of young clusters, and suggest an observational test.

  14. A tale of two anomalies: Depletion, dispersion, and the connection between the stellar lithium spread and inflated radii on the pre-main sequence

    International Nuclear Information System (INIS)

    Somers, Garrett; Pinsonneault, Marc H.

    2014-01-01

    We investigate lithium depletion in standard stellar models (SSMs) and main sequence (MS) open clusters, and explore the origin of the Li dispersion in young, cool stars of equal mass, age, and composition. We first demonstrate that SSMs accurately predict the Li abundances of solar analogs at the zero-age main sequence (ZAMS) within theoretical uncertainties. We then measure the rate of MS Li depletion by removing the [Fe/H]-dependent ZAMS Li pattern from three well-studied clusters, and comparing the detrended data. MS depletion is found to be mass-dependent, in the sense of more depletion at low mass. A dispersion in Li abundance at fixed T eff is nearly universal, and sets in by ∼200 Myr. We discuss mass and age dispersion trends, and the pattern is mixed. We argue that metallicity impacts the ZAMS Li pattern, in agreement with theoretical expectations but contrary to the findings of some previous studies, and suggest Li as a test of cluster metallicity. Finally, we argue that a radius dispersion in stars of fixed mass and age, during the epoch of pre-MS Li destruction, is responsible for the spread in Li abundances and the correlation between rotation and Li in young cool stars, most well known in the Pleiades. We calculate stellar models, inflated to match observed radius anomalies in magnetically active systems, and the resulting range of Li abundances reproduces the observed patterns of young clusters. We discuss ramifications for pre-MS evolutionary tracks and age measurements of young clusters, and suggest an observational test.

  15. Genetic differentiation between fake abalone and genuine Haliotis species using the forensically informative nucleotide sequencing (FINS) method.

    Science.gov (United States)

    Ha, Wai Y; Reid, David G; Kam, Wan L; Lau, Yuk Y; Sham, Wing C; Tam, Silvia Y K; Sin, Della W M; Mok, Chuen S

    2011-05-25

    Abalones ( Haliotis species) are a popular delicacy and commonly preserved in dried form either whole or in slices or small pieces for consumption in Asian countries. Driven by the huge profit from trading abalones, dishonest traders may substitute other molluscan species for processed abalone, of which the morphological characteristics are frequently lost in the processed form. For protection of consumer rights and law enforcement against fraud, there is a need for an effective methodology to differentiate between fake and genuine abalone. This paper describes a method (validated according to the international forensic guidelines provided by SWGDAM) for the identification of fake abalone species using forensically informative nucleotide sequence (FINS) analysis. A study of the local market revealed that many claimed "abalone slice" samples on sale are not genuine. The fake abalone samples were found to be either volutids of the genus Cymbium (93%) or the muricid Concholepas concholepas (7%). This is the first report of Cymbium species being used for the preparation and sale as "abalone" in dried sliced form in Hong Kong.

  16. Lncident: A Tool for Rapid Identification of Long Noncoding RNAs Utilizing Sequence Intrinsic Composition and Open Reading Frame Information

    Directory of Open Access Journals (Sweden)

    Siyu Han

    2016-01-01

    Full Text Available More and more studies have demonstrated that long noncoding RNAs (lncRNAs play critical roles in diversity of biological process and are also associated with various types of disease. How to rapidly identify lncRNAs and messenger RNA is the fundamental step to uncover the function of lncRNAs identification. Here, we present a novel method for rapid identification of lncRNAs utilizing sequence intrinsic composition features and open reading frame information based on support vector machine model, named as Lncident (LncRNAs identification. The 10-fold cross-validation and ROC curve are used to evaluate the performance of Lncident. The main advantage of Lncident is high speed without the loss of accuracy. Compared with the exiting popular tools, Lncident outperforms Coding-Potential Calculator, Coding-Potential Assessment Tool, Coding-Noncoding Index, and PLEK. Lncident is also much faster than Coding-Potential Calculator and Coding-Noncoding Index. Lncident presents an outstanding performance on microorganism, which offers a great application prospect to the analysis of microorganism. In addition, Lncident can be trained by users’ own collected data. Furthermore, R package and web server are simultaneously developed in order to maximize the convenience for the users. The R package “Lncident” can be easily installed on multiple operating system platforms, as long as R is supported.

  17. Scenario-based design: a method for connecting information system design with public health operations and emergency management.

    Science.gov (United States)

    Reeder, Blaine; Turner, Anne M

    2011-12-01

    Responding to public health emergencies requires rapid and accurate assessment of workforce availability under adverse and changing circumstances. However, public health information systems to support resource management during both routine and emergency operations are currently lacking. We applied scenario-based design as an approach to engage public health practitioners in the creation and validation of an information design to support routine and emergency public health activities. Using semi-structured interviews we identified the information needs and activities of senior public health managers of a large municipal health department during routine and emergency operations. Interview analysis identified 25 information needs for public health operations management. The identified information needs were used in conjunction with scenario-based design to create 25 scenarios of use and a public health manager persona. Scenarios of use and persona were validated and modified based on follow-up surveys with study participants. Scenarios were used to test and gain feedback on a pilot information system. The method of scenario-based design was applied to represent the resource management needs of senior-level public health managers under routine and disaster settings. Scenario-based design can be a useful tool for engaging public health practitioners in the design process and to validate an information system design. Copyright © 2011 Elsevier Inc. All rights reserved.

  18. Application of interdisciplinary connections and information technologies for development of motor skills in light athletic of girls - senior form pupils

    Directory of Open Access Journals (Sweden)

    Abdel Baset Al-Ravashdeh

    2015-08-01

    Full Text Available Purpose: to work out and substantiate technologies of motor and intellectual aspects’ integral impact on process of training of light athletic’ throws and run techniques of 15-16 years old girls. Material: in the research 2 groups of pupils participated: control group (n = 22 and experimental group (n = 21. Results: Methodic of run, jumps and throws techniques’ training of senior school girl-pupils has been worked out. The methodic implies mastering of basic light athletic movements on the base of analogies with rational and economic movements in animate nature and laws of mechanic It conditions application of knowledge from physics, biology, mathematic for receiving of more complete understanding of light athletic movements’ correct technique. Conclusions: we have shown that application of interdisciplinary connections permits to make the process of movements’ training more effective in comparison with mastering material of purely physical education.

  19. A genetic algorithm for finding good balanced sequences in a customer assignment problem with no state information

    NARCIS (Netherlands)

    Hordijk, W.; Hordijk, A.; Heidergott, B.F.

    2015-01-01

    In this paper, we study the control problem of optimal assignment of tasks to servers in a multi-server queue with inhomogeneous servers. In order to improve the performance of the system, we use a periodic deterministic sequence of job assignments to servers called a billiard sequence. We then use

  20. Optimizing multiple sequence alignments using a genetic algorithm based on three objectives: structural information, non-gaps percentage and totally conserved columns.

    Science.gov (United States)

    Ortuño, Francisco M; Valenzuela, Olga; Rojas, Fernando; Pomares, Hector; Florido, Javier P; Urquiza, Jose M; Rojas, Ignacio

    2013-09-01

    Multiple sequence alignments (MSAs) are widely used approaches in bioinformatics to carry out other tasks such as structure predictions, biological function analyses or phylogenetic modeling. However, current tools usually provide partially optimal alignments, as each one is focused on specific biological features. Thus, the same set of sequences can produce different alignments, above all when sequences are less similar. Consequently, researchers and biologists do not agree about which is the most suitable way to evaluate MSAs. Recent evaluations tend to use more complex scores including further biological features. Among them, 3D structures are increasingly being used to evaluate alignments. Because structures are more conserved in proteins than sequences, scores with structural information are better suited to evaluate more distant relationships between sequences. The proposed multiobjective algorithm, based on the non-dominated sorting genetic algorithm, aims to jointly optimize three objectives: STRIKE score, non-gaps percentage and totally conserved columns. It was significantly assessed on the BAliBASE benchmark according to the Kruskal-Wallis test (P algorithm also outperforms other aligners, such as ClustalW, Multiple Sequence Alignment Genetic Algorithm (MSA-GA), PRRP, DIALIGN, Hidden Markov Model Training (HMMT), Pattern-Induced Multi-sequence Alignment (PIMA), MULTIALIGN, Sequence Alignment Genetic Algorithm (SAGA), PILEUP, Rubber Band Technique Genetic Algorithm (RBT-GA) and Vertical Decomposition Genetic Algorithm (VDGA), according to the Wilcoxon signed-rank test (P 0.05) with the advantage of being able to use less structures. Structural information is included within the objective function to evaluate more accurately the obtained alignments. The source code is available at http://www.ugr.es/~fortuno/MOSAStrE/MO-SAStrE.zip.

  1. Determination of relevant neuron-neuron connections for neural prosthetics using time-delayed mutual information: tutorial and preliminary results.

    Science.gov (United States)

    Taghva, Alexander; Song, Dong; Hampson, Robert E; Deadwyler, Sam A; Berger, Theodore W

    2012-12-01

    Identification of functional dependence among neurons is a necessary component in both the rational design of neural prostheses as well as in the characterization of network physiology. The objective of this article is to provide a tutorial for neurosurgeons regarding information theory, specifically time-delayed mutual information, and to compare time-delayed mutual information, an information theoretic quantity based on statistical dependence, with cross-correlation, a commonly used metric for this task in a preliminary analysis of rat hippocampal neurons. Spike trains were recorded from rats performing delayed nonmatch-to-sample task using an array of electrodes surgically implanted into the hippocampus of each hemisphere of the brain. In addition, spike train simulations of positively correlated neurons, negatively correlated neurons, and neurons correlated by nonlinear functions were generated. These were evaluated by time-delayed mutual information (MI) and cross-correlation. Application of time-delayed MI to experimental data indicated the optimal bin size for information capture in the CA3-CA1 system was 40 ms, which may provide some insight into the spatiotemporal nature of encoding in the rat hippocampus. On simulated data, time-delayed MI showed peak values at appropriate time lags in positively correlated, negatively correlated, and complexly correlated data. Cross-correlation showed peak and troughs with positively correlated and negatively correlated data, but failed to capture some higher order correlations. Comparison of time-delayed MI to cross-correlation in identification of functionally dependent neurons indicates that the methods are not equivalent. Time-delayed MI appeared to capture some interactions between CA3-CA1 neurons at physiologically plausible time delays missed by cross-correlation. It should be considered as a method for identification of functional dependence between neurons and may be useful in the development of neural

  2. Local sequence information in cellular retinoic acid-binding protein I: specific residue roles in beta-turns.

    Science.gov (United States)

    Rotondi, Kenneth S; Gierasch, Lila M

    2003-01-01

    We have recently shown that two of the beta-turns (III and IV) in the ten-stranded, beta-clam protein, cellular retinoic acid-binding protein I (CRABP I), are favored in short peptide fragments, arguing that they are encoded by local interactions (K. S. Rotondi and L. M. Gierasch, Biochemistry, 2003, Vol. 42, pp. 7976-7985). In this paper we examine these turns in greater detail to dissect the specific local interactions responsible for their observed native conformational biases. Conformations of peptides corresponding to the turn III and IV fragments were examined under conditions designed to selectively disrupt stabilizing interactions, using pH variation, chaotrope addition, or mutagenesis to probe specific side-chain influences. We find that steric constraints imposed by excluded volume effects between near neighbor residues (i,i+2), favorable polar (i,i+2) interactions, and steric permissiveness of glycines are the principal factors accounting for the observed native bias in these turns. Longer-range stabilizing interactions across the beta-turns do not appear to play a significant role in turn stability in these short peptides, in contrast to their importance in hairpins. Additionally, our data add to a growing number of examples of the 3:5 type I turn with a beta-bulge as a class of turns with high propensity to form locally defined structure. Current work is directed at the interplay between the local sequence information in the turns and more long-range influences in the mechanism of folding of this predominantly beta-sheet protein. Copyright 2004 Wiley Periodicals, Inc.

  3. 49 CFR 40.323 - May program participants release drug or alcohol test information in connection with legal...

    Science.gov (United States)

    2010-10-01

    ... 49 Transportation 1 2010-10-01 2010-10-01 false May program participants release drug or alcohol... the Secretary of Transportation PROCEDURES FOR TRANSPORTATION WORKPLACE DRUG AND ALCOHOL TESTING... information pertaining to an employee's drug or alcohol test without the employee's consent in certain legal...

  4. 26 CFR 301.6103(n)-1 - Disclosure of returns and return information in connection with written contracts or agreements...

    Science.gov (United States)

    2010-04-01

    ... administration purposes. 301.6103(n)-1 Section 301.6103(n)-1 Internal Revenue INTERNAL REVENUE SERVICE... and Returns Returns and Records § 301.6103(n)-1 Disclosure of returns and return information in... administration purposes. (a) General rule. (1) Pursuant to the provisions of section 6103(n) of the Internal...

  5. Personal Learning Environments, Social Media, and Self-Regulated Learning: A Natural Formula for Connecting Formal and Informal Learning

    Science.gov (United States)

    Dabbagh, Nada; Kitsantas, Anastasia

    2012-01-01

    A Personal Learning Environment or PLE is a potentially promising pedagogical approach for both integrating formal and informal learning using social media and supporting student self-regulated learning in higher education contexts. The purpose of this paper is to (a) review research that support this claim, (b) conceptualize the connection…

  6. 12 CFR 717.30 - Obtaining or using medical information in connection with a determination of eligibility for credit.

    Science.gov (United States)

    2010-01-01

    ... current and that the consumer has no delinquencies in her repayment history. If the existing debt were... health, condition or history, type of treatment, or prognosis into account as part of any such... use information about: (A) The dollar amount, repayment terms, repayment history, and similar...

  7. 12 CFR 222.30 - Obtaining or using medical information in connection with a determination of eligibility for credit.

    Science.gov (United States)

    2010-01-01

    ... current and that the consumer has no delinquencies in her repayment history. If the existing debt were... health, condition or history, type of treatment, or prognosis into account as part of any such... use information about: (A) The dollar amount, repayment terms, repayment history, and similar...

  8. 12 CFR 334.30 - Obtaining or using medical information in connection with a determination of eligibility for credit.

    Science.gov (United States)

    2010-01-01

    ... current and that the consumer has no delinquencies in her repayment history. If the existing debt were... health, condition or history, type of treatment, or prognosis into account as part of any such... use information about: (A) The dollar amount, repayment terms, repayment history, and similar...

  9. 12 CFR 571.30 - Obtaining or using medical information in connection with a determination of eligibility for credit.

    Science.gov (United States)

    2010-01-01

    ... current and that the consumer has no delinquencies in her repayment history. If the existing debt were... health, condition or history, type of treatment, or prognosis into account as part of any such... use information about: (A) The dollar amount, repayment terms, repayment history, and similar...

  10. 12 CFR 41.30 - Obtaining or using medical information in connection with a determination of eligibility for credit.

    Science.gov (United States)

    2010-01-01

    ... medical information in violation of the prohibition if, for example: (i) In response to a general question... than 90 days past due. Any two debts of this size that are more than 90 days past due would disqualify... she receives $15,000 in long-term disability income each year from her former employer and has no...

  11. Connecting Grammaticalisation

    DEFF Research Database (Denmark)

    Nørgård-Sørensen, Jens; Heltoft, Lars; Schøsler, Lene

    morphological, topological and constructional paradigms often connect to form complex paradigms. The book introduces the concept of connecting grammaticalisation to describe the formation, restructuring and dismantling of such complex paradigms. Drawing primarily on data from Germanic, Romance and Slavic...

  12. An Algorithmic Information Calculus for Causal Discovery and Reprogramming Systems

    KAUST Repository

    Zenil, Hector; Kiani, Narsis A.; Marabita, Francesco; Deng, Yue; Elias, Szabolcs; Schmidt, Angelika; Ball, Gordon; Tegner, Jesper

    2017-01-01

    . By applying sequences of controlled interventions to systems and networks, we estimate how changes in their algorithmic information content are reflected in positive/negative shifts towards and away from randomness. The strong connection between approximations

  13. Sequences for Student Investigation

    Science.gov (United States)

    Barton, Jeffrey; Feil, David; Lartigue, David; Mullins, Bernadette

    2004-01-01

    We describe two classes of sequences that give rise to accessible problems for undergraduate research. These problems may be understood with virtually no prerequisites and are well suited for computer-aided investigation. The first sequence is a variation of one introduced by Stephen Wolfram in connection with his study of cellular automata. The…

  14. Connecting World Heritage Nominations and Monitoring with the Support of the Silk Roads Cultural Heritage Resource Information System

    Science.gov (United States)

    Vileikis, O.; Dumont, B.; Serruys, E.; Van Balen, K.; Tigny, V.; De Maeyer, P.

    2013-07-01

    Serial transnational World Heritage nominations are challenging the way cultural heritage has been managed and evaluated in the past. Serial transnational World Heritage nominations are unique in that they consist of multiple sites listed as one property, distributed in different countries, involving a large diversity of stakeholders in the process. As a result, there is a need for precise baseline information for monitoring, reporting and decision making. This type of nomination requires different methodologies and tools to improve the monitoring cycle from the beginning of the nomination towards the periodic reporting. The case study of the Silk Roads Cultural Heritage Resource Information System (CHRIS) illustrates the use of a Geographical Content Management System (Geo-CMS) supporting the serial transnational World Heritage nomination and the monitoring of the Silk Roads in the five Central Asian countries. The Silk Roads CHRIS is an initiative supported by UNESCO World Heritage Centre (WHC) and the Belgian Federal Science Policy Office (BELSPO), and developed by a consortium headed by the Raymond Lemaire International Centre for Conservation (RLICC) at the KULeuven. The Silk Roads CHRIS has been successfully assisting in the preparation of the nomination dossiers of the Republics of Kazakhstan, Tajikistan and Uzbekistan and will be used as a tool for monitoring tool in the Central Asian countries.

  15. Genome-Wide Prediction and Analysis of 3D-Domain Swapped Proteins in the Human Genome from Sequence Information.

    Science.gov (United States)

    Upadhyay, Atul Kumar; Sowdhamini, Ramanathan

    2016-01-01

    3D-domain swapping is one of the mechanisms of protein oligomerization and the proteins exhibiting this phenomenon have many biological functions. These proteins, which undergo domain swapping, have acquired much attention owing to their involvement in human diseases, such as conformational diseases, amyloidosis, serpinopathies, proteionopathies etc. Early realisation of proteins in the whole human genome that retain tendency to domain swap will enable many aspects of disease control management. Predictive models were developed by using machine learning approaches with an average accuracy of 78% (85.6% of sensitivity, 87.5% of specificity and an MCC value of 0.72) to predict putative domain swapping in protein sequences. These models were applied to many complete genomes with special emphasis on the human genome. Nearly 44% of the protein sequences in the human genome were predicted positive for domain swapping. Enrichment analysis was performed on the positively predicted sequences from human genome for their domain distribution, disease association and functional importance based on Gene Ontology (GO). Enrichment analysis was also performed to infer a better understanding of the functional importance of these sequences. Finally, we developed hinge region prediction, in the given putative domain swapped sequence, by using important physicochemical properties of amino acids.

  16. [Duties of physicians or other healthcare workers connected with diagnosis, treatment, dissemination of information, assessment and registration of TB patients].

    Science.gov (United States)

    Zielonka, Tadeusz M

    2015-01-01

    Effective laws provide a series of duties to be performed by physicians and other medical personnel associated with TB. Every TB case and death resulting from TB as well as any case of undesirable result of BCG test requires notification and filling in of a special form. The physician has a duty to inform TB patients their legal guardians, close relatives or friends about the need to undergo sanitary and diagnostic procedure, treatment or vaccination, as well as on how to prevent disease from spreading. Persons failing to comply with the relevant numerous legal requirements in this respect are subject to a fine.TB patients can use special sick benefits extending up to 270 days. There is a requirement to use appropriate codes to define TB irrespective of LCD-10 classification.

  17. Connected vehicle applications : environment.

    Science.gov (United States)

    2016-01-01

    The U.S. Department of Transportation has developed a number of connected vehicle environmental applications, including the Applications for the Environment Real-Time Information Synthesis (AERIS) research program applications and road weather applic...

  18. IDRC Connect User Guide

    International Development Research Centre (IDRC) Digital Library (Canada)

    Kristina Kamichaitis

    Once an account has been created by IDRC staff, you will receive .... content label in the table to access additional information. Table 3: ... One of the primary functions of IDRC Connect is to enable efficient and automated submission of final.

  19. Connected vehicles and cybersecurity.

    Science.gov (United States)

    2016-01-01

    Connected vehicles are a next-generation technology in vehicles and in infrastructure that will make travel safer, cleaner, and more efficient. The advanced wireless technology enables vehicles to share and communicate information with each other and...

  20. Hydrologically Connected Road Segments

    Data.gov (United States)

    Vermont Center for Geographic Information — Link it ArcGIS Item is HERE.The connectivity layer was created to assist municipalities in preparing for the forthcoming DEC Municipal Roads General Permit in 2018....

  1. Unpacking the performance of a mobile health information messaging program for mothers (MomConnect) in South Africa: evidence on program reach and messaging exposure.

    Science.gov (United States)

    LeFevre, Amnesty E; Dane, Pierre; Copley, Charles J; Pienaar, Cara; Parsons, Annie Neo; Engelhard, Matt; Woods, David; Bekker, Marcha; Benjamin, Peter; Pillay, Yogan; Barron, Peter; Seebregts, Christopher John; Mohan, Diwakar

    2018-01-01

    Despite calls to address broader evidence gaps in linking digital technologies to outcome and impact level health indicators, limited attention has been paid to measuring processes pertaining to the performance of programs. In this paper, we assess the program reach and message exposure of a mobile health information messaging program for mothers (MomConnect) in South Africa. In this descriptive study, we draw from system generated data to measure exposure to the program through registration attempts and conversions, message delivery, opt-outs and drop-outs. Using a logit model, we additionally explore determinants for early registration, opt-outs and drop-outs. From August 2014 to April 2017, 1 159 431 women were registered to MomConnect; corresponding to half of women attending antenatal care 1 (ANC1) and nearly 60% of those attending ANC1 estimated to own a mobile phone. In 2016, 26% of registrations started to get women onto MomConnect did not succeed. If registration attempts were converted to successful registrations, coverage of ANC1 attendees would have been 74% in 2016 and 86% in 2017. When considered as percentage of ANC1 attendees with access to a mobile phone, addressing conversion challenges bring registration coverage to an estimated 83%-89% in 2016 and 97%-100% in 2017. Among women registered, nearly 80% of expected short messaging service messages were received. While registration coverage and message delivery success rates exceed those observed for mobile messaging programs elsewhere, study findings highlight opportunities for program improvement and reinforce the need for rigorous and continuous monitoring of delivery systems.

  2. Inter-laboratory evaluation of the EUROFORGEN Global ancestry-informative SNP panel by massively parallel sequencing using the Ion PGM™.

    Science.gov (United States)

    Eduardoff, M; Gross, T E; Santos, C; de la Puente, M; Ballard, D; Strobl, C; Børsting, C; Morling, N; Fusco, L; Hussing, C; Egyed, B; Souto, L; Uacyisrael, J; Syndercombe Court, D; Carracedo, Á; Lareu, M V; Schneider, P M; Parson, W; Phillips, C; Parson, W; Phillips, C

    2016-07-01

    The EUROFORGEN Global ancestry-informative SNP (AIM-SNPs) panel is a forensic multiplex of 128 markers designed to differentiate an individual's ancestry from amongst the five continental population groups of Africa, Europe, East Asia, Native America, and Oceania. A custom multiplex of AmpliSeq™ PCR primers was designed for the Global AIM-SNPs to perform massively parallel sequencing using the Ion PGM™ system. This study assessed individual SNP genotyping precision using the Ion PGM™, the forensic sensitivity of the multiplex using dilution series, degraded DNA plus simple mixtures, and the ancestry differentiation power of the final panel design, which required substitution of three original ancestry-informative SNPs with alternatives. Fourteen populations that had not been previously analyzed were genotyped using the custom multiplex and these studies allowed assessment of genotyping performance by comparison of data across five laboratories. Results indicate a low level of genotyping error can still occur from sequence misalignment caused by homopolymeric tracts close to the target SNP, despite careful scrutiny of candidate SNPs at the design stage. Such sequence misalignment required the exclusion of component SNP rs2080161 from the Global AIM-SNPs panel. However, the overall genotyping precision and sensitivity of this custom multiplex indicates the Ion PGM™ assay for the Global AIM-SNPs is highly suitable for forensic ancestry analysis with massively parallel sequencing. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  3. Implementing stakeholder-informed research in the substance abuse treatment sector: strategies used by Connections, a Canadian knowledge translation and exchange project.

    Science.gov (United States)

    Henderson, Joanna; Sword, Wendy; Niccols, Alison; Dobbins, Maureen

    2014-05-29

    Researcher-stakeholder collaboration has been identified as critical to bridging research and health system change. While collaboration models vary, meaningful stakeholder involvement over time ("integrated knowledge translation") is advocated to improve the relevance of research to knowledge users. This short report describes the integrated knowledge translation efforts of Connections, a knowledge translation and exchange project to improve services for women with substance abuse problems and their children, and implementation barriers and facilitators. Strategies of varying intensities were used to engage diverse stakeholders, including policy makers and people with lived experience, and executive directors, program managers, and service providers from Canadian addiction agencies serving women. Barriers to participation included individual (e.g., interest), organizational (e.g., funding), and system level (e.g., lack of centralized stakeholder database) barriers. Similarly, facilitators included individual (e.g., perceived relevance) and organizational (e.g., support) facilitators, as well as initiative characteristics (e.g., multiple involvement opportunities). Despite barriers, Connections' stakeholder-informed research efforts proved essential for developing clinically relevant and feasible processes, measures, and implementation strategies. Stakeholder-researcher collaboration is possible and robust integrated knowledge translation efforts can be productive. Future work should emphasize developing and evaluating a range of strategies to address stakeholders' knowledge translation needs and to facilitate sustained and meaningful involvement in research.

  4. Facilitating medical information search using Google Glass connected to a content-based medical image retrieval system.

    Science.gov (United States)

    Widmer, Antoine; Schaer, Roger; Markonis, Dimitrios; Muller, Henning

    2014-01-01

    Wearable computing devices are starting to change the way users interact with computers and the Internet. Among them, Google Glass includes a small screen located in front of the right eye, a camera filming in front of the user and a small computing unit. Google Glass has the advantage to provide online services while allowing the user to perform tasks with his/her hands. These augmented glasses uncover many useful applications, also in the medical domain. For example, Google Glass can easily provide video conference between medical doctors to discuss a live case. Using these glasses can also facilitate medical information search by allowing the access of a large amount of annotated medical cases during a consultation in a non-disruptive fashion for medical staff. In this paper, we developed a Google Glass application able to take a photo and send it to a medical image retrieval system along with keywords in order to retrieve similar cases. As a preliminary assessment of the usability of the application, we tested the application under three conditions (images of the skin; printed CT scans and MRI images; and CT and MRI images acquired directly from an LCD screen) to explore whether using Google Glass affects the accuracy of the results returned by the medical image retrieval system. The preliminary results show that despite minor problems due to the relative stability of the Google Glass, images can be sent to and processed by the medical image retrieval system and similar images are returned to the user, potentially helping in the decision making process.

  5. The use of mycobacterial interspersed repetitive unit typing and whole genome sequencing to inform tuberculosis prevention and control activities.

    Science.gov (United States)

    Gilbert, Gwendolyn L; Sintchenko, Vitali

    2013-07-01

    Molecular strain typing of Mycobacterium tuberculosis has been possible for only about 20 years; it has significantly improved our understanding of the evolution and epidemiology of Mycobacterium tuberculosis and tuberculosis disease. Mycobacterial interspersed repetitive unit typing, based on 24 variable number tandem repeat unit loci, is highly discriminatory, relatively easy to perform and interpret and is currently the most widely used molecular typing system for tuberculosis surveillance. Nevertheless, clusters identified by mycobacterial interspersed repetitive unit typing sometimes cannot be confirmed or adequately defined by contact tracing and additional methods are needed. Recently, whole genome sequencing has been used to identify single nucleotide polymorphisms and other mutations, between genotypically indistinguishable isolates from the same cluster, to more accurately trace transmission pathways. Rapidly increasing speed and quality and reduced costs will soon make large scale whole genome sequencing feasible, combined with the use of sophisticated bioinformatics tools, for epidemiological surveillance of tuberculosis.

  6. Making Connections

    Science.gov (United States)

    Pien, Cheng Lu; Dongsheng, Zhao

    2011-01-01

    Effective teaching includes enabling learners to make connections within mathematics. It is easy to accord with this statement, but how often is it a reality in the mathematics classroom? This article describes an approach in "connecting equivalent" fractions and whole number operations. The authors illustrate how a teacher can combine a common…

  7. A study of archaeal enzymes involved in polar lipid synthesis linking amino acid sequence information, genomic contexts and lipid composition

    Directory of Open Access Journals (Sweden)

    Hiromi Daiyasu

    2005-01-01

    Full Text Available Cellular membrane lipids, of which phospholipids are the major constituents, form one of the characteristic features that distinguish Archaea from other organisms. In this study, we focused on the steps in archaeal phospholipid synthetic pathways that generate polar lipids such as archaetidylserine, archaetidylglycerol, and archaetidylinositol. Only archaetidylserine synthase (ASS, from Methanothermobacter thermautotrophicus, has been experimentally identified. Other enzymes have not been fully examined. Through database searching, we detected many archaeal hypothetical proteins that show sequence similarity to members of the CDP alcohol phosphatidyltransferase family, such as phosphatidylserine synthase (PSS, phosphatidylglycerol synthase (PGS and phosphatidylinositol synthase (PIS derived from Bacteria and Eukarya. The archaeal hypothetical proteins were classified into two groups, based on the sequence similarity. Members of the first group, including ASS from M. thermautotrophicus, were closely related to PSS. The rough agreement between PSS homologue distribution within Archaea and the experimentally identified distribution of archaetidylserine suggested that the hypothetical proteins are ASSs. We found that an open reading frame (ORF tends to be adjacent to that of ASS in the genome, and that the order of the two ORFs is conserved. The sequence similarity of phosphatidylserine decarboxylase to the product of the ORF next to the ASS gene, together with the genomic context conservation, suggests that the ORF encodes archaetidylserine decarboxylase, which may transform archaetidylserine to archaetidylethanolamine. The second group of archaeal hypothetical proteins was related to PGS and PIS. The members of this group were subjected to molecular phylogenetic analysis, together with PGSs and PISs and it was found that they formed two distinct clusters in the molecular phylogenetic tree. The distribution of members of each cluster within Archaea

  8. About Connections

    Directory of Open Access Journals (Sweden)

    Kathleen S Rockland

    2015-05-01

    Full Text Available Despite the attention attracted by connectomics, one can lose sight of the very real questions concerning What are connections? In the neuroimaging community, structural connectivity is ground truth and underlying constraint on functional or effective connectivity. It is referenced to underlying anatomy; but, as increasingly remarked, there is a large gap between the wealth of human brain mapping and the relatively scant data on actual anatomical connectivity. Moreover, connections have typically been discussed as pairwise, point x projecting to point y (or: to points y and z, or more recently, in graph theoretical terms, as nodes or regions and the interconnecting edges. This is a convenient shorthand, but tends not to capture the richness and nuance of basic anatomical properties as identified in the classic tradition of tracer studies. The present short review accordingly revisits connectional weights, heterogeneity, reciprocity, topography, and hierarchical organization, drawing on concrete examples. The emphasis is on presynaptic long-distance connections, motivated by the intention to probe current assumptions and promote discussions about further progress and synthesis.

  9. Brain functional network connectivity based on a visual task: visual information processing-related brain regions are significantly activated in the task state

    Directory of Open Access Journals (Sweden)

    Yan-li Yang

    2015-01-01

    Full Text Available It is not clear whether the method used in functional brain-network related research can be applied to explore the feature binding mechanism of visual perception. In this study, we investigated feature binding of color and shape in visual perception. Functional magnetic resonance imaging data were collected from 38 healthy volunteers at rest and while performing a visual perception task to construct brain networks active during resting and task states. Results showed that brain regions involved in visual information processing were obviously activated during the task. The components were partitioned using a greedy algorithm, indicating the visual network existed during the resting state. Z-values in the vision-related brain regions were calculated, confirming the dynamic balance of the brain network. Connectivity between brain regions was determined, and the result showed that occipital and lingual gyri were stable brain regions in the visual system network, the parietal lobe played a very important role in the binding process of color features and shape features, and the fusiform and inferior temporal gyri were crucial for processing color and shape information. Experimental findings indicate that understanding visual feature binding and cognitive processes will help establish computational models of vision, improve image recognition technology, and provide a new theoretical mechanism for feature binding in visual perception.

  10. Anonymous Connections and Onion Routing

    National Research Council Canada - National Science Library

    Syverson, Paul F; Goldschlag, David M; Reed, Michael G

    1997-01-01

    .... Unmodified Internet applications can use these anonymous connections by means of proxies. The proxies may also make communication anonymous by removing identifying information from the data stream...

  11. Generalized connectivity of graphs

    CERN Document Server

    Li, Xueliang

    2016-01-01

    Noteworthy results, proof techniques, open problems and conjectures in generalized (edge-) connectivity are discussed in this book. Both theoretical and practical analyses for generalized (edge-) connectivity of graphs are provided. Topics covered in this book include: generalized (edge-) connectivity of graph classes, algorithms, computational complexity, sharp bounds, Nordhaus-Gaddum-type results, maximum generalized local connectivity, extremal problems, random graphs, multigraphs, relations with the Steiner tree packing problem and generalizations of connectivity. This book enables graduate students to understand and master a segment of graph theory and combinatorial optimization. Researchers in graph theory, combinatorics, combinatorial optimization, probability, computer science, discrete algorithms, complexity analysis, network design, and the information transferring models will find this book useful in their studies.

  12. Internet Connectivity

    Indian Academy of Sciences (India)

    First page Back Continue Last page Overview Graphics. Internet Connectivity. BSNL, SIFY, HCL in Guwahati; only BSNL elsewhere in NE (local player in Shillong). Service poor; All vendors lease BW from BSNL.

  13. Mathematics Connection

    African Journals Online (AJOL)

    MATHEMATICS CONNECTION aims at providing a forum topromote the development of Mathematics Education in Ghana. Articles that seekto enhance the teaching and/or learning of mathematics at all levels of theeducational system are welcome.

  14. The master two-dimensional gel database of human AMA cell proteins: towards linking protein and genome sequence and mapping information (update 1991)

    DEFF Research Database (Denmark)

    Celis, J E; Leffers, H; Rasmussen, H H

    1991-01-01

    autoantigens" and "cDNAs". For convenience we have included an alphabetical list of all known proteins recorded in this database. In the long run, the main goal of this database is to link protein and DNA sequencing and mapping information (Human Genome Program) and to provide an integrated picture......The master two-dimensional gel database of human AMA cells currently lists 3801 cellular and secreted proteins, of which 371 cellular polypeptides (306 IEF; 65 NEPHGE) were added to the master images during the last 10 months. These include: (i) very basic and acidic proteins that do not focus...

  15. Establishing Connectivity

    DEFF Research Database (Denmark)

    Kjær, Poul F.

    Global law settings are characterised by a structural pre-eminence of connectivity norms, a type of norm which differs from coherency or possibility norms. The centrality of connectivity norms emerges from the function of global law, which is to increase the probability of transfers of condensed ...... and human rights can be understood as serving a constitutionalising function aimed at stabilising and facilitating connectivity. This allows for an understanding of colonialism and contemporary global governance as functional, but not as normative, equivalents.......Global law settings are characterised by a structural pre-eminence of connectivity norms, a type of norm which differs from coherency or possibility norms. The centrality of connectivity norms emerges from the function of global law, which is to increase the probability of transfers of condensed...... social components, such as economic capital and products, religious doctrines and scientific knowledge, from one legally structured context to another within world society. This was the case from colonialism and colonial law to contemporary global supply chains and human rights. Both colonial law...

  16. Development of Highly Informative Genome-Wide Single Sequence Repeat Markers for Breeding Applications in Sesame and Construction of a Web Resource: SisatBase

    Directory of Open Access Journals (Sweden)

    Komivi Dossa

    2017-08-01

    Full Text Available The sequencing of the full nuclear genome of sesame (Sesamum indicum L. provides the platform for functional analyses of genome components and their application in breeding programs. Although the importance of microsatellites markers or simple sequence repeats (SSR in crop genotyping, genetics, and breeding applications is well established, only a little information exist concerning SSRs at the whole genome level in sesame. In addition, SSRs represent a suitable marker type for sesame molecular breeding in developing countries where it is mainly grown. In this study, we identified 138,194 genome-wide SSRs of which 76.5% were physically mapped onto the 13 pseudo-chromosomes. Among these SSRs, up to three primers pairs were supplied for 101,930 SSRs and used to in silico amplify the reference genome together with two newly sequenced sesame accessions. A total of 79,957 SSRs (78% were polymorphic between the three genomes thereby suggesting their promising use in different genomics-assisted breeding applications. From these polymorphic SSRs, 23 were selected and validated to have high polymorphic potential in 48 sesame accessions from different growing areas of Africa. Furthermore, we have developed an online user-friendly database, SisatBase (http://www.sesame-bioinfo.org/SisatBase/, which provides free access to SSRs data as well as an integrated platform for functional analyses. Altogether, the reference SSR and SisatBase would serve as useful resources for genetic assessment, genomic studies, and breeding advancement in sesame, especially in developing countries.

  17. Using structural knowledge in the protein data bank to inform the search for potential host-microbe protein interactions in sequence space: application to Mycobacterium tuberculosis.

    Science.gov (United States)

    Mahajan, Gaurang; Mande, Shekhar C

    2017-04-04

    A comprehensive map of the human-M. tuberculosis (MTB) protein interactome would help fill the gaps in our understanding of the disease, and computational prediction can aid and complement experimental studies towards this end. Several sequence-based in silico approaches tap the existing data on experimentally validated protein-protein interactions (PPIs); these PPIs serve as templates from which novel interactions between pathogen and host are inferred. Such comparative approaches typically make use of local sequence alignment, which, in the absence of structural details about the interfaces mediating the template interactions, could lead to incorrect inferences, particularly when multi-domain proteins are involved. We propose leveraging the domain-domain interaction (DDI) information in PDB complexes to score and prioritize candidate PPIs between host and pathogen proteomes based on targeted sequence-level comparisons. Our method picks out a small set of human-MTB protein pairs as candidates for physical interactions, and the use of functional meta-data suggests that some of them could contribute to the in vivo molecular cross-talk between pathogen and host that regulates the course of the infection. Further, we present numerical data for Pfam domain families that highlights interaction specificity on the domain level. Not every instance of a pair of domains, for which interaction evidence has been found in a few instances (i.e. structures), is likely to functionally interact. Our sorting approach scores candidates according to how "distant" they are in sequence space from known examples of DDIs (templates). Thus, it provides a natural way to deal with the heterogeneity in domain-level interactions. Our method represents a more informed application of local alignment to the sequence-based search for potential human-microbial interactions that uses available PPI data as a prior. Our approach is somewhat limited in its sensitivity by the restricted size and

  18. Connectivity in river deltas

    Science.gov (United States)

    Passalacqua, P.; Hiatt, M. R.; Sendrowski, A.

    2016-12-01

    Deltas host approximately half a billion people and are rich in ecosystem diversity and economic resources. However, human-induced activities and climatic shifts are significantly impacting deltas around the world; anthropogenic disturbance, natural subsidence, and eustatic sea-level rise are major causes of threat to deltas and in many cases have compromised their safety and sustainability, putting at risk the people that live on them. In this presentation, I will introduce a framework called Delta Connectome for studying connectivity in river deltas based on different representations of a delta as a network. Here connectivity indicates both physical connectivity (how different portions of the system interact with each other) as well as conceptual (pathways of process coupling). I will explore several network representations and show how quantifying connectivity can advance our understanding of system functioning and can be used to inform coastal management and restoration. From connectivity considerations, the delta emerges as a leaky network that evolves over time and is characterized by continuous exchanges of fluxes of matter, energy, and information. I will discuss the implications of connectivity on delta functioning, land growth, and potential for nutrient removal.

  19. Connections beyond the margins of the power grid Information technology and the evolution of off-grid solar electricity in the developing world

    Science.gov (United States)

    Alstone, Peter Michael

    This work explores the intersections of information technology and off-grid electricity deployment in the developing world with focus on a key instance: the emergence of pay-as-you-go (PAYG) solar household-scale energy systems. It is grounded in detailed field study by my research team in Kenya between 2013-2014 that included primary data collection across the solar supply chain from global businesses through national and local distribution and to the end-users. We supplement the information with business process and national survey data to develop a detailed view of the markets, technology systems, and individuals who interact within those frameworks. The findings are presented in this dissertation as a series of four chapters with introductory, bridging, and synthesis material between them. The first chapter, Decentralized Energy Systems for Clean Electricity Access, presents a global view of the emerging off-grid power sector. Long-run trends in technology create "a unique moment in history" for closing the gap between global population and access to electricity, which has stubbornly held at 1-2 billion people without power since the initiation of the electric utility business model in the late 1800's. We show the potential for widespread near-term adoption of off-grid solar, which could lead to ten times less inequality in access and also ten times lower household-level climate impacts. Decentralized power systems that replace fuel-based incumbent lighting can advance the causes of climate stabilization, economic and social freedom and human health. Chapters two and three are focused on market and institutional dynamics present circa 2014 in for off-grid solar with a focus on the Kenya market. Chapter 2, "Off-grid Power and Connectivity", presents our findings related to the widespread influence of information technology across the supply chain for solar and in PAYG approaches. Using digital financing and embedded payment verification technology, PAYG

  20. Making connections

    NARCIS (Netherlands)

    Marion Duimel

    2007-01-01

    Original title: Verbinding maken; senioren en internet. More and more older people are finding their way to the Internet. Many people aged over 50 who have only recently gone online say that a new world has opened up for them. By connecting to the Internet they have the feeling that they

  1. CMS Connect

    Science.gov (United States)

    Balcas, J.; Bockelman, B.; Gardner, R., Jr.; Hurtado Anampa, K.; Jayatilaka, B.; Aftab Khan, F.; Lannon, K.; Larson, K.; Letts, J.; Marra Da Silva, J.; Mascheroni, M.; Mason, D.; Perez-Calero Yzquierdo, A.; Tiradani, A.

    2017-10-01

    The CMS experiment collects and analyzes large amounts of data coming from high energy particle collisions produced by the Large Hadron Collider (LHC) at CERN. This involves a huge amount of real and simulated data processing that needs to be handled in batch-oriented platforms. The CMS Global Pool of computing resources provide +100K dedicated CPU cores and another 50K to 100K CPU cores from opportunistic resources for these kind of tasks and even though production and event processing analysis workflows are already managed by existing tools, there is still a lack of support to submit final stage condor-like analysis jobs familiar to Tier-3 or local Computing Facilities users into these distributed resources in an integrated (with other CMS services) and friendly way. CMS Connect is a set of computing tools and services designed to augment existing services in the CMS Physics community focusing on these kind of condor analysis jobs. It is based on the CI-Connect platform developed by the Open Science Grid and uses the CMS GlideInWMS infrastructure to transparently plug CMS global grid resources into a virtual pool accessed via a single submission machine. This paper describes the specific developments and deployment of CMS Connect beyond the CI-Connect platform in order to integrate the service with CMS specific needs, including specific Site submission, accounting of jobs and automated reporting to standard CMS monitoring resources in an effortless way to their users.

  2. Roles of repetitive sequences

    Energy Technology Data Exchange (ETDEWEB)

    Bell, G.I.

    1991-12-31

    The DNA of higher eukaryotes contains many repetitive sequences. The study of repetitive sequences is important, not only because many have important biological function, but also because they provide information on genome organization, evolution and dynamics. In this paper, I will first discuss some generic effects that repetitive sequences will have upon genome dynamics and evolution. In particular, it will be shown that repetitive sequences foster recombination among, and turnover of, the elements of a genome. I will then consider some examples of repetitive sequences, notably minisatellite sequences and telomere sequences as examples of tandem repeats, without and with respectively known function, and Alu sequences as an example of interspersed repeats. Some other examples will also be considered in less detail.

  3. A novel genome-information content-based statistic for genome-wide association analysis designed for next-generation sequencing data.

    Science.gov (United States)

    Luo, Li; Zhu, Yun; Xiong, Momiao

    2012-06-01

    The genome-wide association studies (GWAS) designed for next-generation sequencing data involve testing association of genomic variants, including common, low frequency, and rare variants. The current strategies for association studies are well developed for identifying association of common variants with the common diseases, but may be ill-suited when large amounts of allelic heterogeneity are present in sequence data. Recently, group tests that analyze their collective frequency differences between cases and controls shift the current variant-by-variant analysis paradigm for GWAS of common variants to the collective test of multiple variants in the association analysis of rare variants. However, group tests ignore differences in genetic effects among SNPs at different genomic locations. As an alternative to group tests, we developed a novel genome-information content-based statistics for testing association of the entire allele frequency spectrum of genomic variation with the diseases. To evaluate the performance of the proposed statistics, we use large-scale simulations based on whole genome low coverage pilot data in the 1000 Genomes Project to calculate the type 1 error rates and power of seven alternative statistics: a genome-information content-based statistic, the generalized T(2), collapsing method, multivariate and collapsing (CMC) method, individual χ(2) test, weighted-sum statistic, and variable threshold statistic. Finally, we apply the seven statistics to published resequencing dataset from ANGPTL3, ANGPTL4, ANGPTL5, and ANGPTL6 genes in the Dallas Heart Study. We report that the genome-information content-based statistic has significantly improved type 1 error rates and higher power than the other six statistics in both simulated and empirical datasets.

  4. Gendered Connections

    DEFF Research Database (Denmark)

    Jensen, Steffen Bo

    2009-01-01

    This article explores the gendered nature of urban politics in Cape Town by focusing on a group of female, township politicians. Employing the Deleuzian concept of `wild connectivity', it argues that these politically entrepreneurial women were able to negotiate a highly volatile urban landscape...... by drawing on and operationalizing violent, male networks — from struggle activists' networks, to vigilante groups and gangs, to the police. The fact that they were women helped them to tap into and exploit these networks. At the same time, they were restricted by their sex, as their ability to navigate...... space also drew on quite traditional notions of female respectability. Furthermore, the article argues, the form of wild connectivity to an extent was a function of the political transition, which destabilized formal structures of gendered authority. It remains a question whether this form...

  5. Sequence variants in the bovine silent information regulator 6, their linkage and their associations with body measurements and carcass quality traits in Qinchuan cattle.

    Science.gov (United States)

    Gui, Linsheng; Jiang, Bijie; Zhang, Yaran; Zan, Linsen

    2015-03-15

    Silent information regulator 6 (SIRT6) belongs to the family of class III nicotinamide adenine dinucleotide (NAD)-dependent deacetylase and plays an essential role in DNA repair and metabolism. This study was conducted to detect potential polymorphisms of the bovine SIRT6 gene and explore their relationships with body measurement and carcass quality in Qinchuan cattle. Four sequence variants (SVs) were identified in intron 6, exon 7, exon 9, and 3' UTR, via sequencing technology conducted in 468 individual Qinchuan cattle. Eleven different haplotypes were identified, of which two major haplotypes had a frequency of 45.7% (-CACT-) and 14.8% (-CGTC-). Three SVs (SV2, SV3 and SV4) were significantly associated with some of the body measurements and carcass quality traits (P<0.05 or P<0.01), and the H2H7 (CC-GA-TT-TC) diplotype had better performance than other combinations. Our results suggest that some polymorphisms in SIRT6 are associated with production traits and may be used as candidates for marker-assisted selection (MAS) and management in beef cattle breeding programs. Copyright © 2015 Elsevier B.V. All rights reserved.

  6. NetTurnP--neural network prediction of beta-turns by use of evolutionary information and predicted protein sequence features.

    Directory of Open Access Journals (Sweden)

    Bent Petersen

    Full Text Available UNLABELLED: β-turns are the most common type of non-repetitive structures, and constitute on average 25% of the amino acids in proteins. The formation of β-turns plays an important role in protein folding, protein stability and molecular recognition processes. In this work we present the neural network method NetTurnP, for prediction of two-class β-turns and prediction of the individual β-turn types, by use of evolutionary information and predicted protein sequence features. It has been evaluated against a commonly used dataset BT426, and achieves a Matthews correlation coefficient of 0.50, which is the highest reported performance on a two-class prediction of β-turn and not-β-turn. Furthermore NetTurnP shows improved performance on some of the specific β-turn types. In the present work, neural network methods have been trained to predict β-turn or not and individual β-turn types from the primary amino acid sequence. The individual β-turn types I, I', II, II', VIII, VIa1, VIa2, VIba and IV have been predicted based on classifications by PROMOTIF, and the two-class prediction of β-turn or not is a superset comprised of all β-turn types. The performance is evaluated using a golden set of non-homologous sequences known as BT426. Our two-class prediction method achieves a performance of: MCC=0.50, Qtotal=82.1%, sensitivity=75.6%, PPV=68.8% and AUC=0.864. We have compared our performance to eleven other prediction methods that obtain Matthews correlation coefficients in the range of 0.17-0.47. For the type specific β-turn predictions, only type I and II can be predicted with reasonable Matthews correlation coefficients, where we obtain performance values of 0.36 and 0.31, respectively. CONCLUSION: The NetTurnP method has been implemented as a webserver, which is freely available at http://www.cbs.dtu.dk/services/NetTurnP/. NetTurnP is the only available webserver that allows submission of multiple sequences.

  7. NetTurnP – Neural Network Prediction of Beta-turns by Use of Evolutionary Information and Predicted Protein Sequence Features

    Science.gov (United States)

    Petersen, Bent; Lundegaard, Claus; Petersen, Thomas Nordahl

    2010-01-01

    β-turns are the most common type of non-repetitive structures, and constitute on average 25% of the amino acids in proteins. The formation of β-turns plays an important role in protein folding, protein stability and molecular recognition processes. In this work we present the neural network method NetTurnP, for prediction of two-class β-turns and prediction of the individual β-turn types, by use of evolutionary information and predicted protein sequence features. It has been evaluated against a commonly used dataset BT426, and achieves a Matthews correlation coefficient of 0.50, which is the highest reported performance on a two-class prediction of β-turn and not-β-turn. Furthermore NetTurnP shows improved performance on some of the specific β-turn types. In the present work, neural network methods have been trained to predict β-turn or not and individual β-turn types from the primary amino acid sequence. The individual β-turn types I, I', II, II', VIII, VIa1, VIa2, VIba and IV have been predicted based on classifications by PROMOTIF, and the two-class prediction of β-turn or not is a superset comprised of all β-turn types. The performance is evaluated using a golden set of non-homologous sequences known as BT426. Our two-class prediction method achieves a performance of: MCC  = 0.50, Qtotal = 82.1%, sensitivity  = 75.6%, PPV  = 68.8% and AUC  = 0.864. We have compared our performance to eleven other prediction methods that obtain Matthews correlation coefficients in the range of 0.17 – 0.47. For the type specific β-turn predictions, only type I and II can be predicted with reasonable Matthews correlation coefficients, where we obtain performance values of 0.36 and 0.31, respectively. Conclusion The NetTurnP method has been implemented as a webserver, which is freely available at http://www.cbs.dtu.dk/services/NetTurnP/. NetTurnP is the only available webserver that allows submission of multiple sequences. PMID:21152409

  8. NetTurnP--neural network prediction of beta-turns by use of evolutionary information and predicted protein sequence features.

    Science.gov (United States)

    Petersen, Bent; Lundegaard, Claus; Petersen, Thomas Nordahl

    2010-11-30

    β-turns are the most common type of non-repetitive structures, and constitute on average 25% of the amino acids in proteins. The formation of β-turns plays an important role in protein folding, protein stability and molecular recognition processes. In this work we present the neural network method NetTurnP, for prediction of two-class β-turns and prediction of the individual β-turn types, by use of evolutionary information and predicted protein sequence features. It has been evaluated against a commonly used dataset BT426, and achieves a Matthews correlation coefficient of 0.50, which is the highest reported performance on a two-class prediction of β-turn and not-β-turn. Furthermore NetTurnP shows improved performance on some of the specific β-turn types. In the present work, neural network methods have been trained to predict β-turn or not and individual β-turn types from the primary amino acid sequence. The individual β-turn types I, I', II, II', VIII, VIa1, VIa2, VIba and IV have been predicted based on classifications by PROMOTIF, and the two-class prediction of β-turn or not is a superset comprised of all β-turn types. The performance is evaluated using a golden set of non-homologous sequences known as BT426. Our two-class prediction method achieves a performance of: MCC=0.50, Qtotal=82.1%, sensitivity=75.6%, PPV=68.8% and AUC=0.864. We have compared our performance to eleven other prediction methods that obtain Matthews correlation coefficients in the range of 0.17-0.47. For the type specific β-turn predictions, only type I and II can be predicted with reasonable Matthews correlation coefficients, where we obtain performance values of 0.36 and 0.31, respectively. The NetTurnP method has been implemented as a webserver, which is freely available at http://www.cbs.dtu.dk/services/NetTurnP/. NetTurnP is the only available webserver that allows submission of multiple sequences.

  9. Cosmic Connections

    CERN Document Server

    Ellis, Jonathan Richard

    2003-01-01

    A National Research Council study on connecting quarks with the cosmos has recently posed a number of the more important open questions at the interface between particle physics and cosmology. These questions include the nature of dark matter and dark energy, how the Universe began, modifications to gravity, the effects of neutrinos on the Universe, how cosmic accelerators work, and whether there are new states of matter at high density and pressure. These questions are discussed in the context of the talks presented at this Summer Institute.

  10. Places Connected:

    DEFF Research Database (Denmark)

    Hansen, Annette Skovsted

    This paper argues that development assistance contributed to the globalization of the 20th century by financing truly global networks of people. By focusing on the networks financed by development assistance bound by the national histories of Denmark and Japan, I illustrate how the people who...... experiences of place, however, when it is often the same people who experience many different places? Along with many other so-called donors in the 1950s, Denmark and Japan chose to invest in the education of own and other nationals involved in development and thereby financed personal connections between...... individuals throughout the world. Development assistance , where there are two or three links only between a Bangladeshi farmer, a street child in Sao Paolo and the President of the United States, the Queen of Denmark, or a suburban house wife in Japan, who has never left the Osaka area, but mothered a United...

  11. Sequence co-evolutionary information is a natural partner to minimally-frustrated models of biomolecular dynamics [version 1; referees: 3 approved

    Directory of Open Access Journals (Sweden)

    Jeffrey K Noel

    2016-01-01

    Full Text Available Experimentally derived structural constraints have been crucial to the implementation of computational models of biomolecular dynamics. For example, not only does crystallography provide essential starting points for molecular simulations but also high-resolution structures permit for parameterization of simplified models. Since the energy landscapes for proteins and other biomolecules have been shown to be minimally frustrated and therefore funneled, these structure-based models have played a major role in understanding the mechanisms governing folding and many functions of these systems. Structural information, however, may be limited in many interesting cases. Recently, the statistical analysis of residue co-evolution in families of protein sequences has provided a complementary method of discovering residue-residue contact interactions involved in functional configurations. These functional configurations are often transient and difficult to capture experimentally. Thus, co-evolutionary information can be merged with that available for experimentally characterized low free-energy structures, in order to more fully capture the true underlying biomolecular energy landscape.

  12. The Need for Clinical Decision Support Integrated with the Electronic Health Record for the Clinical Application of Whole Genome Sequencing Information

    Directory of Open Access Journals (Sweden)

    Brandon M. Welch

    2013-12-01

    Full Text Available Whole genome sequencing (WGS is rapidly approaching widespread clinical application. Technology advancements over the past decade, since the first human genome was decoded, have made it feasible to use WGS for clinical care. Future advancements will likely drive down the price to the point wherein WGS is routinely available for care. However, were this to happen today, most of the genetic information available to guide clinical care would go unused due to the complexity of genetics, limited physician proficiency in genetics, and lack of genetics professionals in the clinical workforce. Furthermore, these limitations are unlikely to change in the future. As such, the use of clinical decision support (CDS to guide genome-guided clinical decision-making is imperative. In this manuscript, we describe the barriers to widespread clinical application of WGS information, describe how CDS can be an important tool for overcoming these barriers, and provide clinical examples of how genome-enabled CDS can be used in the clinical setting.

  13. From Sequence to Morphology - Long-Range Correlations in Complete Sequenced Genomes

    NARCIS (Netherlands)

    T.A. Knoch (Tobias)

    2004-01-01

    textabstractThe largely unresolved sequential organization, i.e. the relations within DNA sequences, and its connection to the three-dimensional organization of genomes was investigated by correlation analyses of completely sequenced chromosomes from Viroids, Archaea, Bacteria, Arabidopsis

  14. Allele Re-sequencing Technologies

    DEFF Research Database (Denmark)

    Byrne, Stephen; Farrell, Jacqueline Danielle; Asp, Torben

    2013-01-01

    The development of next-generation sequencing technologies has made sequencing an affordable approach for detection of genetic variations associated with various traits. However, the cost of whole genome re-sequencing still remains too high to be feasible for many plant species with large...... alternative to whole genome re-sequencing to identify causative genetic variations in plants. One challenge, however, will be efficient bioinformatics strategies for data handling and analysis from the increasing amount of sequence information....

  15. Dynamic Sequence Assignment.

    Science.gov (United States)

    1983-12-01

    D-136 548 DYNAMIIC SEQUENCE ASSIGNMENT(U) ADVANCED INFORMATION AND 1/2 DECISION SYSTEMS MOUNTAIN YIELW CA C A 0 REILLY ET AL. UNCLSSIIED DEC 83 AI/DS...I ADVANCED INFORMATION & DECISION SYSTEMS Mountain View. CA 94040 84 u ,53 V,..’. Unclassified _____ SCURITY CLASSIFICATION OF THIS PAGE REPORT...reviews some important heuristic algorithms developed for fas- ter solution of the sequence assignment problem. 3.1. DINAMIC MOGRAMUNIG FORMULATION FOR

  16. Starting-up sequence of the AWEC-60 wind turbine

    International Nuclear Information System (INIS)

    Avia, F.; Cruz, M. de la.

    1991-01-01

    One of the most critical status of the wind turbines operation is the starting-up sequence and the connection to the grid, due to the actuating loads that could be several times the loads during operation at rated conditions. Due to this fact, the control strategy is very important during the starting-up sequence in order to minimize the loads on the machine. For this purpose it is necessary to analyze the behaviour of the wind turbine during that sequence in different wind conditions and machine conditions. This report shows the graphic information about fifty starting-up sequences of the AWEC-60 wind turbine of 60 m. diameter and 1200 kW of rated power, recorded in April 1991 and cut-out wind speed. (author)

  17. NetTurnP – Neural Network Prediction of Beta-turns by Use of Evolutionary Information and Predicted Protein Sequence Features

    DEFF Research Database (Denmark)

    Petersen, Bent; Lundegaard, Claus; Petersen, Thomas Nordahl

    2010-01-01

    is the highest reported performance on a two-class prediction of β-turn and not-β-turn. Furthermore NetTurnP shows improved performance on some of the specific β-turn types. In the present work, neural network methods have been trained to predict β-turn or not and individual β-turn types from the primary amino......β-turns are the most common type of non-repetitive structures, and constitute on average 25% of the amino acids in proteins. The formation of β-turns plays an important role in protein folding, protein stability and molecular recognition processes. In this work we present the neural network method...... NetTurnP, for prediction of two-class β-turns and prediction of the individual β-turn types, by use of evolutionary information and predicted protein sequence features. It has been evaluated against a commonly used dataset BT426, and achieves a Matthews correlation coefficient of 0.50, which...

  18. Valuable Connections

    DEFF Research Database (Denmark)

    Kjærsgaard, Mette Gislev; Smith, Rachel Charlotte

    2014-01-01

    , as well as design, production and use, we might need to rethink the role of ethnography within user centred design and business development. Here the challenge is less about ”getting closer” to user needs and real-life contexts, through familiarization, mediation, and facilitation, and more about creating...... a critical theoretically informed distance from which to perceive and reflect upon complex interconnections between people, technology, business and design, as well as our roles as researchers and designers within these....

  19. Information

    International Nuclear Information System (INIS)

    Boyard, Pierre.

    1981-01-01

    The fear for nuclear energy and more particularly for radioactive wastes is analyzed in the sociological context. Everybody agree on the information need, information is available but there is a problem for their diffusion. Reactions of the public are analyzed and journalists, scientists and teachers have a role to play [fr

  20. Valuable Connections

    DEFF Research Database (Denmark)

    Kjærsgaard, Mette Gislev; Smith, Rachel Charlotte

    2014-01-01

    and blurred boundaries between physical, digital and hybrid contexts, as well as design, production and use, we might need to rethink the role of ethnography within design and business development. Perhaps the aim is less about ”getting closer” to user needs and real-life contexts, through familiarization......, mediation, advocacy and facilitation, as in conventional approaches to ethnography in user centred design, and more about creating a critical theoretically informed distance from which to perceive and reflect upon complex interconnections between people, technology, business and design, as well as our roles...

  1. Sequence assembly

    DEFF Research Database (Denmark)

    Scheibye-Alsing, Karsten; Hoffmann, S.; Frankel, Annett Maria

    2009-01-01

    Despite the rapidly increasing number of sequenced and re-sequenced genomes, many issues regarding the computational assembly of large-scale sequencing data have remain unresolved. Computational assembly is crucial in large genome projects as well for the evolving high-throughput technologies and...... in genomic DNA, highly expressed genes and alternative transcripts in EST sequences. We summarize existing comparisons of different assemblers and provide a detailed descriptions and directions for download of assembly programs at: http://genome.ku.dk/resources/assembly/methods.html....

  2. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based on transcr......The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...

  3. WE-G-BRD-02: Characterizing Information Loss in a Sparse-Sampling-Based Dynamic MRI Sequence (k-T BLAST) for Lung Motion Monitoring

    International Nuclear Information System (INIS)

    Arai, T; Nofiele, J; Sawant, A

    2015-01-01

    Purpose: Rapid MRI is an attractive, non-ionizing tool for soft-tissue-based monitoring of respiratory motion in thoracic and abdominal radiotherapy. One big challenge is to achieve high temporal resolution while maintaining adequate spatial resolution. K-t BLAST, sparse-sampling and reconstruction sequence based on a-priori information represents a potential solution. In this work, we investigated how much “true” motion information is lost as a-priori information is progressively added for faster imaging. Methods: Lung tumor motions in superior-inferior direction obtained from ten individuals were replayed into an in-house, MRI-compatible, programmable motion platform (50Hz refresh and 100microns precision). Six water-filled 1.5ml tubes were placed on it as fiducial markers. Dynamic marker motion within a coronal slice (FOV: 32×32cm"2, resolution: 0.67×0.67mm"2, slice-thickness: 5mm) was collected on 3.0T body scanner (Ingenia, Philips). Balanced-FFE (TE/TR: 1.3ms/2.5ms, flip-angle: 40degrees) was used in conjunction with k-t BLAST. Each motion was repeated four times as four k-t acceleration factors 1, 2, 5, and 16 (corresponding frame rates were 2.5, 4.7, 9.8, and 19.1Hz, respectively) were compared. For each image set, one average motion trajectory was computed from six marker displacements. Root mean square error (RMS) was used as a metric of spatial accuracy where measured trajectories were compared to original data. Results: Tumor motion was approximately 10mm. The mean(standard deviation) of respiratory rates over ten patients was 0.28(0.06)Hz. Cumulative distributions of tumor motion frequency spectra (0–25Hz) obtained from the patients showed that 90% of motion fell on 3.88Hz or less. Therefore, the frame rate must be a double or higher for accurate monitoring. The RMS errors over patients for k-t factors of 1, 2, 5, and 16 were.10(.04),.17(.04), .21(.06) and.26(.06)mm, respectively. Conclusions: K-t factor of 5 or higher can cover the high

  4. In silico site-directed mutagenesis informs species-specific predictions of chemical susceptibility derived from the Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) tool

    Science.gov (United States)

    The Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) tool was developed to address needs for rapid, cost effective methods of species extrapolation of chemical susceptibility. Specifically, the SeqAPASS tool compares the primary sequence (Level 1), functiona...

  5. Hydrophobic cluster analysis of G protein-coupled receptors: a powerful tool to derive structural and functional information from 2D-representation of protein sequences

    NARCIS (Netherlands)

    Lentes, K.U.; Mathieu, E.; Bischoff, Rainer; Rasmussen, U.B.; Pavirani, A.

    1993-01-01

    Current methods for comparative analyses of protein sequences are 1D-alignments of amino acid sequences based on the maximization of amino acid identity (homology) and the prediction of secondary structure elements. This method has a major drawback once the amino acid identity drops below 20-25%,

  6. Sequence History Update Tool

    Science.gov (United States)

    Khanampompan, Teerapat; Gladden, Roy; Fisher, Forest; DelGuercio, Chris

    2008-01-01

    The Sequence History Update Tool performs Web-based sequence statistics archiving for Mars Reconnaissance Orbiter (MRO). Using a single UNIX command, the software takes advantage of sequencing conventions to automatically extract the needed statistics from multiple files. This information is then used to populate a PHP database, which is then seamlessly formatted into a dynamic Web page. This tool replaces a previous tedious and error-prone process of manually editing HTML code to construct a Web-based table. Because the tool manages all of the statistics gathering and file delivery to and from multiple data sources spread across multiple servers, there is also a considerable time and effort savings. With the use of The Sequence History Update Tool what previously took minutes is now done in less than 30 seconds, and now provides a more accurate archival record of the sequence commanding for MRO.

  7. A cloud-based home health care information sharing system to connect patients with home healthcare staff -A case report of a study in a mountainous region.

    Science.gov (United States)

    Nomoto, Shinichi; Utsumi, Momoe; Sasayama, Satoshi; Dekigai, Hiroshi

    2017-01-01

    We have developed a cloud system, the e-Renraku Notebook (e-RN) for sharing of home care information based on the concept of "patient-centricity". In order to assess the likelihood that our system will enhance the communication and sharing of information between home healthcare staff members and home-care patients, we selected patients who were residing in mountainous regions for inclusion in our study. We herein report the findings.Eighteen staff members from 7 medical facilities and 9 patients participated in the present study.The e-RN was developed for two reasons: to allow patients to independently report their health status and to have staff members view and respond to the information received. The patients and staff members were given iPads with the pre-installed applications and the information being exchanged was reviewed over a 54-day period.Information was mainly input by the patients (61.6%), followed by the nurses who performed home visits (19.9%). The amount of information input by patients requiring high-level nursing care and their corresponding staff member was significantly greater than that input by patients who required low-level of nursing care.This patient-centric system in which patients can independently report and share information with a member of the healthcare staff provides a sense of security. It also allows staff members to understand the patient's health status before making a home visit, thereby giving them a sense of security and confidence. It was also noteworthy that elderly patients requiring high-level nursing care and their staff counterpart input information in the system significantly more frequently than patients who required low-level care.

  8. Informe

    Directory of Open Access Journals (Sweden)

    Egon Lichetenberger

    1950-10-01

    Full Text Available Informe del doctor Egon Lichetenberger ante el Consejo Directivo de la Facultad, sobre el  curso de especialización en Anatomía Patológica patrocinado por la Kellogg Foundation (Departamento de Patología

  9. Minimum cost connection networks

    DEFF Research Database (Denmark)

    Hougaard, Jens Leth; Tvede, Mich

    In the present paper we consider the allocation of cost in connection networks. Agents have connection demands in form of pairs of locations they want to be connected. Connections between locations are costly to build. The problem is to allocate costs of networks satisfying all connection demands...

  10. DG connect funded projects on information and communication technologies (ICT) for old age people: Beyond Silos, CareWell and SmartCare

    NARCIS (Netherlands)

    Keijser, Wouter Alexander; de Manuel-Keenoy, E.; D'Angelantonio, M.; Stafylas, P.; Hobson, P.; Apuzzo, G.; Hurtado, M.; Oates, J.

    2016-01-01

    Information and communication technologies (ICT) are promising for the long-term care of older and frequently frail people. These innovations can improve health outcomes, quality of life and efficiency of care processes, while supporting independent living. However, they may be disruptive

  11. The Development of a Code of Ethics: An Online Classroom Approach to Making Connections between Ethical Foundations and the Challenges Presented by Information Technology

    Science.gov (United States)

    Brooks, Rochelle

    2010-01-01

    In today's organizations, ethical challenges relate to areas like fraud, right to privacy for consumers, social responsibility, and trade restrictions. For Information Technology (IT) specifically, these can translate to considerations on how technology is used to violate people's privacy, how automation leads to job reductions, or how management…

  12. Cycle for Science: An informal outreach program connecting K-12 students with renewable energy and physics through miniature 3D-printed, solar-powered bicycles

    Science.gov (United States)

    Woods-Robinson, R.; Case, E.

    2017-12-01

    Engaging communities with renewable energy is key to fighting climate change. Cycle for Science, an innovative STEM outreach organization, has reached more than 3,000 K-12 students across the United States by bringing early-career female scientists into classrooms to teach basic physics and solar energy engineering through hands-on, DIY science activities. We designed a fleet of miniature, 3D-printed, solar-powered bicycles called "Sol Cycles" to use as teaching tools. Traveling by bicycle, Cycle for Science has brought them to rural and urban communities across the U.S. in two major efforts so far: one traversing the country (2015), and one through central California (2017). The program involves (1) introducing the scientists and why they value science, (2) running a skit to demonstrate how electrons and photons interact inside the solar panel, (3) assembling the Sol Cycles, (4) taking students outdoors to test the effects of variables (e.g. light intensity) on the Sol Cycles' movement, (5) and debriefing about the importance of renewable energy. In addition to physics and solar energy, the lessons teach the scientific process, provide tactile engagement with science, and introduce a platform to engage students with climate change impacts. By cycling to classrooms, we provide positive examples of low-impact transportation and a unique avenue for discussing climate action. It was important that this program extend beyond the trips, so the lesson and Sol Cycle design are open source to encourage teachers and students to play, change and improve the design, as well as incorporate new exercises (e.g. could you power the bicycle by wind?). Additionally, it has been permanently added to the XRaise Lending Library at Cornell University, so teachers across the world can implement the lesson. By sharing our project at AGU, we aim to connect with other scientists, educators, and concerned citizens about how to continue to bring renewable energy lessons into classrooms.

  13. Functional Connectivity Bias in the Prefrontal Cortex of Psychopaths.

    Science.gov (United States)

    Contreras-Rodríguez, Oren; Pujol, Jesus; Batalla, Iolanda; Harrison, Ben J; Soriano-Mas, Carles; Deus, Joan; López-Solà, Marina; Macià, Dídac; Pera, Vanessa; Hernández-Ribas, Rosa; Pifarré, Josep; Menchón, José M; Cardoner, Narcís

    2015-11-01

    Psychopathy is characterized by a distinctive interpersonal style that combines callous-unemotional traits with inflexible and antisocial behavior. Traditional emotion-based perspectives link emotional impairment mostly to alterations in amygdala-ventromedial frontal circuits. However, these models alone cannot explain why individuals with psychopathy can regularly benefit from emotional information when placed on their focus of attention and why they are more resistant to interference from nonaffective contextual cues. The present study aimed to identify abnormal or distinctive functional links between and within emotional and cognitive brain systems in the psychopathic brain to characterize further the neural bases of psychopathy. High-resolution anatomic magnetic resonance imaging with a functional sequence acquired in the resting state was used to assess 22 subjects with psychopathy and 22 control subjects. Anatomic and functional connectivity alterations were investigated first using a whole-brain analysis. Brain regions showing overlapping anatomic and functional changes were examined further using seed-based functional connectivity mapping. Subjects with psychopathy showed gray matter reduction involving prefrontal cortex, paralimbic, and limbic structures. Anatomic changes overlapped with areas showing increased degree of functional connectivity at the medial-dorsal frontal cortex. Subsequent functional seed-based connectivity mapping revealed a pattern of reduced functional connectivity of prefrontal areas with limbic-paralimbic structures and enhanced connectivity within the dorsal frontal lobe in subjects with psychopathy. Our results suggest that a weakened link between emotional and cognitive domains in the psychopathic brain may combine with enhanced functional connections within frontal executive areas. The identified functional alterations are discussed in the context of potential contributors to the inflexible behavior displayed by individuals with

  14. DISSECTING HABITAT CONNECTIVITY

    Science.gov (United States)

    abstractConnectivity is increasingly recognized as an important element of a successful reserve design. Connectivity matters in reserve design to the extent that it promotes or hinders the viability of target populations. While conceptually straightforward, connectivity i...

  15. Mixed Connective Tissue Disease

    Science.gov (United States)

    Mixed connective tissue disease Overview Mixed connective tissue disease has signs and symptoms of a combination of disorders — primarily lupus, scleroderma and polymyositis. For this reason, mixed connective tissue disease ...

  16. Undifferentiated Connective Tissue Disease

    Science.gov (United States)

    ... Home Conditions Undifferentiated Connective Tissue Disease (UCTD) Undifferentiated Connective Tissue Disease (UCTD) Make an Appointment Find a Doctor ... by Barbara Goldstein, MD (February 01, 2016) Undifferentiated connective tissue disease (UCTD) is a systemic autoimmune disease. This ...

  17. A New Delay Connection for Long Short-Term Memory Networks.

    Science.gov (United States)

    Wang, Jianyong; Zhang, Lei; Chen, Yuanyuan; Yi, Zhang

    2017-12-17

    Connections play a crucial role in neural network (NN) learning because they determine how information flows in NNs. Suitable connection mechanisms may extensively enlarge the learning capability and reduce the negative effect of gradient problems. In this paper, a new delay connection is proposed for Long Short-Term Memory (LSTM) unit to develop a more sophisticated recurrent unit, called Delay Connected LSTM (DCLSTM). The proposed delay connection brings two main merits to DCLSTM with introducing no extra parameters. First, it allows the output of the DCLSTM unit to maintain LSTM, which is absent in the LSTM unit. Second, the proposed delay connection helps to bridge the error signals to previous time steps and allows it to be back-propagated across several layers without vanishing too quickly. To evaluate the performance of the proposed delay connections, the DCLSTM model with and without peephole connections was compared with four state-of-the-art recurrent model on two sequence classification tasks. DCLSTM model outperformed the other models with higher accuracy and F1[Formula: see text]score. Furthermore, the networks with multiple stacked DCLSTM layers and the standard LSTM layer were evaluated on Penn Treebank (PTB) language modeling. The DCLSTM model achieved lower perplexity (PPL)/bit-per-character (BPC) than the standard LSTM model. The experiments demonstrate that the learning of the DCLSTM models is more stable and efficient.

  18. Intermodal Passenger Connectivity Database -

    Data.gov (United States)

    Department of Transportation — The Intermodal Passenger Connectivity Database (IPCD) is a nationwide data table of passenger transportation terminals, with data on the availability of connections...

  19. Connecting Architecture and Implementation

    Science.gov (United States)

    Buchgeher, Georg; Weinreich, Rainer

    Software architectures are still typically defined and described independently from implementation. To avoid architectural erosion and drift, architectural representation needs to be continuously updated and synchronized with system implementation. Existing approaches for architecture representation like informal architecture documentation, UML diagrams, and Architecture Description Languages (ADLs) provide only limited support for connecting architecture descriptions and implementations. Architecture management tools like Lattix, SonarJ, and Sotoarc and UML-tools tackle this problem by extracting architecture information directly from code. This approach works for low-level architectural abstractions like classes and interfaces in object-oriented systems but fails to support architectural abstractions not found in programming languages. In this paper we present an approach for linking and continuously synchronizing a formalized architecture representation to an implementation. The approach is a synthesis of functionality provided by code-centric architecture management and UML tools and higher-level architecture analysis approaches like ADLs.

  20. Network clustering coefficient approach to DNA sequence analysis

    Energy Technology Data Exchange (ETDEWEB)

    Gerhardt, Guenther J.L. [Universidade Federal do Rio Grande do Sul-Hospital de Clinicas de Porto Alegre, Rua Ramiro Barcelos 2350/sala 2040/90035-003 Porto Alegre (Brazil); Departamento de Fisica e Quimica da Universidade de Caxias do Sul, Rua Francisco Getulio Vargas 1130, 95001-970 Caxias do Sul (Brazil); Lemke, Ney [Programa Interdisciplinar em Computacao Aplicada, Unisinos, Av. Unisinos, 950, 93022-000 Sao Leopoldo, RS (Brazil); Corso, Gilberto [Departamento de Biofisica e Farmacologia, Centro de Biociencias, Universidade Federal do Rio Grande do Norte, Campus Universitario, 59072 970 Natal, RN (Brazil)]. E-mail: corso@dfte.ufrn.br

    2006-05-15

    In this work we propose an alternative DNA sequence analysis tool based on graph theoretical concepts. The methodology investigates the path topology of an organism genome through a triplet network. In this network, triplets in DNA sequence are vertices and two vertices are connected if they occur juxtaposed on the genome. We characterize this network topology by measuring the clustering coefficient. We test our methodology against two main bias: the guanine-cytosine (GC) content and 3-bp (base pairs) periodicity of DNA sequence. We perform the test constructing random networks with variable GC content and imposed 3-bp periodicity. A test group of some organisms is constructed and we investigate the methodology in the light of the constructed random networks. We conclude that the clustering coefficient is a valuable tool since it gives information that is not trivially contained in 3-bp periodicity neither in the variable GC content.

  1. Storing and managing information artifacts collected by information analysts using a computing device

    Science.gov (United States)

    Pike, William A; Riensche, Roderick M; Best, Daniel M; Roberts, Ian E; Whyatt, Marie V; Hart, Michelle L; Carr, Norman J; Thomas, James J

    2012-09-18

    Systems and computer-implemented processes for storage and management of information artifacts collected by information analysts using a computing device. The processes and systems can capture a sequence of interactive operation elements that are performed by the information analyst, who is collecting an information artifact from at least one of the plurality of software applications. The information artifact can then be stored together with the interactive operation elements as a snippet on a memory device, which is operably connected to the processor. The snippet comprises a view from an analysis application, data contained in the view, and the sequence of interactive operation elements stored as a provenance representation comprising operation element class, timestamp, and data object attributes for each interactive operation element in the sequence.

  2. Integrating Resources into Curriculum with the Systems Connect Planning Guide

    Science.gov (United States)

    Oshry, A.; Bean, J. R.

    2017-12-01

    A broadly applicable and guided approach for planning curriculum and instruction around new academic standards or initiatives is critical for implementation success. Curriculum and assessment differs across schools and districts, so built-in adaptability is important for maximal adoption and ease of use by educators. The Systems Connect Planning Guide directs the flow of instruction for building conceptual links between topics in a unit/curriculum through critical vetting and integration of relevant resources. This curricular template is flexible for use in any setting or subject area, and ensures applicability, high impact and responsiveness to academic standards while providing inquiry-based, real-world investigations and action that incorporate authentic research and data. These needs are what informed the creation of the three components of the planning guide:• Curriculum Anchor: alignment with academic standards & learning outcomes and setting the context of the topic• Issues Investigations: informing how students explore topics, and incorporate authentic research and data into learning progressions• Civic Action: development of how students could apply their knowledgeThe Planning Guide also incorporates criteria from transdisciplinary practices, cross-cutting concepts, and organizational charts for outlining guiding questions and conceptual links embedded in the guide. Integration of experiential learning and real-world connections into curricula is important for proficiency and deeper understanding of content, replacing discrete, stand-alone experiences which are not explicitly connected. Rather than information being dispelled through individual activities, relying on students to make the connections, intentionally documenting explicit connections provides opportunities to foster deeper understanding by building conceptual links between topics, which is how fundamental knowledge about earth and living systems is gained. Through the critical vetting

  3. Next-Generation Sequencing Platforms

    Science.gov (United States)

    Mardis, Elaine R.

    2013-06-01

    Automated DNA sequencing instruments embody an elegant interplay among chemistry, engineering, software, and molecular biology and have built upon Sanger's founding discovery of dideoxynucleotide sequencing to perform once-unfathomable tasks. Combined with innovative physical mapping approaches that helped to establish long-range relationships between cloned stretches of genomic DNA, fluorescent DNA sequencers produced reference genome sequences for model organisms and for the reference human genome. New types of sequencing instruments that permit amazing acceleration of data-collection rates for DNA sequencing have been developed. The ability to generate genome-scale data sets is now transforming the nature of biological inquiry. Here, I provide an historical perspective of the field, focusing on the fundamental developments that predated the advent of next-generation sequencing instruments and providing information about how these instruments work, their application to biological research, and the newest types of sequencers that can extract data from single DNA molecules.

  4. Transcranial Direct Current Stimulation Targeting Primary Motor Versus Dorsolateral Prefrontal Cortices: Proof-of-Concept Study Investigating Functional Connectivity of Thalamocortical Networks Specific to Sensory-Affective Information Processing.

    Science.gov (United States)

    Sankarasubramanian, Vishwanath; Cunningham, David A; Potter-Baker, Kelsey A; Beall, Erik B; Roelle, Sarah M; Varnerin, Nicole M; Machado, Andre G; Jones, Stephen E; Lowe, Mark J; Plow, Ela B

    2017-04-01

    The pain matrix is comprised of an extensive network of brain structures involved in sensory and/or affective information processing. The thalamus is a key structure constituting the pain matrix. The thalamus serves as a relay center receiving information from multiple ascending pathways and relating information to and from multiple cortical areas. However, it is unknown how thalamocortical networks specific to sensory-affective information processing are functionally integrated. Here, in a proof-of-concept study in healthy humans, we aimed to understand this connectivity using transcranial direct current stimulation (tDCS) targeting primary motor (M1) or dorsolateral prefrontal cortices (DLPFC). We compared changes in functional connectivity (FC) with DLPFC tDCS to changes in FC with M1 tDCS. FC changes were also compared to further investigate its relation with individual's baseline experience of pain. We hypothesized that resting-state FC would change based on tDCS location and would represent known thalamocortical networks. Ten right-handed individuals received a single application of anodal tDCS (1 mA, 20 min) to right M1 and DLPFC in a single-blind, sham-controlled crossover study. FC changes were studied between ventroposterolateral (VPL), the sensory nucleus of thalamus, and cortical areas involved in sensory information processing and between medial dorsal (MD), the affective nucleus, and cortical areas involved in affective information processing. Individual's perception of pain at baseline was assessed using cutaneous heat pain stimuli. We found that anodal M1 tDCS and anodal DLPFC tDCS both increased FC between VPL and sensorimotor cortices, although FC effects were greater with M1 tDCS. Similarly, anodal M1 tDCS and anodal DLPFC tDCS both increased FC between MD and motor cortices, but only DLPFC tDCS modulated FC between MD and affective cortices, like DLPFC. Our findings suggest that M1 stimulation primarily modulates FC of sensory networks

  5. Cybersecurity for Connected Diabetes Devices.

    Science.gov (United States)

    Klonoff, David C

    2015-04-16

    Diabetes devices are increasingly connected wirelessly to each other and to data-displaying reader devices. Threats to the accurate flow of information and commands may compromise the function of these devices and put their users at risk of health complications. Sound cybersecurity of connected diabetes devices is necessary to maintain confidentiality, integrity, and availability of the data and commands. Diabetes devices can be hacked by unauthorized agents and also by patients themselves to extract data that are not automatically provided by product software. Unauthorized access to connected diabetes devices has been simulated and could happen in reality. A cybersecurity standard designed specifically for connected diabetes devices will improve the safety of these products and increase confidence of users that the products will be secure. © 2015 Diabetes Technology Society.

  6. Red, green, blue equals 1, 2, 3: Digit-color synesthetes can use structured digit information to boost recall of color sequences.

    Science.gov (United States)

    Teichmann, A Lina; Nieuwenstein, Mark R; Rich, Anina N

    2015-01-01

    Digit-color synesthetes report experiencing colors when perceiving letters and digits. The conscious experience is typically unidirectional (e.g., digits elicit colors but not vice versa) but recent evidence shows subtle bidirectional effects. We examined whether short-term memory for colors could be affected by the order of presentation reflecting more or less structure in the associated digits. We presented a stream of colored squares and asked participants to report the colors in order. The colors matched each synesthete's colors for digits 1-9 and the order of the colors corresponded either to a sequence of numbers (e.g., [red, green, blue] if 1 = red, 2 = green, 3 = blue) or no systematic sequence. The results showed that synesthetes recalled sequential color sequences more accurately than pseudo-randomized colors, whereas no such effect was found for the non-synesthetic controls. Synesthetes did not differ from non-synesthetic controls in recall of color sequences overall, providing no evidence of a general advantage in memory for serial recall of colors.

  7. Inter-laboratory evaluation of the EUROFORGEN Global ancestry-informative SNP panel by massively parallel sequencing using the Ion PGM™

    DEFF Research Database (Denmark)

    Eduardoff, M; Gross, T E; Santos, C

    2016-01-01

    Seq™ PCR primers was designed for the Global AIM-SNPs to perform massively parallel sequencing using the Ion PGM™ system. This study assessed individual SNP genotyping precision using the Ion PGM™, the forensic sensitivity of the multiplex using dilution series, degraded DNA plus simple mixtures...

  8. Connecting Numbers with Emotion: Review of Numbers and Nerves: Information, Emotion, and Meaning in a World of Data by Scott Slovic and Paul Slovic (2015

    Directory of Open Access Journals (Sweden)

    Samuel L. Tunstall

    2017-01-01

    Full Text Available Scott Slovic and Paul Slovic (Eds.. Numbers and Nerves: Information, Emotion, and Meaning in a World of Data (Corvallis, OR: Oregon State University Press, 2015. 272 pp. ISBN 978-0-87071-776-5. It is common to view quantitative literacy as reasoning with respect to numbers. In Numbers and Nerves, the contributors to the volume make clear that we should attend not only to how students consciously reason with numbers, but also how our innate biases influence our actions when faced with numbers. Beginning with the concepts of psychic numbing, and then psuedoinefficacy, the contributors to the volume examine how our behaviors when faced with large numbers are often not mathematically rational. I consider the implications of these phenomena for the Numeracy community.

  9. High-Throughput Mapping of Single-Neuron Projections by Sequencing of Barcoded RNA.

    Science.gov (United States)

    Kebschull, Justus M; Garcia da Silva, Pedro; Reid, Ashlan P; Peikon, Ian D; Albeanu, Dinu F; Zador, Anthony M

    2016-09-07

    Neurons transmit information to distant brain regions via long-range axonal projections. In the mouse, area-to-area connections have only been systematically mapped using bulk labeling techniques, which obscure the diverse projections of intermingled single neurons. Here we describe MAPseq (Multiplexed Analysis of Projections by Sequencing), a technique that can map the projections of thousands or even millions of single neurons by labeling large sets of neurons with random RNA sequences ("barcodes"). Axons are filled with barcode mRNA, each putative projection area is dissected, and the barcode mRNA is extracted and sequenced. Applying MAPseq to the locus coeruleus (LC), we find that individual LC neurons have preferred cortical targets. By recasting neuroanatomy, which is traditionally viewed as a problem of microscopy, as a problem of sequencing, MAPseq harnesses advances in sequencing technology to permit high-throughput interrogation of brain circuits. Copyright © 2016 Elsevier Inc. All rights reserved.

  10. Semantic connections: exploring and manipulating connections in smart spaces

    NARCIS (Netherlands)

    Vlist, van der B.J.J.; Niezen, G.; Hu, J.; Feijs, L.M.G.

    2010-01-01

    In envisioned smart environments, enabled by ubiquitous computing technologies, electronic objects will be able to interconnect and interoperate. How will users of such smart environments make sense of the connections that are made and the information that is exchanged? This Internet of Things could

  11. DG Connect Funded Projects on Information and Communication Technologies (ICT) for Old Age People: Beyond Silos, CareWell and SmartCare.

    Science.gov (United States)

    Keijser, W; de Manuel-Keenoy, E; d'Angelantonio, M; Stafylas, P; Hobson, P; Apuzzo, G; Hurtado, M; Oates, J; Bousquet, J; Senn, A

    2016-01-01

    Information and communication technologies (ICT) are promising for the long-term care of older and frequently frail people. These innovations can improve health outcomes, quality of life and efficiency of care processes, while supporting independent living. However, they may be disruptive innovations. As all European member states are facing an increasing complexity of health and social care, good practices in ICT should be identified and evaluated. Three projects funded by DG CNECT are related to Active and Healthy Ageing (AHA) and frailty: (i) BeyondSilos, dealing with independent living and integrated services, (ii) CareWell, providing integrated care coordination, patient empowerment and home support and (iii) SmartCare, proposing a common set of standard functional specifications for an ICT platform enabling the delivery of integrated care to older patients. The three projects described in this paper provide a unique pan-European research field to further study implementation efforts and outcomes of new technologies. Below, based on a description of the projects, the authors display four domains that are in their views fundamental for in-depth exploration of heterogeneity in the European context: 1. Definition of easily transferable, high level pathways with solid evidence-base; 2. Change management in implementing ICT enabled integrated care; 3. Evaluation and data collection methodologies based on existing experience with MAST and MEDAL methodologies; and 4. Construction of new models for delivery of health and social care. Understanding complementarity, synergies and differences between the three unique projects can help to identify a more effective roll out of best practices within a varying European context.

  12. Targeted exome sequencing integrated with clinicopathological information reveals novel and rare mutations in atypical, suspected and unknown cases of Alport syndrome or proteinuria.

    Directory of Open Access Journals (Sweden)

    Rajshekhar Chatterjee

    Full Text Available We applied customized targeted next-generation exome sequencing (NGS to determine if mutations in genes associated with renal malformations, Alport syndrome (AS or nephrotic syndrome are a potential cause of renal abnormalities in patients with equivocal or atypical presentation. We first sequenced 4,041 exons representing 292 kidney disease genes in a Caucasian woman with a history of congenital vesicoureteral reflux (VUR, recurrent urinary tract infections and hydronephrosis who presented with nephrotic range proteinuria at the age of 45. Her biopsy was remarkable for focal segmental glomerulosclerosis (FSGS, a potential complication of longstanding VUR. She had no family history of renal disease. Her proteinuria improved initially, however, several years later she presented with worsening proteinuria and microhematuria. NGS analysis revealed two deleterious COL4A3 mutations, one novel and the other previously reported in AS, and a novel deleterious SALL2 mutation, a gene linked to renal malformations. Pedigree analysis confirmed that COL4A3 mutations were nonallelic and compound heterozygous. The genomic results in conjunction with subsequent abnormal electron microscopy, Collagen IV minor chain immunohistochemistry and progressive sensorineural hearing loss confirmed AS. We then modified our NGS approach to enable more efficient discovery of variants associated with AS or a subset of FSGS by multiplexing targeted exome sequencing of 19 genes associated with AS or FSGS in 14 patients. Using this approach, we found novel or known COL4A3 or COL4A5 mutations in a subset of patients with clinically diagnosed or suspected AS, APOL1 variants associated with FSGS in African Americans and novel mutations in genes associated with nephrotic syndrome. These studies demonstrate the successful application of targeted capture-based exome sequencing to simultaneously evaluate genetic variations in many genes in patients with complex renal phenotypes and

  13. HotSpot Wizard 3.0: web server for automated design of mutations and smart libraries based on sequence input information.

    Science.gov (United States)

    Sumbalova, Lenka; Stourac, Jan; Martinek, Tomas; Bednar, David; Damborsky, Jiri

    2018-05-23

    HotSpot Wizard is a web server used for the automated identification of hotspots in semi-rational protein design to give improved protein stability, catalytic activity, substrate specificity and enantioselectivity. Since there are three orders of magnitude fewer protein structures than sequences in bioinformatic databases, the major limitation to the usability of previous versions was the requirement for the protein structure to be a compulsory input for the calculation. HotSpot Wizard 3.0 now accepts the protein sequence as input data. The protein structure for the query sequence is obtained either from eight repositories of homology models or is modeled using Modeller and I-Tasser. The quality of the models is then evaluated using three quality assessment tools-WHAT_CHECK, PROCHECK and MolProbity. During follow-up analyses, the system automatically warns the users whenever they attempt to redesign poorly predicted parts of their homology models. The second main limitation of HotSpot Wizard's predictions is that it identifies suitable positions for mutagenesis, but does not provide any reliable advice on particular substitutions. A new module for the estimation of thermodynamic stabilities using the Rosetta and FoldX suites has been introduced which prevents destabilizing mutations among pre-selected variants entering experimental testing. HotSpot Wizard is freely available at http://loschmidt.chemi.muni.cz/hotspotwizard.

  14. Minimum cost connection networks

    DEFF Research Database (Denmark)

    Hougaard, Jens Leth; Tvede, Mich

    2015-01-01

    In the present paper we consider the allocation of costs in connection networks. Agents have connection demands in form of pairs of locations they want to have connected. Connections between locations are costly to build. The problem is to allocate costs of networks satisfying all connection...... demands. We use a few axioms to characterize allocation rules that truthfully implement cost minimizing networks satisfying all connection demands in a game where: (1) a central planner announces an allocation rule and a cost estimation rule; (2) every agent reports her own connection demand as well...... as all connection costs; (3) the central planner selects a cost minimizing network satisfying reported connection demands based on the estimated costs; and, (4) the planner allocates the true costs of the selected network. It turns out that an allocation rule satisfies the axioms if and only if relative...

  15. A Building Connecting Separated Communities

    DEFF Research Database (Denmark)

    Axel, Erik

    Producing something for general use involves the designers' anticipation of the use of the object. Personal as well as professional experience is involved in the design anticipations of the process. Using an object means exploring it as a concrete arrangement for our everyday conduct of life....... in no systematic sequence. This, among other things, separates design and use, which is worth investigating in order to understand the problems involved in connecting the design of a house and analyzing the experience of a user. We undertook a preliminary investigation of how a dormitory for visiting students from...... with students from other dormitories, and connect with the Danes from other sections of the building isolating themselves. The janitor was surprised at the supposed function of the washing machines. Since other dormitories at the campus did not provide washing machines, the ones at the house investigated were...

  16. Next-generation sequencing

    DEFF Research Database (Denmark)

    Rieneck, Klaus; Bak, Mads; Jønson, Lars

    2013-01-01

    , Illumina); several millions of PCR sequences were analyzed. RESULTS: The results demonstrated the feasibility of diagnosing the fetal KEL1 or KEL2 blood group from cell-free DNA purified from maternal plasma. CONCLUSION: This method requires only one primer pair, and the large amount of sequence...... information obtained allows well for statistical analysis of the data. This general approach can be integrated into current laboratory practice and has numerous applications. Besides DNA-based predictions of blood group phenotypes, platelet phenotypes, or sickle cell anemia, and the determination of zygosity...

  17. MatrixPlot: visualizing sequence constraints

    DEFF Research Database (Denmark)

    Gorodkin, Jan; Stærfeldt, Hans Henrik; Lund, Ole

    1999-01-01

    MatrixPlot: visualizing sequence constraints. Sub-title Abstract Summary : MatrixPlot is a program for making high-quality matrix plots, such as mutual information plots of sequence alignments and distance matrices of sequences with known three-dimensional coordinates. The user can add information...

  18. Identification and expression of the tig gene coding for trigger factor from psychrophilic bacteria with no information of genome sequence available.

    Science.gov (United States)

    Lee, Kyunghee; Choi, Hyojung; Im, Hana

    2009-08-01

    Trigger factor (TF) plays a key role as a molecular chaperone with a peptidyl-prolyl cis-trans isomerase (PPIase) activity by which cells promote folding of newly synthesized proteins coming out of ribosomes. Since psychrophilic bacteria grow at a quite low temperature, between 4 and 15 degrees C, TF from such bacteria was investigated and compared with that of mesophilic bacteria E. coli in order to offer an explanation of cold-adaptation at a molecular level. Using a combination of gradient PCRs with homologous primers and LA PCR in vitro cloning technology, the tig gene was fully identified from Psychromonas arctica, whose genome sequence is not yet available. The resulting amino acid sequence of the TF was compared with other homologous TFs using sequence alignments to search for common domains. In addition, we have developed a protein expression system, by which TF proteins from P. arctica (PaTF) were produced by IPTG induction upon cloning the tig gene on expression vectors, such as pAED4. We have further examined the role of expressed psychrophilic PaTF on survival against cold treatment at 4 degrees C. Finally, we have attempted the in vitro biochemical characterization of TF proteins with His-tags expressed in a pET system, such as the PPIase activity of PaTF protein. Our results demonstrate that the expressed PaTF proteins helped cells survive against cold environments in vivo and the purified PaTF in vitro display the functional PPIase activity in a concentration dependent manner.

  19. Visualizing neuronal network connectivity with connectivity pattern tables

    Directory of Open Access Journals (Sweden)

    Eilen Nordlie

    2010-01-01

    Full Text Available Complex ideas are best conveyed through well-designed illustrations. Up to now, computational neuroscientists have mostly relied on box-and-arrow diagrams of even complex neuronal networks, often using ad hoc notations with conflicting use of symbols from paper to paper. This significantly impedes the communication of ideas in neuronal network modeling. We present here Connectivity Pattern Tables (CPTs as a clutter-free visualization of connectivity in large neuronal networks containing two-dimensional populations of neurons. CPTs can be generated automatically from the same script code used to create the actual network in the NEST simulator. Through aggregation, CPTs can be viewed at different levels, providing either full detail or summary information. We also provide the open source ConnPlotter tool as a means to create connectivity pattern tables.

  20. Model morphing and sequence assignment after molecular replacement

    Energy Technology Data Exchange (ETDEWEB)

    Terwilliger, Thomas C., E-mail: terwilliger@lanl.gov [Los Alamos National Laboratory, Mail Stop M888, Los Alamos, NM 87545 (United States); Read, Randy J. [University of Cambridge, Cambridge Institute for Medical Research, Cambridge CB2 0XY (United Kingdom); Adams, Paul D. [Lawrence Berkeley National Laboratory, One Cyclotron Road, Bldg 64R0121, Berkeley, CA 94720 (United States); Brunger, Axel T. [Stanford University, 318 Campus Drive West, Stanford, CA 94305 (United States); Afonine, Pavel V. [Lawrence Berkeley National Laboratory, One Cyclotron Road, Bldg 64R0121, Berkeley, CA 94720 (United States); Hung, Li-Wei [Los Alamos National Laboratory, Mail Stop M888, Los Alamos, NM 87545 (United States)

    2013-11-01

    A procedure for model building is described that combines morphing a model to match a density map, trimming the morphed model and aligning the model to a sequence. A procedure termed ‘morphing’ for improving a model after it has been placed in the crystallographic cell by molecular replacement has recently been developed. Morphing consists of applying a smooth deformation to a model to make it match an electron-density map more closely. Morphing does not change the identities of the residues in the chain, only their coordinates. Consequently, if the true structure differs from the working model by containing different residues, these differences cannot be corrected by morphing. Here, a procedure that helps to address this limitation is described. The goal of the procedure is to obtain a relatively complete model that has accurate main-chain atomic positions and residues that are correctly assigned to the sequence. Residues in a morphed model that do not match the electron-density map are removed. Each segment of the resulting trimmed morphed model is then assigned to the sequence of the molecule using information about the connectivity of the chains from the working model and from connections that can be identified from the electron-density map. The procedure was tested by application to a recently determined structure at a resolution of 3.2 Å and was found to increase the number of correctly identified residues in this structure from the 88 obtained using phenix.resolve sequence assignment alone (Terwilliger, 2003 ▶) to 247 of a possible 359. Additionally, the procedure was tested by application to a series of templates with sequence identities to a target structure ranging between 7 and 36%. The mean fraction of correctly identified residues in these cases was increased from 33% using phenix.resolve sequence assignment to 47% using the current procedure. The procedure is simple to apply and is available in the Phenix software package.

  1. Model morphing and sequence assignment after molecular replacement

    International Nuclear Information System (INIS)

    Terwilliger, Thomas C.; Read, Randy J.; Adams, Paul D.; Brunger, Axel T.; Afonine, Pavel V.; Hung, Li-Wei

    2013-01-01

    A procedure for model building is described that combines morphing a model to match a density map, trimming the morphed model and aligning the model to a sequence. A procedure termed ‘morphing’ for improving a model after it has been placed in the crystallographic cell by molecular replacement has recently been developed. Morphing consists of applying a smooth deformation to a model to make it match an electron-density map more closely. Morphing does not change the identities of the residues in the chain, only their coordinates. Consequently, if the true structure differs from the working model by containing different residues, these differences cannot be corrected by morphing. Here, a procedure that helps to address this limitation is described. The goal of the procedure is to obtain a relatively complete model that has accurate main-chain atomic positions and residues that are correctly assigned to the sequence. Residues in a morphed model that do not match the electron-density map are removed. Each segment of the resulting trimmed morphed model is then assigned to the sequence of the molecule using information about the connectivity of the chains from the working model and from connections that can be identified from the electron-density map. The procedure was tested by application to a recently determined structure at a resolution of 3.2 Å and was found to increase the number of correctly identified residues in this structure from the 88 obtained using phenix.resolve sequence assignment alone (Terwilliger, 2003 ▶) to 247 of a possible 359. Additionally, the procedure was tested by application to a series of templates with sequence identities to a target structure ranging between 7 and 36%. The mean fraction of correctly identified residues in these cases was increased from 33% using phenix.resolve sequence assignment to 47% using the current procedure. The procedure is simple to apply and is available in the Phenix software package

  2. Connected vehicle standards.

    Science.gov (United States)

    2016-01-01

    Connected vehicles have the potential to transform the way Americans travel by : allowing cars, buses, trucks, trains, traffic signals, smart phones, and other devices to : communicate through a safe, interoperable wireless network. A connected vehic...

  3. The business case for connectivity

    Science.gov (United States)

    Adams, Dennis; Hirschheim, Rudy

    1991-01-01

    Information systems that provide competitive advantages to organizations can be broadly classified into those that improve the effectiveness of a business function and those that improve the reach of information in the organization. The latter, organizational connectivity systems, can be categorized as intraorganizational and interorganizational systems. Intraorganization systems provide connectivity to function areas within the business, while interorganizational systems support the exchange of business data between independent business units. These system are not confined to a single entity but span organizational boundaries which can be national or international in scope. A series of case studies was undertaken in an effort to better understand the issues and problems associated with providing an increased flow of information within and outside of an organization. Ten issues emerged from this study. In summary, it is necessary for firms to first consider how effective their internal communications systems are before launching projects that tie the organization to external systems.

  4. Connecting to Everyday Practices

    DEFF Research Database (Denmark)

    Iversen, Ole Sejer; Smith, Rachel Charlotte

    2012-01-01

    construction and reproduction of cultural heritage creating novel connections between self and others and between past, present and future. We present experiences from a current research project, the Digital Natives exhibition, in which social media was designed as an integral part of the exhibition to connect...... focusing on the connections between audiences practices and the museum exhibition....

  5. 47 CFR 54.506 - Internal connections.

    Science.gov (United States)

    2010-10-01

    ... instructional building of a school or to a non-administrative building of a library. Internal connections do not... SERVICE Universal Service Support for Schools and Libraries § 54.506 Internal connections. (a) A service... necessary to transport information within one or more instructional buildings of a single school campus or...

  6. Are we connected? : Ports in Global Networks

    NARCIS (Netherlands)

    R.A. Zuidwijk (Rob)

    2015-01-01

    markdownabstractAbstract Global supply chains are built on organizational, information, and logistics networks. Ports are connected via these networks and also need to connect these networks. Synchromodality is an innovative concept for container transportation, and the port plays an important

  7. Google Voice: Connecting Your Telephone to the 21st Century

    Science.gov (United States)

    Johnson, Benjamin E.

    2010-01-01

    The foundation of the mighty Google Empire rests upon an algorithm that connects people to information--things such as websites, maps, and restaurant reviews. Lately it seems that people are less interested in connecting with information than they are with connecting to one another, which begs the question, "Is Facebook the new Google?" Given this…

  8. Green's theorem and Gorenstein sequences

    OpenAIRE

    Ahn, Jeaman; Migliore, Juan C.; Shin, Yong-Su

    2016-01-01

    We study consequences, for a standard graded algebra, of extremal behavior in Green's Hyperplane Restriction Theorem. First, we extend his Theorem 4 from the case of a plane curve to the case of a hypersurface in a linear space. Second, assuming a certain Lefschetz condition, we give a connection to extremal behavior in Macaulay's theorem. We apply these results to show that $(1,19,17,19,1)$ is not a Gorenstein sequence, and as a result we classify the sequences of the form $(1,a,a-2,a,1)$ th...

  9. High accessible experimental information on CPD experiment

    Energy Technology Data Exchange (ETDEWEB)

    Hasegawa, M. [RIAM, Kyushu University, Kasuga, Fukuoka 816-8580 (Japan)], E-mail: hasegawa@triam.kyushu-u.ac.jp; Nakamura, K.; Higashijima, A.; Kawasaki, S.; Nakashima, H.; Sato, K.N.; Zushi, H.; Hanada, K.; Sakamoto, M.; Idei, H. [RIAM, Kyushu University, Kasuga, Fukuoka 816-8580 (Japan)

    2008-04-15

    On CPD [1] (Compact PWI experimental Device) experiment, information of electronic logbook and sequence status are distributed by Web services to prepare future experimental environment such as steady state operation and remote participation. Hence, all the researchers can acquire information with a Web browser installed on a personal computer if they are connected to the Internet. However, to carry a notebook computer all the time is a burden to researchers. Furthermore, the researchers may not be always connected to the Internet. Mobile phones are superior in portability compared to notebook computers, and are easy to connect with Internet through the wireless network of the telecom carriers. Moreover, since recent mobile phones have full browsing function, their affinities to the Web services are becoming high. On this account, Web services for mobile phones are developed to access experimental information. For sequence monitoring, a mobile application MIDlet that utilizes special functions of mobile phone such as sound and vibration is also developed to draw attentions of researchers to sequence status.

  10. High accessible experimental information on CPD experiment

    International Nuclear Information System (INIS)

    Hasegawa, M.; Nakamura, K.; Higashijima, A.; Kawasaki, S.; Nakashima, H.; Sato, K.N.; Zushi, H.; Hanada, K.; Sakamoto, M.; Idei, H.

    2008-01-01

    On CPD [1] (Compact PWI experimental Device) experiment, information of electronic logbook and sequence status are distributed by Web services to prepare future experimental environment such as steady state operation and remote participation. Hence, all the researchers can acquire information with a Web browser installed on a personal computer if they are connected to the Internet. However, to carry a notebook computer all the time is a burden to researchers. Furthermore, the researchers may not be always connected to the Internet. Mobile phones are superior in portability compared to notebook computers, and are easy to connect with Internet through the wireless network of the telecom carriers. Moreover, since recent mobile phones have full browsing function, their affinities to the Web services are becoming high. On this account, Web services for mobile phones are developed to access experimental information. For sequence monitoring, a mobile application MIDlet that utilizes special functions of mobile phone such as sound and vibration is also developed to draw attentions of researchers to sequence status

  11. Network connectivity value.

    Science.gov (United States)

    Dragicevic, Arnaud; Boulanger, Vincent; Bruciamacchie, Max; Chauchard, Sandrine; Dupouey, Jean-Luc; Stenger, Anne

    2017-04-21

    In order to unveil the value of network connectivity, we formalize the construction of ecological networks in forest environments as an optimal control dynamic graph-theoretic problem. The network is based on a set of bioreserves and patches linked by ecological corridors. The node dynamics, built upon the consensus protocol, form a time evolutive Mahalanobis distance weighted by the opportunity costs of timber production. We consider a case of complete graph, where the ecological network is fully connected, and a case of incomplete graph, where the ecological network is partially connected. The results show that the network equilibrium depends on the size of the reception zone, while the network connectivity depends on the environmental compatibility between the ecological areas. Through shadow prices, we find that securing connectivity in partially connected networks is more expensive than in fully connected networks, but should be undertaken when the opportunity costs are significant. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. The processing of positional information in a two-item sequence limits the emergence of symmetry in baboons (Papio papio), but not in humans (Homo sapiens).

    Science.gov (United States)

    Fagot, Joël; Malassis, Raphaelle; Medam, Tiphaine

    2018-03-01

    When trained to associate Stimulus A to Stimulus B, humans can derive the untrained symmetrical B to A relation while nonhuman animals have much more difficulties. Urcuioli (2008, Journal of the Experimental Analysis of Behavior, 90, 257--282; 2015, Conductal, 3, 4--25) proposed that the apparent difficulty of animals in symmetry testing reflects their double encoding of the information on the stimuli (identity and relation) and their positional (i.e., spatial and temporal/ordinal) characteristics. This comparative study tested the emergence of symmetry in humans and baboons in a task in which the position of the stimuli was manipulated independently of their relation. Humans and baboons initially learned to associate pairs of visual shapes on a touch screen in a specific order. Three pairs of (A-B, C-D, and E-F) stimuli were used in training. After training, the two species were tested with the B-A, F-C, and E-D pairs. The B-A pairs preserved the association initially learned with A-B but reversed the positional information relative to training. The F-C pair neither preserved the association nor the positional information of the training pairs, and positional information were the only cues preserved in the E-D pair. Humans showed a response time advantage for B-A, suggesting symmetry, but also for E-D, suggesting that they also process positional information. In baboons, the advantage was found only for E-D, suggesting that they only process positional information. These results confirm that the processing of stimulus pairs differ between nonhuman animals to humans.

  13. Neural Networks and Their Applications in Noise - Information Storage and Retrieval Systems, and in the Rejection of Narrow-Band Interference in Direct Sequence Spread Spectrum Receivers.

    Science.gov (United States)

    Bijjani, Richard

    1990-01-01

    The introduction of neural network models has created new algorithms and application opportunities in parallel signal processing. Here, an M-ary extension of the Hopfield model is presented and is shown to have a substantially higher error correction capability, when compared to the Hopfield model. A digital image processing experiment is successfully conducted to illustrate the new model, and a holographic implementation is proposed. The use of neural networks and of linear combination filters are investigated in connection with the problem of user identification in code division multiple access systems. A multi-layer back-propagation perceptron model is then presented as a means of detecting a wideband signal in the presence of narrowband jammers and additive white Gaussian noise. The performance of the neural network is compared to that of the estimation type filter that uses a least mean squared adaptive filter, in terms of the interference rejection capability, the bit error rate and the overall robustness of the system. The nonlinear neural network filter is found to offer a faster convergence rate and an overall better performance over the LMS Widrow-Hoff filter.

  14. Starting-up sequence of the AWEC-6 0 wind turbine

    International Nuclear Information System (INIS)

    Avia, F.; Cruz, M. de la

    1991-01-01

    One of the most critical status of the wind turbines operation is the starting-up sequence and the connection to the grid, due to the actuating loads that could be several times the loads during operation at rated conditions. Due to this fact, the control strategy is very important during the starting-up sequence in order to minimize the loads on the machine. For this purpose it is necessary to analyze the behaviour of the wind turbine during that sequence in different wind conditions and machine conditions This report shows the graphic Information about fifty starting-up sequences of the AWEC-60 wind turbine of 60 m diameter and 1200 kW of rated power, recorded in April 1991 and covering all the operation range between cut-in and cut-out wind speed. (Author) 2 refs

  15. Connected Component Model for Multi-Object Tracking.

    Science.gov (United States)

    He, Zhenyu; Li, Xin; You, Xinge; Tao, Dacheng; Tang, Yuan Yan

    2016-08-01

    In multi-object tracking, it is critical to explore the data associations by exploiting the temporal information from a sequence of frames rather than the information from the adjacent two frames. Since straightforwardly obtaining data associations from multi-frames is an NP-hard multi-dimensional assignment (MDA) problem, most existing methods solve this MDA problem by either developing complicated approximate algorithms, or simplifying MDA as a 2D assignment problem based upon the information extracted only from adjacent frames. In this paper, we show that the relation between associations of two observations is the equivalence relation in the data association problem, based on the spatial-temporal constraint that the trajectories of different objects must be disjoint. Therefore, the MDA problem can be equivalently divided into independent subproblems by equivalence partitioning. In contrast to existing works for solving the MDA problem, we develop a connected component model (CCM) by exploiting the constraints of the data association and the equivalence relation on the constraints. Based upon CCM, we can efficiently obtain the global solution of the MDA problem for multi-object tracking by optimizing a sequence of independent data association subproblems. Experiments on challenging public data sets demonstrate that our algorithm outperforms the state-of-the-art approaches.

  16. Model morphing and sequence assignment after molecular replacement.

    Science.gov (United States)

    Terwilliger, Thomas C; Read, Randy J; Adams, Paul D; Brunger, Axel T; Afonine, Pavel V; Hung, Li-Wei

    2013-11-01

    A procedure termed `morphing' for improving a model after it has been placed in the crystallographic cell by molecular replacement has recently been developed. Morphing consists of applying a smooth deformation to a model to make it match an electron-density map more closely. Morphing does not change the identities of the residues in the chain, only their coordinates. Consequently, if the true structure differs from the working model by containing different residues, these differences cannot be corrected by morphing. Here, a procedure that helps to address this limitation is described. The goal of the procedure is to obtain a relatively complete model that has accurate main-chain atomic positions and residues that are correctly assigned to the sequence. Residues in a morphed model that do not match the electron-density map are removed. Each segment of the resulting trimmed morphed model is then assigned to the sequence of the molecule using information about the connectivity of the chains from the working model and from connections that can be identified from the electron-density map. The procedure was tested by application to a recently determined structure at a resolution of 3.2 Å and was found to increase the number of correctly identified residues in this structure from the 88 obtained using phenix.resolve sequence assignment alone (Terwilliger, 2003) to 247 of a possible 359. Additionally, the procedure was tested by application to a series of templates with sequence identities to a target structure ranging between 7 and 36%. The mean fraction of correctly identified residues in these cases was increased from 33% using phenix.resolve sequence assignment to 47% using the current procedure. The procedure is simple to apply and is available in the Phenix software package.

  17. POLAR-PALOOZA Polar Researchers and Arctic Residents Engage, Inform and Inspire Diverse Public Audiences by sharing Polar Science and Global Connections during the International Polar Year, using a New Model of Informal Science Education

    Science.gov (United States)

    Haines-Stiles, G.; Akuginow, E.

    2006-12-01

    (Please note that the POLAR-PALOOZA initiative described in this Abstract is-as of 9/7/2006-"pending" for possible support from NSF and NASA as part of this year's IPY solicitation. Subject to decisions expected by 9/30, this presentation would either be withdrawn, or amplified with specific participants, locations and dates.) Despite the success of well-regarded movies like "March of the Penguins", the polar regions remain a great unknown for most people. Public knowledge about the Arctic and Antarctic, and the critical role of the Poles in the entire Earth system, is nonexistent, incomplete or burdened with misperceptions. The International Polar Years of 2007-2009-and associated "I*Y" science years such as IHY, IYPE and eGY-present a unique opportunity to change this. The people who can best effect this change are those who know the Poles best, through living or working there. Based on innovative but proven models, POLAR-PALOOZA will use three complementary strategies to engage, inform and inspire large public audiences. (1) A national tour, under the working title "Stories from a Changing Planet", will include in-person presentations at science centers, museums, libraries and schools across North America, including Canada and Mexico. The presentations will be augmented by High Definition Video taped on location at the Poles, audio and video podcasts, and special education and outreach activities for targeted audiences. "Stories from a Changing Planet" will provide diverse audiences with an exciting opportunity to meet and interact directly with polar experts, and to appreciate why the Poles and the research done there are directly relevant to their lives. (2) The "HiDef Video Science Story Capture Corps" is a team of professional videographers, using the latest generation of low-cost, high-quality cameras, deployed to both Poles. They will document the work of multiple researchers and projects, rather than focusing on one topic for a single broadcast program

  18. Handbook of networking & connectivity

    CERN Document Server

    McClain, Gary R

    1994-01-01

    Handbook of Networking & Connectivity focuses on connectivity standards in use, including hardware and software options. The book serves as a guide for solving specific problems that arise in designing and maintaining organizational networks.The selection first tackles open systems interconnection, guide to digital communications, and implementing TCP/IP in an SNA environment. Discussions focus on elimination of the SNA backbone, routing SNA over internets, connectionless versus connection-oriented networks, internet concepts, application program interfaces, basic principles of layering, proto

  19. 78 FR 55684 - ConnectED Workshop

    Science.gov (United States)

    2013-09-11

    ... tools move everything from homework assignments to testing into the cloud. The workshop will explore possible strategies to connect virtually all of our students to next-generation broadband in a timely, cost-effective way. It will also share promising practices, from NTIA's Broadband Technology Opportunities...

  20. The Connected Traveler

    Energy Technology Data Exchange (ETDEWEB)

    Young, Stanley

    2017-04-24

    The Connected Traveler project is a multi-disciplinary undertaking that seeks to validate potential for transformative transportation system energy savings by incentivizing energy efficient travel behavior.

  1. Connections: All Issues

    Science.gov (United States)

    Goals Recycling Green Purchasing Pollution Prevention Reusing Water Resources Environmental Management Plateau, and more... Connections Newsletter December 2016 December 2016 Science-themed gifts available at

  2. Table 1. Primers sequences information. Primer name Sequence ...

    Indian Academy of Sciences (India)

    Administrator

    Figure 5. Selected microsatellite markers indicated maternal mosaicism was not caused by DNA contamination. We did not find any of the proband's paternal microsatellite markers mixed with the mother's (A). The positive control was generated by mixing 10% proband's sample with 90% his mother's sample (B).

  3. Stratigraphy of fluvial sediment sequences and their palaeoenvironmental information in the foreland of the Serra dos Órgãos, southeastern Brazil

    Science.gov (United States)

    Kirchner, André; Nehren, Udo; Heinrich, Jürgen

    2013-04-01

    In the hinterland of Rio de Janeiro city the rivers Guapiaçu, Macacu and Iconha originate in the Serra dos Órgãos mountain range and drain into the Atlantic Ocean. Since their channelization in the 1950s, higher flow velocities caused an incision of the rivers into the valley fills. These circumstances provide the possibility to study the alluvial deposits along the streams during low water level and allow conclusions on palaeoenvironmental change and landscape history. Sedimentological investigations of 13 exposures as well as AMS 14C measurements were carried out to investigate sediment properties and reconstruct the sedimentation history within the floodplains. These results enable to distinguish three different facies units. A late Pleistocene Unit I can be detected at the base of the observed exposures and consists of clast-supported fine to coarse gravels. It can be assumed that the gravel bodies were formed by a climatically induced erosional-depositional cycle within a braided river system. The gravels are overlaid by Unit II, a grayish to bluish loam mainly of mid-Holocene age. During generally drier climates these loams have been deposited during high water stages or flooding events as a splay facies proximal to the rivers. A reduced flow competence and relatively stable morphodynamic conditions are assumed for that period. Unit III accumulated in the late Holocene typically consists of several meters of planar or cross bedded sands to fine gravels, interfingered by loamy inclusions, buried peat bogs and organic debris. Fining-upward sequences can be frequently studied within Unit III which were completed by loamy sediments in the uppermost parts of the exposures. The increased flow competence from Unit II to Unit III seems to be a fluvial response to the increased humidity of the late Holocene as well as the enhancement of El Niño-Southern Oscillation (ENSO). Heavy rainfall likely caused higher sediment supply from the steep slopes as well as a

  4. TOMATOMICS: A Web Database for Integrated Omics Information in Tomato

    KAUST Repository

    Kudo, Toru; Kobayashi, Masaaki; Terashima, Shin; Katayama, Minami; Ozaki, Soichi; Kanno, Maasa; Saito, Misa; Yokoyama, Koji; Ohyanagi, Hajime; Aoki, Koh; Kubo, Yasutaka; Yano, Kentaro

    2016-01-01

    Solanum lycopersicum (tomato) is an important agronomic crop and a major model fruit-producing plant. To facilitate basic and applied research, comprehensive experimental resources and omics information on tomato are available following their development. Mutant lines and cDNA clones from a dwarf cultivar, Micro-Tom, are two of these genetic resources. Large-scale sequencing data for ESTs and full-length cDNAs from Micro-Tom continue to be gathered. In conjunction with information on the reference genome sequence of another cultivar, Heinz 1706, the Micro-Tom experimental resources have facilitated comprehensive functional analyses. To enhance the efficiency of acquiring omics information for tomato biology, we have integrated the information on the Micro-Tom experimental resources and the Heinz 1706 genome sequence. We have also inferred gene structure by comparison of sequences between the genome of Heinz 1706 and the transcriptome, which are comprised of Micro-Tom full-length cDNAs and Heinz 1706 RNA-seq data stored in the KaFTom and Sequence Read Archive databases. In order to provide large-scale omics information with streamlined connectivity we have developed and maintain a web database TOMATOMICS (http://bioinf.mind.meiji.ac.jp/tomatomics/). In TOMATOMICS, access to the information on the cDNA clone resources, full-length mRNA sequences, gene structures, expression profiles and functional annotations of genes is available through search functions and the genome browser, which has an intuitive graphical interface.

  5. TOMATOMICS: A Web Database for Integrated Omics Information in Tomato

    KAUST Repository

    Kudo, Toru

    2016-11-29

    Solanum lycopersicum (tomato) is an important agronomic crop and a major model fruit-producing plant. To facilitate basic and applied research, comprehensive experimental resources and omics information on tomato are available following their development. Mutant lines and cDNA clones from a dwarf cultivar, Micro-Tom, are two of these genetic resources. Large-scale sequencing data for ESTs and full-length cDNAs from Micro-Tom continue to be gathered. In conjunction with information on the reference genome sequence of another cultivar, Heinz 1706, the Micro-Tom experimental resources have facilitated comprehensive functional analyses. To enhance the efficiency of acquiring omics information for tomato biology, we have integrated the information on the Micro-Tom experimental resources and the Heinz 1706 genome sequence. We have also inferred gene structure by comparison of sequences between the genome of Heinz 1706 and the transcriptome, which are comprised of Micro-Tom full-length cDNAs and Heinz 1706 RNA-seq data stored in the KaFTom and Sequence Read Archive databases. In order to provide large-scale omics information with streamlined connectivity we have developed and maintain a web database TOMATOMICS (http://bioinf.mind.meiji.ac.jp/tomatomics/). In TOMATOMICS, access to the information on the cDNA clone resources, full-length mRNA sequences, gene structures, expression profiles and functional annotations of genes is available through search functions and the genome browser, which has an intuitive graphical interface.

  6. Archives: Mathematics Connection

    African Journals Online (AJOL)

    Items 1 - 9 of 9 ... Archives: Mathematics Connection. Journal Home > Archives: Mathematics Connection. Log in or Register to get access to full text downloads. Username, Password, Remember me, or Register · Journal Home · ABOUT THIS JOURNAL · Advanced Search · Current Issue · Archives. 1 - 9 of 9 Items. 2011 ...

  7. Connective Tissue Disorders

    Science.gov (United States)

    ... of connective tissue. Over 200 disorders that impact connective tissue. There are different types: Genetic disorders, such as Ehlers-Danlos syndrome, Marfan syndrome, and osteogenesis imperfecta Autoimmune disorders, such as lupus and scleroderma Cancers, like some types of soft tissue sarcoma Each ...

  8. [Complete genome sequencing and sequence analysis of BCG Tice].

    Science.gov (United States)

    Wang, Zhiming; Pan, Yuanlong; Wu, Jun; Zhu, Baoli

    2012-10-04

    The objective of this study is to obtain the complete genome sequence of Bacillus Calmette-Guerin Tice (BCG Tice), in order to provide more information about the molecular biology of BCG Tice and design more reasonable vaccines to prevent tuberculosis. We assembled the data from high-throughput sequencing with SOAPdenovo software, with many contigs and scaffolds obtained. There are many sequence gaps and physical gaps remained as a result of regional low coverage and low quality. We designed primers at the end of contigs and performed PCR amplification in order to link these contigs and scaffolds. With various enzymes to perform PCR amplification, adjustment of PCR reaction conditions, and combined with clone construction to sequence, all the gaps were finished. We obtained the complete genome sequence of BCG Tice and submitted it to GenBank of National Center for Biotechnology Information (NCBI). The genome of BCG Tice is 4334064 base pairs in length, with GC content 65.65%. The problems and strategies during the finishing step of BCG Tice sequencing are illuminated here, with the hope of affording some experience to those who are involved in the finishing step of genome sequencing. The microarray data were verified by our results.

  9. Handbook of Brain Connectivity

    CERN Document Server

    Jirsa, Viktor K

    2007-01-01

    Our contemporary understanding of brain function is deeply rooted in the ideas of the nonlinear dynamics of distributed networks. Cognition and motor coordination seem to arise from the interactions of local neuronal networks, which themselves are connected in large scales across the entire brain. The spatial architectures between various scales inevitably influence the dynamics of the brain and thereby its function. But how can we integrate brain connectivity amongst these structural and functional domains? Our Handbook provides an account of the current knowledge on the measurement, analysis and theory of the anatomical and functional connectivity of the brain. All contributors are leading experts in various fields concerning structural and functional brain connectivity. In the first part of the Handbook, the chapters focus on an introduction and discussion of the principles underlying connected neural systems. The second part introduces the currently available non-invasive technologies for measuring struct...

  10. Modeling Structural Brain Connectivity

    DEFF Research Database (Denmark)

    Ambrosen, Karen Marie Sandø

    The human brain consists of a gigantic complex network of interconnected neurons. Together all these connections determine who we are, how we react and how we interpret the world. Knowledge about how the brain is connected can further our understanding of the brain’s structural organization, help...... improve diagnosis, and potentially allow better treatment of a wide range of neurological disorders. Tractography based on diffusion magnetic resonance imaging is a unique tool to estimate this “structural connectivity” of the brain non-invasively and in vivo. During the last decade, brain connectivity...... has increasingly been analyzed using graph theoretic measures adopted from network science and this characterization of the brain’s structural connectivity has been shown to be useful for the classification of populations, such as healthy and diseased subjects. The structural connectivity of the brain...

  11. The text of the amended Protocol to the Agreement between the Kingdom of Swaziland and the International Atomic Energy Agency for the Application of Safeguards in Connection with the Treaty on the Non-Proliferation of Nuclear Weapons, is reproduced in this document for the information of all Member States of the Agency

    International Nuclear Information System (INIS)

    2010-01-01

    The text of the amended Protocol to the Agreement between the Kingdom of Swaziland and the International Atomic Energy Agency for the Application of Safeguards in Connection with the Treaty on the Non-Proliferation of Nuclear Weapons, is reproduced in this document for the information of all Member States of the Agency [es

  12. Functional connectivity of parietal cortex during temporal selective attention.

    Science.gov (United States)

    Tyler, Sarah C; Dasgupta, Samhita; Agosta, Sara; Battelli, Lorella; Grossman, Emily D

    2015-04-01

    Perception of natural experiences requires allocation of attention towards features, objects, and events that are moving and changing over time. This allocation of attention is controlled by large-scale brain networks that, when damaged, cause widespread cognitive deficits. In particular, damage to ventral parietal cortex (right lateralized TPJ, STS, supramarginal and angular gyri) is associated with failures to selectively attend to and isolate features embedded within rapidly changing visual sequences (Battelli, Pascual-Leone, & Cavanagh, 2007; Husain, Shapiro, Martin, & Kennard, 1997). In this study, we used fMRI to investigate the neural activity and functional connectivity of intact parietal cortex while typical subjects judged the relative onsets and offsets of rapidly flickering tokens (a phase discrimination task in which right parietal patients are impaired). We found two regions in parietal cortex correlated with task performance: a bilateral posterior TPJ (pTPJ) and an anterior right-lateralized TPJ (R aTPJ). Both regions were deactivated when subjects engaged in the task but showed different patterns of functional connectivity. The bilateral pTPJ was strongly connected to nodes within the default mode network (DMN) and the R aTPJ was connected to the attention network. Accurate phase discriminations were associated with increased functional correlations between sensory cortex (hMT+) and the bilateral pTPJ, whereas accuracy on a control task was associated with yoked activity in the hMT+ and the R aTPJ. We conclude that temporal selective attention is particularly sensitive for revealing information pathways between sensory and core cognitive control networks that, when damaged, can lead to nonspatial attention impairments in right parietal stroke patients. Copyright © 2015 Elsevier Ltd. All rights reserved.

  13. Scoring protein relationships in functional interaction networks predicted from sequence data.

    Directory of Open Access Journals (Sweden)

    Gaston K Mazandu

    Full Text Available UNLABELLED: The abundance of diverse biological data from various sources constitutes a rich source of knowledge, which has the power to advance our understanding of organisms. This requires computational methods in order to integrate and exploit these data effectively and elucidate local and genome wide functional connections between protein pairs, thus enabling functional inferences for uncharacterized proteins. These biological data are primarily in the form of sequences, which determine functions, although functional properties of a protein can often be predicted from just the domains it contains. Thus, protein sequences and domains can be used to predict protein pair-wise functional relationships, and thus contribute to the function prediction process of uncharacterized proteins in order to ensure that knowledge is gained from sequencing efforts. In this work, we introduce information-theoretic based approaches to score protein-protein functional interaction pairs predicted from protein sequence similarity and conserved protein signature matches. The proposed schemes are effective for data-driven scoring of connections between protein pairs. We applied these schemes to the Mycobacterium tuberculosis proteome to produce a homology-based functional network of the organism with a high confidence and coverage. We use the network for predicting functions of uncharacterised proteins. AVAILABILITY: Protein pair-wise functional relationship scores for Mycobacterium tuberculosis strain CDC1551 sequence data and python scripts to compute these scores are available at http://web.cbio.uct.ac.za/~gmazandu/scoringschemes.

  14. Rapid Diagnostics of Onboard Sequences

    Science.gov (United States)

    Starbird, Thomas W.; Morris, John R.; Shams, Khawaja S.; Maimone, Mark W.

    2012-01-01

    Keeping track of sequences onboard a spacecraft is challenging. When reviewing Event Verification Records (EVRs) of sequence executions on the Mars Exploration Rover (MER), operators often found themselves wondering which version of a named sequence the EVR corresponded to. The lack of this information drastically impacts the operators diagnostic capabilities as well as their situational awareness with respect to the commands the spacecraft has executed, since the EVRs do not provide argument values or explanatory comments. Having this information immediately available can be instrumental in diagnosing critical events and can significantly enhance the overall safety of the spacecraft. This software provides auditing capability that can eliminate that uncertainty while diagnosing critical conditions. Furthermore, the Restful interface provides a simple way for sequencing tools to automatically retrieve binary compiled sequence SCMFs (Space Command Message Files) on demand. It also enables developers to change the underlying database, while maintaining the same interface to the existing applications. The logging capabilities are also beneficial to operators when they are trying to recall how they solved a similar problem many days ago: this software enables automatic recovery of SCMF and RML (Robot Markup Language) sequence files directly from the command EVRs, eliminating the need for people to find and validate the corresponding sequences. To address the lack of auditing capability for sequences onboard a spacecraft during earlier missions, extensive logging support was added on the Mars Science Laboratory (MSL) sequencing server. This server is responsible for generating all MSL binary SCMFs from RML input sequences. The sequencing server logs every SCMF it generates into a MySQL database, as well as the high-level RML file and dictionary name inputs used to create the SCMF. The SCMF is then indexed by a hash value that is automatically included in all command

  15. Filovirus Glycoprotein Sequence, Structure and Virulence

    OpenAIRE

    Phillips, J. C.

    2014-01-01

    Leading Ebola subtypes exhibit a wide mortality range, here explained at the molecular level by using fractal hydropathic scaling of amino acid sequences based on protein self-organized criticality. Specific hydrophobic features in the hydrophilic mucin-like domain suffice to account for the wide mortality range. Significance statement: Ebola virus is spreading rapidly in Africa. The connection between protein amino acid sequence and mortality is identified here.

  16. Galaxy LIMS for next-generation sequencing

    NARCIS (Netherlands)

    Scholtalbers, J.; Rossler, J.; Sorn, P.; Graaf, J. de; Boisguerin, V.; Castle, J.; Sahin, U.

    2013-01-01

    SUMMARY: We have developed a laboratory information management system (LIMS) for a next-generation sequencing (NGS) laboratory within the existing Galaxy platform. The system provides lab technicians standard and customizable sample information forms, barcoded submission forms, tracking of input

  17. Phase-lock loop of Grid-connected Voltage Source Converter under non-ideal grid condition

    DEFF Research Database (Denmark)

    Wang, Haojie; Sun, Hai; Han, Minxiao

    2015-01-01

    It is a normal practice that the DC micro-grid is connected to AC main grid through Grid-connected Voltage Source Converter (G-VSC) for voltage support. Accurate control of DC micro-grid voltage is difficult for G-VSC under unbalanced grid condition as the fundamental positive-sequence component...... and distorted system voltage the proposed PLL can accurately detect the fundamental positive-sequence component of grid voltage thus accurate control of DC micro-grid voltage can be realized....... phase information cannot be accurately tracked. Based on analysis of the cause of double-frequency ripple when unbalance exists in main grid, a phase-locked loop (PLL) detection technique is proposed. Under the conditions of unsymmetrical system voltage, varying system frequency, single-phase system...

  18. PseudoMLSA: a database for multigenic sequence analysis of Pseudomonas species

    Directory of Open Access Journals (Sweden)

    Lalucat Jorge

    2010-04-01

    Full Text Available Abstract Background The genus Pseudomonas comprises more than 100 species of environmental, clinical, agricultural, and biotechnological interest. Although, the recommended method for discriminating bacterial species is DNA-DNA hybridisation, alternative techniques based on multigenic sequence analysis are becoming a common practice in bacterial species discrimination studies. Since there is not a general criterion for determining which genes are more useful for species resolution; the number of strains and genes analysed is increasing continuously. As a result, sequences of different genes are dispersed throughout several databases. This sequence information needs to be collected in a common database, in order to be useful for future identification-based projects. Description The PseudoMLSA Database is a comprehensive database of multiple gene sequences from strains of Pseudomonas species. The core of the database is composed of selected gene sequences from all Pseudomonas type strains validly assigned to the genus through 2008. The database is aimed to be useful for MultiLocus Sequence Analysis (MLSA procedures, for the identification and characterisation of any Pseudomonas bacterial isolate. The sequences are available for download via a direct connection to the National Center for Biotechnology Information (NCBI. Additionally, the database includes an online BLAST interface for flexible nucleotide queries and similarity searches with the user's datasets, and provides a user-friendly output for easily parsing, navigating, and analysing BLAST results. Conclusions The PseudoMLSA database amasses strains and sequence information of validly described Pseudomonas species, and allows free querying of the database via a user-friendly, web-based interface available at http://www.uib.es/microbiologiaBD/Welcome.html. The web-based platform enables easy retrieval at strain or gene sequence information level; including references to published peer

  19. Connected motorcycle system performance.

    Science.gov (United States)

    2016-01-15

    This project characterized the performance of Connected Vehicle Systems (CVS) on motorcycles based on two key components: global positioning and wireless communication systems. Considering that Global Positioning System (GPS) and 5.9 GHz Dedicated Sh...

  20. Connected vehicle applications : safety.

    Science.gov (United States)

    2016-01-01

    Connected vehicle safety applications are designed to increase situational awareness : and reduce or eliminate crashes through vehicle-to-infrastructure, vehicle-to-vehicle, : and vehicle-to-pedestrian data transmissions. Applications support advisor...

  1. IDRC Connect User Guide

    International Development Research Centre (IDRC) Digital Library (Canada)

    Kristina Kamichaitis

    IDRC Extranet home page, which is an umbrella for a number of applications available to IDRC external users. ... IDRC Connect is not formatted for mobile users. ..... Thesis. • Training Material. • Website. • Working Paper. • Workshop Report.

  2. Shotgun protein sequencing.

    Energy Technology Data Exchange (ETDEWEB)

    Faulon, Jean-Loup Michel; Heffelfinger, Grant S.

    2009-06-01

    A novel experimental and computational technique based on multiple enzymatic digestion of a protein or protein mixture that reconstructs protein sequences from sequences of overlapping peptides is described in this SAND report. This approach, analogous to shotgun sequencing of DNA, is to be used to sequence alternative spliced proteins, to identify post-translational modifications, and to sequence genetically engineered proteins.

  3. Directional connectivity in hydrology and ecology

    Science.gov (United States)

    Larsen, Laurel G.; Choi, Jungyill; Nungesser, Martha K.; Harvey, Judson W.

    2012-01-01

    Quantifying hydrologic and ecological connectivity has contributed to understanding transport and dispersal processes and assessing ecosystem degradation or restoration potential. However, there has been little synthesis across disciplines. The growing field of ecohydrology and recent recognition that loss of hydrologic connectivity is leading to a global decline in biodiversity underscore the need for a unified connectivity concept. One outstanding need is a way to quantify directional connectivity that is consistent, robust to variations in sampling, and transferable across scales or environmental settings. Understanding connectivity in a particular direction (e.g., streamwise, along or across gradient, between sources and sinks, along cardinal directions) provides critical information for predicting contaminant transport, planning conservation corridor design, and understanding how landscapes or hydroscapes respond to directional forces like wind or water flow. Here we synthesize progress on quantifying connectivity and develop a new strategy for evaluating directional connectivity that benefits from use of graph theory in ecology and percolation theory in hydrology. The directional connectivity index (DCI) is a graph-theory based, multiscale metric that is generalizable to a range of different structural and functional connectivity applications. It exhibits minimal sensitivity to image rotation or resolution within a given range and responds intuitively to progressive, unidirectional change. Further, it is linearly related to the integral connectivity scale length—a metric common in hydrology that correlates well with actual fluxes—but is less computationally challenging and more readily comparable across different landscapes. Connectivity-orientation curves (i.e., directional connectivity computed over a range of headings) provide a quantitative, information-dense representation of environmental structure that can be used for comparison or detection of

  4. Directional connectivity in hydrology and ecology.

    Science.gov (United States)

    Larsen, Laurel G; Choi, Jungyill; Nungesser, Martha K; Harvey, Judson W

    2012-12-01

    Quantifying hydrologic and ecological connectivity has contributed to understanding transport and dispersal processes and assessing ecosystem degradation or restoration potential. However, there has been little synthesis across disciplines. The growing field of ecohydrology and recent recognition that loss of hydrologic connectivity is leading to a global decline in biodiversity underscore the need for a unified connectivity concept. One outstanding need is a way to quantify directional connectivity that is consistent, robust to variations in sampling, and transferable across scales or environmental settings. Understanding connectivity in a particular direction (e.g., streamwise, along or across gradient, between sources and sinks, along cardinal directions) provides critical information for predicting contaminant transport, planning conservation corridor design, and understanding how landscapes or hydroscapes respond to directional forces like wind or water flow. Here we synthesize progress on quantifying connectivity and develop a new strategy for evaluating directional connectivity that benefits from use of graph theory in ecology and percolation theory in hydrology. The directional connectivity index (DCI) is a graph-theory based, multiscale metric that is generalizable to a range of different structural and functional connectivity applications. It exhibits minimal sensitivity to image rotation or resolution within a given range and responds intuitively to progressive, unidirectional change. Further, it is linearly related to the integral connectivity scale length--a metric common in hydrology that correlates well with actual fluxes--but is less computationally challenging and more readily comparable across different landscapes. Connectivity-orientation curves (i.e., directional connectivity computed over a range of headings) provide a quantitative, information-dense representation of environmental structure that can be used for comparison or detection of

  5. [Connective tissue and inflammation].

    Science.gov (United States)

    Jakab, Lajos

    2014-03-23

    The author summarizes the structure of the connective tissues, the increasing motion of the constituents, which determine the role in establishing the structure and function of that. The structure and function of the connective tissue are related to each other in the resting as well as inflammatory states. It is emphasized that cellular events in the connective tissue are part of the defence of the organism, the localisation of the damage and, if possible, the maintenance of restitutio ad integrum. The organism responds to damage with inflammation, the non specific immune response, as well as specific, adaptive immunity. These processes are located in the connective tissue. Sterile and pathogenic inflammation are relatively similar processes, but inevitable differences are present, too. Sialic acids and glycoproteins containing sialic acids have important roles, and the role of Siglecs is also highlighted. Also, similarities and differences in damages caused by pathogens and sterile agents are briefly summarized. In addition, the roles of adhesion molecules linked to each other, and the whole event of inflammatory processes are presented. When considering practical consequences it is stressed that the structure (building up) of the organism and the defending function of inflammation both have fundamental importance. Inflammation has a crucial role in maintaining the integrity and the unimpaired somato-psychological state of the organism. Thus, inflammation serves as a tool of organism identical with the natural immune response, inseparably connected with the specific, adaptive immune response. The main events of the inflammatory processes take place in the connective tissue.

  6. Quick connect fastener

    Science.gov (United States)

    Weddendorf, Bruce

    1994-01-01

    A quick connect fastener and method of use is presented wherein the quick connect fastener is suitable for replacing available bolts and screws, the quick connect fastener being capable of installation by simply pushing a threaded portion of the connector into a member receptacle hole, the inventive apparatus being comprised of an externally threaded fastener having a threaded portion slidably mounted upon a stud or bolt shaft, wherein the externally threaded fastener portion is expandable by a preloaded spring member. The fastener, upon contact with the member receptacle hole, has the capacity of presenting cylindrical threads of a reduced diameter for insertion purposes and once inserted into the receiving threads of the receptacle member hole, are expandable for engagement of the receptacle hole threads forming a quick connect of the fastener and the member to be fastened, the quick connect fastener can be further secured by rotation after insertion, even to the point of locking engagement, the quick connect fastener being disengagable only by reverse rotation of the mated thread engagement.

  7. Multimodal sequence learning.

    Science.gov (United States)

    Kemény, Ferenc; Meier, Beat

    2016-02-01

    While sequence learning research models complex phenomena, previous studies have mostly focused on unimodal sequences. The goal of the current experiment is to put implicit sequence learning into a multimodal context: to test whether it can operate across different modalities. We used the Task Sequence Learning paradigm to test whether sequence learning varies across modalities, and whether participants are able to learn multimodal sequences. Our results show that implicit sequence learning is very similar regardless of the source modality. However, the presence of correlated task and response sequences was required for learning to take place. The experiment provides new evidence for implicit sequence learning of abstract conceptual representations. In general, the results suggest that correlated sequences are necessary for implicit sequence learning to occur. Moreover, they show that elements from different modalities can be automatically integrated into one unitary multimodal sequence. Copyright © 2015 Elsevier B.V. All rights reserved.

  8. Sequence Read Archive (SRA)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms including Roche 454 GS System®, Illumina Genome...

  9. Starting-up sequence of the AWEC-6 0 wind turbine; Secuencia de Arranaue del Aerogenerador AWEC-60

    Energy Technology Data Exchange (ETDEWEB)

    Avia, F.; Cruz, M. de la

    1991-07-01

    One of the most critical status of the wind turbines operation is the starting-up sequence and the connection to the grid, due to the actuating loads that could be several times the loads during operation at rated conditions. Due to this fact, the control strategy is very important during the starting-up sequence in order to minimize the loads on the machine. For this purpose it is necessary to analyze the behaviour of the wind turbine during that sequence in different wind conditions and machine conditions This report shows the graphic Information about fifty starting-up sequences of the AWEC-60 wind turbine of 60 m diameter and 1200 kW of rated power, recorded in April 1991 and covering all the operation range between cut-in and cut-out wind speed. (Author) 2 refs.

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

    Science.gov (United States)

    Meiler, Arno; Klinger, Claudia; Kaufmann, Michael

    2012-09-08

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

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

    Directory of Open Access Journals (Sweden)

    Meiler Arno

    2012-09-01

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

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

    Science.gov (United States)

    2012-01-01

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

  13. Connectable solar air collectors

    Energy Technology Data Exchange (ETDEWEB)

    Oestergaard Jensen, S.; Bosanac, M.

    2002-02-01

    The project has proved that it is possible to manufacture solar air collector panels, which in an easy way can be connected into large collector arrays with integrated ducting without loss of efficiency. The developed connectable solar air collectors are based on the use of matrix absorbers in the form of perforated metal sheets. Three interconnected solar air collectors of the above type - each with an transparent area of approx. 3 m{sup 2} - was tested and compared with parallel tests on two single solar air collectors also with a transparent area of approx. 3 m{sup 2} One of the single solar air collectors has an identical absorber as the connectable solar air collectors while the absorber of the other single solar air collector was a fibre cloth. The efficiency of the three solar air collectors proved to be almost identical in the investigated range of mass flow rates and temperature differences. The solar air collectors further proved to be very efficient - as efficient as the second most efficient solar air collectors tested in the IEA task 19 project Solar Air Systems. Some problems remain although to be solved: the pressure drop across especially the connectable solar air collectors is too high - mainly across the inlets of the solar air collectors. It should, however, be possible to considerably reduce the pressure losses with a more aerodynamic design of the inlet and outlet of the solar air collectors; The connectable solar air collectors are easy connectable but the air tightness of the connections in the present form is not good enough. As leakage leads to lower efficiencies focus should be put on making the connections more air tight without loosing the easiness in connecting the solar air collectors. As a spin off of the project a simple and easy way to determine the efficiency of solar, air collectors for pre-heating of fresh air has been validated. The simple method of determining the efficiency has with success been compared with an advance method

  14. Connectivity and superconductivity

    CERN Document Server

    Rubinstein, Jacob

    2000-01-01

    The motto of connectivity and superconductivity is that the solutions of the Ginzburg--Landau equations are qualitatively influenced by the topology of the boundaries, as in multiply-connected samples. Special attention is paid to the "zero set", the set of the positions (also known as "quantum vortices") where the order parameter vanishes. The effects considered here usually become important in the regime where the coherence length is of the order of the dimensions of the sample. It takes the intuition of physicists and the awareness of mathematicians to find these new effects. In connectivity and superconductivity, theoretical and experimental physicists are brought together with pure and applied mathematicians to review these surprising results. This volume is intended to serve as a reference book for graduate students and researchers in physics or mathematics interested in superconductivity, or in the Schrödinger equation as a limiting case of the Ginzburg--Landau equations.

  15. A super soliton connection

    International Nuclear Information System (INIS)

    Gurses, M.; Oguz, O.

    1985-07-01

    Integrable super non-linear classical partial differential equations are considered. A super s1(2,R) algebra valued connection 1-form is constructed. It is shown that curvature 2-form of this super connection vanishes by virtue of the integrable super equations of motion. A super extension of the AKNS scheme is presented and a class of super extension of the Lax hierarchy and super non-linear Schroedinger equation are found. O(N) extension and the Baecklund transformations of the above super equations are also considered. (author)

  16. Connecting textual segments

    DEFF Research Database (Denmark)

    Brügger, Niels

    2017-01-01

    history than just the years of the emergence of the web, the chapter traces the history of how segments of text have deliberately been connected to each other by the use of specific textual and media features, from clay tablets, manuscripts on parchment, and print, among others, to hyperlinks on stand......In “Connecting textual segments: A brief history of the web hyperlink” Niels Brügger investigates the history of one of the most fundamental features of the web: the hyperlink. Based on the argument that the web hyperlink is best understood if it is seen as another step in a much longer and broader...

  17. Best connected rectangular arrangements

    Directory of Open Access Journals (Sweden)

    Krishnendra Shekhawat

    2016-03-01

    Full Text Available It can be found quite often in the literature that many well-known architects have employed either the golden rectangle or the Fibonacci rectangle in their works. On contrary, it is rare to find any specific reason for using them so often. Recently, Shekhawat (2015 proved that the golden rectangle and the Fibonacci rectangle are one of the best connected rectangular arrangements and this may be one of the reasons for their high presence in architectural designs. In this work we present an algorithm that generates n-4 best connected rectangular arrangements so that the proposed solutions can be further used by architects for their designs.

  18. Capacity for patterns and sequences in Kanerva's SDM as compared to other associative memory models

    Science.gov (United States)

    Keeler, James D.

    1987-01-01

    The information capacity of Kanerva's Sparse Distributed Memory (SDM) and Hopfield-type neural networks is investigated. Under the approximations used, it is shown that the total information stored in these systems is proportional to the number connections in the network. The proportionality constant is the same for the SDM and Hopfield-type models independent of the particular model, or the order of the model. The approximations are checked numerically. This same analysis can be used to show that the SDM can store sequences of spatiotemporal patterns, and the addition of time-delayed connections allows the retrieval of context dependent temporal patterns. A minor modification of the SDM can be used to store correlated patterns.

  19. Design of Long Period Pseudo-Random Sequences from the Addition of -Sequences over

    Directory of Open Access Journals (Sweden)

    Ren Jian

    2004-01-01

    Full Text Available Pseudo-random sequence with good correlation property and large linear span is widely used in code division multiple access (CDMA communication systems and cryptology for reliable and secure information transmission. In this paper, sequences with long period, large complexity, balance statistics, and low cross-correlation property are constructed from the addition of -sequences with pairwise-prime linear spans (AMPLS. Using -sequences as building blocks, the proposed method proved to be an efficient and flexible approach to construct long period pseudo-random sequences with desirable properties from short period sequences. Applying the proposed method to , a signal set is constructed.

  20. Combining protein sequence, structure, and dynamics: A novel approach for functional evolution analysis of PAS domain superfamily.

    Science.gov (United States)

    Dong, Zheng; Zhou, Hongyu; Tao, Peng

    2018-02-01

    PAS domains are widespread in archaea, bacteria, and eukaryota, and play important roles in various functions. In this study, we aim to explore functional evolutionary relationship among proteins in the PAS domain superfamily in view of the sequence-structure-dynamics-function relationship. We collected protein sequences and crystal structure data from RCSB Protein Data Bank of the PAS domain superfamily belonging to three biological functions (nucleotide binding, photoreceptor activity, and transferase activity). Protein sequences were aligned and then used to select sequence-conserved residues and build phylogenetic tree. Three-dimensional structure alignment was also applied to obtain structure-conserved residues. The protein dynamics were analyzed using elastic network model (ENM) and validated by molecular dynamics (MD) simulation. The result showed that the proteins with same function could be grouped by sequence similarity, and proteins in different functional groups displayed statistically significant difference in their vibrational patterns. Interestingly, in all three functional groups, conserved amino acid residues identified by sequence and structure conservation analysis generally have a lower fluctuation than other residues. In addition, the fluctuation of conserved residues in each biological function group was strongly correlated with the corresponding biological function. This research suggested a direct connection in which the protein sequences were related to various functions through structural dynamics. This is a new attempt to delineate functional evolution of proteins using the integrated information of sequence, structure, and dynamics. © 2017 The Protein Society.

  1. Connections among quantum logics

    International Nuclear Information System (INIS)

    Lock, P.F.; Hardegree, G.M.

    1985-01-01

    This paper gives a brief introduction to the major areas of work in quantum event logics: manuals (Foulis and Randall) and semi-Boolean algebras (Abbott). The two theories are compared, and the connection between quantum event logics and quantum propositional logics is made explicit. In addition, the work on manuals provides us with many examples of results stated in Part I. (author)

  2. Connectivity measures: a review

    Czech Academy of Sciences Publication Activity Database

    Kindlmann, Pavel; Burel, F.

    2008-01-01

    Roč. 23, č. 1 (2008), s. 879-890 ISSN 0921-2973 R&D Projects: GA MŠk LC06073; GA AV ČR(CZ) IAA6087301 Institutional research plan: CEZ:AV0Z60870520 Keywords : Conservation biology * Habitat fragmentation * Landscape connectivity * Measures * Species extinction Subject RIV: EH - Ecology, Behaviour Impact factor: 2.453, year: 2008

  3. Clip, connect, clone

    DEFF Research Database (Denmark)

    Fujima, Jun; Lunzer, Aran; Hornbæk, Kasper

    2010-01-01

    using three mechanisms: clipping of input and result elements from existing applications to form cells on a spreadsheet; connecting these cells using formulas, thus enabling result transfer between applications; and cloning cells so that multiple requests can be handled side by side. We demonstrate...

  4. A Connective Pedagogy.

    Science.gov (United States)

    Goral, Mary

    2000-01-01

    Our increasingly hurried lifestyle, changes in family structure, and intense economic pressures place stress on children and families. Waldorf education provides an educational environment that alleviates this stress through a connective pedagogy that encompasses continuity of people, curriculum, and instruction; a reverence and respect for the…

  5. Connected vehicle application : safety.

    Science.gov (United States)

    2015-01-01

    Connected vehicle safety applications are designed to increase situational awareness : and reduce or eliminate crashes through vehicle-to-infrastructure (V2I), vehicle-to-vehicle (V2V), and vehicle-to-pedestrian (V2P) data transmissions. Applications...

  6. Mathematics Connection: Editorial Policies

    African Journals Online (AJOL)

    Focus and Scope. MATHEMATICS CONNECTION aims at providing a forum to promote the development of Mathematics Education in Ghana. Articles that seek to enhance the teaching and/or learning of mathematics at all levels of the educational system are welcome ...

  7. Making the Connection

    Science.gov (United States)

    Perna, Mark C.

    2006-01-01

    Enrollment marketing is not just about enrollment; it is about creating relationships and serving one's community or target audience for many years. In this article, the author states that the first step in building such relationships is making a connection, and that is what effective marketing is all about. Administrators, teachers and critical…

  8. Connecting numeric models

    International Nuclear Information System (INIS)

    Caremoli, C.; Erhard, P.

    1996-01-01

    Computerized simulation uses calculation codes whose validation is reliable. Reactor simulators should take greater advantage of latest computer technology impact, in particular in the field of parallel processing. Instead of creating more global simulation codes whose validation might be a problem, connecting several existing codes should be a promising solution. (D.L.). 3 figs

  9. From connection to customer

    International Nuclear Information System (INIS)

    Milatz, H.; Soeters, R.

    2001-01-01

    Energy companies can no longer be certain that a customer today will remain a customer tomorrow. They have to work hard to achieve that. They are going from thinking in terms of connections to pampering their customers. Good Customer Relationship Management is a way to achieve a competitive advantage. The whole organisation has to adapt, particularly the customer orientation of employees

  10. Mapping functional connectivity

    Science.gov (United States)

    Peter Vogt; Joseph R. Ferrari; Todd R. Lookingbill; Robert H. Gardner; Kurt H. Riitters; Katarzyna Ostapowicz

    2009-01-01

    An objective and reliable assessment of wildlife movement is important in theoretical and applied ecology. The identification and mapping of landscape elements that may enhance functional connectivity is usually a subjective process based on visual interpretations of species movement patterns. New methods based on mathematical morphology provide a generic, flexible,...

  11. IDRC Connect User Guide

    International Development Research Centre (IDRC) Digital Library (Canada)

    Kristina Kamichaitis

    2 Jul 2015 ... IDRC Connect contribuye a la aplicación de la Política de Acceso abierto de IDRC facilitando ..... Tesis. • Material de capacitación. • Sitio web. • Documento de trabajo ..... incluir planes de estudios, metodologías y manuales.

  12. Connecting multimodality in human communication.

    Science.gov (United States)

    Regenbogen, Christina; Habel, Ute; Kellermann, Thilo

    2013-01-01

    A successful reciprocal evaluation of social signals serves as a prerequisite for social coherence and empathy. In a previous fMRI study we studied naturalistic communication situations by presenting video clips to our participants and recording their behavioral responses regarding empathy and its components. In two conditions, all three channels transported congruent emotional or neutral information, respectively. Three conditions selectively presented two emotional channels and one neutral channel and were thus bimodally emotional. We reported channel-specific emotional contributions in modality-related areas, elicited by dynamic video clips with varying combinations of emotionality in facial expressions, prosody, and speech content. However, to better understand the underlying mechanisms accompanying a naturalistically displayed human social interaction in some key regions that presumably serve as specific processing hubs for facial expressions, prosody, and speech content, we pursued a reanalysis of the data. Here, we focused on two different descriptions of temporal characteristics within these three modality-related regions [right fusiform gyrus (FFG), left auditory cortex (AC), left angular gyrus (AG) and left dorsomedial prefrontal cortex (dmPFC)]. By means of a finite impulse response (FIR) analysis within each of the three regions we examined the post-stimulus time-courses as a description of the temporal characteristics of the BOLD response during the video clips. Second, effective connectivity between these areas and the left dmPFC was analyzed using dynamic causal modeling (DCM) in order to describe condition-related modulatory influences on the coupling between these regions. The FIR analysis showed initially diminished activation in bimodally emotional conditions but stronger activation than that observed in neutral videos toward the end of the stimuli, possibly by bottom-up processes in order to compensate for a lack of emotional information. The

  13. Information Literacy

    OpenAIRE

    Basili, Carla

    2015-01-01

    Information literacy is a concept which is well established in theory while in practice it is only slowly breaking ground in accordance with the understanding of its significance and the possibilities of its realisation. Based on fundamental works, the characteristics of information literacy, its cognitive foundations and significance for individuals as well as for society, are argumented in the article. The analyzed content of this concept is connected with the content of a librarian’s knowl...

  14. Political Connections and Investment in Rural Vietnam

    DEFF Research Database (Denmark)

    Markussen, Thomas; Tarp, Finn

    This paper uses household panel data from rural Vietnam to explore the effects of having a relative in a position of political or bureaucratic power on farmers’ agricultural investment decisions. Our main result is that households significantly increase their investment in land improvement...... as a result of relatives moving into public office. Connections to office holders appear to be important for investment because they strengthen de facto land property rights and improve access to off-farm employment and to informal loans. The findings underline the importance of informal networks for economic...... behaviour in environments with developing institutions and markets. They also suggest the presence of an untapped potential for economic development: if households without connections could obtain equally strong property rights and access to credit and insurance as the well-connected households, investment...

  15. Genome puzzle master (GPM): an integrated pipeline for building and editing pseudomolecules from fragmented sequences.

    Science.gov (United States)

    Zhang, Jianwei; Kudrna, Dave; Mu, Ting; Li, Weiming; Copetti, Dario; Yu, Yeisoo; Goicoechea, Jose Luis; Lei, Yang; Wing, Rod A

    2016-10-15

    Next generation sequencing technologies have revolutionized our ability to rapidly and affordably generate vast quantities of sequence data. Once generated, raw sequences are assembled into contigs or scaffolds. However, these assemblies are mostly fragmented and inaccurate at the whole genome scale, largely due to the inability to integrate additional informative datasets (e.g. physical, optical and genetic maps). To address this problem, we developed a semi-automated software tool-Genome Puzzle Master (GPM)-that enables the integration of additional genomic signposts to edit and build 'new-gen-assemblies' that result in high-quality 'annotation-ready' pseudomolecules. With GPM, loaded datasets can be connected to each other via their logical relationships which accomplishes tasks to 'group,' 'merge,' 'order and orient' sequences in a draft assembly. Manual editing can also be performed with a user-friendly graphical interface. Final pseudomolecules reflect a user's total data package and are available for long-term project management. GPM is a web-based pipeline and an important part of a Laboratory Information Management System (LIMS) which can be easily deployed on local servers for any genome research laboratory. The GPM (with LIMS) package is available at https://github.com/Jianwei-Zhang/LIMS CONTACTS: jzhang@mail.hzau.edu.cn or rwing@mail.arizona.eduSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

  16. Sequence complexity and work extraction

    International Nuclear Information System (INIS)

    Merhav, Neri

    2015-01-01

    We consider a simplified version of a solvable model by Mandal and Jarzynski, which constructively demonstrates the interplay between work extraction and the increase of the Shannon entropy of an information reservoir which is in contact with a physical system. We extend Mandal and Jarzynski’s main findings in several directions: first, we allow sequences of correlated bits rather than just independent bits. Secondly, at least for the case of binary information, we show that, in fact, the Shannon entropy is only one measure of complexity of the information that must increase in order for work to be extracted. The extracted work can also be upper bounded in terms of the increase in other quantities that measure complexity, like the predictability of future bits from past ones. Third, we provide an extension to the case of non-binary information (i.e. a larger alphabet), and finally, we extend the scope to the case where the incoming bits (before the interaction) form an individual sequence, rather than a random one. In this case, the entropy before the interaction can be replaced by the Lempel–Ziv (LZ) complexity of the incoming sequence, a fact that gives rise to an entropic meaning of the LZ complexity, not only in information theory, but also in physics. (paper)

  17. Nonparametric combinatorial sequence models.

    Science.gov (United States)

    Wauthier, Fabian L; Jordan, Michael I; Jojic, Nebojsa

    2011-11-01

    This work considers biological sequences that exhibit combinatorial structures in their composition: groups of positions of the aligned sequences are "linked" and covary as one unit across sequences. If multiple such groups exist, complex interactions can emerge between them. Sequences of this kind arise frequently in biology but methodologies for analyzing them are still being developed. This article presents a nonparametric prior on sequences which allows combinatorial structures to emerge and which induces a posterior distribution over factorized sequence representations. We carry out experiments on three biological sequence families which indicate that combinatorial structures are indeed present and that combinatorial sequence models can more succinctly describe them than simpler mixture models. We conclude with an application to MHC binding prediction which highlights the utility of the posterior distribution over sequence representations induced by the prior. By integrating out the posterior, our method compares favorably to leading binding predictors.

  18. NOMAD - more than a simple sequencer

    International Nuclear Information System (INIS)

    Mutti, P.; Cecillon, F.; Elaazzouzi, A.; Le Goc, Y.; Locatelli, J.; Ortiz, H.; Ratel, J.

    2012-01-01

    NOMAD is the new instrument control software of the Institut Laue-Langevin (ILL). A highly shareable code among all the instruments' suite, a user oriented design for tailored functionality and the improvement of the instrument team's autonomy thanks to a uniform and ergonomic user interface are the essential elements guiding the software development. NOMAD implements a client/server approach. The server is the core business containing all the instrument methods and the hardware drivers, while the GUI (Graphical User Interface) provides all the necessary functionalities for the interaction between user and hardware. All instruments share the same executable while a set of XML configuration files adapts hardware needs and instrument methods to the specific experimental setup. Thanks to a complete graphical representation of experimental sequences, NOMAD provides an overview of past, present and future operations. Users have the freedom to build their own specific work-flows using intuitive drag-and-drop technique. A complete drivers' database to connect and control all possible instrument components has been created, simplifying the inclusion of a new piece of equipment for an experiment. A web application makes available outside the ILL all the relevant information on the status of the experiment. A set of scientific methods facilitates the interaction between users and hardware giving access to instrument control and to complex operations within just one click on the interface. (authors)

  19. Connecting the Production Multiple

    DEFF Research Database (Denmark)

    Lichen, Alex Yu; Mouritsen, Jan

    &OP process itself is a fluid object, but there is still possibility to organise the messy Production. There are connections between the Production multiple and the managerial technology fluid. The fluid enacted the multiplicity of Production thus making it more difficult to be organised because there were...... in opposite directions. They are all part of the fluid object. There is no single chain of circulating references that makes the object a matter of fact. Accounting fluidity means that references drift back and forth and enact new realities also connected to the chain. In this setting future research may......This paper is about objects. It follows post ANT trajectories and finds that objects are multiple and fluid. Extant classic ANT inspired accounting research largely sees accounting inscriptions as immutable mobiles. Although multiplicity of objects upon which accounting acts has been explored...

  20. Evaluation of 604 Connect

    OpenAIRE

    Ladner, S.; Ihnat, M.

    2000-01-01

    The Vancouver Community Network (VCN) is a not-for-profit Internet Service Provider (ISP), based on the “freenet” model of public Internet access. As a VolNet delivery agency, VCN committed to providing participating organizations with the following: (1) A communications protocol, (2) Internet Access, (3) Computer Equipment, (4) Training, and (5) Technical Support. In April 1999, VCN began receiving applications from non-profit organizations for its 604 Connect program, so named for the 604 t...

  1. Tidying up international nucleotide sequence databases: ecological, geographical and sequence quality annotation of its sequences of mycorrhizal fungi.

    Science.gov (United States)

    Tedersoo, Leho; Abarenkov, Kessy; Nilsson, R Henrik; Schüssler, Arthur; Grelet, Gwen-Aëlle; Kohout, Petr; Oja, Jane; Bonito, Gregory M; Veldre, Vilmar; Jairus, Teele; Ryberg, Martin; Larsson, Karl-Henrik; Kõljalg, Urmas

    2011-01-01

    Sequence analysis of the ribosomal RNA operon, particularly the internal transcribed spacer (ITS) region, provides a powerful tool for identification of mycorrhizal fungi. The sequence data deposited in the International Nucleotide Sequence Databases (INSD) are, however, unfiltered for quality and are often poorly annotated with metadata. To detect chimeric and low-quality sequences and assign the ectomycorrhizal fungi to phylogenetic lineages, fungal ITS sequences were downloaded from INSD, aligned within family-level groups, and examined through phylogenetic analyses and BLAST searches. By combining the fungal sequence database UNITE and the annotation and search tool PlutoF, we also added metadata from the literature to these accessions. Altogether 35,632 sequences belonged to mycorrhizal fungi or originated from ericoid and orchid mycorrhizal roots. Of these sequences, 677 were considered chimeric and 2,174 of low read quality. Information detailing country of collection, geographical coordinates, interacting taxon and isolation source were supplemented to cover 78.0%, 33.0%, 41.7% and 96.4% of the sequences, respectively. These annotated sequences are publicly available via UNITE (http://unite.ut.ee/) for downstream biogeographic, ecological and taxonomic analyses. In European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena/), the annotated sequences have a special link-out to UNITE. We intend to expand the data annotation to additional genes and all taxonomic groups and functional guilds of fungi.

  2. Energy storage connection system

    Science.gov (United States)

    Benedict, Eric L.; Borland, Nicholas P.; Dale, Magdelena; Freeman, Belvin; Kite, Kim A.; Petter, Jeffrey K.; Taylor, Brendan F.

    2012-07-03

    A power system for connecting a variable voltage power source, such as a power controller, with a plurality of energy storage devices, at least two of which have a different initial voltage than the output voltage of the variable voltage power source. The power system includes a controller that increases the output voltage of the variable voltage power source. When such output voltage is substantially equal to the initial voltage of a first one of the energy storage devices, the controller sends a signal that causes a switch to connect the variable voltage power source with the first one of the energy storage devices. The controller then causes the output voltage of the variable voltage power source to continue increasing. When the output voltage is substantially equal to the initial voltage of a second one of the energy storage devices, the controller sends a signal that causes a switch to connect the variable voltage power source with the second one of the energy storage devices.

  3. Cutter Connectivity Bandwidth Study

    Science.gov (United States)

    2002-10-01

    The goal of this study was to determine how much bandwidth is required for cutters to meet emerging data transfer requirements. The Cutter Connectivity Business Solutions Team with guidance front the Commandant's 5 Innovation Council sponsored this study. Today, many Coast Guard administrative and business functions are being conducted via electronic means. Although our larger cutters can establish part-time connectivity using commercial satellite communications (SATCOM) while underway, there are numerous complaints regarding poor application performance. Additionally, smaller cutters do not have any standard means of underway connectivity. The R&D study shows the most important factor affecting web performance and enterprise applications onboard cutters was latency. Latency describes the time it takes the signal to reach the satellite and come back down through space. The latency due to use of higher orbit satellites is causing poor application performance and inefficient use of expensive SATCOM links. To improve performance, the CC must, (1) reduce latency by using alternate communications links such as low-earth orbit satellites, (2) tailor applications to the SATCOM link and/or (3) optimize protocols used for data communication to minimize time required by present applications to establish communications between the user and the host systems.

  4. A review of variables of urban street connectivity for spatial connection

    International Nuclear Information System (INIS)

    Mohamad, W S N W; Said, I

    2014-01-01

    Several studies on street connectivity in cities and towns have been modeled on topology, morphology, technology and psychology of people living in the urban environment. Street connectivity means the connection of streets that offers people alternative routes. However, there emerge difficulties to determine the suitable variables and analysis to be chosen in defining the accurate result for studies street connectivity. The aim of this paper is to identify variables of street connectivity by applying GIS and Space Syntax. This paper reviews the variables of street connectivity from 15 past articles done in 1990s to early 2000s from journals of nine disciplines on Environment and Behavior, Planning and Design, Computers, Environment and Urban Systems, Applied Earth Observation and Geo-information, Environment and Planning, Physica A: Statistical Mechanics and its Applications, Environmental Psychology, Social Science and Medicine and Building and Environment. From the review, there are four variables found for street connectivity: link (streets-streets, street-nodes or node-streets, nodes-nodes), accessibility, least-angle, and centrality. Space syntax and GIS are suitable tools to analyze the four variables relating to systematic street systems for pedestrians. This review implies that planners of the street systems, in the aspect of street connectivity in cities and towns, should consider these four variables

  5. A review of variables of urban street connectivity for spatial connection

    Science.gov (United States)

    Mohamad, W. S. N. W.; Said, I.

    2014-02-01

    Several studies on street connectivity in cities and towns have been modeled on topology, morphology, technology and psychology of people living in the urban environment. Street connectivity means the connection of streets that offers people alternative routes. However, there emerge difficulties to determine the suitable variables and analysis to be chosen in defining the accurate result for studies street connectivity. The aim of this paper is to identify variables of street connectivity by applying GIS and Space Syntax. This paper reviews the variables of street connectivity from 15 past articles done in 1990s to early 2000s from journals of nine disciplines on Environment and Behavior, Planning and Design, Computers, Environment and Urban Systems, Applied Earth Observation and Geo-information, Environment and Planning, Physica A: Statistical Mechanics and its Applications, Environmental Psychology, Social Science and Medicine and Building and Environment. From the review, there are four variables found for street connectivity: link (streets-streets, street-nodes or node-streets, nodes-nodes), accessibility, least-angle, and centrality. Space syntax and GIS are suitable tools to analyze the four variables relating to systematic street systems for pedestrians. This review implies that planners of the street systems, in the aspect of street connectivity in cities and towns, should consider these four variables.

  6. Genome Sequence Databases (Overview): Sequencing and Assembly

    Energy Technology Data Exchange (ETDEWEB)

    Lapidus, Alla L.

    2009-01-01

    From the date its role in heredity was discovered, DNA has been generating interest among scientists from different fields of knowledge: physicists have studied the three dimensional structure of the DNA molecule, biologists tried to decode the secrets of life hidden within these long molecules, and technologists invent and improve methods of DNA analysis. The analysis of the nucleotide sequence of DNA occupies a special place among the methods developed. Thanks to the variety of sequencing technologies available, the process of decoding the sequence of genomic DNA (or whole genome sequencing) has become robust and inexpensive. Meanwhile the assembly of whole genome sequences remains a challenging task. In addition to the need to assemble millions of DNA fragments of different length (from 35 bp (Solexa) to 800 bp (Sanger)), great interest in analysis of microbial communities (metagenomes) of different complexities raises new problems and pushes some new requirements for sequence assembly tools to the forefront. The genome assembly process can be divided into two steps: draft assembly and assembly improvement (finishing). Despite the fact that automatically performed assembly (or draft assembly) is capable of covering up to 98% of the genome, in most cases, it still contains incorrectly assembled reads. The error rate of the consensus sequence produced at this stage is about 1/2000 bp. A finished genome represents the genome assembly of much higher accuracy (with no gaps or incorrectly assembled areas) and quality ({approx}1 error/10,000 bp), validated through a number of computer and laboratory experiments.

  7. Internet services for planning embedded generation connections

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2005-12-15

    The required publication by distributed network operators (DNOs) of details of the current state of their network systems and future planned developments in the form of Long Term Development Statements (LTDS) are discussed. This project aims to increase the usefulness of the information in the LTDS by making it available on the internet, by transforming LTDSs into electronic format, and integrating LTDS information with geographical information in a single database. Services developed provide for data loading, data visualisation, initial assessment of connection opportunities, and reporting. The benefits of the services, and the demonstrated feasibility of publishing information concerning UK renewable generation sites are considered. The web address of the site is given.

  8. Astrophysicists' conversational connections on Twitter.

    Directory of Open Access Journals (Sweden)

    Kim Holmberg

    Full Text Available Because Twitter and other social media are increasingly used for analyses based on altmetrics, this research sought to understand what contexts, affordance use, and social activities influence the tweeting behavior of astrophysicists. Thus, the presented study has been guided by three research questions that consider the influence of astrophysicists' activities (i.e., publishing and tweeting frequency and of their tweet construction and affordance use (i.e. use of hashtags, language, and emotions on the conversational connections they have on Twitter. We found that astrophysicists communicate with a variety of user types (e.g. colleagues, science communicators, other researchers, and educators and that in the ego networks of the astrophysicists clear groups consisting of users with different professional roles can be distinguished. Interestingly, the analysis of noun phrases and hashtags showed that when the astrophysicists address the different groups of very different professional composition they use very similar terminology, but that they do not talk to each other (i.e. mentioning other user names in tweets. The results also showed that in those areas of the ego networks that tweeted more the sentiment of the tweets tended to be closer to neutral, connecting frequent tweeting with information sharing activities rather than conversations or expressing opinions.

  9. Empirical validation of directed functional connectivity.

    Science.gov (United States)

    Mill, Ravi D; Bagic, Anto; Bostan, Andreea; Schneider, Walter; Cole, Michael W

    2017-02-01

    Mapping directions of influence in the human brain connectome represents the next phase in understanding its functional architecture. However, a host of methodological uncertainties have impeded the application of directed connectivity methods, which have primarily been validated via "ground truth" connectivity patterns embedded in simulated functional MRI (fMRI) and magneto-/electro-encephalography (MEG/EEG) datasets. Such simulations rely on many generative assumptions, and we hence utilized a different strategy involving empirical data in which a ground truth directed connectivity pattern could be anticipated with confidence. Specifically, we exploited the established "sensory reactivation" effect in episodic memory, in which retrieval of sensory information reactivates regions involved in perceiving that sensory modality. Subjects performed a paired associate task in separate fMRI and MEG sessions, in which a ground truth reversal in directed connectivity between auditory and visual sensory regions was instantiated across task conditions. This directed connectivity reversal was successfully recovered across different algorithms, including Granger causality and Bayes network (IMAGES) approaches, and across fMRI ("raw" and deconvolved) and source-modeled MEG. These results extend simulation studies of directed connectivity, and offer practical guidelines for the use of such methods in clarifying causal mechanisms of neural processing. Copyright © 2016 Elsevier Inc. All rights reserved.

  10. Network structure shapes spontaneous functional connectivity dynamics.

    Science.gov (United States)

    Shen, Kelly; Hutchison, R Matthew; Bezgin, Gleb; Everling, Stefan; McIntosh, Anthony R

    2015-04-08

    The structural organization of the brain constrains the range of interactions between different regions and shapes ongoing information processing. Therefore, it is expected that large-scale dynamic functional connectivity (FC) patterns, a surrogate measure of coordination between brain regions, will be closely tied to the fiber pathways that form the underlying structural network. Here, we empirically examined the influence of network structure on FC dynamics by comparing resting-state FC (rsFC) obtained using BOLD-fMRI in macaques (Macaca fascicularis) to structural connectivity derived from macaque axonal tract tracing studies. Consistent with predictions from simulation studies, the correspondence between rsFC and structural connectivity increased as the sample duration increased. Regions with reciprocal structural connections showed the most stable rsFC across time. The data suggest that the transient nature of FC is in part dependent on direct underlying structural connections, but also that dynamic coordination can occur via polysynaptic pathways. Temporal stability was found to be dependent on structural topology, with functional connections within the rich-club core exhibiting the greatest stability over time. We discuss these findings in light of highly variable functional hubs. The results further elucidate how large-scale dynamic functional coordination exists within a fixed structural architecture. Copyright © 2015 the authors 0270-6474/15/355579-10$15.00/0.

  11. Process connectivity in a naturally prograding river delta

    Science.gov (United States)

    Sendrowski, Alicia; Passalacqua, Paola

    2017-03-01

    River deltas are lowland systems that can display high hydrological connectivity. This connectivity can be structural (morphological connections), functional (control of fluxes), and process connectivity (information flow from system drivers to sinks). In this work, we quantify hydrological process connectivity in Wax Lake Delta, coastal Louisiana, by analyzing couplings among external drivers (discharge, tides, and wind) and water levels recorded at five islands and one channel over summer 2014. We quantify process connections with information theory, a branch of mathematics concerned with the communication of information. We represent process connections as a network; variables serve as network nodes and couplings as network links describing the strength, direction, and time scale of information flow. Comparing process connections at long (105 days) and short (10 days) time scales, we show that tides exhibit daily synchronization with water level, with decreasing strength from downstream to upstream, and that tides transfer information as tides transition from spring to neap. Discharge synchronizes with water level and the time scale of its information transfer compares well to physical travel times through the system, computed with a hydrodynamic model. Information transfer and physical transport show similar spatial patterns, although information transfer time scales are larger than physical travel times. Wind events associated with water level setup lead to increased process connectivity with highly variable information transfer time scales. We discuss the information theory results in the context of the hydrologic behavior of the delta, the role of vegetation as a connector/disconnector on islands, and the applicability of process networks as tools for delta modeling results.

  12. CODAC systems arrangement and connectivity

    Energy Technology Data Exchange (ETDEWEB)

    Gulati, Hitesh Kumar, E-mail: hkgulati@gmail.com; Beltran, David; Kuehn, Ingo; Kotamaki, Miikka; Makijarvi, Petri; Wallander, Anders

    2013-10-15

    termination point for CODAC Network infrastructure. The CODAC Network cables running from the nearest CODAC Network hutch will terminate in these panels. Network panels are installed at strategic locations close to plant system I and C cubicles. This paper will describe more details about the physical arrangement of CODAC systems in different buildings on ITER platform for different purpose and their planned connectivity. This paper will also provide more information about the volume allocations for CODAC components, planned cabling arrangement and other infrastructure requirements like electrical and cooling etc.

  13. Facilitating NCAR Data Discovery by Connecting Related Resources

    Science.gov (United States)

    Rosati, A.

    2012-12-01

    Linking datasets, creators, and users by employing the proper standards helps to increase the impact of funded research. In order for users to find a dataset, it must first be named. Data citations play the important role of giving datasets a persistent presence by assigning a formal "name" and location. This project focuses on the next step of the "name-find-use" sequence: enhancing discoverability of NCAR data by connecting related resources on the web. By examining metadata schemas that document datasets, I examined how Semantic Web approaches can help to ensure the widest possible range of data users. The focus was to move from search engine optimization (SEO) to information connectivity. Two main markup types are very visible in the Semantic Web and applicable to scientific dataset discovery: The Open Archives Initiative-Object Reuse and Exchange (OAI-ORE - www.openarchives.org) and Microdata (HTML5 and www.schema.org). My project creates pilot aggregations of related resources using both markup types for three case studies: The North American Regional Climate Change Assessment Program (NARCCAP) dataset and related publications, the Palmer Drought Severity Index (PSDI) animation and image files from NCAR's Visualization Lab (VisLab), and the multidisciplinary data types and formats from the Advanced Cooperative Arctic Data and Information Service (ACADIS). This project documents the differences between these markups and how each creates connectedness on the web. My recommendations point toward the most efficient and effective markup schema for aggregating resources within the three case studies based on the following assessment criteria: ease of use, current state of support and adoption of technology, integration with typical web tools, available vocabularies and geoinformatic standards, interoperability with current repositories and access portals (e.g. ESG, Java), and relation to data citation tools and methods.

  14. Connecting cognition and consumer choice.

    Science.gov (United States)

    Bartels, Daniel M; Johnson, Eric J

    2015-02-01

    We describe what can be gained from connecting cognition and consumer choice by discussing two contexts ripe for interaction between the two fields. The first-context effects on choice-has already been addressed by cognitive science yielding insights about cognitive process but there is promise for more interaction. The second is learning and representation in choice where relevant theories in cognitive science could be informed by consumer choice, and in return, could pose and answer new questions. We conclude by discussing how these two fields of research stand to benefit from more interaction, citing examples of how interfaces of cognitive science with other fields have been illuminating for theories of cognition. Copyright © 2014 Elsevier B.V. All rights reserved.

  15. Long sequence correlation coprocessor

    Science.gov (United States)

    Gage, Douglas W.

    1994-09-01

    A long sequence correlation coprocessor (LSCC) accelerates the bitwise correlation of arbitrarily long digital sequences by calculating in parallel the correlation score for 16, for example, adjacent bit alignments between two binary sequences. The LSCC integrated circuit is incorporated into a computer system with memory storage buffers and a separate general purpose computer processor which serves as its controller. Each of the LSCC's set of sequential counters simultaneously tallies a separate correlation coefficient. During each LSCC clock cycle, computer enable logic associated with each counter compares one bit of a first sequence with one bit of a second sequence to increment the counter if the bits are the same. A shift register assures that the same bit of the first sequence is simultaneously compared to different bits of the second sequence to simultaneously calculate the correlation coefficient by the different counters to represent different alignments of the two sequences.

  16. Anomaly Detection in Sequences

    Data.gov (United States)

    National Aeronautics and Space Administration — We present a set of novel algorithms which we call sequenceMiner, that detect and characterize anomalies in large sets of high-dimensional symbol sequences that...

  17. DNA sequencing conference, 2

    Energy Technology Data Exchange (ETDEWEB)

    Cook-Deegan, R.M. [Georgetown Univ., Kennedy Inst. of Ethics, Washington, DC (United States); Venter, J.C. [National Inst. of Neurological Disorders and Strokes, Bethesda, MD (United States); Gilbert, W. [Harvard Univ., Cambridge, MA (United States); Mulligan, J. [Stanford Univ., CA (United States); Mansfield, B.K. [Oak Ridge National Lab., TN (United States)

    1991-06-19

    This conference focused on DNA sequencing, genetic linkage mapping, physical mapping, informatics and bioethics. Several were used to study this sequencing and mapping. This article also discusses computer hardware and software aiding in the mapping of genes.

  18. sequenceMiner algorithm

    Data.gov (United States)

    National Aeronautics and Space Administration — Detecting and describing anomalies in large repositories of discrete symbol sequences. sequenceMiner has been open-sourced! Download the file below to try it out....

  19. Finding significantly connected voxels based on histograms of connection strengths

    DEFF Research Database (Denmark)

    Kasenburg, Niklas; Pedersen, Morten Vester; Darkner, Sune

    2016-01-01

    We explore a new approach for structural connectivity based segmentations of subcortical brain regions. Connectivity based segmentations are usually based on fibre connections from a seed region to predefined target regions. We present a method for finding significantly connected voxels based...... on the distribution of connection strengths. Paths from seed voxels to all voxels in a target region are obtained from a shortest-path tractography. For each seed voxel we approximate the distribution with a histogram of path scores. We hypothesise that the majority of estimated connections are false-positives...... and that their connection strength is distributed differently from true-positive connections. Therefore, an empirical null-distribution is defined for each target region as the average normalized histogram over all voxels in the seed region. Single histograms are then tested against the corresponding null...

  20. Entropic fluctuations in DNA sequences

    Science.gov (United States)

    Thanos, Dimitrios; Li, Wentian; Provata, Astero

    2018-03-01

    The Local Shannon Entropy (LSE) in blocks is used as a complexity measure to study the information fluctuations along DNA sequences. The LSE of a DNA block maps the local base arrangement information to a single numerical value. It is shown that despite this reduction of information, LSE allows to extract meaningful information related to the detection of repetitive sequences in whole chromosomes and is useful in finding evolutionary differences between organisms. More specifically, large regions of tandem repeats, such as centromeres, can be detected based on their low LSE fluctuations along the chromosome. Furthermore, an empirical investigation of the appropriate block sizes is provided and the relationship of LSE properties with the structure of the underlying repetitive units is revealed by using both computational and mathematical methods. Sequence similarity between the genomic DNA of closely related species also leads to similar LSE values at the orthologous regions. As an application, the LSE covariance function is used to measure the evolutionary distance between several primate genomes.

  1. Estimating time-dependent connectivity in marine systems

    Science.gov (United States)

    Defne, Zafer; Ganju, Neil K.; Aretxabaleta, Alfredo

    2016-01-01

    Hydrodynamic connectivity describes the sources and destinations of water parcels within a domain over a given time. When combined with biological models, it can be a powerful concept to explain the patterns of constituent dispersal within marine ecosystems. However, providing connectivity metrics for a given domain is a three-dimensional problem: two dimensions in space to define the sources and destinations and a time dimension to evaluate connectivity at varying temporal scales. If the time scale of interest is not predefined, then a general approach is required to describe connectivity over different time scales. For this purpose, we have introduced the concept of a “retention clock” that highlights the change in connectivity through time. Using the example of connectivity between protected areas within Barnegat Bay, New Jersey, we show that a retention clock matrix is an informative tool for multitemporal analysis of connectivity.

  2. Multimodal MR-imaging reveals large-scale structural and functional connectivity changes in profound early blindness

    Science.gov (United States)

    Bauer, Corinna M.; Hirsch, Gabriella V.; Zajac, Lauren; Koo, Bang-Bon; Collignon, Olivier

    2017-01-01

    In the setting of profound ocular blindness, numerous lines of evidence demonstrate the existence of dramatic anatomical and functional changes within the brain. However, previous studies based on a variety of distinct measures have often provided inconsistent findings. To help reconcile this issue, we used a multimodal magnetic resonance (MR)-based imaging approach to provide complementary structural and functional information regarding this neuroplastic reorganization. This included gray matter structural morphometry, high angular resolution diffusion imaging (HARDI) of white matter connectivity and integrity, and resting state functional connectivity MRI (rsfcMRI) analysis. When comparing the brains of early blind individuals to sighted controls, we found evidence of co-occurring decreases in cortical volume and cortical thickness within visual processing areas of the occipital and temporal cortices respectively. Increases in cortical volume in the early blind were evident within regions of parietal cortex. Investigating white matter connections using HARDI revealed patterns of increased and decreased connectivity when comparing both groups. In the blind, increased white matter connectivity (indexed by increased fiber number) was predominantly left-lateralized, including between frontal and temporal areas implicated with language processing. Decreases in structural connectivity were evident involving frontal and somatosensory regions as well as between occipital and cingulate cortices. Differences in white matter integrity (as indexed by quantitative anisotropy, or QA) were also in general agreement with observed pattern changes in the number of white matter fibers. Analysis of resting state sequences showed evidence of both increased and decreased functional connectivity in the blind compared to sighted controls. Specifically, increased connectivity was evident between temporal and inferior frontal areas. Decreases in functional connectivity were observed

  3. Internet services for planning distributed generation connections

    Energy Technology Data Exchange (ETDEWEB)

    Curry, D.; Morgan, A.; Barbier, C.; Reay, P.

    2005-07-01

    The required publication by distributed network operators (DNOs) of details of the current state of their network systems and future planned developments in the form of Long Term Development Statements (LTDS) are discussed. This project aims to increase the usefulness of the information in the LTDS by making it available on the internet and by providing an initial assessment of connection opportunities and the possibility of viewing existing renewable generation projects. The services developed covered data loading, data visualisation, security, connection assessment, reporting, and generation site registration. The benefits of an electronic version of the LTDS are highlighted.

  4. The Berry's connection

    International Nuclear Information System (INIS)

    Le Tourneux, J.

    1989-01-01

    A course on the Berry's connection is presented. The main steps leading to the Berry's discovery are reviewed and the obtained equations are examined. Some applications of Berry's formulation are presented. They include diatomic molecules, dipole-quadrupole interaction in spherical mucleus and diabolic pair transfer. The experimental results presented are the spectrum of the Na 3 molecule, the propagation of photons in an helical optical fiber and the neutron spin rotation. Non-abelian problems and the Aharonow-Anandan phase are discussed [fr

  5. The CONNECT project

    DEFF Research Database (Denmark)

    Assaf, Yaniv; Alexander, Daniel C; Jones, Derek K

    2013-01-01

    Of Neuroimagers for the Non-invasive Exploration of brain Connectivity and Tracts) project aimed to combine tractography and micro-structural measures of the living human brain in order to obtain a better estimate of the connectome, while also striving to extend validation of these measurements. This paper...... summarizes the project and describes the perspective of using micro-structural measures to study the connectome.......In recent years, diffusion MRI has become an extremely important tool for studying the morphology of living brain tissue, as it provides unique insights into both its macrostructure and microstructure. Recent applications of diffusion MRI aimed to characterize the structural connectome using...

  6. Skeletal muscle connective tissue

    DEFF Research Database (Denmark)

    Brüggemann, Dagmar Adeline

    in the structure of fibrous collagen and myofibers at high-resolution. The results demonstrate that the collagen composition in the extra cellular matrix of Gadus morhua fish muscle is much more complex than previously anticipated, as it contains type III, IV, V  and VI collagen in addition to type I. The vascular....... Consequently, functional structures, ensuring "tissue maintenance" must form a major role of connective tissue, in addition that is to the force transmitting structures one typically finds in muscle. Vascular structures have also been shown to change their mechanical properties with age and it has been shown...

  7. Conformally connected universes

    International Nuclear Information System (INIS)

    Cantor, M.; Piran, T.

    1983-01-01

    A well-known difficulty associated with the conformal method for the solution of the general relativistic Hamiltonian constraint is the appearance of an aphysical ''bag of gold'' singularity at the nodal surface of the conformal factor. This happens whenever the background Ricci scalar is too large. Using a simple model, it is demonstrated that some of these singular solutions do have a physical meaning, and that these can be considered as initial data for Universe containing black holes, which are connected, in a conformally nonsingular way with each other. The relation between the ADM mass and the horizon area in this solution supports the cosmic censorship conjecture. (author)

  8. Methylphenidate Modulates Functional Network Connectivity to Enhance Attention

    OpenAIRE

    Rosenberg, Monica D.; Zhang, Sheng; Hsu, Wei-Ting; Scheinost, Dustin; Finn, Emily S.; Shen, Xilin; Constable, R. Todd; Li, Chiang-Shan R.; Chun, Marvin M.

    2016-01-01

    Recent work has demonstrated that human whole-brain functional connectivity patterns measured with fMRI contain information about cognitive abilities, including sustained attention. To derive behavioral predictions from connectivity patterns, our group developed a connectome-based predictive modeling (CPM) approach (Finn et al., 2015; Rosenberg et al., 2016). Previously using CPM, we defined a high-attention network, comprising connections positively correlated with performance on a sustained...

  9. Dynamic effective connectivity of inter-areal brain circuits.

    Directory of Open Access Journals (Sweden)

    Demian Battaglia

    Full Text Available Anatomic connections between brain areas affect information flow between neuronal circuits and the synchronization of neuronal activity. However, such structural connectivity does not coincide with effective connectivity (or, more precisely, causal connectivity, related to the elusive question "Which areas cause the present activity of which others?". Effective connectivity is directed and depends flexibly on contexts and tasks. Here we show that dynamic effective connectivity can emerge from transitions in the collective organization of coherent neural activity. Integrating simulation and semi-analytic approaches, we study mesoscale network motifs of interacting cortical areas, modeled as large random networks of spiking neurons or as simple rate units. Through a causal analysis of time-series of model neural activity, we show that different dynamical states generated by a same structural connectivity motif correspond to distinct effective connectivity motifs. Such effective motifs can display a dominant directionality, due to spontaneous symmetry breaking and effective entrainment between local brain rhythms, although all connections in the considered structural motifs are reciprocal. We show then that transitions between effective connectivity configurations (like, for instance, reversal in the direction of inter-areal interactions can be triggered reliably by brief perturbation inputs, properly timed with respect to an ongoing local oscillation, without the need for plastic synaptic changes. Finally, we analyze how the information encoded in spiking patterns of a local neuronal population is propagated across a fixed structural connectivity motif, demonstrating that changes in the active effective connectivity regulate both the efficiency and the directionality of information transfer. Previous studies stressed the role played by coherent oscillations in establishing efficient communication between distant areas. Going beyond these early

  10. Heritable Disorders of Connective Tissue

    Science.gov (United States)

    ... Home Health Topics English Español Heritable Disorders of Connective Tissue Basics In-Depth Download Download EPUB Download PDF ... they? Points To Remember About Heritable Disorders of Connective Tissue There are more than 200 heritable disorders that ...

  11. Crash sequence based risk matrix for motorcycle crashes.

    Science.gov (United States)

    Wu, Kun-Feng; Sasidharan, Lekshmi; Thor, Craig P; Chen, Sheng-Yin

    2018-04-05

    Considerable research has been conducted related to motorcycle and other powered-two-wheeler (PTW) crashes; however, it always has been controversial among practitioners concerning with types of crashes should be first targeted and how to prioritize resources for the implementation of mitigating actions. Therefore, there is a need to identify types of motorcycle crashes that constitute the greatest safety risk to riders - most frequent and most severe crashes. This pilot study seeks exhibit the efficacy of a new approach for prioritizing PTW crash causation sequences as they relate to injury severity to better inform the application of mitigating countermeasures. To accomplish this, the present study constructed a crash sequence-based risk matrix to identify most frequent and most severe motorcycle crashes in an attempt to better connect causes and countermeasures of PTW crashes. Although the frequency of each crash sequence can be computed from crash data, a crash severity model is needed to compare the levels of crash severity among different crash sequences, while controlling for other factors that also have effects on crash severity such drivers' age, use of helmet, etc. The construction of risk matrix based on crash sequences involve two tasks: formulation of crash sequence and the estimation of a mixed-effects (ME) model to adjust the levels of severities for each crash sequence to account for other crash contributing factors that would have an effect on the maximum level of crash severity in a crash. Three data elements from the National Automotive Sampling System - General Estimating System (NASS-GES) data were utilized to form a crash sequence: critical event, crash types, and sequence of events. A mixed-effects model was constructed to model the severity levels for each crash sequence while accounting for the effects of those crash contributing factors on crash severity. A total of 8039 crashes involving 8208 motorcycles occurred during 2011 and 2013 were

  12. The RNA world, automatic sequences and oncogenetics

    Energy Technology Data Exchange (ETDEWEB)

    Tahir Shah, K

    1993-04-01

    We construct a model of the RNA world in terms of naturally evolving nucleotide sequences assuming only Crick-Watson base pairing and self-cleaving/splicing capability. These sequences have the following properties. (1) They are recognizable by an automation (or automata). That is, to each k-sequence, there exist a k-automation which accepts, recognizes or generates the k-sequence. These are known as automatic sequences. Fibonacci and Morse-Thue sequences are the most natural outcome of pre-biotic chemical conditions. (2) Infinite (resp. large) sequences are self-similar (resp. nearly self-similar) under certain rewrite rules and consequently give rise to fractal (resp.fractal-like) structures. Computationally, such sequences can also be generated by their corresponding deterministic parallel re-write system, known as a DOL system. The self-similar sequences are fixed points of their respective rewrite rules. Some of these automatic sequences have the capability that they can read or ``accept`` other sequences while others can detect errors and trigger error-correcting mechanisms. They can be enlarged and have block and/or palindrome structure. Linear recurring sequences such as Fibonacci sequence are simply Feed-back Shift Registers, a well know model of information processing machines. We show that a mutation of any rewrite rule can cause a combinatorial explosion of error and relates this to oncogenetical behavior. On the other hand, a mutation of sequences that are not rewrite rules, leads to normal evolutionary change. Known experimental results support our hypothesis. (author). Refs.

  13. The RNA world, automatic sequences and oncogenetics

    International Nuclear Information System (INIS)

    Tahir Shah, K.

    1993-04-01

    We construct a model of the RNA world in terms of naturally evolving nucleotide sequences assuming only Crick-Watson base pairing and self-cleaving/splicing capability. These sequences have the following properties. 1) They are recognizable by an automation (or automata). That is, to each k-sequence, there exist a k-automation which accepts, recognizes or generates the k-sequence. These are known as automatic sequences. Fibonacci and Morse-Thue sequences are the most natural outcome of pre-biotic chemical conditions. 2) Infinite (resp. large) sequences are self-similar (resp. nearly self-similar) under certain rewrite rules and consequently give rise to fractal (resp.fractal-like) structures. Computationally, such sequences can also be generated by their corresponding deterministic parallel re-write system, known as a DOL system. The self-similar sequences are fixed points of their respective rewrite rules. Some of these automatic sequences have the capability that they can read or 'accept' other sequences while others can detect errors and trigger error-correcting mechanisms. They can be enlarged and have block and/or palindrome structure. Linear recurring sequences such as Fibonacci sequence are simply Feed-back Shift Registers, a well know model of information processing machines. We show that a mutation of any rewrite rule can cause a combinatorial explosion of error and relates this to oncogenetical behavior. On the other hand, a mutation of sequences that are not rewrite rules, leads to normal evolutionary change. Known experimental results support our hypothesis. (author). Refs

  14. LHCb connects its pipes

    CERN Multimedia

    2006-01-01

    Two weeks ago the first beryllium section of the LHCb beam vacuum chamber was installed. This three-day operation, after requiring lengthy preparation work, demanded patience and precision as the first of four sections of the beampipe was connected to the vertex locator (VeLo) vacuum vessel. The AT-VAC Group with the collaboration of PH/LBD, including Gloria Corti, Tatsuya Nakada, Patrice Mermet, Delios Ramos, Frans Mul, Bruno Versollato, Bernard Corajod, and Raymond Veness. (Not pictured: Adriana Rossi and Laurent Bouvet) This first installed section is composed of a nearly two-metre long conical tube of one-millimetre thick beryllium and of a thin spherical-shaped window, 800 millimeter diameter, made of an aluminum alloy, and has the appearance of a mushroom lying on its side. The window is connected to the conical part of the beampipe through an aluminum alloy bellow, which is needed to allow for mechanical alignment once the assembly is installed. Beryllium was chosen as the material for 12 m of the 19...

  15. Connective tissue activation. XVII

    International Nuclear Information System (INIS)

    Weiss, J.J.; Donakowski, C.; Anderson, B.; Meyers, S.; Castor, C.W.

    1980-01-01

    The platelet-derived connective tissue activating peptide (CTAP-III) has been shown to be an important factor stimulating the metabolism and proliferation of human connective tissue cell strains, including synovial tissue cells. The quantities of CTAP-III affecting the cellular changes and the amounts in various biologic fluids and tissues are small. The objectives of this study were to develop a radioimmunoassay (RIA) for CTAP-III and to ascertain the specificities of the anti-CTAP-III sera reagents. The antisera were shown not to cross-react with a number of polypeptide hormones. However, two other platelet proteins β-thromboglobulin and low affinity platelet factor-4, competed equally as well as CTAP-III for anti-CTAP-III antibodies in the RIA system. Thus, the three platelet proteins are similar or identical with respect to those portions of the molecules constituting the reactive antigenic determinants. The levels of material in normal human platelet-free plasma that inhibited anti-CTAP-III- 125 I-CTAP-III complex formation were determined to be 34+-13 (S.D.) ng/ml. (Auth.)

  16. Nucleotide sequence preservation of human mitochondrial DNA

    International Nuclear Information System (INIS)

    Monnat, R.J. Jr.; Loeb, L.A.

    1985-01-01

    Recombinant DNA techniques have been used to quantitate the amount of nucleotide sequence divergence in the mitochondrial DNA population of individual normal humans. Mitochondrial DNA was isolated from the peripheral blood lymphocytes of five normal humans and cloned in M13 mp11; 49 kilobases of nucleotide sequence information was obtained from 248 independently isolated clones from the five normal donors. Both between- and within-individual differences were identified. Between-individual differences were identified in approximately = to 1/200 nucleotides. In contrast, only one within-individual difference was identified in 49 kilobases of nucleotide sequence information. This high degree of mitochondrial nucleotide sequence homogeneity in human somatic cells is in marked contrast to the rapid evolutionary divergence of human mitochondrial DNA and suggests the existence of mechanisms for the concerted preservation of mammalian mitochondrial DNA sequences in single organisms

  17. Mobile medical device connectivity: real world solutions.

    Science.gov (United States)

    Pettus, Dan

    2004-01-01

    Mobile medical devices, such as infusion pumps, provide an important therapeutic function. They are also valuable sources of information about treatment patterns at the point of care. However, these mobile devices have been independent islands of valuable information, unable to share the data they gather with other hospital information resources on a real time basis. Although data from these devices can provide significant improvements for medical safety and vital information needed for clinical best practice development, gathering that data poses significant challenges when interfacing with hospital information systems. Mobile medical devices move from place to place as independent actors, raising a series of security and identification issues when they need to be disconnected and reconnected using traditional tethered cable connections. The continuing lack of accepted communications protocol standards, in spite of the concentrated efforts of organizations like the IEEE and the Medical Information Bus (IEEE 1073) to establish them, has made integration into the hospital information system a complex and non-standard task. The rapid spread in availability and adoption of high-speed 802.11 wireless systems in hospitals offers a realistic connectivity solution for mobile medical devices. Inspite of this, the 802.11 standard is still evolving, and current security methods designed for user-based products like PDAs and laptop computers are not ideal for unmanned mobile medical devices because they assume the availability of a human operator to authenticate a wireless session. In the absence of accepted standards, manufacturers have created practical and innovative solutions to support the collection of clinical data from mobile medical devices and the integration of that data with hospital information systems. This paper will explore the potential benefits of integrating mobile medical devices into the hospital information system, and describe the challenges in

  18. Connectivity-oriented urban projects

    NARCIS (Netherlands)

    Philibert Petit, E.

    2006-01-01

    This thesis is about connections in the built environment, networked connections for the mobility of people at the smallest scale of the urban realm: the pedestrian scale. It deals with applications of the new science of networks as a tool for observation and assessment of connectivity in the urban

  19. Airport industry connectivity report: 2015

    NARCIS (Netherlands)

    Boonekamp, T.; Lieshout, R.; Burghouwt, G.

    2015-01-01

    This report is an update of the 'Airport Industry Connectivity Report 2004-2014'. It's focused on more recent developments and charting how Europe’s connectivity has evolved over the past 12 months. Airport connectivity is an increasingly discussed topic in European policy circles. With good reason.

  20. Folk Taxonomies. Connected Classroom

    Science.gov (United States)

    Bull, Glen

    2005-01-01

    Early in the 1990s, Tim Berners-Lee had a powerful idea--the concept of the World Wide Web. The success of this vision produced an unparalleled explosion of information, which in turn resulted in a parallel problem--how to locate the right piece of information. A 2005 study by Hanson and Carlson, published by the Educational Development Center,…

  1. Deforestation and rainfall recycling in Brazil: Is decreased forest cover connectivity associated with decreased rainfall connectivity?

    Science.gov (United States)

    Adera, S.; Larsen, L.; Levy, M. C.; Thompson, S. E.

    2017-12-01

    In the Brazilian rainforest-savanna transition zone, deforestation has the potential to significantly affect rainfall by disrupting rainfall recycling, the process by which regional evapotranspiration contributes to regional rainfall. Understanding rainfall recycling in this region is important not only for sustaining Amazon and Cerrado ecosystems, but also for cattle ranching, agriculture, hydropower generation, and drinking water management. Simulations in previous studies suggest complex, scale-dependent interactions between forest cover connectivity and rainfall. For example, the size and distribution of deforested patches has been found to affect rainfall quantity and spatial distribution. Here we take an empirical approach, using the spatial connectivity of rainfall as an indicator of rainfall recycling, to ask: as forest cover connectivity decreased from 1981 - 2015, how did the spatial connectivity of rainfall change in the Brazilian rainforest-savanna transition zone? We use satellite forest cover and rainfall data covering this period of intensive forest cover loss in the region (forest cover from the Hansen Global Forest Change dataset; rainfall from the Climate Hazards Infrared Precipitation with Stations dataset). Rainfall spatial connectivity is quantified using transfer entropy, a metric from information theory, and summarized using network statistics. Networks of connectivity are quantified for paired deforested and non-deforested regions before deforestation (1981-1995) and during/after deforestation (2001-2015). Analyses reveal a decline in spatial connectivity networks of rainfall following deforestation.

  2. Targeted assembly of short sequence reads.

    Directory of Open Access Journals (Sweden)

    René L Warren

    Full Text Available As next-generation sequence (NGS production continues to increase, analysis is becoming a significant bottleneck. However, in situations where information is required only for specific sequence variants, it is not necessary to assemble or align whole genome data sets in their entirety. Rather, NGS data sets can be mined for the presence of sequence variants of interest by localized assembly, which is a faster, easier, and more accurate approach. We present TASR, a streamlined assembler that interrogates very large NGS data sets for the presence of specific variants by only considering reads within the sequence space of input target sequences provided by the user. The NGS data set is searched for reads with an exact match to all possible short words within the target sequence, and these reads are then assembled stringently to generate a consensus of the target and flanking sequence. Typically, variants of a particular locus are provided as different target sequences, and the presence of the variant in the data set being interrogated is revealed by a successful assembly outcome. However, TASR can also be used to find unknown sequences that flank a given target. We demonstrate that TASR has utility in finding or confirming genomic mutations, polymorphisms, fusions and integration events. Targeted assembly is a powerful method for interrogating large data sets for the presence of sequence variants of interest. TASR is a fast, flexible and easy to use tool for targeted assembly.

  3. Diffusion tensor image registration using hybrid connectivity and tensor features.

    Science.gov (United States)

    Wang, Qian; Yap, Pew-Thian; Wu, Guorong; Shen, Dinggang

    2014-07-01

    Most existing diffusion tensor imaging (DTI) registration methods estimate structural correspondences based on voxelwise matching of tensors. The rich connectivity information that is given by DTI, however, is often neglected. In this article, we propose to integrate complementary information given by connectivity features and tensor features for improved registration accuracy. To utilize connectivity information, we place multiple anchors representing different brain anatomies in the image space, and define the connectivity features for each voxel as the geodesic distances from all anchors to the voxel under consideration. The geodesic distance, which is computed in relation to the tensor field, encapsulates information of brain connectivity. We also extract tensor features for every voxel to reflect the local statistics of tensors in its neighborhood. We then combine both connectivity features and tensor features for registration of tensor images. From the images, landmarks are selected automatically and their correspondences are determined based on their connectivity and tensor feature vectors. The deformation field that deforms one tensor image to the other is iteratively estimated and optimized according to the landmarks and their associated correspondences. Experimental results show that, by using connectivity features and tensor features simultaneously, registration accuracy is increased substantially compared with the cases using either type of features alone. Copyright © 2013 Wiley Periodicals, Inc.

  4. Performance assessment on high strength steel endplate connections after fire

    NARCIS (Netherlands)

    Qiang, X.; Wu, N.; Jiang, X.; Bijlaard, F.S.K.; Kolstein, M.H.

    2017-01-01

    Purpose – This study aims to reveal more information and understanding on performance and failure mechanisms of high strength steel endplate connections after fire. Design/methodology/approach – An experimental and numerical study on seven endplate connections after

  5. Developing Information Systems for Competitive Intelligence Support.

    Science.gov (United States)

    Hohhof, Bonnie

    1994-01-01

    Discusses issues connected with developing information systems for competitive intelligence support; defines the elements of an effective competitive information system; and summarizes issues affecting system design and implementation. Highlights include intelligence information; information needs; information sources; decision making; and…

  6. Connectivity Measures in EEG Microstructural Sleep Elements.

    Science.gov (United States)

    Sakellariou, Dimitris; Koupparis, Andreas M; Kokkinos, Vasileios; Koutroumanidis, Michalis; Kostopoulos, George K

    2016-01-01

    During Non-Rapid Eye Movement sleep (NREM) the brain is relatively disconnected from the environment, while connectedness between brain areas is also decreased. Evidence indicates, that these dynamic connectivity changes are delivered by microstructural elements of sleep: short periods of environmental stimuli evaluation followed by sleep promoting procedures. The connectivity patterns of the latter, among other aspects of sleep microstructure, are still to be fully elucidated. We suggest here a methodology for the assessment and investigation of the connectivity patterns of EEG microstructural elements, such as sleep spindles. The methodology combines techniques in the preprocessing, estimation, error assessing and visualization of results levels in order to allow the detailed examination of the connectivity aspects (levels and directionality of information flow) over frequency and time with notable resolution, while dealing with the volume conduction and EEG reference assessment. The high temporal and frequency resolution of the methodology will allow the association between the microelements and the dynamically forming networks that characterize them, and consequently possibly reveal aspects of the EEG microstructure. The proposed methodology is initially tested on artificially generated signals for proof of concept and subsequently applied to real EEG recordings via a custom built MATLAB-based tool developed for such studies. Preliminary results from 843 fast sleep spindles recorded in whole night sleep of 5 healthy volunteers indicate a prevailing pattern of interactions between centroparietal and frontal regions. We demonstrate hereby, an opening to our knowledge attempt to estimate the scalp EEG connectivity that characterizes fast sleep spindles via an "EEG-element connectivity" methodology we propose. The application of the latter, via a computational tool we developed suggests it is able to investigate the connectivity patterns related to the occurrence

  7. Genetic composition and connectivity of the Antillean manatee (Trichechus manatus manatus) in Panama

    Science.gov (United States)

    Díaz-Ferguson, Edgardo; Hunter, Margaret; Guzmán, Héctor M.

    2017-01-01

    Genetic diversity and haplotype composition of the West Indian manatee (Trichechus manatus) population from the San San Pond Sak wetland in Bocas del Toro, Panama was studied using a segment of mitochondrial DNA (D’loop). No genetic information has been published to date for Panamanian populations. Due to the secretive behavior and small population size of the species in the area, DNA extraction was conducted from opportunistically collected fecal (N=20), carcass tissue (N=4) and bone (N=4) samples. However, after DNA processing only 10 samples provided good quality DNA for sequencing (3 fecal, 4 tissue and 3 bone samples). We found three haplotypes in total; two of these haplotypes are reported for the first time, J02 (N=3) and J03 (N=4), and one J01 was previously published (N=3). Genetic diversity showed similar values to previous studies conducted in other Caribbean regions with moderate values of nucleotide diversity (π= 0.00152) and haplotipic diversity (Hd= 0.57). Connectivity assessment was based on sequence similarity, genetic distance and genetic differentiation between San San population and other manatee populations previously studied. The J01 haplotype found in the Panamanian population is shared with populations in the Caribbean mainland and the Gulf of Mexico showing a reduced differentiation corroborated with Fst value between HSSPS and this region of 0.0094. In contrast, comparisons between our sequences and populations in the Eastern Caribbean (South American populations) and North Western Caribbean showed fewer similarities (Fst =0.049 and 0.058, respectively). These results corroborate previous phylogeographic patterns already established for manatee populations and situate Panamanian populations into the Belize and Mexico cluster. In addition, these findings will be a baseline for future studies and comparisons with manatees in other areas of Panama and Central America. These results should be considered to inform management decisions

  8. Data selector group sequencer interface

    International Nuclear Information System (INIS)

    Zizka, G.; Turko, B.

    1984-01-01

    A CAMAC-based module for high rate data selection and transfer to Tracor Northern TN-1700 multichannel analysis system is described. The module can select any group of 4096 consecutive addresses of events, in the range of 24 bits. This module solves the problem of connecting a number of time digitizing systems to the memory of a multichannel analyzer. Continuous processing rate up to 200,000 events per second along with the live display make the testing of the above systems very efficient and relatively inexpensive. The module also can be programmed for storing the preset group of addresses into more than one section of the memory. The events are analyzed in each section of the memory during the preset time. Multiple spectra can thus be taken automatically in a sequence

  9. More features, greater connectivity.

    Science.gov (United States)

    Hunt, Sarah

    2015-09-01

    Changes in our political infrastructure, the continuing frailties of our economy, and a stark growth in population, have greatly impacted upon the perceived stability of the NHS. Healthcare teams have had to adapt to these changes, and so too have the technologies upon which they rely to deliver first-class patient care. Here Sarah Hunt, marketing co-ordinator at Aid Call, assesses how the changing healthcare environment has affected one of its fundamental technologies - the nurse call system, argues the case for wireless such systems in terms of what the company claims is greater adaptability to changing needs, and considers the ever-wider range of features and functions available from today's nurse call equipment, particularly via connectivity with both mobile devices, and ancillaries ranging from enuresis sensors to staff attack alert 'badges'.

  10. Practicing (Dis)connections

    DEFF Research Database (Denmark)

    The paper addresses the reciprocal notions of mobility and mobilisation in medical imaging practice, in view of the contingent and multiple character of the knowledge-practices involving such images – and their interpretation – within and across situated settings. Based on an ethnographically......’s development of in-house examination protocols as a consequence of its having replaced an older, pre-existing MRI scanner with a new model. This re-domestication of MRI as occasioned by the replacement scanner offers a range of sociomaterial and sociotechnical contingencies in the practice to come to light...... of the epistemic underpinnings which render, and condition, how connections are mediated across extended settings of practice (in the MRI unit, at interdisciplinary case conferences, and at other hospitals, etc.). This relational view allows for the heterogeneity entailed in the domestication of the MRI scanner...

  11. Conservation patterns of HIV-1 RT connection and RNase H domains: identification of new mutations in NRTI-treated patients.

    Directory of Open Access Journals (Sweden)

    André F A Santos

    Full Text Available BACKGROUND: Although extensive HIV drug resistance information is available for the first 400 amino acids of its reverse transcriptase, the impact of antiretroviral treatment in C-terminal domains of Pol (thumb, connection and RNase H is poorly understood. METHODS AND FINDINGS: We wanted to characterize conserved regions in RT C-terminal domains among HIV-1 group M subtypes and CRF. Additionally, we wished to identify NRTI-related mutations in HIV-1 RT C-terminal domains. We sequenced 118 RNase H domains from clinical viral isolates in Brazil, and analyzed 510 thumb and connection domain and 450 RNase H domain sequences collected from public HIV sequence databases, together with their treatment status and histories. Drug-naïve and NRTI-treated datasets were compared for intra- and inter-group conservation, and differences were determined using Fisher's exact tests. One third of RT C-terminal residues were found to be conserved among group M variants. Three mutations were found exclusively in NRTI-treated isolates. Nine mutations in the connection and 6 mutations in the RNase H were associated with NRTI treatment in subtype B. Some of them lay in or close to amino acid residues which contact nucleic acid or near the RNase H active site. Several of the residues pointed out herein have been recently associated to NRTI exposure or increase drug resistance to NRTI. CONCLUSIONS: This is the first comprehensive genotypic analysis of a large sequence dataset that describes NRTI-related mutations in HIV-1 RT C-terminal domains in vivo. The findings into the conservation of RT C-terminal domains may pave the way to more rational drug design initiatives targeting those regions.

  12. Capacity for patterns and sequences in Kanerva's SDM as compared to other associative memory models. [Sparse, Distributed Memory

    Science.gov (United States)

    Keeler, James D.

    1988-01-01

    The information capacity of Kanerva's Sparse Distributed Memory (SDM) and Hopfield-type neural networks is investigated. Under the approximations used here, it is shown that the total information stored in these systems is proportional to the number connections in the network. The proportionality constant is the same for the SDM and Hopfield-type models independent of the particular model, or the order of the model. The approximations are checked numerically. This same analysis can be used to show that the SDM can store sequences of spatiotemporal patterns, and the addition of time-delayed connections allows the retrieval of context dependent temporal patterns. A minor modification of the SDM can be used to store correlated patterns.

  13. Evaluating and Redesigning Teaching Learning Sequences at the Introductory Physics Level

    Science.gov (United States)

    Guisasola, Jenaro; Zuza, Kristina; Ametller, Jaume; Gutierrez-Berraondo, José

    2017-01-01

    In this paper we put forward a proposal for the design and evaluation of teaching and learning sequences in upper secondary school and university. We will connect our proposal with relevant contributions on the design of teaching sequences, ground it on the design-based research methodology, and discuss how teaching and learning sequences designed…

  14. Long period pseudo random number sequence generator

    Science.gov (United States)

    Wang, Charles C. (Inventor)

    1989-01-01

    A circuit for generating a sequence of pseudo random numbers, (A sub K). There is an exponentiator in GF(2 sup m) for the normal basis representation of elements in a finite field GF(2 sup m) each represented by m binary digits and having two inputs and an output from which the sequence (A sub K). Of pseudo random numbers is taken. One of the two inputs is connected to receive the outputs (E sub K) of maximal length shift register of n stages. There is a switch having a pair of inputs and an output. The switch outputs is connected to the other of the two inputs of the exponentiator. One of the switch inputs is connected for initially receiving a primitive element (A sub O) in GF(2 sup m). Finally, there is a delay circuit having an input and an output. The delay circuit output is connected to the other of the switch inputs and the delay circuit input is connected to the output of the exponentiator. Whereby after the exponentiator initially receives the primitive element (A sub O) in GF(2 sup m) through the switch, the switch can be switched to cause the exponentiator to receive as its input a delayed output A(K-1) from the exponentiator thereby generating (A sub K) continuously at the output of the exponentiator. The exponentiator in GF(2 sup m) is novel and comprises a cyclic-shift circuit; a Massey-Omura multiplier; and, a control logic circuit all operably connected together to perform the function U(sub i) = 92(sup i) (for n(sub i) = 1 or 1 (for n(subi) = 0).

  15. Haberin Geleceği: Gazetelerle İlgili Bilgi Hizmetlerinin Yapılanması ve Kullanımı / The Future of News: Building and Using Information Services in Connection with Newspapers

    Directory of Open Access Journals (Sweden)

    H. İnci Önal

    2007-04-01

    Full Text Available The purpose of the present research is to specify the current stand and future of information services in providing news. Libraries and archives that collect newspapers, and supply services to let the readers to have quick and easy access to their contents, increase their activities and in conjunction to this, their experience. As an initial step of the present research, by methods of interviewing and administering questionnaires, Ankara branch office responsible of six nationwide distributed daily newspapers were investigated. Data were compiled about the present situation, provided services, problems to be confronted, and work plans. According to the evaluations, it seems that the developments in information technologies would also impose important tasks to librariesin case of disseminating newspaper information.

  16. Protecting genomic sequence anonymity with generalization lattices.

    Science.gov (United States)

    Malin, B A

    2005-01-01

    Current genomic privacy technologies assume the identity of genomic sequence data is protected if personal information, such as demographics, are obscured, removed, or encrypted. While demographic features can directly compromise an individual's identity, recent research demonstrates such protections are insufficient because sequence data itself is susceptible to re-identification. To counteract this problem, we introduce an algorithm for anonymizing a collection of person-specific DNA sequences. The technique is termed DNA lattice anonymization (DNALA), and is based upon the formal privacy protection schema of k -anonymity. Under this model, it is impossible to observe or learn features that distinguish one genetic sequence from k-1 other entries in a collection. To maximize information retained in protected sequences, we incorporate a concept generalization lattice to learn the distance between two residues in a single nucleotide region. The lattice provides the most similar generalized concept for two residues (e.g. adenine and guanine are both purines). The method is tested and evaluated with several publicly available human population datasets ranging in size from 30 to 400 sequences. Our findings imply the anonymization schema is feasible for the protection of sequences privacy. The DNALA method is the first computational disclosure control technique for general DNA sequences. Given the computational nature of the method, guarantees of anonymity can be formally proven. There is room for improvement and validation, though this research provides the groundwork from which future researchers can construct genomics anonymization schemas tailored to specific datasharing scenarios.

  17. 78 FR 50134 - Altus Pharmaceuticals, Inc., Blackhawk Capital Group BDC, Inc., Cargo Connection Logistics...

    Science.gov (United States)

    2013-08-16

    ... SECURITIES AND EXCHANGE COMMISSION [File No. 500-1] Altus Pharmaceuticals, Inc., Blackhawk Capital Group BDC, Inc., Cargo Connection Logistics Holding, Inc., Diapulse Corporation of America, Globus... lack of current and accurate information concerning the securities of Cargo Connection Logistics...

  18. Exploration of noncoding sequences in metagenomes.

    Directory of Open Access Journals (Sweden)

    Fabián Tobar-Tosse

    Full Text Available Environment-dependent genomic features have been defined for different metagenomes, whose genes and their associated processes are related to specific environments. Identification of ORFs and their functional categories are the most common methods for association between functional and environmental features. However, this analysis based on finding ORFs misses noncoding sequences and, therefore, some metagenome regulatory or structural information could be discarded. In this work we analyzed 23 whole metagenomes, including coding and noncoding sequences using the following sequence patterns: (G+C content, Codon Usage (Cd, Trinucleotide Usage (Tn, and functional assignments for ORF prediction. Herein, we present evidence of a high proportion of noncoding sequences discarded in common similarity-based methods in metagenomics, and the kind of relevant information present in those. We found a high density of trinucleotide repeat sequences (TRS in noncoding sequences, with a regulatory and adaptive function for metagenome communities. We present associations between trinucleotide values and gene function, where metagenome clustering correlate with microorganism adaptations and kinds of metagenomes. We propose here that noncoding sequences have relevant information to describe metagenomes that could be considered in a whole metagenome analysis in order to improve their organization, classification protocols, and their relation with the environment.

  19. A neurocomputational model of automatic sequence production.

    Science.gov (United States)

    Helie, Sebastien; Roeder, Jessica L; Vucovich, Lauren; Rünger, Dennis; Ashby, F Gregory

    2015-07-01

    Most behaviors unfold in time and include a sequence of submovements or cognitive activities. In addition, most behaviors are automatic and repeated daily throughout life. Yet, relatively little is known about the neurobiology of automatic sequence production. Past research suggests a gradual transfer from the associative striatum to the sensorimotor striatum, but a number of more recent studies challenge this role of the BG in automatic sequence production. In this article, we propose a new neurocomputational model of automatic sequence production in which the main role of the BG is to train cortical-cortical connections within the premotor areas that are responsible for automatic sequence production. The new model is used to simulate four different data sets from human and nonhuman animals, including (1) behavioral data (e.g., RTs), (2) electrophysiology data (e.g., single-neuron recordings), (3) macrostructure data (e.g., TMS), and (4) neurological circuit data (e.g., inactivation studies). We conclude with a comparison of the new model with existing models of automatic sequence production and discuss a possible new role for the BG in automaticity and its implication for Parkinson's disease.

  20. Multimodal Hyper-connectivity Networks for MCI Classification.

    Science.gov (United States)

    Li, Yang; Gao, Xinqiang; Jie, Biao; Yap, Pew-Thian; Kim, Min-Jeong; Wee, Chong-Yaw; Shen, Dinggang

    2017-09-01

    Hyper-connectivity network is a network where every edge is connected to more than two nodes, and can be naturally denoted using a hyper-graph. Hyper-connectivity brain network, either based on structural or functional interactions among the brain regions, has been used for brain disease diagnosis. However, the conventional hyper-connectivity network is constructed solely based on single modality data, ignoring potential complementary information conveyed by other modalities. The integration of complementary information from multiple modalities has been shown to provide a more comprehensive representation about the brain disruptions. In this paper, a novel multimodal hyper-network modelling method was proposed for improving the diagnostic accuracy of mild cognitive impairment (MCI). Specifically, we first constructed a multimodal hyper-connectivity network by simultaneously considering information from diffusion tensor imaging and resting-state functional magnetic resonance imaging data. We then extracted different types of network features from the hyper-connectivity network, and further exploited a manifold regularized multi-task feature selection method to jointly select the most discriminative features. Our proposed multimodal hyper-connectivity network demonstrated a better MCI classification performance than the conventional single modality based hyper-connectivity networks.

  1. Connecting Network Properties of Rapidly Disseminating Epizoonotics

    Science.gov (United States)

    Rivas, Ariel L.; Fasina, Folorunso O.; Hoogesteyn, Almira L.; Konah, Steven N.; Febles, José L.; Perkins, Douglas J.; Hyman, James M.; Fair, Jeanne M.; Hittner, James B.; Smith, Steven D.

    2012-01-01

    classes of cases, nodes, and networks, generating information usable to revise theory and optimize control measures. Prospective studies that consider pre-outbreak predictors, such as connecting networks, are recommended. PMID:22761900

  2. Genomic sequencing of Pleistocene cave bears

    Energy Technology Data Exchange (ETDEWEB)

    Noonan, James P.; Hofreiter, Michael; Smith, Doug; Priest, JamesR.; Rohland, Nadin; Rabeder, Gernot; Krause, Johannes; Detter, J. Chris; Paabo, Svante; Rubin, Edward M.

    2005-04-01

    Despite the information content of genomic DNA, ancient DNA studies to date have largely been limited to amplification of mitochondrial DNA due to technical hurdles such as contamination and degradation of ancient DNAs. In this study, we describe two metagenomic libraries constructed using unamplified DNA extracted from the bones of two 40,000-year-old extinct cave bears. Analysis of {approx}1 Mb of sequence from each library showed that, despite significant microbial contamination, 5.8 percent and 1.1 percent of clones in the libraries contain cave bear inserts, yielding 26,861 bp of cave bear genome sequence. Alignment of this sequence to the dog genome, the closest sequenced genome to cave bear in terms of evolutionary distance, revealed roughly the expected ratio of cave bear exons, repeats and conserved noncoding sequences. Only 0.04 percent of all clones sequenced were derived from contamination with modern human DNA. Comparison of cave bear with orthologous sequences from several modern bear species revealed the evolutionary relationship of these lineages. Using the metagenomic approach described here, we have recovered substantial quantities of mammalian genomic sequence more than twice as old as any previously reported, establishing the feasibility of ancient DNA genomic sequencing programs.

  3. Design of Tail-Clamp Peptide Nucleic Acid Tethered with Azobenzene Linker for Sequence-Specific Detection of Homopurine DNA

    Directory of Open Access Journals (Sweden)

    Shinjiro Sawada

    2017-10-01

    Full Text Available DNA carries genetic information in its sequence of bases. Synthetic oligonucleotides that can sequence-specifically recognize a target gene sequence are a useful tool for regulating gene expression or detecting target genes. Among the many synthetic oligonucleotides, tail-clamp peptide nucleic acid (TC-PNA offers advantages since it has two homopyrimidine PNA strands connected via a flexible ethylene glycol-type linker that can recognize complementary homopurine sequences via Watson-Crick and Hoogsteen base pairings and form thermally-stable PNA/PNA/DNA triplex structures. Here, we synthesized a series of TC-PNAs that can possess different lengths of azobenzene-containing linkers and studied their binding behaviours to homopurine single-stranded DNA. Introduction of azobenzene at the N-terminus amine of PNA increased the thermal stability of PNA-DNA duplexes. Further extension of the homopyrimidine PNA strand at the N-terminus of PNA-AZO further increased the binding stability of the PNA/DNA/PNA triplex to the target homopurine sequence; however, it induced TC-PNA/DNA/TC-PNA complex formation. Among these TC-PNAs, 9W5H-C4-AZO consisting of nine Watson-Crick bases and five Hoogsteen bases tethered with a beta-alanine conjugated azobenzene linker gave a stable 1:1 TC-PNA/ssDNA complex and exhibited good mismatch recognition. Our design for TC-PNA-AZO can be utilized for detecting homopurine sequences in various genes.

  4. Brain connectivity in normally developing children and adolescents.

    Science.gov (United States)

    Khundrakpam, Budhachandra S; Lewis, John D; Zhao, Lu; Chouinard-Decorte, François; Evans, Alan C

    2016-07-01

    The developing human brain undergoes an astonishing sequence of events that continuously shape the structural and functional brain connectivity. Distinct regional variations in the timelines of maturational events (synaptogenesis and synaptic pruning) occurring at the synaptic level are reflected in brain measures at macroscopic resolution (cortical thickness and gray matter density). Interestingly, the observed brain changes coincide with cognitive milestones suggesting that the changing scaffold of brain circuits may subserve cognitive development. Recent advances in connectivity analysis propelled by graph theory have allowed, on one hand, the investigation of maturational changes in global organization of structural and functional brain networks; and on the other hand, the exploration of specific networks within the context of global brain networks. An emerging picture from several connectivity studies is a system-level rewiring that constantly refines the connectivity of the developing brain. Copyright © 2016 Elsevier Inc. All rights reserved.

  5. Mesoscale Connections Summer 2017

    Energy Technology Data Exchange (ETDEWEB)

    Kippen, Karen Elizabeth [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Bourke, Mark Andrew M. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2017-06-21

    Our challenge derives from the fact that in metals or explosives grains, interfaces and defects control engineering performance in ways that are neither amenable to continuum codes (which fail to rigorously describe the heterogeneities derived from microstructure) nor computationally tractable to first principles atomistic calculations. This is a region called the mesoscale, which stands at the frontier of our desire to translate fundamental science insights into confidence in aging system performance over the range of extreme conditions relevant in a nuclear weapon. For dynamic problems, the phenomena of interest can require extremely good temporal resolutions. A shock wave traveling at 1000 m/s (or 1 mm/μs) passes through a grain with a diameter of 1 micron in a nanosecond (10-9 sec). Thus, to observe the mesoscale phenomena—such as dislocations or phase transformations—as the shock passes, temporal resolution better than picoseconds (10-12 sec) may be needed. As we anticipate the science challenges over the next decade, experimental insights on material performance at the micron spatial scale with picosecond temporal resolution—at the mesoscale— are a clear challenge. This is a challenge fit for Los Alamos in partnership with our sister labs and academia. Mesoscale Connections will draw attention to our progress as we tackle the mesoscale challenge. We hope you like it and encourage suggestions of content you are interested in.

  6. Realise : reconstruction of reality from image sequences

    NARCIS (Netherlands)

    Leymarie, F.; de la Fortelle, A.; Koenderink, Jan J.; Kappers, A. M L; Stavridi, M.; van Ginneken, B.; Muller, S.; Krake, S.; Faugeras, O.; Robert, L.; Gauclin, C.; Laveau, S.; Zeller, C.; Anon,

    1996-01-01

    REALISE has for principal goals to extract from sequences of images, acquired with a moving camera, information necessary for determining the 3D (CAD-like) structure of a real-life scene together with information about the radiometric signatures of surfaces bounding the extracted 3D objects (e.g.

  7. Rapid and Accurate Sequencing of Enterovirus Genomes Using MinION Nanopore Sequencer.

    Science.gov (United States)

    Wang, Ji; Ke, Yue Hua; Zhang, Yong; Huang, Ke Qiang; Wang, Lei; Shen, Xin Xin; Dong, Xiao Ping; Xu, Wen Bo; Ma, Xue Jun

    2017-10-01

    Knowledge of an enterovirus genome sequence is very important in epidemiological investigation to identify transmission patterns and ascertain the extent of an outbreak. The MinION sequencer is increasingly used to sequence various viral pathogens in many clinical situations because of its long reads, portability, real-time accessibility of sequenced data, and very low initial costs. However, information is lacking on MinION sequencing of enterovirus genomes. In this proof-of-concept study using Enterovirus 71 (EV71) and Coxsackievirus A16 (CA16) strains as examples, we established an amplicon-based whole genome sequencing method using MinION. We explored the accuracy, minimum sequencing time, discrimination and high-throughput sequencing ability of MinION, and compared its performance with Sanger sequencing. Within the first minute (min) of sequencing, the accuracy of MinION was 98.5% for the single EV71 strain and 94.12%-97.33% for 10 genetically-related CA16 strains. In as little as 14 min, 99% identity was reached for the single EV71 strain, and in 17 min (on average), 99% identity was achieved for 10 CA16 strains in a single run. MinION is suitable for whole genome sequencing of enteroviruses with sufficient accuracy and fine discrimination and has the potential as a fast, reliable and convenient method for routine use. Copyright © 2017 The Editorial Board of Biomedical and Environmental Sciences. Published by China CDC. All rights reserved.

  8. Connected media and presence

    NARCIS (Netherlands)

    Kort, J.; Nefs, H.T.; Gullström, C.; Greef, T.J. de; Parnes, P.

    2013-01-01

    Effective design of shared mediated spaces, information and connectedness requires theory and practice from a range of disciplines such as found in European projects like Together Anywhere, Together Anytime (TA2) and the EIT ICT Labs Mediating Presence activity. Building on this work we continue to

  9. Isolation, sequence identification and tissue expression profile of a ...

    African Journals Online (AJOL)

    The complete expressed sequence tag (CDS) sequence of Banna mini-pig inbred line (BMI) ribokinase gene (RBKS) was amplified using the reverse transcription-polymerase chain reaction (RT-PCR) based on the conserved sequence information of the cattle or other mammals and known highly homologous swine ESTs.

  10. Nanopore Sequencing as a Rapidly Deployable Ebola Outbreak Tool.

    Science.gov (United States)

    Hoenen, Thomas; Groseth, Allison; Rosenke, Kyle; Fischer, Robert J; Hoenen, Andreas; Judson, Seth D; Martellaro, Cynthia; Falzarano, Darryl; Marzi, Andrea; Squires, R Burke; Wollenberg, Kurt R; de Wit, Emmie; Prescott, Joseph; Safronetz, David; van Doremalen, Neeltje; Bushmaker, Trenton; Feldmann, Friederike; McNally, Kristin; Bolay, Fatorma K; Fields, Barry; Sealy, Tara; Rayfield, Mark; Nichol, Stuart T; Zoon, Kathryn C; Massaquoi, Moses; Munster, Vincent J; Feldmann, Heinz

    2016-02-01

    Rapid sequencing of RNA/DNA from pathogen samples obtained during disease outbreaks provides critical scientific and public health information. However, challenges exist for exporting samples to laboratories or establishing conventional sequencers in remote outbreak regions. We successfully used a novel, pocket-sized nanopore sequencer at a field diagnostic laboratory in Liberia during the current Ebola virus outbreak.

  11. Transnational Connections and Multiple Belongings

    DEFF Research Database (Denmark)

    Galal, Lise Paulsen; Sparre, Sara Cathrine Lei

    With the purpose of presenting DIMECCE key findings, we in this paper present different aspects, potentials and challenges related to the Middle Eastern Christians transnational connections and multiple belonging. We distinguish between individual transnational connections and practices, such as ......, such as family relations, churches as transnational – or global – institutions, and other organisations and associations established to support politically, socially or culturally connections and development in the country or region of origin....

  12. An exploration of the connection between two meaning perspectives: an evidence-based approach to health information delivery to vulnerable groups of Arabic- and Somali-speaking asylum seekers in a Swedish context.

    Science.gov (United States)

    Ekblad, Solvig; Linander, Andrea; Asplund, Maria

    2012-09-01

    The right to health care is significant for asylum seekers, particularly as many of them have experienced traumatic life events in their home country, during flight or in their host country. Post-migration living conditions have more impact than pre-migration conditions on ill health among asylum seekers, which underscores the importance of health care-related refugee reception policies. The purpose of this article is to explore the perceived meaning of comprehensive health information provided by a nurse to Arabic- and Somali-speaking adult asylum seekers, in a Swedish context, during its introduction at the Migration Board. In our study, the endpoint was whether asylum seekers found such health information relevant, understandable and respectful. Following an oral presentation, participants filled in a questionnaire consisting of three close-ended questions. A total of 39 groups of presentation attendees included 626 asylum seekers (415 Arabic- and 211 Somali-speaking). Data were analysed with descriptive statistics. Comments underwent content analysis. We also present some socio-demographic data on these asylum seekers. Independently of gender and language, the participants expressed their gratitude for and the meaningfulness of receiving professional, fact-based information, as well as being treated with concern and respect. They indicated a great need for this and felt relieved by being listened to. They liked the pedagogic group method, the opportunity for dialogue and to practice exercising their rights. These promising results indicate that exercising the asylum-seekers' right to receive such health information would improve future reception policies not only in Sweden, but throughout the EU. A renewed focus on communication and pedagogic skills, instead of just cultural training, should be considered for health care professionals assisting asylum seekers.

  13. The Physics Portal through Physics Connection Website: It's a new way to Stay Connected!

    Science.gov (United States)

    Jacome, D. Z.; Mato, P.; Lopez, J. L.; Zhu, W.; Dong, D.

    2011-12-01

    Our project involves connecting all level of students to science with limited funding available and having necessary resources to keep them updated. Students gain the opportunity to interact with others without having to leave the comfort of their schools. Through the Physics Portal, a door is automatically opened linking students to projects worldwide and expanding their knowledge each day. Through the funds provided we would purchase 2 laptops, a projector, speakers, a microphone, and an HD webcam. This package includes all of the tools needed to communicate and have an interactive experience with other institutions in our local area. Schools receive packages in the mail with every component needed to connect via conferencing to other students, teachers or professors in the field. Information can be recorded on each laptop, reactions of the students, and questions asked to later be updated on the Physics Connection webpage. Physics Connection allows the science community to explore through each recorded session and make recommendations to increase the efficiently of the program. Several applications on the website allow for groups to connect, discuss general ideas, or contact students for admissions to schools. Interviews, event participation, networking, and communication tools are all linked into one complete interactive package. When the experience ends for one student, it begins for another one. The process continues until the majority becomes informed.

  14. Interstate Connections - CEHC [ds619

    Data.gov (United States)

    California Natural Resource Agency — The California Department of Transportation (Caltrans) and California Department of Fish and Game (CDFG) commissioned the California Essential Habitat Connectivity...

  15. Sequencing and comparing whole mitochondrial genomes ofanimals

    Energy Technology Data Exchange (ETDEWEB)

    Boore, Jeffrey L.; Macey, J. Robert; Medina, Monica

    2005-04-22

    Comparing complete animal mitochondrial genome sequences is becoming increasingly common for phylogenetic reconstruction and as a model for genome evolution. Not only are they much more informative than shorter sequences of individual genes for inferring evolutionary relatedness, but these data also provide sets of genome-level characters, such as the relative arrangements of genes, that can be especially powerful. We describe here the protocols commonly used for physically isolating mtDNA, for amplifying these by PCR or RCA, for cloning,sequencing, assembly, validation, and gene annotation, and for comparing both sequences and gene arrangements. On several topics, we offer general observations based on our experiences to date with determining and comparing complete mtDNA sequences.

  16. Disturbed Interhemispheric Functional Connectivity Rather than Structural Connectivity in Irritable Bowel Syndrome

    Directory of Open Access Journals (Sweden)

    Rongfeng Qi

    2016-12-01

    Full Text Available Neuroimaging studies have demonstrated that irritable bowel syndrome (IBS—a relapsing functional bowel disorder—presents with disrupted brain connections. However, little is known about the alterations of interhemispheric functional connectivity and underlying structural connectivity in IBS. This study combined resting-state functional magnetic resonance imaging (MRI and diffusion tensor imaging (DTI to investigate changes in interhemispheric coordination in IBS patients. Resting-state functional and structural magnetic resonance images were acquired from 65 IBS patients and 67 healthy controls (matched for age, sex and educational level. Interhemispheric voxel-mirrored homotopic connectivity (VMHC was calculated and compared between groups. Homotopic regions showing abnormal VMHC in patients were targeted as regions of interest for analysis of DTI tractography. The fractional anisotropy, fiber number, and fiber length were compared between groups. Statistical analysis was also performed by including anxiety and depression as covariates to evaluate their effect. A Pearson correlation analysis between abnormal interhemispheric connectivity and clinical indices of IBS patients was performed. Compared to healthy controls, IBS patients had higher interhemispheric functional connectivity between bilateral thalami, cuneus, posterior cingulate cortices, lingual gyri and inferior occipital/cerebellum lobes, as well as lower interhemispheric functional connectivity between bilateral ventral anterior cingulate cortices (vACC and inferior parietal lobules (IPL. The inclusion of anxiety and depression as covariates abolished VMHC difference in vACC. Microstructural features of white matter tracts connecting functionally abnormal regions did not reveal any differences between the groups. VMHC values in vACC negatively correlated with the quality of life scores of patients. In conclusion, this study provides preliminary evidence of the disrupted

  17. Family Connections: Building Connections among Home, School, and Community

    Science.gov (United States)

    Dikkers, Amy Garrett

    2013-01-01

    Recent research on parental involvement has explored connections between parental involvement in school and children's academic achievement. While many schools have active parent organizations and a base of parents who offer additional support, others struggle to make connections with their parents or community members. Even in places with active…

  18. Joint brain connectivity estimation from diffusion and functional MRI data

    Science.gov (United States)

    Chu, Shu-Hsien; Lenglet, Christophe; Parhi, Keshab K.

    2015-03-01

    Estimating brain wiring patterns is critical to better understand the brain organization and function. Anatomical brain connectivity models axonal pathways, while the functional brain connectivity characterizes the statistical dependencies and correlation between the activities of various brain regions. The synchronization of brain activity can be inferred through the variation of blood-oxygen-level dependent (BOLD) signal from functional MRI (fMRI) and the neural connections can be estimated using tractography from diffusion MRI (dMRI). Functional connections between brain regions are supported by anatomical connections, and the synchronization of brain activities arises through sharing of information in the form of electro-chemical signals on axon pathways. Jointly modeling fMRI and dMRI data may improve the accuracy in constructing anatomical connectivity as well as functional connectivity. Such an approach may lead to novel multimodal biomarkers potentially able to better capture functional and anatomical connectivity variations. We present a novel brain network model which jointly models the dMRI and fMRI data to improve the anatomical connectivity estimation and extract the anatomical subnetworks associated with specific functional modes by constraining the anatomical connections as structural supports to the functional connections. The key idea is similar to a multi-commodity flow optimization problem that minimizes the cost or maximizes the efficiency for flow configuration and simultaneously fulfills the supply-demand constraint for each commodity. In the proposed network, the nodes represent the grey matter (GM) regions providing brain functionality, and the links represent white matter (WM) fiber bundles connecting those regions and delivering information. The commodities can be thought of as the information corresponding to brain activity patterns as obtained for instance by independent component analysis (ICA) of fMRI data. The concept of information

  19. Carl Sagan's Cosmic Connection

    Science.gov (United States)

    Sagan, Carl; Agel, Jerome

    2000-08-01

    Foreword Freeman Dyson; Personal reflections Ann Druyan; Preface; Part I. Cosmic Perspective: 1. A transitional animal; 2. The Unicorn of Cetus; 3. A message from earth; 4. A message to earth; 5. Experiments in utopias; 6. Chauvinism; 7. Space exploration as a human enterprise I. The scientific interest; 8. Space exploration as a human enterprise II. The public interest; 9. Space exploration as a human enterprise III. The historical interest; Part II. The Solar System: 10. On teaching the first grade; 11. 'The ancient and legendary Gods of old'; 12. The Venus detective story; 13. Venus is hell; 14. Science and 'intelligence'; 15. The moons of Barsoom; 16. The mountains of Mars I. Observations from earth; 17. The mountains of Mars II. Observations from space; 18. The canals of Mars; 19. The lost pictures of Mars; 20. The Ice Age and the cauldron; 21. Beginnings and ends of the Earth; 22. Terraforming the plants; 23. The exploration and utlization of the solar system; Part III. Beyond the Solar System: 24. Some of my best friends are dolphins; 25. 'Hello, central casting? Send me twenty extraterrestrials'; 26. The cosmic connection; 27. Extraterrestrial life: an idea whose time has come; 28. Has the Earth been visited?; 29. A search strategy for detecting extraterrestrial intelligence; 30. If we succeed 31. Cables, drums, and seashells; 32. The night freight to the stars; 33. Astroengineering; 34. Twenty questions: a classification of cosmic civilisations; 35. Galactic cultural exchanges; 36. A passage to elsewhere; 37. Starfolk I. A Fable; 38. Starfolk II. A future; 39. Starfolk III. The cosmic Cheshire cats; Epilog David Morrison; Index.

  20. Juno, The Cultural Connection

    Science.gov (United States)

    Clarke, Theodore

    2017-04-01

    After a 5 year journey and a billion miles cartwheeling through the vastness of space, the Juno spacecraft is in orbit about the planet Jupiter. With its suite of scientific instruments Juno scientists will catch a glimpse of the dawn of creation of our own solar system. Juno will address origins, asking for us all, Who am I? Where do I come from? But Juno is more than a space laboratory to study the planet Jupiter. Juno embodies the history of humankind's perception of the universe from Aristotle, Copernicus and Galileo, to the Juno spacecraft peering beneath the clouds of Jupiter. Juno embodies the literature of classical mythology and the timeless masterpieces of the Renaissance and Baroque periods in its very name. Juno carries to Jupiter small statuettes of the gods Jupiter and Juno and the scientist Galileo. Juno embodies cosmic visualization experiences through first ever movies of the moon occulting Earth (>2 million hits on YouTube) and the Galilean satellites orbiting about Jupiter (>1.8 million hits on You Tube). Juno embodies the stirring music of modern Greek composer Vangelis, the Orpheus of Juno, who provided the score for the movies of the moon occulting Earth and of the Galilean satellites orbiting Jupiter. Juno embodies down to Earth visualization experiences through trajectory models created of Juno's passage through the Earth-moon system and Juno's entire orbital mission at Jupiter. Juno is the embodiment of public engagement in its science in a fishbowl program. Indeed, because Juno is the embodiment of this remarkable union of science and technology, history and literature, music and art, and visualization and public engagement, Juno is truly an ambassador to the universe of a New Renaissance. In my paper, "Juno, the Cultural Connection," I will unveil a dimension of the Juno mission to the planet Jupiter that will appeal to a broad sector of the global public.

  1. Polymorphism Sequence - JSNP | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us JSNP Polymorphism Sequence Data detail Data name Polymorphism Sequence DOI 10.18908/lsdba.nb...dc00114-001 Description of data contents Information on polymorphisms (SNPs and insertions/deletions) and th...se Name database name JSNP_SNP: single nucleotide polymorphism JSNP_InsDel_IND: insertion/deletion JSNP_InsD...ved allele observed 3' Flanking Sequence 3' flanking sequence Offset in Flanking Sequence position of the polymorphism...uence Accession No. accession No. of the sequence for polymorphism screening Offset in Record position of the polymorphism

  2. Biomolecule Sequencer: Next-Generation DNA Sequencing Technology for In-Flight Environmental Monitoring, Research, and Beyond

    Science.gov (United States)

    Smith, David J.; Burton, Aaron; Castro-Wallace, Sarah; John, Kristen; Stahl, Sarah E.; Dworkin, Jason Peter; Lupisella, Mark L.

    2016-01-01

    On the International Space Station (ISS), technologies capable of rapid microbial identification and disease diagnostics are not currently available. NASA still relies upon sample return for comprehensive, molecular-based sample characterization. Next-generation DNA sequencing is a powerful approach for identifying microorganisms in air, water, and surfaces onboard spacecraft. The Biomolecule Sequencer payload, manifested to SpaceX-9 and scheduled on the Increment 4748 research plan (June 2016), will assess the functionality of a commercially-available next-generation DNA sequencer in the microgravity environment of ISS. The MinION device from Oxford Nanopore Technologies (Oxford, UK) measures picoamp changes in electrical current dependent on nucleotide sequences of the DNA strand migrating through nanopores in the system. The hardware is exceptionally small (9.5 x 3.2 x 1.6 cm), lightweight (120 grams), and powered only by a USB connection. For the ISS technology demonstration, the Biomolecule Sequencer will be powered by a Microsoft Surface Pro3. Ground-prepared samples containing lambda bacteriophage, Escherichia coli, and mouse genomic DNA, will be launched and stored frozen on the ISS until experiment initiation. Immediately prior to sequencing, a crew member will collect and thaw frozen DNA samples, connect the sequencer to the Surface Pro3, inject thawed samples into a MinION flow cell, and initiate sequencing. At the completion of the sequencing run, data will be downlinked for ground analysis. Identical, synchronous ground controls will be used for data comparisons to determine sequencer functionality, run-time sequence, current dynamics, and overall accuracy. We will present our latest results from the ISS flight experiment the first time DNA has ever been sequenced in space and discuss the many potential applications of the Biomolecule Sequencer for environmental monitoring, medical diagnostics, higher fidelity and more adaptable Space Biology Human

  3. Connecting multimodality in human communication

    Directory of Open Access Journals (Sweden)

    Christina eRegenbogen

    2013-11-01

    Full Text Available A successful reciprocal evaluation of social signals serves as a prerequisite for social coherence and empathy. In a previous fMRI study we studied naturalistic communication situations by presenting video clips to our participants and recording their behavioral responses regarding empathy and its components. In two conditions, all three channels transported congruent emotional or neutral information, respectively. Three conditions selectively presented two emotional channels and one neutral channel and were thus bimodally emotional. We reported channel-specific emotional contributions in modality-related areas, elicited by dynamic video clips with varying combinations of emotionality in facial expressions, prosody, and speech content. However, to better understand the underlying mechanisms accompanying a naturalistically displayed human social interaction in some key regions that presumably serve as specific processing hubs for facial expressions, prosody, and speech content, we pursued a reanalysis of the data. In addition to this specificity of these regions to information channels we demonstrated that they were also sensitive to variations of the respective emotional content.Here, we focused on two different descriptions of temporal characteristics within these three modality-related regions (right fusiform gyrus (FFG, left auditory cortex (AC, left angular gyrus (AG and left dorsomedial prefrontal cortex (dmPFC. By means of a finite impulse response (FIR analysis within each of the three regions we examined the post-stimulus time-courses as a description of the temporal characteristics of the BOLD response during the video clips. Second, effective connectivity between these areas and the left dmPFC was analyzed using dynamic causal modeling (DCM in order to describe condition-related modulatory influences on the coupling between these regions. The FIR analysis showed initially diminished activation in bimodally emotional conditions but

  4. The will to connection

    DEFF Research Database (Denmark)

    Jensen, Ole B.

    2015-01-01

    ’ and designers’ “toolbox” should contain three dimensions: hardware (technological devices), software (operative code), and a manual (here understood as a theoretically informed conceptualization of the socio-cultural embedding of these networked technologies). There is a need for creating operational tools......In this chapter the fields of urban planning and design and their needs for mastering networked technologies are at the center. The chapter discusses what an “Information and Communication Technology Toolbox” for urban planners and designers might mean. Along the road it is argued that a planners...... and understandings that urban planners and designers may utilize next to the technologies and software. The theoretical background for this is derived from the “mobilites turn” as well as theories exploring network technologies and new media....

  5. Effects of Sequences of Cognitions on Group Performance Over Time.

    Science.gov (United States)

    Molenaar, Inge; Chiu, Ming Ming

    2017-04-01

    Extending past research showing that sequences of low cognitions (low-level processing of information) and high cognitions (high-level processing of information through questions and elaborations) influence the likelihoods of subsequent high and low cognitions, this study examines whether sequences of cognitions are related to group performance over time; 54 primary school students (18 triads) discussed and wrote an essay about living in another country (32,375 turns of talk). Content analysis and statistical discourse analysis showed that within each lesson, groups with more low cognitions or more sequences of low cognition followed by high cognition added more essay words. Groups with more high cognitions, sequences of low cognition followed by low cognition, or sequences of high cognition followed by an action followed by low cognition, showed different words and sequences, suggestive of new ideas. The links between cognition sequences and group performance over time can inform facilitation and assessment of student discussions.

  6. Stochastically excited oscillations on the upper main sequence

    DEFF Research Database (Denmark)

    Antoci, Victoria

    2013-01-01

    Convective envelopes in stars on the main sequence are usually connected only with stars of spectral types F5 or later. However, observations as well as theory indicate that the convective outer layers in earlier stars, despite being shallow, are still effective and turbulent enough to stochastic......Convective envelopes in stars on the main sequence are usually connected only with stars of spectral types F5 or later. However, observations as well as theory indicate that the convective outer layers in earlier stars, despite being shallow, are still effective and turbulent enough...... Pulsating B and Be stars, all in the context of solar-like oscillations....

  7. SVX Sequencer Board

    International Nuclear Information System (INIS)

    Utes, M.

    1997-01-01

    The SVX Sequencer boards are 9U by 280mm circuit boards that reside in slots 2 through 21 of each of eight Eurocard crates in the D0 Detector Platform. The basic purpose is to control the SVX chips for data acquisition and when a trigger occurs, to gather the SVX data and relay the data to the VRB boards in the Movable Counting House. Functions and features are as follows: (1) Initialization of eight SVX chip strings using the MIL-STD-1553 data bus; (2) Real time manipulation of the SVX control lines to effect data acquisition, digitization, and readout based on the NRZ/Clock signals from the Controller; (3) Conversion of 8-bit electrical SVX readout data to an optical signal operating at 1.062 Gbit/sec, sent to the VRB. Eight HDIs will be serviced per board; (4) Built-in logic analyzer which can record the most important control and data lines during a data acquisition cycle and put this recorded information onto the 1553 bus; (5) Identification header and end of data trailer tacked onto data stream; (6) 1553 register which can read the current values of the control and data lines; (7) 1553 register which can test the optical link; (8) 1553 registers for crossing pulse width, calibration pulse voltage, and calibration pipeline select; (9) 1553 register for reading the optical drivers status link; (10) 1553 register for power control of SVX chips and ignoring bad SVX strings; (11) Front panel displays and LEDs show the board status at a glance; (12) In-system programmable EPLDs are programmed via 1553 or Altera's 'Bitblaster'; (13) Automatic readout abort after 45us; (14) Supplies BUSY signal back to Trigger Framework; (15) Supports a heartbeat system to prevent excessive SVX current draw; and (16) Supports a SVX power trip feature if heartbeat failure occurs.

  8. Enhanced Dynamic Algorithm of Genome Sequence Alignments

    OpenAIRE

    Arabi E. keshk

    2014-01-01

    The merging of biology and computer science has created a new field called computational biology that explore the capacities of computers to gain knowledge from biological data, bioinformatics. Computational biology is rooted in life sciences as well as computers, information sciences, and technologies. The main problem in computational biology is sequence alignment that is a way of arranging the sequences of DNA, RNA or protein to identify the region of similarity and relationship between se...

  9. HIV Sequence Compendium 2015

    Energy Technology Data Exchange (ETDEWEB)

    Foley, Brian Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Leitner, Thomas Kenneth [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Apetrei, Cristian [Univ. of Pittsburgh, PA (United States); Hahn, Beatrice [Univ. of Pennsylvania, Philadelphia, PA (United States); Mizrachi, Ilene [National Center for Biotechnology Information, Bethesda, MD (United States); Mullins, James [Univ. of Washington, Seattle, WA (United States); Rambaut, Andrew [Univ. of Edinburgh, Scotland (United Kingdom); Wolinsky, Steven [Northwestern Univ., Evanston, IL (United States); Korber, Bette Tina Marie [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-10-05

    This compendium is an annual printed summary of the data contained in the HIV sequence database. We try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2015. Hence, though it is published in 2015 and called the 2015 Compendium, its contents correspond to the 2014 curated alignments on our website. The number of sequences in the HIV database is still increasing. In total, at the end of 2014, there were 624,121 sequences in the HIV Sequence Database, an increase of 7% since the previous year. This is the first year that the number of new sequences added to the database has decreased compared to the previous year. The number of near complete genomes (>7000 nucleotides) increased to 5834 by end of 2014. However, as in previous years, the compendium alignments contain only a fraction of these. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/ content/sequence/NEWALIGN/align.html As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

  10. Mapping sequences by parts

    Directory of Open Access Journals (Sweden)

    Guziolowski Carito

    2007-09-01

    Full Text Available Abstract Background: We present the N-map method, a pairwise and asymmetrical approach which allows us to compare sequences by taking into account evolutionary events that produce shuffled, reversed or repeated elements. Basically, the optimal N-map of a sequence s over a sequence t is the best way of partitioning the first sequence into N parts and placing them, possibly complementary reversed, over the second sequence in order to maximize the sum of their gapless alignment scores. Results: We introduce an algorithm computing an optimal N-map with time complexity O (|s| × |t| × N using O (|s| × |t| × N memory space. Among all the numbers of parts taken in a reasonable range, we select the value N for which the optimal N-map has the most significant score. To evaluate this significance, we study the empirical distributions of the scores of optimal N-maps and show that they can be approximated by normal distributions with a reasonable accuracy. We test the functionality of the approach over random sequences on which we apply artificial evolutionary events. Practical Application: The method is illustrated with four case studies of pairs of sequences involving non-standard evolutionary events.

  11. Perception Enhancement using Visual Attributes in Sequence Motif Visualization

    OpenAIRE

    Oon, Yin; Lee, Nung; Kok, Wei

    2016-01-01

    Sequence logo is a well-accepted scientific method to visualize the conservation characteristics of biological sequence motifs. Previous studies found that using sequence logo graphical representation for scientific evidence reports or arguments could seriously cause biases and misinterpretation by users. This study investigates on the visual attributes performance of a sequence logo in helping users to perceive and interpret the information based on preattentive theories and Gestalt principl...

  12. Quantifying Riverscape Connectivity with Graph Theory

    Science.gov (United States)

    Carbonneau, P.; Milledge, D.; Sinha, R.; Tandon, S. K.

    2013-12-01

    connectivity structure of the Gangetic riverscape with fluvial remote sensing. Our study reach extends from the heavily dammed headwaters of the Bhagirathi, Mandakini and Alaknanda rivers which form the source of the Ganga to Allahabad ~900 km downstream on the main stem. We use Landsat-8 imagery as the baseline dataset. Channel width along the Ganga (i.e. Ganges) is often several kilometres. Therefore, the pan-sharpened 15m pixels of Landsat-8 are in fact capable of resolving inner channel features for over 80% of the channel length thus allowing a riverscape approach to be adopted. We examine the following connectivity metrics: size distribution of connected components, betweeness centrality and the integrated index of connectivity. A geographic perspective is added by mapping local (25 km-scale) values for these metrics in order to examine spatial patterns of connectivity. This approach allows us to map impacts of dam construction and has the potential to inform policy decisions in the area as well as open-up new avenues of investigation.

  13. Social network models predict movement and connectivity in ecological landscapes

    Science.gov (United States)

    Fletcher, Robert J.; Acevedo, M.A.; Reichert, Brian E.; Pias, Kyle E.; Kitchens, Wiley M.

    2011-01-01

    Network analysis is on the rise across scientific disciplines because of its ability to reveal complex, and often emergent, patterns and dynamics. Nonetheless, a growing concern in network analysis is the use of limited data for constructing networks. This concern is strikingly relevant to ecology and conservation biology, where network analysis is used to infer connectivity across landscapes. In this context, movement among patches is the crucial parameter for interpreting connectivity but because of the difficulty of collecting reliable movement data, most network analysis proceeds with only indirect information on movement across landscapes rather than using observed movement to construct networks. Statistical models developed for social networks provide promising alternatives for landscape network construction because they can leverage limited movement information to predict linkages. Using two mark-recapture datasets on individual movement and connectivity across landscapes, we test whether commonly used network constructions for interpreting connectivity can predict actual linkages and network structure, and we contrast these approaches to social network models. We find that currently applied network constructions for assessing connectivity consistently, and substantially, overpredict actual connectivity, resulting in considerable overestimation of metapopulation lifetime. Furthermore, social network models provide accurate predictions of network structure, and can do so with remarkably limited data on movement. Social network models offer a flexible and powerful way for not only understanding the factors influencing connectivity but also for providing more reliable estimates of connectivity and metapopulation persistence in the face of limited data.

  14. Social network models predict movement and connectivity in ecological landscapes.

    Science.gov (United States)

    Fletcher, Robert J; Acevedo, Miguel A; Reichert, Brian E; Pias, Kyle E; Kitchens, Wiley M

    2011-11-29

    Network analysis is on the rise across scientific disciplines because of its ability to reveal complex, and often emergent, patterns and dynamics. Nonetheless, a growing concern in network analysis is the use of limited data for constructing networks. This concern is strikingly relevant to ecology and conservation biology, where network analysis is used to infer connectivity across landscapes. In this context, movement among patches is the crucial parameter for interpreting connectivity but because of the difficulty of collecting reliable movement data, most network analysis proceeds with only indirect information on movement across landscapes rather than using observed movement to construct networks. Statistical models developed for social networks provide promising alternatives for landscape network construction because they can leverage limited movement information to predict linkages. Using two mark-recapture datasets on individual movement and connectivity across landscapes, we test whether commonly used network constructions for interpreting connectivity can predict actual linkages and network structure, and we contrast these approaches to social network models. We find that currently applied network constructions for assessing connectivity consistently, and substantially, overpredict actual connectivity, resulting in considerable overestimation of metapopulation lifetime. Furthermore, social network models provide accurate predictions of network structure, and can do so with remarkably limited data on movement. Social network models offer a flexible and powerful way for not only understanding the factors influencing connectivity but also for providing more reliable estimates of connectivity and metapopulation persistence in the face of limited data.

  15. The Colliding Beams Sequencer

    International Nuclear Information System (INIS)

    Johnson, D.E.; Johnson, R.P.

    1989-01-01

    The Colliding Beam Sequencer (CBS) is a computer program used to operate the pbar-p Collider by synchronizing the applications programs and simulating the activities of the accelerator operators during filling and storage. The Sequencer acts as a meta-program, running otherwise stand alone applications programs, to do the set-up, beam transfers, acceleration, low beta turn on, and diagnostics for the transfers and storage. The Sequencer and its operational performance will be described along with its special features which include a periodic scheduler and command logger. 14 refs., 3 figs

  16. Phylogenetic Trees From Sequences

    Science.gov (United States)

    Ryvkin, Paul; Wang, Li-San

    In this chapter, we review important concepts and approaches for phylogeny reconstruction from sequence data.We first cover some basic definitions and properties of phylogenetics, and briefly explain how scientists model sequence evolution and measure sequence divergence. We then discuss three major approaches for phylogenetic reconstruction: distance-based phylogenetic reconstruction, maximum parsimony, and maximum likelihood. In the third part of the chapter, we review how multiple phylogenies are compared by consensus methods and how to assess confidence using bootstrapping. At the end of the chapter are two sections that list popular software packages and additional reading.

  17. The Always-Connected Generation

    Science.gov (United States)

    Bull, Glen

    2010-01-01

    The Pew Internet and American Life project characterizes the millennials--the first generation to come of age in the new millennium--as the first "always-connected" generation. Significant aspects of culture are changing as a result. A changing world where all students are connected all the time has substantial educational implications. Despite…

  18. Partitioning graphs into connected parts

    NARCIS (Netherlands)

    Hof, van 't P.; Paulusma, D.; Woeginger, G.J.; Frid, A.; Morozov, A.S.; Rybalchenko, A.; Wagner, K.W.

    2009-01-01

    The 2-DISJOINT CONNECTED SUBGRAPHS problem asks if a given graph has two vertex-disjoint connected subgraphs containing pre-specified sets of vertices. We show that this problem is NP-complete even if one of the sets has cardinality 2. The LONGEST PATH CONTRACTIBILITY problem asks for the largest

  19. Connections for Small Vertex Models

    Indian Academy of Sciences (India)

    This paper is a first attempt at calssifying connections on small vertex models i.e., commuting squares of the form displayed in (1.2) below. ... obtain necessary conditions for two such `model connections' in (2, ) to be ... Current Issue : Vol.

  20. Information technology made simple

    CERN Document Server

    Carter, Roger

    1991-01-01

    Information Technology: Made Simple covers the full range of information technology topics, including more traditional subjects such as programming languages, data processing, and systems analysis. The book discusses information revolution, including topics about microchips, information processing operations, analog and digital systems, information processing system, and systems analysis. The text also describes computers, computer hardware, microprocessors, and microcomputers. The peripheral devices connected to the central processing unit; the main types of system software; application soft

  1. Transcultural Tectonic Connections

    DEFF Research Database (Denmark)

    Carter, Adrian

    2014-01-01

    have been informed by his understanding of boat-building, reference to nature, extensive travels and broad transcultural influences. The paper will also consider to what extent Utzon’s work can be seen to have been a precursor and direct influence upon subsequent developments within architecture......, together with his continuing contemporary relevance. With particular consideration of the ways in which Utzon’s approach to architectural design and form provide a pedagogic model for the creative development of students of architecture and source of inspiration to current practitioners. Jørn Utzon...

  2. Connecting Science with Society

    DEFF Research Database (Denmark)

    awareness of the important questions of our society reflected in scientific research and of the answers produced by these research activities. The CRIS2010 conference, entitled “Bringing Science to Society”, therefore seeks to highlight the role of Current Research Information Systems for communicating......, for driving innovation or for disseminating results to the scientific community and beyond. And, as a look at the CRIS2010 conference program will tell, there are many more, often little known purposes for which CRIS are used. These applications stimulate with their demands the progress in designing, building...

  3. Spanning k-ended trees of 3-regular connected graphs

    Directory of Open Access Journals (Sweden)

    Hamed Ghasemian Zoeram

    2017-10-01

    Full Text Available A vertex of degree one is called an end-vertex and the set of end-vertices of G is denoted by End(G. For a positive integer k, a tree T be called k-ended tree if $|End(T| \\leq k$. In this paper, we obtain sufficient conditions for spanning k-trees of 3-regular connected graphs. We give a construction sequence of graphs satisfying the condition. At the end, we present a conjecture about spanning k-ended trees of 3-regular connected graphs.

  4. Privacy and the Connected Society

    DEFF Research Database (Denmark)

    Sørensen, Lene Tolstrup; Khajuria, Samant; Skouby, Knud Erik

    The Vision of the 5G enabled connected society is highly based on the evolution and implementation of Internet of Things. This involves, amongst others, a significant raise in devices, sensors and communication in pervasive interconnections as well as cooperation amongst devices and entities across...... the society. Enabling the vision of the connected society, researchers point in the direction of security and privacy as areas to challenge the vision. By use of the Internet of Things reference model as well as the vision of the connected society, this paper identifies privacy of the individual with respect...... to three selected areas: Shopping, connected cars and online gaming. The paper concludes that privacy is a complexity within the connected society vision and that thee is a need for more privacy use cases to shed light on the challenge....

  5. Network Connection Management

    CERN Document Server

    IT Department, Communication Systems and Network Group

    2005-01-01

    The CERN network database is a key element of the CERN network infrastructure. It is absolutely essential that its information is kept up-to-date for security reasons and to ensure a smooth running of the network infrastructure. Over the years, some of the information in the database has become obsolete. The database therefore needs to be cleaned up, for which we are requesting your help. In the coming weeks, you may receive an electronic mail from Netops.database@cern.ch relating to the clean-up. If you receive such a message, it will be for one of the following reasons: You are the person responsible for or the main user of a system for which a problem has been detected, or You have been the supervisor of a person who has now left CERN (according to the HR database), or The problem has been passed up to you because someone under your supervision has not taken the necessary action within four weeks of notification. Just open the link that will be included in the message and follow the instructions....

  6. Network Connection Management

    CERN Multimedia

    IT Department

    2005-01-01

    The CERN network database is a key element of the CERN network infrastructure. It is absolutely essential that its information is kept up-to-date for security reasons and to ensure smooth running of the network infrastructure. Over the years, some of the information in the database has become obsolete. The database therefore needs to be cleaned up, for which we are requesting your help. In the coming weeks, you may receive an electronic mail from Netops.database@cern.ch relating to the clean-up. If you receive such a message, it will be for one of the following reasons: You are the person responsible for or the main user of a system for which a problem has been detected, or You have been the supervisor of a person who has now left CERN (according to the HR database), or The problem has been passed up to you because someone under your supervision has not taken the necessary action within four weeks of notification. Just open the link that will be included in the message and follow the instructions. Thank ...

  7. Gomphid DNA sequence data

    Data.gov (United States)

    U.S. Environmental Protection Agency — DNA sequence data for several genetic loci. This dataset is not publicly accessible because: It's already publicly available on GenBank. It can be accessed through...

  8. Yeast genome sequencing:

    DEFF Research Database (Denmark)

    Piskur, Jure; Langkjær, Rikke Breinhold

    2004-01-01

    For decades, unicellular yeasts have been general models to help understand the eukaryotic cell and also our own biology. Recently, over a dozen yeast genomes have been sequenced, providing the basis to resolve several complex biological questions. Analysis of the novel sequence data has shown...... of closely related species helps in gene annotation and to answer how many genes there really are within the genomes. Analysis of non-coding regions among closely related species has provided an example of how to determine novel gene regulatory sequences, which were previously difficult to analyse because...... they are short and degenerate and occupy different positions. Comparative genomics helps to understand the origin of yeasts and points out crucial molecular events in yeast evolutionary history, such as whole-genome duplication and horizontal gene transfer(s). In addition, the accumulating sequence data provide...

  9. Incongruent genetic connectivity patterns for VME indicator taxa: implications for the management of New Zealand's vulnerable marine ecosystems

    Science.gov (United States)

    Clark, M. R.; Gardner, J.; Holland, L.; Zeng, C.; Hamilton, J. S.; Rowden, A. A.

    2016-02-01

    In the New Zealand region vulnerable marine ecosystems (VMEs) are at risk from commercial fishing activity and future seabed mining. Understanding connectivity among VMEs is important for the design of effective spatial management strategies, i.e. a network of protected areas. To date however, genetic connectivity in the New Zealand region has rarely been documented. As part of a project developing habitat suitability models and spatial management options for VMEs we used DNA sequence data and microsatellite genotyping to assess genetic connectivity for a range of VME indicator taxa, including the coral Desmophyllum dianthus, and the sponges Poecilastra laminaris and Penares palmatoclada. Overall, patterns of connectivity were inconsistent amonst taxa. Nonetheless, genetic data from each taxon were relevant to inform management at a variety of spatial scales. D. dianthus populations in the Kermadec volcanic arc and the Louisville Seamount Chain were indistinguishable, highlighting the importance of considering source-sink dynamics between populations beyond the EEZ in conservation planning. Poecilastra laminaris populations showed significant divergence across the Chatham Rise, in contrast to P. palmatoclada, which had a uniform haplotypic distribution. However, both sponge species exhibited the highest genetic diversity on the Chatham Rise, suggesting that this area is a genetic hotspot. The spatial heterogeneity of genetic patterns of structure suggest that inclusion of several taxa is necessary to facilitate understanding of regional connectivity patterns, variation in which may be attributed to alternate life history strategies, local hydrodynamic regimes, or in some cases, suboptimal sample sizes. Our findings provide important information for use by environmental managers, including summary maps of genetic diversity and barriers to gene flow, which will be used in spatial management decision-support tools.

  10. HIV Sequence Compendium 2010

    Energy Technology Data Exchange (ETDEWEB)

    Kuiken, Carla [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Foley, Brian [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Leitner, Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Apetrei, Christian [Univ. of Pittsburgh, PA (United States); Hahn, Beatrice [Univ. of Alabama, Tuscaloosa, AL (United States); Mizrachi, Ilene [National Center for Biotechnology Information, Bethesda, MD (United States); Mullins, James [Univ. of Washington, Seattle, WA (United States); Rambaut, Andrew [Univ. of Edinburgh, Scotland (United Kingdom); Wolinsky, Steven [Northwestern Univ., Evanston, IL (United States); Korber, Bette [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2010-12-31

    This compendium is an annual printed summary of the data contained in the HIV sequence database. In these compendia we try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2010. Hence, though it is called the 2010 Compendium, its contents correspond to the 2009 curated alignments on our website. The number of sequences in the HIV database is still increasing exponentially. In total, at the time of printing, there were 339,306 sequences in the HIV Sequence Database, an increase of 45% since last year. The number of near complete genomes (>7000 nucleotides) increased to 2576 by end of 2009, reflecting a smaller increase than in previous years. However, as in previous years, the compendium alignments contain only a small fraction of these. Included in the alignments are a small number of sequences representing each of the subtypes and the more prevalent circulating recombinant forms (CRFs) such as 01 and 02, as well as a few outgroup sequences (group O and N and SIV-CPZ). Of the rarer CRFs we included one representative each. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/content/sequence/NEWALIGN/align.html. Reprints are available from our website in the form of both HTML and PDF files. As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

  11. General LTE Sequence

    OpenAIRE

    Billal, Masum

    2015-01-01

    In this paper,we have characterized sequences which maintain the same property described in Lifting the Exponent Lemma. Lifting the Exponent Lemma is a very powerful tool in olympiad number theory and recently it has become very popular. We generalize it to all sequences that maintain a property like it i.e. if p^{\\alpha}||a_k and p^\\b{eta}||n, then p^{{\\alpha}+\\b{eta}}||a_{nk}.

  12. Pairwise Sequence Alignment Library

    Energy Technology Data Exchange (ETDEWEB)

    2015-05-20

    Vector extensions, such as SSE, have been part of the x86 CPU since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprint that features complex data dependencies. The trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. Therefore, a novel SIMD implementation of a parallel scan-based sequence alignment algorithm that can better exploit wider SIMD units was implemented as part of the Parallel Sequence Alignment Library (parasail). Parasail features: Reference implementations of all known vectorized sequence alignment approaches. Implementations of Smith Waterman (SW), semi-global (SG), and Needleman Wunsch (NW) sequence alignment algorithms. Implementations across all modern CPU instruction sets including AVX2 and KNC. Language interfaces for C/C++ and Python.

  13. Optimizing and benchmarking de novo transcriptome sequencing: from library preparation to assembly evaluation.

    Science.gov (United States)

    Hara, Yuichiro; Tatsumi, Kaori; Yoshida, Michio; Kajikawa, Eriko; Kiyonari, Hiroshi; Kuraku, Shigehiro

    2015-11-18

    RNA-seq enables gene expression profiling in selected spatiotemporal windows and yields massive sequence information with relatively low cost and time investment, even for non-model species. However, there remains a large room for optimizing its workflow, in order to take full advantage of continuously developing sequencing capacity. Transcriptome sequencing for three embryonic stages of Madagascar ground gecko (Paroedura picta) was performed with the Illumina platform. The output reads were assembled de novo for reconstructing transcript sequences. In order to evaluate the completeness of transcriptome assemblies, we prepared a reference gene set consisting of vertebrate one-to-one orthologs. To take advantage of increased read length of >150 nt, we demonstrated shortened RNA fragmentation time, which resulted in a dramatic shift of insert size distribution. To evaluate products of multiple de novo assembly runs incorporating reads with different RNA sources, read lengths, and insert sizes, we introduce a new reference gene set, core vertebrate genes (CVG), consisting of 233 genes that are shared as one-to-one orthologs by all vertebrate genomes examined (29 species)., The completeness assessment performed by the computational pipelines CEGMA and BUSCO referring to CVG, demonstrated higher accuracy and resolution than with the gene set previously established for this purpose. As a result of the assessment with CVG, we have derived the most comprehensive transcript sequence set of the Madagascar ground gecko by means of assembling individual libraries followed by clustering the assembled sequences based on their overall similarities. Our results provide several insights into optimizing de novo RNA-seq workflow, including the coordination between library insert size and read length, which manifested in improved connectivity of assemblies. The approach and assembly assessment with CVG demonstrated here would be applicable to transcriptome analysis of other species as

  14. Population Coding in Sparsely Connected Networks of Noisy Neurons

    Directory of Open Access Journals (Sweden)

    Bryan Patrick Tripp

    2012-05-01

    Full Text Available This study examines the relationship between population coding and spatial connection statistics in networks of noisy neurons. Encoding of sensory information in the neocortex is thought to require coordinated neural populations, because individual cortical neurons respond to a wide range of stimuli, and exhibit highly variable spiking in response to repeated stimuli. Population coding is rooted in network structure, because cortical neurons receive information only from other neurons, and because the information they encode must be decoded by other neurons, if it is to affect behaviour. However, population coding theory has often ignored network structure, or assumed discrete, fully-connected populations (in contrast with the sparsely connected, continuous sheet of the cortex. In this study, we model a sheet of cortical neurons with sparse, primarily local connections, and find that a network with this structure can encode multiple internal state variables with high signal-to-noise ratio. However, in our model, although connection probability varies with the distance between neurons, we find that the connections cannot be instantiated at random according to these probabilities, but must have additional structure if information is to be encoded with high fidelity.

  15. How Analysts Cognitively “Connect the Dots”

    Energy Technology Data Exchange (ETDEWEB)

    Bradel, Lauren; Self, Jessica S.; Endert, Alexander; Hossain, Shahriar M.; North, Chris; Ramakrishnan, Naren

    2013-06-04

    As analysts attempt to make sense of a collection of documents, such as intelligence analysis reports, they may wish to “connect the dots” between pieces of information that may initially seem unrelated. This process of synthesizing information between information requires users to make connections between pairs of documents, creating a conceptual story. We conducted a user study to analyze the process by which users connect pairs of documents and how they spatially arrange information. Users created conceptual stories that connected the dots using organizational strategies that ranged in complexity. We propose taxonomies for cognitive connections and physical structures used when trying to “connect the dots” between two documents. We compared the user-created stories with a data-mining algorithm that constructs chains of documents using co-occurrence metrics. Using the insight gained into the storytelling process, we offer design considerations for the existing data mining algorithm and corresponding tools to combine the power of data mining and the complex cognitive processing of analysts.

  16. Methods of information geometry

    CERN Document Server

    Amari, Shun-Ichi

    2000-01-01

    Information geometry provides the mathematical sciences with a new framework of analysis. It has emerged from the investigation of the natural differential geometric structure on manifolds of probability distributions, which consists of a Riemannian metric defined by the Fisher information and a one-parameter family of affine connections called the \\alpha-connections. The duality between the \\alpha-connection and the (-\\alpha)-connection together with the metric play an essential role in this geometry. This kind of duality, having emerged from manifolds of probability distributions, is ubiquitous, appearing in a variety of problems which might have no explicit relation to probability theory. Through the duality, it is possible to analyze various fundamental problems in a unified perspective. The first half of this book is devoted to a comprehensive introduction to the mathematical foundation of information geometry, including preliminaries from differential geometry, the geometry of manifolds or probability d...

  17. Cognitive control network connectivity in adolescent women with and without a parental history of depression

    Directory of Open Access Journals (Sweden)

    Peter C. Clasen

    2014-01-01

    Conclusions: Depressed parents may transmit depression vulnerability to their adolescent daughters via alterations in functional connectivity within neural circuits that underlie cognitive control of emotional information.

  18. Divide and conquer: enriching environmental sequencing data.

    Directory of Open Access Journals (Sweden)

    Anne Bergeron

    2007-09-01

    Full Text Available In environmental sequencing projects, a mix of DNA from a whole microbial community is fragmented and sequenced, with one of the possible goals being to reconstruct partial or complete genomes of members of the community. In communities with high diversity of species, a significant proportion of the sequences do not overlap any other fragment in the sample. This problem will arise not only in situations with a relatively even distribution of many species, but also when the community in a particular environment is routinely dominated by the same few species. In the former case, no genomes may be assembled at all, while in the latter case a few dominant species in an environment will always be sequenced at high coverage to the detriment of coverage of the greater number of sparse species.Here we show that, with the same global sequencing effort, separating the species into two or more sub-communities prior to sequencing can yield a much higher proportion of sequences that can be assembled. We first use the Lander-Waterman model to show that, if the expected percentage of singleton sequences is higher than 25%, then, under the uniform distribution hypothesis, splitting the community is always a wise choice. We then construct simulated microbial communities to show that the results hold for highly non-uniform distributions. We also show that, for the distributions considered in the experiments, it is possible to estimate quite accurately the relative diversity of the two sub-communities.Given the fact that several methods exist to split microbial communities based on physical properties such as size, density, surface biochemistry, or optical properties, we strongly suggest that groups involved in environmental sequencing, and expecting high diversity, consider splitting their communities in order to maximize the information content of their sequencing effort.

  19. Impact of Negative Sequence Current Injection by Wind Power Plants

    DEFF Research Database (Denmark)

    Chaudhary, Sanjay; Göksu, Ömer; Teodorescu, Remus

    2013-01-01

    This paper presents an analysis of the impact from negative sequence current injection by wind power plants in power systems under steady-state and short-term unbalanced conditions, including faults. The separate positive and negative sequence current control capability of the grid-side converters...... of full scale converter type wind turbines may be utilized to alter voltage imbalance at the point of connection and further into the grid, in turn changing the resultant negative sequence current flow in the grid. The effects of such control actions have been analyzed and discussed through theoretical...

  20. Accelerated Distributed Dual Averaging Over Evolving Networks of Growing Connectivity

    Science.gov (United States)

    Liu, Sijia; Chen, Pin-Yu; Hero, Alfred O.

    2018-04-01

    We consider the problem of accelerating distributed optimization in multi-agent networks by sequentially adding edges. Specifically, we extend the distributed dual averaging (DDA) subgradient algorithm to evolving networks of growing connectivity and analyze the corresponding improvement in convergence rate. It is known that the convergence rate of DDA is influenced by the algebraic connectivity of the underlying network, where better connectivity leads to faster convergence. However, the impact of network topology design on the convergence rate of DDA has not been fully understood. In this paper, we begin by designing network topologies via edge selection and scheduling. For edge selection, we determine the best set of candidate edges that achieves the optimal tradeoff between the growth of network connectivity and the usage of network resources. The dynamics of network evolution is then incurred by edge scheduling. Further, we provide a tractable approach to analyze the improvement in the convergence rate of DDA induced by the growth of network connectivity. Our analysis reveals the connection between network topology design and the convergence rate of DDA, and provides quantitative evaluation of DDA acceleration for distributed optimization that is absent in the existing analysis. Lastly, numerical experiments show that DDA can be significantly accelerated using a sequence of well-designed networks, and our theoretical predictions are well matched to its empirical convergence behavior.