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

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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...

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.

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/.

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.

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)

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.

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

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…

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.

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.

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.

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

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

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.

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.

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.

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.

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.

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.

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

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.

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.

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)

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

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

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...

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...

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)

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.

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

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.

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.

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/.

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...

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.

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.

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

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.

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

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.

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...

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...

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.

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.

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.

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

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

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

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.

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...

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…

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).

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.

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.

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.

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

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.

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

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.

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.

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.

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.

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...

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

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.

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.

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.

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.

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

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

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

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…

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

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.

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.

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

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.

Effective Connectivity of Cortical Sensorimotor Networks During Finger Movement Tasks: A Simultaneous fNIRS, fMRI, EEG Study.

Science.gov (United States)

Anwar, A R; Muthalib, M; Perrey, S; Galka, A; Granert, O; Wolff, S; Heute, U; Deuschl, G; Raethjen, J; Muthuraman, Muthuraman

2016-09-01

Recently, interest has been growing to understand the underlying dynamic directional relationship between simultaneously activated regions of the brain during motor task performance. Such directionality analysis (or effective connectivity analysis), based on non-invasive electrophysiological (electroencephalography-EEG) and hemodynamic (functional near infrared spectroscopy-fNIRS; and functional magnetic resonance imaging-fMRI) neuroimaging modalities can provide an estimate of the motor task-related information flow from one brain region to another. Since EEG, fNIRS and fMRI modalities achieve different spatial and temporal resolutions of motor-task related activation in the brain, the aim of this study was to determine the effective connectivity of cortico-cortical sensorimotor networks during finger movement tasks measured by each neuroimaging modality. Nine healthy subjects performed right hand finger movement tasks of different complexity (simple finger tapping-FT, simple finger sequence-SFS, and complex finger sequence-CFS). We focused our observations on three cortical regions of interest (ROIs), namely the contralateral sensorimotor cortex (SMC), the contralateral premotor cortex (PMC) and the contralateral dorsolateral prefrontal cortex (DLPFC). We estimated the effective connectivity between these ROIs using conditional Granger causality (GC) analysis determined from the time series signals measured by fMRI (blood oxygenation level-dependent-BOLD), fNIRS (oxygenated-O2Hb and deoxygenated-HHb hemoglobin), and EEG (scalp and source level analysis) neuroimaging modalities. The effective connectivity analysis showed significant bi-directional information flow between the SMC, PMC, and DLPFC as determined by the EEG (scalp and source), fMRI (BOLD) and fNIRS (O2Hb and HHb) modalities for all three motor tasks. However the source level EEG GC values were significantly greater than the other modalities. In addition, only the source level EEG showed a

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…

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.

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.

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.

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

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.

Neural Sequence Generation Using Spatiotemporal Patterns of Inhibition.

Directory of Open Access Journals (Sweden)

Jonathan Cannon

2015-11-01

Full Text Available Stereotyped sequences of neural activity are thought to underlie reproducible behaviors and cognitive processes ranging from memory recall to arm movement. One of the most prominent theoretical models of neural sequence generation is the synfire chain, in which pulses of synchronized spiking activity propagate robustly along a chain of cells connected by highly redundant feedforward excitation. But recent experimental observations in the avian song production pathway during song generation have shown excitatory activity interacting strongly with the firing patterns of inhibitory neurons, suggesting a process of sequence generation more complex than feedforward excitation. Here we propose a model of sequence generation inspired by these observations in which a pulse travels along a spatially recurrent excitatory chain, passing repeatedly through zones of local feedback inhibition. In this model, synchrony and robust timing are maintained not through redundant excitatory connections, but rather through the interaction between the pulse and the spatiotemporal pattern of inhibition that it creates as it circulates the network. These results suggest that spatially and temporally structured inhibition may play a key role in sequence generation.

Neural Sequence Generation Using Spatiotemporal Patterns of Inhibition.

Science.gov (United States)

Cannon, Jonathan; Kopell, Nancy; Gardner, Timothy; Markowitz, Jeffrey

2015-11-01

Stereotyped sequences of neural activity are thought to underlie reproducible behaviors and cognitive processes ranging from memory recall to arm movement. One of the most prominent theoretical models of neural sequence generation is the synfire chain, in which pulses of synchronized spiking activity propagate robustly along a chain of cells connected by highly redundant feedforward excitation. But recent experimental observations in the avian song production pathway during song generation have shown excitatory activity interacting strongly with the firing patterns of inhibitory neurons, suggesting a process of sequence generation more complex than feedforward excitation. Here we propose a model of sequence generation inspired by these observations in which a pulse travels along a spatially recurrent excitatory chain, passing repeatedly through zones of local feedback inhibition. In this model, synchrony and robust timing are maintained not through redundant excitatory connections, but rather through the interaction between the pulse and the spatiotemporal pattern of inhibition that it creates as it circulates the network. These results suggest that spatially and temporally structured inhibition may play a key role in sequence generation.

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.

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…

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.

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.

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.

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

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.

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.

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...

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...

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

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.

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.

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

[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.

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....

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.

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.

Visualizing neuronal network connectivity with connectivity pattern tables

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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.

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.

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.

Entropy and Information Approaches to Genetic Diversity and its Expression: Genomic Geography

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William B. Sherwin

2010-07-01

Full Text Available This article highlights advantages of entropy-based genetic diversity measures, at levels from gene expression to landscapes. Shannon’s entropy-based diversity is the standard for ecological communities. The exponentials of Shannon’s and the related “mutual information” excel in their ability to express diversity intuitively, and provide a generalised method of considering microscopic behaviour to make macroscopic predictions, under given conditions. The hierarchical nature of entropy and information allows integrated modeling of diversity along one DNA sequence, and between different sequences within and among populations, species, etc. The aim is to identify the formal connections between genetic diversity and the flow of information to and from the environment.

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…

[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.

Heteroassociative storage of hippocampal pattern sequences in the CA3 subregion

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Raphael Y. de Camargo

2018-01-01

Full Text Available Background Recent research suggests that the CA3 subregion of the hippocampus has properties of both autoassociative network, due to its ability to complete partial cues, tolerate noise, and store associations between memories, and heteroassociative one, due to its ability to store and retrieve sequences of patterns. Although there are several computational models of the CA3 as an autoassociative network, more detailed evaluations of its heteroassociative properties are missing. Methods We developed a model of the CA3 subregion containing 10,000 integrate-and-fire neurons with both recurrent excitatory and inhibitory connections, and which exhibits coupled oscillations in the gamma and theta ranges. We stored thousands of pattern sequences using a heteroassociative learning rule with competitive synaptic scaling. Results We showed that a purely heteroassociative network model can (i retrieve pattern sequences from partial cues with external noise and incomplete connectivity, (ii achieve homeostasis regarding the number of connections per neuron when many patterns are stored when using synaptic scaling, (iii continuously update the set of retrievable patterns, guaranteeing that the last stored patterns can be retrieved and older ones can be forgotten. Discussion Heteroassociative networks with synaptic scaling rules seem sufficient to achieve many desirable features regarding connectivity homeostasis, pattern sequence retrieval, noise tolerance and updating of the set of retrievable patterns.

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

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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.

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.

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.

Conservation patterns of HIV-1 RT connection and RNase H domains: identification of new mutations in NRTI-treated patients.

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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.

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.

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...

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

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.

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

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

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.

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…

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

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.

Phylogeography and connectivity of molluscan parasites: Perkinsus spp. in Panama and beyond.

Science.gov (United States)

Pagenkopp Lohan, Katrina M; Hill-Spanik, Kristina M; Torchin, Mark E; Fleischer, Robert C; Carnegie, Ryan B; Reece, Kimberly S; Ruiz, Gregory M

2018-02-01

Panama is a major hub for commercial shipping between two oceans, making it an ideal location to examine parasite biogeography, potential invasions, and the spread of infectious agents. Our goals were to (i) characterise the diversity and genetic connectivity of Perkinsus spp. haplotypes across the Panamanian Isthmus and (ii) combine these data with sequences from around the world to evaluate the current phylogeography and genetic connectivity of these widespread molluscan parasites. We collected 752 bivalves from 12 locations along the coast of Panama including locations around the Bocas del Toro archipelago and the Caribbean and Pacific entrances to the Panama Canal, from December 2012 to February 2013. We used molecular genetic methods to screen for Perkinsus spp. and obtained internal transcribed spacer region (ITS) ribosomal DNA (rDNA) sequences for all positive samples. Our sequence data were used to evaluate regional haplotype diversity and distribution across both coasts of Panama, and were then combined with publicly available sequences to create global haplotype networks. We found 26 ITS haplotypes from four Perkinsus spp. (1-12 haplotypes per species) in Panama. Perkinsus beihaiensis haplotypes had the highest genetic diversity, were the most regionally widespread, and were associated with the greatest number of hosts. On a global scale, network analyses demonstrated that some haplotypes found in Panama were cosmopolitan (Perkinsus chesapeaki, Perkinsus marinus), while others were more geographically restricted (Perkinsus olseni, P. beihaiensis), indicating different levels of genetic connectivity and dispersal. We found some Perkinsus haplotypes were shared across the Isthmus of Panama and several regions around the world, including across ocean basins. We also found that haplotype diversity is currently underestimated and directly related to the number of sequences. Nevertheless, our results demonstrate long-range dispersal and global connectivity for

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.

Cell density signal protein suitable for treatment of connective tissue injuries and defects

Science.gov (United States)

Schwarz, Richard I.

2002-08-13

Identification, isolation and partial sequencing of a cell density protein produced by fibroblastic cells. The cell density signal protein comprising a 14 amino acid peptide or a fragment, variant, mutant or analog thereof, the deduced cDNA sequence from the 14 amino acid peptide, a recombinant protein, protein and peptide-specific antibodies, and the use of the peptide and peptide-specific antibodies as therapeutic agents for regulation of cell differentiation and proliferation. A method for treatment and repair of connective tissue and tendon injuries, collagen deficiency, and connective tissue defects.

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

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).

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

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

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.

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? ...

Intrinsic connections and architectonics of posterior parietal cortex in the rhesus monkey

International Nuclear Information System (INIS)

Pandya, D.N.; Seltzer, B.

1982-01-01

By means of autoradiographic and ablation-degeneration techniques, the intrinsic cortical connections of the posterior parietal cortex in the rhesus monkey were traced and correlated with a reappraisal of cerebral architectonics. Two major rostral-to-caudal connectional sequences exist. One begins in the dorsal postcentral gyrus (area 2) and proceeds, through architectonic divisions of the superior parietal lobule (areas PE and PEc), to a cortical region on the medial surface of the parietal lobe (area PGm). This area has architectonic features similar to those of the caudal inferior parietal lobule (area PG). The second sequence begins in the ventral post/central gyrus (area 2) and passes through the rostral inferior parietal lobule (areas PG and PFG) to reach the caudal inferior parietal lobule (area PG). Both the superior parietal lobule and the rostral inferior parietal lobule also send projections to various other zones located in the parietal opercular region, the intraparietal sulcus, and the caudalmost portion of the cingulate sulcus. Areas PGm and PG, on the other hand, project to each other, to the cingulate region, to the caudalmost portion of the superior temporal gyrus, and to the upper bank of the superior temporal sulcus. Finally, a reciprocal sequence of connections, directed from caudal to rostral, links together many of the above-mentioned parietal zones. With regard to the laminar pattern of termination, the rostral-to-caudal connections are primarily distributed in the form of cortical ''columns'' while the caudal-to-rostral connections are found mainly over the first cortical cell layer

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....

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.

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.

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

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.

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.

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…

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.

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.

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.

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.

A simple component-connection method for building binary decision diagrams encoding a fault tree

International Nuclear Information System (INIS)

Way, Y.-S.; Hsia, D.-Y.

2000-01-01

A simple new method for building binary decision diagrams (BDDs) encoding a fault tree (FT) is provided in this study. We first decompose the FT into FT-components. Each of them is a single descendant (SD) gate-sequence. Following the node-connection rule, the BDD-component encoding an SD FT-component can each be found to be an SD node-sequence. By successively connecting the BDD-components one by one, the BDD for the entire FT is thus obtained. During the node-connection and component-connection, reduction rules might need to be applied. An example FT is used throughout the article to explain the procedure step by step. Our method proposed is a hybrid one for FT analysis. Some algorithms or techniques used in the conventional FT analysis or the newer BDD approach may be applied to our case; our ideas mentioned in the article might be referred by the two methods

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.

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.

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

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.)

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.

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...

Structural and Functional Brain Connectivity of People with Obesity and Prediction of Body Mass Index Using Connectivity.

Directory of Open Access Journals (Sweden)

Bo-yong Park

Full Text Available Obesity is a medical condition affecting billions of people. Various neuroimaging methods including magnetic resonance imaging (MRI have been used to obtain information about obesity. We adopted a multi-modal approach combining diffusion tensor imaging (DTI and resting state functional MRI (rs-fMRI to incorporate complementary information and thus better investigate the brains of non-healthy weight subjects. The objective of this study was to explore multi-modal neuroimaging and use it to predict a practical clinical score, body mass index (BMI. Connectivity analysis was applied to DTI and rs-fMRI. Significant regions and associated imaging features were identified based on group-wise differences between healthy weight and non-healthy weight subjects. Six DTI-driven connections and 10 rs-fMRI-driven connectivities were identified. DTI-driven connections better reflected group-wise differences than did rs-fMRI-driven connectivity. We predicted BMI values using multi-modal imaging features in a partial least-square regression framework (percent error 15.0%. Our study identified brain regions and imaging features that can adequately explain BMI. We identified potentially good imaging biomarker candidates for obesity-related diseases.

New approaches in mathematical biology: Information theory and molecular machines

International Nuclear Information System (INIS)

Schneider, T.

1995-01-01

My research uses classical information theory to study genetic systems. Information theory was founded by Claude Shannon in the 1940's and has had an enormous impact on communications engineering and computer sciences. Shannon found a way to measure information. This measure can be used to precisely characterize the sequence conservation at nucleic-acid binding sites. The resulting methods, by completely replacing the use of ''consensus sequences'', provide better models for molecular biologists. An excess of conservation led us to do experimental work on bacteriophage T7 promoters and the F plasmid IncD repeats. The wonderful fidelity of telephone communications and compact disk (CD) music can be traced directly to Shannon's channel capacity theorem. When rederived for molecular biology, this theorem explains the surprising precision of many molecular events. Through connections with the Second Law of Thermodyanmics and Maxwell's Demon, this approach also has implications for the development of technology at the molecular level. Discussions of these topics are held on the internet news group bionet.info-theo. (author). (Abstract only)

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...

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

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

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....

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...

Asymmetrical Grid Fault Ride-Through Strategy of Three-phase Grid-connected Inverter Considering Network Impedance Impact in Low Voltage Grid

DEFF Research Database (Denmark)

Guo, Xiaoqiang; Zhang, Xue; Wang, Baocheng

2014-01-01

This letter presents a new control strategy of threephase grid-connected inverter for the positive sequence voltage recovery and negative sequence voltage reduction under asymmetrical grid faults. Unlike the conventional control strategy based on an assumption that the network impedance is mainly...... of the proposed solution for the flexible voltage support in a low-voltage grid, where thenetwork impedance is mainly resistive.......This letter presents a new control strategy of threephase grid-connected inverter for the positive sequence voltage recovery and negative sequence voltage reduction under asymmetrical grid faults. Unlike the conventional control strategy based on an assumption that the network impedance is mainly...... inductive, the proposed control strategy is more flexible and effective by considering the network impedance impact, which is of great importance for the high penetration of grid-connected renewable energy systems into low-voltage grids. The experimental tests are carried out to validate the effectiveness...

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

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

Decoding spatiotemporal spike sequences via the finite state automata dynamics of spiking neural networks

International Nuclear Information System (INIS)

Jin, Dezhe Z

2008-01-01

Temporally complex stimuli are encoded into spatiotemporal spike sequences of neurons in many sensory areas. Here, we describe how downstream neurons with dendritic bistable plateau potentials can be connected to decode such spike sequences. Driven by feedforward inputs from the sensory neurons and controlled by feedforward inhibition and lateral excitation, the neurons transit between UP and DOWN states of the membrane potentials. The neurons spike only in the UP states. A decoding neuron spikes at the end of an input to signal the recognition of specific spike sequences. The transition dynamics is equivalent to that of a finite state automaton. A connection rule for the networks guarantees that any finite state automaton can be mapped into the transition dynamics, demonstrating the equivalence in computational power between the networks and finite state automata. The decoding mechanism is capable of recognizing an arbitrary number of spatiotemporal spike sequences, and is insensitive to the variations of the spike timings in the sequences

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.

Population coding in sparsely connected networks of noisy neurons.

Science.gov (United States)

Tripp, Bryan P; Orchard, Jeff

2012-01-01

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 behavior. 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 modeled a sheet of cortical neurons with sparse, primarily local connections, and found that a network with this structure could encode multiple internal state variables with high signal-to-noise ratio. However, we were unable to create high-fidelity networks by instantiating connections at random according to spatial connection probabilities. In our models, high-fidelity networks required additional structure, with higher cluster factors and correlations between the inputs to nearby neurons.

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.

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...

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.

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...

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...

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.

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...

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.

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.

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.

Quantum control of ultra-cold atoms: uncovering a novel connection between two paradigms of quantum nonlinear dynamics

DEFF Research Database (Denmark)

Wang, Jiao; Mouritzen, Anders Sørrig; Gong, Jiangbin

2009-01-01

Controlling the translational motion of cold atoms using optical lattice potentials is of both theoretical and experimental interest. By designing two on-resonance time sequences of kicking optical lattice potentials, a novel connection between two paradigms of nonlinear mapping systems, i.e. the...... sequences of control fields. Extensions of this study are also discussed. The results are intended to open up a new generation of cold-atom experiments of quantum nonlinear dynamics.......Controlling the translational motion of cold atoms using optical lattice potentials is of both theoretical and experimental interest. By designing two on-resonance time sequences of kicking optical lattice potentials, a novel connection between two paradigms of nonlinear mapping systems, i...

Connective tissue activation. XXXII. Structural and biologic characteristics of mesenchymal cell-derived connective tissue activating peptide-V.

Science.gov (United States)

Cabral, A R; Cole, L A; Walz, D A; Castor, C W

1987-12-01

Connective tissue activating peptide-V (CTAP-V) is a single-chain, mesenchymal cell-derived anionic protein with large and small molecular forms (Mr of 28,000 and 16,000, respectively), as defined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The proteins have similar specific activities with respect to stimulation of hyaluronic acid and DNA formation in human synovial fibroblast cultures. S-carboxymethylation or removal of sialic acid residues did not modify CTAP-V biologic activity. Rabbit antibodies raised separately against each of the purified CTAP-V proteins reacted, on immunodiffusion and on Western blot, with each antigen and neutralized mitogenic activity. The amino-terminal amino acid sequence of the CTAP-V proteins, determined by 2 laboratories, confirmed their structural similarities. The amino-terminal sequence through 37 residues was demonstrated for the smaller protein. The first 10 residues of CTAP-V (28 kd) were identical to the N-terminal decapeptide of CTAP-V (16 kd). The C-terminal sequence, determined by carboxypeptidase Y digestion, was the same for both CTAP-V molecular species. The 2 CTAP-V peptides had similar amino acid compositions, whether residues were expressed as a percent of the total or were normalized to mannose. Reduction of native CTAP-V protein released sulfhydryl groups in a protein:disulfide ratio of 1:2; this suggests that CTAP-V contains 2 intramolecular disulfide bonds. Clearly, CTAP-V is a glycoprotein. The carbohydrate content of CTAP-V (16 kd) and CTAP-V (28 kd) is 27% and 25%, respectively. CTAP-V may have significance in relation to autocrine mechanisms for growth regulation of connective tissue cells and other cell types.

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.

Perfusion deficits and functional connectivity alterations in patients with post-traumatic stress disorder

Science.gov (United States)

Liu, Yang; Li, Baojuan; Zhang, Xi; Zhang, Linchuan; Li, Liang; Lu, Hongbing

2016-03-01

To explore the alteration in cerebral blood flow (CBF) and functional connectivity between survivors with recent onset post-traumatic stress disorder (PTSD) and without PTSD, survived from the same coal mine flood disaster. In this study, a processing pipeline using arterial spin labeling (ASL) sequence was proposed. Considering low spatial resolution of ASL sequence, a linear regression method was firstly used to correct the partial volume (PV) effect for better CBF estimation. Then the alterations of CBF between two groups were analyzed using both uncorrected and PV-corrected CBF maps. Based on altered CBF regions detected from the CBF analysis as seed regions, the functional connectivity abnormities in PTSD patients was investigated. The CBF analysis using PV-corrected maps indicates CBF deficits in the bilateral frontal lobe, right superior frontal gyrus and right corpus callosum of PTSD patients, while only right corpus callosum was identified in uncorrected CBF analysis. Furthermore, the regional CBF of the right superior frontal gyrus exhibits significantly negative correlation with the symptom severity in PTSD patients. The resting-state functional connectivity indicates increased connectivity between left frontal lobe and right parietal lobe. These results indicate that PV-corrected CBF exhibits more subtle perfusion changes and may benefit further perfusion and connectivity analysis. The symptom-specific perfusion deficits and aberrant connectivity in above memory-related regions may be putative biomarkers for recent onset PTSD induced by a single prolonged trauma exposure and help predict the severity of PTSD.

Technical guide to the connection of generation to the distribution network

Energy Technology Data Exchange (ETDEWEB)

Jarrett, K.; Hedgecock, J.; Gregory, R.; Warham, T.

2003-07-01

This guide provides a 'route map' of the processes of getting a generation scheme connected to the network and is intended to help developers of any form of distributed generation connected to the UK's local electricity networks, eg: renewable energy schemes; waste-to-energy schemes; on-site generation and combined heat and power (CHP) schemes; and peak lopping schemes using back-up generators. Where necessary, the guide distinguishes between arrangements that apply in Scotland and those that apply in England and Wales. The guide aims to: provide background information about the electricity industry; highlight common technical issues that arise during connection negotiation and their implications for distribution network operators (DNOs) and developers; examine the main factors affecting connection costs and timescales for achieving connections; and identify the different types of contracts relating to connection. The report considers the connection process, the connection application process and timescales, costs and charges, competition in connection, the structure of the UK electricity industry, the statutory framework, the effects of distributed generation of the distribution system, earthing and protection design, safety issues and DNO network information. It includes a glossary, checklists, useful contact details and information about standards and other useful documents.

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.

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

A microfabricated hybrid device for DNA sequencing.

Science.gov (United States)

Liu, Shaorong

2003-11-01

We have created a hybrid device of a microfabricated round-channel twin-T injector incorporated with a separation capillary in order to extend the straight separation distance for high speed and long readlength DNA sequencing. Semicircular grooves on glass wafers are obtained using a photomask with a narrow line-width and a standard isotropic photolithographic etching process. Round channels are made when two etched wafers are face-to-face aligned and bonded. A two-mask fabrication process has been developed to make channels of two different diameters. The twin-T injector is formed by the smaller channels whose diameter matches the bore of the separation capillary, and the "usual" separation channel, now called the connection channel, is formed by the larger ones whose diameter matches the outer diameter of the separation capillary. The separation capillary is inserted through the connection channel all the way to the twin-T injector to allow the capillary bore flush with the twin-T injector channels. The total dead-volume of the connection is estimated to be approximately 5 pL. To demonstrate the efficiency of this hybrid device, we have performed four-color DNA sequencing on it. Using a 200 microm twin-T injector coupled with a separation capillary of 20 cm effective separation distance, we have obtained readlengths of 800 plus bases at an accuracy of 98.5% in 56 min, compared to about 650 bases in 100 min on a conventional 40 cm long capillary sequencing machine under similar conditions. At an increased separation field strength and using a diluted sieving matrix, the separation time has been reduced to 20 min with a readlength of 700 bases at 98.5% base-calling accuracy.

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.

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.

Multiband multi-echo imaging of simultaneous oxygenation and flow timeseries for resting state connectivity.

Science.gov (United States)

Cohen, Alexander D; Nencka, Andrew S; Lebel, R Marc; Wang, Yang

2017-01-01

A novel sequence has been introduced that combines multiband imaging with a multi-echo acquisition for simultaneous high spatial resolution pseudo-continuous arterial spin labeling (ASL) and blood-oxygenation-level dependent (BOLD) echo-planar imaging (MBME ASL/BOLD). Resting-state connectivity in healthy adult subjects was assessed using this sequence. Four echoes were acquired with a multiband acceleration of four, in order to increase spatial resolution, shorten repetition time, and reduce slice-timing effects on the ASL signal. In addition, by acquiring four echoes, advanced multi-echo independent component analysis (ME-ICA) denoising could be employed to increase the signal-to-noise ratio (SNR) and BOLD sensitivity. Seed-based and dual-regression approaches were utilized to analyze functional connectivity. Cerebral blood flow (CBF) and BOLD coupling was also evaluated by correlating the perfusion-weighted timeseries with the BOLD timeseries. These metrics were compared between single echo (E2), multi-echo combined (MEC), multi-echo combined and denoised (MECDN), and perfusion-weighted (PW) timeseries. Temporal SNR increased for the MECDN data compared to the MEC and E2 data. Connectivity also increased, in terms of correlation strength and network size, for the MECDN compared to the MEC and E2 datasets. CBF and BOLD coupling was increased in major resting-state networks, and that correlation was strongest for the MECDN datasets. These results indicate our novel MBME ASL/BOLD sequence, which collects simultaneous high-resolution ASL/BOLD data, could be a powerful tool for detecting functional connectivity and dynamic neurovascular coupling during the resting state. The collection of more than two echoes facilitates the use of ME-ICA denoising to greatly improve the quality of resting state functional connectivity MRI.

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

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.

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.

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.

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...

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.

Googling DNA sequences on the World Wide Web.

Science.gov (United States)

Hajibabaei, Mehrdad; Singer, Gregory A C

2009-11-10

New web-based technologies provide an excellent opportunity for sharing and accessing information and using web as a platform for interaction and collaboration. Although several specialized tools are available for analyzing DNA sequence information, conventional web-based tools have not been utilized for bioinformatics applications. We have developed a novel algorithm and implemented it for searching species-specific genomic sequences, DNA barcodes, by using popular web-based methods such as Google. We developed an alignment independent character based algorithm based on dividing a sequence library (DNA barcodes) and query sequence to words. The actual search is conducted by conventional search tools such as freely available Google Desktop Search. We implemented our algorithm in two exemplar packages. We developed pre and post-processing software to provide customized input and output services, respectively. Our analysis of all publicly available DNA barcode sequences shows a high accuracy as well as rapid results. Our method makes use of conventional web-based technologies for specialized genetic data. It provides a robust and efficient solution for sequence search on the web. The integration of our search method for large-scale sequence libraries such as DNA barcodes provides an excellent web-based tool for accessing this information and linking it to other available categories of information on the web.

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

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...

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.

Homology groups for particles on one-connected graphs

Science.gov (United States)

MaciÄ Żek, Tomasz; Sawicki, Adam

2017-06-01

We present a mathematical framework for describing the topology of configuration spaces for particles on one-connected graphs. In particular, we compute the homology groups over integers for different classes of one-connected graphs. Our approach is based on some fundamental combinatorial properties of the configuration spaces, Mayer-Vietoris sequences for different parts of configuration spaces, and some limited use of discrete Morse theory. As one of the results, we derive the closed-form formulae for ranks of the homology groups for indistinguishable particles on tree graphs. We also give a detailed discussion of the second homology group of the configuration space of both distinguishable and indistinguishable particles. Our motivation is the search for new kinds of quantum statistics.

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.

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 ...

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

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

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

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.

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

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.

ASAP: Amplification, sequencing & annotation of plastomes

Directory of Open Access Journals (Sweden)

Folta Kevin M

2005-12-01

Full Text Available Abstract Background Availability of DNA sequence information is vital for pursuing structural, functional and comparative genomics studies in plastids. Traditionally, the first step in mining the valuable information within a chloroplast genome requires sequencing a chloroplast plasmid library or BAC clones. These activities involve complicated preparatory procedures like chloroplast DNA isolation or identification of the appropriate BAC clones to be sequenced. Rolling circle amplification (RCA is being used currently to amplify the chloroplast genome from purified chloroplast DNA and the resulting products are sheared and cloned prior to sequencing. Herein we present a universal high-throughput, rapid PCR-based technique to amplify, sequence and assemble plastid genome sequence from diverse species in a short time and at reasonable cost from total plant DNA, using the large inverted repeat region from strawberry and peach as proof of concept. The method exploits the highly conserved coding regions or intergenic regions of plastid genes. Using an informatics approach, chloroplast DNA sequence information from 5 available eudicot plastomes was aligned to identify the most conserved regions. Cognate primer pairs were then designed to generate ~1 – 1.2 kb overlapping amplicons from the inverted repeat region in 14 diverse genera. Results 100% coverage of the inverted repeat region was obtained from Arabidopsis, tobacco, orange, strawberry, peach, lettuce, tomato and Amaranthus. Over 80% coverage was obtained from distant species, including Ginkgo, loblolly pine and Equisetum. Sequence from the inverted repeat region of strawberry and peach plastome was obtained, annotated and analyzed. Additionally, a polymorphic region identified from gel electrophoresis was sequenced from tomato and Amaranthus. Sequence analysis revealed large deletions in these species relative to tobacco plastome thus exhibiting the utility of this method for structural and

Sequence Capture versus Restriction Site Associated DNA Sequencing for Shallow Systematics.

Science.gov (United States)

Harvey, Michael G; Smith, Brian Tilston; Glenn, Travis C; Faircloth, Brant C; Brumfield, Robb T

2016-09-01

Sequence capture and restriction site associated DNA sequencing (RAD-Seq) are two genomic enrichment strategies for applying next-generation sequencing technologies to systematics studies. At shallow timescales, such as within species, RAD-Seq has been widely adopted among researchers, although there has been little discussion of the potential limitations and benefits of RAD-Seq and sequence capture. We discuss a series of issues that may impact the utility of sequence capture and RAD-Seq data for shallow systematics in non-model species. We review prior studies that used both methods, and investigate differences between the methods by re-analyzing existing RAD-Seq and sequence capture data sets from a Neotropical bird (Xenops minutus). We suggest that the strengths of RAD-Seq data sets for shallow systematics are the wide dispersion of markers across the genome, the relative ease and cost of laboratory work, the deep coverage and read overlap at recovered loci, and the high overall information that results. Sequence capture's benefits include flexibility and repeatability in the genomic regions targeted, success using low-quality samples, more straightforward read orthology assessment, and higher per-locus information content. The utility of a method in systematics, however, rests not only on its performance within a study, but on the comparability of data sets and inferences with those of prior work. In RAD-Seq data sets, comparability is compromised by low overlap of orthologous markers across species and the sensitivity of genetic diversity in a data set to an interaction between the level of natural heterozygosity in the samples examined and the parameters used for orthology assessment. In contrast, sequence capture of conserved genomic regions permits interrogation of the same loci across divergent species, which is preferable for maintaining comparability among data sets and studies for the purpose of drawing general conclusions about the impact of

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

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.

SDSS-IV MaNGA: Spatially Resolved Star Formation Main Sequence and LI(N)ER Sequence

Science.gov (United States)

Hsieh, B. C.; Lin, Lihwai; Lin, J. H.; Pan, H. A.; Hsu, C. H.; Sánchez, S. F.; Cano-Díaz, M.; Zhang, K.; Yan, R.; Barrera-Ballesteros, J. K.; Boquien, M.; Riffel, R.; Brownstein, J.; Cruz-González, I.; Hagen, A.; Ibarra, H.; Pan, K.; Bizyaev, D.; Oravetz, D.; Simmons, A.

2017-12-01

We present our study on the spatially resolved Hα and M * relation for 536 star-forming and 424 quiescent galaxies taken from the MaNGA survey. We show that the star formation rate surface density ({{{Σ }}}{SFR}), derived based on the Hα emissions, is strongly correlated with the M * surface density ({{{Σ }}}* ) on kiloparsec scales for star-forming galaxies and can be directly connected to the global star-forming sequence. This suggests that the global main sequence may be a consequence of a more fundamental relation on small scales. On the other hand, our result suggests that ∼20% of quiescent galaxies in our sample still have star formation activities in the outer region with lower specific star formation rate (SSFR) than typical star-forming galaxies. Meanwhile, we also find a tight correlation between {{{Σ }}}{{H}α } and {{{Σ }}}* for LI(N)ER regions, named the resolved “LI(N)ER” sequence, in quiescent galaxies, which is consistent with the scenario that LI(N)ER emissions are primarily powered by the hot, evolved stars as suggested in the literature.

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)

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

Jubilite: A 4-,8-connected Cubic Structural Pattern in Space Group Pm3

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Eduardo A. Castro

2005-05-01

Full Text Available Abstract: In the course of investigating structural modifications of the 3-,4-connected net known as the Pt3O4 structure-type (waserite, a novel 4-,8-connected structure-type was discovered. This lattice is generated by replacing the 3-connected trigonal planar vertices of the Pt3O4 structure-type with 4-connected tetrahedral vertices, to achieve a structure which possesses a generic empirical formula of JK6L8. In such a topological modification, the four 3-fold axes of the parent cubic, Pm3n, Pt3O4 structure-type are retained. Thus the 4-connected tetrahedral vertices are oriented so as to preserve cubic symmetry in the resulting Pm3, JK6L8 (jubilite lattice. The unit cell contains a single 8-connected cubecentered vertex, six 4-connected distorted square planar vertices and eight 4-connected distorted tetrahedral vertices. It is a Wellsean structure with a Wells point symbol given by (4166484(42826(43838 and a Schläfli symbol of (53/4, 4.2667. This latter index reveals a decrease in the lattice’s polygonality and concomitant increase in the connectivity through the transformation from waserite to jubilite. The topology of the parent waserite lattice (Pt3O4 corresponds to that of the Catalan structures with the Wells point symbol (843(834, which has the Schläfli symbol (8, 3.4285. Finally, it can be seen that a sequence of structure-types starting with waserite (Pt3O4 and moving to jubilite (JK6L8 and finally to fluorite (CaF2 represents a continuous crystallographic structural transformation in which the symmetry and topology undergo concomitant changes from one structure-type (waserite to the other structure-types. The topology of the fluorite lattice, represented by the Wells point symbol (424(462, and the Schläfli symbol (4, 51/3, indicates a discontinuous topological transformation from the intermediate jubilite lattice; like the discontinuous topological transformation from Pt3O4 to JK6L8; in which the

Sequencing of BAC pools by different next generation sequencing platforms and strategies

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Scholz Uwe

2011-10-01

Full Text Available Abstract Background Next generation sequencing of BACs is a viable option for deciphering the sequence of even large and highly repetitive genomes. In order to optimize this strategy, we examined the influence of read length on the quality of Roche/454 sequence assemblies, to what extent Illumina/Solexa mate pairs (MPs improve the assemblies by scaffolding and whether barcoding of BACs is dispensable. Results Sequencing four BACs with both FLX and Titanium technologies revealed similar sequencing accuracy, but showed that the longer Titanium reads produce considerably less misassemblies and gaps. The 454 assemblies of 96 barcoded BACs were improved by scaffolding 79% of the total contig length with MPs from a non-barcoded library. Assembly of the unmasked 454 sequences without separation by barcodes revealed chimeric contig formation to be a major problem, encompassing 47% of the total contig length. Masking the sequences reduced this fraction to 24%. Conclusion Optimal BAC pool sequencing should be based on the longest available reads, with barcoding essential for a comprehensive assessment of both repetitive and non-repetitive sequence information. When interest is restricted to non-repetitive regions and repeats are masked prior to assembly, barcoding is non-essential. In any case, the assemblies can be improved considerably by scaffolding with non-barcoded BAC pool MPs.

Establishing a framework for comparative analysis of genome sequences

Energy Technology Data Exchange (ETDEWEB)

Bansal, A.K.

1995-06-01

This paper describes a framework and a high-level language toolkit for comparative analysis of genome sequence alignment The framework integrates the information derived from multiple sequence alignment and phylogenetic tree (hypothetical tree of evolution) to derive new properties about sequences. Multiple sequence alignments are treated as an abstract data type. Abstract operations have been described to manipulate a multiple sequence alignment and to derive mutation related information from a phylogenetic tree by superimposing parsimonious analysis. The framework has been applied on protein alignments to derive constrained columns (in a multiple sequence alignment) that exhibit evolutionary pressure to preserve a common property in a column despite mutation. A Prolog toolkit based on the framework has been implemented and demonstrated on alignments containing 3000 sequences and 3904 columns.

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

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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

Design of Tail-Clamp Peptide Nucleic Acid Tethered with Azobenzene Linker for Sequence-Specific Detection of Homopurine DNA

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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.

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

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.

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.

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

Habenula functional resting-state connectivity in pediatric CRPS.

Science.gov (United States)

Erpelding, Nathalie; Sava, Simona; Simons, Laura E; Lebel, Alyssa; Serrano, Paul; Becerra, Lino; Borsook, David

2014-01-01

The habenula (Hb) is a small brain structure located in the posterior end of the medial dorsal thalamus and through medial (MHb) and lateral (LHb) Hb connections, it acts as a conduit of information between forebrain and brainstem structures. The role of the Hb in pain processing is well documented in animals and recently also in acute experimental pain in humans. However, its function remains unknown in chronic pain disorders. Here, we investigated Hb resting-state functional connectivity (rsFC) in patients with complex regional pain syndrome (CRPS) compared with healthy controls. Twelve pediatric patients with unilateral lower-extremity CRPS (9 females; 10-17 yr) and 12 age- and sex-matched healthy controls provided informed consent to participate in the study. In healthy controls, Hb functional connections largely overlapped with previously described anatomical connections in cortical, subcortical, and brainstem structures. Compared with controls, patients exhibited an overall Hb rsFC reduction with the rest of the brain and, specifically, with the anterior midcingulate cortex, dorsolateral prefrontal cortex, supplementary motor cortex, primary motor cortex, and premotor cortex. Our results suggest that Hb rsFC parallels anatomical Hb connections in the healthy state and that overall Hb rsFC is reduced in patients, particularly connections with forebrain areas. Patients' decreased Hb rsFC to brain regions implicated in motor, affective, cognitive, and pain inhibitory/modulatory processes may contribute to their symptomatology.

Human Genome Sequencing in Health and Disease

Science.gov (United States)

Gonzaga-Jauregui, Claudia; Lupski, James R.; Gibbs, Richard A.

2013-01-01

Following the “finished,” euchromatic, haploid human reference genome sequence, the rapid development of novel, faster, and cheaper sequencing technologies is making possible the era of personalized human genomics. Personal diploid human genome sequences have been generated, and each has contributed to our better understanding of variation in the human genome. We have consequently begun to appreciate the vastness of individual genetic variation from single nucleotide to structural variants. Translation of genome-scale variation into medically useful information is, however, in its infancy. This review summarizes the initial steps undertaken in clinical implementation of personal genome information, and describes the application of whole-genome and exome sequencing to identify the cause of genetic diseases and to suggest adjuvant therapies. Better analysis tools and a deeper understanding of the biology of our genome are necessary in order to decipher, interpret, and optimize clinical utility of what the variation in the human genome can teach us. Personal genome sequencing may eventually become an instrument of common medical practice, providing information that assists in the formulation of a differential diagnosis. We outline herein some of the remaining challenges. PMID:22248320

Estimating migratory connectivity of birds when re-encounter probabilities are heterogeneous

Science.gov (United States)

Cohen, Emily B.; Hostelter, Jeffrey A.; Royle, J. Andrew; Marra, Peter P.

2014-01-01

Understanding the biology and conducting effective conservation of migratory species requires an understanding of migratory connectivity – the geographic linkages of populations between stages of the annual cycle. Unfortunately, for most species, we are lacking such information. The North American Bird Banding Laboratory (BBL) houses an extensive database of marking, recaptures and recoveries, and such data could provide migratory connectivity information for many species. To date, however, few species have been analyzed for migratory connectivity largely because heterogeneous re-encounter probabilities make interpretation problematic. We accounted for regional variation in re-encounter probabilities by borrowing information across species and by using effort covariates on recapture and recovery probabilities in a multistate capture–recapture and recovery model. The effort covariates were derived from recaptures and recoveries of species within the same regions. We estimated the migratory connectivity for three tern species breeding in North America and over-wintering in the tropics, common (Sterna hirundo), roseate (Sterna dougallii), and Caspian terns (Hydroprogne caspia). For western breeding terns, model-derived estimates of migratory connectivity differed considerably from those derived directly from the proportions of re-encounters. Conversely, for eastern breeding terns, estimates were merely refined by the inclusion of re-encounter probabilities. In general, eastern breeding terns were strongly connected to eastern South America, and western breeding terns were strongly linked to the more western parts of the nonbreeding range under both models. Through simulation, we found this approach is likely useful for many species in the BBL database, although precision improved with higher re-encounter probabilities and stronger migratory connectivity. We describe an approach to deal with the inherent biases in BBL banding and re-encounter data to demonstrate

Rfam: annotating families of non-coding RNA sequences.

Science.gov (United States)

Daub, Jennifer; Eberhardt, Ruth Y; Tate, John G; Burge, Sarah W

2015-01-01

The primary task of the Rfam database is to collate experimentally validated noncoding RNA (ncRNA) sequences from the published literature and facilitate the prediction and annotation of new homologues in novel nucleotide sequences. We group homologous ncRNA sequences into "families" and related families are further grouped into "clans." We collate and manually curate data cross-references for these families from other databases and external resources. Our Web site offers researchers a simple interface to Rfam and provides tools with which to annotate their own sequences using our covariance models (CMs), through our tools for searching, browsing, and downloading information on Rfam families. In this chapter, we will work through examples of annotating a query sequence, collating family information, and searching for data.

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.

Research based teaching sequence for enhancing electrical capacitance understanding at first fist year of university

Directory of Open Access Journals (Sweden)

Jenaro Guisasola

2011-04-01

Full Text Available In the electricity curriculum for introductory university physics courses and final secondary school courses, no provision is normally made for a teaching sequence which analyses the transition of specific charges to charged bodies, thus preventing the construction of a model able to explain the aspects connected with the process of charging a body, accumulating the charge and its relation to the potential acquired. This constituted a relevant historical problem and demanded the introduction of a new concept, that of electrical capacitance, to solve it. The aim of the work presented here is to design and assess a teaching sequence which endeavours to overcome the difficulties in learning found in the bibliography. The structure of the sequence was established in activities following a “problematised structure” design. The problems defining the sequence appeared when a step-by-step analysis of the transfer of charges from one body to another was made, by establishing connections between the movement of charges (microscopic level. The results of implementing the sequence indicate that a considerable number of students have achieved a more satisfactory understanding of the electrical capacitance of bodies and charging processes. This seems to confirm that the aspects highlighted in the sequence are relevant to the objectives specified.

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.

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.

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...

Task-related functional connectivity of the caudate mediates the association between trait mindfulness and implicit learning in older adults.

Science.gov (United States)

Stillman, Chelsea M; You, Xiaozhen; Seaman, Kendra L; Vaidya, Chandan J; Howard, James H; Howard, Darlene V

2016-08-01

Accumulating evidence shows a positive relationship between mindfulness and explicit cognitive functioning, i.e., that which occurs with conscious intent and awareness. However, recent evidence suggests that there may be a negative relationship between mindfulness and implicit types of learning, or those that occur without conscious awareness or intent. Here we examined the neural mechanisms underlying the recently reported negative relationship between dispositional mindfulness and implicit probabilistic sequence learning in both younger and older adults. We tested the hypothesis that the relationship is mediated by communication, or functional connectivity, of brain regions once traditionally considered to be central to dissociable learning systems: the caudate, medial temporal lobe (MTL), and prefrontal cortex (PFC). We first replicated the negative relationship between mindfulness and implicit learning in a sample of healthy older adults (60-90 years old) who completed three event-related runs of an implicit sequence learning task. Then, using a seed-based connectivity approach, we identified task-related connectivity associated with individual differences in both learning and mindfulness. The main finding was that caudate-MTL connectivity (bilaterally) was positively correlated with learning and negatively correlated with mindfulness. Further, the strength of task-related connectivity between these regions mediated the negative relationship between mindfulness and learning. This pattern of results was limited to the older adults. Thus, at least in healthy older adults, the functional communication between two interactive learning-relevant systems can account for the relationship between mindfulness and implicit probabilistic sequence learning.

LookSeq: A browser-based viewer for deep sequencing data

OpenAIRE

Manske, Heinrich Magnus; Kwiatkowski, Dominic P.

2009-01-01

Sequencing a genome to great depth can be highly informative about heterogeneity within an individual or a population. Here we address the problem of how to visualize the multiple layers of information contained in deep sequencing data. We propose an interactive AJAX-based web viewer for browsing large data sets of aligned sequence reads. By enabling seamless browsing and fast zooming, the LookSeq program assists the user to assimilate information at different levels of resolution, from an ov...

Connected smart sensors make super-smart buildings; Connected smart sensors maken gebouwen superslim

Energy Technology Data Exchange (ETDEWEB)

Van der Veen, J.K.

2012-10-15

In 2020, between 20 and 50 billion appliances will be connected to the internet and exchange information, usually without human intervention. A large part will consist of smart, autonomous sensors that generate their own supply voltage and have wireless connection with the web. The 'internet of things' offers dazzling opportunities for smart buildings [Dutch] In 2020 zullen tussen de twintig en vijftig miljard apparaten met internet verbonden zijn en, veelal zonder tussenkomst van mensen, informatie uitwisselen. Een groot deel hiervan zal bestaan uit slimme, autonome sensoren, die hun eigen voedingsspanning opwekken en draadloos met het web zijn verbonden. Voor slimme gebouwen biedt 'the internet of things' duizelingwekkende mogelijkheden.

Genetic diversity and connectivity in the East African giant mud crab Scylla serrata: Implications for fisheries management.

Directory of Open Access Journals (Sweden)

Cyrus Rumisha

Full Text Available The giant mud crab Scylla serrata provides an important source of income and food to coastal communities in East Africa. However, increasing demand and exploitation due to the growing coastal population, export trade, and tourism industry are threatening the sustainability of the wild stock of this species. Because effective management requires a clear understanding of the connectivity among populations, this study was conducted to assess the genetic diversity and connectivity in the East African mangrove crab S. serrata. A section of 535 base pairs of the cytochrome oxidase subunit I (COI gene and eight microsatellite loci were analysed from 230 tissue samples of giant mud crabs collected from Kenya, Tanzania, Mozambique, Madagascar, and South Africa. Microsatellite genetic diversity (He ranged between 0.56 and 0.6. The COI sequences showed 57 different haplotypes associated with low nucleotide diversity (current nucleotide diversity = 0.29%. In addition, the current nucleotide diversity was lower than the historical nucleotide diversity, indicating overexploitation or historical bottlenecks in the recent history of the studied population. Considering that the coastal population is growing rapidly, East African countries should promote sustainable fishing practices and sustainable use of mangrove resources to protect mud crabs and other marine fauna from the increasing pressure of exploitation. While microsatellite loci did not show significant genetic differentiation (p > 0.05, COI sequences revealed significant genetic divergence between sites on the East coast of Madagascar (ECM and sites on the West coast of Madagascar, mainland East Africa, as well as the Seychelles. Since East African countries agreed to achieve the Convention on Biological Diversity (CBD target to protect over 10% of their marine areas by 2020, the observed pattern of connectivity and the measured genetic diversity can serve to provide useful information for designing

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...

Optimizing and benchmarking de novo transcriptome sequencing: from library preparation to assembly evaluation.

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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

LookSeq: a browser-based viewer for deep sequencing data.

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Manske, Heinrich Magnus; Kwiatkowski, Dominic P

2009-11-01

Sequencing a genome to great depth can be highly informative about heterogeneity within an individual or a population. Here we address the problem of how to visualize the multiple layers of information contained in deep sequencing data. We propose an interactive AJAX-based web viewer for browsing large data sets of aligned sequence reads. By enabling seamless browsing and fast zooming, the LookSeq program assists the user to assimilate information at different levels of resolution, from an overview of a genomic region to fine details such as heterogeneity within the sample. A specific problem, particularly if the sample is heterogeneous, is how to depict information about structural variation. LookSeq provides a simple graphical representation of paired sequence reads that is more revealing about potential insertions and deletions than are conventional methods.

Mobile medical device connectivity: real world solutions.

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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

Design of Long Period Pseudo-Random Sequences from the Addition of m -Sequences over 𝔽 p

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 m -sequences with pairwise-prime linear spans (AMPLS. Using m -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 𝔽 2 , a signal set ( ( 2 n − 1 ( 2 m − 1 , ( 2 n + 1 ( 2 m + 1 , ( 2 ( n + 1 / 2 + 1 ( 2 ( m + 1 / 2 + 1 is constructed.

Empirical validation of directed functional connectivity.

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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.

Accelerated Distributed Dual Averaging Over Evolving Networks of Growing Connectivity

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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.

Auditory and visual connectivity gradients in frontoparietal cortex.

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Braga, Rodrigo M; Hellyer, Peter J; Wise, Richard J S; Leech, Robert

2017-01-01

A frontoparietal network of brain regions is often implicated in both auditory and visual information processing. Although it is possible that the same set of multimodal regions subserves both modalities, there is increasing evidence that there is a differentiation of sensory function within frontoparietal cortex. Magnetic resonance imaging (MRI) in humans was used to investigate whether different frontoparietal regions showed intrinsic biases in connectivity with visual or auditory modalities. Structural connectivity was assessed with diffusion tractography and functional connectivity was tested using functional MRI. A dorsal-ventral gradient of function was observed, where connectivity with visual cortex dominates dorsal frontal and parietal connections, while connectivity with auditory cortex dominates ventral frontal and parietal regions. A gradient was also observed along the posterior-anterior axis, although in opposite directions in prefrontal and parietal cortices. The results suggest that the location of neural activity within frontoparietal cortex may be influenced by these intrinsic biases toward visual and auditory processing. Thus, the location of activity in frontoparietal cortex may be influenced as much by stimulus modality as the cognitive demands of a task. It was concluded that stimulus modality was spatially encoded throughout frontal and parietal cortices, and was speculated that such an arrangement allows for top-down modulation of modality-specific information to occur within higher-order cortex. This could provide a potentially faster and more efficient pathway by which top-down selection between sensory modalities could occur, by constraining modulations to within frontal and parietal regions, rather than long-range connections to sensory cortices. Hum Brain Mapp 38:255-270, 2017. © 2016 Wiley Periodicals, Inc. © 2016 The Authors Human Brain Mapping Published by Wiley Periodicals, Inc.

Augmented brain function by coordinated reset stimulation with slowly varying sequences

Directory of Open Access Journals (Sweden)

Magteld eZeitler

2015-03-01

Full Text Available Several brain disorders are characterized by abnormally strong neuronal synchrony. Coordinated Reset (CR stimulation was developed to selectively counteract abnormal neuronal synchrony by desynchronization. For this, phase resetting stimuli are delivered to different subpopulations in a timely coordinated way. In neural networks with spike timing-dependent plasticity CR stimulation may eventually lead to an anti-kindling, i.e. an unlearning of abnormal synaptic connectivity and abnormal synchrony. The spatiotemporal sequence by which all stimulation sites are stimulated exactly once is called the stimulation site sequence, or briefly sequence. So far, in simulations, pre-clinical and clinical applications CR was applied either with fixed sequences or rapidly varying sequences (RVS. In this computational study we show that appropriate repetition of the sequence with occasional random switching to the next sequence may significantly improve the anti-kindling effect of CR. To this end, a sequence is applied many times before randomly switching to the next sequence. This new method is called SVS CR stimulation, i.e. CR with slowly varying sequences. In a neuronal network with strong short-range excitatory and weak long-range inhibitory dynamic couplings SVS CR stimulation turns out to be superior to CR stimulation with fixed sequences or RVS.

Augmented brain function by coordinated reset stimulation with slowly varying sequences.

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Zeitler, Magteld; Tass, Peter A

2015-01-01

Several brain disorders are characterized by abnormally strong neuronal synchrony. Coordinated Reset (CR) stimulation was developed to selectively counteract abnormal neuronal synchrony by desynchronization. For this, phase resetting stimuli are delivered to different subpopulations in a timely coordinated way. In neural networks with spike timing-dependent plasticity CR stimulation may eventually lead to an anti-kindling, i.e., an unlearning of abnormal synaptic connectivity and abnormal synchrony. The spatiotemporal sequence by which all stimulation sites are stimulated exactly once is called the stimulation site sequence, or briefly sequence. So far, in simulations, pre-clinical and clinical applications CR was applied either with fixed sequences or rapidly varying sequences (RVS). In this computational study we show that appropriate repetition of the sequence with occasional random switching to the next sequence may significantly improve the anti-kindling effect of CR. To this end, a sequence is applied many times before randomly switching to the next sequence. This new method is called SVS CR stimulation, i.e., CR with slowly varying sequences. In a neuronal network with strong short-range excitatory and weak long-range inhibitory dynamic couplings SVS CR stimulation turns out to be superior to CR stimulation with fixed sequences or RVS.

(D,A)∞-modules over (D,A)∞-algebras and spectral sequences

International Nuclear Information System (INIS)

Lapin, S V

2002-01-01

We introduce the construction of a (D,A) ∞ -(co)module over a (D,A) ∞ -(co) algebra and study its main homotopy properties. We establish a connection between (D,A) ∞ -(co)modules over (D,A) ∞ -(co)algebras and spectral sequences, and thus obtain the structure of an A ∞ -comodule over the Milnor A ∞ -coalgebra on the homology of any spectrum directly from the differentials of the Adams spectral sequence of this spectrum

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

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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.

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

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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.

Social network models predict movement and connectivity in ecological landscapes

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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.

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.

Salt tectonics and sequence-stratigraphic history of minibasins near the Sigsbee Escarpment, Gulf of Mexico

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Montoya, Patricia

The focus of this research is to understand the stratigraphic and structural evolution of lower-slope minibasins in the Gulf of Mexico by examining the influence of salt tectonics on sediment transport systems and deep-water facies architecture. Results showed that gravitational subsidence and shortening can cause variations in the relief of salt massifs on opposing sides of a minibasin. These bathymetric variations, combined with changes in sedimentation rates through time, affected not only the distribution of deep-water facies inside the minibasins, but also influenced the evolution of sediment transport systems between minibasins. In order to understand the evolution of salt massifs, this dissertation presents a new approach to evaluate qualitatively the rate of relative massif uplift based on depoaxis shifts and channel geometries identified in minibasins surrounded by mobile salt. From these results it was established that compression was long-lived, and that extension only dominated during late intervals. Stratigraphic analyses showed that there is a strong cyclicity in deep-water facies stacking patterns within lower-slope minibasins, related primarily to cyclical changes in sedimentation rates. A typical sequence starts with a period of slow sedimentation associated with drape facies above each sequence boundary. Then, towards the middle and final stages of the sequence, sedimentation rates increase and turbidity flows fill the minibasin. Previous studies describe processes of fill-and-spill for two adjacent minibasins in the upper and middle slope. However, these models fail to adequately explain fill-and-spill processes in lower slope minibasins surrounded by mobile salt. In particular, they do not consider the effect of variations in bathymetric relief of the intervening massif, nor do they examine multidirectional connections between proximal and distal minibasins. A new dynamic-salt fill-and-spill model is proposed in this dissertation in order to

Quasirandom geometric networks from low-discrepancy sequences

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Estrada, Ernesto

2017-08-01

We define quasirandom geometric networks using low-discrepancy sequences, such as Halton, Sobol, and Niederreiter. The networks are built in d dimensions by considering the d -tuples of digits generated by these sequences as the coordinates of the vertices of the networks in a d -dimensional Id unit hypercube. Then, two vertices are connected by an edge if they are at a distance smaller than a connection radius. We investigate computationally 11 network-theoretic properties of two-dimensional quasirandom networks and compare them with analogous random geometric networks. We also study their degree distribution and their spectral density distributions. We conclude from this intensive computational study that in terms of the uniformity of the distribution of the vertices in the unit square, the quasirandom networks look more random than the random geometric networks. We include an analysis of potential strategies for generating higher-dimensional quasirandom networks, where it is know that some of the low-discrepancy sequences are highly correlated. In this respect, we conclude that up to dimension 20, the use of scrambling, skipping and leaping strategies generate quasirandom networks with the desired properties of uniformity. Finally, we consider a diffusive process taking place on the nodes and edges of the quasirandom and random geometric graphs. We show that the diffusion time is shorter in the quasirandom graphs as a consequence of their larger structural homogeneity. In the random geometric graphs the diffusion produces clusters of concentration that make the process more slow. Such clusters are a direct consequence of the heterogeneous and irregular distribution of the nodes in the unit square in which the generation of random geometric graphs is based on.

Internally connected graphs and the Kashiwara-Vergne Lie algebra

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Felder, Matteo

2018-02-01

It is conjectured that the Kashiwara-Vergne Lie algebra \\widehat{krv}_2 is isomorphic to the direct sum of the Grothendieck-Teichmüller Lie algebra grt_1 and a one-dimensional Lie algebra. In this paper, we use the graph complex of internally connected graphs to define a nested sequence of Lie subalgebras of \\widehat{krv}_2 whose intersection is grt_1 , thus giving a way to interpolate between these two Lie algebras.

Unsupervised classification of major depression using functional connectivity MRI.

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Zeng, Ling-Li; Shen, Hui; Liu, Li; Hu, Dewen

2014-04-01

The current diagnosis of psychiatric disorders including major depressive disorder based largely on self-reported symptoms and clinical signs may be prone to patients' behaviors and psychiatrists' bias. This study aims at developing an unsupervised machine learning approach for the accurate identification of major depression based on single resting-state functional magnetic resonance imaging scans in the absence of clinical information. Twenty-four medication-naive patients with major depression and 29 demographically similar healthy individuals underwent resting-state functional magnetic resonance imaging. We first clustered the voxels within the perigenual cingulate cortex into two subregions, a subgenual region and a pregenual region, according to their distinct resting-state functional connectivity patterns and showed that a maximum margin clustering-based unsupervised machine learning approach extracted sufficient information from the subgenual cingulate functional connectivity map to differentiate depressed patients from healthy controls with a group-level clustering consistency of 92.5% and an individual-level classification consistency of 92.5%. It was also revealed that the subgenual cingulate functional connectivity network with the highest discriminative power primarily included the ventrolateral and ventromedial prefrontal cortex, superior temporal gyri and limbic areas, indicating that these connections may play critical roles in the pathophysiology of major depression. The current study suggests that subgenual cingulate functional connectivity network signatures may provide promising objective biomarkers for the diagnosis of major depression and that maximum margin clustering-based unsupervised machine learning approaches may have the potential to inform clinical practice and aid in research on psychiatric disorders. Copyright © 2013 Wiley Periodicals, Inc.

Methods of information geometry

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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...

Decreased triple network connectivity in patients with post-traumatic stress disorder

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Liu, Yang; Li, Liang; Li, Baojuan; Zhang, Xi; Lu, Hongbing

2017-03-01

The triple network model provides a common framework for understanding affective and neurocognitive dysfunctions across multiple disorders, including central executive network (CEN), default mode network (DMN), and salience network (SN). Considering the effect of traumatic experience on post-traumatic stress disorder (PTSD), this study aims to explore the alteration of triple network connectivity in a specific PTSD induced by a single prolonged trauma exposure. With arterial spin labeling sequence, three networks were identified using independent component analysis in 10 PTSD patients and 10 healthy survivors, who experienced the same coal mining flood disaster. In PTSD patients, decreased connectivity was identified in left middle frontal gyrus of CEN, left precuneus and bilateral superior frontal gyrus of DMN, and right anterior insula of SN. The decreased connectivity in left middle frontal gyrus was identified to associate with clinical severity. These results indicated the decreased triple network connectivity, which not only supported the proposal of the triple network model, but also prompted possible neurobiology mechanism of cognitive dysfunction for this kind of PTSD.

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

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

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

Asymmetrical Fault Analysis at the Offshore Network of HVDC connected Wind Power Plants

DEFF Research Database (Denmark)

Goksu, Omer; Cutululis, Nicolaos Antonio; Sorensen, Poul

2017-01-01

Short-circuit faults for HVDC connected Wind Power Plants (WPPs) have been studied mostly for dc link and onshore ac grid faults, while the offshore ac faults, especially asymmetrical faults, have been mostly omitted in the literature. Requirements related to the offshore asymmetrical faults have...... been kept as future development at national levels in the recent ENTSO-E HVDC network code. In this paper offshore ac faults are studied using the classical power system fault analysis methods. It is shown that suppression of negative sequence current flow is not applicable and negative sequence...

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.

Quantitative comparison between a multiecho sequence and a single-echo sequence for susceptibility-weighted phase imaging.

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Gilbert, Guillaume; Savard, Geneviève; Bard, Céline; Beaudoin, Gilles

2012-06-01

The aim of this study was to investigate the benefits arising from the use of a multiecho sequence for susceptibility-weighted phase imaging using a quantitative comparison with a standard single-echo acquisition. Four healthy adult volunteers were imaged on a clinical 3-T system using a protocol comprising two different three-dimensional susceptibility-weighted gradient-echo sequences: a standard single-echo sequence and a multiecho sequence. Both sequences were repeated twice in order to evaluate the local noise contribution by a subtraction of the two acquisitions. For the multiecho sequence, the phase information from each echo was independently unwrapped, and the background field contribution was removed using either homodyne filtering or the projection onto dipole fields method. The phase information from all echoes was then combined using a weighted linear regression. R2 maps were also calculated from the multiecho acquisitions. The noise standard deviation in the reconstructed phase images was evaluated for six manually segmented regions of interest (frontal white matter, posterior white matter, globus pallidus, putamen, caudate nucleus and lateral ventricle). The use of the multiecho sequence for susceptibility-weighted phase imaging led to a reduction of the noise standard deviation for all subjects and all regions of interest investigated in comparison to the reference single-echo acquisition. On average, the noise reduction ranged from 18.4% for the globus pallidus to 47.9% for the lateral ventricle. In addition, the amount of noise reduction was found to be strongly inversely correlated to the estimated R2 value (R=-0.92). In conclusion, the use of a multiecho sequence is an effective way to decrease the noise contribution in susceptibility-weighted phase images, while preserving both contrast and acquisition time. The proposed approach additionally permits the calculation of R2 maps. Copyright © 2012 Elsevier Inc. All rights reserved.

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

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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.

Highly accurate sequence imputation enables precise QTL mapping in Brown Swiss cattle.

Science.gov (United States)

Frischknecht, Mirjam; Pausch, Hubert; Bapst, Beat; Signer-Hasler, Heidi; Flury, Christine; Garrick, Dorian; Stricker, Christian; Fries, Ruedi; Gredler-Grandl, Birgit

2017-12-29

Within the last few years a large amount of genomic information has become available in cattle. Densities of genomic information vary from a few thousand variants up to whole genome sequence information. In order to combine genomic information from different sources and infer genotypes for a common set of variants, genotype imputation is required. In this study we evaluated the accuracy of imputation from high density chips to whole genome sequence data in Brown Swiss cattle. Using four popular imputation programs (Beagle, FImpute, Impute2, Minimac) and various compositions of reference panels, the accuracy of the imputed sequence variant genotypes was high and differences between the programs and scenarios were small. We imputed sequence variant genotypes for more than 1600 Brown Swiss bulls and performed genome-wide association studies for milk fat percentage at two stages of lactation. We found one and three quantitative trait loci for early and late lactation fat content, respectively. Known causal variants that were imputed from the sequenced reference panel were among the most significantly associated variants of the genome-wide association study. Our study demonstrates that whole-genome sequence information can be imputed at high accuracy in cattle populations. Using imputed sequence variant genotypes in genome-wide association studies may facilitate causal variant detection.

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.

A safe an easy method for building consensus HIV sequences from 454 massively parallel sequencing data.

Science.gov (United States)

Fernández-Caballero Rico, Jose Ángel; Chueca Porcuna, Natalia; Álvarez Estévez, Marta; Mosquera Gutiérrez, María Del Mar; Marcos Maeso, María Ángeles; García, Federico

2018-02-01

To show how to generate a consensus sequence from the information of massive parallel sequences data obtained from routine HIV anti-retroviral resistance studies, and that may be suitable for molecular epidemiology studies. Paired Sanger (Trugene-Siemens) and next-generation sequencing (NGS) (454 GSJunior-Roche) HIV RT and protease sequences from 62 patients were studied. NGS consensus sequences were generated using Mesquite, using 10%, 15%, and 20% thresholds. Molecular evolutionary genetics analysis (MEGA) was used for phylogenetic studies. At a 10% threshold, NGS-Sanger sequences from 17/62 patients were phylogenetically related, with a median bootstrap-value of 88% (IQR83.5-95.5). Association increased to 36/62 sequences, median bootstrap 94% (IQR85.5-98)], using a 15% threshold. Maximum association was at the 20% threshold, with 61/62 sequences associated, and a median bootstrap value of 99% (IQR98-100). A safe method is presented to generate consensus sequences from HIV-NGS data at 20% threshold, which will prove useful for molecular epidemiological studies. Copyright © 2016 Elsevier España, S.L.U. and Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

Design and Evaluation of a Protection Relay for a Wind Generator Based on the Positive- and Negative-Sequence Fault Components

DEFF Research Database (Denmark)

Zheng, T. Y.; Cha, Seung-Tae; Crossley, P. A.

2013-01-01

To avoid undesirable disconnection of healthy wind generators (WGs) or a wind power plant, a WG protection relay should discriminate among faults, so that it can operate instantaneously for WG, connected feeder or connection bus faults, it can operate after a delay for inter-tie or grid faults......, and it can avoid operating for parallel WG or adjacent feeder faults. A WG protection relay based on the positive- and negativesequence fault components is proposed in the paper. At stage 1, the proposed relay uses the magnitude of the positive-sequence component in the fault current to distinguish faults...... at a parallel WG connected to the same feeder or at an adjacent feeder, from other faults at a connected feeder, an inter-tie, or a grid. At stage 2, the fault type is first determined using the relationships between the positive- and negative-sequence fault components. Then, the relay differentiates between...

Gene flow connects coastal populations of a habitat specialist, the Clapper Rail Rallus crepitans

Science.gov (United States)

Coster, Stephanie S.; Welsh, Amy B.; Costanzo, Gary R.; Harding, Sergio R.; Anderson, James T.; Katzner, Todd

2018-01-01

Examining population genetic structure can reveal patterns of reproductive isolation or population mixing and inform conservation management. Some avian species are predicted to exhibit minimal genetic differentiation among populations as a result of the species high mobility, with habitat specialists tending to show greater fine‐scale genetic structure. To explore the relationship between habitat specialization and gene flow, we investigated the genetic structure of a saltmarsh specialist with high potential mobility across a wide geographic range of fragmented habitat. Little variation among mitochondrial sequences (620 bp from ND2) was observed among 149 individual Clapper Rails Rallus crepitans sampled along the Atlantic coast of North America, with the majority of individuals at all sampling sites sharing a single haplotype. Genotyping of nine microsatellite loci across 136 individuals revealed moderate genetic diversity, no evidence of bottlenecks, and a weak pattern of genetic differentiation that increased with geographic distance. Multivariate analyses, Bayesian clustering and an AMOVA all suggested a lack of genetic structuring across the North American Atlantic coast, with all individuals grouped into a single interbreeding population. Spatial autocorrelation analyses showed evidence of weak female philopatry and a lack of male philopatry. We conclude that high gene flow connecting populations of this habitat specialist may result from the interaction of ecological and behavioral factors that promote dispersal and limit natal philopatry and breeding‐site fidelity. As climate change threatens saltmarshes, the genetic diversity and population connectivity of Clapper Rails may promote resilience of their populations. This finding helps inform about potential fates of other similarly behaving saltmarsh specialists on the Atlantic coast.

A modified strategy for sequence specific assignment of protein NMR spectra based on amino acid type selective experiments

International Nuclear Information System (INIS)

Schubert, Mario; Labudde, Dirk; Leitner, Dietmar; Oschkinat, Hartmut; Schmieder, Peter

2005-01-01

The determination of the three-dimensional structure of a protein or the study of protein-ligand interactions requires the assignment of all relevant nuclei as an initial step. This is nowadays almost exclusively performed using triple-resonance experiments. The conventional strategy utilizes one or more pairs of three dimensional spectra to obtain redundant information and thus reliable assignments. Here, a modified strategy for obtaining sequence specific assignments based on two dimensional amino acid type selective triple-resonance experiments is proposed. These experiments can be recorded with good resolution in a relatively short time. They provide very specific and redundant information, in particular on sequential connectivities, that drastically increases the ease and reliability of the assignment procedure, done either manually or in an automated fashion. The new strategy is demonstrated with the protein domain PB1 from yeast CDC24p

Internally connected graphs and the Kashiwara-Vergne Lie algebra

OpenAIRE

Felder, Matteo

2016-01-01

It is conjectured that the Kashiwara-Vergne Lie algebra $\\widehat{\\mathfrak{krv}}_2$ is isomorphic to the direct sum of the Grothendieck-Teichm\\"uller Lie algebra $\\mathfrak{grt}_1$ and a one-dimensional Lie algebra. In this paper, we use the graph complex of internally connected graphs to define a nested sequence of Lie subalgebras of $\\widehat{\\mathfrak{krv}}_2$ whose intersection is $\\mathfrak{grt}_1$, thus giving a way to interpolate between these two Lie algebras.

NBAS mutations cause a multisystem disorder involving bone, connective tissue, liver, immune system, and retina

NARCIS (Netherlands)

Segarra, Nuria Garcia; Ballhausen, Diana; Crawford, Heather; Perreau, Matthieu; Campos-Xavier, Belinda; van Spaendonck-Zwarts, Karin; Vermeer, Cees; Russo, Michel; Zambelli, Pierre-Yves; Stevenson, Brian; Royer-Bertrand, Beryl; Rivolta, Carlo; Candotti, Fabio; Unger, Sheila; Munier, Francis L.; Superti-Furga, Andrea; Bonafé, Luisa

2015-01-01

We report two unrelated patients with a multisystem disease involving liver, eye, immune system, connective tissue, and bone, caused by biallelic mutations in the neuroblastoma amplified sequence (NBAS) gene. Both presented as infants with recurrent episodes triggered by fever with vomiting,

MIPS: a database for genomes and protein sequences.

Science.gov (United States)

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

2002-01-01

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

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.

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.

MIPS: a database for protein sequences and complete genomes.

Science.gov (United States)

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

1998-01-01

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

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...

Mutual Connectivity Analysis (MCA) Using Generalized Radial Basis Function Neural Networks for Nonlinear Functional Connectivity Network Recovery in Resting-State Functional MRI.

Science.gov (United States)

DSouza, Adora M; Abidin, Anas Zainul; Nagarajan, Mahesh B; Wismüller, Axel

2016-03-29

We investigate the applicability of a computational framework, called mutual connectivity analysis (MCA), for directed functional connectivity analysis in both synthetic and resting-state functional MRI data. This framework comprises of first evaluating non-linear cross-predictability between every pair of time series prior to recovering the underlying network structure using community detection algorithms. We obtain the non-linear cross-prediction score between time series using Generalized Radial Basis Functions (GRBF) neural networks. These cross-prediction scores characterize the underlying functionally connected networks within the resting brain, which can be extracted using non-metric clustering approaches, such as the Louvain method. We first test our approach on synthetic models with known directional influence and network structure. Our method is able to capture the directional relationships between time series (with an area under the ROC curve = 0.92 ± 0.037) as well as the underlying network structure (Rand index = 0.87 ± 0.063) with high accuracy. Furthermore, we test this method for network recovery on resting-state fMRI data, where results are compared to the motor cortex network recovered from a motor stimulation sequence, resulting in a strong agreement between the two (Dice coefficient = 0.45). We conclude that our MCA approach is effective in analyzing non-linear directed functional connectivity and in revealing underlying functional network structure in complex systems.

Metabolic connectivity mapping reveals effective connectivity in the resting human brain.

Science.gov (United States)

Riedl, Valentin; Utz, Lukas; Castrillón, Gabriel; Grimmer, Timo; Rauschecker, Josef P; Ploner, Markus; Friston, Karl J; Drzezga, Alexander; Sorg, Christian

2016-01-12

Directionality of signaling among brain regions provides essential information about human cognition and disease states. Assessing such effective connectivity (EC) across brain states using functional magnetic resonance imaging (fMRI) alone has proven difficult, however. We propose a novel measure of EC, termed metabolic connectivity mapping (MCM), that integrates undirected functional connectivity (FC) with local energy metabolism from fMRI and positron emission tomography (PET) data acquired simultaneously. This method is based on the concept that most energy required for neuronal communication is consumed postsynaptically, i.e., at the target neurons. We investigated MCM and possible changes in EC within the physiological range using "eyes open" versus "eyes closed" conditions in healthy subjects. Independent of condition, MCM reliably detected stable and bidirectional communication between early and higher visual regions. Moreover, we found stable top-down signaling from a frontoparietal network including frontal eye fields. In contrast, we found additional top-down signaling from all major clusters of the salience network to early visual cortex only in the eyes open condition. MCM revealed consistent bidirectional and unidirectional signaling across the entire cortex, along with prominent changes in network interactions across two simple brain states. We propose MCM as a novel approach for inferring EC from neuronal energy metabolism that is ideally suited to study signaling hierarchies in the brain and their defects in brain disorders.

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.

Reliability evaluation of linear multi-state consecutively-connected systems constrained by m consecutive and n total gaps

International Nuclear Information System (INIS)

Yu, Huan; Yang, Jun; Peng, Rui; Zhao, Yu

2016-01-01

This paper extends the linear multi-state consecutively-connected system (LMCCS) to the case of LMCCS-MN, where MN denotes the dual constraints of m consecutive gaps and n total gaps. All the nodes are distributed along a line and form a sequence. The distances between the adjacent nodes are usually non-uniform. The nodes except the last one can contain statistically independent multi-state connection elements (MCEs). Each MCE can provide a connection between the node at which it is located and the next nodes along the sequence. The LMCCS-MN fails if it meets either of the two constraints. The universal generating function technique is adopted to evaluate the system reliability. The optimal allocations of LMCCS-MN with two different types of failures are solved by genetic algorithm. Finally, two examples are given for the demonstration of the proposed model. - Highlights: • A new model of multi-state consecutively-connected system (LMCCS-MN) is proposed. • The non-uniform distributed nodes are involved in the proposed LMCCS-MN model. • An algorithm for system reliability evaluation is provided by the UGF method. • The computational complexity of the proposed algorithm is discussed in detail. • Optimal element allocation problem is formulated and solved.

Brain oscillation and connectivity during a chemistry visual working memory task.

Science.gov (United States)

Huang, Li-Yu; She, Hsiao-Ching; Chou, Wen-Chi; Chuang, Ming-Hua; Duann, Jeng-Ren; Jung, Tzyy-Ping

2013-11-01

Many studies have reported that frontal theta and posterior alpha activities are associated with working memory tasks. However, fewer studies have focused on examining whether or not the frontal alpha or posterior theta can play a role in the working memory task. This study investigates electroencephalography (EEG) dynamics and connectivity among different brain regions' theta and alpha oscillations. The EEG was collected from undergraduate students (n = 64) while they were performing a Sternberg-like working memory task involving chemistry concepts. The results showed that the frontal midline cluster exhibited sustained theta augmentation across the periods of stimulus presentations, maintenance, and probe presentation, suggesting that the frontal midline theta might associate with facilitating the central execute function to maintain information in the working memory. Study of the central parietal and the occipital clusters revealed a sequence of theta augmentation followed by alpha suppression at constant intervals after the onset of stimulus and probe presentations, suggesting that the posterior theta might be associated with sensory processing, theta gating, or stimulus selection. It further suggests that the posterior alpha event-related de-synchronization (ERD) might be linked to direct information flow into and out of the long-term memory (LTM) and precede stimulus recognition. An alternating phasic alpha event-related synchronization (ERS) and ERD following the 1st stimulus and probe presentations were observed at the occipital cluster, in which alpha ERS might be linked to the inhibition of irrelevant information. © 2013.

Facilitating genome navigation : survey sequencing and dense radiation-hybrid gene mapping

NARCIS (Netherlands)

Hitte, C; Madeoy, J; Kirkness, EF; Priat, C; Lorentzen, TD; Senger, F; Thomas, D; Derrien, T; Ramirez, C; Scott, C; Evanno, G; Pullar, B; Cadieu, E; Oza, [No Value; Lourgant, K; Jaffe, DB; Tacher, S; Dreano, S; Berkova, N; Andre, C; Deloukas, P; Fraser, C; Lindblad-Toh, K; Ostrander, EA; Galibert, F

Accurate and comprehensive sequence coverage for large genomes has been restricted to only a few species of specific interest. Lower sequence coverage (survey sequencing) of related species can yield a wealth of information about gene content and putative regulatory elements. But survey sequences

In the search for the low-complexity sequences in prokaryotic and eukaryotic genomes: how to derive a coherent picture from global and local entropy measures

Energy Technology Data Exchange (ETDEWEB)

Acquisti, Claudia; Allegrini, Paolo E-mail: allegrip@ilc.cnr.it; Bogani, Patrizia; Buiatti, Marcello; Catanese, Elena; Fronzoni, Leone; Grigolini, Paolo; Mersi, Giuseppe; Palatella, Luigi

2004-04-01

We investigate on a possible way to connect the presence of low-complexity sequences (LCS) in DNA genomes and the non-stationary properties of base correlations. Under the hypothesis that these variations signal a change in the DNA function, we use a new technique, called non-stationarity entropic index (NSEI) method, and we prove that this technique is an efficient way to detect functional changes with respect to a random baseline. The remarkable aspect is that NSEI does not imply any training data or fitting parameter, the only arbitrarity being the choice of a marker in the sequence. We make this choice on the basis of biological information about LCS distributions in genomes. We show that there exists a correlation between changing the amount in LCS and the ratio of long- to short-range correlation.

In the search for the low-complexity sequences in prokaryotic and eukaryotic genomes: how to derive a coherent picture from global and local entropy measures

Science.gov (United States)

Acquisti, Claudia; Allegrini, Paolo; Bogani, Patrizia; Buiatti, Marcello; Catanese, Elena; Fronzoni, Leone; Grigolini, Paolo; Mersi, Giuseppe; Palatella, Luigi

2004-04-01

We investigate on a possible way to connect the presence of Low-Complexity Sequences (LCS) in DNA genomes and the nonstationary properties of base correlations. Under the hypothesis that these variations signal a change in the DNA function, we use a new technique, called Non-Stationarity Entropic Index (NSEI) method, and we prove that this technique is an efficient way to detect functional changes with respect to a random baseline. The remarkable aspect is that NSEI does not imply any training data or fitting parameter, the only arbitrarity being the choice of a marker in the sequence. We make this choice on the basis of biological information about LCS distributions in genomes. We show that there exists a correlation between changing the amount in LCS and the ratio of long- to short-range correlation.

In the search for the low-complexity sequences in prokaryotic and eukaryotic genomes: how to derive a coherent picture from global and local entropy measures

International Nuclear Information System (INIS)

Acquisti, Claudia; Allegrini, Paolo; Bogani, Patrizia; Buiatti, Marcello; Catanese, Elena; Fronzoni, Leone; Grigolini, Paolo; Mersi, Giuseppe; Palatella, Luigi

2004-01-01

We investigate on a possible way to connect the presence of low-complexity sequences (LCS) in DNA genomes and the non-stationary properties of base correlations. Under the hypothesis that these variations signal a change in the DNA function, we use a new technique, called non-stationarity entropic index (NSEI) method, and we prove that this technique is an efficient way to detect functional changes with respect to a random baseline. The remarkable aspect is that NSEI does not imply any training data or fitting parameter, the only arbitrarity being the choice of a marker in the sequence. We make this choice on the basis of biological information about LCS distributions in genomes. We show that there exists a correlation between changing the amount in LCS and the ratio of long- to short-range correlation

Accelerating Information Retrieval from Profile Hidden Markov Model Databases.

Science.gov (United States)

Tamimi, Ahmad; Ashhab, Yaqoub; Tamimi, Hashem

2016-01-01

Profile Hidden Markov Model (Profile-HMM) is an efficient statistical approach to represent protein families. Currently, several databases maintain valuable protein sequence information as profile-HMMs. There is an increasing interest to improve the efficiency of searching Profile-HMM databases to detect sequence-profile or profile-profile homology. However, most efforts to enhance searching efficiency have been focusing on improving the alignment algorithms. Although the performance of these algorithms is fairly acceptable, the growing size of these databases, as well as the increasing demand for using batch query searching approach, are strong motivations that call for further enhancement of information retrieval from profile-HMM databases. This work presents a heuristic method to accelerate the current profile-HMM homology searching approaches. The method works by cluster-based remodeling of the database to reduce the search space, rather than focusing on the alignment algorithms. Using different clustering techniques, 4284 TIGRFAMs profiles were clustered based on their similarities. A representative for each cluster was assigned. To enhance sensitivity, we proposed an extended step that allows overlapping among clusters. A validation benchmark of 6000 randomly selected protein sequences was used to query the clustered profiles. To evaluate the efficiency of our approach, speed and recall values were measured and compared with the sequential search approach. Using hierarchical, k-means, and connected component clustering techniques followed by the extended overlapping step, we obtained an average reduction in time of 41%, and an average recall of 96%. Our results demonstrate that representation of profile-HMMs using a clustering-based approach can significantly accelerate data retrieval from profile-HMM databases.

Migration of TCP Connections with Layer-2 Support in Wireless Environments

NARCIS (Netherlands)

Bosch, H.G.P.; Cortes, Mauricio; Janiszewski, Tom J.; McKie, Jim B.; Mullender, Sape J.; Rajkumar, Ajay; Recchione, Michael C.; Rossetti, David A.; Turner, Michael D.

2008-01-01

Example embodiments provide methods of transparently migrating a reliable transport layer connection between a user and a first base station and a second base station in a wireless network. The method includes receiving at least one transport layer connection state information parameter from the

Genome sequence of Stachybotrys chartarum Strain 51-11

Science.gov (United States)

Stachybotrys chartarum strain 51-11 genome was sequenced by shotgun sequencing utilizing Illumina Hiseq 2000 and PacBio long read technology. Since Stachybotrys chartarum has been implicated in health impacts within water-damaged buildings, any information extracted from the geno...

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.

Secure and robust cloud computing for high-throughput forensic microsatellite sequence analysis and databasing.

Science.gov (United States)

Bailey, Sarah F; Scheible, Melissa K; Williams, Christopher; Silva, Deborah S B S; Hoggan, Marina; Eichman, Christopher; Faith, Seth A

2017-11-01

Next-generation Sequencing (NGS) is a rapidly evolving technology with demonstrated benefits for forensic genetic applications, and the strategies to analyze and manage the massive NGS datasets are currently in development. Here, the computing, data storage, connectivity, and security resources of the Cloud were evaluated as a model for forensic laboratory systems that produce NGS data. A complete front-to-end Cloud system was developed to upload, process, and interpret raw NGS data using a web browser dashboard. The system was extensible, demonstrating analysis capabilities of autosomal and Y-STRs from a variety of NGS instrumentation (Illumina MiniSeq and MiSeq, and Oxford Nanopore MinION). NGS data for STRs were concordant with standard reference materials previously characterized with capillary electrophoresis and Sanger sequencing. The computing power of the Cloud was implemented with on-demand auto-scaling to allow multiple file analysis in tandem. The system was designed to store resulting data in a relational database, amenable to downstream sample interpretations and databasing applications following the most recent guidelines in nomenclature for sequenced alleles. Lastly, a multi-layered Cloud security architecture was tested and showed that industry standards for securing data and computing resources were readily applied to the NGS system without disadvantageous effects for bioinformatic analysis, connectivity or data storage/retrieval. The results of this study demonstrate the feasibility of using Cloud-based systems for secured NGS data analysis, storage, databasing, and multi-user distributed connectivity. Copyright © 2017 Elsevier B.V. All rights reserved.

Functional connectivity mapping of regions associated with self- and other-processing.

Science.gov (United States)

Murray, Ryan J; Debbané, Martin; Fox, Peter T; Bzdok, Danilo; Eickhoff, Simon B

2015-04-01

Neuroscience literature increasingly suggests a conceptual self composed of interacting neural regions, rather than independent local activations, yet such claims have yet to be investigated. We, thus, combined task-dependent meta-analytic connectivity modeling (MACM) with task-independent resting-state (RS) connectivity analysis to delineate the neural network of the self, across both states. Given psychological evidence implicating the self's interdependence on social information, we also delineated the neural network underlying conceptual other-processing. To elucidate the relation between the self-/other-networks and their function, we mined the MACM metadata to generate a cognitive-behavioral profile for an empirically identified region specific to conceptual self, the pregenual anterior cingulate (pACC), and conceptual other, posterior cingulate/precuneus (PCC/PC). Mining of 7,200 published, task-dependent, neuroimaging studies, using healthy human subjects, yielded 193 studies activating the self-related seed and were conjoined with RS connectivity analysis to delineate a differentiated self-network composed of the pACC (seed) and anterior insula, relative to other functional connectivity. Additionally, 106 studies activating the other-related seed were conjoined with RS connectivity analysis to delineate a differentiated other-network of PCC/PC (seed) and angular gyrus/temporoparietal junction, relative to self-functional connectivity. The self-network seed related to emotional conflict resolution and motivational processing, whereas the other-network seed related to socially oriented processing and contextual information integration. Notably, our findings revealed shared RS connectivity between ensuing self-/other-networks within the ventromedial prefrontal cortex and medial orbitofrontal cortex, suggesting self-updating via integration of self-relevant social information. We, therefore, present initial neurobiological evidence corroborating the increasing

Optimal rotation sequences for active perception

Science.gov (United States)

Nakath, David; Rachuy, Carsten; Clemens, Joachim; Schill, Kerstin

2016-05-01

One major objective of autonomous systems navigating in dynamic environments is gathering information needed for self localization, decision making, and path planning. To account for this, such systems are usually equipped with multiple types of sensors. As these sensors often have a limited field of view and a fixed orientation, the task of active perception breaks down to the problem of calculating alignment sequences which maximize the information gain regarding expected measurements. Action sequences that rotate the system according to the calculated optimal patterns then have to be generated. In this paper we present an approach for calculating these sequences for an autonomous system equipped with multiple sensors. We use a particle filter for multi- sensor fusion and state estimation. The planning task is modeled as a Markov decision process (MDP), where the system decides in each step, what actions to perform next. The optimal control policy, which provides the best action depending on the current estimated state, maximizes the expected cumulative reward. The latter is computed from the expected information gain of all sensors over time using value iteration. The algorithm is applied to a manifold representation of the joint space of rotation and time. We show the performance of the approach in a spacecraft navigation scenario where the information gain is changing over time, caused by the dynamic environment and the continuous movement of the spacecraft

PINGU: PredIction of eNzyme catalytic residues usinG seqUence information.

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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.

Multimodal frontostriatal connectivity underlies individual differences in self-esteem.

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Chavez, Robert S; Heatherton, Todd F

2015-03-01

A heightened sense of self-esteem is associated with a reduced risk for several types of affective and psychiatric disorders, including depression, anxiety and eating disorders. However, little is known about how brain systems integrate self-referential processing and positive evaluation to give rise to these feelings. To address this, we combined diffusion tensor imaging (DTI) and functional magnetic resonance imaging (fMRI) to test how frontostriatal connectivity reflects long-term trait and short-term state aspects of self-esteem. Using DTI, we found individual variability in white matter structural integrity between the medial prefrontal cortex and the ventral striatum was related to trait measures of self-esteem, reflecting long-term stability of self-esteem maintenance. Using fMRI, we found that functional connectivity of these regions during positive self-evaluation was related to current feelings of self-esteem, reflecting short-term state self-esteem. These results provide convergent anatomical and functional evidence that self-esteem is related to the connectivity of frontostriatal circuits and suggest that feelings of self-worth may emerge from neural systems integrating information about the self with positive affect and reward. This information could potentially inform the etiology of diminished self-esteem underlying multiple psychiatric conditions and inform future studies of evaluative self-referential processing. © The Author (2014). Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

TurboFold: Iterative probabilistic estimation of secondary structures for multiple RNA sequences

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Sharma Gaurav

2011-04-01

Full Text Available Abstract Background The prediction of secondary structure, i.e. the set of canonical base pairs between nucleotides, is a first step in developing an understanding of the function of an RNA sequence. The most accurate computational methods predict conserved structures for a set of homologous RNA sequences. These methods usually suffer from high computational complexity. In this paper, TurboFold, a novel and efficient method for secondary structure prediction for multiple RNA sequences, is presented. Results TurboFold takes, as input, a set of homologous RNA sequences and outputs estimates of the base pairing probabilities for each sequence. The base pairing probabilities for a sequence are estimated by combining intrinsic information, derived from the sequence itself via the nearest neighbor thermodynamic model, with extrinsic information, derived from the other sequences in the input set. For a given sequence, the extrinsic information is computed by using pairwise-sequence-alignment-based probabilities for co-incidence with each of the other sequences, along with estimated base pairing probabilities, from the previous iteration, for the other sequences. The extrinsic information is introduced as free energy modifications for base pairing in a partition function computation based on the nearest neighbor thermodynamic model. This process yields updated estimates of base pairing probability. The updated base pairing probabilities in turn are used to recompute extrinsic information, resulting in the overall iterative estimation procedure that defines TurboFold. TurboFold is benchmarked on a number of ncRNA datasets and compared against alternative secondary structure prediction methods. The iterative procedure in TurboFold is shown to improve estimates of base pairing probability with each iteration, though only small gains are obtained beyond three iterations. Secondary structures composed of base pairs with estimated probabilities higher than a

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

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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.

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...

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

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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.

Neural network connectivity and response latency modelled by stochastic processes

DEFF Research Database (Denmark)

Tamborrino, Massimiliano

is connected to thousands of other neurons. The rst question is: how to model neural networks through stochastic processes? A multivariate Ornstein-Uhlenbeck process, obtained as a diffusion approximation of a jump process, is the proposed answer. Obviously, dependencies between neurons imply dependencies......Stochastic processes and their rst passage times have been widely used to describe the membrane potential dynamics of single neurons and to reproduce neuronal spikes, respectively.However, cerebral cortex in human brains is estimated to contain 10-20 billions of neurons and each of them...... between their spike times. Therefore, the second question is: how to detect neural network connectivity from simultaneously recorded spike trains? Answering this question corresponds to investigate the joint distribution of sequences of rst passage times. A non-parametric method based on copulas...

Implicit sequence learning in people with Parkinson’s disease

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Katherine R Gamble

2014-08-01

Full Text Available Implicit sequence learning involves learning about dependencies in sequences of events without intent to learn or awareness of what has been learned. Sequence learning is related to striatal dopamine levels, striatal activation, and integrity of white matter connections. People with Parkinson’s disease (PD have degeneration of dopamine-producing neurons, leading to dopamine deficiency and therefore striatal deficits, and they have difficulties with sequencing, including complex language comprehension and postural stability. Most research on implicit sequence learning in PD has used motor-based tasks. However, because PD presents with motor deficits, it is difficult to assess whether learning itself is impaired in these tasks. The present study used an implicit sequence learning task with a reduced motor component, the Triplets Learning Task (TLT. People with PD and age- and education-matched healthy older adults completed three sessions (each consisting of 10 blocks of 50 trials of the TLT. Results revealed that the PD group was able to learn the sequence, however, when learning was examined using a Half Blocks analysis (Nemeth et al., 2013, which compared learning in the 1st 25/50 trials of all blocks to that in the 2nd 25/50 trials, the PD group showed significantly less learning than Controls in the 2nd Half Blocks, but not in the 1st. Nemeth et al. hypothesized that the 1st Half Blocks involve recall and reactivation of the sequence learned, thus reflecting hippocampal-dependent learning, while the 2nd Half Blocks involve proceduralized behavior of learned sequences, reflecting striatal-based learning. The present results suggest that the PD group had intact hippocampal-dependent implicit sequence learning, but impaired striatal-dependent learning. Thus, sequencing deficits in PD are likely due to striatal impairments, but other brain systems, such as the hippocampus, may be able to partially compensate for striatal decline to improve

Dispersal Ecology Informs Design of Large-Scale Wildlife Corridors.

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Benz, Robin A; Boyce, Mark S; Thurfjell, Henrik; Paton, Dale G; Musiani, Marco; Dormann, Carsten F; Ciuti, Simone

Landscape connectivity describes how the movement of animals relates to landscape structure. The way in which movement among populations is affected by environmental conditions is important for predicting the effects of habitat fragmentation, and for defining conservation corridors. One approach has been to map resistance surfaces to characterize how environmental variables affect animal movement, and to use these surfaces to model connectivity. However, current connectivity modelling typically uses information on species location or habitat preference rather than movement, which unfortunately may not capture dispersal limitations. Here we emphasize the importance of implementing dispersal ecology into landscape connectivity, i.e., observing patterns of habitat selection by dispersers during different phases of new areas' colonization to infer habitat connectivity. Disperser animals undertake a complex sequence of movements concatenated over time and strictly dependent on species ecology. Using satellite telemetry, we investigated the movement ecology of 54 young male elk Cervus elaphus, which commonly disperse, to design a corridor network across the Northern Rocky Mountains. Winter residency period is often followed by a spring-summer movement phase, when young elk migrate with mothers' groups to summering areas, and by a further dispersal bout performed alone to a novel summer area. After another summer residency phase, dispersers usually undertake a final autumnal movement to reach novel wintering areas. We used resource selection functions to identify winter and summer habitats selected by elk during residency phases. We then extracted movements undertaken during spring to move from winter to summer areas, and during autumn to move from summer to winter areas, and modelled them using step selection functions. We built friction surfaces, merged the different movement phases, and eventually mapped least-cost corridors. We showed an application of this tool by

A Unified Theoretical Framework for Cognitive Sequencing.

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Savalia, Tejas; Shukla, Anuj; Bapi, Raju S

2016-01-01

The capacity to sequence information is central to human performance. Sequencing ability forms the foundation stone for higher order cognition related to language and goal-directed planning. Information related to the order of items, their timing, chunking and hierarchical organization are important aspects in sequencing. Past research on sequencing has emphasized two distinct and independent dichotomies: implicit vs. explicit and goal-directed vs. habits. We propose a theoretical framework unifying these two streams. Our proposal relies on brain's ability to implicitly extract statistical regularities from the stream of stimuli and with attentional engagement organizing sequences explicitly and hierarchically. Similarly, sequences that need to be assembled purposively to accomplish a goal require engagement of attentional processes. With repetition, these goal-directed plans become habits with concomitant disengagement of attention. Thus, attention and awareness play a crucial role in the implicit-to-explicit transition as well as in how goal-directed plans become automatic habits. Cortico-subcortical loops basal ganglia-frontal cortex and hippocampus-frontal cortex loops mediate the transition process. We show how the computational principles of model-free and model-based learning paradigms, along with a pivotal role for attention and awareness, offer a unifying framework for these two dichotomies. Based on this framework, we make testable predictions related to the potential influence of response-to-stimulus interval (RSI) on developing awareness in implicit learning tasks.

A Unified Theoretical Framework for Cognitive Sequencing

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Tejas Savalia

2016-11-01

Full Text Available The capacity to sequence information is central to human performance. Sequencing ability forms the foundation stone for higher order cognition related to language and goal-directed planning. Information related to the order of items, their timing, chunking and hierarchical organization are important aspects in sequencing. Past research on sequencing has emphasized two distinct and independent dichotomies: implicit versus explicit and goal-directed versus habits. We propose a theoretical framework unifying these two streams. Our proposal relies on brain's ability to implicitly extract statistical regularities from the stream of stimuli and with attentional engagement organizing sequences explicitly and hierarchically. Similarly, sequences that need to be assembled purposively to accomplish a goal require engagement of attentional processes. With repetition, these goal-directed plans become habits with concomitant disengagement of attention. Thus attention and awareness play a crucial role in the implicit-to-explicit transition as well as in how goal-directed plans become automatic habits. Cortico-subcortical loops ─ basal ganglia-frontal cortex and hippocampus-frontal cortex loops ─ mediate the transition process. We show how the computational principles of model-free and model-based learning paradigms, along with a pivotal role for attention and awareness, offer a unifying framework for these two dichotomies. Based on this framework, we make testable predictions related to the potential influence of response-to-stimulus interval (RSI on developing awareness in implicit learning tasks.

How does farmer connectivity influence livestock genetic structure?

DEFF Research Database (Denmark)

Berthouly, C; Do, Duy Ngoc; Thévenon, S

2009-01-01

Assessing how genes flow across populations is a key component of conservation genetics. Gene flow in a natural population depends on ecological traits and the local environment, whereas for a livestock population, gene flow is driven by human activities. Spatial organization, relationships between...... farmers and their husbandry practices will define the farmer's network and so determine farmer connectivity. It is thus assumed that farmer connectivity will affect the genetic structure of their livestock. To test this hypothesis, goats reared by four different ethnic groups in a Vietnamese province were......, ethnicity and husbandry practices. In this study, we clearly linked the livestock genetic pattern to farmer connectivity and showed the importance of taking into account spatial information in genetic studies....

Statistical approaches to use a model organism for regulatory sequences annotation of newly sequenced species.

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Pietro Liò

Full Text Available A major goal of bioinformatics is the characterization of transcription factors and the transcriptional programs they regulate. Given the speed of genome sequencing, we would like to quickly annotate regulatory sequences in newly-sequenced genomes. In such cases, it would be helpful to predict sequence motifs by using experimental data from closely related model organism. Here we present a general algorithm that allow to identify transcription factor binding sites in one newly sequenced species by performing Bayesian regression on the annotated species. First we set the rationale of our method by applying it within the same species, then we extend it to use data available in closely related species. Finally, we generalise the method to handle the case when a certain number of experiments, from several species close to the species on which to make inference, are available. In order to show the performance of the method, we analyse three functionally related networks in the Ascomycota. Two gene network case studies are related to the G2/M phase of the Ascomycota cell cycle; the third is related to morphogenesis. We also compared the method with MatrixReduce and discuss other types of validation and tests. The first network is well known and provides a biological validation test of the method. The two cell cycle case studies, where the gene network size is conserved, demonstrate an effective utility in annotating new species sequences using all the available replicas from model species. The third case, where the gene network size varies among species, shows that the combination of information is less powerful but is still informative. Our methodology is quite general and could be extended to integrate other high-throughput data from model organisms.

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…

Biophysical and structural considerations for protein sequence evolution

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Grahnen Johan A

2011-12-01

Full Text Available Abstract Background Protein sequence evolution is constrained by the biophysics of folding and function, causing interdependence between interacting sites in the sequence. However, current site-independent models of sequence evolutions do not take this into account. Recent attempts to integrate the influence of structure and biophysics into phylogenetic models via statistical/informational approaches have not resulted in expected improvements in model performance. This suggests that further innovations are needed for progress in this field. Results Here we develop a coarse-grained physics-based model of protein folding and binding function, and compare it to a popular informational model. We find that both models violate the assumption of the native sequence being close to a thermodynamic optimum, causing directional selection away from the native state. Sampling and simulation show that the physics-based model is more specific for fold-defining interactions that vary less among residue type. The informational model diffuses further in sequence space with fewer barriers and tends to provide less support for an invariant sites model, although amino acid substitutions are generally conservative. Both approaches produce sequences with natural features like dN/dS Conclusions Simple coarse-grained models of protein folding can describe some natural features of evolving proteins but are currently not accurate enough to use in evolutionary inference. This is partly due to improper packing of the hydrophobic core. We suggest possible improvements on the representation of structure, folding energy, and binding function, as regards both native and non-native conformations, and describe a large number of possible applications for such a model.

Studying hemispheric lateralization during a Stroop task through near-infrared spectroscopy-based connectivity

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Zhang, Lei; Sun, Jinyan; Sun, Bailei; Luo, Qingming; Gong, Hui

2014-05-01

Near-infrared spectroscopy (NIRS) is a developing and promising functional brain imaging technology. Developing data analysis methods to effectively extract meaningful information from collected data is the major bottleneck in popularizing this technology. In this study, we measured hemodynamic activity of the prefrontal cortex (PFC) during a color-word matching Stroop task using NIRS. Hemispheric lateralization was examined by employing traditional activation and novel NIRS-based connectivity analyses simultaneously. Wavelet transform coherence was used to assess intrahemispheric functional connectivity. Spearman correlation analysis was used to examine the relationship between behavioral performance and activation/functional connectivity, respectively. In agreement with activation analysis, functional connectivity analysis revealed leftward lateralization for the Stroop effect and correlation with behavioral performance. However, functional connectivity was more sensitive than activation for identifying hemispheric lateralization. Granger causality was used to evaluate the effective connectivity between hemispheres. The results showed increased information flow from the left to the right hemispheres for the incongruent versus the neutral task, indicating a leading role of the left PFC. This study demonstrates that the NIRS-based connectivity can reveal the functional architecture of the brain more comprehensively than traditional activation, helping to better utilize the advantages of NIRS.

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

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.

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.

Nanopore Sequencing as a Rapidly Deployable Ebola Outbreak Tool.

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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.

Amygdala Functional Connectivity is Reduced After the Cold Pressor Task

Science.gov (United States)

Clewett, David; Schoeke, Andrej; Mather, Mara

2013-01-01

The amygdala forms a crucial link between central pain and stress systems. There is much evidence that psychological stress affects amygdala activity, but it is less clear how painful stressors influence subsequent amygdala functional connectivity. In the present study, we used pulsed arterial spin labeling (PASL) to investigate differences in healthy male adults’ resting-state amygdala functional connectivity following a cold pressor versus control task, with the stressor and control conditions conducted on different days. During the period of peak cortisol response to acute stress (approximately fifteen to thirty minutes after stressor onset), participants were asked to rest for six minutes with their eyes closed during a PASL scanning sequence. The cold pressor task led to reduced resting-state functional connectivity between the amygdalae and orbitofrontal cortex (OFC) and ventromedial prefrontal cortex (VMPFC), which occurred irrespective of cortisol release. The stressor also induced greater inverse connectivity between the left amygdala and dorsal anterior cingulate cortex (dACC), a brain region implicated in the down-regulation of amygdala responsivity. Furthermore, the degree of post-stressor left amygdala decoupling with the lateral OFC varied according to self-reported pain intensity during the cold pressor task. These findings indicate that the cold pressor task alters amygdala interactions with prefrontal and ACC regions 15–30 minutes after the stressor, and that these altered functional connectivity patterns are related to pain perception rather than cortisol feedback. PMID:23645370

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...

Population connectivity of the plating coral Agaricia lamarcki from southwest Puerto Rico

Science.gov (United States)

Hammerman, Nicholas M.; Rivera-Vicens, Ramon E.; Galaska, Matthew P.; Weil, Ernesto; Appledoorn, Richard S.; Alfaro, Monica; Schizas, Nikolaos V.

2018-03-01

Identifying genetic connectivity and discrete population boundaries is an important objective for management of declining Caribbean reef-building corals. A double digest restriction-associated DNA sequencing protocol was utilized to generate 321 single nucleotide polymorphisms to estimate patterns of horizontal and vertical gene flow in the brooding Caribbean plate coral, Agaricia lamarcki. Individual colonies ( n = 59) were sampled from eight locations throughout southwestern Puerto Rico from six shallow ( 10-20 m) and two mesophotic habitats ( 30-40 m). Descriptive summary statistics (fixation index, F ST), analysis of molecular variance, and analysis through landscape and ecological associations and discriminant analysis of principal components estimated high population connectivity with subtle subpopulation structure among all sampling localities.

Brain activation during anticipation of sound sequences.

Science.gov (United States)

Leaver, Amber M; Van Lare, Jennifer; Zielinski, Brandon; Halpern, Andrea R; Rauschecker, Josef P

2009-02-25

Music consists of sound sequences that require integration over time. As we become familiar with music, associations between notes, melodies, and entire symphonic movements become stronger and more complex. These associations can become so tight that, for example, hearing the end of one album track can elicit a robust image of the upcoming track while anticipating it in total silence. Here, we study this predictive "anticipatory imagery" at various stages throughout learning and investigate activity changes in corresponding neural structures using functional magnetic resonance imaging. Anticipatory imagery (in silence) for highly familiar naturalistic music was accompanied by pronounced activity in rostral prefrontal cortex (PFC) and premotor areas. Examining changes in the neural bases of anticipatory imagery during two stages of learning conditional associations between simple melodies, however, demonstrates the importance of fronto-striatal connections, consistent with a role of the basal ganglia in "training" frontal cortex (Pasupathy and Miller, 2005). Another striking change in neural resources during learning was a shift between caudal PFC earlier to rostral PFC later in learning. Our findings regarding musical anticipation and sound sequence learning are highly compatible with studies of motor sequence learning, suggesting common predictive mechanisms in both domains.

A Process Mining Based Service Composition Approach for Mobile Information Systems

Directory of Open Access Journals (Sweden)

Chengxi Huang

2017-01-01

Full Text Available Due to the growing trend in applying big data and cloud computing technologies in information systems, it is becoming an important issue to handle the connection between large scale of data and the associated business processes in the Internet of Everything (IoE environment. Service composition as a widely used phase in system development has some limits when the complexity of relationship among data increases. Considering the expanding scale and the variety of devices in mobile information systems, a process mining based service composition approach is proposed in this paper in order to improve the adaptiveness and efficiency of compositions. Firstly, a preprocessing is conducted to extract existing service execution information from server-side logs. Then process mining algorithms are applied to discover the overall event sequence with preprocessed data. After that, a scene-based service composition is applied to aggregate scene information and relocate services of the system. Finally, a case study that applied the work in mobile medical application proves that the approach is practical and valuable in improving service composition adaptiveness and efficiency.

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.

Improving Cancer-Related Outcomes with Connected Health - Part 2: Objective 2

Science.gov (United States)

A core principle of connected health is that individuals are empowered to decide when, whether, and how much to participate in their health and healthcare (see Principles of Connected Health in Part 1). Decisions about participation may change over time. Connected health tools are needed to ensure that people at risk for cancer, cancer patients, and cancer survivors have access to the information they need when they need it and in formats that meet their needs.

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...

Exploring the Associations Between Intrinsic Brain Connectivity and Creative Ability Using Functional Connectivity Strength and Connectome Analysis.

Science.gov (United States)

Gao, Zhenni; Zhang, Delong; Liang, Aiying; Liang, Bishan; Wang, Zengjian; Cai, Yuxuan; Li, Junchao; Gao, Mengxia; Liu, Xiaojin; Chang, Song; Jiao, Bingqing; Huang, Ruiwang; Liu, Ming

2017-11-01

The present study aimed to explore the association between resting-state functional connectivity and creativity ability. Toward this end, the figural Torrance Tests of Creative Thinking (TTCT) scores were collected from 180 participants. Based on the figural TTCT measures, we collected resting-state functional magnetic resonance imaging data for participants with two different levels of creativity ability (a high-creativity group [HG, n = 22] and a low-creativity group [LG, n = 20]). For the aspect of group difference, this study combined voxel-wise functional connectivity strength (FCS) and seed-based functional connectivity to identify brain regions with group-change functional connectivity. Furthermore, the connectome properties of the identified regions and their associations with creativity were investigated using the permutation test, discriminative analysis, and brain-behavior correlation analysis. The results indicated that there were 4 regions with group differences in FCS, and these regions were linked to 30 other regions, demonstrating different functional connectivity between the groups. Together, these regions form a creativity-related network, and we observed higher network efficiency in the HG compared with the LG. The regions involved in the creativity network were widely distributed across the modality-specific/supramodality cerebral cortex, subcortex, and cerebellum. Notably, properties of regions in the supramodality networks (i.e., the default mode network and attention network) carried creativity-level discriminative information and were significantly correlated with the creativity performance. Together, these findings demonstrate a link between intrinsic brain connectivity and creative ability, which should provide new insights into the neural basis of creativity.

A Window Into Clinical Next-Generation Sequencing-Based Oncology Testing Practices.

Science.gov (United States)

Nagarajan, Rakesh; Bartley, Angela N; Bridge, Julia A; Jennings, Lawrence J; Kamel-Reid, Suzanne; Kim, Annette; Lazar, Alexander J; Lindeman, Neal I; Moncur, Joel; Rai, Alex J; Routbort, Mark J; Vasalos, Patricia; Merker, Jason D

2017-12-01

- Detection of acquired variants in cancer is a paradigm of precision medicine, yet little has been reported about clinical laboratory practices across a broad range of laboratories. - To use College of American Pathologists proficiency testing survey results to report on the results from surveys on next-generation sequencing-based oncology testing practices. - College of American Pathologists proficiency testing survey results from more than 250 laboratories currently performing molecular oncology testing were used to determine laboratory trends in next-generation sequencing-based oncology testing. - These presented data provide key information about the number of laboratories that currently offer or are planning to offer next-generation sequencing-based oncology testing. Furthermore, we present data from 60 laboratories performing next-generation sequencing-based oncology testing regarding specimen requirements and assay characteristics. The findings indicate that most laboratories are performing tumor-only targeted sequencing to detect single-nucleotide variants and small insertions and deletions, using desktop sequencers and predesigned commercial kits. Despite these trends, a diversity of approaches to testing exists. - This information should be useful to further inform a variety of topics, including national discussions involving clinical laboratory quality systems, regulation and oversight of next-generation sequencing-based oncology testing, and precision oncology efforts in a data-driven manner.

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.

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....

Spread the Word: The Stop.Think.Connect.[TM] Community Outreach Guide

Science.gov (United States)

US Department of Homeland Security, 2013

2013-01-01

The "Stop.Think.Connect. Community Outreach Toolkit" was adapted from the Federal Trade Commission's "OnGuardOnline.gov," a project that provides practical tips to help guard against Internet fraud and protect your privacy. The kit will help you offer your community information about protecting kids online. It includes "Stop.Think.Connect.," a…

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.

Connection Setup Signaling Scheme with Flooding-Based Path Searching for Diverse-Metric Network

Science.gov (United States)

Kikuta, Ko; Ishii, Daisuke; Okamoto, Satoru; Oki, Eiji; Yamanaka, Naoaki

Connection setup on various computer networks is now achieved by GMPLS. This technology is based on the source-routing approach, which requires the source node to store metric information of the entire network prior to computing a route. Thus all metric information must be distributed to all network nodes and kept up-to-date. However, as metric information become more diverse and generalized, it is hard to update all information due to the huge update overhead. Emerging network services and applications require the network to support diverse metrics for achieving various communication qualities. Increasing the number of metrics supported by the network causes excessive processing of metric update messages. To reduce the number of metric update messages, another scheme is required. This paper proposes a connection setup scheme that uses flooding-based signaling rather than the distribution of metric information. The proposed scheme requires only flooding of signaling messages with requested metric information, no routing protocol is required. Evaluations confirm that the proposed scheme achieves connection establishment without excessive overhead. Our analysis shows that the proposed scheme greatly reduces the number of control messages compared to the conventional scheme, while their blocking probabilities are comparable.

Examining Neuronal Connectivity and Its Role in Learning and Memory

Science.gov (United States)

Gala, Rohan

Learning and long-term memory formation are accompanied with changes in the patterns and weights of synaptic connections in the underlying neuronal network. However, the fundamental rules that drive connectivity changes, and the precise structure-function relationships within neuronal networks remain elusive. Technological improvements over the last few decades have enabled the observation of large but specific subsets of neurons and their connections in unprecedented detail. Devising robust and automated computational methods is critical to distill information from ever-increasing volumes of raw experimental data. Moreover, statistical models and theoretical frameworks are required to interpret the data and assemble evidence into understanding of brain function. In this thesis, I first describe computational methods to reconstruct connectivity based on light microscopy imaging experiments. Next, I use these methods to quantify structural changes in connectivity based on in vivo time-lapse imaging experiments. Finally, I present a theoretical model of associative learning that can explain many stereotypical features of experimentally observed connectivity.

Application of next generation sequencing in clinical microbiology and infection prevention

NARCIS (Netherlands)

Deurenberg, Ruud H.; Bathoorn, Erik; Chlebowicz, Monika A.; Couto, Natacha; Ferdous, Mithila; Garcia-Cobos, Silvia; Kooistra-Smid, Anna M. D.; Raangs, Erwin C.; Rosema, Sigrid; Veloo, Alida C. M.; Zhou, Kai; Friedrich, Alexander W.; Rossen, John W. A.

2017-01-01

Current molecular diagnostics of human pathogens provide limited information that is often not sufficient for outbreak and transmission investigation. Next generation sequencing (NGS) determines the DNA sequence of a complete bacterial genome in a single sequence run, and from these data,

Out-of-Sequence Prevention for Multicast Input-Queuing Space-Memory-Memory Clos-Network

DEFF Research Database (Denmark)

Yu, Hao; Ruepp, Sarah; Berger, Michael Stübert

2011-01-01

This paper proposes two cell dispatching algorithms for the input-queuing space-memory-memory (IQ-SMM) Closnetwork to reduce out-of-sequence (OOS) for multicast traffic. The frequent connection pattern change of DSRR results in a severe OOS problem. Based on the principle of DSRR, MFDSRR is able ...

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…

Making Connections: Where STEM Learning and Earth Science Data Services Meet

Science.gov (United States)

Bugbee, Kaylin; Ramachandran, Rahul; Maskey, Manil; Gatlin, Patrick; Weigel, Amanda

2016-01-01

STEM (Science, Technology, Engineering, Mathematics) learning is most effective when students are encouraged to see the connections between science, technology and real world problems. Helping to make these connections has become an increasingly important aspect of Earth Science data research. The Global Hydrology Resource Center (GHRC), one of NASA's 12 EOSDIS (Earth Observing System Data Information System) data centers, has developed a new type of documentation called the micro article to facilitate making connections between data and Earth science research problems.

Low-coverage MiSeq next generation sequencing reveals the mitochondrial genome of the Eastern Rock Lobster, Sagmariasus verreauxi.

Science.gov (United States)

Doyle, Stephen R; Griffith, Ian S; Murphy, Nick P; Strugnell, Jan M

2015-01-01

The complete mitochondrial genome of the Eastern Rock lobster, Sagmariasus verreauxi, is reported for the first time. Using low-coverage, long read MiSeq next generation sequencing, we constructed and determined the mtDNA genome organization of the 15,470 bp sequence from two isolates from Eastern Tasmania, Australia and Northern New Zealand, and identified 46 polymorphic nucleotides between the two sequences. This genome sequence and its genetic polymorphisms will likely be useful in understanding the distribution and population connectivity of the Eastern Rock Lobster, and in the fisheries management of this commercially important species.

Functional Connectivity of the Precuneus in Female University Students with Long-Term Musical Training.

Science.gov (United States)

Tanaka, Shoji; Kirino, Eiji

2016-01-01

Conceiving concrete mental imagery is critical for skillful musical expression and performance. The precuneus, a core component of the default mode network (DMN), is a hub of mental image processing that participates in functions such as episodic memory retrieval and imagining future events. The precuneus connects with many brain regions in the frontal, parietal, temporal, and occipital cortices. The aim of this study was to examine the effects of long-term musical training on the resting-state functional connectivity of the precuneus. Our hypothesis was that the functional connectivity of the precuneus is altered in musicians. We analyzed the functional connectivity of the precuneus using resting-state functional magnetic resonance imaging (fMRI) data recorded in female university students majoring in music and nonmusic disciplines. The results show that the music students had higher functional connectivity of the precuneus with opercular/insular regions, which are associated with interoceptive and emotional processing; Heschl's gyrus (HG) and the planum temporale (PT), which process complex tonal information; and the lateral occipital cortex (LOC), which processes visual information. Connectivity of the precuneus within the DMN did not differ between the two groups. Our finding suggests that functional connections between the precuneus and the regions outside of the DMN play an important role in musical performance. We propose that a neural network linking the precuneus with these regions contributes to translate mental imagery into information relevant to musical performance.

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

Overlapping genomic sequences: a treasure trove of single-nucleotide polymorphisms.

Science.gov (United States)

Taillon-Miller, P; Gu, Z; Li, Q; Hillier, L; Kwok, P Y

1998-07-01

An efficient strategy to develop a dense set of single-nucleotide polymorphism (SNP) markers is to take advantage of the human genome sequencing effort currently under way. Our approach is based on the fact that bacterial artificial chromosomes (BACs) and P1-based artificial chromosomes (PACs) used in long-range sequencing projects come from diploid libraries. If the overlapping clones sequenced are from different lineages, one is comparing the sequences from 2 homologous chromosomes in the overlapping region. We have analyzed in detail every SNP identified while sequencing three sets of overlapping clones found on chromosome 5p15.2, 7q21-7q22, and 13q12-13q13. In the 200.6 kb of DNA sequence analyzed in these overlaps, 153 SNPs were identified. Computer analysis for repetitive elements and suitability for STS development yielded 44 STSs containing 68 SNPs for further study. All 68 SNPs were confirmed to be present in at least one of the three (Caucasian, African-American, Hispanic) populations studied. Furthermore, 42 of the SNPs tested (62%) were informative in at least one population, 32 (47%) were informative in two or more populations, and 23 (34%) were informative in all three populations. These results clearly indicate that developing SNP markers from overlapping genomic sequence is highly efficient and cost effective, requiring only the two simple steps of developing STSs around the known SNPs and characterizing them in the appropriate populations.

Behaviour of High Strength Steel Endplate Connections in Fire and after Fire

NARCIS (Netherlands)

Qiang, X.

2013-01-01

The aim of this research is to reveal more information and understanding on behaviour and failure mechanisms of high strength steel endplate connections (combining high strength steel endplates with either mild steel or high strength steel beams and columns in endplate connections) in fire and after

Accelerating Information Retrieval from Profile Hidden Markov Model Databases.

Directory of Open Access Journals (Sweden)

Ahmad Tamimi

Full Text Available Profile Hidden Markov Model (Profile-HMM is an efficient statistical approach to represent protein families. Currently, several databases maintain valuable protein sequence information as profile-HMMs. There is an increasing interest to improve the efficiency of searching Profile-HMM databases to detect sequence-profile or profile-profile homology. However, most efforts to enhance searching efficiency have been focusing on improving the alignment algorithms. Although the performance of these algorithms is fairly acceptable, the growing size of these databases, as well as the increasing demand for using batch query searching approach, are strong motivations that call for further enhancement of information retrieval from profile-HMM databases. This work presents a heuristic method to accelerate the current profile-HMM homology searching approaches. The method works by cluster-based remodeling of the database to reduce the search space, rather than focusing on the alignment algorithms. Using different clustering techniques, 4284 TIGRFAMs profiles were clustered based on their similarities. A representative for each cluster was assigned. To enhance sensitivity, we proposed an extended step that allows overlapping among clusters. A validation benchmark of 6000 randomly selected protein sequences was used to query the clustered profiles. To evaluate the efficiency of our approach, speed and recall values were measured and compared with the sequential search approach. Using hierarchical, k-means, and connected component clustering techniques followed by the extended overlapping step, we obtained an average reduction in time of 41%, and an average recall of 96%. Our results demonstrate that representation of profile-HMMs using a clustering-based approach can significantly accelerate data retrieval from profile-HMM databases.

Distributed generation connected to the local network - a guide

Energy Technology Data Exchange (ETDEWEB)

NONE

2005-07-01

This guide provides advice to the developers and operators of small distributed generation plant (including microgenerators) in the UK about the practical issues associated with connecting their plant and trading their output. Particular attention is given to sales revenues and how to access these revenue streams, including the mechanisms for purchasing Renewable Obligation Certificates (ROCs). The guide clarifies key terms, explains the wholesale trading system and provides an overview of sales opportunities (including ROCs and Levy Exemption Certificates (LECs)). Requirements on small distributed generation (including licensing, claiming class exemptions and metering) are described and the commercial aspects of connection (including the recent reduction in the barriers to connection) examined. Microgeneration (ie generators below 10 kW) issues are covered in their own chapter. The six appendices contain: background information about the industry; a list of purchasers of electricity from small distributed generators; descriptions of the generation, transmission and supply industries; information about industry standards and their governance; the role of government departments and institutions; and a glossary and other links.

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.

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

Science.gov (United States)

Owens, John

2009-01-01

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

An Ambystoma mexicanum EST sequencing project: analysis of 17,352 expressed sequence tags from embryonic and regenerating blastema cDNA libraries

Science.gov (United States)

Habermann, Bianca; Bebin, Anne-Gaelle; Herklotz, Stephan; Volkmer, Michael; Eckelt, Kay; Pehlke, Kerstin; Epperlein, Hans Henning; Schackert, Hans Konrad; Wiebe, Glenis; Tanaka, Elly M

2004-01-01

Background The ambystomatid salamander, Ambystoma mexicanum (axolotl), is an important model organism in evolutionary and regeneration research but relatively little sequence information has so far been available. This is a major limitation for molecular studies on caudate development, regeneration and evolution. To address this lack of sequence information we have generated an expressed sequence tag (EST) database for A. mexicanum. Results Two cDNA libraries, one made from stage 18-22 embryos and the other from day-6 regenerating tail blastemas, generated 17,352 sequences. From the sequenced ESTs, 6,377 contigs were assembled that probably represent 25% of the expressed genes in this organism. Sequence comparison revealed significant homology to entries in the NCBI non-redundant database. Further examination of this gene set revealed the presence of genes involved in important cell and developmental processes, including cell proliferation, cell differentiation and cell-cell communication. On the basis of these data, we have performed phylogenetic analysis of key cell-cycle regulators. Interestingly, while cell-cycle proteins such as the cyclin B family display expected evolutionary relationships, the cyclin-dependent kinase inhibitor 1 gene family shows an unusual evolutionary behavior among the amphibians. Conclusions Our analysis reveals the importance of a comprehensive sequence set from a representative of the Caudata and illustrates that the EST sequence database is a rich source of molecular, developmental and regeneration studies. To aid in data mining, the ESTs have been organized into an easily searchable database that is freely available online. PMID:15345051

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.

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

The genome sequence of a widespread apex Predator, the golden eagle (Aquila chrysaetos)

Science.gov (United States)

Jacqueline M. Doyle; Todd E. Katzner; Peter H. Bloom; Yanzhu Ji; Bhagya K. Wijayawardena; J. Andrew DeWoody; Ludovic. Orlando

2014-01-01

Biologists routinely use molecular markers to identify conservation units, to quantify genetic connectivity, to estimate population sizes, and to identify targets of selection. Many imperiled eagle populations require such efforts and would benefit from enhanced genomic resources. We sequenced, assembled, and annotated the first eagle genome using DNA from a male...

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)

Study of RNA structures with a connection to random matrix theory

International Nuclear Information System (INIS)

Bhadola, Pradeep; Deo, Nivedita

2015-01-01

This manuscript investigates the level of complexity and thermodynamic properties of the real RNA structures and compares the properties with the random RNA sequences. A discussion on the similarities of thermodynamical properties of the real structures with the non linear random matrix model of RNA folding is presented. The structural information contained in the PDB file is exploited to get the base pairing information. The complexity of an RNA structure is defined by a topological quantity called genus which is calculated from the base pairing information. Thermodynamic analysis of the real structures is done numerically. The real structures have a minimum free energy which is very small compared to the randomly generated sequences of the same length. This analysis suggests that there are specific patterns in the structures which are preserved during the evolution of the sequences and certain sequences are discarded by the evolutionary process. Further analyzing the sequences of a fixed length reveal that the RNA structures exist in ensembles i.e. although all the sequences in the ensemble have different series of nucleotides (sequence) they fold into structures that have the same pairs of hydrogen bonding as well as the same minimum free energy. The specific heat of the RNA molecule is numerically estimated at different lengths. The specific heat curve with temperature shows a bump and for some RNA, a double peak behavior is observed. The same behavior is seen in the study of the random matrix model with non linear interaction of RNA folding. The bump in the non linear matrix model can be controlled by the change in the interaction strength.

The LncRNA Connectivity Map: Using LncRNA Signatures to Connect Small Molecules, LncRNAs, and Diseases.

Science.gov (United States)

Yang, Haixiu; Shang, Desi; Xu, Yanjun; Zhang, Chunlong; Feng, Li; Sun, Zeguo; Shi, Xinrui; Zhang, Yunpeng; Han, Junwei; Su, Fei; Li, Chunquan; Li, Xia

2017-07-27

Well characterized the connections among diseases, long non-coding RNAs (lncRNAs) and drugs are important for elucidating the key roles of lncRNAs in biological mechanisms in various biological states. In this study, we constructed a database called LNCmap (LncRNA Connectivity Map), available at http://www.bio-bigdata.com/LNCmap/ , to establish the correlations among diseases, physiological processes, and the action of small molecule therapeutics by attempting to describe all biological states in terms of lncRNA signatures. By reannotating the microarray data from the Connectivity Map database, the LNCmap obtained 237 lncRNA signatures of 5916 instances corresponding to 1262 small molecular drugs. We provided a user-friendly interface for the convenient browsing, retrieval and download of the database, including detailed information and the associations of drugs and corresponding affected lncRNAs. Additionally, we developed two enrichment analysis methods for users to identify candidate drugs for a particular disease by inputting the corresponding lncRNA expression profiles or an associated lncRNA list and then comparing them to the lncRNA signatures in our database. Overall, LNCmap could significantly improve our understanding of the biological roles of lncRNAs and provide a unique resource to reveal the connections among drugs, lncRNAs and diseases.

Just-in-time connectivity for large spiking networks.

Science.gov (United States)

Lytton, William W; Omurtag, Ahmet; Neymotin, Samuel A; Hines, Michael L

2008-11-01

The scale of large neuronal network simulations is memory limited due to the need to store connectivity information: connectivity storage grows as the square of neuron number up to anatomically relevant limits. Using the NEURON simulator as a discrete-event simulator (no integration), we explored the consequences of avoiding the space costs of connectivity through regenerating connectivity parameters when needed: just in time after a presynaptic cell fires. We explored various strategies for automated generation of one or more of the basic static connectivity parameters: delays, postsynaptic cell identities, and weights, as well as run-time connectivity state: the event queue. Comparison of the JitCon implementation to NEURON's standard NetCon connectivity method showed substantial space savings, with associated run-time penalty. Although JitCon saved space by eliminating connectivity parameters, larger simulations were still memory limited due to growth of the synaptic event queue. We therefore designed a JitEvent algorithm that added items to the queue only when required: instead of alerting multiple postsynaptic cells, a spiking presynaptic cell posted a callback event at the shortest synaptic delay time. At the time of the callback, this same presynaptic cell directly notified the first postsynaptic cell and generated another self-callback for the next delay time. The JitEvent implementation yielded substantial additional time and space savings. We conclude that just-in-time strategies are necessary for very large network simulations but that a variety of alternative strategies should be considered whose optimality will depend on the characteristics of the simulation to be run.

Formatt: Correcting protein multiple structural alignments by incorporating sequence alignment

Directory of Open Access Journals (Sweden)

Daniels Noah M

2012-10-01

Full Text Available Abstract Background The quality of multiple protein structure alignments are usually computed and assessed based on geometric functions of the coordinates of the backbone atoms from the protein chains. These purely geometric methods do not utilize directly protein sequence similarity, and in fact, determining the proper way to incorporate sequence similarity measures into the construction and assessment of protein multiple structure alignments has proved surprisingly difficult. Results We present Formatt, a multiple structure alignment based on the Matt purely geometric multiple structure alignment program, that also takes into account sequence similarity when constructing alignments. We show that Formatt outperforms Matt and other popular structure alignment programs on the popular HOMSTRAD benchmark. For the SABMark twilight zone benchmark set that captures more remote homology, Formatt and Matt outperform other programs; depending on choice of embedded sequence aligner, Formatt produces either better sequence and structural alignments with a smaller core size than Matt, or similarly sized alignments with better sequence similarity, for a small cost in average RMSD. Conclusions Considering sequence information as well as purely geometric information seems to improve quality of multiple structure alignments, though defining what constitutes the best alignment when sequence and structural measures would suggest different alignments remains a difficult open question.

Algebraic solution of the synthesis problem for coded sequences

International Nuclear Information System (INIS)

Leukhin, Anatolii N

2005-01-01

The algebraic solution of a 'complex' problem of synthesis of phase-coded (PC) sequences with the zero level of side lobes of the cyclic autocorrelation function (ACF) is proposed. It is shown that the solution of the synthesis problem is connected with the existence of difference sets for a given code dimension. The problem of estimating the number of possible code combinations for a given code dimension is solved. It is pointed out that the problem of synthesis of PC sequences is related to the fundamental problems of discrete mathematics and, first of all, to a number of combinatorial problems, which can be solved, as the number factorisation problem, by algebraic methods by using the theory of Galois fields and groups. (fourth seminar to the memory of d.n. klyshko)

1H NMR studies of plastocyanin from Scenedesmus obliquus: Complete sequence-specific assignment, secondary structure analysis, and global fold

International Nuclear Information System (INIS)

Moore, J.M.; Chazin, W.J.; Wright, P.E.; Powls, R.

1988-01-01

Two-dimensional 1 H NMR methods have been used to make sequence-specific resonance assignments for the 97 amino acid residues of the plastocyanin from the green alga Scenedesmus obliquus. Assignments were obtained for all backbone protons and the majority of the side-chain protons. Spin system identification relied heavily on the observation of relayed connectivities to the backbone amide proton. Sequence-specific assignments were made by using the sequential assignment procedure. During this process, an extra valine residue was identified that had not been detected in the original amino acid sequence. Elements of regular secondary structure were identified from characteristic NOE connectivities between backbone protons, coupling constant values, and the observation of slowly exchanging amide protons. The protein in solution contains eight β-strands, one short segment of helix, five reverse turns, and five loops. The β-strands may be arranged into two βsheets on the basis of extensive cross-strand NOE connectivities. The chain-folding topology determined from the NMR experiments is that of a Greek key β-barrel and is similar to that observed for French bean plastocyanin in solution and poplar plastocyanin in the crystalline state. While the overall structures are similar, several differences in local structure between the S. obliquus and higher plant plastocyanins have been identified

Bio-AIMS Collection of Chemoinformatics Web Tools based on Molecular Graph Information and Artificial Intelligence Models.

Science.gov (United States)

Munteanu, Cristian R; Gonzalez-Diaz, Humberto; Garcia, Rafael; Loza, Mabel; Pazos, Alejandro

2015-01-01

The molecular information encoding into molecular descriptors is the first step into in silico Chemoinformatics methods in Drug Design. The Machine Learning methods are a complex solution to find prediction models for specific biological properties of molecules. These models connect the molecular structure information such as atom connectivity (molecular graphs) or physical-chemical properties of an atom/group of atoms to the molecular activity (Quantitative Structure - Activity Relationship, QSAR). Due to the complexity of the proteins, the prediction of their activity is a complicated task and the interpretation of the models is more difficult. The current review presents a series of 11 prediction models for proteins, implemented as free Web tools on an Artificial Intelligence Model Server in Biosciences, Bio-AIMS (http://bio-aims.udc.es/TargetPred.php). Six tools predict protein activity, two models evaluate drug - protein target interactions and the other three calculate protein - protein interactions. The input information is based on the protein 3D structure for nine models, 1D peptide amino acid sequence for three tools and drug SMILES formulas for two servers. The molecular graph descriptor-based Machine Learning models could be useful tools for in silico screening of new peptides/proteins as future drug targets for specific treatments.

Fine-structured multi-scaling long-range correlations in completely sequenced genomes - features, origin and classification.

NARCIS (Netherlands)

T.A. Knoch (Tobias); M. Göcker; R. Lohner (Rudolf); A. Abuseiris (Anis); F.G. Grosveld (Frank)

2009-01-01

textabstractThe sequential organization of genomes, i.e. the relations between distant base pairs and regions within sequences, and its connection to the three-dimensional organization of genomes is still a largely unresolved problem. Long-range power-law correlations were found using correlation

Knowledge Access in Rural Inter-connected Areas Network ...

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

Knowledge Access in Rural Inter-connected Areas Network (KariaNet) - Phase II ... and indigenous knowledge using information and communication technologies (ICTs) ... for research proposals on the aforementioned topics, action-research projects, ... Evaluating knowledge-sharing methods to improve land utilization and ...

Connecting Music, Art, and Science for Increased Creativity and Topic Engagement

Directory of Open Access Journals (Sweden)

Tamara L. McNealy

2013-08-01

Full Text Available ‘Attention spans have shortened,’ is a common phrase often used in reference to today’s college students. As faculty and instructors, we need to address this issue through the utilization of innovative and creative techniques that aid in making our subjects accessible to our students. Connecting a serious topic such as microbiology with a ‘fun’ activity can increase student engagement and learning. Ideas to maintain student attention on a subject include providing information in 15- to 20-minute blocks, giving one- to two-minute assignments, and providing an active learning activity at least once per hour. But what if we could also increase their engagement with science by connecting it to things they already think of outside of class, and, in addition, make science thinking interdisciplinary? I have recently introduced exercises that connect music and art to various microbiology topics in my class. The creative processes in art and science have much in common. Albert Einstein recognized that both science and art delve into the mysterious by stating, “The most beautiful thing we can experience is the mysterious. It is the source of all true art and all science” (1. Connecting these subjects in the minds of our students will help them realize the importance of technology, industry, and progress in science and simultaneously emphasize the importance of art, music, and the humanities. The tools presented here will encourage students to connect new science information through the music and art they already know and, therefore, provide increased engagement and retention of the new knowledge. These techniques used in a microbiology class increased the amount of time spent thinking about new information, increased engagement with the information being presented, and encouraged critical thinking of microbiology topics. These tools were used in an upper level microbiology course, but the techniques can be easily incorporated into any course

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

Exploring brain function from anatomical connectivity

Directory of Open Access Journals (Sweden)

Gorka eZamora-López

2011-06-01

Full Text Available The intrinsic relationship between the architecture of the brain and the range of sensory and behavioral phenomena it produces is a relevant question in neuroscience. Here, we review recent knowledge gained on the architecture of the anatomical connectivity by means of complex network analysis. It has been found that corticocortical networks display a few prominent characteristics: (i modular organization, (ii abundant alternative processing paths and (iii the presence of highly connected hubs. Additionally, we present a novel classification of cortical areas of the cat according to the role they play in multisensory connectivity. All these properties represent an ideal anatomical substrate supporting rich dynamical behaviors, as-well-as facilitating the capacity of the brain to process sensory information of different modalities segregated and to integrate them towards a comprehensive perception of the real world. The result here exposed are mainly based in anatomical data of cats’ brain, but we show how further observations suggest that, from worms to humans, the nervous system of all animals might share fundamental principles of organization.

An innovative experimental sequence on electromagnetic induction and eddy currents based on video analysis and cheap data acquisition

International Nuclear Information System (INIS)

Bonanno, A; Sapia, P; Bozzo, G

2017-01-01

In this work, we present a coherent sequence of experiments on electromagnetic (EM) induction and eddy currents, appropriate for university undergraduate students, based on a magnet falling through a drilled aluminum disk. The sequence, leveraging on the didactical interplay between the EM and mechanical aspects of the experiments, allows us to exploit the students’ awareness of mechanics to elicit their comprehension of EM phenomena. The proposed experiments feature two kinds of measurements: (i) kinematic measurements (performed by means of high-speed video analysis) give information on the system’s kinematics and, via appropriate numerical data processing, allow us to get dynamic information, in particular on energy dissipation; (ii) induced electromagnetic field (EMF) measurements (by using a homemade multi-coil sensor connected to a cheap data acquisition system) allow us to quantitatively determine the inductive effects of the moving magnet on its neighborhood. The comparison between experimental results and the predictions from an appropriate theoretical model (of the dissipative coupling between the moving magnet and the conducting disk) offers many educational hints on relevant topics related to EM induction, such as Maxwell’s displacement current, magnetic field flux variation, and the conceptual link between induced EMF and induced currents. Moreover, the didactical activity gives students the opportunity to be trained in video analysis, data acquisition and numerical data processing. (paper)

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.

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

'Information Seeking in Context' and the development of information systems

Directory of Open Access Journals (Sweden)

Irina Gaslikova

1999-01-01

Full Text Available This paper reports on some findings of the explorations represented at the conference "Information Seeking in Context" (ISIC’98. These findings are investigated with the aim to evaluate their practical usefulness for the design of information computer systems. The paper discusses some common problems connected with the conceptual approaches to the information system development.

A priori Considerations When Conducting High-Throughput Amplicon-Based Sequence Analysis

Directory of Open Access Journals (Sweden)

Aditi Sengupta

2016-03-01

Full Text Available Amplicon-based sequencing strategies that include 16S rRNA and functional genes, alongside “meta-omics” analyses of communities of microorganisms, have allowed researchers to pose questions and find answers to “who” is present in the environment and “what” they are doing. Next-generation sequencing approaches that aid microbial ecology studies of agricultural systems are fast gaining popularity among agronomy, crop, soil, and environmental science researchers. Given the rapid development of these high-throughput sequencing techniques, researchers with no prior experience will desire information about the best practices that can be used before actually starting high-throughput amplicon-based sequence analyses. We have outlined items that need to be carefully considered in experimental design, sampling, basic bioinformatics, sequencing of mock communities and negative controls, acquisition of metadata, and in standardization of reaction conditions as per experimental requirements. Not all considerations mentioned here may pertain to a particular study. The overall goal is to inform researchers about considerations that must be taken into account when conducting high-throughput microbial DNA sequencing and sequences analysis.

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.

Evaluating and redesigning teaching learning sequences at the introductory physics level

Science.gov (United States)

Guisasola, Jenaro; Zuza, Kristina; Ametller, Jaume; Gutierrez-Berraondo, José

2017-12-01

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 according to our proposal relate to learning progressions. An iterative methodology for evaluating and redesigning the teaching and learning sequence (TLS) is presented. The proposed assessment strategy focuses on three aspects: (a) evaluation of the activities of the TLS, (b) evaluation of learning achieved by students in relation to the intended objectives, and (c) a document for gathering the difficulties found when implementing the TLS to serve as a guide to teachers. Discussion of this guide with external teachers provides feedback used for the TLS redesign. The context of our implementation and evaluation is an innovative calculus-based physics course for first-year engineering and science degree students at the University of the Basque Country.

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

Using sequence similarity networks for visualization of relationships across diverse protein superfamilies.

Directory of Open Access Journals (Sweden)

Holly J Atkinson

Full Text Available The dramatic increase in heterogeneous types of biological data--in particular, the abundance of new protein sequences--requires fast and user-friendly methods for organizing this information in a way that enables functional inference. The most widely used strategy to link sequence or structure to function, homology-based function prediction, relies on the fundamental assumption that sequence or structural similarity implies functional similarity. New tools that extend this approach are still urgently needed to associate sequence data with biological information in ways that accommodate the real complexity of the problem, while being accessible to experimental as well as computational biologists. To address this, we have examined the application of sequence similarity networks for visualizing functional trends across protein superfamilies from the context of sequence similarity. Using three large groups of homologous proteins of varying types of structural and functional diversity--GPCRs and kinases from humans, and the crotonase superfamily of enzymes--we show that overlaying networks with orthogonal information is a powerful approach for observing functional themes and revealing outliers. In comparison to other primary methods, networks provide both a good representation of group-wise sequence similarity relationships and a strong visual and quantitative correlation with phylogenetic trees, while enabling analysis and visualization of much larger sets of sequences than trees or multiple sequence alignments can easily accommodate. We also define important limitations and caveats in the application of these networks. As a broadly accessible and effective tool for the exploration of protein superfamilies, sequence similarity networks show great potential for generating testable hypotheses about protein structure-function relationships.

Using sequence similarity networks for visualization of relationships across diverse protein superfamilies.

Science.gov (United States)

Atkinson, Holly J; Morris, John H; Ferrin, Thomas E; Babbitt, Patricia C

2009-01-01

The dramatic increase in heterogeneous types of biological data--in particular, the abundance of new protein sequences--requires fast and user-friendly methods for organizing this information in a way that enables functional inference. The most widely used strategy to link sequence or structure to function, homology-based function prediction, relies on the fundamental assumption that sequence or structural similarity implies functional similarity. New tools that extend this approach are still urgently needed to associate sequence data with biological information in ways that accommodate the real complexity of the problem, while being accessible to experimental as well as computational biologists. To address this, we have examined the application of sequence similarity networks for visualizing functional trends across protein superfamilies from the context of sequence similarity. Using three large groups of homologous proteins of varying types of structural and functional diversity--GPCRs and kinases from humans, and the crotonase superfamily of enzymes--we show that overlaying networks with orthogonal information is a powerful approach for observing functional themes and revealing outliers. In comparison to other primary methods, networks provide both a good representation of group-wise sequence similarity relationships and a strong visual and quantitative correlation with phylogenetic trees, while enabling analysis and visualization of much larger sets of sequences than trees or multiple sequence alignments can easily accommodate. We also define important limitations and caveats in the application of these networks. As a broadly accessible and effective tool for the exploration of protein superfamilies, sequence similarity networks show great potential for generating testable hypotheses about protein structure-function relationships.

Using high-throughput barcode sequencing to efficiently map connectomes.

Science.gov (United States)

Peikon, Ian D; Kebschull, Justus M; Vagin, Vasily V; Ravens, Diana I; Sun, Yu-Chi; Brouzes, Eric; Corrêa, Ivan R; Bressan, Dario; Zador, Anthony M

2017-07-07

The function of a neural circuit is determined by the details of its synaptic connections. At present, the only available method for determining a neural wiring diagram with single synapse precision-a 'connectome'-is based on imaging methods that are slow, labor-intensive and expensive. Here, we present SYNseq, a method for converting the connectome into a form that can exploit the speed and low cost of modern high-throughput DNA sequencing. In SYNseq, each neuron is labeled with a unique random nucleotide sequence-an RNA 'barcode'-which is targeted to the synapse using engineered proteins. Barcodes in pre- and postsynaptic neurons are then associated through protein-protein crosslinking across the synapse, extracted from the tissue, and joined into a form suitable for sequencing. Although our failure to develop an efficient barcode joining scheme precludes the widespread application of this approach, we expect that with further development SYNseq will enable tracing of complex circuits at high speed and low cost. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Environmental Reform in the Information Age. The Contours of Informational Governance.

NARCIS (Netherlands)

Mol, A.P.J.

2008-01-01

As the information revolution continues to accelerate, the environment remains high on public and political agendas around the world. These two topics are rarely connected, but information - its collection, processing, accessibility and verification - is crucial in dealing with environmental

DNA Polymerases Drive DNA Sequencing-by-Synthesis Technologies: Both Past and Present

Directory of Open Access Journals (Sweden)

Cheng-Yao eChen

2014-06-01

Full Text Available Next-generation sequencing (NGS technologies have revolutionized modern biological and biomedical research. The engines responsible for this innovation are DNA polymerases; they catalyze the biochemical reaction for deriving template sequence information. In fact, DNA polymerase has been a cornerstone of DNA sequencing from the very beginning. E. coli DNA polymerase I proteolytic (Klenow fragment was originally utilized in Sanger's dideoxy chain terminating DNA sequencing chemistry. From these humble beginnings followed an explosion of organism-specific, genome sequence information accessible via public database. Family A/B DNA polymerases from mesophilic/thermophilic bacteria/archaea were modified and tested in today's standard capillary electrophoresis (CE and NGS sequencing platforms. These enzymes were selected for their efficient incorporation of bulky dye-terminator and reversible dye-terminator nucleotides respectively. Third generation, real-time single molecule sequencing platform requires slightly different enzyme properties. Enterobacterial phage ⱷ29 DNA polymerase copies long stretches of DNA and possesses a unique capability to efficiently incorporate terminal phosphate-labeled nucleoside polyphosphates. Furthermore, ⱷ29 enzyme has also been utilized in emerging DNA sequencing technologies including nanopore-, and protein-transistor-based sequencing. DNA polymerase is, and will continue to be, a crucial component of sequencing technologies.

Increased cortico-striatal connectivity during motor practice contributes to the consolidation of motor memory in writer's cramp patients

Directory of Open Access Journals (Sweden)

C. Gallea

2015-01-01

Full Text Available Sensorimotor representations of movements are created in the sensorimotor network through repeated practice to support successful and effortless performance. Writer's cramp (WC is a disorder acquired through extensive practice of finger movements, and it is likely associated with the abnormal acquisition of sensorimotor representations. We investigated (i the activation and connectivity changes in the brain network supporting the acquisition of sensorimotor representations of finger sequences in patients with WC and (ii the link between these changes and consolidation of motor performance 24 h after the initial practice. Twenty-two patients with WC and 22 age-matched healthy volunteers practiced a complex sequence with the right (pathological hand during functional MRI recording. Speed and accuracy were measured immediately before and after practice (day 1 and 24 h after practice (day 2. The two groups reached equivalent motor performance on day 1 and day 2. During motor practice, patients with WC had (i reduced hippocampal activation and hippocampal–striatal functional connectivity; and (ii overactivation of premotor–striatal areas, whose connectivity correlated with motor performance after consolidation. These results suggest that patients with WC use alternative networks to reach equiperformance in the acquisition of new motor memories.

Sequence-based classification and identification of Fungi.

Science.gov (United States)

Hibbett, David; Abarenkov, Kessy; Kõljalg, Urmas; Öpik, Maarja; Chai, Benli; Cole, James; Wang, Qiong; Crous, Pedro; Robert, Vincent; Helgason, Thorunn; Herr, Joshua R; Kirk, Paul; Lueschow, Shiloh; O'Donnell, Kerry; Nilsson, R Henrik; Oono, Ryoko; Schoch, Conrad; Smyth, Christopher; Walker, Donald M; Porras-Alfaro, Andrea; Taylor, John W; Geiser, David M

Fungal taxonomy and ecology have been revolutionized by the application of molecular methods and both have increasing connections to genomics and functional biology. However, data streams from traditional specimen- and culture-based systematics are not yet fully integrated with those from metagenomic and metatranscriptomic studies, which limits understanding of the taxonomic diversity and metabolic properties of fungal communities. This article reviews current resources, needs, and opportunities for sequence-based classification and identification (SBCI) in fungi as well as related efforts in prokaryotes. To realize the full potential of fungal SBCI it will be necessary to make advances in multiple areas. Improvements in sequencing methods, including long-read and single-cell technologies, will empower fungal molecular ecologists to look beyond ITS and current shotgun metagenomics approaches. Data quality and accessibility will be enhanced by attention to data and metadata standards and rigorous enforcement of policies for deposition of data and workflows. Taxonomic communities will need to develop best practices for molecular characterization in their focal clades, while also contributing to globally useful datasets including ITS. Changes to nomenclatural rules are needed to enable validPUBLICation of sequence-based taxon descriptions. Finally, cultural shifts are necessary to promote adoption of SBCI and to accord professional credit to individuals who contribute to community resources.

Insights from 20 years of bacterial genome sequencing

DEFF Research Database (Denmark)

Land, Miriam; Hauser, Loren; Jun, Se-Ran

2015-01-01

Since the first two complete bacterial genome sequences were published in 1995, the science of bacteria has dramatically changed. Using third-generation DNA sequencing, it is possible to completely sequence a bacterial genome in a few hours and identify some types of methylation sites along...... the genome as well. Sequencing of bacterial genome sequences is now a standard procedure, and the information from tens of thousands of bacterial genomes has had a major impact on our views of the bacterial world. In this review, we explore a series of questions to highlight some insights that comparative...... genomics has produced. To date, there are genome sequences available from 50 different bacterial phyla and 11 different archaeal phyla. However, the distribution is quite skewed towards a few phyla that contain model organisms. But the breadth is continuing to improve, with projects dedicated to filling...

WebPrInSeS: automated full-length clone sequence identification and verification using high-throughput sequencing data.

Science.gov (United States)

Massouras, Andreas; Decouttere, Frederik; Hens, Korneel; Deplancke, Bart

2010-07-01

High-throughput sequencing (HTS) is revolutionizing our ability to obtain cheap, fast and reliable sequence information. Many experimental approaches are expected to benefit from the incorporation of such sequencing features in their pipeline. Consequently, software tools that facilitate such an incorporation should be of great interest. In this context, we developed WebPrInSeS, a web server tool allowing automated full-length clone sequence identification and verification using HTS data. WebPrInSeS encompasses two separate software applications. The first is WebPrInSeS-C which performs automated sequence verification of user-defined open-reading frame (ORF) clone libraries. The second is WebPrInSeS-E, which identifies positive hits in cDNA or ORF-based library screening experiments such as yeast one- or two-hybrid assays. Both tools perform de novo assembly using HTS data from any of the three major sequencing platforms. Thus, WebPrInSeS provides a highly integrated, cost-effective and efficient way to sequence-verify or identify clones of interest. WebPrInSeS is available at http://webprinses.epfl.ch/ and is open to all users.

Approaches for in silico finishing of microbial genome sequences

Directory of Open Access Journals (Sweden)

Frederico Schmitt Kremer

Full Text Available Abstract The introduction of next-generation sequencing (NGS had a significant effect on the availability of genomic information, leading to an increase in the number of sequenced genomes from a large spectrum of organisms. Unfortunately, due to the limitations implied by the short-read sequencing platforms, most of these newly sequenced genomes remained as “drafts”, incomplete representations of the whole genetic content. The previous genome sequencing studies indicated that finishing a genome sequenced by NGS, even bacteria, may require additional sequencing to fill the gaps, making the entire process very expensive. As such, several in silico approaches have been developed to optimize the genome assemblies and facilitate the finishing process. The present review aims to explore some free (open source, in many cases tools that are available to facilitate genome finishing.

Approaches for in silico finishing of microbial genome sequences.

Science.gov (United States)

Kremer, Frederico Schmitt; McBride, Alan John Alexander; Pinto, Luciano da Silva

The introduction of next-generation sequencing (NGS) had a significant effect on the availability of genomic information, leading to an increase in the number of sequenced genomes from a large spectrum of organisms. Unfortunately, due to the limitations implied by the short-read sequencing platforms, most of these newly sequenced genomes remained as "drafts", incomplete representations of the whole genetic content. The previous genome sequencing studies indicated that finishing a genome sequenced by NGS, even bacteria, may require additional sequencing to fill the gaps, making the entire process very expensive. As such, several in silico approaches have been developed to optimize the genome assemblies and facilitate the finishing process. The present review aims to explore some free (open source, in many cases) tools that are available to facilitate genome finishing.

SEQATOMS: a web tool for identifying missing regions in PDB in sequence context

NARCIS (Netherlands)

Brandt, B.W.; Heringa, J.; Leunissen, J.A.M.

2008-01-01

With over 46 000 proteins, the Protein Data Bank (PDB) is the most important database with structural information of biological macromolecules. PDB files contain sequence and coordinate information. Residues present in the sequence can be absent from the coordinate section, which means their

Adaptive GDDA-BLAST: fast and efficient algorithm for protein sequence embedding.

Directory of Open Access Journals (Sweden)

Yoojin Hong

2010-10-01

Full Text Available A major computational challenge in the genomic era is annotating structure/function to the vast quantities of sequence information that is now available. This problem is illustrated by the fact that most proteins lack comprehensive annotations, even when experimental evidence exists. We previously theorized that embedded-alignment profiles (simply "alignment profiles" hereafter provide a quantitative method that is capable of relating the structural and functional properties of proteins, as well as their evolutionary relationships. A key feature of alignment profiles lies in the interoperability of data format (e.g., alignment information, physio-chemical information, genomic information, etc.. Indeed, we have demonstrated that the Position Specific Scoring Matrices (PSSMs are an informative M-dimension that is scored by quantitatively measuring the embedded or unmodified sequence alignments. Moreover, the information obtained from these alignments is informative, and remains so even in the "twilight zone" of sequence similarity (<25% identity. Although our previous embedding strategy was powerful, it suffered from contaminating alignments (embedded AND unmodified and high computational costs. Herein, we describe the logic and algorithmic process for a heuristic embedding strategy named "Adaptive GDDA-BLAST." Adaptive GDDA-BLAST is, on average, up to 19 times faster than, but has similar sensitivity to our previous method. Further, data are provided to demonstrate the benefits of embedded-alignment measurements in terms of detecting structural homology in highly divergent protein sequences and isolating secondary structural elements of transmembrane and ankyrin-repeat domains. Together, these advances allow further exploration of the embedded alignment data space within sufficiently large data sets to eventually induce relevant statistical inferences. We show that sequence embedding could serve as one of the vehicles for measurement of low

Sequence modelling and an extensible data model for genomic database

Energy Technology Data Exchange (ETDEWEB)

Li, Peter Wei-Der [California Univ., San Francisco, CA (United States); Univ. of California, Berkeley, CA (United States)

1992-01-01

The Human Genome Project (HGP) plans to sequence the human genome by the beginning of the next century. It will generate DNA sequences of more than 10 billion bases and complex marker sequences (maps) of more than 100 million markers. All of these information will be stored in database management systems (DBMSs). However, existing data models do not have the abstraction mechanism for modelling sequences and existing DBMS`s do not have operations for complex sequences. This work addresses the problem of sequence modelling in the context of the HGP and the more general problem of an extensible object data model that can incorporate the sequence model as well as existing and future data constructs and operators. First, we proposed a general sequence model that is application and implementation independent. This model is used to capture the sequence information found in the HGP at the conceptual level. In addition, abstract and biological sequence operators are defined for manipulating the modelled sequences. Second, we combined many features of semantic and object oriented data models into an extensible framework, which we called the ``Extensible Object Model``, to address the need of a modelling framework for incorporating the sequence data model with other types of data constructs and operators. This framework is based on the conceptual separation between constructors and constraints. We then used this modelling framework to integrate the constructs for the conceptual sequence model. The Extensible Object Model is also defined with a graphical representation, which is useful as a tool for database designers. Finally, we defined a query language to support this model and implement the query processor to demonstrate the feasibility of the extensible framework and the usefulness of the conceptual sequence model.

Sequence modelling and an extensible data model for genomic database

Energy Technology Data Exchange (ETDEWEB)

Li, Peter Wei-Der (California Univ., San Francisco, CA (United States) Lawrence Berkeley Lab., CA (United States))

1992-01-01

The Human Genome Project (HGP) plans to sequence the human genome by the beginning of the next century. It will generate DNA sequences of more than 10 billion bases and complex marker sequences (maps) of more than 100 million markers. All of these information will be stored in database management systems (DBMSs). However, existing data models do not have the abstraction mechanism for modelling sequences and existing DBMS's do not have operations for complex sequences. This work addresses the problem of sequence modelling in the context of the HGP and the more general problem of an extensible object data model that can incorporate the sequence model as well as existing and future data constructs and operators. First, we proposed a general sequence model that is application and implementation independent. This model is used to capture the sequence information found in the HGP at the conceptual level. In addition, abstract and biological sequence operators are defined for manipulating the modelled sequences. Second, we combined many features of semantic and object oriented data models into an extensible framework, which we called the Extensible Object Model'', to address the need of a modelling framework for incorporating the sequence data model with other types of data constructs and operators. This framework is based on the conceptual separation between constructors and constraints. We then used this modelling framework to integrate the constructs for the conceptual sequence model. The Extensible Object Model is also defined with a graphical representation, which is useful as a tool for database designers. Finally, we defined a query language to support this model and implement the query processor to demonstrate the feasibility of the extensible framework and the usefulness of the conceptual sequence model.

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.

Capturing connectivity and causality in complex industrial processes

CERN Document Server

Yang, Fan; Shah, Sirish L; Chen, Tongwen

2014-01-01

This brief reviews concepts of inter-relationship in modern industrial processes, biological and social systems. Specifically ideas of connectivity and causality within and between elements of a complex system are treated; these ideas are of great importance in analysing and influencing mechanisms, structural properties and their dynamic behaviour, especially for fault diagnosis and hazard analysis. Fault detection and isolation for industrial processes being concerned with root causes and fault propagation, the brief shows that, process connectivity and causality information can be captured in two ways: ·      from process knowledge: structural modeling based on first-principles structural models can be merged with adjacency/reachability matrices or topology models obtained from process flow-sheets described in standard formats; and ·      from process data: cross-correlation analysis, Granger causality and its extensions, frequency domain methods, information-theoretical methods, and Bayesian ne...

Learning sequences on the subject of energy

International Nuclear Information System (INIS)

1986-01-01

The ten learning sequences follow on one another. Each picks on a particular aspect from the energy field. The subject notebooks are self-contained and can therefore be used independently. Apart from actual data and energy-related information, the information for the teacher contains: - proposals for teaching - suggestions for further activities - sample solutions for the pupil's sheets - references to the literature and media. The worksheets for the pupils are different; it should be possible to use the learning sequences in all classes of secondary school stage 1. The multicoloured foils for projectors should motivate, on the one hand, and on the other hand should help to check the results of learning. (orig./HP) [de

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.

Stomach-brain synchrony reveals a novel, delayed-connectivity resting-state network in humans.

Science.gov (United States)